##maf version=1 scoring=autoMZ.v1
a score=-1801.000000
s hg19.chrY                          7646594 43 +  59373566 ca-aaaa----------CAGTATACTTTtcttagacaccatttcatagcagtac
s tarSyr1.scaffold_304549                518 18 -      1751 CA-TCAA----------TAGTGTCCTCCT-------------------------
q tarSyr1.scaffold_304549                                   76-9969----------999996979999-------------------------
i tarSyr1.scaffold_304549          N 0 N 0
s rheMac2.chr2                     158755265 44 + 189746636 aacaaaa----------cagtatacttttcttagagaccatttcatagcagtac
q rheMac2.chr2                                              9999999----------9999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027099 53 - 202140232 aa-aaaaaacaacaaatcagtatacttttcttagagaccatttcatagcagtac
q ponAbe2.chr3                                              99-999999999099999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        500129 43 +  23952694 ca-aaaa----------CAGTATACTTTtcttagagaccatttcatagcagtac
q panTro2.chrY                                              00-0000----------0000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s loxAfr3.scaffold_36                 507773 42 -  24123610 --attaa----------cagtacatttttcttagtgatctttccatataaggac
q loxAfr3.scaffold_36                                       --99999----------9999999999999999999999999999999999999
i loxAfr3.scaffold_36              I 299 C 0
s oryCun2.chr14                      2463501 14 + 163896628 --------------------CATCTTTCCC----ACAC----------------
q oryCun2.chr14                                             --------------------9999999999----9999----------------
i oryCun2.chr14                    C 0 C 0
s equCab2.chr16                     22206090 37 -  87365405 ------a----------cagtgtacttgtcttagagacc-ttcaatggcagtac
q equCab2.chr16                                             ------9----------9999999999999999999999-99999999999999
i equCab2.chr16                    C 0 C 0
s myoLuc1.scaffold_164119             117468 13 -    117938 -----------------------attctttttaaag------------------
q myoLuc1.scaffold_164119                                   -----------------------9999999999999------------------
i myoLuc1.scaffold_164119          I 1572 N 0
e cavPor3.scaffold_0                 8217733 200 -  88675666 I
e rn4.chr9                         107342142 164 - 113440463 I
e mm9.chr17                         50246941 148 +  95272651 I
e bosTau4.chr1                     156977363 218 + 161106243 I
e canFam2.chr23                     25986606  8 -  55389570 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                96558 2330 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               7696 130 +     88154 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=37212.000000
s hg19.chrY                          7646637 65 +  59373566 acagagtgttttctcag--tcttttct------acaga----------tccatt----gtgtgatataccatggtctatgaaaactt
s rheMac2.chr2                     158755309 65 + 189746636 acagagttctttctcat--tcttttct------acaga----------tccatt----gtgtgatataccatggagtatgcaaactt
q rheMac2.chr2                                              99999999999999999--99999999------99999----------999999----99999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027152 65 - 202140232 acagagtgctttctcac--tcttttct------acaga----------tccatt----gtgtgatataccatggagtatgcaaactt
q ponAbe2.chr3                                              99999999999999999--99999999------99999----------999999----99999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        500172 65 +  23952694 acagagtgttttctcag--tcttttct------acaga----------tccatt----gtgtgatataccatggtctatGAAAActt
q panTro2.chrY                                              00000000000000000--00000000------00000----------000000----00000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107342306 40 - 113440463 -------------------TGTTTTTT------GTAGA----------TCT-------GTGTTGC-----AAAGGTTATAAAACCTT
q rn4.chr9                                                  -------------------99999999------99999----------999-------9999999-----99999999999999999
i rn4.chr9                         I 164 C 0
s mm9.chr17                         50247089 68 +  95272651 ACAGAGCACTTCCTGCTTTATTTTTTT------GTAGA----------TCTATTCA-CGTGTTACAT--TAGTGATTATAAAAGCTT
i mm9.chr17                        I 148 C 0
s oryCun2.chr14                      2463515 36 + 163896628 ---------------------------------------------------ATGCGTCATGTTAGATACCATACACCATACAAGCtt
q oryCun2.chr14                                             ---------------------------------------------------999999999999999999999999999999999999
i oryCun2.chr14                    C 0 C 0
s equCab2.chr16                     22206127 71 -  87365405 acagggctcttcctcac--tctttt-t------acagatgca--gt-ttccatt----gtgtgatggaccacagattattcaaactt
q equCab2.chr16                                             99999999999999999--999999-9------999999999--99-9999999----99999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s loxAfr3.scaffold_36                 507815 81 -  24123610 acagagctcttcctctt--tcttttttctttacacaaatgcatggtgtcccatt----gcatgatgtaccatagattattcaaactc
q loxAfr3.scaffold_36                                       99999999999999999--99999999999999999999999999999999999----99999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8217733 200 -  88675666 I
e bosTau4.chr1                     156977363 218 + 161106243 I
e canFam2.chr23                     25986606  8 -  55389570 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                96558 2330 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               7696 130 +     88154 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=110408.000000
s hg19.chrY                          7646702 68 +  59373566 ttgcttttataagtaatcgtttagtgaaaaatatcattcctatatgattttgcacat----gtgcgcttgta
s rheMac2.chr2                     158755374 68 + 189746636 ttgcttttgtaagtaatctcttagtgaaaaatatcattcctacatgatttcacatgt----gtgtgcttata
q rheMac2.chr2                                              999999999999999999999999999999999999999999999999999999999----99999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027217 68 - 202140232 ttgctcttacaagtagtcttttagtgaaaaatatcattcctacatgattttgcatgt----gtgcgcttata
q ponAbe2.chr3                                              999999999999999099999999999999999999999999999999999999999----99999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        500237 68 +  23952694 ttgcttttataagtaatcgtttagtgaaaaatatcattcctatatgattttgcacat----gtgcgcttata
q panTro2.chrY                                              000000000000000000000000000000000000000000000000000000000----00000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107342346 63 - 113440463 TTGTTTCTACATG----GCTGTAGTAAGAAATA-CATTCCTATATGACTTCACACGC----ACACATATATA
q rn4.chr9                                                  9999999999999----9999999999999999-99999999999999999999999----99999999999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50247157 63 +  95272651 TCGTTTCTTCATA----GCTTTAATAAGAGTAT-CATCCCTACATGATTTCACATGC----GCGAGCGCGCG
i mm9.chr17                        C 0 I 3
s oryCun2.chr14                      2463551 66 + 163896628 ctgtttgtataagtaacgcttcactcataaatt--attcctacatgatttcacatgt----gtgcacatata
q oryCun2.chr14                                             999999999999999999999999999999999--9999999999999999999999----99999999999
i oryCun2.chr14                    C 0 C 0
s canFam2.chr23                     25986614 66 -  55389570 TTATTACCATAAGTAATGTTG--ATGAAAAATACGACTCCTACATAATTTCACATGG----ATGTACATAGA
q canFam2.chr23                                             999999999999999999999--9999999999999999999999999999999999----99999999999
i canFam2.chr23                    I 8 C 0
s equCab2.chr16                     22206198 72 -  87365405 ttgcttttataagtaatgctgcagtgaaaaacattgctcctacatgatttcacatgggtgcatgtatatata
q equCab2.chr16                                             999999999999999999999999999999999999999999999999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s loxAfr3.scaffold_36                 507896 71 -  24123610 ttgcttttatgagtaatgctgcaaggaaaaata-tactcctacatgacttcacctacctatgtgcacatgga
q loxAfr3.scaffold_36                                       999999999999999999999999999999999-99999999999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8217733 200 -  88675666 I
e bosTau4.chr1                     156977363 218 + 161106243 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                96558 2330 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               7696 130 +     88154 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=22033.000000
s hg19.chrY                          7646770 59 +  59373566 gtacat-----ataaaaaataaattcatagatgttgaattgctgggttaaaAATACATGcattg
s rheMac2.chr2                     158755442 59 + 189746636 gtacgt-----acaaaaaataaattcctagacgtggaattgctgggttaaaAATAtatgcattg
q rheMac2.chr2                                              999999-----99999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027285 59 - 202140232 gtacat-----ataaaaaataaattcctagatgtggaattgctgggttaaaaatatatgcagtg
q ponAbe2.chr3                                              999999-----99999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        500305 59 +  23952694 gtacat-----acaaaaaataaattcatagacgttgaattgctgggttaaaAATACATGcattg
q panTro2.chrY                                              000000-----00000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107342409 26 - 113440463 ACACAT-----TCAGAAAACACATTTGTAAA---------------------------------
q rn4.chr9                                                  999999-----99999999999999999999---------------------------------
i rn4.chr9                         C 0 I 141
s mm9.chr17                         50247223  9 +  95272651 Gcacac-----aca--------------------------------------------------
i mm9.chr17                        I 3 I 187
s oryCun2.chr14                      2463617 50 + 163896628 gtatat-----ctaaagaaaattgcgaga--tgtggaattgctgggttaaacttaca-------
q oryCun2.chr14                                             999999-----999999999999999999--99999999999999999999999999-------
i oryCun2.chr14                    C 0 C 0
s ochPri2.scaffold_2292                98888 15 +    188698 AAAGAA-----CCAAAACAA--------------------------------------------
q ochPri2.scaffold_2292                                     999999-----999999999--------------------------------------------
i ochPri2.scaffold_2292            I 2330 I 1220
s canFam2.chr23                     25986680 51 -  55389570 GTACATCATACCCAGGGATTCCatacctag----gaatttgctggaccaaagata---------
q canFam2.chr23                                             999999999999999999999999999999----999999999999999999999---------
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22206270 60 -  87365405 gtacct----ctaaaagaataaattcctaggtgtggaattgctgggctaaagataaatgcattg
q equCab2.chr16                                             999999----999999999999999999999999999999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s loxAfr3.scaffold_36                 507967 57 -  24123610 gtctac-----ctaaaaaataagtttctaagtgtggagttgctgggttaaagatacatgcat--
q loxAfr3.scaffold_36                                       999999-----999999999999999999999999999999999999999999999999999--
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8217733 200 -  88675666 I
e bosTau4.chr1                     156977363 218 + 161106243 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               7696 130 +     88154 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=41295.000000
s hg19.chrY                          7646829  97 +  59373566 cgtgcatgtatcaaaacatctcatgtaccctataaatatatacacctactatgtacccacaaaaattaaaaATA---------AAATCAAAAATCAGAGGTGTAAA
s rheMac2.chr2                     158755501 105 + 189746636 tgtgcctgcatcaaaacatctcatgtaccctgtaaatatatacacctactatgtacccacaaaaaataaaaaaattaaaaaataaataaataattaGAGGTGTAA-
q rheMac2.chr2                                               999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027344  89 - 202140232 tgtgcctgtatcaaaacatctcatgtaccctataaatatatacacctactatgtacccacaaaaaat----------------aaataaaaaatcagagatgtaa-
q ponAbe2.chr3                                               9999999999999999999999999999999999999999999999999999999999999999999----------------9999999999999999999999-
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        500364  97 +  23952694 cgtgcatgtatcaaaacatctcatgtaccctataaatatatacacctactatgtacccacaaaaattaaaaATA---------AAATCAAAAATCAGAGGTGTAAA
q panTro2.chrY                                               00000000000000000000000000000000000000000000000000000000000000000000000000---------00000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8217733 200 -  88675666 I
e rn4.chr9                         107342435 141 - 113440463 I
e mm9.chr17                         50247232 187 +  95272651 I
e oryCun2.chr14                      2463667   0 + 163896628 C
e equCab2.chr16                     22206330   0 -  87365405 C
e bosTau4.chr1                     156977363 218 + 161106243 I
e loxAfr3.scaffold_36                 508024   0 -  24123610 C
e canFam2.chr23                     25986731   0 -  55389570 C
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802  28 + 312544902 I
e eriEur1.scaffold_377961               7696 130 +     88154 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-2813.000000
s hg19.chrY                          7646926 52 +  59373566 AAatatatatatatatatatatatacacacatatatatgtcatacatatGTC
s panTro2.chrY                        500461 46 +  23952694 AAAAatatatctatatata------cacacatatatataccatacatatgtC
q panTro2.chrY                                              0000000000000000000------000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71027433 32 - 202140232 ----atatatatatatat-------cacaca---------catatacatgtg
q ponAbe2.chr3                                              ----99999999999999-------999999---------999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158755606 30 + 189746636 ------ATATATATATAT-------CACACA---------CATATATATGTg
q rheMac2.chr2                                              ------999999999999-------999999---------999999999999
i rheMac2.chr2                     C 0 C 0
s canFam2.chr23                     25986731  2 -  55389570 -aa-------------------------------------------------
q canFam2.chr23                                             -99-------------------------------------------------
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               7826 40 +     88154 ----atgtgtgtatgtgt-------agtacATGAAAATG-CCTAGGTGTGAC
q eriEur1.scaffold_377961                                   ----99999999999999-------99999999999999-999999999999
i eriEur1.scaffold_377961          I 130 C 0
e cavPor3.scaffold_0                 8217733 200 -  88675666 I
e rn4.chr9                         107342435 141 - 113440463 I
e mm9.chr17                         50247232 187 +  95272651 I
e oryCun2.chr14                      2463667  0 + 163896628 C
e equCab2.chr16                     22206330  0 -  87365405 C
e bosTau4.chr1                     156977363 218 + 161106243 I
e loxAfr3.scaffold_36                 508024  0 -  24123610 C
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=52638.000000
s hg19.chrY                          7646978 83 +  59373566 TGCATTG-------------------TAA-TTTTTTCAGATAGTGCTAGA---TTTCTTCTATAC-AGTAC-TATGGATTTATCTGGCATCAGTGATGT------------ATA-AAGTTG
s eriEur1.scaffold_377961               7866 99 +     88154 ATTACTGGGGTAAAAtaaatgtgtgacat-ttctctaAGATCTTGCCAGG-----TTTTTCCATG-ATTAG-CACAG--TTACTGCCTATCAACGATGT------------ATAGAAGGTA
q eriEur1.scaffold_377961                                   99999999999999999999999999999-99999999999999999999-----9999999999-99999-99999--99999999999999999999------------9999999999
i eriEur1.scaffold_377961          C 0 C 0
s canFam2.chr23                     25986733 83 -  55389570 agtattg-------------------tac-ttttttcatatatggccaga---tttcttccacag-agtag-catggatttacctcctatcagcaatgt------------ata-aaggca
q canFam2.chr23                                             9999999-------------------999-99999999999999999999---999999999999-99999-999999999999999999999999999------------999-999999
i canFam2.chr23                    C 0 C 0
s rn4.chr9                         107342576 70 - 113440463 ---ACTG-------------------TGA-TGAGCTCAGATGTCACCAGA---CTTCATTCATAA-AGAGG-TAAAGATTTACTTCTCCATAGAAAGC-----------------------
q rn4.chr9                                                  ---9999-------------------999-99999999999999999999---999999999999-99999-99999999999999999999999999-----------------------
i rn4.chr9                         I 141 C 0
s oryCun2.chr14                      2463667 83 + 163896628 agcattg-------------------taa-cattttccaattttg-aaga---ttttctccacag-tacag-aacacatttacctcccagcagggagcc--acacaggggc----------
q oryCun2.chr14                                             9999999-------------------999-999999999999999-9999---999999999999-99999-999999999999999999999999999--9999999999----------
i oryCun2.chr14                    C 0 C 0
s panTro2.chrY                        500507 83 +  23952694 TGCATTG-------------------TAA-TTTTTTCAGATAGTGCTAGA---TTTCTTCTATAC-AGTAC-TATGGATTTATCTGGCATCAGTGATGT------------ATA-GAGTTG
q panTro2.chrY                                              0000000-------------------000-00000000000000000000---000000000000-00000-000000000000000000000000000------------000-000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71027465 81 - 202140232 tgcattg-------------------taa-ttttttcagttagtgct--a---tttcctccatag-agtag-tatggatttatctgccatcagtgatgt------------ata-aagtta
q ponAbe2.chr3                                              9999999-------------------999-99999999999999999--9---999999999999-99999-999999999999999999999999999------------999-999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158755636 84 + 189746636 tgcattg-------------------taatttttttcaacgagtgctaca---tttcctccatag-agtag-tatggatttatctgctatcagtgatgt------------ata-aagttg
q rheMac2.chr2                                              9999999-------------------999999999999999999999999---999999999999-99999-999999999999999999999999999------------999-999999
i rheMac2.chr2                     C 0 C 0
s loxAfr3.scaffold_36                 508024 80 -  24123610 ----ttg-------------------taa-ttttttcaggaattaccaga---tttcctccatagaagtaa-tacaaattcgcctctcatctgtgattt------------aca-agagca
q loxAfr3.scaffold_36                                       ----999-------------------999-99999999999999999999---999999999999999999-999999999999999999999999999------------999-999999
i loxAfr3.scaffold_36              C 0 C 0
s sorAra1.scaffold_217076                 35 73 -      8965 ------------------------------ttttCCTAGATATTGCCAGA---CTCTCTTCACAA-AGTAA-CTCAACTTTGGTTCCCACCAGAAAGAT------------ACA-AAAGTC
q sorAra1.scaffold_217076                                   ------------------------------99998888999999998799---999999998999-99999-999746999999999999999999999------------999-999999
i sorAra1.scaffold_217076          N 0 C 0
s equCab2.chr16                     22206330 76 -  87365405 --------------------------tag-ttttttcagatattgccaga----ttcctccataa-agtagatacagctttacctcccatcagcgctgt------------aca-aaggca
q equCab2.chr16                                             --------------------------999-99999999999999999999----99999999999-999999999999999999999999999999999------------999-999999
i equCab2.chr16                    C 0 C 0
s mm9.chr17                         50247419 72 +  95272651 --------------------------TCA-TGGGCTCAGATAGCGCCAGACTTCTTCGTTCATAA-AGAAG-TAAAGACTTACATCTCTCTATAAAACTTT--------------------
i mm9.chr17                        I 187 I 180
s cavPor3.scaffold_0                 8217933 44 -  88675666 -----------------------------------------------------TTTCCTCCATAT-AGTAG-TAGAGATTTACCTCCCATCAGTGATAT----------------------
q cavPor3.scaffold_0                                        -----------------------------------------------------999999999999-99999-999999999999999999999999999----------------------
i cavPor3.scaffold_0               I 200 C 0
e bosTau4.chr1                     156977363 218 + 161106243 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=290805.000000
s hg19.chrY                          7647061 321 +  59373566 TTTGTTTTCCCATACTG----------------------------------TGGCTATTGTC-----AGTGGAA-AAAAAAA-----AAATGATCCC--TGTGAGATGTTAA-CTTATATTtctcttattgtgt---aatttgt------atttttttcttattaaacatttcacatttaaatgc----tgtttctccttctctgtgaactgtctgtccattatctttgcctggcatccttttggg-tcattggaccttttttc-tattggtt-----tgtaagaactgtttacatattaggaaATTTGGTTT-------CT-AT--------------------TTATCTGTC--CCCGATTTGTTGCTTGCCTTTTGACTTTGTATATGGTAGGTTTTGCTATGAAAttt-----ttttttt
s rheMac2.chr2                     158755720 319 + 189746636 tttcttttcccatactc----------------------------------tggctactctc-----agta-ga-aaaaaa----------gatccc--tgtgagatggtaa-cttatatttctcttattatgt---aatttgt------atttttttcttattaaacatttcatatttaaatgc----tgtgtttccttgtctgtgaactctctgtccgttatctttgcctggtgtcctattggg-tcattggac-gtttttc-tattggtt-----tgtaagaactctttacatattaggaaatttagttt-------tt-at--------------------ttatctgtc--cccaatttggtgcttgccttttgactttgcatatggtgggttttgccatgaaACACtttttttttttt
q rheMac2.chr2                                               99999999999999999----------------------------------99999999999-----9999-99-999999----------999999--9999999999999-999999999999999999999---9999999------99999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999-999999999-9999999-99999999-----99999999999999999999999999999999999-------99-99--------------------999999999--99999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027546 315 - 202140232 tttcttttcccatactc----------------------------------tgactattctc-----agtg-aa-aaaaaaa---------gatctc--tgtgagatggtaa-cttatatttatcttattatgt---aatttgt------a-ttttttcttattaaacatttcgtatttaaatgc----tgtgtctccttgtctgtgaactgtctgtccattatctttgcctcgtgtcctattgag-tcattgggctttttttc-tattggtt-----tgtaagaactctttacatattaggaaatttagttt-------ttaat--------------------gtatcagcc--cccaatttgtcacttgccttttgactttgcatatagtgggttttgccatgaaAAt------ttttttt
q ponAbe2.chr3                                               99999999999999999----------------------------------99999999999-----9999-99-9999999---------999999--9999999999999-999999999999999999999---9999999------9-999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999-99999999999999999-99999999-----99999999999999999999999999999999999-------99999--------------------999999999--9999999999999999999999999999999999999999999999999999999------9999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        500590 325 +  23952694 TTTGTCTTCCCATACTG----------------------------------TGGCTATTATC-----AGTG-AA-AAAAAAA-----ACATGatccc--tgtgagatgttaa-cttatatttctcttattgtgt---aatttgt------atttttttcttattaaacatttcacatttaaatgc----tgtttttccttctctgtgaactgtctgtccattatctttgcctggcatccttttggg-tcattggaccttttttc-tattggtt-----tgtaagaactgtttacatattaggaaatttggttt-------tt-at--------------------ttatctgtc--cccaatttgttgcttgccttttgactttgtatatggtgggttttgctatgaaAtttcttttttttttt
q panTro2.chrY                                               00000000000000000----------------------------------00000000000-----0000-00-0000000-----0000000000--0000000000000-000000000000000000000---0000000------00000000000000000000000000000000000----000000000000000000000000000000000000000000000000000000000-00000000000000000-00000000-----00000000000000000000000000000000000-------00-00--------------------000000000--00000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s bosTau4.chr1                     156977581 309 + 161106243 TTCTTTTCCCCACGCCC----------------------------------TGGCTACTGTC-----ACAg-tg-aaa---------agatgattcc--taggaggtggtaa-ttcatagttctcttgttatgt---aatttgt------acttttttcatactaaacatttcacgtttaaatgctatttatgttgtcttttctgttaa-------ttcataatttttgcctagttgtcaactggg-ttattgatc---------tgttggtt-----tgt---aattcttaatatattaggaaatccagttc-------tt-atttgtgataa----tgcaa--atacctctc-----aattcgt---ttgtcttttgactttgcataacatgagttttc-catgaaaaatgtttt-----tt
q bosTau4.chr1                                               99999999999999999----------------------------------99999999999-----9999-99-999---------9999999999--9999999999999-999999999999999999999---9999999------99999999999999999999999999999999999999999999999999999999999-------999999999999999999999999999999-999999999---------99999999-----999---99999999999999999999999999999-------99-99999999999----99999--999999999-----9999999---99999999999999999999999999999999-999999999999999-----99
i bosTau4.chr1                     I 218 I 375
s equCab2.chr16                     22206406 283 -  87365405 tttcccttctcacgccc----------------------------------cggctaatctc-----atag-tg-aaa---------aaatgacccc--tgtgaggtggtaa-tttgtatttctcttattatgt---aatttta------a-ttttttcttattaaacattttatgtttaaatgctatcagtgttgccttttctgttaa----ctgttcatagtcgctgcctagttttcttttggg-ttattggtccttttttcttattGGTT----------------CTTATTTGT-----GATGCCGGTG-------gc-a------------------a--atatcttcc--cacaattta----ttgtcttttgacttggtgaaaggtgcctttcgctatg------------------
q equCab2.chr16                                              99999999999999999----------------------------------99999999999-----9999-99-999---------9999999999--9999999999999-999999999999999999999---9999999------9-999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999-99999999999999999999999999----------------999999999-----9999999999-------99-9------------------9--999999999--999999999----9999999999999999999999999999999999999------------------
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961               7965 268 +     88154 TTTCTTTTTCCAT--------------------------------------------GTCTT-----AATT-AC---------------------CT--AGCAAAATG---------TGTGTCTCTTGCTGTGt---taattat------a--tttttcttattagcCAGTCCATGTCTAAAttctatttgtattatttttcctGTTAA----CTGCTCACAATC-CTCCTTGCTTGTCCATtgag-ttatttttccttttttcctactGGCTTGTGTTGTGGGGGTCTCAT---TAGTGGGAAATTTAGTT------------TTTGTGATGCCGGTTGCAA--ATATCTGTT--ctcaactta----cttttttt-----------------tttttac-catgat----------------
q eriEur1.scaffold_377961                                    9999999999999--------------------------------------------99999-----9999-99---------------------99--999999999---------99999999999999999---9999999------9--99999999999999999999999999999999999999999999999999999999----999999999999-99999999999999999999-999999999999999999999999999999999999999999999---99999999999999999------------9999999999999999999--999999999--999999999----99999999-----------------9999999-999999----------------
i eriEur1.scaffold_377961          C 0 C 0
s sorAra1.scaffold_217076                108 236 -      8965 TTTGTTTTTCCATAGTC----------------------------------TGGCTAATCTC-----ATTA-TC---------------------CT--TTTGagatg-------------------gctatatatatatatat------a--tttctcttgttG------------------------TGTGCT-----------------------------------TTGTTCATCATTTG--------TTTCATCTTCTAGTATTAATT----TTGTAAGAACTCTTTATATAGGAGGAATTTTAGTTC-------TT-ATTTGTGAGGCCAGTTCTAA--CTATCT-TT--CTGA---TA----CATTCTTT-GACTTTGCATGAAGAGTTTtttc-cataataattttttt-----gg
q sorAra1.scaffold_217076                                    99999999999999999----------------------------------99999999999-----9999-99---------------------99--999999999-------------------99999999999999999------9--999999999999------------------------999999-----------------------------------99999999999999--------999999999999999999999----999999999999999999999999999999999999-------99-99999999999999999999--999999-99--9999---99----99999999-99999999999999999999999-999999999999999-----99
i sorAra1.scaffold_217076          C 0 I 38
s canFam2.chr23                     25986816 295 -  55389570 -ttccttttccatgtcc----------------------------------tggctaatttc-----atag-tgaaaa---------aaatgatctt--tat--tgtggcaa-tttgtatttctcttactacat---aacttat------a-ttttttcttactgaacatctcatgtttaaatactatctgtgtcaccttttctattaa----ctgttcataatctttgcctagttttctattggg-ttattggtccttttctc-tattgatt-----tgtcaaaactctttatatattaggaaatttagttg-------tc-at-------------tgc-a--atagctttc--ccaaattta----ttgttttttgactttgcataaggtgggttttg-----------------------
q canFam2.chr23                                              -9999999999999999----------------------------------99999999999-----9999-999999---------9999999999--999--99999999-999999999999999999999---9999999------9-999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999-99999999999999999-99999999-----99999999999999999999999999999999999-------99-99-------------999-9--999999999--999999999----99999999999999999999999999999999-----------------------
i canFam2.chr23                    C 0 I 1
s oryCun2.chr14                      2463750 318 + 163896628 -tcctttgcccatgccc----------------------------------cgcccactctc-----agag----------------aaatgactgctgtgtgaggtgctga-cgtacatttctcctattttgt---aatttgt----------atttcttattaaatgttacatatgcaaatgc----tgtgcctccttttctgtgga----ctttgcatcatctttccctggttttctgttggatttattggtc-ctttttc-tattggtt-----tacagacactctttacatattaggaaaattagtcctaaattgtt-gt-------atccgttacaa--gtatctttc--cctaatatgttgtttg-cttttgactttccataaagtggttttgc-catgaagaatgtttt-------
q oryCun2.chr14                                              -9999999999999999----------------------------------99999999999-----9999----------------9999999999999999999999999-999999999999999999999---9999999----------9999999999999999999999999999999----99999999999999999999----9999999999999999999999999999999999999999999-9999999-99999999-----99999999999999999999999999999999999999999999-99-------99999999999--999999999--9999999999999999-9999999999999999999999999999-999999999999999-------
i oryCun2.chr14                    C 0 C 0
s cavPor3.scaffold_0                 8217977 295 -  88675666 -CTCTTTTCTCATA-CC----------------------------------TGGATATCCTATTTTTAAAA----------------ATATGATGCC--TGTGAAGTGACAA-TTTACACTTC-----TCTTAT---TAGGTGT------T-AGTGTTTTtattaaacatttcatatttaaatgc----tctacttctttctctgtgaa----atgtgcataatctgttc-------tctattgga-ttactggtc-ttgttta-tgttggtg-----tgtagtaactctttatatactaggaaatttaactc-aaattgtg-ct-------accagtgccaa---tatctttt--cccaatttgttgcttgtcttttgactttgtataaggtaggtttcgc----------------------
q cavPor3.scaffold_0                                         -9999999999999-99----------------------------------99999999999999999999----------------9999999999--9999999999999-9999999999-----999999---9999999------9-999999999999999999999999999999999----99999999999999999999----99999999999999999-------999999999-999999999-9999999-99999999-----99999999999999999999999999999999999-99999999-99-------99999999999---99999999--9999999999999999999999999999999999999999999999----------------------
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107342646 283 - 113440463 -CTCTCTTCCTGTGCCC----------------------------------TGGATAATCTC---AGAGAA-GA-AAAGGAAAGAGGAAACGATCCC--TGTGAGATG-CGA-TATATACTTC-----CTATGC---GACCTGTAATAGCG-GAAGCTATTAATAAACCTTCCTTATTTAAA--------------TTGTGCACATGAG----CTGTGGGAACTCAGCCC---GGTGTTTATTGGA-TCACTGACCAATGTTCC-ACCTGATC-----CACAGGACCTATT-ATATATGAGAGAATTTAGTTT---GTGATG-AT----------------AGGAGTGTCTCTC--ATTAATCCATTACTTGCCTGTTGACGTCGCA-------------------------------------
q rn4.chr9                                                   -9999999999999999----------------------------------99999999999---999999-99-9999999999999999999999--999999999-999-9999999999-----999999---99999999999999-999999999999999999999999999999--------------9999999999999----99999999999999999---9999999999999-99999999999999999-99999999-----9999999999999-999999999999999999999---999999-99----------------9999999999999--9999999999999999999999999999999-------------------------------------
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50247671 285 +  95272651 -TTCTCTTCCCATGCCC----------------------------------TGGA-AATCTCATAATAAAA-GG-AAAGGAAAGAGAAAACGATCCC--TGTGTGGTG-CCA-TCTACACTTT-----CTATGC---AATCCAT------G-GCTTCTCTTATTAACCCTTCCTTATTCAAA--------------CTGTGCCTATGAG----CTGTGGGAACTCTGCCC---AGTTTTTATTGGA-TTCTTGACCAATTTTCC-ACCTGGTC-----CACAAGAACGATC------TTAGAGAATTTAGTTC---TTGATG-AT-------ACAGGCTGCAAGTGTGTCTCTCCTATCAATTCAATACTTCCCTTTTGACTTTGCA-------------------------------------
i mm9.chr17                        I 180 C 0
s loxAfr3.scaffold_36                 508104 348 -  24123610 tttctcttcctctgccctagcaaaaaagtgtgtcactaaatttttttatcttggctcatctc-----atag-gt-gaaa--------aagtgatctc--tgtgaggttgtaattttgtatttctcttattatat---aactcac------g-ttttctctttttgaacatttcatatttaaacgctttctgtatgtccttttctgtgaa----ctgttcataacctttggctgcttttctattggg-ttattgatccttctttc-------------------------tttacctattaggaaatttagctc-------tt-atttgtgaaaccagttgcaa--atatctttc--cccaatttgttg-ttttcttttcactctgcataaggtgatttttgtcatgaaatgttttgtt------
q loxAfr3.scaffold_36                                        99999999999999999999999999999999999999999999999999999999999999-----9999-99-9999--------9999999999--99999999999999999999999999999999999---9999999------9-999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999-99999999999999999-------------------------999999999999999999999999-------99-99999999999999999999--999999999--999999999999-9999999999999999999999999999999999999999999999999------
i loxAfr3.scaffold_36              C 0 C 0
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802  28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=21311.000000
s hg19.chrY                          7647382  92 +  59373566 tttgg-----acaaagtctctctctggtgcccaag-------ctggagtgcagtgacactatctcagttcactgcaaactccacctcctgggttcaagtgatt---------c
s panTro2.chrY                        500915  92 +  23952694 tttgg-----acaaagtctctctctggtgcccaag-------ctggagtgcagtgacactatctcagttcactgcaaactccacctcctgggttcaagcgatt---------c
q panTro2.chrY                                               00000-----0000000000000000000000000-------0000000000000000000000000000000000000000000000000000000000000---------0
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71027861  92 - 202140232 ttaag-----acaaagtctctctctgttgcccagg-------ctggagtgcagtggcgctatccccactcactgcaaactctgcctcctgggttcaagtgatt---------c
q ponAbe2.chr3                                               99999-----9999999999999999999999999-------9999999999999999999999999999999999999999999999999999999999999---------9
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158756039  92 + 189746636 tttag-----atgaagtcttgctctgttgcccagg-------ctggagtgcagtggcgctatccccactcactgcaaactctgcctcctgggttcaagtgatt---------c
q rheMac2.chr2                                               99999-----9999999999999999999999999-------9999999999999999999999999999999999999999999999999999999999999---------9
i rheMac2.chr2                     C 0 C 0
s sorAra1.scaffold_217076                382 102 -      8965 tctgcactcaagaattacccctggcggtgctcaggggaccatatgggatgctgggaatcaaacccaggtcg----accacctacctgctgtgct------attgctccagcc-
q sorAra1.scaffold_217076                                    99999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999------999999999999-
i sorAra1.scaffold_217076          I 38 C 0
s eriEur1.scaffold_377961               8233  21 +     88154 tCTGC-------------------------------------ATGAGATG---------------------------------------GAGTT------ATT----------
q eriEur1.scaffold_377961                                    99999-------------------------------------99999649---------------------------------------99999------999----------
i eriEur1.scaffold_377961          C 0 C 0
e cavPor3.scaffold_0                 8218272   0 -  88675666 C
e rn4.chr9                         107342929   0 - 113440463 C
e mm9.chr17                         50247956   0 +  95272651 C
e oryCun2.chr14                      2464068   0 + 163896628 C
e equCab2.chr16                     22206689   0 -  87365405 C
e bosTau4.chr1                     156977890 375 + 161106243 I
e loxAfr3.scaffold_36                 508452   0 -  24123610 C
e canFam2.chr23                     25987111   1 -  55389570 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802  28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-518.000000
s hg19.chrY                          7647474 40 +  59373566 CATGGAAAA-CTTTTTAAA---TAAAGCTAAAT---TTACCAATCTT
s sorAra1.scaffold_217076                484 46 -      8965 cccataaca-atttttaaaagctgaaatTGAAGTCATTGTCACCTTG
q sorAra1.scaffold_217076                                   999999999-9999999999999999999999999999999999999
i sorAra1.scaffold_217076          C 0 C 0
s eriEur1.scaffold_377961               8254 37 +     88154 ----TTACACACTTTTATA---TGAAGTTGAAT---TTATCAATCTT
q eriEur1.scaffold_377961                                   ----988999647999999---99999989999---99999999889
i eriEur1.scaffold_377961          C 0 C 0
s equCab2.chr16                     22206689 36 -  87365405 ----gagaa-ttttttttg---taaaggtgaat---ttatcaatctt
q equCab2.chr16                                             ----99999-999999999---99999999999---99999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25987112 38 -  55389570 cataaagaa-ttttttaTG-----GAGCTAAAT---TACTCAATATT
q canFam2.chr23                                             999999999-999999999-----999999999---99999999999
i canFam2.chr23                    I 1 I 184
s cavPor3.scaffold_0                 8218272 40 -  88675666 catgaataa-tttttttca---taaagttaagt---ttatcagtcct
q cavPor3.scaffold_0                                        999999999-999999999---99999999999---99999999999
i cavPor3.scaffold_0               C 0 C 0
s panTro2.chrY                        501007 40 +  23952694 CATGGAAAA-CTTTTTAAA---TAAAGCTAAAT---TTACCAATCTT
q panTro2.chrY                                              000000000-000000000---00000000000---00000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71027953 40 - 202140232 CATGAAAAA-CTTTTTAAA---TGAAGCTGAAT---TTACCAATCTT
q ponAbe2.chr3                                              999999999-999999999---99999999999---99999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158756131 40 + 189746636 CATGAAAAA-CTTTTTAAA---TGAAGCTGAAT---TTACCAATCTT
q rheMac2.chr2                                              999999999-999999999---99999999999---99999999999
i rheMac2.chr2                     C 0 C 0
s loxAfr3.scaffold_36                 508452 20 -  24123610 ---------------------atgcagttaaat---ttatcaat---
q loxAfr3.scaffold_36                                       ---------------------999999999999---99999999---
i loxAfr3.scaffold_36              C 0 C 0
s mm9.chr17                         50247956  9 +  95272651 -----------------------AAAGTTGAG---------------
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107342929  9 - 113440463 -----------------------AAAGTGGAG---------------
q rn4.chr9                                                  -----------------------999999999---------------
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2464068 23 + 163896628 ------------------a---tgaacttgaat---gtatcattctt
q oryCun2.chr14                                             ------------------9---99999999999---99999999999
i oryCun2.chr14                    C 0 C 0
e bosTau4.chr1                     156977890 375 + 161106243 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=163173.000000
s hg19.chrY                          7647514 67 +  59373566 GCTTTCAATGGCTTCTGAGTTTTATGTCATAGGAGA--AAGACCTGGAATTGTAAAACAGTTATCTTGT
s rheMac2.chr2                     158756171 67 + 189746636 GCTTTCAGTGGCTTCCGAGTTTTATGTCATAACAGA--AAGACCTGGGATTATAAAACAATTCTCTTGT
q rheMac2.chr2                                              999999999999999999999999999999999999--9999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71027993 67 - 202140232 GCTTTCAATGGCTTCTGAGTTTTATGTCATAGCAGA--AAGACGTGGGATTATAAAACAATTCTCTTGT
q ponAbe2.chr3                                              999999999999999999999999999999999999--9999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501047 67 +  23952694 GCTTTCAATGGCTTCTGAGTTTTATGTCATAGGAGA--AAGACCTGGAATTGTAAAACAGTTATCTTGT
q panTro2.chrY                                              000000000000000000000000000000000000--0000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218312 67 -  88675666 gtcttcagtggctTTGAAAATGTGTGTCATGGCACA--AAGACCTGGGACTACAAAACCGTTTTCCTGT
q cavPor3.scaffold_0                                        999999999999999999999999999999999999--9999999999999999999999999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464091 67 + 163896628 gttttcaatggcttctgagttttatgttatagcaga--aagacccaggattataaaacagttctcctgt
q oryCun2.chr14                                             999999999999999999999999999999999999--9999999999999999999999999999999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107342938 54 - 113440463 ------------TTTGCATGTGTG-ACGACAGCAGA--AAGGCACTGGACCGTGCGACAACTTTTCTGT
q rn4.chr9                                                  ------------999999999999-99999999999--9999999999999999999999999999999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50247965 50 +  95272651 -------------TTGCATATGTT-ATTATAGCAAA--AAGATGTTGGAATAT---ATAACTTTTCTGT
i mm9.chr17                        C 0 C 0
s canFam2.chr23                     25987334 65 -  55389570 GCCTTCAATGACT--TGAATTTTATGTCATAGCAGA--GAGATCAGGGATCATAAAACAATTTTCCTGT
q canFam2.chr23                                             9999999999999--999999999999999999999--9999999999999999999999999999999
i canFam2.chr23                    I 184 C 0
s equCab2.chr16                     22206725 67 -  87365405 gtcttcaacagcttctgagttttatgtcacagcaga--gagatctgggattataaaacaattctcctgt
q equCab2.chr16                                             999999999999999999999999999999999999--9999999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961               8291 59 +     88154 -CCTTGAACAGCTTCTGGGTCTTATAGCAGAGAGCCCTGATACTATA------AAAATAATTCTGT---
q eriEur1.scaffold_377961                                   -9999999999999999999999999998795689988997999999------9999899999888---
i eriEur1.scaffold_377961          C 0 C 0
s sorAra1.scaffold_217076                530 63 -      8965 -ACTTTATTGTCTTCTGAGTTTTATGCCACAGTGAA--GATATCAAAGAGTGGAAAACAATTCCAT---
q sorAra1.scaffold_217076                                   -99999999999999999999999999999999999--9999999999999999999999999999---
i sorAra1.scaffold_217076          C 0 C 0
s loxAfr3.scaffold_36                 508472 65 -  24123610 --tttctatagcttttgagttttatgtcatagtaga--aagacctgagattataaaaccattctcctgt
q loxAfr3.scaffold_36                                       --9999999999999999999999999999999999--9999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e bosTau4.chr1                     156977890 375 + 161106243 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=64302.000000
s hg19.chrY                          7647581 58 +  59373566 GAATTCTCAT-----AAAACT-----TATTTCATTTTTTTGCAT------AAAAATCTTTGATTG-ATTTGGGAT
s rheMac2.chr2                     158756238 57 + 189746636 GAATTCTCAT-----AATACA-----TATTTCA-TTTTTTGCAT------ATAAATCTTTTATCG-ATTTGGCAT
q rheMac2.chr2                                              9999999999-----999999-----9999999-9999999999------999999999999999-999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028060 50 - 202140232 GAATTCCCA-----------------TATTTTA-TTTTTTGCAT------ATAAATCTTTTATCG-ATTTGGAAT
q ponAbe2.chr3                                              999999999-----------------9999999-9999999999------999999999999999-999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501114 58 +  23952694 GAATTCTCAT-----AAAACT-----TATTTCATTTTTTTGCAT------AAAAATCTTTGATTG-ATTTGGGAT
q panTro2.chrY                                              0000000000-----000000-----000000000000000000------000000000000000-000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218379 56 -  88675666 GAATCCTGAT-----GACACA-----TATATCA--TTTTTGCAT------ATACATCTTGACTGT-TTTGGGGAA
q cavPor3.scaffold_0                                        9999999999-----999999-----9999999--999999999------999999999999999-999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464158 56 + 163896628 gaatgctggt-----aataca-----tatttca--tttctgtat------ataaatctttgatcc-atttggaat
q oryCun2.chr14                                             9999999999-----999999-----9999999--999999999------999999999999999-999999999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107342992 50 - 113440463 TAATGCTT-----------TA-----TATCACA-TTTTTTACGT------GTGAATCTTACATAT-ATTTCATA-
q rn4.chr9                                                  99999999-----------99-----9999999-9999999999------999999999999999-99999999-
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50248015 54 +  95272651 TAATGCTT-----------CATAAGGTATCACA--TTTTTGCAT------GTAAATCTTAAATAT-ATTTCAGA-
i mm9.chr17                        C 0 C 0
s bosTau4.chr1                     156978265 51 + 161106243 AAATTCTT-C-----ATGGCA-----AAACTCA-TGTTATGCAT------ATAAATATTATACAG-GTTT-----
q bosTau4.chr1                                              99999999-9-----999999-----9999999-9999999999------999999999999999-9999-----
i bosTau4.chr1                     I 375 I 80
s equCab2.chr16                     22206792 57 -  87365405 gatttcttgt-----agtgca-----tatttca-ttttttacat------gtaaatctttgatgc-atttggaat
q equCab2.chr16                                             9999999999-----999999-----9999999-9999999999------999999999999999-999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25987399 49 -  55389570 ---------T-----AAGACA-----TATTTCA-TTTTTCAGAT------GTGAATCTTTGAGCCAATTTGGAAT
q canFam2.chr23                                             ---------9-----999999-----9999999-9999999999------9999999999999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               8350 56 +     88154 GCTTTCCTTA-----GGTACA-----TAGTT-A-CTTTCTGTAT------ATAAATGCTAGCTAC-ATTTGGTAC
q eriEur1.scaffold_377961                                   9999999999-----997999-----99999-9-9999999799------999999998899889-999999699
i eriEur1.scaffold_377961          C 0 C 0
s sorAra1.scaffold_217076                593 66 -      8965 GGTTTCTTGATTTCTAGGACA-----Aagtg-g-ttctttttattttttaaaagattct-gaTGC-TTTTAGTAT
q sorAra1.scaffold_217076                                   999999999999999999999-----99999-9-9999999999999999999999999-99999-999999999
i sorAra1.scaffold_217076          C 0 N 0
s loxAfr3.scaffold_36                 508537 57 -  24123610 tatttcttgt-----aATACA-----TATTTCA-TTTTTTGCCT------ATAAACACTTGATAC-ATTTGGAAT
q loxAfr3.scaffold_36                                       9999999999-----999999-----9999999-9999999999------999999999999999-999999999
i loxAfr3.scaffold_36              C 0 C 0
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=15064.000000
s hg19.chrY                          7647639 58 +  59373566 TTATCCCAGGTAAACTAT-GCAATATGAATTTAAC----------------TCCCCCACACAC--CCACACACAGGG
s rheMac2.chr2                     158756295 51 + 189746636 TTATCCCATGTAAAGTGT-GCAGTACGAATTTAAC----------------TCCCCCCCAC---------CACAGGG
q rheMac2.chr2                                              999999999999999999-9999999999999999----------------9999999999---------9999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028110 51 - 202140232 TTATCCCATGTAAAGTGT-GCAATATGAATTTAAC----------------TCCCCCCCAC---------CACAGGG
q ponAbe2.chr3                                              999999999999999999-9999999999999999----------------9999999999---------9999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501172 58 +  23952694 TTATCCCATGTAAACTAT-GCAATATGAATTTAAC----------------TCCCCCACACAC--CCACACACAGGG
q panTro2.chrY                                              000000000000000000-0000000000000000----------------000000000000--000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218435 46 -  88675666 GTGTCTTTTGTAAGGCATGAAGTTATGAATTCAACA---------------TCCTCCC----------------AGA
q cavPor3.scaffold_0                                        999999999999999999999999999999999999---------------9999999----------------999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464214 60 + 163896628 ttatCCCATGTAGAGCAT-ACGATCTGAATTCAATATCCAGACATCCACTTTCCTCAG----------------GGG
q oryCun2.chr14                                             999999999999999999-999999999999999999999999999999999999999----------------999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107343042 43 - 113440463 -TTTACCTTGCAAAGCGT-ACACTATGAGTTCAAC----------------CCCCCCT----------------GAA
q rn4.chr9                                                  -99999999999999999-9999999999999999----------------9999999----------------999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50248069 41 +  95272651 -TTTACTTTGCAAAGCAT-ACACTATGAATTCAA------------------CCCCCT----------------GAA
i mm9.chr17                        C 0 C 0
s canFam2.chr23                     25987448 28 -  55389570 --------------TTAT-GCAATATGAATTCAAC----------------ATCCCACC------------------
q canFam2.chr23                                             --------------9999-9999999999999999----------------99999999------------------
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22206849 32 -  87365405 --------------ttat-GCAACATGAATTAAAC----------------ATTTTCCCATTT--------------
q equCab2.chr16                                             --------------9999-9999999999999999----------------999999999999--------------
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961               8406 34 +     88154 --------------TTAT-GCAAAATGAAttcacc----------------ccccccacacccag------------
q eriEur1.scaffold_377961                                   --------------9999-9979998999998799----------------99999958588969------------
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 508594 48 -  24123610 TTATCTGGTATAACGTAT-GCGATATGAATTCAATATAC------------TTCCCCagac----------------
q loxAfr3.scaffold_36                                       999999999999999999-99999999999999999999------------9999999999----------------
i loxAfr3.scaffold_36              C 0 C 0
e bosTau4.chr1                     156978316 80 + 161106243 I
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=338188.000000
s hg19.chrY                          7647697 376 +  59373566 GTTTATCTATT-TTTCC---------------------TCATTGATTTCA----------------GA--TGCCATATATTATATGCCATTTATCAT----TCATTATATTC---------CCAGATA----TG----AGTTTA------TGACTGtgatccatc---------aatctatt---tgtataaa--acactacttcaa-acaattttaatttcacat------------------------tatgt-ttta--atatctggtt-----------------------aaaccatt------tctcaaat----tttccta------------tattcctgtt--ta--tgttttgtatcctc-------------ctaatttgtttttctaaatga---tcttt-aaaaaatctgctcagtaaattc--cctttcctccaccagaaaa-----------------aaacttgtgggtatttttactaggtcatgttcaaa-tcatag-ctaactg---------aaaatgaata-ttttcaccaagctgcaagttcccatgcaag--aaactggca
s rheMac2.chr2                     158756346 376 + 189746636 GTTTATCCATT-TTTTC---------------------TCATTGATTTGA----------------GAGGTGCCATATATCATATGCCATTTGTCAT----TCGTTATATTC---------CCAAATA----TC----AGTTTA------TGACTGTGATCCATG---------AATCTATT---TGTATAAA--ACCCTAGTTTAA-ACAATTTTAATTTCGTAT------------------------TGTCT-TTTA--ATATCTGCTT-----------------------AACCTATT------TATCAAAT----CTTCCTA------------TATTCCTGTT--TA--TATTTTGAATCTTC-------------CTAAtttgtttttctacatga---tcttt--aaaaatcagctcagtaagttt--cccttcctccact--aaaa-----------------aagtctgtgggtatttttattgggtcacattcaaa-tcattgcttaactg---------agaatgagta-ttttcaccatgctgcaagttcccatgcaag--aaactggca
q rheMac2.chr2                                               99999999999-99999---------------------999999999999----------------9999999999999999999999999999999----99999999999---------9999999----99----999999------999999999999999---------99999999---99999999--999999999999-999999999999999999------------------------99999-9999--9999999999-----------------------99999999------99999999----9999999------------9999999999--99--99999999999999-------------999999999999999999999---99999--999999999999999999999--9999999999999--9999-----------------99999999999999999999999999999999999-99999999999999---------9999999999-999999999999999999999999999999--999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028161 369 - 202140232 GTTTATCcatt-tttcc---------------------tcattgatttga----------------ga--tgccatatatcatgtgccatttatcat----tcattatattc---------ccaaata----tg----agttta------tgACTGTGATCCAT--------------TATT---TGTATAAA--ACACTACTTCAA-ACAATTTtaatttcatat------------------------tatgt-ttta--atatctggtt-----------------------aaactact------tgtcaaat----cttccta------------tattcctgtt--ta--tattttgaattttc-------------ctaatttgtttttctaaatga---tcttt--aaaaatcagctcagtaaatac--cccttcctccact--aaaa-----------------aagtttgtgggtatttttaatgcgtcatgttcaaa-tcatagcctaactg---------agaatgaata-ttttcaccacgctgcaagttcccatgcaag--aaactggca
q ponAbe2.chr3                                               99999999999-99999---------------------999999999999----------------99--999999999999999999999999999----99999999999---------9999999----99----999999------99999999999999--------------9999---99999999--999999999999-999999999999999999------------------------99999-9999--9999999999-----------------------99999999------99999999----9999999------------9999999999--99--99999999999999-------------999999999999999999999---99999--999999999999999999999--9999999999999--9999-----------------99999999999999999999999999999999999-99999999999999---------9999999999-999999999999999999999999999999--999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501230 376 +  23952694 GTTTATCTATT-TTTCC---------------------TCATTGATTTCA----------------GA--TGCCATATATTATATGACATTTATCAT----TCATTATATTC---------CCAGATA----TG----AGTTTA------TGACTGtgatccatc---------aatctatt---tgtataaa--acactactttaa-acaattttaatttcacat------------------------tatgt-ttta--atatctggtt-----------------------aaaccatt------tctcaaat----tttccta------------tattcctgtt--ta--tgttttgaatcttc-------------ctaatttgtttttctaaatga---tcttt-aaaaaatctgctcagtaaattc--cctttcctccaccagaaaa-----------------aaatttgtgggtatttttactaggtcatgttcaaa-tcatag-ctaactg---------aaaatgaata-ttttcaccaagctgcaagttcccatgcaag--aaactggca
q panTro2.chrY                                               00000000000-00000---------------------000000000000----------------00--000000000000000000000000000----00000000000---------0000000----00----000000------000000000000000---------00000000---00000000--000000000000-000000000000000000------------------------00000-0000--0000000000-----------------------00000000------00000000----0000000------------0000000000--00--00000000000000-------------000000000000000000000---00000-0000000000000000000000--0000000000000000000-----------------00000000000000000000000000000000000-000000-0000000---------0000000000-000000000000000000000000000000--000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218481 347 -  88675666 GTTTATCCATT-TTT--------------------------TAAATTTGA----------------AA--TGCAA------------CTTTTATCATCTAGTAA------------------TGAATA----T------ATTTAAGTTT-AGGCTATAATACA-T---------AATTTA-----TGCATTAACAGTATTGTTTTGA-ACAATGTTAGTTCATAA-------------------------CATAT-TTTT--GTATCTGGTT-----------------------AGGCTGTT------CCTTGACT----TTC----------------TCTTCCTCTT---------TCTGAATCTTC-------------CTAATTTATTTTTCCAAATGG---TCTTT--ACAAATCACCTCATCAAATTCTGTCATACCttcccc--caaa-----------------a----tgctgaaacttttattagaccatgttcaaa-ttacagcttaactgtggg-----agaatgaataatttttaccacgcagagcactcccattcgag--aacatggaa
q cavPor3.scaffold_0                                         99999999999-999--------------------------999999999----------------99--99999------------99999999999999999------------------999999----9------9999999999-9999999999999-9---------999999-----9999999999999999999999-99999999999999999-------------------------99999-9999--9999999999-----------------------99999999------99999999----999----------------9999999999---------99999999999-------------999999999999999999999---99999--999999999999999999999999999999999999--9999-----------------9----999999999999999999999999999999-999999999999999999-----99999999999999999999999999999999999999999--999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464274 337 + 163896628 GTctattcgag-ttc-c---------------------tcattgatttga----------------ga--t-cca------------cctttaccat----atattatattc---------ctgaata----c------atttaagtttacgactgtgattcatt---------tgtccact---tgtaggta----acatttttta-cccactttagtttcatat------------------------tatat-tttt--gtatctagta-----------------------agctattt------cctgaa-------------------------tcctcctaat----------------------------------ttgtttgtttttccaaatgg---tcttt--aaaaatcagttcattaaattcc-ccctccctccaaa--gaaa-----------------c----tgctgatatttttattggatcatgttccaa-ctattgcttaacagagag-----agagaggata-tgttcaccatgccgccagtttccatccaag--aacatggca
q oryCun2.chr14                                              99999999999-999-9---------------------999999999999----------------99--9-999------------9999999999----99999999999---------9999999----9------99999999999999999999999999---------99999999---99999999----9999999999-999999999999999999------------------------99999-9999--9999999999-----------------------99999999------999999-------------------------9999999999----------------------------------99999999999999999999---99999--9999999999999999999999-9999999999999--9999-----------------9----999999999999999999999999999999-999999999999999999-----9999999999-999999999999999999999999999999--999999999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107343085 337 - 113440463 AGTTACCTGTT-TTTTC---------------------TTATTGATTTGA----------------GA--AGTGA------------CTTTTCTCGT----GAA------------------TGAATA----T------ATTTG------TGACCGCAATAAATT---------AACTTATT---TGCGTTAC----ACTATCTTTC-ATCACGTTAGTTTTGTA-------------------------AGTATGTTTT--GGGTTTG-------------------------------TTT------CCTGAAAT----TTT--TG------------TCTCCCTGTT--TA--ACCTCTAAACCTTCT------------TTACTTTCTTTTTCAAAATCG---TTTTT-TTTAAACCAACTAATCAAATCCC-CCTTTCATTCCCT--TAAA-----------------A---GTGTTAATATTTTTATTGAATCATATTCAAA-CTGAAGCTTGACCAGGAGCATTAAAACCGAGCCTTTCCCACCATGC-------TGGTGTCCGCA-------AACA
q rn4.chr9                                                   99999999999-99999---------------------999999999999----------------99--99999------------9999999999----999------------------999999----9------99999------999999999999999---------99999999---99999999----9999999999-99999999999999999-------------------------9999999999--9999999-------------------------------999------99999999----999--99------------9999999999--99--999999999999999------------999999999999999999999---99999-99999999999999999999999-9999999999999--9999-----------------9---9999999999999999999999999999999-9999999999999999999999999999999999999999999999-------99999999999-------9999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50248110 356 +  95272651 GGTTACCTACT-TTTCC---------------------TTATTGATTTGA----------------GA--GGCGA------------CTTTTCGCTT----AAA------------------TGAATAGAGTT------GTTTG------TGACTGTAATAAATT---------AACTCATT---TGCATTAA----ACTCTCGTTC-ACCACCCTAGCTTCATA-------------------------AGTATGTTTT--GGGTCTG-------------------------------TTT------CCTGCACT----TTT----------------TCTTTCTGTT--TA--ATTTCTAAACCTCCT------------TTAATGTCTTTTTCAAAATCA---TTTTTAAAAAAATCAACTAACCAAGTTCC-CCCTTCATTCTCT--TAAA-----------------AAG-GTGTTGATGTTTTTACTGAATCGTATTCAAA-CTGTAGCTTAAGCAAGAGCATTAAAACTTCGCGGTTTCCACCGTGCTGCTAGTTGCTATCCACAACAGCCCAGCG
i mm9.chr17                        C 0 C 0
s bosTau4.chr1                     156978396 488 + 161106243 GTTTATTTGTT-TTT-CTGAGTGGTCTTTAAAATAAGTTCATTAAATTACCCCTCAAAAAAATCTTGT--TGCTA------------TTTTTATCA------GATCATGTTCACATTATAGCTGAGAA----TG---GATTTTC------Ttctttttactcatttttaattgaaatatagttaatttacaat---------------attgtgttagtttcaggtgtacagaaaagtgattcagttatacatat-cttaatatatctattctttttcaaattccgtttcattataggttattacaagatcctgaatatggttccctgtactgcacagtaggtccctgttgata--gtagtttgatatattagtCTCCAATTCCTAACTTATCACTCT---------CCCCT---CAGACTATCTGATTTTCTTT--TTAATC---CATA--GGAATTGGA-------AATTGAAGCCAAACAATACT----TTAGAGAAAGTTAAGA-----ATGTCAACACCCCg-----agaatggata-ttttcatcgtgccacaagtttccacccaag--aacatggca
q bosTau4.chr1                                               99999999999-999-9999999999999999999999999999999999999999999999999999--99999------------999999999------99999999999999999999999999----99---9999999------9999999999999999999999999999999999999999999---------------99999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999---------99999---99999999999999999999--999999---9999--999999999-------99999999999999999999----9999999999999999-----99999999999999-----9999999999-999999999999999999999999999999--999999999
i bosTau4.chr1                     I 80 C 0
s equCab2.chr16                     22206881 361 -  87365405 -TTTATCCATT-TTC-C---------------------TCATTGATTTGA----------------GT--TACCA------------CCTTTATCAT----ATATTATATTC---------CTGAATA----TATTTAAGTTTA------TGACTGTAATCCATT---------AATACATT---TTAGCAAT--------------------GTtagtttcatat------------------------tatat-ttta--atatctgctc-----------------------tggctatt------tcctgaat----cttccta------------gcttcctgtt--ta--ttttctgaatcttcctgtctattcttacttatttgtttttccaaagga---tcttt---aaaatcagctcatcaaattc--cccctc---caca--aaaa-----------------aatggtgttaatatttttattggatcatgttcaaatttatagctttactgaggg-----agaatggata-ttttcatcatgctacaagttcccacacaag--aacacagca
q equCab2.chr16                                              -9999999999-999-9---------------------999999999999----------------99--99999------------9999999999----99999999999---------9999999----999999999999------999999999999999---------99999999---99999999--------------------9999999999999------------------------99999-9999--9999999999-----------------------99999999------99999999----9999999------------9999999999--99--999999999999999999999999999999999999999999999999---99999---99999999999999999999--999999---9999--9999-----------------999999999999999999999999999999999999999999999999999999-----9999999999-999999999999999999999999999999--999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25987476 329 -  55389570 ------CCCTT-TTT-C---------------------TCATTAATTTGA----------------GC--TGTCA------------CCTTTATCA---------TATATTC---------TTGAACA----TA--TAAATTTA------TTATTGTGATCCATT---------AATctgtt---ttaacaat-------------------------tttaatgt------------------------catgt-ttta--acatctggtc-----------------------aggctatt------tcctgaaa----cttctta-------------tttcctttt--ta--gtttctgaatcttcctttctttttt----------ttttttttaatga---ccttt---aaaactaactcatcaaacct--tccttc-----ca--aaaa-----------------aatcttattggtattattattggatcatgttaaaa-ttatagcttaactgaggg-----agaatggata-tcttcatcacactgtaagttcccatccaag--gacaagga-
q canFam2.chr23                                              ------99999-999-9---------------------999999999999----------------99--99999------------999999999---------9999999---------9999999----99--99999999------999999999999999---------99999999---99999999-------------------------99999999------------------------99999-9999--9999999999-----------------------99999999------99999999----9999999-------------999999999--99--9999999999999999999999999----------9999999999999---99999---99999999999999999999--999999-----99--9999-----------------99999999999999999999999999999999999-999999999999999999-----9999999999-999999999999999999999999999999--99999999-
i canFam2.chr23                    C 0 I 1
s eriEur1.scaffold_377961               8440 366 +     88154 GTTTACCCATTCCTT-C---------------------TTATTAGAGACA----------------GC-------------------CCTTCATTGT----ACACTGCAACC---------CTAAATT----TATTCAAGGTTA------TGGACACAGCCTATT---------AACCTCTT---TTGACAAC--------------------TTTGGATTCATAT------------------------TTTGC-TTTA--ATCTGTAGTC-----------------------TGGTTATT------TTCTAAAT----CTTCCAA------------GATTGCTGTT--TACTTTTTCTGAATCTTCATGTctattct----tgtttgtttttccaaatgGTCTTCTTT---AAATTCAGCTCATCAAATTc--ccctcc---agaa--aaaaaaaaaaaagagcaaagagatCTTCTTGATATTTTGATCAGCTCATCTTCAA--TTATAGCTT-ACTGGGAG-----AGC---GATG-TTTTCAT---GCTACAGATTCCCAC-TGAG--GACATGACG
q eriEur1.scaffold_377961                                    969979995877767-6---------------------699778988745----------------88-------------------8878747887----65486855679---------8858869----857853878367------698564859683866---------86555859---98756588--------------------5887853986585------------------------89996-6885--8687637737-----------------------39526549------97645855----6585526------------5627344838--75538887665453557635756456642----762664146675646534416535274---35557425555335486254--884553---1544--6776776777642111373344435435443212267523353333332313224--323234432-51146221-----331---2012-2665323---443331232336323-9979--166679998
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 508642 355 -  24123610 --ttatccatt-tt------------------------tcattgatttga----------------ga--tgcta------------cctttatcat----acactataatc---------ctgaata----tatttaagttca------tgactgtcatccatt---------aatctatc---tattcttt----atctctacaacactactttagtttcctat------------------------tacat-ttta--atatccagcc-----------------------aggctatt------tcctgaat----attccta------------------tctt--ta--ttttctgaatcttcctgtatatt----cttgtttgtttttccaaatgg---ttttt---aaaatcagct------------cgttccctcccaa--aaaa-----------------aatcatgttgatatttttattggatcatattcaag-ttatatcttcactgaac------agaatggaga-tattcatgatgttgcaagttcctttccaaa--gaggtggta
q loxAfr3.scaffold_36                                        --999999999-99------------------------999999999999----------------99--99999------------9999999999----99999999999---------9999999----999999999999------999999999999999---------99999999---99999999----99999999999999999999999999999------------------------99999-9999--9999999999-----------------------99999999------99999999----9999999------------------9999--99--99999999999999999999999----999999999999999999999---99999---9999999999------------9999999999999--9999-----------------99999999999999999999999999999999999-99999999999999999------9999999999-999999999999999999999999999999--999999999
i loxAfr3.scaffold_36              C 0 I 1
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e felCat3.scaffold_206809                532 2602 -    143945 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802  28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=232500.000000
s hg19.chrY                          7648073 62 +  59373566 aaattttga-tttgttcaagtcttcctttgggttcctctggagcata---ctaaagttttcttcac
s rheMac2.chr2                     158756722 62 + 189746636 aaattttga-ttcgttcaattgttcctttgggtccctctggagcata---ctaaagttttcttcac
q rheMac2.chr2                                              999999999-9999999999999999999999999999999999999---9999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028530 62 - 202140232 aaattttga-tttgctcaagtcttcctttgggtccctctggagcata---ctaaagttttcttcac
q ponAbe2.chr3                                              999999999-9999999999999999999999999999999999999---9999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501606 62 +  23952694 aaattttga-tttgttcaagtcttcctttgggttcctctggagcaca---ctaaagttttcttcac
q panTro2.chrY                                              000000000-0000000000000000000000000000000000000---0000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218828 62 -  88675666 taactttga-cttactcaagtcttccactaggtccctcaggagcata---ttaaggttttcctcac
q cavPor3.scaffold_0                                        999999999-9999999999999999999999999999999999999---9999999999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464611 62 + 163896628 taactttga-tttactcaagtcttcttttagatccctcgggagcgta---ttaaagtttccttcac
q oryCun2.chr14                                             999999999-9999999999999999999999999999999999999---9999999999999999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107343422 61 - 113440463 CCGTTTGGA-TTTACTTGAGTTGTCCTTTTGGTCCCTCTGGAGCATA---TTAAAA-TTCTGTCAC
q rn4.chr9                                                  999999999-9999999999999999999999999999999999999---999999-999999999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50248466 61 +  95272651 CCATTTTGA-TTTACTTGAGTTGTATTTTTCGTCCCTTGAGAGCATA---TTAAAA-TTTCGTCAC
i mm9.chr17                        C 0 C 0
s bosTau4.chr1                     156978884 61 + 161106243 tgactttca-tttattcaagac-tttttggggtccctcagatgcata---ttataatttttttcat
q bosTau4.chr1                                              999999999-999999999999-999999999999999999999999---9999999999999999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22207242 59 -  87365405 caactttcg-tttattcaag---tcttttcagtccttcagatgcata---ttaaagttttcttcac
q equCab2.chr16                                             999999999-9999999999---999999999999999999999999---9999999999999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4120 61 -      4973 -AATTTTTGTTTTATTCAAGACTTCTTTGGGGTCCTTCAGGCACGTA---TTAAAGTTTTC-TCAC
q felCat3.scaffold_111908                                   -6667654226733165464526626835883424344355555565---55694568953-5455
i felCat3.scaffold_111908          n 2602 C 0
s canFam2.chr23                     25987806 61 -  55389570 -aatttttg-tttattcaagatttctttggggtccctcaggcacatt---ttaaagttttcttcac
q canFam2.chr23                                             -99999999-9999999999999999999999999999999999999---9999999999999999
i canFam2.chr23                    I 1 C 0
s eriEur1.scaffold_377961               8806 65 +     88154 TAATTTTCA-TTGATTTGAGACTTCTCTAGAGTCCCTCAGGAGCCTGCCCTGCCAAGTTTCTTCAC
q eriEur1.scaffold_377961                                   899999966-99999996342359999999999999999999999999999989999999999989
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 508998 53 -  24123610 gactctcca-tgtatttaagccctcttttgagtccctcaggagcatg---tgaaagt---------
q loxAfr3.scaffold_36                                       999999999-9999999999999999999999999999999999999---9999999---------
i loxAfr3.scaffold_36              I 1 C 0
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e turTru1.scaffold_111402               8317 1443 -     37689 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=173281.000000
s hg19.chrY                          7648135  80 +  59373566 acagatagta------------------------------------------------------------------------------------------------------------catattt-atcaag-ttaatttctagttatcctgtatt-ttattcctattggaatactata----------t-------------------------------------------------ttt-cc-tttttc-
s rheMac2.chr2                     158756784 129 + 189746636 acagatagta------------------------------------------------------------------------------------------------------------catattt-atcagg-tttattcctagttattctatatt-ttattgctattggaataattta----------tcaggtttattcctagttattctatattttattgctattggaatGATATGTTT-TC-TTTTTC-
q rheMac2.chr2                                               9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999999999-9999999999999999999999----------99999999999999999999999999999999999999999999999999999-99-999999-
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028592  80 - 202140232 acagatagca------------------------------------------------------------------------------------------------------------catattt-atcagg-tttattcctagttattctatatt-ttattgctattggaaTAATACA----------T-------------------------------------------------TTT-CC-TTTTTC-
q ponAbe2.chr3                                               9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999999999-9999999999999999999999----------9-------------------------------------------------999-99-999999-
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501668  80 +  23952694 acagatagta------------------------------------------------------------------------------------------------------------catattt-atcaag-ttaatttctagttatcctgtatt-ttattcctattggaagactata----------t-------------------------------------------------ttt-cc-tttttc-
q panTro2.chrY                                               0000000000------------------------------------------------------------------------------------------------------------0000000-000000-00000000000000000000000-0000000000000000000000----------0-------------------------------------------------000-00-000000-
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218890  78 -  88675666 atggatatta------------------------------------------------------------------------------------------------------------catattt-attaaa-tgtatttctagttgttttatgtt-ttatttctagtagaat---aga----------t-------------------------------------------------ttt-ttaaatttt-
q cavPor3.scaffold_0                                         9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999999999-9999999999999999---999----------9-------------------------------------------------999-999999999-
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464673  80 + 163896628 atagacatta------------------------------------------------------------------------------------------------------------catattt-atcagg-tctattcctagttgttttatatc-tcattgctattggaaTAATAAA----------T-------------------------------------------------CTC-CT-TGTTTT-
q oryCun2.chr14                                              9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999999999-9999999999999999999999----------9-------------------------------------------------999-99-999999-
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107343483  81 - 113440463 GTGGCTATTA------------------------------------------------------------------------------------------------------------TATATTT-ATCAAG-TTTATTCCTAGTCACTTTATAATGTCGCTTCTATTACAGTAACAGA----------T-------------------------------------------------TCT-CT-GGCTTC-
q rn4.chr9                                                   9999999999------------------------------------------------------------------------------------------------------------9999999-999999-9999999999999999999999999999999999999999999999----------9-------------------------------------------------999-99-999999-
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50248527  81 +  95272651 ATGGATATTA------------------------------------------------------------------------------------------------------------TATATTT-ATCAAGTTTTACTCCTAGTCATTTTGTATTCTTGTTTCTA-GAGAGTATCAGA----------T-------------------------------------------------TCT-CT-GGCTTC-
i mm9.chr17                        C 0 C 0
s bosTau4.chr1                     156978945  80 + 161106243 gtagctactg------------------------------------------------------------------------------------------------------------cacactt-atgaag-tctcttcctagttattttatatt-ttattgctatttgaatag----------attct-------------------------------------------------ttt-CT-CCTTTT-
q bosTau4.chr1                                               9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999999999-999999999999999999----------99999-------------------------------------------------999-99-999999-
i bosTau4.chr1                     C 0 C 0
s turTru1.scaffold_111402               9760 188 -     37689 atggatattttcatcacgctgcaagtttccatccaagaacattgcatgatttttgtttattcaagactctttaggggtcccctgggtgcatattaaaattttcttcacatagatactgcacactt-gtgaag-tttattcctagttattttatatt-ttattgctatttgaattg----------ttttt-------------------------------------------------ttt-ct-CCTTTT-
q turTru1.scaffold_111402                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999-99999999999999999999999-999999999999999999----------99999-------------------------------------------------999-99-999999-
i turTru1.scaffold_111402          I 1443 C 0
s equCab2.chr16                     22207301  84 -  87365405 gtaaatactg------------------------------------------------------------------------------------------------------------cacactt-actaag-tttattcctagttactttataat-gtactgctattggaatagtaca------attat-------------------------------------------------ttt-tT-CTTTTT-
q equCab2.chr16                                              9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999999999-9999999999999999999999------99999-------------------------------------------------999-99-999999-
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4181  72 -      4973 ATAGATATTG------------------------------------------------------------------------------------------------------------CACACTTAAACAAG-TTTATTC-TACTAA-----------TATTGCTATTGGAATAATAGA------ATTTT-------------------------------------------------TTT----CTTTTT-
q felCat3.scaffold_111908                                    4645465554------------------------------------------------------------------------------------------------------------54655667936655-5965883-663696-----------664685666566956756567------69999-------------------------------------------------999----579996-
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25987867  78 -  55389570 atagatattg------------------------------------------------------------------------------------------------------------tacactt-atcaat-tttactcttatttatct--------tactgttattggagtaataga------atttt-------------------------------------------------tttCCC-CTTTTT-
q canFam2.chr23                                              9999999999------------------------------------------------------------------------------------------------------------9999999-999999-99999999999999999--------999999999999999999999------99999-------------------------------------------------999999-999999-
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               8871  91 +     88154 ATAAATACTG------------------------------------------------------------------------------------------------------------CACACTTAACTGAG-CTTAATCCtagtttctctgtatc-tttttgcTGCTGGAgtaatggactttttttttt-------------------------------------------------ttt-tt-cttttt-
q eriEur1.scaffold_377961                                    9999999999------------------------------------------------------------------------------------------------------------99999999999999-99999999999999999999999-999999999999999999999999999999999-------------------------------------------------999-99-989999-
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 509051  68 -  24123610 --------------------------------------------------------------------------------------------------------------------------ttt-ATCAAG-ATTAATCCCAGTTACTTTATATTTTTGTTCTTATTAGAATAATAGT----------T-------------------------------------------------TTT-TC-TTTTTTT
q loxAfr3.scaffold_36                                        --------------------------------------------------------------------------------------------------------------------------999-999999-9999999999999999999999999999999999999999999999----------9-------------------------------------------------999-99-9999999
i loxAfr3.scaffold_36              C 0 C 0
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e echTel1.scaffold_321361             111564 5226 +    198078 I
e monDom5.chr8                     276496802  28 + 312544902 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=187572.000000
s hg19.chrY                          7648215 78 +  59373566 acttCTGtaatattcattgtgtgt------aaaggtgttggggaaacaggc-acgcccct--tgtc--a-tggtggga-----gtgaacctttct
s rheMac2.chr2                     158756913 78 + 189746636 ACTTCTGTAATCGTCCCTGCGTgc------aagggtgctggggaaacaggc-atggccct--catc--g-tggtggca-----gtgaacctttct
q rheMac2.chr2                                              999999999999988999996766------669999999999999999999-99999999--9999--9-99999999-----999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028672 78 - 202140232 ACTTCTGtaatattcactgcatgc------aagggtgttggggaaacaggc-atggccct--catc--g-tggtggga-----gtgaacctttct
q ponAbe2.chr3                                              999999999999999999999999------999999999999999999999-99999999--9999--9-99999999-----999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501748 78 +  23952694 acttCTGtaatattcattgtgtgt------aaaggtgttggggaaacaggc-acgcccct--tgtc--a-tggtggga-----gtgaacctttct
q panTro2.chrY                                              000000000000000000000000------000000000000000000000-00000000--0000--0-00000000-----000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8218968 66 -  88675666 acttCTAGAATACCT-------------------ACACTGGAGAAACAGCT-ATCCTTCT--CACA--GCTGGTTGGA-----GCAAACCTTTCT
q cavPor3.scaffold_0                                        999999999999999-------------------99999999999999999-99999999--9999--9999999999-----999999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464753 79 + 163896628 ACTCCCATAGCATCCGCCGTGGGC------AAGGATGCTGGGGAGAGAGGC-GAGCTCAT--CACA--GCTGGTCCGA-----GCAAATCTTTCC
q oryCun2.chr14                                             999999999999999999999999------999999999999999999999-99999999--9999--9999999999-----999999999999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107343564 67 - 113440463 AGGCCCATAATGTCC-------------------CTGCTGGGGAATCAGAC-AGACTCTT--GTCACTGCTGA-TGGA-----GGGGATCCCTCT
q rn4.chr9                                                  999999999999999-------------------99999999999999999-99999999--99999999999-9999-----999999999999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50248608 64 +  95272651 AGCTCCAACATG-CC-------------------CCGCTGGGGAGGCAGAC-AGGCTCAT--GCCA--GCTGA-TGGA-----GCGAATCTCTGT
i mm9.chr17                        C 0 C 0
s bosTau4.chr1                     156979025 79 + 161106243 ACTTCTATGATACTCATCGTGGGC------AAGAACGTTGGGGCAACAGTC-TCGCTCGT--CGTG--GCTGACAGGG-----GAGAACCTTTGC
q bosTau4.chr1                                              999999999999999999999999------999999999999999999999-99999999--9999--9999999999-----999999999999
i bosTau4.chr1                     C 0 C 0
s turTru1.scaffold_111402               9948 79 -     37689 ACTTCTGTGATCTCcattgtgggc------aagaatgttggagaaacagtc-atgctcat--ggcg--gctgacagtg-----gtgaacctttct
q turTru1.scaffold_111402                                   999999999999999999999999------999999999999999999999-99999999--9999--9999999999-----999999999999
i turTru1.scaffold_111402          C 0 C 0
s equCab2.chr16                     22207385 78 -  87365405 ACTTCTATGATATCAATCACGGGC------AAGAAGATtggggaaacagacaacgctcat--caca--gttgat-ggg-----gtg-acctttct
q equCab2.chr16                                             999999999999999999999999------999999999999999999999999999999--9999--999999-999-----999-99999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4253 78 -      4973 ACTTCTATGCTATCcattgtgggc------aagaatgttggggaaacaggc-atgctcat--catg--gttgat-cgg-----gtaaactttttt
q felCat3.scaffold_111908                                   967969867695768666767967------968966788999889696979-77869858--9669--977687-699-----775995999992
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25987945 76 -  55389570 ATTCCTATGCTACCCATT-CAggc------aagaatgttggggaaatagcc-atattcat--catg--g-tgat-gtg-----gtgaacttctct
q canFam2.chr23                                             999999999999999999-99999------999999999999999999999-99999999--9999--9-9999-999-----999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               8962 79 +     88154 gctttgatGCTAGCTTTTGTGAGC------AAGAATA-TGGAGAAGCAGGC-AAGTTCATCGCACA--GTGGAC-GGG-----CTGAATCTTTCT
q eriEur1.scaffold_377961                                   999999999999999999999999------9999999-9999999999999-99999999999999--999999-999-----999999999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 509119 78 -  24123610 ACTTTTATGGTATCcattgtgggc------aaggatgttggggaaacaggc-atggccct--catg--gttggt-agg-----gtgaccctttct
q loxAfr3.scaffold_36                                       999999999999999999999999------999999999999999999999-99999999--9999--999999-999-----999999999999
i loxAfr3.scaffold_36              C 0 C 0
s echTel1.scaffold_321361             116790 88 +    198078 ACTTTTGTGATGCCCTCAGTGAGTGAAAAAGAAAAAGCCGGGAGAAGGAGT-GT-GCCCT--CACG--ACTGGT-GGGCATGCCTGATACCTTCT
q echTel1.scaffold_321361                                   999999999999999999999997999999999999999999999999999-96-98999--9989--999999-99999999999999999997
i echTel1.scaffold_321361          I 5226 C 0
e vicPac1.scaffold_6092                36957 1906 -     83534 I
e speTri1.scaffold_135460              75393 1253 -    203079 I
e micMur1.scaffold_734                256013 12562 -    418489 I
e ochPri2.scaffold_2292                98903 1220 +    188698 I
e tupBel1.scaffold_130011.1-168288     38871 4238 -    168288 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e calJac1.Contig102                  1024939 4716 -   1157145 I
e monDom5.chr8                     276496802 28 + 312544902 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e papHam1.scaffold12353                38119 19689 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=326629.000000
s hg19.chrY                          7648293 82 +  59373566 tgagg------gcagg-----gtg--atattggccttcat-acctaaaaatgcacacactgtttgtccagcaaccccactatt-ggcagtacttcta
s rheMac2.chr2                     158756991 82 + 189746636 tgagg------gcagg-----atg--ctatcggccttcaa-acctaaaaatgcacacactctttgcccagcaaccccactact-ggtagtacttcta
q rheMac2.chr2                                              99999------99999-----999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028750 82 - 202140232 tgagg------gcacg-----gtg--gtattggccttcaa-acctaaaaatgcacacactctttgtccagcaaccctactact-ggtagtacttcta
q ponAbe2.chr3                                              99999------99999-----999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501826 82 +  23952694 tgagg------gcagg-----gtg--gtattggccttcat-acctaaaaatgcacacactgtttgtccagcaaccccactatt-ggcagtacttcta
q panTro2.chrY                                              00000------00000-----000--00000000000000-000000000000000000000000000000000000000000-0000000000000
i panTro2.chrY                     C 0 C 0
s calJac1.Contig102                  1029655 82 -   1157145 ctagg------gcaga-----gtg--gtattggccttcaa-tcctaaaaatgcacatactctctgtccagcaacccctctact-ggcagtactccta
q calJac1.Contig102                                         99999------99999-----999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i calJac1.Contig102                I 4716 C 0
s cavPor3.scaffold_0                 8219034 74 -  88675666 --GCG----G-AGTAG-----GCA--CATT-------CAA-ACCTCAAAATGTACACACTTCCTGTCCAAAAACCCCACTACT-GGTGTTAAACCTA
q cavPor3.scaffold_0                                        --999----9-99999-----999--9999-------999-999999999999999999999999999999999999999999-9999999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2464832 79 + 163896628 --AGA----GGACCAG-----GTG--TGCTT--GCCCTAC-ACCTAGCGATGCACACACCCTGTGCCCAGCAACCCCACTACT-GGAACTGGTTCT-
q oryCun2.chr14                                             --999----9999999-----999--99999--9999999-999999999999999999999999999999999999999999-999999999999-
i oryCun2.chr14                    C 0 I 1577
s rn4.chr9                         107343631 74 - 113440463 --GAGGGCAG-GTAAG-----GTG--CCTC---------G-ATCCCCCAGTGCATGGA--CTCTGCCCAGGGTCGCCATCATT-TGGAGCAGTCCTA
q rn4.chr9                                                  --99999999-99999-----999--9999---------9-99999999999999999--99999999999999999999999-9999999999999
i rn4.chr9                         C 0 I 821
s mm9.chr17                         50248672 72 +  95272651 --GAG----G-GTAAG-----GCG--CATT---------A-ATCTCCTAGTGCATGGACGCTCTGTGCAGGATCTCCACCATT-TGGAGCATTCCTA
i mm9.chr17                        C 0 I 1211
s ochPri2.scaffold_2292               100123 57 +    188698 -----------GCGGG-----AGG--CGTTC--CCTCCGG-ACTCAGTCAT------------------GCAGCCTCACTACT-AGAAGTGCACCTA
q ochPri2.scaffold_2292                                     -----------99999-----999--99999--9999999-9999999999------------------99999999999999-9999999999999
i ochPri2.scaffold_2292            I 1220 C 0
s micMur1.scaffold_734                268575 74 -    418489 --------------ag-----gga--gtgtttgccttcaa-ttataaaaacacacacaccctttgtccagcaaccttgctact-ggtattattctgg
q micMur1.scaffold_734                                      --------------99-----999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i micMur1.scaffold_734             I 12562 C 0
s gorGor1.Supercontig_0191774          12775 75 -     13449 -------------agg-----gtg--gtattgcccttcaa-acctaaaaatgcacacactctttgtccagcaaccctactact-ggtagtacttcta
q gorGor1.Supercontig_0191774                               -------------999-----999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i gorGor1.Supercontig_0191774      N 0 C 0
s papHam1.scaffold12353                57808 75 +     70985 -------------agg-----atg--ctattgaccttcaa-acctaaaaatgcacacactctttgtccagcaaccccactact-ggtagtacttcta
q papHam1.scaffold12353                                     -------------999-----999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i papHam1.scaffold12353            I 19689 C 0
s tupBel1.scaffold_130011.1-168288     43109 69 -    168288 ------------TAAG-----GTA--GTGTTTACCTCCAA-GCCT-AAAATGCACACACCCTTAGTCCAGCAGCTCC-TTACT------TACTCCCA
q tupBel1.scaffold_130011.1-168288                          ------------9999-----999--99999999999999-9999-9999999999999999999999999999999-99999------99999999
i tupBel1.scaffold_130011.1-168288 I 4238 C 0
s bosTau4.chr1                     156979104 83 + 161106243 -----------GGAGGGTTGTGTG--GTGTTTGCCTTCAG-TCTTAAAAGTGCATTCACCCTGCATCCAACAGCCTCACCACTGGGTATTATGCCTA
q bosTau4.chr1                                              -----------9999999999999--99999999999999-99999999999999999999999999999999999999999999999999999999
i bosTau4.chr1                     C 0 C 0
s turTru1.scaffold_111402              10027 83 -     37689 -----------ggagggccgtgtg--gcattttccctcaa-tcctaaaagtgcatttgcactttgtccagcaacctcgccactgagttttatgcctg
q turTru1.scaffold_111402                                   -----------9999999999999--99999999999999-99999999999999999999999999999999999999999999999999999999
i turTru1.scaffold_111402          C 0 C 0
s equCab2.chr16                     22207463 82 -  87365405 -----------ggagggcaatgtg--gtgactgcctccaa-actgaaaagtgtctgcgccctttgtccagcaactccgctgct-ggtattacgccta
q equCab2.chr16                                             -----------9999999999999--99999999999999-999999999999999999999999999999999999999999-9999999999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4331 83 -      4973 -----------gaaggggaatatg--atgcttgccttcca-acctaaaagtacacacaccctttgtccaacaaccccactactggatactgcatcta
q felCat3.scaffold_111908                                   -----------6998997989979--97977959599899-99998999989999997999999999999999999999999999999999999999
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25988021 85 -  55389570 -----------ggagggtaatatagtgtgtttgtcttcaa-acctaaaagtacacacaccctttgtccaacaatcccactactaggtattttgccta
q canFam2.chr23                                             -----------99999999999999999999999999999-99999999999999999999999999999999999999999999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               9041 67 +     88154 -----------GAACGGCAGTGTG--GTATCTGCCTTCA-----------------TACCCTCTGTGCCGCAGCCTCTCTACAGGGTAGTCAGCAAA
q eriEur1.scaffold_377961                                   -----------9999999999999--9999999999999-----------------99999999999999999999999999999999999999999
i eriEur1.scaffold_377961          C 0 C 0
s vicPac1.scaffold_6092                38863 73 -     83534 ---------------------gtg--gtgtctgccttcaa-aacttaaagtgcacacaccctttgtccagcaaactccctgctgggtatcacgctta
q vicPac1.scaffold_6092                                     ---------------------999--99999999999999-99999999999999999999999999999999999999999999999999999999
i vicPac1.scaffold_6092            I 1906 C 0
s speTri1.scaffold_135460              76646 28 -    203079 ---------------------ATG--CATT-------CAG-ACCTAAACTcacacacac--------------------------------------
q speTri1.scaffold_135460                                   ---------------------968--6999-------998-621128769876767555--------------------------------------
i speTri1.scaffold_135460          I 1253 I 1205
s loxAfr3.scaffold_36                 509197 83 -  24123610 tgagg------gcgag-----gtg--gtgtttgccttcaa-acctaaaaatgcccataccctttgtctagcagccccacaactgggtatcactccta
q loxAfr3.scaffold_36                                       99999------99999-----999--99999999999999-99999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s echTel1.scaffold_321361             116878 84 +    198078 GGAGG------CCAAG-----GTA--GGGTTTCCCTTTAGCCCCTAAAAGTGCACATCCCATTTGTCCAGCAGCACCAGCACTGGGTACTAATCCTA
q echTel1.scaffold_321361                                   89998------86856-----456--68859989999784499388999758566469998696548998675455979789589568997467998
i echTel1.scaffold_321361          C 0 C 0
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802 28 + 312544902 I
e otoGar1.scaffold_99909.1-31737        5376 1877 -     31737 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=311785.000000
s hg19.chrY                          7648375 39 +  59373566 tggctggaatcataaatgcctttc-aagatatatggacaa
s rheMac2.chr2                     158757073 39 + 189746636 tgactggactcacaaatgtctttc-aagatatatggacaa
q rheMac2.chr2                                              666666665655655676666666-666666664554346
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028832 35 - 202140232 tggctggactcacgaatgtctttc-aagatatatgg----
q ponAbe2.chr3                                              999999999999999999999999-99999999999----
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501908 39 +  23952694 tggctggaatcataaatgcctttc-aagatatatggacaa
q panTro2.chrY                                              000000000000000000000000-000000000000000
i panTro2.chrY                     C 0 C 0
s calJac1.Contig102                  1029737 39 -   1157145 tggctggactcataaatgtcttcc-aagatatatggacaa
q calJac1.Contig102                                         999999999999999999999999-999999999999999
i calJac1.Contig102                C 0 C 0
s papHam1.scaffold12353                57883 39 +     70985 tgactggactcacaaatgtctttc-aagatatatggacaa
q papHam1.scaffold12353                                     999999999999999999999999-999999999999999
i papHam1.scaffold12353            C 0 C 0
s gorGor1.Supercontig_0191774          12850 39 -     13449 cggctggactcatgaatgtctttc-aagatatatggacaa
q gorGor1.Supercontig_0191774                               999999999999999999999999-999999999999999
i gorGor1.Supercontig_0191774      C 0 C 0
s micMur1.scaffold_734                268649 39 -    418489 tggctggactcataactgtctttc-aagatatatggagaa
q micMur1.scaffold_734                                      999999999999999999999999-999999999999999
i micMur1.scaffold_734             C 0 C 0
s otoGar1.scaffold_99909.1-31737        7253 39 -     31737 tgaatggacttataaatgtcttac-aagatatataaacaa
q otoGar1.scaffold_99909.1-31737                            999999999999999999999999-999999999999999
i otoGar1.scaffold_99909.1-31737   I 1877 I 1
s tupBel1.scaffold_130011.1-168288     43178 39 -    168288 TGACTGGACACGTGGATGTCTTTT-GAGGAATACTGGcaa
q tupBel1.scaffold_130011.1-168288                          999999999999999999999999-999999999999999
i tupBel1.scaffold_130011.1-168288 C 0 C 0
s cavPor3.scaffold_0                 8219108 35 -  88675666 TGGCTGGACTCATG----TCTTTC-AAAATAAATGGACAA
q cavPor3.scaffold_0                                        99999999999999----999999-999999999999999
i cavPor3.scaffold_0               C 0 I 765
s ochPri2.scaffold_2292               100180 20 +    188698 AGTATGCACTCCTG-------------GATTAA-------
q ochPri2.scaffold_2292                                     99999999999999-------------999999-------
i ochPri2.scaffold_2292            C 0 C 0
s vicPac1.scaffold_6092                38936 40 -     83534 tggctggactcagaaatgtttctcaaagatatctggacaa
q vicPac1.scaffold_6092                                     9999999999999999999999999999999999999999
i vicPac1.scaffold_6092            C 0 C 0
s turTru1.scaffold_111402              10110 39 -     37689 tggctggactcctaaatgtttctc-aagatatatgggcaa
q turTru1.scaffold_111402                                   999999999999999999999999-999999999999999
i turTru1.scaffold_111402          C 0 C 0
s bosTau4.chr1                     156979187 38 + 161106243 C-GCTGGACACACAGATGTGTCTC-AAGATACATGCGCAA
q bosTau4.chr1                                              9-9999999999999999999999-999999999999999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22207545 39 -  87365405 tggctgggttcataaaagtttttc-aagatgtatggacaa
q equCab2.chr16                                             999999999999999999999999-999999999999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4414 39 -      4973 tggctggactcctagatgtttttc-aggctttatggacaa
q felCat3.scaffold_111908                                   999999999999999999999999-999999999999999
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25988106 34 -  55389570 tggctggactcataga-----atc-aagatatacggacaa
q canFam2.chr23                                             9999999999999999-----999-999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               9108 20 +     88154 GGACTAGACCCACGGG----CTTC----------------
q eriEur1.scaffold_377961                                   9999999999999999----9999----------------
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 509280 39 -  24123610 tgtctggactcacaaatgcttttc-aagatatatggacaa
q loxAfr3.scaffold_36                                       999999999999999999999999-999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s echTel1.scaffold_321361             116962 38 +    198078 TGTCCAGACTCGGGAATGCTTTTC-AAGATAT-TGAGCAA
q echTel1.scaffold_321361                                   567887778967878865859988-6975988-6885599
i echTel1.scaffold_321361          C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802 28 + 312544902 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=211004.000000
s hg19.chrY                          7648414 32 +  59373566 agat----atttaCTACTGGGTTGCTC-TAGT-AGCAA
s rheMac2.chr2                     158757112 32 + 189746636 agat----atttactactgggttgctc-taat-agcaa
q rheMac2.chr2                                              5555----5566666766666666666-5522-22226
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028867 29 - 202140232 ---t----atttgctactgggttgctc-taac-agcaa
q ponAbe2.chr3                                              ---9----9999999999999999999-9999-99999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501947 32 +  23952694 agat----atttactacTGGGTTGCTC-TAGT-AGCAA
q panTro2.chrY                                              0000----0000000000000000000-0000-00000
i panTro2.chrY                     C 0 C 0
s calJac1.Contig102                  1029776 32 -   1157145 acat----atttaCTACTGGGTTGCCC-TCAT-AGCAA
q calJac1.Contig102                                         9999----9999999999999999999-9999-99999
i calJac1.Contig102                C 0 C 0
s papHam1.scaffold12353                57922 32 +     70985 agat----atttactactgggttgctc-taat-agcaa
q papHam1.scaffold12353                                     9999----9999999999999999999-9999-99999
i papHam1.scaffold12353            C 0 C 0
s gorGor1.Supercontig_0191774          12889 32 -     13449 aggt----atttaCTACTGGGTTGCTC-TAAC-AGCAA
q gorGor1.Supercontig_0191774                               9999----9999999999999999999-9999-99999
i gorGor1.Supercontig_0191774      C 0 C 0
s micMur1.scaffold_734                268688 32 -    418489 aggt----atttactaaaaggttgttc-ttgg-aacca
q micMur1.scaffold_734                                      9999----9999999999999999999-9999-99999
i micMur1.scaffold_734             C 0 I 6
s otoGar1.scaffold_99909.1-31737        7293 33 -     31737 atat----ataaacaaagtggttgttc-ttggaaacca
q otoGar1.scaffold_99909.1-31737                            9999----9999999999999999999-9999999999
i otoGar1.scaffold_99909.1-31737   I 1 I 6
s tupBel1.scaffold_130011.1-168288     43217 31 -    168288 agat----attcactaccgggtt-ttc-tcat-agcaa
q tupBel1.scaffold_130011.1-168288                          9999----999999999999999-999-9999-99999
i tupBel1.scaffold_130011.1-168288 C 0 I 19
s cavPor3.scaffold_0                 8219908 32 -  88675666 AGAT----ATCCACTATAGTGCTGATC-TAAT-AGCAG
q cavPor3.scaffold_0                                        9999----9999999999999999999-9999-99999
i cavPor3.scaffold_0               I 765 I 3
s ochPri2.scaffold_2292               100200 32 +    188698 AGAT----ACTTACTACTGACTTGTTT-TAAC-AAAAA
q ochPri2.scaffold_2292                                     9999----9999999999999999999-9999-99999
i ochPri2.scaffold_2292            C 0 I 363
s vicPac1.scaffold_6092                38976 32 -     83534 agat----aatcactacagggtcactg-caat-ggcaa
q vicPac1.scaffold_6092                                     9999----9999999999999999999-9999-99999
i vicPac1.scaffold_6092            C 0 I 19
s turTru1.scaffold_111402              10149 32 -     37689 agtt----attcactacagggtcatca-caac-agcaa
q turTru1.scaffold_111402                                   9999----9999999999999999999-9999-99999
i turTru1.scaffold_111402          C 0 I 19
s bosTau4.chr1                     156979225 26 + 161106243 AGAT----GCTCACCACGGGATT-------AC-TGCAA
q bosTau4.chr1                                              9999----999999999999999-------99-99999
i bosTau4.chr1                     C 0 I 19
s equCab2.chr16                     22207584 36 -  87365405 agaaagacattcactactgggctgttc-atac-agcaa
q equCab2.chr16                                             999999999999999999999999999-9999-99999
i equCab2.chr16                    C 0 I 19
s felCat3.scaffold_111908               4453 28 -      4973 agat--------actacagatatgttc-acat-agcaa
q felCat3.scaffold_111908                                   9999--------999999999999999-9999-99999
i felCat3.scaffold_111908          C 0 I 19
s canFam2.chr23                     25988140 32 -  55389570 atat----actcactacaggcttgttc-ctat-agcaa
q canFam2.chr23                                             9999----9999999999999999999-9999-99999
i canFam2.chr23                    C 0 I 19
s eriEur1.scaffold_377961               9128 32 +     88154 AGAT----GTTCACTGCAGGGCTGTCT-GAAG-ggcaa
q eriEur1.scaffold_377961                                   9999----9999999999999999999-9999-99999
i eriEur1.scaffold_377961          C 0 I 18
s loxAfr3.scaffold_36                 509319 33 -  24123610 acat----attcactacagagttgtctgtaat-agcaa
q loxAfr3.scaffold_36                                       9999----999999999999999999999999-99999
i loxAfr3.scaffold_36              C 0 I 19
s echTel1.scaffold_321361             117000 33 +    198078 AACC----GGtcattgcagagttatttgtaat-atcaa
q echTel1.scaffold_321361                                   9397----786979269898799999699688-78999
i echTel1.scaffold_321361          C 0 I 23
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802 28 + 312544902 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=714867.000000
s hg19.chrY                          7648446 106 +  59373566 TCT-TAATTGCAGGAAT----AGTTATA----TACTGGAA----TATCCCAGTGATT-AATCCTATAAAC----CA-TTCAGaagattaaagtaaatctgttatgtgctgatatagaaacaagtc
s rheMac2.chr2                     158757144 106 + 189746636 TCT-TAATTGCAGGACC----AGTtaaa----cactggaa----taccccagtgatt-aatcctaggaac----ca-ttaagaagattagagtaaatctgttatgtgctgatacagaaatgagtc
q rheMac2.chr2                                               799-9999997878999----9999999----99999999----9999955789999-676665999999----99-999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71028896 106 - 202140232 tct-taattgcaggact----agttaaa----cactggaa----taccccagtgatt-aatcctatgaac----ca-ttaagaagattaaagtaaatctgttatgtgctgatatagaaacaagtc
q ponAbe2.chr3                                               999-9999999999999----9999999----99999999----9999999999999-999999999999----99-999999990999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        501979 106 +  23952694 TCT-TAATTGCAGGAAT----AGTTATA----TACTGGAA----TATCCCAGTGATT-AATCCTATAAAC----CA-TTCAGaagattaaagtaaatctgttatgtgctgatatagaaacaagtc
q panTro2.chrY                                               000-0000000000000----0000000----00000000----0000000000000-000000000000----00-000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s calJac1.Contig102                  1029808 102 -   1157145 TCT-TAATTGCAGGAC--------TAAA----CACTGAAA----CACTCCAGTGATT-aatcctatgaac----ca-ttaagaagattaaaataaatctgttatgtgctgatacggaaacgagtc
q calJac1.Contig102                                          999-999999999999--------9999----99999999----9999999999999-999999999999----99-999999999999999999999999999999999999999999999999
i calJac1.Contig102                C 0 C 0
s papHam1.scaffold12353                57954 106 +     70985 tct-taattgcaggacc----agttaaa----cactggaa----taccccagtgatt-aatcctaggaac----ca-ttaagaagattagagtaaatctgttatgtgctgatacagaaatgagtc
q papHam1.scaffold12353                                      999-9999999999999----9999999----99999999----9999999999999-999999999999----99-999999999999999999999999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s gorGor1.Supercontig_0191774          12921 106 -     13449 TCT-TAATTGCAGgact----agttaaa----cactggaa----taccccagtgatt-aatcctatgaac----cg-ttaagaagattaaagtaaatctgttatgtgctgatatagaaacaagtc
q gorGor1.Supercontig_0191774                                999-9999999999999----9999999----99999999----9999999999999-999999999999----99-999999999999999999999999999959995999939998777777
i gorGor1.Supercontig_0191774      C 0 C 0
s micMur1.scaffold_734                268726 101 -    418489 tct-tcactggaagac--------taaa----t-atcgga----cacccctatgatg-aatcctatgaaa----ca-ttaagaagattaaagtaaatctgttaagtcctgataaagaaatctgcc
q micMur1.scaffold_734                                       999-999999999999--------9999----9-999999----9999999999999-998999999997----79-999999999999999999889999999999999999999998999999
i micMur1.scaffold_734             I 6 C 0
s otoGar1.scaffold_99909.1-31737        7332  99 -     31737 tct-tcattggaggat--------taaa----caatggga----cactccaatgatg-aatcccacgaaggaacca-ttaagaagattta-------ctattcagtgctgataaagaaacctatc
q otoGar1.scaffold_99909.1-31737                             999-999999999999--------9999----99999996----9999999999999-997999699999997999-9999999999999-------9977999879999999999999999999
i otoGar1.scaffold_99909.1-31737   I 6 C 0
s tupBel1.scaffold_130011.1-168288     43267 104 -    168288 tct-tcgttggaagact----agttcaa----tcctgggg----caccccaatgatg-aatcctgtgaac----ta-ctaaaaagattcaggtaaatctgttacgtgctgatatggaaac--gtc
q tupBel1.scaffold_130011.1-168288                           999-9999999999999----9999999----99999999----9999999999999-999999999999----99-9999999999999999999999999999999999999999999--999
i tupBel1.scaffold_130011.1-168288 I 19 C 0
s cavPor3.scaffold_0                 8219943 113 -  88675666 TCTGGAACCAAAGAATTCTTCAG-TAAG----TACTAGTTAACATATTCCAATGGTA-AGTCTTAAGAA-----TG-TTAAGAAAGTCAAGGTAAATCTGCTATGTGTTAAAATGGAAATGTGTC
q cavPor3.scaffold_0                                         99999999999999999999999-9999----9999999999999999999999999-99999999999-----99-999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0               I 3 C 0
s ochPri2.scaffold_2292               100595  88 +    188698 TCT-TCATCAAAGCACT----AG-TAAA----TACTGGGC----TACCCCAGTGACG-AATTCTAGGAAC----CA-TTAAGATGACTAAAGCA--------ATGTGTT---ACGGAAA------
q ochPri2.scaffold_2292                                      999-9999979999999----99-9999----99999999----9999999999999-999999999999----99-99999999999999999--------9999999---9999999------
i ochPri2.scaffold_2292            I 363 C 0
s vicPac1.scaffold_6092                39027 101 -     83534 tct-t---tggagggct----agctaaa----cactggga----caccccaatgatg-aatcctataaac----ca-ttaagaaaattaaggtaaacctgttacgtgctact--gaaaatatgcc
q vicPac1.scaffold_6092                                      999-9---999999999----9999999----99999999----9999999999999-999999999999----99-99999999999999999999999999999999999--99999999999
i vicPac1.scaffold_6092            I 19 C 0
s turTru1.scaffold_111402              10200  91 -     37689 TCT-TCATTGGAGGGCT----AGCTCAA----CATTGGGA----CACCCCAATGATG-AATCCTCTGAAC----CA-TTAATA-------------TGTGTTACATGAGGAT--GAAAATGTGCC
q turTru1.scaffold_111402                                    999-9999999999999----9999999----99999999----9999999999999-999999999999----99-999999-------------9999999999999999--99999999999
i turTru1.scaffold_111402          I 19 C 0
s bosTau4.chr1                     156979270  90 + 161106243 TCC-TCACTGTAGGGCA----AGCTCAA----CACTGGGA----CACCCCAGTGATG-AATCCTATGAAC----CG-TTAAGA--------------GGATTACACACTAAT--GAAAACGTGTC
q bosTau4.chr1                                               999-9999999999999----9999999----99999999----9999999999999-999999999999----99-999999--------------999999999999999--99999999999
i bosTau4.chr1                     I 19 C 0
s equCab2.chr16                     22207639  91 -  87365405 TCT-TCACTGGTGTGCC----AGTTAAA---------------------CAATGATG-AATCCTATGAAC-----GTTTAAGGAGATTAAGGTAAATCTGTCATGTGCTGAT--GGAAACATGTC
q equCab2.chr16                                              999-9999999999999----9999999---------------------99999999-999999999999-----9999999999999999999999999999999999999--99999999999
i equCab2.chr16                    I 19 C 0
s felCat3.scaffold_111908               4500 108 -      4973 tct-tcattggcgagct----ggctaaataaacactggga----cacc-cagtgatg-aatcctatgggc----tatttaacaagattaaggtaaatctgttatgtgctgat--ggcaatgtgtc
q felCat3.scaffold_111908                                    999-9999999999999----9999999999999999999----9999-99999999-999999999999----99999999999999999999999999999999999999--99999999999
i felCat3.scaffold_111908          I 19 C 0
s canFam2.chr23                     25988191 109 -  55389570 tct-tcattggagggct----ggctagctaaccactggga----cacctcagtgatg-aattctatgggc----catttaacaagactaagataaatctgttatgtacagat--ggaaatgtatc
q canFam2.chr23                                              999-9999999999999----9999999999999999999----9999999999999-999999999999----99999999999999999999999999999999999999--99999999999
i canFam2.chr23                    I 19 C 0
s eriEur1.scaffold_377961               9178 104 +     88154 TCT-TCACTGAAGGGCT----ACTTGGG----TGCTAGGC----TTCCACACTGATG-AAACCTGTGGGT----GA-TTACAAAGCTTTAGGTAAATACGTTATGTGCTGAT--GAAAGAACAGC
q eriEur1.scaffold_377961                                    999-9999999999999----9999999----99999999----9999999999999-999999999999----99-99999999999999999999999999999999999--99999999999
i eriEur1.scaffold_377961          I 18 C 0
s loxAfr3.scaffold_36                 509371 105 -  24123610 tct-tcattggaggact----agttaaa----cactgggc-----aacccaatgatgaaatcctattaac----ta-ttaagaagatt-aagtaaatccgttaagtgttgacatagaAACACGCC
q loxAfr3.scaffold_36                                        999-9999999999999----9999999----99999999-----9999999999999999999999999----99-99999999999-999999999999999999999999999999999999
i loxAfr3.scaffold_36              I 19 I 106
s echTel1.scaffold_321361             117056  94 +    198078 cct-tttttgggaga--------ttgaa----ccctggga-----gccccattgatgaaatccca-caac----tc-ttaggaagattaaagtaaatctgttgtgtgctgatactgaa-------
q echTel1.scaffold_321361                                    997-99998799999--------98779----57967999-----87869998896899478996-9999----99-99899988869899899978978988798987899996699-------
i echTel1.scaffold_321361          I 23 I 174
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802  28 + 312544902 I
e proCap1.scaffold_51344                8235 8796 -     18560 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=309249.000000
s hg19.chrY                          7648552 45 +  59373566 caagataca-ttgctaagtttaaaa---aaaaa-----aggtaact-acagtgtt
s rheMac2.chr2                     158757250 45 + 189746636 caagataca-ttgctaagttaaaaa---aaaag------ggtgcctaacagtgtt
q rheMac2.chr2                                              999999999-999999999999999---99999------9999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71029002 49 - 202140232 caagataca-ctgctaagttaaaaa---aaaaaaa--aaggtgcctaacagtgtt
q ponAbe2.chr3                                              999999999-999999999999999---9999999--999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        502085 44 +  23952694 caagataca-ttgctaagtttaaaa---aaaaa------ggtaact-acagtgtt
q panTro2.chrY                                              000000000-000000000000000---00000------0000000-00000000
i panTro2.chrY                     C 0 C 0
s calJac1.Contig102                  1029910 45 -   1157145 caagataca-ctgctaagttaaaaa---aaaga------ggtgcacaacagtgtt
q calJac1.Contig102                                         999999999-999999999999999---99999------9999999999999999
i calJac1.Contig102                C 0 C 0
s papHam1.scaffold12353                58060 45 +     70985 cgagataca-ttgctaagttaaaaa---aaaaa------ggtgcctaacagtgtt
q papHam1.scaffold12353                                     999999999-999999999999999---99999------9999999999999999
i papHam1.scaffold12353            C 0 C 0
s gorGor1.Supercontig_0191774          13027 47 -     13449 caagataca-ctgctaagtttaaaa---aaaaa----aaggtgcctaacagtgtt
q gorGor1.Supercontig_0191774                               788777877-277277774888999---99999----999999799998999999
i gorGor1.Supercontig_0191774      C 0 C 0
s micMur1.scaffold_734                268827 47 -    418489 caagacaca-ttgctaagttaaaaaaagaaaaa-------atgcctaacagtgtt
q micMur1.scaffold_734                                      999999999-99999999999999999999999-------998999999999999
i micMur1.scaffold_734             C 0 C 0
s otoGar1.scaffold_99909.1-31737        7431 44 -     31737 caagataca-ttgttaagttaaaaa---ataaa-------gtgcctaactttatt
q otoGar1.scaffold_99909.1-31737                            979999996-978967989999999---99999-------999999969999999
i otoGar1.scaffold_99909.1-31737   C 0 C 0
s tupBel1.scaffold_130011.1-168288     43371 50 -    168288 tgggataca-ttgctaaattaaaaa---cagaaaagccaggtgcCT-GCTGTGTT
q tupBel1.scaffold_130011.1-168288                          999999999-999999999999999---999999999999999999-99999999
i tupBel1.scaffold_130011.1-168288 C 0 I 5578
s cavPor3.scaffold_0                 8220056 35 -  88675666 TAAGACACA-TCACTGACTTT---T---TAAAG-------GTGTC------TGTT
q cavPor3.scaffold_0                                        999999999-99999999999---9---99999-------99999------9999
i cavPor3.scaffold_0               C 0 C 0
s ochPri2.scaffold_2292               100683 42 +    188698 CCAGACACA-TTACTAAGTTTAAAA---CAAAT-------GTGTA--AGGGTGCT
q ochPri2.scaffold_2292                                     999999999-999999999999999---99999-------99999--99999999
i ochPri2.scaffold_2292            C 0 C 0
s vicPac1.scaffold_6092                39128 42 -     83534 taaaacaca-ttactcagttaagag---acaag-------gtgtcta--agggtt
q vicPac1.scaffold_6092                                     999999999-999999999999999---99999-------9999999--999999
i vicPac1.scaffold_6092            C 0 C 0
s turTru1.scaffold_111402              10291 44 -     37689 CAAGACCCA-TGACTAAGTTAAGAG---ACAAG-------GTGTCTAACAGTGTT
q turTru1.scaffold_111402                                   999999999-999999999999999---99999-------999999999999999
i turTru1.scaffold_111402          C 0 C 0
s bosTau4.chr1                     156979360 44 + 161106243 CGAGACCCA-CGACTAAGTTAAGAG---TCAGG-------GGGTCTAGCAGTACT
q bosTau4.chr1                                              999999999-999999999999999---99999-------999999999999999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22207730 44 -  87365405 CAAGATACA-TTACTAAGTTAAGAC---GTAAG-------GTGTCTAACAGTGTC
q equCab2.chr16                                             999999999-999999999999999---99999-------999999999999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4608 41 -      4973 cgagataaa-ttattaagttaagag---gcaag-------gggtca---agtgtt
q felCat3.scaffold_111908                                   999999999-999999999999999---99999-------999999---999999
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25988300 44 -  55389570 caaggtaag-tttttaagttaagac---gcgac-------gtgtcaaacagtgtt
q canFam2.chr23                                             999999999-999999999999999---99999-------999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961               9282 45 +     88154 CAAGAGGTAGTCACTAGGCTAAGAG---ACAAG-------GTACCAACTGGTGTT
q eriEur1.scaffold_377961                                   9999999999999999999999999---99999-------999999999999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 509582 44 -  24123610 TAAGATACA-TTACTAAGTTAAAAA---TCCAG-------GTACCTACCAGTGTT
q loxAfr3.scaffold_36                                       999999999-999999999999999---99999-------999999999999999
i loxAfr3.scaffold_36              I 106 C 0
s proCap1.scaffold_15753                 114 41 -     39409 -AAGATACA-TCACTAA--TAAAAC---TCCTG-------GTACCTAGCAGTATT
q proCap1.scaffold_15753                                    -99999998-9999999--999999---99989-------979999925956999
i proCap1.scaffold_15753           n 8796 C 0
s echTel1.scaffold_321361             117324 44 +    198078 TAAGATACA-TTATGAAGTTAAAAC---TCCCA-------GTCCCTCACAGTGTT
q echTel1.scaffold_321361                                   999999999-999999999999999---99999-------999999999999999
i echTel1.scaffold_321361          I 174 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802 28 + 312544902 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=49109.000000
s hg19.chrY                          7648597 39 +  59373566 aatggtatggccactcttgtg--ta------aATAATATTAGAAGGA--------------
s rheMac2.chr2                     158757295 39 + 189746636 aatggtatggtcactcttgtg--ta------aATAATATTAGAAGGA--------------
q rheMac2.chr2                                              999999999999999999999--99------9999999999999999--------------
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71029051 39 - 202140232 aatggtatggtcactcttgtg--ta------aATAACATTAGAAAGA--------------
q ponAbe2.chr3                                              999999999999999999999--99------9999999999999999--------------
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        502129 39 +  23952694 aatggtatggccactcttgtg--ta------aATAATATTAGAAGGA--------------
q panTro2.chrY                                              000000000000000000000--00------0000000000000000--------------
i panTro2.chrY                     C 0 C 0
s calJac1.Contig102                  1029955 37 -   1157145 aatggtatggccactcttgtg--ta------aagaaTATTAGAAG----------------
q calJac1.Contig102                                         999999999999999999999--99------99999999999999----------------
i calJac1.Contig102                C 0 I 325
s papHam1.scaffold12353                58105 39 +     70985 aatggtatggtcactcttgtg--ta------aATAATATTAGAAGGA--------------
q papHam1.scaffold12353                                     999999999999999999999--99------9999999999999999--------------
i papHam1.scaffold12353            C 0 C 0
s gorGor1.Supercontig_0191774          13074 39 -     13449 aatggtatggtcactcttgtg--ta------aATAACATTAGAAGGA--------------
q gorGor1.Supercontig_0191774                               999999999999999998888--98------8777378888888888--------------
i gorGor1.Supercontig_0191774      C 0 C 0
s micMur1.scaffold_734                268874 40 -    418489 aatggtatggtcactcttgcattta------aaaaaagttggaa-GG--------------
q micMur1.scaffold_734                                      9999999997999999999999999------9999999999999-99--------------
i micMur1.scaffold_734             C 0 I 1
s otoGar1.scaffold_99909.1-31737        7475 39 -     31737 aatggtatgatcactcttaca-taa------aaaaaaGTTAAAA-GA--------------
q otoGar1.scaffold_99909.1-31737                            999999999999999999999-999------9999999999999-99--------------
i otoGar1.scaffold_99909.1-31737   C 0 I 332
s cavPor3.scaffold_0                 8220091 37 -  88675666 AATAGAATGGGCACTCATATT--TA------AAAAA--TTAAAAGTA--------------
q cavPor3.scaffold_0                                        999999999999999999999--99------99999--999999999--------------
i cavPor3.scaffold_0               C 0 C 0
s ochPri2.scaffold_2292               100725 36 +    188698 AACGGTGT-GTCACTCTTGCA--TG------AAAAA--CTAGAAGGA--------------
q ochPri2.scaffold_2292                                     99999999-999999999999--99------99999--999999999--------------
i ochPri2.scaffold_2292            C 0 C 0
s vicPac1.scaffold_6092                39170 37 -     83534 tatCACATGAT-ACTCTTACA--TT------AAAAGA-TCAGAAGGA--------------
q vicPac1.scaffold_6092                                     99999999999-999999999--99------999999-999999999--------------
i vicPac1.scaffold_6092            C 0 C 0
s turTru1.scaffold_111402              10335 37 -     37689 TATCGTAGGAT-ACTTTAGTA--TA------AAAAAA-TTCGAAGGA--------------
q turTru1.scaffold_111402                                   99999999999-999999999--99------999999-999999999--------------
i turTru1.scaffold_111402          C 0 C 0
s bosTau4.chr1                     156979404 37 + 161106243 CATCACAGGAT-ACTAACATA--TA------AAGAAA-ATGGAAGAA--------------
q bosTau4.chr1                                              99999999999-999999999--99------999999-999999999--------------
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22207774 31 -  87365405 TATCATATGAT-GCTCTTGTA--TT------GAAAAA------AAG---------------
q equCab2.chr16                                             99999999999-999999999--99------999999------999---------------
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4649 28 -      4973 tatcctatgct-agtcttgta--ga------aaaata------------------------
q felCat3.scaffold_111908                                   99999999999-999999999--99------999999------------------------
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25988344 33 -  55389570 -----tatGAC-AGTCTTGTA--TA------AAAATAATTAGAAAGA--------------
q canFam2.chr23                                             -----999999-999999999--99------9999999999999999--------------
i canFam2.chr23                    C 0 I 181
s eriEur1.scaffold_377961               9327 33 +     88154 TC---TAGCAT-GCTTTCATG--CA------AAAA-A-TTAGAAGCA--------------
q eriEur1.scaffold_377961                                   99---999999-999999999--99------9999-9-999999999--------------
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 509626 40 -  24123610 TATTGTATGATCACCCTTGTG--TA------AAAAGAAAAAAAAAAAT-------------
q loxAfr3.scaffold_36                                       999999999999999999999--99------99999999999999999-------------
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                 155 54 -     39409 TATTGTATAATCAGTCTTGTA--TAAAAAAGAAAAGAAAAAAAAAAAC-----TGGAAGAA
q proCap1.scaffold_15753                                    999999999999999999999--9999999999999999999999997-----78399999
i proCap1.scaffold_15753           C 0 C 0
s echTel1.scaffold_321361             117368 47 +    198078 TACTGCACGATCACCCT--------------GTGAGAAAAATATGTGTGTGTGTAGGAGGG
q echTel1.scaffold_321361                                   99999999999999999--------------999999999999999999999999999999
i echTel1.scaffold_321361          C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802 28 + 312544902 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=266532.000000
s hg19.chrY                          7648636 59 +  59373566 TGGAC------AGata---------taaataaaaata-------ttttttttCC------TGGAAGAAATCAC-AAAAACATCAACAT
s panTro2.chrY                        502168 59 +  23952694 TGGAC------AGata---------taaataaaaata-------ttttttttCC------TGGAAGAAATCAC-AAAAACATCAACAT
q panTro2.chrY                                              00000------00000---------000000000000-------0000000000------0000000000000-00000000000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0191774          13113 59 -     13449 TGGAC------AGATA---------TAAATAAAAATC-------TTTTTTTTCC------TGGAAGAAATTAC-AAAAACATCAACAT
q gorGor1.Supercontig_0191774                               99999------99999---------999999999996-------7999999999------9999999999999-99989999999999
i gorGor1.Supercontig_0191774      C 0 C 0
s ponAbe2.chr3                      71029090 59 - 202140232 TGGAC------AGACA---------TAAATAAAAATC-------TTTTTTTTCC------TGGAAGAAAACAT-ACAAACATCAACAT
q ponAbe2.chr3                                              99999------99999---------999999999999-------9999999999------9999999999999-99999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158757334 64 + 189746636 TGGAC------AGata---------taaataaaaatc--tttttttttttttCC------TGGAAGAAATCAC-AAAAACATCAACGT
q rheMac2.chr2                                              99999------99999---------999999999999--999999999999999------9999949999999-99999999999999
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                58144 66 +     70985 TGGAC------AGata---------taaataaaaatctttttttttttttttCC------TGGAAGAAATCAC-AAAAACATCAACAT
q papHam1.scaffold12353                                     99999------99999---------99999999999999999999999999999------9999999999999-99999999999999
i papHam1.scaffold12353            C 0 C 0
s calJac1.Contig102                  1030317 61 -   1157145 TGGAC------AGACA---------TAAATAAAAATC-----TTTTTTTTTTTC------TGGAAGGAATCAC-AAAAACATCAACAT
q calJac1.Contig102                                         99999------99999---------999999999999-----999999999999------9999999999999-99999999999999
i calJac1.Contig102                I 325 I 315
s micMur1.scaffold_734                268915 62 -    418489 TGGACAGACATAGACA---------TAAATAAAAATA----------TTTTTTC------TGGAAGAAATCAC-AAAAACATCAAAAC
q micMur1.scaffold_734                                      9999999999999999---------999999999999----------9999999------9999999999999-99999999999999
i micMur1.scaffold_734             I 1 C 0
s cavPor3.scaffold_0                 8220128 46 -  88675666 T-------------------------GAATAAAAATA----------CTTTTTC------TGGAGGAAATTAC-AAAGATACCAACAT
q cavPor3.scaffold_0                                        9-------------------------99999999999----------9999999------9999999999999-99999999999999
i cavPor3.scaffold_0               C 0 C 0
s ochPri2.scaffold_2292               100761 49 +    188698 TGTGT------AGACA---------CGAATAAAAA-------------CTCTTC------TGGGGGAAGCTAC-AG----TCTAGCGT
q ochPri2.scaffold_2292                                     99999------99999---------9999999999-------------999999------9999999999999-99----99999999
i ochPri2.scaffold_2292            C 0 C 0
s vicPac1.scaffold_6092                39207 55 -     83534 TAGAG------AGACA---------TGAATAAAAAT-----------TTTTTTC------TGGAAGAAATCAC-AAAAACATCAATAT
q vicPac1.scaffold_6092                                     99999------99999---------99999999999-----------9999999------9999999999999-99999999999999
i vicPac1.scaffold_6092            C 0 C 0
s turTru1.scaffold_111402              10372 54 -     37689 TAGAT------AGACA---------TGAATAAAAT------------TTTTTTC------TGGAAGAAATAAC-AAAAACATCAATAT
q turTru1.scaffold_111402                                   99999------99999---------9999999999------------9999999------9999999999999-99999999999999
i turTru1.scaffold_111402          C 0 C 0
s bosTau4.chr1                     156979441 56 + 161106243 GAGAG------AGACA---------TGAGTGAAATTC----------TCTTTTC------TGGAAGAAATCAC-AAAAACATCGATAT
q bosTau4.chr1                                              99999------99999---------999999999999----------9999999------9999999999999-99999999999999
i bosTau4.chr1                     C 0 C 0
s eriEur1.scaffold_377961               9360 58 +     88154 CAATG------TGgca---------taaat--gat------------ttttttccccttatggaAGAAACCTC-AAAAACATGAATAT
q eriEur1.scaffold_377961                                   99999------99999---------99999--999------------99999999999999999999999999-99999999999999
i eriEur1.scaffold_377961          C 0 C 0
s equCab2.chr16                     22207805 51 -  87365405 --GAT------AGACA---------AGAAT--AAT------------TTTTTTC------TGGAAGGAATCACAAAAAACATCAATAT
q equCab2.chr16                                             --999------99999---------99999--999------------9999999------9999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4677 61 -      4973 --gag------agataatCTTTTTCAGAATAAAAT------------TTTTTTC------TGAAAGAAATCAC-AAAAATATGAATAT
q felCat3.scaffold_111908                                   --999------999999999999999999999999------------9999999------9999999999999-99999999999999
i felCat3.scaffold_111908          C 0 C 0
s canFam2.chr23                     25988558 56 -  55389570 --GAA------AGATAAT-TTTTTTAGAATAAAAT------------TTTTTTC------TGAAATAAA-----AAACATATGAATGT
q canFam2.chr23                                             --999------9999909-9999999999999999------------9999999------999999999-----99999999999999
i canFam2.chr23                    I 181 C 0
s loxAfr3.scaffold_36                 509666 52 -  24123610 ---GG------AAGGA---------TGAATAAAAAAT--------TTTGG---G------GGGGAAAAATCAC-AGGAGCAACAGAAT
q loxAfr3.scaffold_36                                       ---99------99999---------999999999999--------99999---9------9999999999999-99999999999999
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                 209 57 -     39409 -TGGA------AAGTA---------TGAGTAAAGATT--------TTTTTTTCT------GGAAAAAAATCAC-AAGACTGACAAAAT
q proCap1.scaffold_15753                                    -9999------99979---------999999999999--------999999999------9999999999935-49999999999999
i proCap1.scaffold_15753           C 0 C 0
s echTel1.scaffold_321361             117415 56 +    198078 -T-GG------AGATA---------TGAACTAAAATT--------TGTTATCTG------GAAAAATAATCAC-AGGCATGACAGCAT
q echTel1.scaffold_321361                                   -9-99------99999---------999999999999--------999999999------9999999999999-99999999990999
i echTel1.scaffold_321361          C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802 28 + 312544902 I
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=305211.000000
s hg19.chrY                          7648695  81 +  59373566 TGAAGAGAAGGATTGGAGTAG------------------GGAGGAAAGCATAGA----AA-GTGGTTTTTGCTTTATTTTATACTTTTGATC----CCATTACCACCA
s panTro2.chrY                        502227  81 +  23952694 TGAAGAGAGGGATTGGAGTAG------------------GGAGGAAAGCATAGA----AA-GTGGTTTTTGCTTTATTTCATACTTTTGATC----CTATTACCACCA
q panTro2.chrY                                               000000000000000000000------------------000000000000000----00-0000000000000000000000000000000----000000000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0191774          13172  80 -     13449 TGAAGAGAGGGACTGGAGTAG------------------GGAGGAAAGGGTAGA----AA-GTCATTTTTACTGTATTTTATACTTTCGATC----CCATTACCACC-
q gorGor1.Supercontig_0191774                                999999999999999999999------------------999999999999999----99-9799999999999999999999999999999----99999999999-
i gorGor1.Supercontig_0191774      C 0 C 0
s ponAbe2.chr3                      71029149  80 - 202140232 TGAAGAGAGGGACTGGAGTAG------------------GGAGGAAAGGGTAGA----AA-GTCGTTTTTACTGTATTTTATACTTTCCATC----CCATTACCACC-
q ponAbe2.chr3                                               999999999999999999999------------------999999999999999----99-9999999999999999999999999999999----99999999999-
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158757398  81 + 189746636 TGAAGAGAGGGACTGGAAGAG------------------GGAGGAAATGGTAGA----AA-GTCGTTTTTACTGTATTTTATACTTTTGATC----CCATTACCACCA
q rheMac2.chr2                                               999979999999999999999------------------999999999999969----99-9999999999999999999999999999999----999999999999
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                58210  81 +     70985 TGAAGAGAGGGACTGGAAGAG------------------GGAGGAAAGGGTAGA----AA-GTCGTTTTTTCTGTATTTTATACTTTTGATC----CCATTACCACCA
q papHam1.scaffold12353                                      999999999999999999999------------------999999999999999----99-9999999999999999999999999999999----999999999999
i papHam1.scaffold12353            C 0 C 0
s calJac1.Contig102                  1030693  81 -   1157145 TGAAGAGATGGACTAGAGTAG------------------AGATTAAAGGATAGA----AG-GTCATTTTTATTTTATCTTACACTTTTGATT----CCATTACCATCA
q calJac1.Contig102                                          999999999999999999999------------------999999999999999----99-9999999999999999999999999999999----999999999999
i calJac1.Contig102                I 315 C 0
s micMur1.scaffold_734                268977  77 -    418489 TGAAGAGAGGGACTAGAGAAG------------------GGAGGAAAGGGTGGA----AAGGTCATCCT-----TATTTTATACTTTCAATA----CTATTGCCTTCA
q micMur1.scaffold_734                                       999999999999999999999------------------999999999999999----99999999999-----999999999999999999----999999999999
i micMur1.scaffold_734             C 0 C 0
s cavPor3.scaffold_0                 8220174  72 -  88675666 TAGAAAAAGGGGCAAAAATAG------------------GAAGAAAACAGTGGA----AA-AGTTGTTTTAATATTTTCAAAACTATTACTA----GCA---------
q cavPor3.scaffold_0                                         999999999999999999999------------------999999999999999----99-9999999999999999999999999999999----999---------
i cavPor3.scaffold_0               C 0 C 0
s ochPri2.scaffold_2292               100810  55 +    188698 GAGAAAA-----CCCAAACAG------------------G------TCATT-----------TCTGCTTTAGTTTGTACTATCCATCCTCTC----GTA---------
q ochPri2.scaffold_2292                                      9999999-----999999999------------------9------99999-----------999999999999999999999999999999----999---------
i ochPri2.scaffold_2292            C 0 I 1
s vicPac1.scaffold_6092                39262  73 -     83534 TGGAGA----GACTGGAGTAG------------------GGAGGGGAGGGTGGG----AAGGTAG-TTCTACTTTGTTCT----TTTGAGTA----CTATTACCATCA
q vicPac1.scaffold_6092                                      999999----99999999999------------------999999999999999----9999999-99999999999999----99999999----999999999999
i vicPac1.scaffold_6092            C 0 C 0
s turTru1.scaffold_111402              10426  78 -     37689 TGGAGA----GACTGGAGTAG------------------AGAGGTGAGGATGAG----AAGGTAGTTTTTGCTTTATTTTGTACTTTCAATA----CTATTACTGTCA
q turTru1.scaffold_111402                                    999999----99999999999------------------999999999999999----9999999999999999999999999999999999----999999999999
i turTru1.scaffold_111402          C 0 I 2
s bosTau4.chr1                     156979497  78 + 161106243 TGGAGA----GACTGGAGAAG------------------GGAGCGGAGGGTGGA----AAGGTAGATTTTACTTTATTATGTACTTTCAACA----CTATTACCGTCA
q bosTau4.chr1                                               999999----99999999999------------------999999999999999----9999999999999999999999999999999999----999999999999
i bosTau4.chr1                     C 0 C 0
s canFam2.chr23                     25988614  72 -  55389570 AGGAGAAAGGGGCTGGAGTAT------------------AGAGGGAAGG---------AAGATGGTTTTTA-----TTTTGTACTCACAGTA----CTATTACCATCC
q canFam2.chr23                                              999999999999999999999------------------9999999999---------9999999999999-----9999999999999999----999999999999
i canFam2.chr23                    C 0 C 0
s felCat3.scaffold_111908               4738  86 -      4973 TGGAGAAAAGGGCTGGAGAAT------------------AGAGGGAAGGATGGA----AAGGTGGCTTTTACTTTCTTTTGTACTTGCAGTAGGTGCTGTTACCATCC
q felCat3.scaffold_111908                                    999999999999999999999------------------999999999999999----99999999999999999999999999999999999999999999999999
i felCat3.scaffold_111908          C 0 C 0
s equCab2.chr16                     22207856  78 -  87365405 TGGAAAGAGAGACTGTAGTAG------------------AGAGGGGAGGATGGG----AAGGTGGTTTTTACTTTATTACGTACTTCTAGCA--------CAACATCA
q equCab2.chr16                                              999999999999999999999------------------999999999999999----9999999999999999999999999999999999--------99999999
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961               9418  50 +     88154 TGGAGA------CTGGAGGAC------------------AGTGAATAGGAATGA----AAggcggtcttttttttttt------------------------------
q eriEur1.scaffold_377961                                    999999------999999999------------------999999999999999----99999999999999999999------------------------------
i eriEur1.scaffold_377961          C 0 I 1285
s loxAfr3.scaffold_36                 509718 100 -  24123610 CAGAGAAAGGAACTAGAGGGGAGCAGAGAGGAGAGTAGGGCAGGAAAGGATACA----AAGTTAGTTTTTACTTTATTTTGTTCTTTCAGTG----CTATTATCATCA
q loxAfr3.scaffold_36                                        999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999999----999999999999
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                 266  75 -     39409 CTAAGACAGGAAATAAACGAG-------------------------AGGGTCGA----AAGACAGCTTTCACTCTATTTTGTGCTTTCAGTA----CTATTATTACCA
q proCap1.scaffold_15753                                     625999759999997286499-------------------------99999999----9999999999999999999999999999746338----658537999947
i proCap1.scaffold_15753           C 0 C 0
s echTel1.scaffold_321361             117471  79 +    198078 TGGTGCGAGGAACTGGAGTAA-------------------------GGGGTCCAGGGTAAAGCCGTGTGTACTTTATTTTATACTTTCCGAA----CAATTATCATCC
q echTel1.scaffold_321361                                    999999999999999999999-------------------------9999999999999999999999999999999999999999990899----999999999999
i echTel1.scaffold_321361          C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2464911 1577 + 163896628 I
e speTri1.scaffold_135460              76674 1205 -    203079 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e pteVam1.scaffold_30179                1440 3486 -      7387 M
e monDom5.chr8                     276496802  28 + 312544902 I
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=354616.000000
s hg19.chrY                          7648776 72 +  59373566 ACAGGAGTCA-TTTAAGTGGAAGGTTTATGAGTCATTT-TT------ATTTTCCTCTTTATATATAAAAAC----AATA-----TTATT
s panTro2.chrY                        502308 72 +  23952694 ACAGGAGTCA-TTTAAGTGGAAGGTTTATGAGTCATTT-TT------ATTTTCCTCTTTATATATAAAAAC----AATA-----TTATT
q panTro2.chrY                                              0000000000-000000000000000000000000000-00------000000000000000000000000----0000-----00000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0191774          13252 64 -     13449 -----AGTGA-TTTGGGTGGAAAGTTTATGAGTCATTT-TT------ATTTTCCTCtt--tatataaaaac----aata-----ttat-
q gorGor1.Supercontig_0191774                               -----99999-999999999999999999999999999-99------99999998999--99999999999----9999-----9999-
i gorGor1.Supercontig_0191774      C 0 C 0
s ponAbe2.chr3                      71029229 66 - 202140232 -----AGTGA-TTTGGGTGGAAAGTTTATGAGTCATTT-TT------ATTTTCCTCTTTACatataaaaac----aata-----ttat-
q ponAbe2.chr3                                              -----99999-999999999999999999999999999-99------999999999999999999999999----9999-----9999-
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158757479 69 + 189746636 ACAGGAGTCA-TTTGGGTGGAAGGCTTATGAGTCATTT-TT------ATTTTTCTCCC--TATATAAAAAC----AATA-----TTAT-
q rheMac2.chr2                                              9999999999-999999999999999999999999999-99------99999999999--99999999999----9999-----9999-
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                58291 69 +     70985 ACAGGAGTCA-TTTGGGTGGAAGGCTTATGAGTCATTT-TT------ATTTTTCTCTC--TATATAAAAAC----AATA-----TTAT-
q papHam1.scaffold12353                                     9999999999-999999999999999999999999999-99------99999999999--99999999999----9999-----9999-
i papHam1.scaffold12353            C 0 C 0
s calJac1.Contig102                  1030774 68 -   1157145 ACAGGAGTCA-TTTGGGTGGAAGGTTTATGAGTCATTT-AT------ATTTTGCTCtttatatataaa-------aata-----ttat-
q calJac1.Contig102                                         9999999999-999999999999999999999999999-99------999999999999999999999-------9999-----9999-
i calJac1.Contig102                C 0 C 0
s micMur1.scaffold_734                269054 61 -    418489 ACAGGGATTG-TTTGGATGGAGGATTTATGAGACATTT-TT------ATTTTCTTCTGtatatata-------------------tat-
q micMur1.scaffold_734                                      9999999999-999999999999999999999999999-99------9999999999999999999-------------------999-
i micMur1.scaffold_734             C 0 C 0
s cavPor3.scaffold_0                 8220246 66 -  88675666 ATAGGGATCA-TTTCAGTGAGAACTTTATAAGACATT-----------TTATGTTCTTTATATGTAAAA------AATATTATT-----
q cavPor3.scaffold_0                                        9999999999-99999999999999999999999999-----------999999999999999999999------999999999-----
i cavPor3.scaffold_0               C 0 I 23
s speTri1.scaffold_135460              77879 62 -    203079 ACAGGGATCA-TTTCAATGGAGAGTTTATAAGGCATTC-TT------ATTTTCTTCtttatatttaaaaa-------------------
q speTri1.scaffold_135460                                   9958955455-998434876779959999787646798-86------99999987788999697888798-------------------
i speTri1.scaffold_135460          I 1205 I 210
s ochPri2.scaffold_2292               100866 56 +    188698 ACAGGGATCA-CTTGGCTGGAT-----------CTTCT-TT------ACTTTCTTCCTTTAATATGAAGAC----AATT----------
q ochPri2.scaffold_2292                                     9999999999-99999999999-----------99999-99------999999999999999999999999----9999----------
i ochPri2.scaffold_2292            I 1 C 0
s oryCun2.chr14                      2466488 64 + 163896628 --AGGCACCA-TTTGGATAGAGGG-CAATGAAACACTT-CT------GTTTTCTTCCTTAAATATGAAAAC----AAGT----------
q oryCun2.chr14                                             --99999999-9999999999999-9999999999999-99------999999999999999999999999----9999----------
i oryCun2.chr14                    I 1577 C 0
s vicPac1.scaffold_6092                39335 65 -     83534 ACGGAAATCA-TTTGAGTGGAGGATTTATGAAACACTT-TA------ATTTTCTTCtttatatgtaaaaat----a-t-----------
q vicPac1.scaffold_6092                                     9999999999-999999999999999999999999999-99------999999999999999999999999----9-9-----------
i vicPac1.scaffold_6092            C 0 I 1
s turTru1.scaffold_111402              10506 64 -     37689 ACAGCAATCA-TTTGGGTGGAGGGTTCATGAGACATTT-TA------ATTTTCTTCTTTACATGTGAAA------AAT-----------
q turTru1.scaffold_111402                                   9999999999-999999999999999999999999999-99------9999999999999999999999------999-----------
i turTru1.scaffold_111402          I 2 I 1
s bosTau4.chr1                     156979575 64 + 161106243 ACAGTAATCG-TTTGGGTGGA--GCTTAGGAGACattt-ta------attttcttctttataaataaaaat----att-----------
q bosTau4.chr1                                              9999999999-9999999999--999999999999999-99------999999999999999999999999----999-----------
i bosTau4.chr1                     C 0 I 1
s canFam2.chr23                     25988686 65 -  55389570 ACAGGGGCCA-T-TGGGTGGAGGGTCTATGAGATATTT-TA------ATTTTCTTATTTATATGCAAAAAC----ATC-----------
q canFam2.chr23                                             9999999999-9-9999999999999999999999999-99------999999999899989999999999----999-----------
i canFam2.chr23                    C 0 I 1
s felCat3.scaffold_111908               4824 66 -      4973 ATCAGGGTCA-T-TGGGTGGAGGGTTGATAAGACATTGAAA------ATTTTCTGATTTATATGTAAAAAC----ATT-----------
q felCat3.scaffold_111908                                   9999999999-9-9999999999999999999999999999------999999999999999999999999----999-----------
i felCat3.scaffold_111908          C 0 I 1
s equCab2.chr16                     22207934 69 -  87365405 ACAGGGACCATT-TGGGGAGAGGGTTTATGAGACATTT-TA------ATTGTCTTCTTTATATGTAAAAAC-AATATT-----------
q equCab2.chr16                                             999999999999-9999999999999999999999999-99------999999999999999999999999-999999-----------
i equCab2.chr16                    C 0 I 1
s pteVam1.scaffold_30179                4955 64 -      7387 -------------TGGGTGGAGGGTTTATGGGACACTT-TAATTTTCATTTTCTTCtttatatttaaaaaataatatt-----------
q pteVam1.scaffold_30179                                    -------------4996699759839376999744999-899999942999999999956429641777789999999-----------
i pteVam1.scaffold_30179           M 3486 I 1
s loxAfr3.scaffold_36                 509818 73 -  24123610 ATAG-GGTCA-TCTGAGTGGTGGATTTATGTCATATTT-TA------ATTATACTCTTTATATGTAAAAAC----AATAGAGTGTT---
q loxAfr3.scaffold_36                                       9999-99999-999999999999999999999999999-99------999999999999999999999999----99999999999---
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                 341 73 -     39409 ATAG-GGCCA-TCTGAGTGGTGGATTTATGGGAAATCT-TC------ATTTTATTCTTTATATGCAAAAAC----AACACGGTGTT---
q proCap1.scaffold_15753                                    9999-99999-989999995399999999999999999-99------999999999999999999999999----99999999999---
i proCap1.scaffold_15753           C 0 C 0
s echTel1.scaffold_321361             117550 72 +    198078 ACAG-GGCCA-TTT-AGCAGTGGGTTTGTGGCATCTTT-CA------ATTTTATTCTTTATATGTACAAAG----AAGATGATGTT---
q echTel1.scaffold_321361                                   7979-99999-999-99999999999999999999999-90------999999999999999999999999----99999999999---
i echTel1.scaffold_321361          C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-76901.000000
s hg19.chrY                          7648848 60 +  59373566 GTTAAAATGTTTT-TAATGTACTTT-----AAAAAATG-----------TGCTTTTCAAATTTTCTAAtttttctta
s panTro2.chrY                        502380 60 +  23952694 GTTAAAATGTTTT-TGATGTACTTT-----AAAAAATG-----------TGCTTTTCAAATTTTCTAAtttttctta
q panTro2.chrY                                              0000000000000-00000000000-----00000000-----------0000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0191774          13316 61 -     13449 -ttaaaa-gtttt-taatgtacttt--taaaaataatG-----------TGCCTTTTAAATTTTCTAAtttttctta
q gorGor1.Supercontig_0191774                               -999999-99999-99999999999--99999999999-----------9999999999999999999999997999
i gorGor1.Supercontig_0191774      C 0 N 0
s ponAbe2.chr3                      71029295 61 - 202140232 -ttaaaa-gtttt-taatgtacttt--taaaaataatG-----------TGCTTTTTAAATTTTCTAAtttttctta
q ponAbe2.chr3                                              -999999-99999-99999999999--98999999999-----------9999999999999999799999999999
i ponAbe2.chr3                     C 0 I 16
s rheMac2.chr2                     158757548 60 + 189746636 -TAAAAA-GTTTT-TAATGTACCTT---AAAAATAATG-----------TGCTTTCTAAATTTTCTAAtttttctta
q rheMac2.chr2                                              -999999-99999-99999999999---9999999999-----------9999999999999999999999999999
i rheMac2.chr2                     C 0 I 16
s papHam1.scaffold12353                58360 60 +     70985 -TAAAAA-GTTTT-TAATGTACCTT---AAAAATAATG-----------TGCTTTTTAAATTTTCTAATTTTTCTTA
q papHam1.scaffold12353                                     -999999-99999-99999999999---9999999999-----------9999999999999999999999999999
i papHam1.scaffold12353            C 0 I 16
s calJac1.Contig102                  1030842 48 -   1157145 -ttaaaa-ctttt-taat---------------taatG-----------TGCTTTTTAAATTTTCTAAtttttctta
q calJac1.Contig102                                         -999999-99999-9999---------------99999-----------9999999999999999999999999999
i calJac1.Contig102                C 0 I 16
s micMur1.scaffold_734                269115 37 -    418489 -ttaaaa-gttct-taatgtatttttttaaaaataatt-----------tg--------------------------
q micMur1.scaffold_734                                      -999999-99999-999999999999999999999999-----------99--------------------------
i micMur1.scaffold_734             C 0 C 0
s oryCun2.chr14                      2466552 38 + 163896628 -ATTTAA-GTTTT-TCATGCATATT---TTAAATGATG-----------CA-TTAT---------------------
q oryCun2.chr14                                             -999999-99999-99999999999---9999999999-----------99-9999---------------------
i oryCun2.chr14                    C 0 I 2
s ochPri2.scaffold_2292               100922 49 +    188698 -TTTGAA-GTCTT-TAACGCGTCtt---ttaaatgattattattttttaaa-aaat---------------------
q ochPri2.scaffold_2292                                     -999999-99999-99999999999---99999999999999999999999-9999---------------------
i ochPri2.scaffold_2292            C 0 I 1
s vicPac1.scaffold_6092                39401 26 -     83534 tttaaat-tttta--aatttatttt--taaa----------------------------------------------
q vicPac1.scaffold_6092                                     9999999-99999--9999999999--9999----------------------------------------------
i vicPac1.scaffold_6092            I 1 I 1
s turTru1.scaffold_111402              10571 27 -     37689 TTTTGAA-TTTT---AATGTATTTT--TAAAAA--------------------------------------------
q turTru1.scaffold_111402                                   9999999-9999---9999999999--999999--------------------------------------------
i turTru1.scaffold_111402          I 1 C 0
s bosTau4.chr1                     156979640 28 + 161106243 tttaaaa-attt---tatgtattta--aaaaaat-------------------------------------------
q bosTau4.chr1                                              9999999-9999---9999999999--9999999-------------------------------------------
i bosTau4.chr1                     I 1 C 0
s equCab2.chr16                     22208004 29 -  87365405 TTTACAA-GTTTT--TATGTATTTT--TTAAAAC-------------------------------------------
q equCab2.chr16                                             9999999-99999--9999999999--9999999-------------------------------------------
i equCab2.chr16                    I 1 I 134
s felCat3.scaffold_111908               4891 30 -      4973 TCTGCAA-GTTCT-TTATGTATTTT--TAAAAAT-------------------------------------------
q felCat3.scaffold_111908                                   9999999-99999-99999999999--9999999-------------------------------------------
i felCat3.scaffold_111908          I 1 C 0
s canFam2.chr23                     25988752 30 -  55389570 TTTAAAA-GTTTC-GCATATATTTC--TGAGAAT-------------------------------------------
q canFam2.chr23                                             9999999-99999-99999999999--9999888-------------------------------------------
i canFam2.chr23                    I 1 I 204
s pteVam1.scaffold_30179                5020 28 -      7387 tttaaaa-GTTTCTTTATGTATTTA--AAAA----------------------------------------------
q pteVam1.scaffold_30179                                    9999999-99999999999999999--9999----------------------------------------------
i pteVam1.scaffold_30179           I 1 I 2
s loxAfr3.scaffold_36                 509891 29 -  24123610 GTTTAAA-GCTTT--AATGTACttt--taaaaat-------------------------------------------
q loxAfr3.scaffold_36                                       9999999-99999--9999999999--9999999-------------------------------------------
i loxAfr3.scaffold_36              C 0 I 7
s proCap1.scaffold_15753                 414 43 -     39409 ATGTAAA-ATTTT--AATGTATTTT--TAAAAACGATGTATTATT-----------TAA------------------
q proCap1.scaffold_15753                                    9999999-99999--9999999999--999999999999999999-----------999------------------
i proCap1.scaffold_15753           C 0 C 0
s echTel1.scaffold_321361             117622 25 +    198078 CATTAAC-ATTTT--AATGCA---T--CAAAAA--------------------------------------------
q echTel1.scaffold_321361                                   9999999-79999--999997---9--999999--------------------------------------------
i echTel1.scaffold_321361          C 0 I 1
e cavPor3.scaffold_0                 8220312 23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e speTri1.scaffold_135460              77941 210 -    203079 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=104076.000000
s hg19.chrY                          7648908 91 +  59373566 tttattttgagactgaacctcgctctgccacccaggctggactgcagtggtgcgatcacagctcactgcagccttgatcccctgggctcaa
s panTro2.chrY                        502440 91 +  23952694 tttattttgagactgaaccttgctctgccacccaggctggactgcagtggtgtgatcacagctcactgcagccttgatcccctgggctcaa
q panTro2.chrY                                              0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71029372 91 - 202140232 tttattttgagacagagcctctctctgtcacccgggctggagtaaagtggtgcgatcacagctccctgaagccttgatctcctgggctcaa
q ponAbe2.chr3                                              9999999999999999999999999999999999999999999889999999799999999999978999999889996999999999989
i ponAbe2.chr3                     I 16 C 0
s rheMac2.chr2                     158757624 91 + 189746636 tttattttgagacagagtctcgttctgtcacccaggctggagtaaagtggtgccatcacagctccctgcagccttaatctcttgggctcaa
q rheMac2.chr2                                              9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     I 16 C 0
s papHam1.scaffold12353                58436 91 +     70985 tttattttgagacagagtctcgttctgtcacccaggctggagcaaagtggtgcgatcacagctccctgcagccttaatctcttgggatcaa
q papHam1.scaffold12353                                     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i papHam1.scaffold12353            I 16 I 4
s calJac1.Contig102                  1030906 91 -   1157145 tttattttgagacagagcattgctctgtcacccaggctggagtacagtggtacaatcacagctcactgcactcttgatctcctgggctcaa
q calJac1.Contig102                                         9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i calJac1.Contig102                I 16 C 0
e cavPor3.scaffold_0                 8220312 23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590  2 + 163896628 I
e equCab2.chr16                     22208033 134 -  87365405 I
e bosTau4.chr1                     156979668  0 + 161106243 C
e loxAfr3.scaffold_36                 509920  7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427  1 -     83534 I
e speTri1.scaffold_135460              77941 210 -    203079 I
e micMur1.scaffold_734                269152  0 -    418489 C
e ochPri2.scaffold_2292               100971  1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921  0 -      4973 C
e pteVam1.scaffold_30179                5048  2 -      7387 I
e echTel1.scaffold_321361             117647  1 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598  0 -     37689 C
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e proCap1.scaffold_15753                 457  0 -     39409 C
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=98089.000000
s hg19.chrY                          7648999 132 +  59373566 gtgatcctcttattgcttcagcctccagagtttctgggactgtaggcacatgccagcatgtccagctaatttttaaatttcttgtggagacagtgtcttgccatgttgcccaggctagtcccaaactcctgg
s panTro2.chrY                        502531 132 +  23952694 gcgatcctcttattgcttcagcctccagagtttctgggactgtaggcacatgccagcatgtccagctaatttttaaatttcttgtggagacagtgtcttgccatgttgcccaggctagtcccaaactcctgg
q panTro2.chrY                                               000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71029463 132 - 202140232 gcgatcctcctattgtctcagcctccagagttgctgggactacaggcacatgccagcatgtccagctaatttttaaatttcttgtagagatggggtcttgccatgttgcccaggctggtcacaaactcctgg
q ponAbe2.chr3                                               979979999899999979999999998999999999999899999999999999999999999999999999999999999999999999999999994245535989999999999999997899999999
i ponAbe2.chr3                     C 0 M 349
s rheMac2.chr2                     158757715 132 + 189746636 gggatcctcctattgcctcagcctccagagttgctgggactacaggcacatgccggcatgtcccgctaatttttaaatttcttgtagagacagggtcttgccatgttgcccaggctggtcacaaactcctgg
q rheMac2.chr2                                               999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999899999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s calJac1.Contig102                  1030997 117 -   1157145 gtgatcctcctattgactcaacctccagagttgctgggactt------catgccagcatgtcccgctaattttttaatttcttgtagagacagga---------gtggtccaggctggtcacaaactcctgg
q calJac1.Contig102                                          999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999---------9999999999999999999999999999
i calJac1.Contig102                C 0 C 0
e cavPor3.scaffold_0                 8220312  23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590   2 + 163896628 I
e equCab2.chr16                     22208033 134 -  87365405 I
e bosTau4.chr1                     156979668   0 + 161106243 C
e loxAfr3.scaffold_36                 509920   7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427   1 -     83534 I
e speTri1.scaffold_135460              77941 210 -    203079 I
e micMur1.scaffold_734                269152   0 -    418489 C
e ochPri2.scaffold_2292               100971   1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921   0 -      4973 C
e pteVam1.scaffold_30179                5048   2 -      7387 I
e echTel1.scaffold_321361             117647   1 +    198078 I
e monDom5.chr8                     276496802  28 + 312544902 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598   0 -     37689 C
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e proCap1.scaffold_15753                 457   0 -     39409 C
e papHam1.scaffold12353                58527   4 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=17346.000000
s hg19.chrY                          7649131 33 +  59373566 ttttaaatgatcttcctgcctgggcctTAATGT
s calJac1.Contig102                  1031114 33 -   1157145 ttttaaatgatcttcctgcctgggcctAAATGT
q calJac1.Contig102                                         999999999999999999999999999999999
i calJac1.Contig102                C 0 I 11
s rheMac2.chr2                     158757847 33 + 189746636 ttttaaacgatcttcctgcctgggcctTAACGT
q rheMac2.chr2                                              999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s panTro2.chrY                        502663 33 +  23952694 ttttaaatgatcttcctgcctgggcctTAATGT
q panTro2.chrY                                              000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8220312 23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590  2 + 163896628 I
e equCab2.chr16                     22208033 134 -  87365405 I
e bosTau4.chr1                     156979668  0 + 161106243 C
e loxAfr3.scaffold_36                 509920  7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427  1 -     83534 I
e speTri1.scaffold_135460              77941 210 -    203079 I
e micMur1.scaffold_734                269152  0 -    418489 C
e ochPri2.scaffold_2292               100971  1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921  0 -      4973 C
e pteVam1.scaffold_30179                5048  2 -      7387 I
e echTel1.scaffold_321361             117647  1 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598  0 -     37689 C
e otoGar1.scaffold_99909.1-31737        7514 332 -     31737 I
e proCap1.scaffold_15753                 457  0 -     39409 C
e papHam1.scaffold12353                58527  4 +     70985 I
e ponAbe2.chr3                      71029595 349 - 202140232 M
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=29985.000000
s hg19.chrY                          7649164 80 +  59373566 ACtt--------------------ttttttctttttttttt--gagacagagtctccctccttcgcc-caggctggagtgcagtggtgcaatttcagctcact
s otoGar1.scaffold_99909.1-31737        7846 68 -     31737 -------------------------------tttttttttg--gagac--agtctctctctgtcaccttggggttcagtgctgtggtgtcagcccagttcaca
q otoGar1.scaffold_99909.1-31737                            -------------------------------9999999999--99999--99999999999999999999999999999999999999999999999999999
i otoGar1.scaffold_99909.1-31737   I 332 C 0
s ponAbe2.chr3                      71029944 76 - 202140232 ------------------------ttttttttttttttttt--gagacagagtctccctctttggcc-caggctggagtgcagtggcatcatcttggctcact
q ponAbe2.chr3                                              ------------------------79999999999999993--768596854628594949935664-97986576895696859864795779599699876
i ponAbe2.chr3                     M 349 C 0
s equCab2.chr16                     22208167 63 -  87365405 acct--------------------tcctttattttgtatgt--gagac-------accaccacagca-tggcttgatgagtggtga---------aggtc-ct
q equCab2.chr16                                             9999--------------------99999999999999999--99999-------999999999999-999999999999999999---------99999-99
i equCab2.chr16                    I 134 C 0
s rheMac2.chr2                     158757880 98 + 189746636 ACTGtttttttttgggttttgttttgttttgttttgttttt--gagac--agtctccctctttggcc-taggctggagtgcagtggcacgatcttggctcact
q rheMac2.chr2                                              99998999999999986662222222253354565544435--35546--56445666332333334-56556554466654344654556333366666443
i rheMac2.chr2                     C 0 C 0
s panTro2.chrY                        502696 81 +  23952694 ACtt--------------------ttttttcttttttttttttgagacagagtctccctc-ttcgcc-caggctggagtgcagtggtgcaatttcagctcact
q panTro2.chrY                                              0000--------------------000000000000000000000000000000000000-000000-00000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8220312 23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590  2 + 163896628 I
e bosTau4.chr1                     156979668  0 + 161106243 C
e loxAfr3.scaffold_36                 509920  7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427  1 -     83534 I
e speTri1.scaffold_135460              77941 210 -    203079 I
e micMur1.scaffold_734                269152  0 -    418489 C
e ochPri2.scaffold_2292               100971  1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921  0 -      4973 C
e pteVam1.scaffold_30179                5048  2 -      7387 I
e calJac1.Contig102                  1031147 11 -   1157145 I
e echTel1.scaffold_321361             117647  1 +    198078 I
e monDom5.chr8                     276496802 28 + 312544902 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598  0 -     37689 C
e proCap1.scaffold_15753                 457  0 -     39409 C
e papHam1.scaffold12353                58527  4 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=68830.000000
s hg19.chrY                          7649244 100 +  59373566 gcaacctccacctccctgattaaagtgattctcctgcctcagctt-cctgaatag-ctgggactacaggcacatgccaccatgcctggctaatttttg-tatt
s panTro2.chrY                        502777 100 +  23952694 gcaacctccacctccctgattaaagtgattctcctgcctcagctt-cctgaatag-ctgggactacaggcacatgccaccatgcctggctaatttttg-tatt
q panTro2.chrY                                               000000000000000000000000000000000000000000000-000000000-000000000000000000000000000000000000000000-0000
i panTro2.chrY                     C 0 C 0
s rheMac2.chr2                     158757978  99 + 189746636 gcaacctctgcctcccaggttcaagtgattctcctgcctcagcct-cctaagtag-ct-agactacaggcacacgacagcatgcctagctaatttttg-taat
q rheMac2.chr2                                               566664223356665666654566666666665565545566545-633554443-43-442226899999999899999999798998876377778-9987
i rheMac2.chr2                     C 0 C 0
s equCab2.chr16                     22208230  53 -  87365405 gggatccaaacccacaaagccaa------------------------------ag-cagagcacacaaactta-acaaccatgcc------------------
q equCab2.chr16                                              99999999999999999999999------------------------------99-99999999999999999-99999999999------------------
i equCab2.chr16                    C 0 C 0
s ponAbe2.chr3                      71030020 100 - 202140232 gcaacctccgcctcccaggttcaagtgattctcctgcctcagcct-cctgagtag-ctgggactacaggcacatgccagcatgcctagctaatttttg-tatt
q ponAbe2.chr3                                               798692676662556979975699969649499999929999948-967999999-949999799999999999999999999999999999999939-9999
i ponAbe2.chr3                     C 0 C 0
s otoGar1.scaffold_99909.1-31737        7914 101 -     31737 gcaacctcaaaatcctaggctcagacgatcttcatgcctcagctt-ccagagtag-ctgagactacagccatcagccacaatgcccaactagttttttctatt
q otoGar1.scaffold_99909.1-31737                             999999999999999999999999999999999999999999999-999999999-99999999999999999999999999999999999999999999999
i otoGar1.scaffold_99909.1-31737   C 0 C 0
s monDom5.chr8                     276496830 102 + 312544902 GCGTCCTTCCCCTGCCAGACAACAACCACGATCTAATCTGAGCCTACCTTAACAGACTATCCTCAATGAGTCATTCTACGTGGACCGTCCAATTCTTT-CCTT
q monDom5.chr8                                               99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999
i monDom5.chr8                     I 28 C 0
s gorGor1.Supercontig_0555359             15  77 +       585 -----------------------agtgattctcctgcctcagcct-cctaagtag-ctgggactacaggcacacgccagcatgcctagctaatttttg-tatt
q gorGor1.Supercontig_0555359                                -----------------------9999999999999999999999-999999999-999999999999999999999999999999999999999999-9999
i gorGor1.Supercontig_0555359      N 0 C 0
e cavPor3.scaffold_0                 8220312  23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590   2 + 163896628 I
e bosTau4.chr1                     156979668   0 + 161106243 C
e loxAfr3.scaffold_36                 509920   7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427   1 -     83534 I
e speTri1.scaffold_135460              77941 210 -    203079 I
e micMur1.scaffold_734                269152   0 -    418489 C
e ochPri2.scaffold_2292               100971   1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921   0 -      4973 C
e pteVam1.scaffold_30179                5048   2 -      7387 I
e calJac1.Contig102                  1031147  11 -   1157145 I
e echTel1.scaffold_321361             117647   1 +    198078 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598   0 -     37689 C
e proCap1.scaffold_15753                 457   0 -     39409 C
e papHam1.scaffold12353                58527   4 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=25104.000000
s hg19.chrY                          7649344 38 +  59373566 ---------tttagtagatac-gggtttcaccatgttggccaggatgg
s rheMac2.chr2                     158758077 38 + 189746636 ---------tttagtagagac-aggtttcaccatgttggccaggatga
q rheMac2.chr2                                              ---------899999999999-99999999999999999699999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71030120 38 - 202140232 ---------tttagtagagac-aggtttcaccatgttggccaggatga
q ponAbe2.chr3                                              ---------999999999999-99999998999999999999999999
i ponAbe2.chr3                     C 0 C 0
s gorGor1.Supercontig_0555359             92 38 +       585 ---------tttagtagagac-aggtttcaccatgttggccaggatga
q gorGor1.Supercontig_0555359                               ---------999999999999-99999999999999999999999999
i gorGor1.Supercontig_0555359      C 0 C 0
s panTro2.chrY                        502877 38 +  23952694 ---------tttagtagatac-gggtttcaccatgttggccaggatgg
q panTro2.chrY                                              ---------000000000000-00000000000000000000000000
i panTro2.chrY                     C 0 C 0
s otoGar1.scaffold_99909.1-31737        8015 37 -     31737 ---------tttagtagagatggggtctcac--tcttgctcaggctgg
q otoGar1.scaffold_99909.1-31737                            ---------9999999999999999999999--999999999999999
i otoGar1.scaffold_99909.1-31737   C 0 C 0
s speTri1.scaffold_135460              78151 38 -    203079 ---------TTGAGTTGATTa-gtgtctcactaaattgctgaagctgg
q speTri1.scaffold_135460                                   ---------658855734363-22659674466766676697696666
i speTri1.scaffold_135460          I 210 C 0
s equCab2.chr16                     22208283 10 -  87365405 --------------------------------------acagggctgg
q equCab2.chr16                                             --------------------------------------9999999999
i equCab2.chr16                    C 0 C 0
s monDom5.chr8                     276496932 33 + 312544902 TTCCATCTCTTGGGAAAATGA-GAAATTCACCTC--------------
q monDom5.chr8                                              999999999999999999999-999999999999--------------
i monDom5.chr8                     C 0 C 0
e cavPor3.scaffold_0                 8220312 23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590  2 + 163896628 I
e bosTau4.chr1                     156979668  0 + 161106243 C
e loxAfr3.scaffold_36                 509920  7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427  1 -     83534 I
e micMur1.scaffold_734                269152  0 -    418489 C
e ochPri2.scaffold_2292               100971  1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921  0 -      4973 C
e pteVam1.scaffold_30179                5048  2 -      7387 I
e calJac1.Contig102                  1031147 11 -   1157145 I
e echTel1.scaffold_321361             117647  1 +    198078 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598  0 -     37689 C
e proCap1.scaffold_15753                 457  0 -     39409 C
e papHam1.scaffold12353                58527  4 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=82856.000000
s hg19.chrY                          7649382 69 +  59373566 tctcgatctcctgacct--tgtgatccatctgcctctgcctctccctaaagttctgggattacaggcgtga
s panTro2.chrY                        502915 69 +  23952694 tcttgatctcctgacct--tgtgatccatctgcctctgcctctccctaaagttctgggattacaggtgtga
q panTro2.chrY                                              00000000000000000--0000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            130 69 +       585 tcttgatctcctgacct--agtgatctacccacctcagcctctccctaaagcactgggattacaggcgtga
q gorGor1.Supercontig_0555359                               99999999999999999--9999999999999999999998999999999899999999999999999999
i gorGor1.Supercontig_0555359      C 0 I 13
s ponAbe2.chr3                      71030158 69 - 202140232 tctggatctcctgacct--agtgatctacccacctcagcctctccctaaagtgctgggattacaggcatga
q ponAbe2.chr3                                              99999999999999999--9999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 I 13
s rheMac2.chr2                     158758115 69 + 189746636 tctcgatctcctgacct--agtgatctacccacctcagcctctccctaaagtgctgggattacaggcgtga
q rheMac2.chr2                                              99999999999999749--9999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 I 39
s papHam1.scaffold12353                58531 69 +     70985 tctcgatctcctgacct--agtgatctacccacctcagcctctccctaaagtgctgggattacaggcgtga
q papHam1.scaffold12353                                     99999999999999999--9999999999999999999999999999999999999999999999999999
i papHam1.scaffold12353            I 4 I 13
s otoGar1.scaffold_99909.1-31737        8052 69 -     31737 tcttgaactcctgagctcaaacattctgcccatcttggc--ctcccagagttgccaggattataggcatga
q otoGar1.scaffold_99909.1-31737                            999999999999999999999999999999999999999--999999999999999999999999999999
i otoGar1.scaffold_99909.1-31737   C 0 I 207
s speTri1.scaffold_135460              78189 58 -    203079 --------ctttgaact--cacgatcctcctgcctcaccct---ccagagtcactgggattacaggcgtgt
q speTri1.scaffold_135460                                   --------576799999--9999999998999989889999---998999995899999999959999999
i speTri1.scaffold_135460          C 0 C 0
s equCab2.chr16                     22208293  7 -  87365405 -------------------------------------------ccccAAT---------------------
q equCab2.chr16                                             -------------------------------------------9999999---------------------
i equCab2.chr16                    C 0 C 0
s monDom5.chr8                     276496965 46 + 312544902 ------TTCCCTCACCT-------TTCATTCGCCTC-------TCTCGGATTTTTGGGAGGAGGGG-----
q monDom5.chr8                                              ------99999999999-------999999999999-------99999999999999999999999-----
i monDom5.chr8                     C 0 C 0
e cavPor3.scaffold_0                 8220312 23 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590  2 + 163896628 I
e bosTau4.chr1                     156979668  0 + 161106243 C
e loxAfr3.scaffold_36                 509920  7 -  24123610 I
e canFam2.chr23                     25988782 204 -  55389570 I
e vicPac1.scaffold_6092                39427  1 -     83534 I
e micMur1.scaffold_734                269152  0 -    418489 C
e ochPri2.scaffold_2292               100971  1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4921  0 -      4973 C
e pteVam1.scaffold_30179                5048  2 -      7387 I
e calJac1.Contig102                  1031147 11 -   1157145 I
e echTel1.scaffold_321361             117647  1 +    198078 I
e eriEur1.scaffold_377961               9468 1285 +     88154 I
e turTru1.scaffold_111402              10598  0 -     37689 C
e proCap1.scaffold_15753                 457  0 -     39409 C
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-46946.000000
s hg19.chrY                          7649451 26 +  59373566 gccaATGTAC------------TATTTTAAGAAACA----------------AA
s vicPac1.scaffold_6092                39428 22 -     83534 --CAATGTGT------------TACCTTAAAACTAA------------------
q vicPac1.scaffold_6092                                     --99999999------------99999999999999------------------
i vicPac1.scaffold_6092            I 1 C 0
s turTru1.scaffold_111402              10598 22 -     37689 --CACTGTGT------------TACTTTAAAACAAA------------------
q turTru1.scaffold_111402                                   --99999999------------99999999999999------------------
i turTru1.scaffold_111402          C 0 C 0
s papHam1.scaffold12353                58613 26 +     70985 gTCAGTGTCC------------TCtttttaaaaaaa----------------aa
q papHam1.scaffold12353                                     9999999999------------99999994869999----------------99
i papHam1.scaffold12353            I 13 C 0
s panTro2.chrY                        502984 26 +  23952694 gccaATGTAC------------TATTTTAAGAAACA----------------AA
q panTro2.chrY                                              0000000000------------00000000000000----------------00
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            212 26 +       585 gccAATGTAC------------TCTTTTTAAAAACA----------------AA
q gorGor1.Supercontig_0555359                               9999999999------------99999999999999----------------99
i gorGor1.Supercontig_0555359      I 13 C 0
s ponAbe2.chr3                      71030240 26 - 202140232 gccAATGTAC------------TCTTTTTAAAAACA----------------AA
q ponAbe2.chr3                                              9999999999------------99999999999999----------------99
i ponAbe2.chr3                     I 13 C 0
s speTri1.scaffold_135460              78247 54 -    203079 gccatggtgcctggcAAGATAATGTTTTTTTAAATGATGCTTGGTTTTTAAAAA
q speTri1.scaffold_135460                                   989999949999998789999999899999999999999999999999999999
i speTri1.scaffold_135460          C 0 C 0
s loxAfr3.scaffold_36                 509927 13 -  24123610 -------------------------tttaaaacata----------------aa
q loxAfr3.scaffold_36                                       -------------------------99999999999----------------99
i loxAfr3.scaffold_36              I 7 C 0
s proCap1.scaffold_15753                 457  6 -     39409 --------------------------------AAGA----------------CA
q proCap1.scaffold_15753                                    --------------------------------9999----------------99
i proCap1.scaffold_15753           C 0 C 0
s echTel1.scaffold_321361             117648 20 +    198078 ---AATGTGC------------T---TTAAAAAATA----------------AA
q echTel1.scaffold_321361                                   ---9999899------------9---9999999989----------------96
i echTel1.scaffold_321361          I 1 C 0
s cavPor3.scaffold_0                 8220335 22 -  88675666 ---AATGTG-------------TATTTTTAGAAATG----------------AA
q cavPor3.scaffold_0                                        ---999999-------------99999999999999----------------99
i cavPor3.scaffold_0               I 23 C 0
s calJac1.Contig102                  1031158  7 -   1157145 -------------------------------AAACA----------------AA
q calJac1.Contig102                                         -------------------------------99999----------------99
i calJac1.Contig102                I 11 C 0
s otoGar1.scaffold_99909.1-31737        8328 19 -     31737 -------TGC------------TATTTTTAAAAACA----------------AA
q otoGar1.scaffold_99909.1-31737                            -------999------------99999999999999----------------99
i otoGar1.scaffold_99909.1-31737   I 207 C 0
s micMur1.scaffold_734                269152 17 -    418489 ---------t------------tatttttaaaaaca----------------aa
q micMur1.scaffold_734                                      ---------9------------99999999999999----------------99
i micMur1.scaffold_734             C 0 C 0
s eriEur1.scaffold_377961              10753 23 +     88154 ---AATGCAt------------gactttaaataaaa----------------ag
q eriEur1.scaffold_377961                                   ---9999999------------99999999999999----------------99
i eriEur1.scaffold_377961          I 1285 C 0
s bosTau4.chr1                     156979668 21 + 161106243 ---aatGTGT------------TACTTTAAAAACAA------------------
q bosTau4.chr1                                              ---9999999------------99999999999999------------------
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22208300 23 -  87365405 ---AATGTGT------------TCTTTTAAAACACA----------------AA
q equCab2.chr16                                             ---9999999------------99999999999999----------------99
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_111908               4921 22 -      4973 ---AATGTGT------------TATTTTAAAACACA----------------A-
q felCat3.scaffold_111908                                   ---9999999------------99999999999999----------------9-
i felCat3.scaffold_111908          C 0 I 2
s canFam2.chr23                     25988986 21 -  55389570 -----TGTAC------------TTTTTTAAAACACA----------------AA
q canFam2.chr23                                             -----99999------------99999999999999----------------99
i canFam2.chr23                    I 204 I 220
s pteVam1.scaffold_30179                5050 23 -      7387 ---AATGTGT------------TATTTTAAAACACA----------------AA
q pteVam1.scaffold_30179                                    ---9999999------------99999999999999----------------99
i pteVam1.scaffold_30179           I 2 C 0
s myoLuc1.scaffold_164117               3621  9 -     50790 -----------------------------AAACACA----------------CA
q myoLuc1.scaffold_164117                                   -----------------------------5654231----------------22
i myoLuc1.scaffold_164117          N 0 C 0
s monDom5.chr8                     276497011 17 + 312544902 -----------------CCCAGCTTCCTAACAAG--------------------
q monDom5.chr8                                              -----------------99999999999999999--------------------
i monDom5.chr8                     C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466590  2 + 163896628 I
e ochPri2.scaffold_2292               100971  1 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e rheMac2.chr2                     158758184 39 + 189746636 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=339782.000000
s hg19.chrY                          7649477 30 +  59373566 TTTTAAAACAAAACCTAGGGGTACTT----AA-GA
s papHam1.scaffold12353                58639 30 +     70985 atttaaaaCAAAACCTAGGGGTACTT----AA-GA
q papHam1.scaffold12353                                     99999999999999999999999999----99-99
i papHam1.scaffold12353            C 0 C 0
s panTro2.chrY                        503010 30 +  23952694 TTTTAAAACAAAACCTAGGGGTACTT----AA-GA
q panTro2.chrY                                              00000000000000000000000000----00-00
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            238 30 +       585 TTTTAAAATAAAACCTAGGGGTACTT----AA-GA
q gorGor1.Supercontig_0555359                               99999999999999999999999999----99-99
i gorGor1.Supercontig_0555359      C 0 C 0
s ponAbe2.chr3                      71030266 30 - 202140232 TTTTAAAATAAAACCTAGGGGTACTT----AA-GA
q ponAbe2.chr3                                              99999999999999999999999999----99-99
i ponAbe2.chr3                     C 0 C 0
s speTri1.scaffold_135460              78301 29 -    203079 TTTAAAATCAAGATCTA-GGGTACTT----AA-GA
q speTri1.scaffold_135460                                   99999999999999999-99999999----99-99
i speTri1.scaffold_135460          C 0 C 0
s cavPor3.scaffold_0                 8220357 29 -  88675666 TTTAAAAATAAAATCCA-GGGGACTT----AA-TA
q cavPor3.scaffold_0                                        99999999999999999-99999999----99-99
i cavPor3.scaffold_0               C 0 C 0
s calJac1.Contig102                  1031165 30 -   1157145 TGTTAAAAGAAAACCTAGGGGTGCTT----AA-CA
q calJac1.Contig102                                         99999999999999999999999999----99-99
i calJac1.Contig102                C 0 C 0
s rheMac2.chr2                     158758223 29 + 189746636 -tttaaaaCAAAACCTAGGGGTACTT----AA-GA
q rheMac2.chr2                                              -9999999999999999999999999----99-99
i rheMac2.chr2                     I 39 C 0
s otoGar1.scaffold_99909.1-31737        8347 30 -     31737 TTTATAAACAAAAACTAAGGGTACTT----AG-AA
q otoGar1.scaffold_99909.1-31737                            99999999999999999999999999----99-99
i otoGar1.scaffold_99909.1-31737   C 0 I 5
s micMur1.scaffold_734                269169 31 -    418489 tttataaaCAAAATCTAGGGGTACTT----AACGA
q micMur1.scaffold_734                                      99999999999999999999999999----99999
i micMur1.scaffold_734             C 0 I 5
s vicPac1.scaffold_6092                39450 30 -     83534 CTTAAAAACAAAATCTAGGGGTACTT----AA-GA
q vicPac1.scaffold_6092                                     99999999999999999999999999----99-99
i vicPac1.scaffold_6092            C 0 I 1
s turTru1.scaffold_111402              10620 27 -     37689 CTTAACAA---AATCTAGGGGTACTT----AA-GA
q turTru1.scaffold_111402                                   99999999---999999999999999----99-99
i turTru1.scaffold_111402          C 0 I 1
s bosTau4.chr1                     156979689 30 + 161106243 GCTAAAGATGCAATCTAAGGGTACTT----AA-GA
q bosTau4.chr1                                              99999999999999999999999999----99-99
i bosTau4.chr1                     C 0 I 1
s felCat3.scaffold_111908               4945 28 -      4973 TTAAAAA--CAAATCTAGGGGTCCTT----AA-GA
q felCat3.scaffold_111908                                   9999999--99999999999999999----99-99
i felCat3.scaffold_111908          I 2 n 2
s canFam2.chr23                     25989227 30 -  55389570 TTAAAAAACTAAATCTAGGGCTACTT----AA-GA
q canFam2.chr23                                             99999999999999999999999999----99-99
i canFam2.chr23                    I 220 I 2
s pteVam1.scaffold_30179                5073 30 -      7387 CTTAAAAACAAAATCTAGAGGTACTT----AA-GG
q pteVam1.scaffold_30179                                    99999999999999999999999999----99-99
i pteVam1.scaffold_30179           C 0 I 2
s myoLuc1.scaffold_164117               3630 28 -     50790 CTTAAAA--CAAATCTAGAGGTACTT----AG-GA
q myoLuc1.scaffold_164117                                   2446772--25844543254333245----32-33
i myoLuc1.scaffold_164117          C 0 I 2
s eriEur1.scaffold_377961              10776 27 +     88154 ---aacaacaaaatttCAAGGAACTT----TA-GA
q eriEur1.scaffold_377961                                   ---99999999999999999999999----99-99
i eriEur1.scaffold_377961          C 0 I 5
s equCab2.chr16                     22208323 24 -  87365405 ------AACAAAATCTAGGGGTACTT----AG-GA
q equCab2.chr16                                             ------99999999999999999999----99-99
i equCab2.chr16                    C 0 I 2
s oryCun2.chr14                      2466592 12 + 163896628 ------------------TTAAGAAC----TA-AG
q oryCun2.chr14                                             ------------------99999999----99-99
i oryCun2.chr14                    I 2 C 0
s ochPri2.scaffold_2292               100972 27 +    188698 --TTACAATGAGCTCTA-GAGTTCTT----TA-GG
q ochPri2.scaffold_2292                                     --999999999999999-99999999----99-99
i ochPri2.scaffold_2292            I 1 C 0
s echTel1.scaffold_321361             117668 30 +    198078 TGTGAAAATGAAATGTAGGGGCACTT----AA-GA
q echTel1.scaffold_321361                                   99999999999979999999996899----99-99
i echTel1.scaffold_321361          C 0 C 0
s proCap1.scaffold_15753                 463 30 -     39409 TTTAAAAATAAATTCTAGGGGCACTT----CA-GA
q proCap1.scaffold_15753                                    99999999999999999999999998----89-99
i proCap1.scaffold_15753           C 0 C 0
s loxAfr3.scaffold_36                 509940 30 -  24123610 tttaaaaataaaatCTAGGGGCACTT----AA-GA
q loxAfr3.scaffold_36                                       99999999999999999999999999----99-99
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497028 31 + 312544902 ---ATGACTCAATCCCAGAGGCATTCCCCAAA-GA
q monDom5.chr8                                              ---99999999999999999999999999999-99
i monDom5.chr8                     C 0 I 1
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=1732958.000000
s hg19.chrY                          7649507 148 +  59373566 A---CCACCTGACATCAGATACTGTAGCTGTCA---------------TTTCCATATATCATGCAAGAAATTGACA--GG--ACAAAAAA----ATCTGCAGCAATGATTCAC------TCTAAAACAAGCATTCAGCATCCTGGAG----AAGTCTCCATT---AATAAGAGTGACAAAT-GTAGGA
s papHam1.scaffold12353                58669 147 +     70985 A---CCACCTAACATCAGATACTGTAACTCTCA---------------TTTCCATACATCGTGCAAGAAATTTATA--GG--A-AAAAAT----ATCTATAGCAATGATTGAC------TCTAACACAAGCATTCAGCATCCTGGAG----AAGGCTCTATT---AGTAAGAGTGACAAAT-GTAGGA
q papHam1.scaffold12353                                      9---99999999999999999999999999999---------------9999999999999999999999999999--99--9-999999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i papHam1.scaffold12353            C 0 C 0
s panTro2.chrY                        503040 146 +  23952694 A---CCACCTGACATCAGATACTGTAGCTGTCA---------------TTTCCATATATCATGCAAGAAATTGACA--GG--ACAAAAAA----ATCTGCAGCAATGATTCAC------TCTAAAACAAGCATTCAGCATCCTGGAG----AAGTCTCCATT---AAT--GAGTGACAAAT-GTAGGA
q panTro2.chrY                                               0---00000000000000000000000000000---------------0000000000000000000000000000--00--00000000----0000000000000000000------0000000000000000000000000000----00000000000---000--00000000000-000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            268 149 +       585 A---CCACCTAACATCAGATACTGTAGCTCTCA---------------TTTCCATACATCATGCAAGAAATTTACA--GG-AAAAAAAAA----ATCTATAGCCATGATTCAC------TCTAAAACAAGCATTCAGCATCCTGGAG----AAGGCTCCATT---AATAAGAGTGACAAAT-GTAGGA
q gorGor1.Supercontig_0555359                                9---99999999999999999999999999999---------------9999999999999989999999999999--99-999999999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i gorGor1.Supercontig_0555359      C 0 C 0
s ponAbe2.chr3                      71030296 148 - 202140232 A---CCACCTAACATCAGATACTGTAGCTCTCA---------------TTTCCATACATCATGCAAGAAATTTACA--GG--AAAAAAAA----ATCTATAGCCATGATTCAC------TCTAAAACAAGCATTCAGCATCCTGGAG----AAGGCTCCATT---AATAAGAGTGACAAAT-GTAGGA
q ponAbe2.chr3                                               9---99999999999999999999999999999---------------9999999999999999999999999999--99--99999999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i ponAbe2.chr3                     C 0 C 0
s micMur1.scaffold_734                269205 153 -    418489 A---CCACATAACATCAGA-ACTGTAGCTCTCA---------------TTTCCATACATCACACAAGAAATTTACA--GGAAAAAAAAAA----ATCTATAGCAATGATTCAC------TCTAAAGCAAGCATTCAGCATCCTGGAATCCTAAAGCGCCATT---AATAATGGTGACAAAT-AAAAGA
q micMur1.scaffold_734                                       8---998899999999999-6999999999996---------------8976969796996859999999999999--999999999999----9999999999999999989------9987997899587799999689989996998999999789999---9999989999999999-899999
i micMur1.scaffold_734             I 5 C 0
s otoGar1.scaffold_99909.1-31737        8382 154 -     31737 A---CCGTATAATATCAGATACTGTAGTTCTTA----------------TTCCATATATCATGTAAGAAATTTACA--GG--AAAAAAAA----ATCTATAGCAATGATTCACGCTGAGTCTAAAGCAAGCACTCAGCATCCTGGAG----AAAGTGCCATT---AATAACAGTGACAAATAAAAAGA
q otoGar1.scaffold_99909.1-31737                             9---99999999999999999999999999999----------------999999999999999999999999999--99--99999999----99999999999999999999999999999999799877798777679976666----99977438667---76697667785669968999966
i otoGar1.scaffold_99909.1-31737   I 5 C 0
s rheMac2.chr2                     158758252 147 + 189746636 A---CCACCTAACATCAGATACTGTAACTCTCA---------------TTTCCATACATCGTGCAAGAAATTTATA--GG--A-AAAAAT----ATCTATAGCAATGATTGAC------TCTAACACAAGCATTCAGCATCCTGGAG----AAGGCTCTATT---AATAAGAGTGACAAAT-GTAGGA
q rheMac2.chr2                                               9---99999999999999999999999999999---------------9999999999999999999999999999--99--9-999999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i rheMac2.chr2                     C 0 C 0
s calJac1.Contig102                  1031195 147 -   1157145 A---CCACCTAACATCAGATACTGTAGCTCTCA---------------TTTCCATACATCATGCAAGAAATTTACA--GG--A-AAAAAA----ATCTACAGCAATGATTCAC------TCTAAAACAAGCATTCAGCATCCTGGAG----AAGGCTCCATT---AATAAGAGTGACAAAT-GTAGGG
q calJac1.Contig102                                          9---99999999999999999999999999999---------------9999999999999999999999999999--99--9-999999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i calJac1.Contig102                C 0 C 0
s cavPor3.scaffold_0                 8220386 145 -  88675666 ----TCATGTAGCACAAGACACAATAGTTCTCA---------------TTTCCATGGATTGTGCAAGAAATTTACA--GG---AAAAAGG----ATCCATAGCAATGATTCAC------TCTAAATCAGGT-TCCAGTAGCCTAAAG----AAACCTTCATT---AACAAGAGTGACAAAT-GTAAGG
q cavPor3.scaffold_0                                         ----99999999999999999999999999999---------------9999999999999999999999999999--99---9999999----9999999999999999999------999999999999-999999999999999----99999999999---9999999999999999-999999
i cavPor3.scaffold_0               C 0 C 0
s speTri1.scaffold_135460              78330 151 -    203079 A-TTCTATGTATCATTAGATACTGTGGCTTTCA---------------TTTCCATACATCATGTAAGAAATTTACA--GG-AAAAAAAAA----ATCCATAGCAATGATTCAC------TCTAAATCAAGTGTCCAGCATCGTGGAG----GAACCTCCATT---AATAACAATGACAAAT-GTAAGA
q speTri1.scaffold_135460                                    9-9999999999999999999999999999999---------------9999999999999999999999999999--99-999999999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i speTri1.scaffold_135460          C 0 C 0
s ochPri2.scaffold_2292               100999 140 +    188698 G-ATATCACTAACGCCAGAGTCCATAGCTCTCA---------------TTTCCATACCTCATACAAGACATTTACA--GTTAAAACAAAA----ATCTATCG------------------CCAAAGCAAGTATACTGCATGCTGGAG----ACACCTCTATC---GACAACAGTGATAAAC-GCAAGA
q ochPri2.scaffold_2292                                      9-9999999999999999999999999999999---------------9999999999999999999999999999--999999999999----99999999------------------999999999999999999999999999----99999999999---9999999999999999-999999
i ochPri2.scaffold_2292            C 0 I 5426
s oryCun2.chr14                      2466604 138 + 163896628 A-TTACCCCTAACATCAGATTCTGTAGCTCTCA---------------TTTTCATATATCATGCAAAAAATTTACA--GT--AAAAAAAA----ATCTACAG------------------CTAAAGCAAGCATCGAGCATCCTGCAG----CAGCCTCCATT---AACAGCAGTGGCAAAC-AGAAGA
q oryCun2.chr14                                              9-9999999999999999999999999999999---------------9999999999999999999999999999--99--99999999----99999999------------------999999999999999999999999999----99999999999---9999999999999999-999999
i oryCun2.chr14                    C 0 C 0
s vicPac1.scaffold_6092                39481 102 -     83534 ---TACTCTT---------TACTGTAGCTCTCA----------------------------GACAAGAAATTTACA--GG--GGGAAA----------------------------------AAAGCAAAAGTCCGGCATCTTGGAG----AAATCTCCATT---AATAACAGTGACAGAG-CCATGG
q vicPac1.scaffold_6092                                      ---9999999---------99999999999999----------------------------999999999999999--99--999999----------------------------------9999999999999999999999999----99999999999---9999999999999999-999999
i vicPac1.scaffold_6092            I 1 C 0
s turTru1.scaffold_111402              10648 140 -     37689 ---TGCTCTTAACATCAGCCACTGTAGCCCTCA---------------CTTCCATACATCAGGCAAGAAATTTACA--AG--GAAGAAAA----ATCTACAGCAATGATTCAT------TCTAAAGCAAGTGTCCAGCATCCTGGAG----AAATCACCATG---AATAACAGTGACAG---------
q turTru1.scaffold_111402                                    ---999999999999999999999999999999---------------9999999999999999999999999999--99--99999999----9999999999999999999------9999999999999999999999999999----99999999999---99999999999999---------
i turTru1.scaffold_111402          I 1 I 11
s bosTau4.chr1                     156979720 146 + 161106243 ---TGTACTTAAAGTCAGACACTATAACTCTCA----------------TTCCACACATCACACACAAAATTTATA--CG--AAAAGAAA----ATCTATAGCAGTGTTTTAT------TCTAAAGCAAATGACCAGCATCCTGGAG----AAATTGCCATG----ATAACACTGACAAAG-ATAAGG
q bosTau4.chr1                                               ---999999999999999999999999999999----------------999999999999999999999999999--99--99999999----9999999999999999999------9999999999999999999999999999----99999999999----999999999999999-999999
i bosTau4.chr1                     I 1 C 0
s equCab2.chr16                     22208349 145 -  87365405 ---ATTATTTAACATCAGATACTGTAGCTCTCA---------------TTTCCATACACCATGCAGGAGATTTACAGGGG--AAAA-AAA----ACCTATAGCAATGACT--C------CCTAGACCAAGTGTCCAGCAACCTAGAG----AAATCTCCATT---CACAACAGTGACAAAC-AGAC--
q equCab2.chr16                                              ---999999999999999999999999999999---------------99999999999999999999999999999999--9999-999----9999999999999999--9------9999999999999999999999999999----99999999999---9999999999999999-9999--
i equCab2.chr16                    I 2 I 5
s canFam2.chr23                     25989259 143 -  55389570 ---ACTACTTAACATCAGCTACT---GCTCTCA---------------TTTCCATACATCATGCAAGGAATTTACA--GG--AAAA-AAA----ATCTATAGCAATGATTCAC------TCTAAAGC-AGTGCCCAGCATCCTGGAG----AAATCTCCATT---AATAACAATGACAAAT-AGAAGA
q canFam2.chr23                                              ---99999999999999999999---9999999---------------9999999999999999999999999999--99--9999-999----9999999999999999999------99999999-9999999999999999999----99999999999---9999999999999999-999999
i canFam2.chr23                    I 2 C 0
s pteVam1.scaffold_30179                5105 146 -      7387 ---ACTACTTAACATCGGATACTGTAGCTCTCA---------------TTTCCATACATCATGCAAGAAATTTATG--GG--GAA--AAA----ATCTATAGCAATGATTCAC------TCTAAAGCAAGAGTCTGGCATCCTGGAG----AGACCTCCATC---AATAACAGGGACAAAG-ATGAGA
q pteVam1.scaffold_30179                                     ---999999999999999999999999999999---------------9999999999999999999999999999--99--999--999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i pteVam1.scaffold_30179           I 2 C 0
s myoLuc1.scaffold_164117               3660 140 -     50790 ---GCTACTTCCCATTAGATACTCTAGCTCTCA---------------TTTCCATACATCATGCAAGAAATTTACG--GG--AAAATAAA----ATCTATAGCAATGATTCAC------CC-----------TCATGCATCCTGGAG----AGACCTCCATCAATAATAACAGTGACAAAG-ATAAGA
q myoLuc1.scaffold_164117                                    ---556255457544334222455533346565---------------3856745454666335445584386545--65--57735688----6545665466545756547------94-----------756535352635465----563556655559565554586555468857-696584
i myoLuc1.scaffold_164117          I 2 C 0
s eriEur1.scaffold_377961              10808 145 +     88154 ---ACTACTTAAC-TTAACTACT-TAACTCTCA---------------TTCCCATTCATCCTACAAGaaatttaca--gg--aaaa-aaa----atctatagcaaTGATTCAC------TCTAAAGCAAGTGTCCAATATCCTGGAG----AACTCTACATC---AATAACAGTGACAAAT-ATAGGT
q eriEur1.scaffold_377961                                    ---9999999999-999999999-999999999---------------9999999997999999999999999999--99--9999-999----9999999999999999999------9999999999999999999999999999----99999999999---9999999999999999-999999
i eriEur1.scaffold_377961          I 5 C 0
s echTel1.scaffold_321361             117698 141 +    198078 A-TTTCACGTAACATC---------ATTTCTCA---------------TTTCCATCTATCATGTGAGA-ACTTACA--GG--AAAAACTA----ATCTATAGCGATGATTCAC------TGGAAAGCAAGCATCCAGCATCCTGGAG---GAAACCTCCATT---AATAATAGTGACAAAT-AAATGC
q echTel1.scaffold_321361                                    7-89996899998798---------69999777---------------99998399999789979989-9799896--99--99997799----9976999999879769976------8978998869866998487779779698---799594778599---9879879789886997-997797
i echTel1.scaffold_321361          C 0 I 4
s proCap1.scaffold_15753                 493 154 -     39409 CTTTTCATGCAACATCAGTTACTACAGTTCTCA---------------TTTCTACTCATCACGCAAGA-ATTCACA--GG--AAAAAAAAAATCACCTATGGGGACGATTTAC------TCTAAAGCAAGTGTCCAGCATTGTGGAG---AAAACCTCCATT---AGTAACAGTGACGAAC-ACAGG-
q proCap1.scaffold_15753                                     999999999999999997989999999999999---------------99999999999999999999-9999799--99--9999999996794887979855999999999------9999999999999998749676848577---999471939697---7777496869879859-69899-
i proCap1.scaffold_15753           C 0 C 0
s loxAfr3.scaffold_36                 509970 152 -  24123610 A-TTTCACGCAACATCAGCTACTATAGTTCTCA---------------TTTCCACTCATCACGCGAGA-ATTGACA--GG--AAAAAAAGAA--ATCTATGGTGATGATTCAC------TCCAAAGCAAGCGTCCAGCATCCTGGAG---AAAACCTCCATT---AATAACAGTGACAAAC-AGAAGC
q loxAfr3.scaffold_36                                        9-9999999999999999999999999999999---------------99999999999999999999-9999999--99--9999999999--9999999999999999999------9999999999999999999999999999---999999999999---9999999999999999-999999
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497060 153 + 312544902 ---GCTATCTCCCATCAGGCATCGCAGCCCCCTCCCCACCACACACACTTTTCATAAACAACAAAAGGGCTTCGTG--GA--A----AGA----ATCTGTGGTCGTGATTCAC------CACCGAGGAGGAGGCAAGCATCCTGGAC---CTGACCTCCATG---GGCAATGGCAGCAAA--------
q monDom5.chr8                                               ---9999999999999999999999999999999999999999999999999999999999999999999999999--99--9----999----9999999999999999999------9999999999999999999999999999---999999999999---999999999999999--------
i monDom5.chr8                     I 1 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973   2 -      4973 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=289571.000000
s hg19.chrY                          7649655 38 +  59373566 -------CTCATCAGGTAAGCAGAAAAG----TATGCAATCTTTCCCCT
s papHam1.scaffold12353                58816 38 +     70985 -------CTGGTCAGGAAAGCAGAAAAG----TATGCAATCTTTCTCCT
q papHam1.scaffold12353                                     -------999999999999999999999----99999999999999999
i papHam1.scaffold12353            C 0 I 1
s panTro2.chrY                        503186 38 +  23952694 -------CTCACCAGGTAAGCAGAAAAG----TATGCAATCTTTCCCCT
q panTro2.chrY                                              -------000000000000000000000----00000000000000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            417 38 +       585 -------CTGGCCAGGAAAGCAGAAAAG----TATGCAATCTTTCCCCC
q gorGor1.Supercontig_0555359                               -------999999999999999999999----99999999999917755
i gorGor1.Supercontig_0555359      C 0 I 2
s ponAbe2.chr3                      71030444 38 - 202140232 -------CTGGCCAGGAAAGCAGTAAAG----TATGCAATCTTTCCCCT
q ponAbe2.chr3                                              -------999999999999999999999----99999999999999999
i ponAbe2.chr3                     C 0 I 1
s micMur1.scaffold_734                269358 37 -    418489 -------CTGGCCAGGAGAGCAGAAAA-----TATGCACTCTTTCCTTT
q micMur1.scaffold_734                                      -------99978999999988899999-----99988699999989999
i micMur1.scaffold_734             C 0 I 1
s otoGar1.scaffold_99909.1-31737        8536 38 -     31737 -------CTGGCCAGGAGAGCAGAAAAG----TATGCAATCTCCGCCTT
q otoGar1.scaffold_99909.1-31737                            -------566256566558456658965----47552435773535476
i otoGar1.scaffold_99909.1-31737   C 0 I 1
s rheMac2.chr2                     158758399 38 + 189746636 -------CTGGTCAGGAAAGCAGAAAAG----TATGCAATCTTTCTCCT
q rheMac2.chr2                                              -------999999999999999999999----99999999999999999
i rheMac2.chr2                     C 0 I 1
s calJac1.Contig102                  1031342 38 -   1157145 -------TTAGCCAGGAAAGCAGAAAAG----TATGCAATCTCTCCCTG
q calJac1.Contig102                                         -------999999999999999999999----99999999999999999
i calJac1.Contig102                C 0 C 0
s cavPor3.scaffold_0                 8220531 38 -  88675666 -------CCGGGTAGGAAAGCAGAAAAG----TAAGTAATTCCTCCCTT
q cavPor3.scaffold_0                                        -------999999999999999999999----99999999999999999
i cavPor3.scaffold_0               C 0 I 1
s speTri1.scaffold_135460              78481 30 -    203079 -------CTGGTTAGAAAAGCAT------------GCAATCTCTCCCCT
q speTri1.scaffold_135460                                   -------9999999999999999------------99999999999999
i speTri1.scaffold_135460          C 0 I 1
s oryCun2.chr14                      2466742 30 + 163896628 -------CTGAGCAGGAGAGCAG------------GTGTCTTTACCTCG
q oryCun2.chr14                                             -------9999999999999999------------99999999999999
i oryCun2.chr14                    C 0 I 1
s vicPac1.scaffold_6092                39583 38 -     83534 -------CTGATCAGGAGAGTTGAAAAG----TATGCACCCTTTCCCTT
q vicPac1.scaffold_6092                                     -------999999999999999999999----99999999999999999
i vicPac1.scaffold_6092            C 0 I 1
s bosTau4.chr1                     156979866 38 + 161106243 -------CTGATGGAGAAAGCTGGAAAG----CATGCAATGTTTCCCTT
q bosTau4.chr1                                              -------999999999999999999999----99999999999999999
i bosTau4.chr1                     C 0 I 1
s canFam2.chr23                     25989402 30 -  55389570 -------TTGGCCAGG--------AAAG----TGTGCAGTCTTTTCCCT
q canFam2.chr23                                             -------999999999--------9999----99999999999999999
i canFam2.chr23                    C 0 C 0
s pteVam1.scaffold_30179                5251 38 -      7387 -------CTGGCCAGGAAAGCAGAAAAG----TCTGTACTCTTCCCCTT
q pteVam1.scaffold_30179                                    -------999999999999999999999----99999999999999999
i pteVam1.scaffold_30179           C 0 I 1
s myoLuc1.scaffold_164117               3800 38 -     50790 -------CTGGCCAGGAAAGCAGAAAAG----TCTGCACTCTTTCCCCT
q myoLuc1.scaffold_164117                                   -------945259555893455769948----69556678899999995
i myoLuc1.scaffold_164117          C 0 I 1
s eriEur1.scaffold_377961              10953 42 +     88154 -------CTGGCCAGGAAAGCAGCATGGTGCATATGCAGTCTTTCCTTT
q eriEur1.scaffold_377961                                   -------999999999999999999999999999999999999999999
i eriEur1.scaffold_377961          C 0 C 0
s echTel1.scaffold_321361             117843 26 +    198078 -------CTGGTCAGGAAAGCAGAAGGG----------------CCCTT
q echTel1.scaffold_321361                                   -------799999799999998899999----------------99999
i echTel1.scaffold_321361          I 4 C 0
s proCap1.scaffold_15753                 647 31 -     39409 --------------AGGGAGCAGGAAAG----TACCACGACTTTCCCTT
q proCap1.scaffold_15753                                    --------------79958799969995----96786798899979597
i proCap1.scaffold_15753           C 0 C 0
s loxAfr3.scaffold_36                 510122 38 -  24123610 -------CTGGTCAGGAAAGCAGAAAAG----TACGACGGCTTTCCCTT
q loxAfr3.scaffold_36                                       -------999999999999999999999----99999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497213 28 + 312544902 CCATCTTCTAACGGG-----------------CAAGGAACCCTCC----
q monDom5.chr8                                              999999999999999-----------------9999999999999----
i monDom5.chr8                     C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e equCab2.chr16                     22208494  5 -  87365405 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e turTru1.scaffold_111402              10788 11 -     37689 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=26325.000000
s hg19.chrY                          7649693 31 +  59373566 G--AAGGTACATTCAGG----------------------------------------------------ATATGCTGCTA-----------GAT-------------------AA
s papHam1.scaffold12353                58855 31 +     70985 A--AAGGTACATTCAGG----------------------------------------------------ACATGCTGCTA-----------GAT-------------------AA
q papHam1.scaffold12353                                     9--99999999999999----------------------------------------------------99999999999-----------999-------------------99
i papHam1.scaffold12353            I 1 C 0
s panTro2.chrY                        503224 31 +  23952694 G--AAGGTACATTCAGG----------------------------------------------------ATATGCTGCTA-----------GAT-------------------AA
q panTro2.chrY                                              0--00000000000000----------------------------------------------------00000000000-----------000-------------------00
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            457 31 +       585 A--AGGGTACATTCAGG----------------------------------------------------ATATGCTGCTA-----------GAT-------------------AA
q gorGor1.Supercontig_0555359                               9--99999999999999----------------------------------------------------99999999999-----------999-------------------99
i gorGor1.Supercontig_0555359      I 2 C 0
s ponAbe2.chr3                      71030483 31 - 202140232 A--AGGGTACATTCAGG----------------------------------------------------ATATGCTGCTA-----------GAT-------------------AA
q ponAbe2.chr3                                              9--99999999999999----------------------------------------------------99999999999-----------999-------------------99
i ponAbe2.chr3                     I 1 C 0
s micMur1.scaffold_734                269396 31 -    418489 A--AAGGTTCATTCTGG----------------------------------------------------ATATGCTGCTA-----------GAT-------------------AA
q micMur1.scaffold_734                                      9--99988998999999----------------------------------------------------99999999999-----------999-------------------99
i micMur1.scaffold_734             I 1 C 0
s otoGar1.scaffold_99909.1-31737        8575 26 -     31737 A--AAGGTACATTCTGG----------------------------------------------------ATCTTCTG----------------G-------------------AC
q otoGar1.scaffold_99909.1-31737                            6--97453456676543----------------------------------------------------24656556----------------6-------------------34
i otoGar1.scaffold_99909.1-31737   I 1 C 0
s rheMac2.chr2                     158758438 31 + 189746636 A--AAGGTACATTCAGG----------------------------------------------------ACATGTTGCTA-----------GAT-------------------AA
q rheMac2.chr2                                              9--99999999999999----------------------------------------------------99999999999-----------999-------------------99
i rheMac2.chr2                     I 1 C 0
s calJac1.Contig102                  1031380 31 -   1157145 A--AGGGTACATTCAGG----------------------------------------------------ATATGCTTCTA-----------GAT-------------------AG
q calJac1.Contig102                                         9--99999999999999----------------------------------------------------99999999999-----------999-------------------99
i calJac1.Contig102                C 0 C 0
s cavPor3.scaffold_0                 8220570 90 -  88675666 A--AGGCTAGGttttgttttttttttttttttttttttttttttttttttttGGAAGGGTAGGCTTTAGATATACTGCTGAAGAGAA----AAA-------------------AA
q cavPor3.scaffold_0                                        9--999999997999419999999999999999999999999999999993102545446523429356522318478135399999----999-------------------99
i cavPor3.scaffold_0               I 1 C 0
s speTri1.scaffold_135460              78512 60 -    203079 A--AGGATAATTTCCAGATACATTTTTTTCCTTTC----------------------------------CTCTTTTCCTAAAGAGGAAAGGAAA-------------------AA
q speTri1.scaffold_135460                                   9--99999999999999999999999999999999----------------------------------9999999999999999999999999-------------------99
i speTri1.scaffold_135460          I 1 C 0
s oryCun2.chr14                      2466773 37 + 163896628 GC-AGGGTAGGTTCCAA----------------------------------------------------GTACACAGCTAGAGGG------AAA-------------------AA
q oryCun2.chr14                                             99-99999999999999----------------------------------------------------9999999999999999------999-------------------99
i oryCun2.chr14                    I 1 C 0
s vicPac1.scaffold_6092                39622 30 -     83534 A--AGAGTACATTCTAG----------------------------------------------------ATATGCTGCCA-----------GAT--------------------G
q vicPac1.scaffold_6092                                     9--99999999999999----------------------------------------------------99999999999-----------999--------------------9
i vicPac1.scaffold_6092            I 1 C 0
s bosTau4.chr1                     156979905 49 + 161106243 A--AGAGTA-GTTCTAA----------------------------------------------------ATAAGGTGTTA-----------GATTTATAAAAAAACAGAACAAAA
q bosTau4.chr1                                              9--999999-9999999----------------------------------------------------99999999999-----------999999999999999999999999
i bosTau4.chr1                     I 1 C 0
s pteVam1.scaffold_30179                5290 27 -      7387 A--AGGATGCATGCTG------------------------------------------------------TATGCTGCTA-----------GAT---------------------
q pteVam1.scaffold_30179                                    9--9999999999999------------------------------------------------------9999999999-----------999---------------------
i pteVam1.scaffold_30179           I 1 C 0
s myoLuc1.scaffold_164117               3839 29 -     50790 G--AGGGTACATTCTGC----------------------------------------------------CTATGCTGCTG-----------GAT---------------------
q myoLuc1.scaffold_164117                                   8--85567476668458----------------------------------------------------97858855836-----------589---------------------
i myoLuc1.scaffold_164117          I 1 C 0
s eriEur1.scaffold_377961              10995 32 +     88154 G--AGGGTACATTCTGG----------------------------------------------------CTATGTTGCTG-----------GAT------------------AAA
q eriEur1.scaffold_377961                                   9--99999999999999----------------------------------------------------99999999999-----------999------------------999
i eriEur1.scaffold_377961          C 0 C 0
s echTel1.scaffold_321361             117869 20 +    198078 -------------CTGG----------------------------------------------------ATCTGAGGCTG-----------GCT-------------------GC
q echTel1.scaffold_321361                                   -------------9999----------------------------------------------------99989999999-----------999-------------------99
i echTel1.scaffold_321361          C 0 C 0
s proCap1.scaffold_15753                 678 32 -     39409 -GAAGGCTGCGTCCTGG----------------------------------------------------TCACGTGGCTG-----------GAT-------------------GA
q proCap1.scaffold_15753                                    -7999968975999566----------------------------------------------------79888688849-----------997-------------------89
i proCap1.scaffold_15753           C 0 I 12
s loxAfr3.scaffold_36                 510160 32 -  24123610 -GAAGGGTGCATCCTGG----------------------------------------------------ATACGCTACTG-----------GAT-------------------GC
q loxAfr3.scaffold_36                                       -9999999999999999----------------------------------------------------99999999999-----------999-------------------99
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497241 28 + 312544902 -----GGGAGCTTCCTA----------------------------------------------------ACAAGCTTCCG-----------GAT-------------------GA
q monDom5.chr8                                              -----999999999999----------------------------------------------------99999999999-----------999-------------------99
i monDom5.chr8                     C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e equCab2.chr16                     22208494  5 -  87365405 I
e canFam2.chr23                     25989432  0 -  55389570 C
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e turTru1.scaffold_111402              10788 11 -     37689 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=97887.000000
s hg19.chrY                          7649724 32 +  59373566 -----ACAAATCCAAAG-GTAAGTCTCGTAA-AGAATGC
s papHam1.scaffold12353                58886 32 +     70985 -----ACAAATCCAAAG-GTAAGTATGGTAA-AGAATCC
q papHam1.scaffold12353                                     -----999999999999-9999999999999-9999999
i papHam1.scaffold12353            C 0 C 0
s panTro2.chrY                        503255 32 +  23952694 -----ACAAATCCAAAG-GTAAGTCTCGTAA-AGAATGC
q panTro2.chrY                                              -----000000000000-0000000000000-0000000
i panTro2.chrY                     C 0 C 0
s gorGor1.Supercontig_0555359            488 32 +       585 -----ACAAATCCAAAG-GTAAGTCTGGTAA-AGAATCC
q gorGor1.Supercontig_0555359                               -----999999999999-9999999999999-9999999
i gorGor1.Supercontig_0555359      C 0 C 0
s ponAbe2.chr3                      71030514 10 - 202140232 -----ACAAATCCAA------------------------
q ponAbe2.chr3                                              -----9999999999------------------------
i ponAbe2.chr3                     C 0 T 77
s micMur1.scaffold_734                269427 32 -    418489 -----ACAAATCCAAAG-TCAAGTCTAGTAA-AGAATGC
q micMur1.scaffold_734                                      -----999999999999-9999999999999-9999999
i micMur1.scaffold_734             C 0 C 0
s otoGar1.scaffold_99909.1-31737        8601 32 -     31737 -----TTAAATCCAAAG-TTAAGTCTCATGA-AGGATGC
q otoGar1.scaffold_99909.1-31737                            -----656865435855-5365556555562-5455456
i otoGar1.scaffold_99909.1-31737   C 0 I 4
s rheMac2.chr2                     158758469 32 + 189746636 -----ACAAATCCAAAG-GTAAGTATGGTAA-AGAATCC
q rheMac2.chr2                                              -----999999999999-9999999999999-9999999
i rheMac2.chr2                     C 0 C 0
s calJac1.Contig102                  1031411 32 -   1157145 -----ACAAATCCAAAG-GTAAGTCTGGTAA-AGAATCC
q calJac1.Contig102                                         -----999999999999-9999999999999-9999999
i calJac1.Contig102                C 0 C 0
s cavPor3.scaffold_0                 8220660 32 -  88675666 -----AAAAATCCAAAG-GTGAGGCTGGTAA-TAAATGC
q cavPor3.scaffold_0                                        -----999999999999-9999999999999-9999999
i cavPor3.scaffold_0               C 0 I 110
s speTri1.scaffold_135460              78572 28 -    203079 -----AAAAATCCAAAG-GCAAATCTGGTAA-Aga----
q speTri1.scaffold_135460                                   -----999999999999-9999999999999-999----
i speTri1.scaffold_135460          C 0 I 25574
s oryCun2.chr14                      2466810 16 + 163896628 -----ACATATAGAAGG-GTGA-----------------
q oryCun2.chr14                                             -----999999999999-9999-----------------
i oryCun2.chr14                    C 0 I 626
s vicPac1.scaffold_6092                39652 31 -     83534 -----AAAAACTGAAAG-GTAAGTCTG-GAA-AGAACGC
q vicPac1.scaffold_6092                                     -----999999999999-999999999-999-9999999
i vicPac1.scaffold_6092            C 0 C 0
s bosTau4.chr1                     156979954 30 + 161106243 -----CAAAACTTGAAG-GTAAGTCTG-GAA-AGAGCG-
q bosTau4.chr1                                              -----999999999999-999999999-999-999999-
i bosTau4.chr1                     C 0 C 0
s pteVam1.scaffold_30179                5317 32 -      7387 -----AAAAACCTAAAG-GTAAGTCTGTTAA-GGAATGC
q pteVam1.scaffold_30179                                    -----999999999999-9999999999999-9999999
i pteVam1.scaffold_30179           C 0 C 0
s myoLuc1.scaffold_164117               3868 32 -     50790 -----AAAAACCTAAAA-GGAAATCTAGGCG-AGAATGC
q myoLuc1.scaffold_164117                                   -----999939978997-8798978858797-8987744
i myoLuc1.scaffold_164117          C 0 C 0
s eriEur1.scaffold_377961              11027 32 +     88154 -----AATAACCTAAAGTTTAGGTGTG-TAA-AGTACAC
q eriEur1.scaffold_377961                                   -----9999999999999999999999-999-9999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 510192 31 -  24123610 ------AAATTCTAAAG-GTGAGGCTCCTAA-AGAACGA
q loxAfr3.scaffold_36                                       ------99999999999-9999999999999-9999999
i loxAfr3.scaffold_36              C 0 C 0
s echTel1.scaffold_321361             117889 32 +    198078 ------AAATTCTAAAG-GGGAGACTGGTGATTGACTAA
q echTel1.scaffold_321361                                   ------79999999999-999999998999999999999
i echTel1.scaffold_321361          C 0 C 0
s monDom5.chr8                     276497269 32 + 312544902 AAATTCCCAACCCAGAG-ACAAGGC-----G-AGCATGC
q monDom5.chr8                                              99999999999999999-9999999-----9-9999999
i monDom5.chr8                     C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e equCab2.chr16                     22208494  5 -  87365405 I
e canFam2.chr23                     25989432  0 -  55389570 C
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e turTru1.scaffold_111402              10788 11 -     37689 I
e proCap1.scaffold_15753                 710 12 -     39409 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=50291.000000
s hg19.chrY                          7649756 49 +  59373566 TAAGCCTCTCTGTATACCCCAT----GCATGGAAACCTGTCAAGGTAGGACTG
s gorGor1.Supercontig_0555359            520 42 +       585 TGATCCTCTCCGTATTCCCCGT----GCACAGAAACCTGTCAAGGT-------
q gorGor1.Supercontig_0555359                               9999999999999999999999----99999999999999998887-------
i gorGor1.Supercontig_0555359      C 0 N 0
s panTro2.chrY                        503287 49 +  23952694 TAAGCCTCTCTGTATACCCCAT----GCATGGAAACCTGTCAAGGTAGGATTG
q panTro2.chrY                                              0000000000000000000000----000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s rheMac2.chr2                     158758501 43 + 189746636 CGAGCCTCTCCGTATTCCCCGT----GCATGGAAACCTGTCAAGGTA------
q rheMac2.chr2                                              9999999999999999999999----999999999999999999999------
i rheMac2.chr2                     C 0 T 142
s papHam1.scaffold12353                58918 34 +     70985 CCAGCCTCTCCGTATTCCCCGT----GCATGGAAACCT---------------
q papHam1.scaffold12353                                     9999999999999999999999----999999999999---------------
i papHam1.scaffold12353            C 0 C 0
s calJac1.Contig102                  1031443 34 -   1157145 TGAGCCTCTCCGGATTCCCCAT----GCACGGAAACCT---------------
q calJac1.Contig102                                         9999999999999999999999----999999999999---------------
i calJac1.Contig102                C 0 C 0
s otoGar1.scaffold_99909.1-31737        8637 34 -     31737 AGGATCCCTCCCAATTCCCCAT----GCACAGAAACCC---------------
q otoGar1.scaffold_99909.1-31737                            3751558455774578769667----955459997796---------------
i otoGar1.scaffold_99909.1-31737   I 4 C 0
s micMur1.scaffold_734                269459 34 -    418489 TGAGCCCCTCTGAGTTCCCCCG----GCATGGAAACCT---------------
q micMur1.scaffold_734                                      9999999999999999999999----999999999999---------------
i micMur1.scaffold_734             C 0 C 0
s vicPac1.scaffold_6092                39683 42 -     83534 CAAGCC-CCTCCACACTCCCAG----GCACAGAAACCCGGTAGG------CCA
q vicPac1.scaffold_6092                                     999999-999999999999999----999999999999999999------999
i vicPac1.scaffold_6092            C 0 I 207
s bosTau4.chr1                     156979984 30 + 161106243 -------------TACTCCCAG----GCACAGAAACCCAGCAGG------CCA
q bosTau4.chr1                                              -------------999999999----999999999999999999------999
i bosTau4.chr1                     C 0 I 1046
s pteVam1.scaffold_30179                5349 39 -      7387 TGAGCC-CCCCCACATTCTCAT----GCACAGAAACCCACCAAG---------
q pteVam1.scaffold_30179                                    999999-999999999999999----999999999999999999---------
i pteVam1.scaffold_30179           C 0 I 251
s myoLuc1.scaffold_164117               3900 40 -     50790 CGAGCCGCTCCCTAATTCCCAC----GCACAGAAACCCATCAGG---------
q myoLuc1.scaffold_164117                                   8775678888789864999978----887689988999599999---------
i myoLuc1.scaffold_164117          C 0 I 46
s eriEur1.scaffold_377961              11059 37 +     88154 TCCTCC-TTTCCTGTTACCCAT----GCACAAAATCCTGGCA-----------
q eriEur1.scaffold_377961                                   999999-999999999999999----9999999999999999-----------
i eriEur1.scaffold_377961          C 0 I 644
s loxAfr3.scaffold_36                 510223 31 -  24123610 -CAGCCCCTCTGCATTCCTCAT----GCTGGAAAAT-----------------
q loxAfr3.scaffold_36                                       -999999999999999999999----9999999999-----------------
i loxAfr3.scaffold_36              C 0 T 129
s echTel1.scaffold_321361             117921 24 +    198078 -GAGCCTCTCTGTGTTTCATGT----GTA------------------------
q echTel1.scaffold_321361                                   -999999999999999999899----999------------------------
i echTel1.scaffold_321361          C 0 I 6038
s monDom5.chr8                     276497301 41 + 312544902 -AAATCCCTGCGAATCCCACGTCCTGGCAAGGGAGCATCCTT-----------
q monDom5.chr8                                              -99999999999999999999999999999999999999999-----------
i monDom5.chr8                     C 0 I 23
e cavPor3.scaffold_0                 8220692 110 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208494  5 -  87365405 I
e canFam2.chr23                     25989432  0 -  55389570 C
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e turTru1.scaffold_111402              10788 11 -     37689 I
e proCap1.scaffold_15753                 710 12 -     39409 I
e ponAbe2.chr3                      71030524 77 - 202140232 T
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=58475.000000
s hg19.chrY                          7649805 34 +  59373566 GCCAGGTAAGCAGAAAAGTATGCAATCTTTCCCC
s panTro2.chrY                        503336 34 +  23952694 GCCAGGTAAGCAGAAAAGTATACAATCTTTCCCC
q panTro2.chrY                                              0000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71030447 34 - 202140232 GCCAGGAAAGCAGTAAAGTATGCAATCTTTCCCC
q ponAbe2.chr3                                              9999999999999999999999999999999999
i ponAbe2.chr3                     T 77 C 0
s rheMac2.chr2                     158758402 34 + 189746636 GTCAGGAAAGCAGAAAAGTATGCAATCTTTCTCC
q rheMac2.chr2                                              9999999999999999999999999999999999
i rheMac2.chr2                     T 142 C 0
s turTru1.scaffold_111402              10799 34 -     37689 GTCAGGAAAGCTAGAGAGCATGCAATCTCTGCCT
q turTru1.scaffold_111402                                   9999999999999999999999999999999999
i turTru1.scaffold_111402          I 11 C 0
s pteVam1.scaffold_38887                 242 34 -      4039 GCCAGGAAAGCAGAAAAGTCTGTACTCTTCCCCT
q pteVam1.scaffold_38887                                    9999999999999999999999999999999999
i pteVam1.scaffold_38887           n 251 C 0
s equCab2.chr16                     22208499 34 -  87365405 ACCAGGGAAGCCGAGATGCACGCAATCTTTCTCT
q equCab2.chr16                                             9999999999999999999999999999999999
i equCab2.chr16                    I 5 C 0
s loxAfr3.scaffold_36                 510125 34 -  24123610 GTCAGGAAAGCAGAAAAGTACGACGGCTTTCCCT
q loxAfr3.scaffold_36                                       9999999999999999999999999999999999
i loxAfr3.scaffold_36              T 129 C 0
s micMur1.scaffold_140973                541 16 -      1081 ------------------TATGCACTCTTTCCTT
q micMur1.scaffold_140973                                   ------------------9999999999999999
i micMur1.scaffold_140973          n 0 C 0
e cavPor3.scaffold_0                 8220692 110 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989432  0 -  55389570 C
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e calJac1.Contig102                  1031477  0 -   1157145 C
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e otoGar1.scaffold_99909.1-31737        8671  0 -     31737 C
e proCap1.scaffold_15753                 710 12 -     39409 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e papHam1.scaffold12353                58952  0 +     70985 C
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=87564.000000
s hg19.chrY                          7649839 47 +  59373566 TGAAGGGTATATTCAAGATAGGCTGCTAGACAAACAAA---TCCAAAGGT
s panTro2.chrY                        503370 47 +  23952694 TGAAGGGTATATTCAAGATAGGCTGCTAGACAAACAAA---TCCAAAGGT
q panTro2.chrY                                              00000000000000000000000000000000000000---000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71030481 44 - 202140232 TGAAGGGTACATTCAGGATATGCTGCTAGATAAACAAA---TCCAAG---
q ponAbe2.chr3                                              99999999999999999999999999999999999999---999999---
i ponAbe2.chr3                     C 0 I 17
s rheMac2.chr2                     158758436 47 + 189746636 TGAAAGGTACATTCAGGACATGTTGCTAGATAAACAAA---TCCAAAGGT
q rheMac2.chr2                                              99999999999999999999999999999999999999---999999999
i rheMac2.chr2                     C 0 C 0
s micMur1.scaffold_140973                557 47 -      1081 TGAAAGGTTCATTCTGGATATGCTGCTAGATAAACAAA---TCCAAAGTC
q micMur1.scaffold_140973                                   99999999999999999999999999999999999999---999999999
i micMur1.scaffold_140973          C 0 C 0
s turTru1.scaffold_111402              10833 50 -     37689 TGAAGAGTACGTTCTACATATGCTGCCAGATAGAAAAAAATCTTGAAGGT
q turTru1.scaffold_111402                                   99999999999999999999999999999999999999999999999999
i turTru1.scaffold_111402          C 0 C 0
s equCab2.chr16                     22208533 47 -  87365405 TAAAGGGTACACTGTGGATATGCTGCTAGATAAAAAAG---TCTAAAACT
q equCab2.chr16                                             99999999999999999999999999999999999999---999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25989432 47 -  55389570 TGAAGTGTACCTTCTGGATATGCAGCTAGTCAAAAAAA---TCTAAAGAC
q canFam2.chr23                                             99999999999999999999999999999999999999---999999999
i canFam2.chr23                    C 0 C 0
s pteVam1.scaffold_38887                 276 43 -      4039 TGAAGGATGCATGCTG--TATGCTGCTAGATAAAAA-----CCTAAAGGT
q pteVam1.scaffold_38887                                    9999999999999999--999999999999999999-----999999999
i pteVam1.scaffold_38887           C 0 C 0
s loxAfr3.scaffold_36                 510159 34 -  24123610 TGAAGGGTGCATCCTGGATACGCTACTGGATGCA----------------
q loxAfr3.scaffold_36                                       9999999999999999999999999999999999----------------
i loxAfr3.scaffold_36              C 0 I 61
e cavPor3.scaffold_0                 8220692 110 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e calJac1.Contig102                  1031477  0 -   1157145 C
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e otoGar1.scaffold_99909.1-31737        8671  0 -     31737 C
e proCap1.scaffold_15753                 710 12 -     39409 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e papHam1.scaffold12353                58952  0 +     70985 C
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=86247.000000
s hg19.chrY                          7649886 47 +  59373566 AAGTCTGGT--AAAGAATCCTGAGCCTCTCCATACTCGCCATGCATGGA
s micMur1.scaffold_140973                604 47 -      1081 AAGTCTAGT--AAAGAATGCTGAGCCCCTCTGAGTTCCCCCGGCATGGA
q micMur1.scaffold_140973                                   999999999--99999999999998999999997999994899992133
i micMur1.scaffold_140973          C 0 n 0
s panTro2.chrY                        503417 47 +  23952694 AAGTCTGGT--AAAGAATCCTGAGCCTCTCCATACTCCCCATGCATGGA
q panTro2.chrY                                              000000000--00000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71030542 47 - 202140232 AAGTCTGGT--AAAGAATCCTGAGCCTCTCCGTATTCCCCGTGCACGGA
q ponAbe2.chr3                                              999999999--99999999999999999999999999999999999999
i ponAbe2.chr3                     I 17 I 6
s rheMac2.chr2                     158758483 47 + 189746636 AAGTATGGT--AAAGAATCCCGAGCCTCTCCGTATTCCCCGTGCATGGA
q rheMac2.chr2                                              999999999--99999999999999999999999999999999999999
i rheMac2.chr2                     C 0 I 14
s cavPor3.scaffold_0                 8220802 30 -  88675666 -------------------CTAAGCCCCTTTGTATTCCCCGTGCATGGA
q cavPor3.scaffold_0                                        -------------------999999999999999999999999999999
i cavPor3.scaffold_0               I 110 I 6
s turTru1.scaffold_111402              10883 45 -     37689 AAGTCGGGA---GAGATCGCTGAGCCCGTCCACACTC-CTAGGCACAGC
q turTru1.scaffold_111402                                   999999999---9999999999999999999999999-99999999999
i turTru1.scaffold_111402          C 0 I 10
s equCab2.chr16                     22208580 45 -  87365405 AAGTCTGGT---AAAGACGCTGAGCCCCTTTGCATTC-CCACACACAGA
q equCab2.chr16                                             999999999---9999999999999999999999999-99999999999
i equCab2.chr16                    C 0 I 5
s canFam2.chr23                     25989479 48 -  55389570 AGGTCTGGTAAAAAAAATGCTGAGCCCCTCTGAATTC-CCATGCAAAGA
q canFam2.chr23                                             9999999999999999999999999999999999999-99999999999
i canFam2.chr23                    C 0 I 5
s pteVam1.scaffold_38887                 319 46 -      4039 AAGTCTGTT--AAGGAATGCTGAGCCCCCCCACATTC-TCATGCACAGA
q pteVam1.scaffold_38887                                    999999999--99999999999999999999999999-99999999999
i pteVam1.scaffold_38887           C 0 n 0
s proCap1.scaffold_15753                 722 44 -     39409 GAGACTGGG-----GAATAAAGGATCCTTCTGCATGCTTTATGCTGGAA
q proCap1.scaffold_15753                                    999997999-----99999999978959987899999999999868999
i proCap1.scaffold_15753           I 12 I 3
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510193 61 -  24123610 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e calJac1.Contig102                  1031477  0 -   1157145 C
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e otoGar1.scaffold_99909.1-31737        8671  0 -     31737 C
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e papHam1.scaffold12353                58952  0 +     70985 C
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=102077.000000
s hg19.chrY                          7649933 46 +  59373566 GTCAAGGTGTCTCATAAGCAGCTTCTTGGATGCAGGCGAGAGG--GAC
s panTro2.chrY                        503464 46 +  23952694 GTCAAGGTGTCTCATAAGCAGCTTCTTGGATGCAGGCGAGAGG--GAC
q panTro2.chrY                                              0000000000000000000000000000000000000000000--000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71030595 46 - 202140232 GTCAAGGTGTCTCACAAGCAGCTTCTTGGATGCAGGCGAGAGA--GAC
q ponAbe2.chr3                                              9999999999999999999999999999999999999999999--999
i ponAbe2.chr3                     I 6 C 0
s papHam1.scaffold12353                58952 46 +     70985 GTCAAGGTGTCTCACAAGCAGCTTCTTGGATGCAGGCGAGAGG--GAC
q papHam1.scaffold12353                                     9999999999999999999999999999999999999999999--999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158758544 37 + 189746636 ---------TCTCACAAGCAGCTTCTTGGATGCAGGCGAGAGG--GAC
q rheMac2.chr2                                              ---------9999999999999999999999999999999999--999
i rheMac2.chr2                     I 14 C 0
s calJac1.Contig102                  1031477 46 -   1157145 GTCAAGGTGTCTCACAAGTGGCTTCTTAGATGCAGGCGAGGGG--CCC
q calJac1.Contig102                                         9999999999999999999999999999999999999999999--999
i calJac1.Contig102                C 0 C 0
s micMur1.scaffold_734                269493 45 -    418489 GTCAAGGGGTCTCAC-AGCAGCTCCTAAGACCCAGGCAAGAAG--AAC
q micMur1.scaffold_734                                      999999999999999-999999999999999999999999999--999
i micMur1.scaffold_734             C 0 C 0
s otoGar1.scaffold_99909.1-31737        8671 42 -     31737 ATCAAGGGGTCTCAC-AGCAGCTCC---GACCCAGGCAAGAGG--ACC
q otoGar1.scaffold_99909.1-31737                            788499986799877-767765636---755986999699889--469
i otoGar1.scaffold_99909.1-31737   C 0 C 0
s cavPor3.scaffold_0                 8220838 46 -  88675666 GCCAACCTGTCCCACGATCAGTTCATTGTACTCAGACAACAGG--GAC
q cavPor3.scaffold_0                                        9999999999999999999999999999999999999999999--999
i cavPor3.scaffold_0               I 6 I 104
s turTru1.scaffold_111402              10938 18 -     37689 GCCAGAGGG--------GCAGCCtct----------------------
q turTru1.scaffold_111402                                   999999999--------999999999----------------------
i turTru1.scaffold_111402          I 10 I 62
s equCab2.chr16                     22208630 43 -  87365405 GTCAAGGGCT--CACAAGCAGCTccttagacccaggcaagcgg--gc-
q equCab2.chr16                                             9999999999--9999999999999999999999999999999--99-
i equCab2.chr16                    I 5 C 0
s canFam2.chr23                     25989532 33 -  55389570 GCCAaatac------------ctccttagacccaggcaagggg--tc-
q canFam2.chr23                                             999999999------------9999999999999999999999--99-
i canFam2.chr23                    I 5 C 0
s loxAfr3.scaffold_36                 510254 48 -  24123610 GCCAAAGTGTCTCAGAAGCAGCAGctgagacccaggcataagaacgac
q loxAfr3.scaffold_36                                       999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36              I 61 C 0
s proCap1.scaffold_15753                 769 46 -     39409 GCAGAAGTGTCTCAGCACCAGAGACTGAGACCCAGGGACCTGG--GAC
q proCap1.scaffold_15753                                    9999999999598889799999998999999999999999999--999
i proCap1.scaffold_15753           I 3 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e pteVam1.scaffold_38887                 365  0 -      4039 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-44583.000000
s hg19.chrY                          7649979 71 +  59373566 TACTGCTCT------------AAAGCTTGTTCTGAACACCAGGGTTT--------ACATcaagggtccccaaacctggggccacagactgg
s panTro2.chrY                        503510 71 +  23952694 TACTGCTCT------------AAAGCTTGTCCTGAACACCAGGGTTT--------ACATcaagtgtccccaaacctggggccacagactgg
q panTro2.chrY                                              000000000------------00000000000000000000000000--------000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71030641 32 - 202140232 CCCTGCTCT------------AAAGCTTGTCCTGAACCCCAAGG-----------------------------------------------
q ponAbe2.chr3                                              999999999------------99999999999999999999999-----------------------------------------------
i ponAbe2.chr3                     C 0 C 0
s papHam1.scaffold12353                58998 54 +     70985 C-CTGCTCT------------AAACCTTGTT----ACAGcaggg--------------------gtccccaagcctggggccacggacagg
q papHam1.scaffold12353                                     9-9999999------------9999999999----999999999--------------------999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158758581 54 + 189746636 C-CTGCTCT------------AAACCTTGTT----ACAGcaggg--------------------gtccccaagcctggggccacagacggg
q rheMac2.chr2                                              9-9999999------------9999999999----999999999--------------------999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s calJac1.Contig102                  1031523 58 -   1157145 T-CTGCTCT------------AAAGCTTGTCCTGAATCCCAAGGCTT--------ACAGCAGGGGTCCCTAACCCTgga------------
q calJac1.Contig102                                         9-9999999------------99999999999999999999999999--------999999999999999999999999------------
i calJac1.Contig102                C 0 C 0
s micMur1.scaffold_734                269538 55 -    418489 TCGGACTCT------------GCACCCTGAGCTTCAGAGCAAGGGTTCTGATCCAGCACCAAgggcc------------------------
q micMur1.scaffold_734                                      999999999------------9999999999999999999999999999999999999999999999------------------------
i micMur1.scaffold_734             C 0 I 35
s otoGar1.scaffold_99909.1-31737        8713 27 -     31737 CT--ACTCT------------GTACCTTGAGCTTCAGAGCA--------------------------------------------------
q otoGar1.scaffold_99909.1-31737                            69--95779------------99999999698999799997--------------------------------------------------
i otoGar1.scaffold_99909.1-31737   C 0 I 68
s equCab2.chr16                     22208673 38 -  87365405 ccctaccct------------ggaccccgagcttcagagCAGGGAGC--------------------CTC---------------------
q equCab2.chr16                                             999999999------------99999999999999999999999999--------------------999---------------------
i equCab2.chr16                    C 0 I 58
s canFam2.chr23                     25989565 21 -  55389570 tcccaccctggaccccttgct----------------------------------------------------------------------
q canFam2.chr23                                             999999999999999999999----------------------------------------------------------------------
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 510302 58 -  24123610 -cctgctct------------gaaccccacactttagagctggggtcctc--------------------agagtgtggtccccaggccag
q loxAfr3.scaffold_36                                       -99999999------------99999999999999999999999999999--------------------999999999999999999999
i loxAfr3.scaffold_36              C 0 I 28
s proCap1.scaffold_15753                 815 35 -     39409 -CCTGTGCT------------GGACCCCATACTTTACAGcaggggtcc-------------------------------------------
q proCap1.scaffold_15753                                    -99999999------------999999999999999999999999998-------------------------------------------
i proCap1.scaffold_15753           C 0 I 59
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e pteVam1.scaffold_38887                 365  0 -      4039 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956 62 -     37689 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=121056.000000
s hg19.chrY                          7650050 140 +  59373566 ta-tgggggt--------------gctgcacagcaggagttgagtgaacattactacctaagctctgcctcctgtcagatcaatagcagtattagattctcttaggagcatgaaccctaatgtgaactgtgcatgcaagggacctatgttgcatg
s panTro2.chrY                        503581 140 +  23952694 tg-tgggggt--------------gctgcacagcaggagttgagtgaacattactacctaagctctgcctcctgtcagatcaatagcagtattaggttctcttaggagcatgaaccctaatgtgaactgtgcatgcaagggacctatgttgcatg
q panTro2.chrY                                               00-0000000--------------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71030673 115 - 202140232 ----------------------------------------TGAGCGAgcattaccacctgagctctgcctcctgtcagatcaacagcggtattagattctcttaggagcgtgaaccctattgtgaactgcgcatatgagggatctatgttgtgta
q ponAbe2.chr3                                               ----------------------------------------9999999999999999999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s papHam1.scaffold12353                59052 148 +     70985 tactaggggctgtccgtactacaggctgcacagcaggaggtgagcgagcattatcacctgagctctgcctcctgtcagatcaacagcggtattagattctcttagcagagtgaaccctattgtgaaccgcgcatatgagcgatctatg-------
q papHam1.scaffold12353                                      9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------
i papHam1.scaffold12353            C 0 I 4
s rheMac2.chr2                     158758635 139 + 189746636 tactaggggctgtccgtactagaggctgcacagcaggaggtgagcgagcattatcacctgagctctgcctcctgtcagatcaacagcggtattagattctcttaggagagtgaaccctattgtgaactgcgcatatgag----------------
q rheMac2.chr2                                               9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------
i rheMac2.chr2                     C 0 I 4
s calJac1.Contig102                  1031581 131 -   1157145 ------------------------gctgcccagcagcagatgagcaagcattactacctgagctctgcctcctgtcctgtcaacagtggtatttaattcttttaggagcgtgaactctattgtgaactgtgcatgcgagggatctaggttgtata
q calJac1.Contig102                                          ------------------------99999999999999999999909999999999999999999999999999999099999999999999990999999999999999999999999999999999999999999999999999999999999
i calJac1.Contig102                C 0 C 0
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711  58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510360  28 -  24123610 I
e canFam2.chr23                     25989586   0 -  55389570 C
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593  35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973   2 -      4973 I
e pteVam1.scaffold_38887                 365   0 -      4039 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956  62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740  68 -     31737 I
e proCap1.scaffold_15753                 850  59 -     39409 I
e myoLuc1.scaffold_164117               3940  46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=316604.000000
s hg19.chrY                          7650190 285 +  59373566 ctccttatgagaatctaatgcctgatgatctgtcattgtcctccataacccctagatgggaccatcttgttgcaggaaaacaagctcagggctctcactgattc---------------cacattatggtgagttgtataattatttcaatacata-tataatgtaataataatataaataaagtgtacagtaaacgtaatgcacttgaatcgtcccaaaatcacc------cccacaaccccatctgtagaaaaactgccttccata-aaccagtccctagtgccaaaaaggttggggaccactgGT
s calJac1.Contig102                  1031712 284 -   1157145 ctccatacgagaatctaatgcctgataatctgtcactgtcttccattacccctagataggactgtctagttgcaggaaaacaagctcaggactctcactgattc---------------tacatt---gtgagctgtataatgatttcaatatatattacaatgtaataataacagaaataaagcatagagtaaatgtaattcatttgaatcaaccccaaatcacc------cccctacccccatccacgtaaaatctgccttccatacaaccaggccctggtgtcaaaaaggtttgggaccattgCT
q calJac1.Contig102                                          99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999999
i calJac1.Contig102                C 0 C 0
s rheMac2.chr2                     158758778 286 + 189746636 ----ttatgagaatctaatgcctgatgatctgtcactgtctcccatcacctatagatgggaccgtctagttgcaggaaaacaagctcaggactcgcactgagtc---------------tgcattatggtgagttgtataattatttcaatatatattataatgtaataacaatagaaataaagtgtacagtaaatgtaatgcacttgaatcatcccaaaatcaccaccc--cgcccaaccctatatgtggaaaaactgccttccata-aaccagtccctggtgccaaaaaggctgggaactgctgCT
q rheMac2.chr2                                               ----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999-999999999999999999999999999999999999999
i rheMac2.chr2                     I 4 C 0
s papHam1.scaffold12353                59204 290 +     70985 ctccttacgagaatccaatgcctgatgatctgtcactgtctcccatcacctctagatgggaccgtctagttgcaggaaaacaagctcagggctcgcactgagtc---------------tgcattatggtgagtcgtataattatttcaatatatattataatgtaataataatagaaataaagtgtaccgtaaatataatgcacttgaatcatcccaaaatcaccaccc--cgcccaaccctatctgtggaaaaactgccttccata-aaccagtccctggtgccaaaaagggtggaaactgctgCT
q papHam1.scaffold12353                                      99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999-999999999999999999999999999999999999999
i papHam1.scaffold12353            I 4 C 0
s ponAbe2.chr3                      71030788 307 - 202140232 ctccttatgagaatctaatgcctgatgatctgtcactgtctttcatcacccctagatgggaccctctagttgcaggaaaacaagctcaggactctcaccgagttgtataattatttcaatatattatgatgagttgtataattatttcaatatatattataatgtaataaaaatagaaataaagtgtacagtaaatgtaatgcgcttgaatcatcccaaaatcactcccccacccccaaccccatccgtggaaaaactgccttccgta-aaccagtccctggtgccaaaaaggctggggactgctgCT
q ponAbe2.chr3                                               9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999976099424999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        503721 285 +  23952694 ctccttatgagaatctaatgcctgatgatctgtcattgtcttccataacccctagatgggaccatctagttgcaggaaaacaagctcagggctctcactgattc---------------cacattatggtgagttgtataattatttcaatacata-tataatgtaataataatataaataaagtgtacagtaaatgtaatgcacttgaatcatcccaaaatcacc------cccacaaccccatctgtagaaaaactgccttccata-aaccagtccctggtgccaaaaaggttggggaccactgGT
q panTro2.chrY                                               00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000---------------0000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000------000000000000000000000000000000000000-000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711  58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510360  28 -  24123610 I
e canFam2.chr23                     25989586   0 -  55389570 C
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593  35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973   2 -      4973 I
e pteVam1.scaffold_38887                 365   0 -      4039 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956  62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740  68 -     31737 I
e proCap1.scaffold_15753                 850  59 -     39409 I
e myoLuc1.scaffold_164117               3940  46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=84956.000000
s hg19.chrY                          7650475 65 +  59373566 TTAGAGCAAGTGTCCTCAAAATCCACACCCTTGTCcagcaacacc----------tgagaacttgttagaaatga
s panTro2.chrY                        504006 65 +  23952694 TTAGAGCAAGTGTCCTCAAAATCCACACCCTCGTCcagcaacacc----------tgagaacttattagaaatga
q panTro2.chrY                                              000000000000000000000000000000000000000000000----------00000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031095 65 - 202140232 TTAGAGCAAGggtcctcaaagtgcacatcctggtccagcagcacc----------tgggaacttgttagaaatga
q ponAbe2.chr3                                              999999999999999999999999999999999999999999999----------99999999999999999999
i ponAbe2.chr3                     C 0 C 0
s papHam1.scaffold12353                59494 65 +     70985 TTAGAGCAAGggtcctcaaagcacacaacctggtccagcagcact----------tgggaacttgttagaaatgA
q papHam1.scaffold12353                                     999999999999999999999999999999999999999999999----------99999999999999999999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158759064 65 + 189746636 TTAGAGcaagggtcctcaaagcacacaacctggtccagcagcagt----------tgggaacttgttagaaatgA
q rheMac2.chr2                                              999999999999999999999999999999999999999999999----------99999999999999999999
i rheMac2.chr2                     C 0 C 0
s calJac1.Contig102                  1031996 65 -   1157145 TTAGAGCAAggttcctcaaagtgcatgctctggtccagcagcggc----------tgggaacttgatagaaatga
q calJac1.Contig102                                         999999999999999999999999999999999999999999999----------99999999999999999999
i calJac1.Contig102                C 0 I 11
s canFam2.chr23                     25989586 73 -  55389570 ttagagCAAGggtcctccaagtgtgctccttagtccaccagcagcaccagcaacacagagattcattagaaat--
q canFam2.chr23                                             9999999909999999999999999999999999999999999999999999999999999999999999999--
i canFam2.chr23                    C 0 I 783
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711 58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510360 28 -  24123610 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593 35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e pteVam1.scaffold_38887                 365  0 -      4039 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956 62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740 68 -     31737 I
e proCap1.scaffold_15753                 850 59 -     39409 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=37507.000000
s hg19.chrY                          7650540 52 +  59373566 caaaccttgtctgggagttgtggctcatgcctgtaatcccagcactttggga
s panTro2.chrY                        504071 52 +  23952694 caaactttgtctgggagttgtggctcatgcctgtaatcccagcactttggga
q panTro2.chrY                                              0000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031160 52 - 202140232 gaaaacttgcccgggggtggtggctcatgcctgtaatctcagtactttggga
q ponAbe2.chr3                                              9999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s papHam1.scaffold12353                59559 52 +     70985 GAAAACTTACccgggcgcggcggctcatgcctgtaatcttagcactttggga
q papHam1.scaffold12353                                     9999999999999999999999999999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158759129 52 + 189746636 Gaaaacttacccgggcgcggtggctcaggcctgtaatcttagcactttggga
q rheMac2.chr2                                              9999999999999999999999999993999999999999999999999999
i rheMac2.chr2                     C 0 I 51
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711 58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510360 28 -  24123610 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593 35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e pteVam1.scaffold_38887                 365  0 -      4039 I
e calJac1.Contig102                  1032061 11 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956 62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740 68 -     31737 I
e proCap1.scaffold_15753                 850 59 -     39409 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=69185.000000
s hg19.chrY                          7650592 152 +  59373566 ggctgaggtgagcatatcatcaggtcaggagttcaagatcatcctgactaacacagtgaaacccagtctctactaaaaatacaagaaattaggcaggtgtggtggcacacacccatagtcccagctactcaggaggctgaagcaggagaatt
s ponAbe2.chr3                      71031212 152 - 202140232 agccgaggcgggcggatcataaggtcaggagatcaagaccattctggctaacatggtgaaaccccgtctctactaaaaacacaaaaaattagctgggtgtggtggtgggtgcctgtagtcccagctactcgggaggctgaggcaggagaatc
q ponAbe2.chr3                                               99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        504123 152 +  23952694 ggctgaggtgagcatatcatcaggtcaggagttcaagatcatcctggctaacacagtgaaacccagtctctactaaaaatacaagaaattaggcaggtgtggtggcacacacccgtagtcccagctactcaggaggctgaagcaggagaatt
q panTro2.chrY                                               00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s papHam1.scaffold12353                59611 152 +     70985 agccaaggcgggcggatcagaaggtcaagagatcaagaccatcctggctaacacggtgaaaccctgtctttactaaaaatacaaaaaattagccaggtgtggtggcgggcacctgtagtcccagctactcgggaggctgaggcaggagaatc
q papHam1.scaffold12353                                      99999999999999999999999999999999999999999979999799998999999999997895729769999999999996666898888998989989889999999999999999999999999999899999999999989999
i papHam1.scaffold12353            C 0 C 0
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711  58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510360  28 -  24123610 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593  35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973   2 -      4973 I
e pteVam1.scaffold_38887                 365   0 -      4039 I
e rheMac2.chr2                     158759181  51 + 189746636 I
e calJac1.Contig102                  1032061  11 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956  62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740  68 -     31737 I
e proCap1.scaffold_15753                 850  59 -     39409 I
e myoLuc1.scaffold_164117               3940  46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=61721.000000
s hg19.chrY                          7650744 85 +  59373566 gcttgaacctaggatgcagaggttgcagtgagacaagatcatgccactgaactccagcctgggcaacagagccagactctgtctc
s papHam1.scaffold12353                59763 85 +     70985 gcttgaacctgggaggcggaggttgcagtgagccgagatggcgccactgcactccaacctgggtgacagagcaagactccatctc
q papHam1.scaffold12353                                     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158759232 84 + 189746636 gcttgaacctgggaggcggaggttgcagtgagtcgagatggcgccactgcactccagcctgggcgacagagcgagactc-gtccc
q rheMac2.chr2                                              3555435545656455555766666656567676522111111224556666669999999993999999999999995-48889
i rheMac2.chr2                     I 51 C 0
s ponAbe2.chr3                      71031364 85 - 202140232 acttgaacccaggaggtggagggtgcagtgagccgagatcacgccactgcactccagcctgggtgacagagtgagactccgtctc
q ponAbe2.chr3                                              9999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        504275 85 +  23952694 gcttgaacctaggatgcagagcttgcagtgagacaagatcatgccactgaactccagcctgggcaacagagccagactctgtctc
q panTro2.chrY                                              0000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711 58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510360 28 -  24123610 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593 35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e pteVam1.scaffold_38887                 365  0 -      4039 I
e calJac1.Contig102                  1032061 11 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956 62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740 68 -     31737 I
e proCap1.scaffold_15753                 850 59 -     39409 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=2824.000000
s hg19.chrY                          7650829 22 +  59373566 aaaaagacaaaaaaaaa----------------------------aaacc-
s pteVam1.scaffold_30179                5639 22 -      7387 aaaaagaaaaaagaaaagaaat-----------------------------
q pteVam1.scaffold_30179                                    9999999999999999999999-----------------------------
i pteVam1.scaffold_30179           I 251 C 0
s papHam1.scaffold12353                59848 50 +     70985 aaaaaaaaaaaaaaaaaaaacccaaaaaaaCCCCCAAAAACAAagaaatg-
q papHam1.scaffold12353                                     99999999999999999999999999999999999999999999999999-
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158759316 37 + 189746636 aaaaaaaaaaaaaaaaaaaa-------------ccaaaaacaaagaaatg-
q rheMac2.chr2                                              99999999999999999999-------------99999999999999999-
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71031449 30 - 202140232 aaaaaaaaaaaaaaaaa--------------------aaggaaagaaatg-
q ponAbe2.chr3                                              99999999999999999--------------------9999999999999-
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        504360 22 +  23952694 aaaaaggaaaaaaaaaa----------------------------aaaag-
q panTro2.chrY                                              00000000000000000----------------------------00000-
i panTro2.chrY                     C 0 C 0
s loxAfr3.scaffold_36                 510388  8 -  24123610 -------------------------------------------agaaatgc
q loxAfr3.scaffold_36                                       -------------------------------------------99999999
i loxAfr3.scaffold_36              I 28 C 0
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e equCab2.chr16                     22208711 58 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                39725 207 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                269593 35 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e calJac1.Contig102                  1032061 11 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              10956 62 -     37689 I
e otoGar1.scaffold_99909.1-31737        8740 68 -     31737 I
e proCap1.scaffold_15753                 850 59 -     39409 I
e myoLuc1.scaffold_164117               3940 46 -     50790 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=128962.000000
s hg19.chrY                          7650851 40 +  59373566 aga--atatttggttcctaccttagacttacagaatcagaat
s calJac1.Contig102                  1032072 28 -   1157145 --------------tcccaccctagacctacagaatcagaag
q calJac1.Contig102                                         --------------9999999999999999999999999999
i calJac1.Contig102                I 11 C 0
s otoGar1.scaffold_99909.1-31737        8808 32 -     31737 ----------tggcccccaccccagacttagaaagtcagaat
q otoGar1.scaffold_99909.1-31737                            ----------99689999999999999999999999999999
i otoGar1.scaffold_99909.1-31737   I 68 C 0
s micMur1.scaffold_734                269628 39 -    418489 ---agaatcttgggccctaccccagactcaccaagtcagaat
q micMur1.scaffold_734                                      ---999999999999999999999999999999999999999
i micMur1.scaffold_734             I 35 C 0
s panTro2.chrY                        504382 42 +  23952694 agagaatatttggctcctaccttagacttacagaatcagaat
q panTro2.chrY                                              000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031479 39 - 202140232 aga--aaacttgggtcctacgctagacttacagaatc-gaat
q ponAbe2.chr3                                              999--99999999999999999999999999999999-9999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158759353 40 + 189746636 aga--aagcttgggtcctaccctagacttacagaatcagaat
q rheMac2.chr2                                              999--9999999999999999999999999999999989999
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                59898 40 +     70985 aga--aagcttgggtcctaccctagacttacagaatcagaat
q papHam1.scaffold12353                                     999--9999999999999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s equCab2.chr16                     22208769 34 -  87365405 --------tctgggccccaccccagatctactgaatcagaat
q equCab2.chr16                                             --------9999999999999999999999999999999999
i equCab2.chr16                    I 58 C 0
s pteVam1.scaffold_30179                5661 39 -      7387 ---ggagacctgagtccttccccagatctactaaatcagaat
q pteVam1.scaffold_30179                                    ---999999999999999999999999999999999999999
i pteVam1.scaffold_30179           C 0 C 0
s vicPac1.scaffold_6092                39932 32 -     83534 ----------tgggcaccacctaggacctaccgaatcagaat
q vicPac1.scaffold_6092                                     ----------99999999999999999999999999999999
i vicPac1.scaffold_6092            I 207 C 0
s turTru1.scaffold_111402              11018 33 -     37689 ---------ttgggcgccaccccagacctactgaatcggaat
q turTru1.scaffold_111402                                   ---------999999999999999999999999999999999
i turTru1.scaffold_111402          I 62 C 0
s myoLuc1.scaffold_164117               3986 27 -     50790 ---------------cccactccagacctactgtatcaggat
q myoLuc1.scaffold_164117                                   ---------------999999999999999999999999999
i myoLuc1.scaffold_164117          I 46 C 0
s loxAfr3.scaffold_36                 510396 38 -  24123610 -ag---aatcgtggccccatcttagacttgctgaatcaggat
q loxAfr3.scaffold_36                                       -99---999999999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                 909 38 -     39409 ----aatatctctgccccatccctgacccgcagcatcagaat
q proCap1.scaffold_15753                                    ----98999998947899899999999999999999999899
i proCap1.scaffold_15753           I 59 C 0
e cavPor3.scaffold_0                 8220884 104 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973  2 -      4973 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=202897.000000
s hg19.chrY                          7650891  89 +  59373566 ctgagcca-----------tttgtgtct-cacaacctccccaggGAGTTTGACTGC------------GCCAAAGAGTTTCACTC-----CTGCAATG-----------------GCCCTCCTCCACACACTCTC
s papHam1.scaffold12353                59938  83 +     70985 ctgagcca-----------tctgtgtct-cacaagctccccagggagttcgACTGC------------CCCCAAGGGTTTCACCT-----------TG-----------------GCCCTCTTCCGCCCACTCTA
q papHam1.scaffold12353                                      99999999-----------999999999-999999999999999999999999999------------99999999999999999-----------99-----------------99999999999999999999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158759393  83 + 189746636 ctgagcca-----------tctgtgtct-cacaagctccccagggagttcGACTGC------------CCCCAAGGGTTTCACCT-----------TG-----------------GCCCTCTTCCACCCACTCTA
q rheMac2.chr2                                               99999999-----------999999999-999999999999999999999999999------------99999999999999999-----------99-----------------99999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71031518  83 - 202140232 ctgagcca-----------tctgtgtct-cacaagctccccagggagttcGACTGC------------CCCAAAGAGTTTCAGCT-----------TG-----------------GCCCTCCTCCACCCACTCTC
q ponAbe2.chr3                                               99999999-----------999999999-999999999999999999999999999------------99999999999999999-----------99-----------------99999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        504424  89 +  23952694 ctgagcca-----------tttgtgtct-cacaacctccccagggagtttgaCTGC------------GCCAAAGAGTTTCACTC-----CTGCAATG-----------------GCCCTCCTCCACACACTCTC
q panTro2.chrY                                               00000000-----------000000000-000000000000000000000000000------------00000000000000000-----00000000-----------------00000000000000000000
i panTro2.chrY                     C 0 C 0
s micMur1.scaffold_734                269667  83 -    418489 ctgagcca-----------tctgtgtctccacaacccctcttggagattcACCAGA------------TCTGCAGAGCTCTGCTT-----------CG-----------------G-CCTCCTCCAATCACTCCC
q micMur1.scaffold_734                                       99999999-----------9999999999999999999999999999999999999------------99999999999999999-----------99-----------------9-999999999999999999
i micMur1.scaffold_734             C 0 C 0
s otoGar1.scaffold_99909.1-31737        8840  84 -     31737 ctgagcca-----------tctgtctctccacaacccctccaggAGGCTCACCAGC------------TCCATAGAGCTGTGCTT-----------CG-----------------GCCCTCCTCCAACCACATTC
q otoGar1.scaffold_99909.1-31737                             99999999-----------9999999999989999999989999997999999999------------99999999999999799-----------99-----------------66999999999999999999
i otoGar1.scaffold_99909.1-31737   C 0 C 0
s calJac1.Contig102                  1032100  83 -   1157145 ctgagcca-----------tctgtgtcc-cacaagcctcccagggagttcAACTGC------------CCCAAAGAGTTTCACCT-----------TG-----------------TCCCTCCTCCATCCATTTTC
q calJac1.Contig102                                          99999999-----------999999999-999999999999999999999999999------------99999999999999999-----------99-----------------99999999999999999999
i calJac1.Contig102                C 0 C 0
s cavPor3.scaffold_0                 8220988  90 -  88675666 CTGAACCA-----------CTTGTGCCCCTACAGTCTCGCCCAGAAGTACAAATGC------------CAAGAACAACTGCTCCTGGGAGCTGCTGTG-----------------GTCCTC--CAACCCA---TC
q cavPor3.scaffold_0                                         99999999-----------9999999999999999999999999999999999999------------999999999999999999999999999999-----------------999999--9999999---99
i cavPor3.scaffold_0               I 104 C 0
s turTru1.scaffold_111402              11051  98 -     37689 cagagcca-----------tctatggcttcacaagccctcgaggaga-tAAGAGGCTGAGAACTACCTTCTAGAGGGTTTCCTCT-----------AGAGGATCTAAGGCCACACACCCAC--------------
q turTru1.scaffold_111402                                    99999999-----------9999999999999999999999999999-9999999999999999999999999999999999999-----------9999999999999999999999999--------------
i turTru1.scaffold_111402          C 0 C 0
s vicPac1.scaffold_6092                39964  82 -     83534 cggagcca-----------tccgtgtcctcacaggctctgcaggagattcagaggcTGAGAACTATTCTGCAGGGGGTTTCCCTT-----------TG-----------------GCCCTC--------------
q vicPac1.scaffold_6092                                      99999999-----------999999999999999999999999999999999999999999999999999999999999999999-----------99-----------------999999--------------
i vicPac1.scaffold_6092            C 0 C 0
s equCab2.chr16                     22208803  95 -  87365405 ctgagcca-----------cctacaccttcacaagccctccaggagattctgaggcTGAGAAGTACTctccagaaagttccactt-----------gg-----------------gccctcctccaa-cactctc
q equCab2.chr16                                              99999999-----------999999999999999999999999999999999999999999999999999999999999999999-----------99-----------------999999999999-9999999
i equCab2.chr16                    C 0 C 0
s myoLuc1.scaffold_164117               4013  94 -     50790 ctgagcga-----------gcttcatcttcacagg-cctccaagagactctggtgctgagaattactctccaga-ggttccactt-----------cg-----------------gccctcctccaaccactctc
q myoLuc1.scaffold_164117                                    99999999-----------9999999999999999-99999999999999999999999999999999999999-9999999999-----------99-----------------99999999999999999999
i myoLuc1.scaffold_164117          C 0 C 0
s pteVam1.scaffold_30179                5700 100 -      7387 ctgagggatg-------ggtatatgtcctcgcaagtcctcgaggagattctgTGGCTGCAAACCACTCTCCCgaggggttcattt-----------tg-----------------gccctcttccaaccactgcc
q pteVam1.scaffold_30179                                     9999999999-------99999999999999999999999999999999999999999999999999999999999999999999-----------99-----------------99999999999999999999
i pteVam1.scaffold_30179           C 0 C 0
s loxAfr3.scaffold_36                 510434 106 -  24123610 ctgggacaaggcccggagatgcctgttttcgcag-ccccccaggtggtgctgatgctgagaacccctgctctggatggtatccct-----------tg-----------------gccttcctccacccactctc
q loxAfr3.scaffold_36                                        9999999999999999999999999999999999-99999999999999999999999999999999999999999998999999-----------99-----------------99999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                 947  90 -     39409 ctggggcaaggcctggagatgcacattttcacag--cccccaggtggtgctgatgccgagaacc---------------acCCCT-----------TG-----------------GCCTCCGCCCAGCCACTCTC
q proCap1.scaffold_15753                                     9965799999999999999999999999988899--9999999999999999999999999999---------------999999-----------99-----------------99999996999999999999
i proCap1.scaffold_15753           C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_111908               4973   2 -      4973 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=8085.000000
s hg19.chrY                          7650980 25 +  59373566 CTCTCCACAGGCAAGGAAACCTTTG------------------------------------------------------------
s papHam1.scaffold12353                60021 22 +     70985 CTCTCCACAGGCAAGAAAACCT---------------------------------------------------------------
q papHam1.scaffold12353                                     9999999999999999999999---------------------------------------------------------------
i papHam1.scaffold12353            C 0 I 52
s rheMac2.chr2                     158759476 22 + 189746636 CTCTCCACAGGCAAGAAAACCT---------------------------------------------------------------
q rheMac2.chr2                                              9999999999999999999999---------------------------------------------------------------
i rheMac2.chr2                     C 0 I 52
s ponAbe2.chr3                      71031601 25 - 202140232 CTCTCCACAGGCAAGAAAACCTGTG------------------------------------------------------------
q ponAbe2.chr3                                              9999999999999999999999999------------------------------------------------------------
i ponAbe2.chr3                     C 0 I 49
s panTro2.chrY                        504513 25 +  23952694 CTCTCCACAGGCAAGGAAATCTTTG------------------------------------------------------------
q panTro2.chrY                                              0000000000000000000000000------------------------------------------------------------
i panTro2.chrY                     C 0 C 0
s micMur1.scaffold_734                269750 22 -    418489 CTCTCCACGTGCAAGGGATCTG---------------------------------------------------------------
q micMur1.scaffold_734                                      9999999999999999999999---------------------------------------------------------------
i micMur1.scaffold_734             C 0 I 66
s otoGar1.scaffold_99909.1-31737        8924 22 -     31737 CTCTCCACGGGCAAGGGGACAG---------------------------------------------------------------
q otoGar1.scaffold_99909.1-31737                            9999999999999999999999---------------------------------------------------------------
i otoGar1.scaffold_99909.1-31737   C 0 I 73
s calJac1.Contig102                  1032183 22 -   1157145 TTCTCCACAGGCAAGGAAACCT---------------------------------------------------------------
q calJac1.Contig102                                         9999999999999999999999---------------------------------------------------------------
i calJac1.Contig102                C 0 I 49
s cavPor3.scaffold_0                 8221078 22 -  88675666 CTGCACACAGGCAAGGAAACTG---------------------------------------------------------------
q cavPor3.scaffold_0                                        9999999999999999999999---------------------------------------------------------------
i cavPor3.scaffold_0               C 0 I 69
s turTru1.scaffold_111402              11149  9 -     37689 CT-------------GTGACCT---------------------------------------------------------------
q turTru1.scaffold_111402                                   99-------------9999999---------------------------------------------------------------
i turTru1.scaffold_111402          C 0 I 46
s vicPac1.scaffold_6092                40046 20 -     83534 CT-TCAATGGGCA-GGGGACCT---------------------------------------------------------------
q vicPac1.scaffold_6092                                     99-9999999999-99999999---------------------------------------------------------------
i vicPac1.scaffold_6092            C 0 I 34
s equCab2.chr16                     22208898 22 -  87365405 ctcttcatgggcccggaaacct---------------------------------------------------------------
q equCab2.chr16                                             9999999999999999999999---------------------------------------------------------------
i equCab2.chr16                    C 0 I 32
s felCat3.scaffold_206809               3134 20 -    143945 cttcccacaggcc--aagacct---------------------------------------------------------------
q felCat3.scaffold_206809                                   1495555512253--6242774---------------------------------------------------------------
i felCat3.scaffold_206809          I 2602 I 17
s myoLuc1.scaffold_164117               4107 21 -     50790 ctctccatgagca-aggaacct---------------------------------------------------------------
q myoLuc1.scaffold_164117                                   9999999999999-99999999---------------------------------------------------------------
i myoLuc1.scaffold_164117          C 0 I 81
s pteVam1.scaffold_30179                5800 21 -      7387 ctctccatgagca-aggaacct---------------------------------------------------------------
q pteVam1.scaffold_30179                                    9999999999999-99999999---------------------------------------------------------------
i pteVam1.scaffold_30179           C 0 I 78
s loxAfr3.scaffold_36                 510540 82 -  24123610 ctctccactggcacaggaactg---tggacctaagggttgatgcccacctgtgacctgttctcaacctccagagctcactgcatg
q loxAfr3.scaffold_36                                       9999999999999999999999---999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                1037 63 -     39409 CCCTCCACCTGTCTGGAAACTG---CAGACTTCACAGTGGGTGGCCACCTATGACCT--------------GAGCCCAC-----A
q proCap1.scaffold_15753                                    6679999899999996999999---99999999999999999999999999999999--------------99999999-----9
i proCap1.scaffold_15753           C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-17594.000000
s hg19.chrY                          7651005 28 +  59373566 ---------------------CAGCC-------------A---TA--------GGCCCAATCTGGAGGCC------------------------------------------------------ATG--
s panTro2.chrY                        504538 28 +  23952694 ---------------------CAGCC-------------A---TA--------GGCCCAATCTGGAGGCC------------------------------------------------------ATG--
q panTro2.chrY                                              ---------------------00000-------------0---00--------00000000000000000------------------------------------------------------000--
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031675 28 - 202140232 ---------------------CAGCC-------------A---TG--------GGCTCAATCTGGGGGCC------------------------------------------------------ATG--
q ponAbe2.chr3                                              ---------------------99999-------------9---99--------99999999999999999------------------------------------------------------999--
i ponAbe2.chr3                     I 49 C 0
s rheMac2.chr2                     158759550 28 + 189746636 ---------------------CAGCC-------------C---TG--------GGCCCGATCTGGGGACC------------------------------------------------------ATG--
q rheMac2.chr2                                              ---------------------99999-------------9---99--------99999999999999999------------------------------------------------------999--
i rheMac2.chr2                     I 52 C 0
s papHam1.scaffold12353                60095 28 +     70985 ---------------------CAGCC-------------C---TG--------GGCCCGATCTGGGGACC------------------------------------------------------ATG--
q papHam1.scaffold12353                                     ---------------------99999-------------9---99--------99999999999999999------------------------------------------------------999--
i papHam1.scaffold12353            I 52 C 0
s calJac1.Contig102                  1032254 28 -   1157145 ---------------------CAGCC-------------C---TG--------GGCCCAATCTGGGGGCC------------------------------------------------------GTT--
q calJac1.Contig102                                         ---------------------99999-------------9---99--------99999999999999999------------------------------------------------------999--
i calJac1.Contig102                I 49 C 0
s micMur1.scaffold_734                269838 28 -    418489 ---------------------CAATC-------------C---CG--------GGCTGGCTCTCAAAGCT------------------------------------------------------GCT--
q micMur1.scaffold_734                                      ---------------------99999-------------9---99--------99999999999999999------------------------------------------------------999--
i micMur1.scaffold_734             I 66 C 0
s otoGar1.scaffold_99909.1-31737        9019 82 -     31737 ---------------------CAGTC-------------C---CG--------GGCCCACTGTGGAATCTGTGCCCAGATCCAAGCACATGTACCCACCTGTGACCCGCACCCACCGTCACACAGTG--
q otoGar1.scaffold_99909.1-31737                            ---------------------99999-------------9---99--------99999999999999999999999999999999999999999999999999999999999999999999999999--
i otoGar1.scaffold_99909.1-31737   I 73 C 0
s cavPor3.scaffold_0                 8221169 28 -  88675666 ---------------------TGACA-------------C---GG--------AGCCTTTTCTGGGGGCC------------------------------------------------------ACG--
q cavPor3.scaffold_0                                        ---------------------99999-------------9---99--------99999999999999899------------------------------------------------------999--
i cavPor3.scaffold_0               I 69 C 0
s turTru1.scaffold_111402              11204 27 -     37689 ---------------------CAGCC-------------C---CA--------GGCCCACTGCGGGGGTC-------------------------------------------------------TG--
q turTru1.scaffold_111402                                   ---------------------99999-------------9---99--------99989999999999999-------------------------------------------------------99--
i turTru1.scaffold_111402          I 46 I 2
s vicPac1.scaffold_6092                40100 39 -     83534 ---------------------CACCCCAACTTGACACAGC---CA--------AGCCC-CTGGCGGTCCC-------------------------------------------------------TG--
q vicPac1.scaffold_6092                                     ---------------------9999999999999999999---99--------99999-99999999999-------------------------------------------------------99--
i vicPac1.scaffold_6092            I 34 I 2
s equCab2.chr16                     22208952 58 -  87365405 ---------------------caccc-------------c---aacttcacacggcctagacccgggaat---------------------------tctctggcctgacagccccagc-----ctg--
q equCab2.chr16                                             ---------------------99999-------------9---999999999999999999999999999---------------------------9999999999999999999999-----999--
i equCab2.chr16                    I 32 I 2
s felCat3.scaffold_206809               3171 27 -    143945 ---------------------gagcc-------------c---ag--------ggcccactttgggggat-------------------------------------------------------tg--
q felCat3.scaffold_206809                                   ---------------------77679-------------5---45--------95997979935779666-------------------------------------------------------45--
i felCat3.scaffold_206809          I 17 I 2
s myoLuc1.scaffold_164117               4209 26 -     50790 ---------------------gagcc-------------c---t---------ggtgcaatttgggggcc-------------------------------------------------------tg--
q myoLuc1.scaffold_164117                                   ---------------------99999-------------9---9---------99999999999999999-------------------------------------------------------99--
i myoLuc1.scaffold_164117          I 81 I 2
s pteVam1.scaffold_30179                5899 27 -      7387 ---------------------cagcc-------------c---cg--------ggcccactttgagagcc-------------------------------------------------------tg--
q pteVam1.scaffold_30179                                    ---------------------99999-------------9---99--------99999999999999999-------------------------------------------------------99--
i pteVam1.scaffold_30179           I 78 I 2
s loxAfr3.scaffold_36                 510622 53 -  24123610 tagccaagaccctggaacttcctgct-------------caaaca--------ggcccaccttgggggcc-------------------------------------------------------tgca
q loxAfr3.scaffold_36                                       99999999999999999999999999-------------999999--------99999999999999999-------------------------------------------------------9999
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                1100 44 -     39409 CAGCCAA--------AAGTCCCTGCT-------------C-AATG--------GGCCCACTTTGGGGATC-------------------------------------------------------TTTC
q proCap1.scaffold_15753                                    9999999--------99999999999-------------9-9999--------99999999999999999-------------------------------------------------------9958
i proCap1.scaffold_15753           C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2466826 626 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=307836.000000
s hg19.chrY                          7651033  95 +  59373566 CAGACTT----CTTC------------------CT-CA-----------------GTCTGCAGTGAGGCCG-----GATGGTG-CC-TATTTGTGTG--CACTCC----TAGGCCCAAGGca---gggaaaaaa-------ctaagaggaggaaagtg
s panTro2.chrY                        504566  95 +  23952694 CAGACTT----CTTC------------------CT-CA-----------------GTCTGCAGTGAGGCTG-----GATGGTG-CC-TATTTGTGTG--CACTCC----TAGGCCCAAGGca---gggaaaaaa-------ttaagaggaggcaagtg
q panTro2.chrY                                               0000000----0000------------------00-00-----------------0000000000000000-----0000000-00-0000000000--000000----0000000000000---000000000-------00000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031703  95 - 202140232 CAGACTT----CCTC------------------CT-TA-----------------GTCTTCAGTAAGGGTG-----GATGGTG-CC-CCTTTGTGTG--CACTCC----CAGGCCCAAGGca---ggacagaga-------ctaagaggaggcaagtg
q ponAbe2.chr3                                               9999999----9999------------------99-99-----------------9999999999999999-----9999999-99-9999999999--999999----9999999999999---999999999-------99999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158759578 101 + 189746636 CAGACTT----ACTC------------------CT-CA-----------------GTCTGCAGGGAGGGTG-----GATGGTG-CC-C-TTTGTGTG--CACTCC----CAGGCCCAAGGca---gggcagagactaagagctaagaggaggcaagtg
q rheMac2.chr2                                               9999999----9999------------------99-99-----------------9999999999999999-----9999999-99-9-99999999--999999----9999999999999---999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                60123 101 +     70985 CAGACTT----ACTC------------------CT-CA-----------------GTCTGCAGGGAGGGTG-----GATGGTG-CC-C-TTTGTGTG--CACTCC----CAGGCCCAAGGca---gggcagagactaagagctaagaggaggcaagtg
q papHam1.scaffold12353                                      9999999----9999------------------99-99-----------------9999999999999999-----9999999-99-9-99999999--999999----9999999999999---999999999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s calJac1.Contig102                  1032282  95 -   1157145 CGGGATT----CTTC------------------CT-CC-----------------ATCTGCAGTGAGGGTG-----GATGGTG-CC-CCTTTGTGTG--CACTCC----CAGGCCCGAGGca---gggcagaaa-------ctaagaggaggcaagtg
q calJac1.Contig102                                          9999999----9999------------------99-99-----------------9999999999999999-----9999999-99-9999999999--999999----9999999999999---999999999-------99999999999999999
i calJac1.Contig102                C 0 C 0
s micMur1.scaffold_734                269866  85 -    418489 CAGGCTT-----CTC------------------CC-CG-----------------GTCTGCAGCGAGGGTG-----GGCCGTG-CC-TT----------CACCC-----TGGGCCCAAGGca---ggggtgaga-------cgagggtgaggggagta
q micMur1.scaffold_734                                       9999999-----999------------------99-99-----------------9999999999999999-----9999999-99-99----------99999-----9999999999999---999999999-------99999999999999999
i micMur1.scaffold_734             C 0 C 0
s otoGar1.scaffold_99909.1-31737        9101 120 -     31737 CAGGCCCTGGAACTC------------------CC-TGCTACCAGCCCTGGGCCCCTCTGCAGCAAGGGCA-----GACAGTG-TC-CCTATGGGCA--CACCCACCTGCAGGCCCAGGGca---gggatgcga-------ctagggtcagaggagtg
q otoGar1.scaffold_99909.1-31737                             999999999999999------------------99-99999999989999976999999999999999999-----9999999-99-9999999999--99999999999999999999999---999999999-------99999999999999999
i otoGar1.scaffold_99909.1-31737   C 0 C 0
s cavPor3.scaffold_0                 8221197  93 -  88675666 CAAGCCT----TTTC------------------TC-CA-----------------GTCCACAGTGAGGGTG-----GTAGCAA-AC-CATGAAGCTG---ACCCC----CAGACCcaaggcaatggggcagagg-------ttaa----aggcaagtc
q cavPor3.scaffold_0                                         9999999----9999------------------99-99-----------------9999999999999999-----9999999-99-9999999999---99999----9999999999999999999999999-------9999----999999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2467452  75 + 163896628 CGGGCTT----CTCC------------------CCACA-----------------GTCTGCAGTAGGGGCC-----AACGGTG-CC-CCTGGGGCCA--CACTCC----CAAGTCTAAGGCA--GGGGC-----------------------------
q oryCun2.chr14                                              9999999----9999------------------99999-----------------9999999999999999-----9999999-99-9999999999--999999----9999999999999--99999-----------------------------
i oryCun2.chr14                    I 626 C 0
s turTru1.scaffold_111402              11233  69 -     37689 CAGGCTT----CTCC------------------CC-CA-----------------GTCTGT-------GTG----------------------------CACCCC----CAGGCCCAAGGCG---GCACAgaga-------ctagggagaggcgagtg
q turTru1.scaffold_111402                                    9999999----9999------------------99-99-----------------999999-------999----------------------------999999----9999999999999---999999999-------99999999999999999
i turTru1.scaffold_111402          I 2 C 0
s vicPac1.scaffold_6092                40141  87 -     83534 CGGACAG----CCCCAGGCCTACTGTGCCTCTTCG-CA-----------------ATCTGT-------GCG----------------------------CACCCC----CAGGCCCCAGGCg---gcccagagc-------ccaggcggaggtgagta
q vicPac1.scaffold_6092                                      9999999----999999999999999999999999-99-----------------999999-------999----------------------------999999----9999999999999---999999999-------99999999999999999
i vicPac1.scaffold_6092            I 2 C 0
s equCab2.chr16                     22209012 101 -  87365405 caggctt----cttc------------------cc-ca-----------------gtctgtagctagggtggtcctgatggt--cc-ccgctgtatgcccacccc----caggcccaagCTG---ggacagaga-------ctagggcaaggcgagtg
q equCab2.chr16                                              9999999----9999------------------99-99-----------------999999999999999999999999999--99-999999999999999999----9999999999999---999999999-------99999999999999999
i equCab2.chr16                    I 2 C 0
s felCat3.scaffold_206809               3200  72 -    143945 caggctt----ct---------------------c-ca-----------------atctgcagcaagggtg-----gatggtg-cc-ccaatgtgtg--catccg----caagcccaaggga---gggcag---------------------------
q felCat3.scaffold_206809                                    9977479----59---------------------5-97-----------------7647787997699589-----9846968-99-9997259989--969958----9799999897989---999999---------------------------
i felCat3.scaffold_206809          I 2 C 0
s myoLuc1.scaffold_164117               4237  96 -     50790 caggctt----cttc------------------cc-tg-----------------gtctatggcgagggtg-----gacactgttc-cctatctgtg--cacccc----caggcccaaggtg---ggactgagg-------ctaccatgaggtaagtg
q myoLuc1.scaffold_164117                                    9999999----9999------------------99-99-----------------9999999999999999-----9999999999-9999999999--999999----9999999999999---999999999-------99999999999999999
i myoLuc1.scaffold_164117          I 2 C 0
s pteVam1.scaffold_30179                5928  96 -      7387 caggctt----ctcc------------------cc-ag-----------------gtctgtgtcaagggtg-----gatggtgttt-catatgcaca--cacccc----tgggcccaagaca---ggacaggga-------caagggtgaggtgagtg
q pteVam1.scaffold_30179                                     9999999----9999------------------99-99-----------------9999999999999999-----9999999999-9999999999--999999----9999999999999---999999999-------99999999999999999
i pteVam1.scaffold_30179           I 2 C 0
s loxAfr3.scaffold_36                 510675  91 -  24123610 caggctt----ttcc------------------cc-ta-----------------gcctgtactgagggag-----gatggtg-ccacctatgagca--cac-cc----ccggcccaaagTa---aggctgaaa-------ctagggtgaggtg----
q loxAfr3.scaffold_36                                        9999999----9999------------------99-99-----------------9999999999999999-----9999999-9999999999999--999-99----9999999999999---999999999-------9999999999999----
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_15753                1144  95 -     39409 CAGGC-T----TTCC------------------CT-CA-----------------GCCTGTGTTAAAAGTG-----GATGGTG-CCACCTGTGAGCA--TTCACC----CAAGCCCCAAGCA---GTGCTGAAA-------TGAGGGTGAGGGGAGTG
q proCap1.scaffold_15753                                     99999-9----9999------------------99-99-----------------9999999999999999-----9999999-9999999899999--999977----8999999999999---998935999-------47999936999999742
i proCap1.scaffold_15753           C 0 I 23823
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=539747.000000
s hg19.chrY                          7651128 147 +  59373566 aggatataacttaccacaagtgcaaattttaa-ggga-gcaccaaaagctcaatgatcaagatg----aataaatattcaatgtaatat-----tttaaaaaat-a--aaaatcaatgt--aaaacttaatgatgaacaaagtatcaatacttttcataaaga
s panTro2.chrY                        504661 147 +  23952694 aggatataacttaccacaagtgcaaattttaa-ggga-gcaccaaaagctcaatgatcaagatg----aataaatattcaatgtaatat-----tttaaaaaat-a--aaaatcaatgt--aaaacttaatgatgaacaaagtatcaatacttttcataaaga
q panTro2.chrY                                               00000000000000000000000000000000-0000-00000000000000000000000000----000000000000000000000-----0000000000-0--00000000000--000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031798 148 - 202140232 aggagataactcaccacaggtgtaaactttaa-agga-gcaccaaaagctcaataaccaagata----aataaatatttaatataatat-----gtgaaaaaat-a--aaaatcagtgc-aaaaaattaatgatgaacaacatatcaaaatttttgataaaga
q ponAbe2.chr3                                               99999999999999999999999999999999-9999-99999999999999999999999999----999999999999999999999-----9999999999-9--99999999999-9999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158759679 139 + 189746636 aggagataactcaccacaggtacaaactttaa-agg----------agctcaatatccaagata----aataaatatttaatgtaatat-----gtgataaaat-a--aaaatcagggc-aaaaaattaatgatgaacaacatatcaaaatttttgataaaga
q rheMac2.chr2                                               99999999999999999999999999999999-999----------999999999999999999----999999999999999999999-----9999999999-9--99999999999-9999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                60224 139 +     70985 aggagataactcaccgcaggtacaaactttaa-agg----------agctcaatatccaagata----aataaatatttaatgtaatac-----gtgataaaat-a--aaaatcagggc-aaaaaattaatgatgaacaacatatcaaaatttttgataaaga
q papHam1.scaffold12353                                      99999999999999999999999999999999-999----------999999999999999999----999999999999999999999-----9999999999-9--99999999999-9999999999999999999999999999999999999999999
i papHam1.scaffold12353            C 0 C 0
s calJac1.Contig102                  1032377 148 -   1157145 aggagatatctcaccacaggcagaaaccttaa-ggga-gcaccacaatctcagtaatcaagata----aataaatatttcatgtaatat-----gctaaaatat-a--aaaatcaatgc-aaaaagtcaatgataagcaaagtatcaaaatttttgataaatg
q calJac1.Contig102                                          99999999999999999999999999999999-9999-99999999999999999999999999----999999999999999999999-----9999999999-9--99999999999-9999999999999999999999999999999999999999999
i calJac1.Contig102                C 0 C 0
s micMur1.scaffold_734                269951 135 -    418489 aggagaca-ctcaccactgctgcaaaatttaa-ggga-gcaccaaaaattcagagatcaaga--------taaatatttaatgca--at-----gttaaaaaataa--aaaataaagca-aaaatactcatgatgaacatagcatcaaattttttc-------
q micMur1.scaffold_734                                       99999999-99999999999999999999999-9999-999999999999999999999999--------999999999999999--99-----999999999999--99999999999-999999999999999999999999999999999999-------
i micMur1.scaffold_734             C 0 I 6625
s otoGar1.scaffold_99909.1-31737        9221 141 -     31737 aggacata-cccactgcaggtgcaaaatataa-ggga-gtaaggaaaactcagtgaccaagata----agtaaatacttaatgtaatat-----gttaaaaagtaa--aaaattaatgc-aaaaaagtcatgatgaacaaagcatcaaaaattttt-------
q otoGar1.scaffold_99909.1-31737                             99999999-99999999999999999999999-9999-96776999989999999989999999----999999999999989999997-----998999986869--99989999667-999999999989979967998887989999689996-------
i otoGar1.scaffold_99909.1-31737   C 0 I 1524
s cavPor3.scaffold_0                 8221290 124 -  88675666 atgagaaa-ttcaccgtaggttcaaaaat--a-ggga-gcaccaaaaactcagaaattaaa---------taaatatttagtgcaatga-aaaacttaaaaaat-g--c---------c--aaaaatccatgatcaacaaaggactaaacttt----------
q cavPor3.scaffold_0                                         99999999-99999999999999999999--9-9999-79899999999999999999999---------9999999999999999998-99999898999999-9--9---------9--99997797789999999999999999999999----------
i cavPor3.scaffold_0               C 0 I 1
s oryCun2.chr14                      2467527 131 + 163896628 -----------CAATGgggtgtcaaacat--a-aggatgtgccgaacacacaataacgagg---------ccaa----gtgtgcaatgctgctccttacaaaat-g--caaatcaatgc--aaacaaacgggataaacaaagcatcaaaattgttcacaaaga
q oryCun2.chr14                                              -----------999999999999999999--9-9999999999999999999999999999---------9999----99999999999999999999999999-9--99999999999--999999999999999999999999999999999999999999
i oryCun2.chr14                    C 0 I 6
s turTru1.scaffold_111402              11302 144 -     37689 gggagaca-c-tgctgcgggggcaacatttaa-gga--gcatcaaaa-ctcagtaaccagtacg----aatcaacattaaatgaaatat-----gttaaaaagt-g--aacatgaatgc-cgaaagtccataatgaacaaactatcaaaaattttactaagga
q turTru1.scaffold_111402                                    99999999-9-999999999999989999992-711--253637998-4562341134346124----325253835369645683977-----7969999995-9--85965999989-7999999897999798499998979799998999976999999
i turTru1.scaffold_111402          C 0 C 0
s vicPac1.scaffold_6092                40228 144 -     83534 aggaggca-c-tcctgcaggtgcaaaattgaacggg--gaaccaaagccttagtaacca----a----gataaagatgtaatgcagtat-----gtcagaaagt-gaaaaaatcaatgc-agaaagtccattacgaacaaactatccaaaagtttactaaaga
q vicPac1.scaffold_6092                                      99999999-9-9999999999999999999999999--999999999999999999999----9----999999999999999999999-----9999999999-99999999999999-9999999999999999999999999999999999999999999
i vicPac1.scaffold_6092            C 0 C 0
s equCab2.chr16                     22209113 141 -  87365405 aggagaca-c-tgccataggtgcaaaatttaa-ggg--gcaccaaaaactcagcaatca----a----cataaatatttaatgcaatat-----gttaaaaagt-g--aaaattaatgc-aaaaaatccataacaaacaaaatatcaaaaattttaataagga
q equCab2.chr16                                              99999999-9-999999999999999999999-999--999999999999999999999----9----999999999999999999999-----9999999999-9--99999999999-9999999999999999999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s felCat3.scaffold_206809               3272 144 -    143945 -ggagaca-c-ccccacagccgcaaaatttag-ggg--gcaccaaaaactcagtaagaa----agatcaataaaaatttaatgcaatat-----gttacaaagt-g--aaaattcatgc-aagaagtctacaacaaacaaaatatccaaaattttaataaata
q felCat3.scaffold_206809                                    -9999999-9-999999989979999999989-999--999999999999999999999----99999999999999999999999999-----9999999999-9--99999999999-9999999999999999999999999999999999999999999
i felCat3.scaffold_206809          C 0 C 0
s myoLuc1.scaffold_164117               4333 129 -     50790 aggagacg-cttgctataggtgcataattg-a-ggg--gcaccaaaaactcagtagccacgata----aataaatatttaatgcaatat-----gttaaaaagt-g--aaaaggaatgc-aaaaagtctgtaatggacaaaatatca----------------
q myoLuc1.scaffold_164117                                    99999999-999999999999999999999-9-999--99999999999999999999899999----999999999999999999999-----9999999999-9--99999999999-999999999999999999999999999----------------
i myoLuc1.scaffold_164117          C 0 C 0
s pteVam1.scaffold_30179                6024 113 -      7387 aggagatg-cttgccacaggtgcaaaatttca-ggg--gcactaaaaactcagtaacca----a----gataaatatgtaatgcaatac-----gttaaaaagt-a--aaaagaaatgc---gaagtccataatga---------------------------
q pteVam1.scaffold_30179                                     99999999-99999999999999999999999-999--999999999999999999999----9----999999999999999999999-----9999999999-9--99999999999---99999999999999---------------------------
i pteVam1.scaffold_30179           C 0 I 6
s loxAfr3.scaffold_36                 510766 145 -  24123610 agcacctcactcacctccagtgcaaaatttaa-gggg-gcaccaaaaactcagtaaccaggata----aaccatatctcaatgcgatat-----gctaaaaaat-g--aaaattaatgcaaaaaaatccatgataaaccaaatatcaaaattttaaata----
q loxAfr3.scaffold_36                                        99999999999999999999999999999999-9999-99999999999999999999999999----999999999999999999999-----9999999999-9--999999999999999999999999999999999999999999999999999----
i loxAfr3.scaffold_36              C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-7327.000000
s hg19.chrY                          7651275 17 +  59373566 taagatcag--------------gctgggtg
s myoLuc1.scaffold_164117               4462  5 -     50790 ----aaaat----------------------
q myoLuc1.scaffold_164117                                   ----99999----------------------
i myoLuc1.scaffold_164117          C 0 C 0
s felCat3.scaffold_206809               3416  9 -    143945 caggatcag----------------------
q felCat3.scaffold_206809                                   999999999----------------------
i felCat3.scaffold_206809          C 0 C 0
s equCab2.chr16                     22209254  9 -  87365405 caggatcag----------------------
q equCab2.chr16                                             999999999----------------------
i equCab2.chr16                    C 0 C 0
s vicPac1.scaffold_6092                40372  4 -     83534 ------gagg---------------------
q vicPac1.scaffold_6092                                     ------9999---------------------
i vicPac1.scaffold_6092            C 0 I 136
s turTru1.scaffold_111402              11446 17 -     37689 ------cagcatctgtattattg--------
q turTru1.scaffold_111402                                   ------99897989999999979--------
i turTru1.scaffold_111402          C 0 I 4906
s calJac1.Contig102                  1032525 17 -   1157145 taagttcag--------------GGTgggtg
q calJac1.Contig102                                         999999999--------------99999999
i calJac1.Contig102                C 0 C 0
s papHam1.scaffold12353                60363 17 +     70985 taagatcag--------------gctgagtg
q papHam1.scaffold12353                                     999999999--------------99999999
i papHam1.scaffold12353            C 0 C 0
s rheMac2.chr2                     158759818 17 + 189746636 taagatcag--------------gctgagtg
q rheMac2.chr2                                              999999999--------------99999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71031946 17 - 202140232 taagattag--------------gctgagtg
q ponAbe2.chr3                                              999999999--------------99999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        504808 17 +  23952694 taagatcag--------------gctgggtg
q panTro2.chrY                                              000000000--------------00000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8221414  1 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467658  6 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510911  0 -  24123610 C
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e pteVam1.scaffold_30179                6137  6 -      7387 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=11951.000000
s hg19.chrY                          7651292 55 +  59373566 ccagtggctcaggactgtaat-----------------------cccagcacttgtgggtgtcccagacaggaggatt
s panTro2.chrY                        504825 55 +  23952694 ccagtggctcacgactgtaat-----------------------cccagcacttgtgggtgtcccaggcaggaggatt
q panTro2.chrY                                              000000000000000000000-----------------------0000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71031963 55 - 202140232 ccagtggctcacgcctgtaat-----------------------cccagcacttgtgggaggctgaggcaggagaatc
q ponAbe2.chr3                                              999999999999999999999-----------------------9999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158759835 55 + 189746636 ccagtggctcacgcctgtaat-----------------------cccagcacttgtgggaggccgaggcaggagaatt
q rheMac2.chr2                                              999999999999999999999-----------------------9999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s papHam1.scaffold12353                60380 46 +     70985 ccagtggctcacgcctgtaat-----------------------cccagcacttgtgggaggccgaggc---------
q papHam1.scaffold12353                                     999999999999999999999-----------------------9999999999999999999999999---------
i papHam1.scaffold12353            C 0 I 8117
s calJac1.Contig102                  1032542 55 -   1157145 ccagtggctcacacctgtaat-----------------------cccagcacttgatggaggccaaggcaggaggatc
q calJac1.Contig102                                         999999999999999999999-----------------------9999999999999999999999999999999999
i calJac1.Contig102                C 0 I 7661
s equCab2.chr16                     22209263 37 -  87365405 ---------------tgttattgatttttcctttggcctgaggctccagcac--------------------------
q equCab2.chr16                                             ---------------9999999999999999999999999999999999999--------------------------
i equCab2.chr16                    C 0 I 185
s felCat3.scaffold_206809               3425  8 -    143945 ---------------tattattg-------------------------------------------------------
q felCat3.scaffold_206809                                   ---------------99999999-------------------------------------------------------
i felCat3.scaffold_206809          C 0 I 251
s myoLuc1.scaffold_164117               4467  6 -     50790 ---------------tgtaat---------------------------------------------------------
q myoLuc1.scaffold_164117                                   ---------------999999---------------------------------------------------------
i myoLuc1.scaffold_164117          C 0 I 597
s loxAfr3.scaffold_36                 510911  9 -  24123610 ----------------------------------------------------------------caggcagga-----
q loxAfr3.scaffold_36                                       ----------------------------------------------------------------999999999-----
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8221414  1 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467658  6 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                40376 136 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e pteVam1.scaffold_30179                6137  6 -      7387 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=62322.000000
s hg19.chrY                          7651347 129 +  59373566 gcttgagcacaggagtttgagaccaacctggggaatatggcaaaactccatctgtaccaaaaaacacaaaaattagctgggcatagtggcatgtgcctgaagtcccagctactagggaggctgagatgg
s panTro2.chrY                        504880 129 +  23952694 gcttgagcacaggagtttgagaccaacctggggaatatggcaaaactccatctgtaccaaaaaatacaaaaattagctgggcatagtggcatgtgcctgaagtcccagctactagggaggctgagatgg
q panTro2.chrY                                               000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032018 129 - 202140232 gcttgagcccaggagtttgagactagcctaggcaatatggcaaaactccatctgtacaaaaaaatacaaaaattagctgagtgtggtggcatgtgcctatagtgccagctactagggaggctgagatgg
q ponAbe2.chr3                                               999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158759890 129 + 189746636 gcctgagcccaggagtttgagaccagcctaggcaataagccaaaactccatatgtacaaaaaaatacaaaaattagctgagtgtggtggcatgtgcctgtagggccagctactagggaggctgagatgg
q rheMac2.chr2                                               999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
e cavPor3.scaffold_0                 8221414   1 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467658   6 + 163896628 I
e equCab2.chr16                     22209300 185 -  87365405 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510920   0 -  24123610 C
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                40376 136 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3433 251 -    143945 I
e pteVam1.scaffold_30179                6137   6 -      7387 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=18269.000000
s hg19.chrY                          7651476 41 +  59373566 gaggatcgcttgagcctggggagaccaaggatgcagtgacc
s equCab2.chr16                     22209485 29 -  87365405 gaggttc------gccagttgggatcccgggtgca------
q equCab2.chr16                                             9999999------9999999999999999999999------
i equCab2.chr16                    I 185 C 0
s panTro2.chrY                        505009 41 +  23952694 gaggatcgcttgagcctagggagaccaaggatgcagtgacc
q panTro2.chrY                                              00000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032147 41 - 202140232 gaggatcacttgagcccagagaggtcaaggaggcagtgagc
q ponAbe2.chr3                                              99999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760019 41 + 189746636 gaggatcacttgagcccagagaggtcgaggatgcagtgagc
q rheMac2.chr2                                              99999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
e cavPor3.scaffold_0                 8221414  1 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467658  6 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e loxAfr3.scaffold_36                 510920  0 -  24123610 C
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                40376 136 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3433 251 -    143945 I
e pteVam1.scaffold_30179                6137  6 -      7387 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=11962.000000
s hg19.chrY                          7651517 30 +  59373566 tgagattgcaccact--gcactccagcctggg
s rheMac2.chr2                     158760060 30 + 189746636 tgagattgcaccact--gcactccagcctgga
q rheMac2.chr2                                              999999999999999--999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71032188 30 - 202140232 tgagatcgcaccact--gcattccagcctgga
q ponAbe2.chr3                                              999999999999999--999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505050 30 +  23952694 tgagattgcaccact--gcactccagcctggg
q panTro2.chrY                                              000000000000000--000000000000000
i panTro2.chrY                     C 0 C 0
s equCab2.chr16                     22209514 31 -  87365405 -gacatggcactgcttggcaagccacgctgtg
q equCab2.chr16                                             -9999999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s loxAfr3.scaffold_36                 510920  4 -  24123610 tgag----------------------------
q loxAfr3.scaffold_36                                       9999----------------------------
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8221414  1 -  88675666 I
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467658  6 + 163896628 I
e bosTau4.chr1                     156980014 1046 + 161106243 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                40376 136 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3433 251 -    143945 I
e pteVam1.scaffold_30179                6137  6 -      7387 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=-43358.000000
s hg19.chrY                          7651547 44 +  59373566 GTAAGAGATTTAC----TAAATAAATAAATAATTA--aaagataggatca
s rheMac2.chr2                     158760090 47 + 189746636 gtgaccgagTTACCTTataaataaataaataaat---aaggataggatcg
q rheMac2.chr2                                              9999999999999999999999999999999999---9999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71032218 48 - 202140232 gtgacagagTTACtaaataaataaataaataaata--aaagataggatcg
q ponAbe2.chr3                                              99999999999999999999999999999999999--9999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505080 44 +  23952694 GTAAGAGAGTTAC----TAAATAAATAAATAATTA--aaagataggatca
q panTro2.chrY                                              0000000000000----000000000000000000--0000000000000
i panTro2.chrY                     C 0 C 0
s pteVam1.scaffold_30179                6143 27 -      7387 ----gcg-------------------ataattttaataaagacaggatca
q pteVam1.scaffold_30179                                    ----999-------------------999999999999999999999999
i pteVam1.scaffold_30179           I 6 I 6
s equCab2.chr16                     22209545 35 -  87365405 gtaggcg-----------tcccacatataaagtagaggaagatgga----
q equCab2.chr16                                             9999999-----------9999999999999999999999999999----
i equCab2.chr16                    C 0 I 116
s vicPac1.scaffold_6092                40512 30 -     83534 -------atatgt----tatataaCTATATGATTA---------TGATTA
q vicPac1.scaffold_6092                                     -------999999----999999999999999999---------999999
i vicPac1.scaffold_6092            I 136 I 4348
s bosTau4.chr1                     156981060 13 + 161106243 -------------------------------------aaagataggatca
q bosTau4.chr1                                              -------------------------------------9999999999999
i bosTau4.chr1                     I 1046 C 0
s oryCun2.chr14                      2467664  7 + 163896628 -------------------------------------------agtatta
q oryCun2.chr14                                             -------------------------------------------9999999
i oryCun2.chr14                    I 6 C 0
s cavPor3.scaffold_0                 8221415 19 -  88675666 -----------------------------taataa--atatggggtatta
q cavPor3.scaffold_0                                        -----------------------------999999--9999999999999
i cavPor3.scaffold_0               I 1 C 0
s loxAfr3.scaffold_36                 510924  9 -  24123610 ----------------------tattacata-------------------
q loxAfr3.scaffold_36                                       ----------------------999999999-------------------
i loxAfr3.scaffold_36              C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e canFam2.chr23                     25989659 783 -  55389570 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3433 251 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=43635.000000
s hg19.chrY                          7651591 56 +  59373566 ctgtt----ttttccttt-cacttcaagctccaatatgact-ctcacgctactgtcactgat
s panTro2.chrY                        505124 56 +  23952694 ctgtt----ttttccttt-cacttcaagctccaatatggct-cgcacgctactgtcactgat
q panTro2.chrY                                              00000----000000000-0000000000000000000000-00000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032266 56 - 202140232 gtgtt----ttttccttt-cactttaagctccaatacagct-cgcacagtactgtcactgat
q ponAbe2.chr3                                              99999----999999999-9999999999999999999999-99999999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760137 56 + 189746636 gtgtt----ttttccttt-caccttaagccccaatacagct-cgcagagtactgtcactaat
q rheMac2.chr2                                              99999----999999999-9999999999999999999999-99999999999999999999
i rheMac2.chr2                     C 0 C 0
s cavPor3.scaffold_0                 8221434 56 -  88675666 ctgtt----tttttcttttcaactcaagcatgactgaagct-cacatgatacttttacc-at
q cavPor3.scaffold_0                                        99999----99999999999999999999999999999999-99999999999999999-99
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2467671 49 + 163896628 ccatc----ctctccttg--ggctctagctcccctgtggtt-ccaaggctacag------at
q oryCun2.chr14                                             99999----999999999--999999999999999999999-999999999999------99
i oryCun2.chr14                    C 0 C 0
s bosTau4.chr1                     156981073 62 + 161106243 gtgttatcgattttccttttgcctcaagctccagtacagctcgacacggtactgctccggat
q bosTau4.chr1                                              99999999999999999999999999999999999999999999999999999999999999
i bosTau4.chr1                     C 0 C 0
s felCat3.scaffold_206809               3684 46 -    143945 ctgtc----tctctctctctctctcaaaaataaata------aacattaaacaaaT------
q felCat3.scaffold_206809                                   99999----999999999999999999999999999------99999999999999------
i felCat3.scaffold_206809          I 251 I 5129
s pteVam1.scaffold_30179                6176 58 -      7387 ttgat----ttttcttttttgtctcaagctccaatacggtttagcacaacactgttactgac
q pteVam1.scaffold_30179                                    99999----99999999999999999999999999999999999999999999999999999
i pteVam1.scaffold_30179           I 6 C 0
s loxAfr3.scaffold_36                 510933 52 -  24123610 ---------ctttccttt-tgcctcaagctccaatatggctcagcctccaactgttattcaa
q loxAfr3.scaffold_36                                       ---------999999999-9999999999999999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e equCab2.chr16                     22209580 116 -  87365405 I
e canFam2.chr23                     25989659 783 -  55389570 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342 23 + 312544902 I
e eriEur1.scaffold_377961              11096 644 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=129156.000000
s hg19.chrY                          7651647  98 +  59373566 cttgtcttt---aTTGTA-----A----AA-CGTTGCCTTATTCCCCTCACCCTAATCCTGGC-CCAT-CCCAAGATCTCCTTTCGTCCTCTAGTTCCAGA-TCCTCCAAATGC
s loxAfr3.scaffold_36                 510985  98 -  24123610 cctaccttt---TTT-CA-----A----AA-TGCTGCCTCACTTGCCTTACCCCATTCCTGGC-CCAGGCACAAgacctctattcgtactctcctcccagg-ccctgcaaatgt
q loxAfr3.scaffold_36                                        999999999---999-99-----9----99-99999999999999999999999999999999-9999999999999999999999999999999999999-999999999999
i loxAfr3.scaffold_36              C 0 C 0
s eriEur1.scaffold_377961              11740  88 +     88154 -----ctttataTTA-AA-----ACTCCAA-CATAGCTTCTATGATCTC--CCTGGTGCTGGC-CCAG-CCCACGGC---CTTCTGCACTGTTGT-------CCCTGCACGTGA
q eriEur1.scaffold_377961                                    -----9999999999-99-----9999999-999999999999999999--999999999999-9999-99999999---999999999999999-------999999999999
i eriEur1.scaffold_377961          I 644 I 16
s bosTau4.chr1                     156981135  94 + 161106243 ctcctcttt---tta-aa-----a----CA-TGTTGCCTCGCTTGCCTCACCCGAGTGCCAGC-CCAG-TCCAGCAT---CTCTTGCACTCTTGTCTGGGG-CCCTGCAAACAA
q bosTau4.chr1                                               999999999---999-99-----9----99-99999999999999999999999999999999-9999-99999999---999999999999999999999-999999999999
i bosTau4.chr1                     C 0 I 4
s canFam2.chr23                     25990442  97 -  55389570 CTTGTCTTT---TTA-AA-----A----AACTGTTGCCTCACCTGCCTCACCCTAATGCTGGCTCATG-CCCAGTAT---CTCttgcactcttgacctgggcccctgcaaatga
q canFam2.chr23                                              999999999---999-99-----9----9999999999999999999999999999999999999990-99999999---9999999999999999999999999999999999
i canFam2.chr23                    I 783 I 16
s pteVam1.scaffold_30179                6234  97 -      7387 cacatcttt---ttt-aa-----a----aa-tgttgCCTCACTCGTCTCATCCTAGTGCTGGC-CAGG-CCCAATATCTCCTCTTGCAGCATCGCCCTAGG-CCCTGCGAATGA
q pteVam1.scaffold_30179                                     999999999---899-99-----9----99-99999999999999999999999999999999-9999-99999999999999999999999999999999-999999999999
i pteVam1.scaffold_30179           C 0 I 16
s oryCun2.chr14                      2467720  91 + 163896628 cttgccctt---G-T-CA-----C----AG-CGTAGCCTTCTTTGCCTCACCCTGCTCCCAG-------CCCGTGGTCTCCCTGCCTAGCCCTGAACCAGG-CCCTACCCACGC
q oryCun2.chr14                                              999999999---9-9-99-----9----99-9999999999999999999999999999999-------99999999999999999999999999999999-999999999999
i oryCun2.chr14                    C 0 C 0
s cavPor3.scaffold_0                 8221490  93 -  88675666 cttgtattt---act-ta-----a----aa-tcttgCCTCATTCGCTTCACCTTGGTCCCAGC-CAGGACCCAAGACCTTCCTCTCTCATCTTGCAAAAG------CTTCATTT
q cavPor3.scaffold_0                                         999999999---999-99-----9----99-99999999999999999999999999999999-999999999999999999999999999999999999------99999999
i cavPor3.scaffold_0               C 0 C 0
s rheMac2.chr2                     158760193 102 + 189746636 cctgtcttt---aTT-TATTATAA----AA-TGTTGCCTCACTCCCCTCACCCTAATCCTGGC-CCAG-CCCAAgatctccttttgtcctcttgtcccaga-tcctgcaaatgc
q rheMac2.chr2                                               999999999---999-99999999----99-99999999999999999999999999999999-9999-99999999999999999999999999999999-999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71032322 101 - 202140232 cttgtcttt---aTT-TATTAT-A----AA-TGTTGCCTCACTCCCCTCACCCTAATCCTGGC-CCAG-CCCAAGATCTCCTTTTGTCCTCTTGTCCCAGA-TCCTGCAAATGC
q ponAbe2.chr3                                               999999999---999-999999-9----99-99999999999999999999999999999999-9999-99999999999999999999999999999999-999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505180  98 +  23952694 cttgtcttt---aTTGTA-----A----AA-CGTTGCCTTATTCCCCTAACCCTAATCCTGGC-CCAT-CCCAAGATCTCCTTTCATCCTCTAGTTCCAGA-TCCTCCAAATGC
q panTro2.chrY                                               000000000---000000-----0----00-00000000000000000000000000000000-0000-00000000000000000000000000000000-000000000000
i panTro2.chrY                     C 0 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e equCab2.chr16                     22209580 116 -  87365405 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497342  23 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6803230 4589 +   6934412 I

a score=108748.000000
s hg19.chrY                          7651745 145 +  59373566 ----TGGGTG-TGGACCTTATGGAAACCAGGGGCATGTT------------------TCATCTGCTGTCAACAGATTACAAGGCTGCTGAACCAAAAGGGCAAAACCACATGTAGCGGAGACA-----CTGTTTTA----------TTTGAAA-AACTG---AATGGACTTTAGGTAGGAGTGTAAG
s loxAfr3.scaffold_36                 511083 166 -  24123610 ----taggag-cgg----------ggctAGATGTAGGTTGTGCGAGGGAACTTGGCAGTCTCTGCTGTCAAGAGATTACAAAGCTATTGAACCAAAAGGGTATAACCACAGGTGGCAGAGACACT-GGTTGTTTTTTTTTTTTTTTTTTGGAA-ACGTG----ATGGACTTTTGGTGGGAGTGCAAA
q loxAfr3.scaffold_36                                        ----999999-999----------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999-99999----999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s eriEur1.scaffold_377961              11844 146 +     88154 ----TGTAGG-CCGTTCAAAGGA-AGACAGGG-CGGGTC------------------TCCTCTG--GGCCAAGGAACAAGAAGAGACTAACGTGGATGGACATT--AACACGTGACAGAGTTGCT-GGCTGCTGCT----------TTTAAAC-AAGTGAATAATGGACCTTAGGTAGGAGTATGAG
q eriEur1.scaffold_377961                                    ----999999-999999999999-99999999-999999------------------9999999--99999999999999999999999999999999999999--9999999999999999999-9999999999----------9999999-999999999999999999999999999999999
i eriEur1.scaffold_377961          I 16 C 0
s pteVam1.scaffold_30179                6347 132 -      7387 ----TGTCGG-TTGTGCCCAGGG-AACCAGAGGCAGGTT------------------TTCTTTGCTGTCAAGAGGTTACAAAGCAACTGAACCGAAAGAGTAT---TTCTTGCGGCATAGATGC------------------------TGAAA-AATGG---CATGGACTTTTGGTAGGGGTGTAGG
q pteVam1.scaffold_30179                                     ----999999-999999999999-999999999999999------------------9999999999999999999999999999999999999999999999---999999999999999999------------------------99999-99999---9999999222269999999999999
i pteVam1.scaffold_30179           I 16 C 0
s canFam2.chr23                     25990555 143 -  55389570 ----TGCAGG-TTGTGCCCAGAG--AACAGGGGCAGGTT------------------TCCTCTGCTGTCAAGAGATTACAAAGTGGCTGACCTGAACAAGCATCACTGTGTGTGGCATAGACGCT-GGCTGTTTCG----------TTTGCAA-AACCG---AACAGACTTTTGGTAG----GTGGG
q canFam2.chr23                                              ----999999-999999999999--99999999999999------------------99999999999999999999999999999999999999999999999999999999999999999999-9999999999----------9999999-99999---9999999999999999----99999
i canFam2.chr23                    I 16 I 5
s equCab2.chr16                     22209696 138 -  87365405 ----TGTATA-TTGT-CCCAAAGGAAACAGGGTTGGGTT------------------TCCTCTGCTGTCAAGAGATTAGGAAGCGACTGAACCCAGAGGGCACAAGTGCGTGTGGCATAGACACT-GGTTGTTTTA----------TTTGAAA-AACTG---AATGGACTTTT----------TTGG
q equCab2.chr16                                              ----999999-9999-99999999999999999999999------------------99999999999999999999999999999999999999999999999999999999999999999999-9999999999----------9999999-99999---99999999999----------9999
i equCab2.chr16                    I 116 C 0
s bosTau4.chr1                     156981233 130 + 161106243 ----AGTGGGCCTGTGTAAAGGG-AACCAGGGGCGGGTT------------------TCCCCCACTGTC---AGATGACGAAGCAACTGAAGTG------------TGTGTGTGGCACAGACACT-GGGCGTTTCA---------TTTTAAAA-ACCTG---AATGGACTTTTGGCAGGAGT-----
q bosTau4.chr1                                               ----9999999999999999999-999999999999999------------------999999999999---9999999999999999999999------------9999999999999999999-9999999999---------99999999-99999---99999999999999999999-----
i bosTau4.chr1                     I 4 I 212
s oryCun2.chr14                      2467811 117 + 163896628 ----TGAGTG-TGGACCTCACAGAAACCTGGGGCAGCTG------------------TCCCCTACTGCTTAGAGCTAACCAAGCCACCACATCCAAAGGG--CATCCACGTGCTGCACACCAG-----CTGCTCTC----------TGAAAAA-AAtt-----------------------------
q oryCun2.chr14                                              ----999999-9999999999999999999999999999------------------9999999999999999999999999999999999999999999--999999999999999999999-----99999999----------9999999-9999-----------------------------
i oryCun2.chr14                    C 0 I 1275
s cavPor3.scaffold_0                 8221583 115 -  88675666 ----GGAGAA-TGG--------GAGAATATGGCCAGGTT------------------GCTTGTGCTGTGAGCAGCTCACAAAGCTAC----TGAAAAGGGTTCAACCATGTGCGGCCAAGACA-----CTGC-------------------------------ATGAAC-ACAGGTAGATGTGAAAG
q cavPor3.scaffold_0                                         ----999999-999--------99999999999999999------------------999999999999999999999999999999----99999999999999999999999999999999-----9999-------------------------------999999-99999999999999999
i cavPor3.scaffold_0               C 0 C 0
s rheMac2.chr2                     158760295 149 + 189746636 ----tgggtg-tggacttCATGGAAATCAGGGGCAGGTT------------------TCATCTGCTGTCAACAGATTACAAGGCTGCTGAACCAAAAGGGCAAAACCACACGTGGCGGAGACACT-GTTTGTTTTA----------TTTGAAA-AACTG---AATGGACTTTTGGTGGGAGTGTAAG
q rheMac2.chr2                                               ----999999-9999999999999999999999999999------------------99999999999999999999999999999999999999999999999999999999999999999999-9999999999----------9999999-99999---9999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71032423 146 - 202140232 ----TGGGTG-TCGACCTTATGGAAACCAGGGGCAGGTT------------------TCATCTGCTGTCAACAGATTACAAGGCTGCTGAACCGAAAGGGCAAAACCACATGTGGCGGAGACA----GTTGTTTTG----------TTTGAAA-AACTG---AATGTACTTTTGGTAGGAGTGTAAG
q ponAbe2.chr3                                               ----999999-9999999999999999999999999999------------------999999999999999999999999999999999999999999999999999999999999999999----999999999----------9999999-99999---9999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505278 145 +  23952694 ----TGGGTG-TGGACCTTATGGAAACCAGGGGCATGTT------------------TCATCTGCTGTCAACAGATTACAAGGCTGCTGAACCAAAAGGGCAAAACCACATGTAGCGGAGACA-----CTGTTTTA----------TTTGAAA-AACTG---AATGGACTTTAGGTAGGAGTGTAAG
q panTro2.chrY                                               ----000000-0000000000000000000000000000------------------000000000000000000000000000000000000000000000000000000000000000000-----00000000----------0000000-00000---0000000000000000000000000
i panTro2.chrY                     C 0 C 0
s monDom5.chr8                     276497365 101 + 312544902 -------GTG-TGGA------GGAAACCAGGCTCAGGTT------------------CCTGCCATGGTCAGGAGATTACCAGGCTACTGTATTC--------TGCCTGTACAGAGCACGGATG-----TGATTATG----------------------G---GATGGATGT----------------
q monDom5.chr8                                               -------999-9999------999999999999999999------------------9999999999999999999999999999999999999--------999999999999999999999-----99999999----------------------9---999999999----------------
i monDom5.chr8                     I 23 C 0
s ornAna1.Ultra117                   6807819 151 +   6934412 GGTATCTAGG-CTGTGCGGAGGA-AAACAGATGCATGCT------------------TCCTCTGATAATGAGAGTTTACAAGGCTACTGTACTAAGATGGCTTTCCCCGGCATTTCCCAATCATCAGGCTATTTTA----------TCAGAAGCATCCG---AATGCATTT---GGAGAGGTTTCAT
q ornAna1.Ultra117                                           9999999999-999999999999-999999999999999------------------9999999999999999999999999999999999999999999999999999999999999999999999999999999----------9999999999999---999999999---9999999999999
i ornAna1.Ultra117                 I 4589 C 0
e rn4.chr9                         107343705 821 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=172051.000000
s hg19.chrY                          7651890 103 +  59373566 CCTTGATGGAGGGCAACTGCATGTTGTCAATCAAACCTAAAAATACTACCCAGCACCAAGATCCC-CTCTTCTTTGATAAA--------ACTATATA----------------CAAACAGCATCTGTG
s panTro2.chrY                        505423 103 +  23952694 CCTTGATGGAGGGCAACTGCACGTTGTCAATCAAACCTAAAAATACTACCCAGCACCAAGATCCC-CTCTTCTTTGATAAA--------ACTATATA----------------CAAACAGCATTTGTG
q panTro2.chrY                                               00000000000000000000000000000000000000000000000000000000000000000-000000000000000--------00000000----------------000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032569 103 - 202140232 CCTTTATGGGAGGCAACTGCACGTTGTCAATCAAACCTAAGAATACTATCCAGCACCAAGATCCC-CTCTTCTTTGATAAA--------ACTATATA----------------CAAACAGCATCTGTG
q ponAbe2.chr3                                               99999999999999999999999999999999999999999999999999999999999999999-799999999999999--------99999999----------------999999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760444 103 + 189746636 CCTTTATGGAGGGCAACTGCACGTTGTCAATCAAACCTAAAACTACTATCCAGCACCGAGATCCC-CTCTTCTTTGATAAA--------ACTATATA----------------CAAACAGCATCTGTG
q rheMac2.chr2                                               99999999999999999999999999999999999999999999999999999999999999999-999999999999999--------99999999----------------999999999999999
i rheMac2.chr2                     C 0 C 0
s cavPor3.scaffold_0                 8221698  89 -  88675666 CCTTT---------CACAACA-----TCCACTGAACCTAAACACACCGTGCAACTCTCAGATCTT-CTCTTTTATGACACA--------ACTCTATAT---------------AAAAGTGCGTCAGT-
q cavPor3.scaffold_0                                         99999---------9999999-----999999999999999999999999999999999999999-999999999999999--------999999999---------------99999999999999-
i cavPor3.scaffold_0               C 0 C 0
s bosTau4.chr1                     156981575 104 + 161106243 ccTTTCTGGAGGGTAATTTTATAATATCCATCAAACCTAAAAATACCACACAGCATGGAGACCACCCTCCTCTTTGATGAA--------ACTGTACA----------------TAAAGAGCATCTGTG
q bosTau4.chr1                                               999999999999999999999999999999999999999999999999999999999999999999999999999999999--------99999999----------------999999999999999
i bosTau4.chr1                     I 212 C 0
s equCab2.chr16                     22209834 103 -  87365405 cctttctggagggtaatttcatgatatgcatcaaacctaaaaaCACTATGCAGCACTAAGATCCC-CTTTTCTTTGACAAT--------ACTGCAAA----------------TAAAGAGCATCTGTG
q equCab2.chr16                                              99999999999999999999999999999999999999999999999999999999999999999-999999999999999--------99999999----------------999999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25990703 102 -  55389570 CCTTTTCGGAGGGTAATTTTACAATGTCGATCAAACCTAAAAATACCATGCAGCATTAAGCTGCC-C-CCTCTTTGATGAA--------AGCATATA----------------TGAAGAGCATCTGTG
q canFam2.chr23                                              99999999999999999999999999999999999999999999999999999999999999999-9-9999999999999--------99999999----------------999999999999999
i canFam2.chr23                    I 5 C 0
s pteVam1.scaffold_30179                6479  87 -      7387 CCTTTCAGGAGGGTAATTTCATGATATCGATCAA-----------------AGCACTTAGATCCTACTCTTCCTTGATAAA--------ACCATATG----------------TAAAGAGCATCTCTG
q pteVam1.scaffold_30179                                     9999999999999999999999999999999999-----------------999999999662111122189911431167--------41311001----------------344432352114113
i pteVam1.scaffold_30179           C 0 N 0
s eriEur1.scaffold_377961              11990  90 +     88154 CCCTTCTGGGGG------------TATCAGTCAGACCT-AGAATACTGGACAGCACTCAGAGCCT-TTCTTCCTTAATAAA--------CCAATATG----------------CAAAGACTATCAGCA
q eriEur1.scaffold_377961                                    999999999999------------99999999999999-99999999999999999999999999-999999999999999--------99999999----------------999999999999999
i eriEur1.scaffold_377961          C 0 C 0
s rn4.chr9                         107344526  70 - 113440463 --------------------------TTGATTAAAGCTGAAAA-----TCCTATCTTTGGAGCTT-CTCCTCGAAG--AAA--------AGTGTACA----------------AAAAGGGCTTTGGCG
q rn4.chr9                                                   --------------------------99999999999999999-----99999999999999999-9999999999--999--------99999999----------------999999999999999
i rn4.chr9                         I 821 C 0
s loxAfr3.scaffold_36                 511249 118 -  24123610 -CCTTTGGAAGGGCATTTTTACCATATATATTAAAGCTAAAAATGCTATGCAGCCCTAAAATGCC-CTCTTCTTTGCTAAA--------ACTATATATACACACATACATGTATAAAGAACATCTGGG
q loxAfr3.scaffold_36                                        -9999999999999999999999999999999999999999999999999999999999999999-999999999999999--------999999999999999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497466  76 + 312544902 -------GGAGGGTTCTC------TGTCCACGGAAC-------------------TGTACATTCC-ATTTTCTCTGATAAG--------AA-ATATG----------GCTGTCAAGAGAGCATCTGTG
q monDom5.chr8                                               -------99999999999------999999999999-------------------9999999999-999999999999999--------99-99999----------999999999999999999999
i monDom5.chr8                     C 0 C 0
s ornAna1.Ultra117                   6807970  64 +   6934412 ------------------------------------------CCGTTGCACTGCT----GATGCC-ATTTTCTTGGATAAATAAGAATTATTATCTG-----------------AAGGAAAGTCTGCA
q ornAna1.Ultra117                                           ------------------------------------------9999999999999----999999-9999999999999999999999999999999-----------------99999999999999
i ornAna1.Ultra117                 C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=58362.000000
s hg19.chrY                          7651993 55 +  59373566 AGTCATCAAACATGAGCCCTCAAACTCA---------------------------GCCAGTCTCTAC-AGTTCAATATTCTTT-
s panTro2.chrY                        505526 55 +  23952694 AGTCATCAAACATGAGCCCTCAAACTCA---------------------------GCCAGTCTCTAC-AGTTCAATATTCTTT-
q panTro2.chrY                                              0000000000000000000000000000---------------------------000000000000-000000000000000-
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032672 73 - 202140232 TGTCATCGAATATGGGCCCTCAAACTCATATTTAACTCAAA-----CTCAT----ATTGGTCTCTAC-AGTTCAATATTCTTT-
q ponAbe2.chr3                                              99999999999999999999999999999999999999999-----99999----999999999999-999999999999999-
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760547 55 + 189746636 AGGCATTGAATACGAGCCCTCAAACTCA---------------------------GCCAGTCTCTAC-AGTTCAATATTCTTT-
q rheMac2.chr2                                              9999999999999999999999999999---------------------------999999999999-999999999999999-
i rheMac2.chr2                     C 0 C 0
s cavPor3.scaffold_0                 8221787 24 -  88675666 ---------------------------------------------------------CTGTTTCTAG-AGTTGTCT-TTTTAA-
q cavPor3.scaffold_0                                        ---------------------------------------------------------9999999999-99999999-999999-
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107344596 46 - 113440463 --------AAAATAAACCTTCAGGCCCA---------------------------A-CTGTTTCGAGCAGCAGGCT-TTCTGT-
q rn4.chr9                                                  --------99999999999999999999---------------------------9-9999999999999999999-999999-
i rn4.chr9                         C 0 C 0
s bosTau4.chr1                     156981679 51 + 161106243 AGTCATCAAAGATGAGACTTTCA----A---------------------------GTAAGTCTCTAC-AGGTTGGTATTTGAT-
q bosTau4.chr1                                              99999999999999999999999----9---------------------------999999999999-999999999999999-
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22209937 55 -  87365405 AGTCATCAAATATGAGACCTCAAACTCA---------------------------GCCAGTCTCAAC-AGTTCAATATTTTGT-
q equCab2.chr16                                             9999999999999999999999999999---------------------------999999999999-999999999999999-
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25990805 55 -  55389570 AGTCAACCAATATGAGACCACCCACTCA---------------------------GCCGGTCTCCAC-AGCACAGTGTTTTGT-
q canFam2.chr23                                             9999999999999999999999999999---------------------------999999999999-999999999999999-
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              12080 50 +     88154 AATCATCTCAGACCAGAC-----ACTCA---------------------------ACCAGGCTCCac-agtgcactttttttt-
q eriEur1.scaffold_377961                                   999999999999999999-----99999---------------------------999999999999-999999999999999-
i eriEur1.scaffold_377961          C 0 I 678
s loxAfr3.scaffold_36                 511367 51 -  24123610 ACTTATCAAGTATCAGCCCTCAAACTCA-------------------------------GTCTCTAC-AGCTCAATCTTCTTG-
q loxAfr3.scaffold_36                                       9999999999999999999999999999-------------------------------99999999-999999999999999-
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497542 78 + 312544902 AGCCATTAAGCATTGGGCCTCAAGCTCACTCCCAATTAAAAG----GTCATGTCAACCAGTTTCCAC-AGCTTAAATCTTTTT-
q monDom5.chr8                                              999999999999999999999999999999999999999999----999999999999999999999-999999999999999-
i monDom5.chr8                     C 0 C 0
s ornAna1.Ultra117                   6808034 78 +   6934412 AGTTATTAAGCACTAGACCTTGAACTCACCCCCAACTTAAAGTCATGTCA-----ACTAATTTCCAC-AGCTTGAACTTTCTTT
q ornAna1.Ultra117                                          99999999999999999999999999999999999999999999999999-----999999999999-9999999999999999
i ornAna1.Ultra117                 C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=63534.000000
s hg19.chrY                          7652048 42 +  59373566 AAATGTTTCAAATCTTTCAAG--CTCTTCAAGCTATAATAAAAT
s panTro2.chrY                        505581 42 +  23952694 AAATGTTTCAAATCTTTCAAG--CTCTTCAAGCTATAATAAAAT
q panTro2.chrY                                              000000000000000000000--000000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032745 42 - 202140232 AAATGTTTCAAATTTTTCAAA--CTTTTCCTGCTATAATAAAAT
q ponAbe2.chr3                                              999999999999999999999--999999998557975999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760602 42 + 189746636 AAACGTTTCAAATTTTTCAAA--CTCTTTCTGCTATAATAAAAT
q rheMac2.chr2                                              999999999999999999999--999999999999999999999
i rheMac2.chr2                     C 0 C 0
s cavPor3.scaffold_0                 8221811 24 -  88675666 AAATGTGCC----------AC--CCTTTGCATGGAT--------
q cavPor3.scaffold_0                                        999999999----------99--9999999999999--------
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107344642 34 - 113440463 AAATGCATCAAAGATTTCAAA--CTCTTACTTGTAT--------
q rn4.chr9                                                  999999999999999999999--9999999999999--------
i rn4.chr9                         C 0 C 0
s bosTau4.chr1                     156981730 42 + 161106243 AAATGTTTCAAGTATCTTAGA--CTCTTTCTGCAATGATAAAAT
q bosTau4.chr1                                              999999999999999999999--999999999999999999999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22209992 42 -  87365405 GAATGTTTCAAGTATTTCAAA--CTCTTACTGCTATAATAAAAT
q equCab2.chr16                                             999999999999999999999--999999999999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25990860 42 -  55389570 AAATGTTTCAAGTATTTCAAA--TTCTTACTGCTATAATAAAAT
q canFam2.chr23                                             999999999999999999999--999999999999999999999
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 511418 42 -  24123610 GAACTTTTCATGGGTTTCAAA--CTTTTATCGTTGTAGTAACAT
q loxAfr3.scaffold_36                                       999999999999999999999--999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276497620 28 + 312544902 ---TTTTTTAAACTTGGGATG--TTTTGCAAGC-----------
q monDom5.chr8                                              ---999999999999999999--9999999999-----------
i monDom5.chr8                     C 0 I 4885
s ornAna1.Ultra117                   6808112 44 +   6934412 AAACCTGTCATGTTTTTCATATGCCCTTCTAACTTAAAAAAAAT
q ornAna1.Ultra117                                          99999999999999999999999999999999999999999999
i ornAna1.Ultra117                 C 0 I 754
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=91145.000000
s hg19.chrY                          7652090 86 +  59373566 GAACCTTTATTGAGAGATCGATAATTTAT-------------ATACATGTTTCCTCTTATGCACCACACTAAAATAAAAAATAAAA-GTAGTTAATATGT
s panTro2.chrY                        505623 86 +  23952694 GAACCTTTATTGAGAGATTGATAATTTAT-------------ATACATGTTTCCTCTTATGCACCACACTAAAATAAAAAATAAAA-GTAGTTAATATGT
q panTro2.chrY                                              00000000000000000000000000000-------------00000000000000000000000000000000000000000000-0000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032787 86 - 202140232 AAACCTTTATTGAGAGTTTGATAATTTAT-------------ACATTTGTTTCCTCTTATGCAACACACTAAAATAAAAAATAAAA-GTAGTTAATATGT
q ponAbe2.chr3                                              99999999999997999999999999999-------------99999999966556783868867377783647444479999999-9993999979634
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760644 82 + 189746636 AAACC----TTGAGAGTTTGGTAATTAAT-------------ATATTTGTTTCCTCTTATGCACCACACTAAAATAAAAAATAAAA-GCAGTTAATATGT
q rheMac2.chr2                                              99999----99999999999999999999-------------99999999999999999999999999999999999999999999-9999999999999
i rheMac2.chr2                     C 0 C 0
s cavPor3.scaffold_0                 8221835 61 -  88675666 ----------------TTCAATAATTTAT-------------ATATTTGCCTGGTCTCATGCACTGCTCTGTAATAAAAAGTAAAA-GCAG---------
q cavPor3.scaffold_0                                        ----------------9999999999999-------------99999999999999999999999999999999999999999999-9999---------
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107344676 67 - 113440463 -------------------AATGAATGAA-------------TTCTTTACTAGGACTTTTGTGTTTACATGTATGTTTGTGCGTGG-GTAGTGAGTACAT
q rn4.chr9                                                  -------------------9999999999-------------99999999999999999999999999999999999999999999-9999999999999
i rn4.chr9                         C 0 I 241
s bosTau4.chr1                     156981772 72 + 161106243 AAGCCTGTACCAAAATTTTGATCATTTGT-------------ATGC--GTTTCCTCTTACACATCATCCTATAATTAAAACAATAAA-------------
q bosTau4.chr1                                              99999999999999999999999999999-------------9999--999999999999999999999999999999999999999-------------
i bosTau4.chr1                     C 0 I 40
s equCab2.chr16                     22210034 74 -  87365405 AAACCTTCACCAAGATTTTGATAATTTAT-------------ATACTTGTTTCCTTTTATGCATCATGCTGTAATAAAAACATGAAA-------------
q equCab2.chr16                                             99999999999999999999999999999-------------999999999999999999999999999999999999999999999-------------
i equCab2.chr16                    C 0 I 294
s canFam2.chr23                     25990902 87 -  55389570 AAGCCTTTACTAAGATTCTGATCATTTAT-------------AGATTTGTTCCCCCTTATACATTATGCTGTAATAAAGAAATAAAAGTAGTCGGTGTCT
q canFam2.chr23                                             99999999999999999999999999999-------------9999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 511460 99 -  24123610 AAACCTTTACTAAGATTTTGATAATTTATATAAATGTAAGAGATATTAGTTTTCTCTAGTGCGTAACACTATAATAAAAAATAAAA-GCAGTCAATGTGT
q loxAfr3.scaffold_36                                       99999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=21558.000000
s hg19.chrY                          7652176 19 +  59373566 TTAGAAGGC--AGGGTTCTgg
s rheMac2.chr2                     158760726 19 + 189746636 TTAGAAGAC--AGGGTTCTTg
q rheMac2.chr2                                              999999999--9999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71032873 19 - 202140232 TTAGAAGAC--AGGGTTCTTg
q ponAbe2.chr3                                              667389692--4999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505709 19 +  23952694 TTAGAAGGC--AGGATTCTgg
q panTro2.chrY                                              000000000--0000000000
i panTro2.chrY                     C 0 C 0
s bosTau4.chr1                     156981884 21 + 161106243 TTAGAAGCCTTGGGATTCTAG
q bosTau4.chr1                                              999999999999999999999
i bosTau4.chr1                     I 40 I 591
s canFam2.chr23                     25990989 20 -  55389570 TTAGAAGACTTGGGATTCTA-
q canFam2.chr23                                             99999999999999999999-
i canFam2.chr23                    C 0 I 2
s loxAfr3.scaffold_36                 511559 21 -  24123610 ttagaagacttgggattctag
q loxAfr3.scaffold_36                                       999999999999999999999
i loxAfr3.scaffold_36              C 0 I 339
e cavPor3.scaffold_0                 8221896  0 -  88675666 C
e rn4.chr9                         107344743 241 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e equCab2.chr16                     22210108 294 -  87365405 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=48432.000000
s hg19.chrY                          7652195 106 +  59373566 ctggggacggtggctcacgcttgtaattgcagcactttgggaggccaaggcaggtggatcacttgagagtgggagtttgagaccagcctggcccacatggtgaaac
s rheMac2.chr2                     158760745 106 + 189746636 ctgggcatggtggctcacacttgtaatcgcagcactttgggagactgaggcgagtagatcacttgacagcaggagttcgagaccagcctggccaacatggtgaaac
q rheMac2.chr2                                               9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71032892 105 - 202140232 ctgggcatggtggctcatgcttgtaatcgcagcacttt-agaggccgagctgggtggatcatttgagagcaggagttcgaaaccagcctggccaacatggtgaaac
q ponAbe2.chr3                                               99999999999999999999999999993996999999-9997999996999999999999999998999959979998999997899999899998999799949
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505728 106 +  23952694 ctggggactgtggctcacgcttgtaattgcagcactttgggaggccaaggcaggtggatcacttgagagtgggagtttgagaccagcctggcccacatggtgaaac
q panTro2.chrY                                               0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8221896   0 -  88675666 C
e rn4.chr9                         107344743 241 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e equCab2.chr16                     22210108 294 -  87365405 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e canFam2.chr23                     25991009   2 -  55389570 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_15753                1239 23823 -     39409 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=24975.000000
s hg19.chrY                          7652301 70 +  59373566 cctgtctctaccaaaaattcaaaaattagctgggcatgttggtgtgcgcgtacagtcctagttactcagg--
s panTro2.chrY                        505834 70 +  23952694 cccgtctctaccaaaaattcaaaaattagctgggcatgttggtgtgtgcctacagtcctagttattcagg--
q panTro2.chrY                                              0000000000000000000000000000000000000000000000000000000000000000000000--
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71032997 70 - 202140232 cctgtctctacccaaaatacaaatattagctgcgcatgttggcgtgcacctatagtcccagctactcagg--
q ponAbe2.chr3                                              8999998998766089699979798999499994858949597999968988957889977988998209--
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158760851 70 + 189746636 tctgtctctaccaaaaatacaaaaattagccgtgcatgttggcgtgggcctataatcccggctactctgg--
q rheMac2.chr2                                              9999999999999999999999999999999999999999999999999999998999999999999999--
i rheMac2.chr2                     C 0 C 0
s proCap1.scaffold_51344               17031 53 -     18560 --GGTCATC----AGAATAAAAGGA----------GTGCTGGTG---GCACAATGGTTTAAATGCTCAGCtg
q proCap1.scaffold_51344                                    --9999999----999999999999----------999999999---9999999999999999999999999
i proCap1.scaffold_51344           I 8796 C 0
e cavPor3.scaffold_0                 8221896  0 -  88675666 C
e rn4.chr9                         107344743 241 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e equCab2.chr16                     22210108 294 -  87365405 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e canFam2.chr23                     25991009  2 -  55389570 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=7926.000000
s hg19.chrY                          7652371 34 +  59373566 gggat--gaagtgggatgatcacttgagtccagg-ag
s cavPor3.scaffold_0                 8221896 18 -  88675666 AGGAT--GAGGTTGGAAGAT-----------------
q cavPor3.scaffold_0                                        99999--9999999999999-----------------
i cavPor3.scaffold_0               C 0 C 0
s rheMac2.chr2                     158760921 34 + 189746636 gggct--gaggtggaaggatcacttgagtccagg-ag
q rheMac2.chr2                                              99999--999999999999999999999999999-99
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71033067 37 - 202140232 ggggctgaaggcgggaggatcacttgagtccaggaag
q ponAbe2.chr3                                              9793595835446969584313399770768705822
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        505904 34 +  23952694 gggat--gaagcgggatgatcacttgagtgcagg-ag
q panTro2.chrY                                              00000--000000000000000000000000000-00
i panTro2.chrY                     C 0 C 0
s proCap1.scaffold_51344               17084 33 -     18560 atgat--caaa-aggctggccattcaaaaccacc-ag
q proCap1.scaffold_51344                                    99999--9999-9999999999999999999999-99
i proCap1.scaffold_51344           C 0 I 1340
e rn4.chr9                         107344743 241 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e equCab2.chr16                     22210108 294 -  87365405 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e canFam2.chr23                     25991009  2 -  55389570 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=16845.000000
s hg19.chrY                          7652405 36 +  59373566 gttgaggttgcagtgagccgagatcatgccactgca
s rheMac2.chr2                     158760955 36 + 189746636 gcggaggttgcagtgagccgaaatcacaccactgca
q rheMac2.chr2                                              999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71033104 36 - 202140232 gctaaggttgcagtgagccgatatcgtgccactgca
q ponAbe2.chr3                                              352094596675599907601009956999854434
i ponAbe2.chr3                     C 0 I 687
s panTro2.chrY                        505938 36 +  23952694 gttgaggctgcagtgagccgagatcatgccactgca
q panTro2.chrY                                              000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
e cavPor3.scaffold_0                 8221914  0 -  88675666 C
e rn4.chr9                         107344743 241 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e equCab2.chr16                     22210108 294 -  87365405 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e canFam2.chr23                     25991009  2 -  55389570 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=7994.000000
s hg19.chrY                          7652441 35 +  59373566 atccagcctggcagacagagtaagacctgtgtctc
s rheMac2.chr2                     158760991 35 + 189746636 ctccagcctgggagacagagtaagacctctgtctc
q rheMac2.chr2                                              99999999999999999999999999999999999
i rheMac2.chr2                     C 0 I 5
s panTro2.chrY                        505974 35 +  23952694 atccagcctggcagacagagtaagacctgtgtctc
q panTro2.chrY                                              00000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8221914 14 -  88675666 ---------------------GAGATCTAGATCTA
q cavPor3.scaffold_0                                        ---------------------99999999999999
i cavPor3.scaffold_0               C 0 C 0
e rn4.chr9                         107344743 241 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e equCab2.chr16                     22210108 294 -  87365405 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e canFam2.chr23                     25991009  2 -  55389570 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e myoLuc1.scaffold_164117               4473 597 -     50790 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ponAbe2.chr3                      71033140 687 - 202140232 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=67425.000000
s hg19.chrY                          7652476 109 +  59373566 aagaagaaaGCAGACAGAGTTCTG-TACCAGTTGCTCTCCTCACTGCCTGGTAACCCCA---GGTATG-tgaacactcaatttctttgtataaaatggtgat----aataacatcaac
s canFam2.chr23                     25991011  71 -  55389570 --------------------------------TACATTCTTCACTGGT-ATTAATCCTG---GGCATG-tgaacacccagtttccttgtttaagatgggcat----actaac------
q canFam2.chr23                                              --------------------------------9999999999999999-9999999999---999999-999999999999999999999999999999999----999999------
i canFam2.chr23                    I 2 C 0
s myoLuc1.scaffold_164117               5070  93 -     50790 -----------------gaatttagtatcagctacattcctcactagc-attaaccctg---ggcatgaggaacactcagtttcctcatataaaatggacat----cataacatcagc
q myoLuc1.scaffold_164117                                    -----------------9999999999999999999999999999999-9999999999---9999999999999999999999999999999999999999----999999999999
i myoLuc1.scaffold_164117          I 597 N 0
s equCab2.chr16                     22210402  93 -  87365405 --------------cgggattctagcatcagctgcatttctcactagc-gttaatcctg---ggcaca-tggaca--cagtcttctcgtataaaatggagat----aacaacatcagc
q equCab2.chr16                                              --------------9999999999999999999999999999999999-9999999999---999999-999999--9999999999999999999999999----999999999999
i equCab2.chr16                    I 294 C 0
s rheMac2.chr2                     158761031 109 + 189746636 aaaaaaaaagaaGACAGGGTTCTA-TACCAGCTGCTTTCCTCACTGCTTGCTAACCCCC---GGCATG-tgaacactcaatttctttgtataaaatggtgat----aacaacatcaac
q rheMac2.chr2                                               999999999999999999999999-9999999999999999996777676676999999---999999-999999999999999999999999999999999----999999999999
i rheMac2.chr2                     I 5 C 0
s ponAbe2.chr3                      71033827 109 - 202140232 aaaaaaaaagaaGACAGGGTTCTA-TACCAGCTGCTCTCCTCACTGCCTGCTAACCCCA---GGCATG-tgaacactcaatttctttgtataaaatagtgat----aacaacatcaac
q ponAbe2.chr3                                               689634483397599999999999-9999999999999999999999999999999999---999999-999999999999999999999999999999999----999999999999
i ponAbe2.chr3                     I 687 C 0
s panTro2.chrY                        506009 109 +  23952694 aagaagaaaGCAGACAGGGTTCTC-TACCAGTTGCTCTCCTCACTGCCTGGTAACCCCA---GGTATG-tgaacactcaatttctttgtataaaatggtgat----aataacatcaac
q panTro2.chrY                                               000000000000000000000000-0000000000000000000000000000000000---000000-000000000000000000000000000000000----000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8221928  71 -  88675666 -----------A-----CATT--------AACTGCATTCTTCACCAGCCGTTAATTCTGAATGCAATA-AA---------------TGAAtgaagtagagat-------gacacagtc
q cavPor3.scaffold_0                                         -----------9-----9999--------999999999999999999999999999999999999999-99---------------9999999999999999-------999999999
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107344984  75 - 113440463 ------------GACAGCATT----------CCATGTTTCTCATGAGCTGTTAGCTCTA---GCCATG-A-----------------GAACATAGTAAGGTTCTACATAGGCACCAGT
q rn4.chr9                                                   ------------999999999----------9999999999999999999999999999---999999-9-----------------9999999999999999999999999999999
i rn4.chr9                         I 241 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              12130 678 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=56027.000000
s hg19.chrY                          7652585 52 +  59373566 gtgtcttccatcatagagtggttgtgaggatcaagtgggatgac------------------------------------------gtgt---gtaa
s eriEur1.scaffold_377961              12808 45 +     88154 CTGTCTTCCACCAAATGGCA---GTGAGACTCCAATGGGA----------------------------------------------GTGT---GTGA
q eriEur1.scaffold_377961                                   99999999999999999999---99999999999999999----------------------------------------------9999---9999
i eriEur1.scaffold_377961          I 678 C 0
s canFam2.chr23                     25991082 45 -  55389570 ---------atcataccgcacctagaagagtccaatgggatgat----------------------------------------gcatgt---gaaA
q canFam2.chr23                                             ---------99999999999999999999999999999999999----------------------------------------999999---9999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22210495 54 -  87365405 ctgttttctatcatagggtggttgtgagaaccaaatgggataat----------------------------------------gtgtgt---gtaa
q equCab2.chr16                                             99999999999999999999999999999999999999999999----------------------------------------999999---9999
i equCab2.chr16                    C 0 C 0
s rn4.chr9                         107345059 97 - 113440463 CCGTCTGCCATCAAATGGTGGCTATAAGACTCAGTTGGGATGACAATGgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtAATGTAA
q rn4.chr9                                                  9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rn4.chr9                         C 0 C 0
s cavPor3.scaffold_0                 8221999 52 -  88675666 ctgcctaccatcacaaagtggctgtgagagtcggatggg---------------------------------------------gtGTCTTGCACAC
q cavPor3.scaffold_0                                        999999999999999999999999999999999999999---------------------------------------------9999999999999
i cavPor3.scaffold_0               C 0 C 0
s panTro2.chrY                        506118 54 +  23952694 gtgtcttccatcatagagtggttgtgaggatcaagtgggatgac----------------------------------------atgtgt---gtaa
q panTro2.chrY                                              00000000000000000000000000000000000000000000----------------------------------------000000---0000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71033936 54 - 202140232 ctgtcttccatcatagcgtcattgtgaggatcaagtgggatgat----------------------------------------gtgtgt---gtaa
q ponAbe2.chr3                                              99999999999999999999999999999999999999999999----------------------------------------999999---9999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158761140 54 + 189746636 cagtcttccatcatagcatcattgtgaggatcaagtgggatgat----------------------------------------gtgtgt---GTAA
q rheMac2.chr2                                              99999999999999969999999999999999999999999999----------------------------------------999999---9999
i rheMac2.chr2                     C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e loxAfr3.scaffold_36                 511580 339 -  24123610 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=67038.000000
s hg19.chrY                          7652637 105 +  59373566 tatacagagcacaaaa--caatcacgggcaGTGGCGCTGGCCA-TGGT--GAAT-TGGGG-----------GACTACCCACCCGGGGATGGTGATGACAACAAGGTGT--GGGACCATGAAATC
s rheMac2.chr2                     158761194 104 + 189746636 TCTACAGAGCACAAAA--CAATCACGGGCGGTGGCACTGGCTG-TGGC--TAAT-GGAAG-----------GAGTGGTCACCCTGGGATGG-GATGACAACATGATAT--GGGGCCATGAAATC
q rheMac2.chr2                                               9999999889999999--9999999999999999999999999-9999--9999-98898-----------99999999999999999999-9999999999999999--99999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71033990 105 - 202140232 TCTACAGAACACAAAA--CAATCACGGATGGTGGCACTGGCTG-TGGT--GAAT-GGGAG-----------GACTGGTCACCCCGGGATGGTGATGACAACATGATGC--GGGGCCATGAAATC
q ponAbe2.chr3                                               9999999999999999--9999999999999999999999999-9999--9999-99999-----------9999999999999999999999999999999999999--99999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        506172 105 +  23952694 tctacagagcacaAAA--CAATCACGGGCAGTGGCGCTGGCCA-TGGT--GAAT-TGGGG-----------GACTACCCACCCGGGGATGGTGATGACAACAAGGTGT--GGGACCATGAAATC
q panTro2.chrY                                               0000000000000000--0000000000000000000000000-0000--0000-00000-----------0000000000000000000000000000000000000--00000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8222051  93 -  88675666 TTGACAAAGCCCAAAA--CCGTCACAGTCAGTGGCA-----TG-TGCC--TGGT-GGA----------------GGCCTGCTCAGGGAGGGTGCTGACAGTCCAGGAT--AGGGCCATTGG--T
q cavPor3.scaffold_0                                         9999999999999999--999999999999999999-----99-9999--9999-999----------------9999999999999999999999999999999999--99999999999--9
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107345156  87 - 113440463 TCAACACAGCCAAACAATCAGTCAGGATGGGTGGGG-----AGCTGGC--AGAT-GGA----------------TACC------------ATGTTGACCCTAAGGGGTC-AGGGTCATTAGACT
q rn4.chr9                                                   999999999999999999999999999999999999-----9999999--9999-999----------------9999------------9999999999999999999-99999999999999
i rn4.chr9                         C 0 C 0
s equCab2.chr16                     22210549 116 -  87365405 TCCATAAAGCTCAGAA--TTGTCATAGGCAGT-GTGCTGGCAG-TGGT--GGATGGGGAGTGGGCCAGGGAGAGCGGTCAGCCGCGGGTGGTGAGGACATCATGGTGC--TGGGCCCTTAAATC
q equCab2.chr16                                              9999999999999999--99999999999999-9999999999-9999--9999999999999999999999999999999999999999999999999999999999--99999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25991127 116 -  55389570 TCGATGAAGCTACAAA--CTACCACTGTCAGTGGTGGTAGCAG-TGGT--GGAT-GGGAGTTGGTCAGGGATACTGGTCAGCTGAGGCCAGTGATGACACCATGGTGC--CAGGCCACTAAATC
q canFam2.chr23                                              9999999999999999--9999999999999999999999999-9999--9999-99999999999999999999999999999999999999999999999999999--99999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              12853  96 +     88154 TTC-TAAAACTCACAT--TTTTCAT--------ATTCTA--AG-TGGT--GGGT-AGGGTTAAG---------ATGGTCACTTGCAGATGGTGATTACAGCTCAGCGT--TGGGCCACTGAAGC
q eriEur1.scaffold_377961                                    999-999999999999--9999999--------999999--99-9999--9999-999999999---------99999999999999999999999999999999999--99999999999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 511919 117 -  24123610 --GATACAGCTCAGCA--C-GTTGCACCCACCGGCAGTGGCAG-TGGTGGGGGT-GGAGCTGGGTCAGGGGGACCGATCAGCTGGAGATAGTGATGACATTATGGCGCTGGGGGCCAACAAATC
q loxAfr3.scaffold_36                                        --99999999999999--9-99999999999999999999999-9999999999-999999999999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36              I 339 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e bosTau4.chr1                     156981905 591 + 161106243 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=200981.000000
s hg19.chrY                          7652742 89 +  59373566 CTTCCCCATTCCCACCCACACCTCTTAACCTCCATGC------------TCCC--AAGTCAGTGCACTAGAAATATTTTAGTGGTC--AATCAACCACTTTATAT
s rheMac2.chr2                     158761298 84 + 189746636 CTTCCCCATTCCCACCCACACCCCTTAACCTCCATGC------------TCCC--AAATCAGTGCACTAAAAATGT-----TACTC--CATCAACCACTTTATAT
q rheMac2.chr2                                              9999999999999999999999999999999999999------------9999--999999999999999999999-----99999--99999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034095 84 - 202140232 CTTCCCCATTCCCACCCACACCCCTTAACCTCCATGC------------TCCC--AAATCGGTGCACCAAAAATGT-----TAGTC--AATCAACCACTTTATAT
q ponAbe2.chr3                                              9999999999999999999999999999999999999------------9999--999999999999999999999-----99999--99999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        506277 89 +  23952694 CTTCCCCATTCCCACCCACACCTCTTAACCTCCATGC------------TCCC--AAGTCAGTGCACTAGAAATATTTTAGTGGTC--AATCAACCACTTTATAT
q panTro2.chrY                                              0000000000000000000000000000000000000------------0000--0000000000000000000000000000000--00000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8222144 83 -  88675666 ATTCTCCATCCTCCCCCACATCTC-TAATCTCTGTGC------------TCCC--CAATCAGTGCACTAAAAATAT-----TAGTC--AACCAGCTGCTTTATGG
q cavPor3.scaffold_0                                        999999999999999999999999-999999999999------------9999--999999999999999999999-----99999--99999999999999999
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107345243 85 - 113440463 GTGCTCCCTCCCCACCCAGACCTT-TATCCTTTATAT------------TCCCGAAAATCAGTGCGCTATAAATAT-----TAAGC--AATCAACTGCCTAATAC
q rn4.chr9                                                  999999999999999999999999-999999999999------------999999999999999999999999999-----99999--99999999999999999
i rn4.chr9                         C 0 C 0
s bosTau4.chr1                     156982496 81 + 161106243 CCTCCCCA--ACCCCCCGCACCCCTTCACCTCCA-CC------------CCGC--CAGTCAGGGCACTAAAAATAT-----TAGTC--AATCAACCATGTTACGG
q bosTau4.chr1                                              99999999--999999999999999999999999-99------------9999--999999999999999999999-----99999--99999999999999999
i bosTau4.chr1                     I 591 C 0
s canFam2.chr23                     25991243 84 -  55389570 ATTCTCCATTTCCTCCCATACCCCATAACCACCAGGC------------TTAC--AAATCACTGTATTAAAAACAG-----TAGTT--GATCAACCACTTTACAG
q canFam2.chr23                                             9999999999999999999999999999999999999------------9999--999999999999999999999-----99999--99999999999999999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22210665 84 -  87365405 GCTTCTCATTCCCACCCACACCTCTTAATATCCAGGC------------TCTC--AAATCAGTGTACTAAAAATAT-----TAGTC--AATCAATTACTTTACTG
q equCab2.chr16                                             9999999999999999999999999999999999999------------9999--999999999999999999999-----99999--99999999999999999
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961              12949 77 +     88154 -CTCCCTA----ACCCCACACTTCTTACCCTCCGGGC------------TTCT--AAATCAAAGCAC--GAAATAT-----TAGTC--AATCAACTACTTTGTAG
q eriEur1.scaffold_377961                                   -9999999----9999999999989999999999999------------9999--999999999999--9999999-----65467--64699999999937799
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 512036 98 -  24123610 AATGCCCATCCCCACCCACATCCCTTAACCTCCACGCAGAAAACATGGATCCC--AGATCAGTGCGCTAAAAATAC-----TAGTCAAAATCAACCAATTTAGAG
q loxAfr3.scaffold_36                                       99999999999999999999999999999999999999999999999999999--999999999999999999999-----999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2467928 1275 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=898050.000000
s hg19.chrY                          7652831 269 +  59373566 TTAAATGCTCCCTGAATAAAACATAA-AGCTTTAAAATTTTTATC-TTATAATCTAAAAATGAATCTCTTGTCAAAACTAAGC-AGTTTTGTGGCTTTAA-TCTTTGGTAAGCATGCTGTCAAAGTAAGTTTAGCTTCATGGTTAAAAGAAAAA-AATAAAAATG-T----------TCTCAATGATCTTAAAGCA-AT-----TAAAAAAAA-------------GGCTCCTACTGCAAATATGATTAAAGGCCTTAATGTCTTGTTTCTATTTGAACCCTAACCTT-AAAAT-----------ACAAAAGAAAA
s rheMac2.chr2                     158761382 274 + 189746636 TTAAATGCTGCCTGAATAAAACATAATACCTTTTAAATTTTTATCTTTAAAATCTAAAGATGTATTTCCTGTCAAAGCTAAGC-AATTTTATGGCTTTAA-TTTTTGGTATGCATGCTGTCAAAGTAAGTTTAGCTTCATGGTTAAAAGAAACA-AATAAAAATGAA----------TCTCAATGATCTTAAAGCA-AT----AAAAAAAAAA-------------GGCTCCTATTGTAAGTATGATTAAAGACCTTAATCTCATGTTTCTATTTGAACCCTAACCTTAAAAAT-----------ACAAAAGAAAA
q rheMac2.chr2                                               99999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999-99999999999999999999999999999999999999999999999999999-999999999999----------9999999999999999999-99----9999999999-------------99999999999999999999999999999999999999999999999999999999999999999999-----------99999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034179 270 - 202140232 TTAAATGCTTCCTGAATAAAACATAATACCTTTTAAATTTTTATC-TTAAAATCTAAAGATGTATCTCCTGTCAAAGCTAAGC-AATTTTATGGCTTTAA-TTTTTGGTATGCATGCTGTCAAAGTAAGTTTAGCTTCATGGTTAAAAGAAACA-AATAAAAATGAA----------TCTCAATGATCTTAAAGCA-AT-------AAAAAAA-------------GGCTCCTATTGTAAATATGATTAAAGGCCTTAATCTCATGTTTCTATTTGAACCTTAACCTTAAAAAT-----------ACAAAAGAAAA
q ponAbe2.chr3                                               999999999999999999999999999999999999999999999-9999999999999999999999999999999999999-9999999999999999-99999999999999999999999999999999999999999999997999999-999999999999----------9999999999999999999-99-------9999999-------------99999999999999999999999999999999999999999999999999999999999999999999-----------99999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        506366 267 +  23952694 TTAAATGCTCCCTGAATAAAACATAA-AGCTTTAAAATTTTTATC-TTATAATCTAAAAATGAATCTCTTGTCAAAACTAAGC-AGTTTTGTGGCTTTAA-TCTTTGGTAAGCATGCTGTCAAAGTAAGTTTAGCTTCATGGTAAAAAGAAAAA-AATAAAAATG-G----------TCTCAATGATCTTAAAGCA-AT------AAAAAAAA-------------GGCTCCTACTGCAA-TATGATTAAAGGCCTTAATGTCTTGTTTCTATTTGAACCCTAACGTT-AAAAT-----------ACAAAAGAAAA
q panTro2.chrY                                               00000000000000000000000000-000000000000000000-0000000000000000000000000000000000000-0000000000000000-00000000000000000000000000000000000000000000000000000-0000000000-0----------0000000000000000000-00------00000000-------------00000000000000-00000000000000000000000000000000000000000000000-00000-----------00000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8222227 261 -  88675666 TAAATTGCTTCCTGAATAAAACATAATACCTTTTAAATTTTTATC-TTAAAATCTAAAGATATACCTTTTGTCCAAACTCAGC-AGTTTTATGACTTTAA-TTTTTGGTATGCAAGCTGTCA----AAGTTTAGCTTCATGGTT-----AACAAAAACAAAAATGAA----------TCTCAACAATCTTATCACA-AT---------AAAAA-------------GGCTTCTATTATTAATATGATCAAAGGCCTTAATTTCATGTTTTTATGTGAACCTTAACTTTAAAGATA----------ACAAAGACAAA
q cavPor3.scaffold_0                                         999999999999999999999999999999999999999999999-9999999999999999999999999999999999999-9999999999999999-999999999999999999999----999999999999999999-----999999999999999999----------9999999999999999999-99---------99999-------------999999999999999999999999999999999999999999999999999999999999999999999----------99999999999
i cavPor3.scaffold_0               C 0 I 3
s rn4.chr9                         107345328 267 - 113440463 TTAAAAACTTCCTGAATAAAACACAGCACCCTTTATTTTTTTAAT-CTAATATTTG-----------TTTGTCAAAAGTCAAC-CACTTTGTGACATCAA-TTTTTGGTAAGTGTAACATCAGAATAAGTTTAGCTTTGCCGCTAAAACAACAACAATAAAAACAAACAAAATAAACTCTCAACGGAAATACTGCA-AT---------AAAAA-------------GGCTTATACTATAAGTATCATTAAAGATCTTTAGTTCGTGTTTCTATTTGAACCTTAAC-CCACAAAT-----------ACAGAAGCAAA
q rn4.chr9                                                   999999999999999999999999999999999999999999999-9999999999-----------9999999999999999-9999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99---------99999-------------99999999999999999999999999999999999999999999999999999999999-99999999-----------99999999999
i rn4.chr9                         C 0 I 254
s oryCun2.chr14                      2469203 276 + 163896628 TTCAGTGTTTCCTAAAT-AAACATAACACTTTTAAA--TTTTATC-TTAAAATCTAAAGCTGCATCTCCTGTC-AAACACAGC-AGTTTTATGGCTTTAA-TTTTTCGTGTGCATGCTGTCAAAGTAAGTTTAGCTTCAAGGTTAAAACAGCA--AATAAAAATGAA----------TCTCAACAATCTTATCACA-GG---------AAAAAAAAAAAAAAACCTAGCTCCTATTGTAAACAGGATTCGAGACCTTAACTCCATGTTTGTATTTGAACCTTAACCTTAAAAGT-----------ACAAGAAAAAA
q oryCun2.chr14                                              33555324642223610-183533111032752271--2773143-222796554465575432464262522-696315354-4358856553438644-5887735253466456544369564553486655656643565599585645--857599953454----------7556535555555257465-43---------59999997999999466955599986827699595985458878569969599698698948898937946999936796899787-----------39959779931
i oryCun2.chr14                    I 1275 I 3
s bosTau4.chr1                     156982577 273 + 161106243 CTAAATGCTTCCTGAATAAAACATAACATCTTTAAAATTTTTATC-TCCAAATCTAAAGATGCATTTCCTGTCAAAACTCAAGGGATTTTATGGCTTTAA-TTTTTGGTATGTGTGCTGTCAAAGTAAGTTGATCTTCATGGTTAAAAAAACA--AATAAAAATGAA----------TCTCAACCATCTTATGGCA-AT---TAAAAAAAAAA-------------GGTCCCTATTGTAAATATGATTAAAGGCCTTAATTCCATGTTTCTTTTTGAACCTTAACCTTAAAAA------------AAAAAAAAAAG
q bosTau4.chr1                                               999999999999999999999999999999999999999999997-999999979999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999--999999999999----------9999999999999999999-99---99999999999-------------9999999999999999999999999999999999999999999999999999999999999999999------------99999999999
i bosTau4.chr1                     C 0 I 1
s canFam2.chr23                     25991327 263 -  55389570 TTAAATGCTTCCTGAATAAAACATAATACCTTTAAAATTTTCATC-TTAAAATCTAAAGATGTATCTCTTGTCAAAACTCAGCAAACTTTATGGTTTTAATTTTTTGGTATGCATGCTGGCAAAGTAAGTTTAGCTTCATGGCT-AAAAAACA--AATAAAAATGAA----------TCTCAACAATCTTGTTGCA-AT-----AAAAAAAAA-------------GGCTCTTGTTGTAAATATGATTAAAGGCCTTAATTTCTTGTTTCTGTTTGAACCTTAACCTTCAG--------------------AAAAA
q canFam2.chr23                                              999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999--999999999999----------9999999999999999999-99-----999999999-------------99999999999999999999999999999999999999999999999999999999999999999--------------------99999
i canFam2.chr23                    C 0 I 1
s equCab2.chr16                     22210749 264 -  87365405 TTAAATGCTTCCTGAATAAAACATAATAGCTTTTAAATTTTTATC-TTAAAATCTAAAGATATATCTCCTGTCAAAACTCAGC-AATTTTATGGCTTTAA-TTTTTGGTACGCATGCTGTCAAAGTAAGTTTAGCTTCAGGATT-AAAAAACA--AACAAAAATGAA----------TCTCAACAATCATATCACA-AT---TAAAAAAAAAA-------------GGCTCTTGGTGTAAATATGATTAAAGACCTTAATTTCATGTTTCTATTTGAACCTTAACCTTAAA-------------------CAAAAG
q equCab2.chr16                                              999999999999999999999999999999999999999999999-9999999999999999999999999999999999999-9999999999999999-9999999999999999999999999999999999999999999-99999999--999999999999----------9999999999999999999-99---99999999999-------------99999999999999999999999999999999999999999999999999999999999999999-------------------999999
i equCab2.chr16                    C 0 I 1
s eriEur1.scaffold_377961              13026 273 +     88154 TTAAATGCCTCCTGAATAAAACATCATGCCTTTTAAATTTTCATC-TTAAAATCTAAAGA---------TGTCAGAACTCAAC-AATTTTATGGCTTTAA-TTTTTGGTATGCATGCTATCAAAGTAAGTTTAGCTCCATGGTT-AGAAAAC----ATCAAAATGAA----------TCTGACCCATCTTACCATACAA---TATAAAACACC-------------GGTAACTATTGTAAATATGATTAAAGGCCTTAATTTCGTGTTTCTATTTGAATTTTATCCCTGAAAAACAAacaccaccaacaaaaaaaa
q eriEur1.scaffold_377961                                    999964369899369677994546976369588588659856465-94799476889687---------46775794767955-9479979596799997-8999689796579678987999999996996879999958999-7999959----89899995995----------9979379969999499996999---99999969698-------------999989999499999996999999983999999999997999999999799899996999989999889996959948999999999999
i eriEur1.scaffold_377961          C 0 I 1
s loxAfr3.scaffold_36                 512134 274 -  24123610 TTAAATGGTTCCTAAACAAAAGACAACATCTTGGAAATTTTAACC-TTAAAATCTAGAGATACATCGCCTGTCAAAACTCAGC-AATTTTATGGCTTTAA-TTTTTGGTACACAGGCTGTCAAAGTAAGTTTAGGTTCATGGCTCAAAAACC---AATAATAATGAA----------TCTCAACAATCTTATCACA-ATAATAATAATAATAA-------------AGCTCCCATTGTAAATATGATTCAAGGCCTTAATTTCATGTTTTCATTTGAACCATAACTGtaaaaaa-----------aaaaaaaaaa-
q loxAfr3.scaffold_36                                        999999999999999999999999999999999999999999999-9999999999999999999999999999999999999-9999999999999999-999999999999999999999999999999999999999999999999999---999999999999----------9999999999999999999-9999999999999999-------------99999999999999999999999999999999999999999999999999999999999999999999-----------9999999999-
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=725230.000000
s hg19.chrY                          7653100 281 +  59373566 -CATAGTTCTCATAAAGTGACCAATCCCTCAG-------------------TGTTACTCCTAGGCAAATAAA-------------------------------------------CAAAGGAATGATTTCTC-------------------TATTTGGATAGACATACCAATTGCA-GCCTGTTGGTCTGTTT--CTCAACCTGCTTA-TCAGAGTAACCTCTCCACTATT-TTGTTTTCTAATAGTTGCCTGATTTcgtttacaaattatgt-aaccatgggcaagctatatatctccctctccatctcttggg---accctcatt-----tacaaaatgaaga--c--taaatggtcAATTGCAAAAGGATATTTCAAC
s rheMac2.chr2                     158761656 268 + 189746636 -CACAGTTCTTACGAAGTGACCAATTCCCCAG-------------------TGTTGCTCCTAGGTAAACAAA-------------------------------------------CAAAGGAATGGTTTCTC-------------------CATTTGGATGGACATAGCAATTGTA-GCCTGTTGGTCTCTTT--CTCACCCTACTTA-TCAGAGTAACCTCTCCACTATT-TTGTTTTGTAATAGTTGCCTGATTTcatttacaaattatgt-aaccttgggcaaactatatagctccctccccatctcttggg---accctcatt-----tacaaaatgaaga--ctttgaatgggcaattgca---------------
q rheMac2.chr2                                               -9999999999999999999999999999999-------------------999999999999999999999-------------------------------------------99999999999999999-------------------9999999999999999999999999-9999999999999999--9999999999999-9999999999999999999999-99999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999999999--9999999999999999999---------------
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034449 268 - 202140232 -CATAGTTCTTATGAAGTGACCAATTCCCCAG-------------------TGTTACTCCTAGGCAAATAAA-------------------------------------------CAAAGGAATGATTTCTC-------------------CGTTTGGATGGACATACCAGTTGTA-GCCTGTTGGTCTGTTT--CTCACCCTACTTA-TCAGAGTAACCTCTCCACTATT-TTGTTTTGTAATAGTTGCCTGATTTcatttacaaattatgt-aaccttgggcaagctatatagttccctccccatctcttggg---accctcatt-----tacaaaatgaaga--ctttggatgggcaattgca---------------
q ponAbe2.chr3                                               -9999999999999999999999999999999-------------------999999999999999999999-------------------------------------------99999999999999999-------------------9999999999999999999999999-9999999999999999--9999999999999-9999999999999999999999-99999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999999999--9999999999999999999---------------
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        506633 281 +  23952694 -CATAGTTCTCATAAAGTGACCAATCCCTCAG-------------------TGTTACTCCTAGGCAAATAAA-------------------------------------------CAAAGGAATGATTTCTC-------------------TATTTGGATAGACATACCAATTGTA-GCCTATTGGTCTGTTT--CTCAACCTGCTTA-TCAGAGTAACCTCTCCACTATT-TTGTTTTCTAATAGTTGCCTGATTTcgtttacaaattatgt-aaccatgggcaagctatatatctccctctccatctcttggg---accctcatt-----tacaaaatgaaga--c--taaatggtcaattgcaaaaggataTTTCAAC
q panTro2.chrY                                               -0000000000000000000000000000000-------------------000000000000000000000-------------------------------------------00000000000000000-------------------0000000000000000000000000-0000000000000000--0000000000000-0000000000000000000000-00000000000000000000000000000000000000000-00000000000000000000000000000000000000000---000000000-----0000000000000--0--0000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107345849 347 - 113440463 -CCTGGTTCTTGTAGAGTTGTCAGCCCCTCAATGCTATGTCAATCTCTTAATATTACTACTAGAAAACTAAACTATGAAACGTAATACAAAACTATTGAATAGTATTAAAAATAAGGAAAGGTTGGTCTATCAACATATCGAATGATGGGATGTTCAGATGGAAACACTGATT--ATAGTTGTTGGCCTGT-----TCTACCCACCCAGTCAGAGAAATCGCCCTAGCATT-CTGCTTTGTAATAACTGTCTGATTTCA-CTGCTGCTTATGT-AACCTTGGGTAGATGACAGAAATCCCTCCCCATCTCTAGGG---TCCTTTACTATGAAAGTGAGA--------TCTTGGATACACATTTGGGTAA------------
q rn4.chr9                                                   -9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999-----99999999999999999999999999999999999-999999999999999999999999999-9999999999999-99999999999999999999999999999999999999999---999999999999999999999--------9999999999999999999999------------
i rn4.chr9                         I 254 C 0
s cavPor3.scaffold_0                 8222491 238 -  88675666 -CTTAGTTCTCTTAAAGTGATCAGTCCCCCAA--------------------GTTATTACTAGAAAAACAAA----------------------------------------------------------------------------------------GGATTTACTGTTTGGATACCCCTTGGTCTGTTT--CTCGCCCTACCCA-TGAGAAAAATCTCTCCAATACT--TGTTTTGTAATTGTTGCCTGATTTcatttacagattatgt-aaccttgcgtaagtcatataactcccttcccatctcttggg---tcctttatt-----tataaga--------CCCTAGATAGGCAATTGTGAAA------------
q cavPor3.scaffold_0                                         -9999999999999999999999999999999--------------------99999999999999999999----------------------------------------------------------------------------------------999999999999999999999999999999999--9999999999999-9999999999999999999999--9999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999--------9999999999999999999999------------
i cavPor3.scaffold_0               I 3 C 0
s oryCun2.chr14                      2469482 252 + 163896628 -TCTAGTTCTTATAAAGTAATCAACCCTCCCG-----------------------------------ACAAG-----------------------------------------------GGGATGATTTATC-------------------TGTTTAGTTGGACATACCAAACGCA-GCCTTTTGGTCCGTTT--TTCACCCTGCCCA-GGGGAGTAACCTCTTTGCTATT------TTGTAACAGTTGCCTGCTCTCTTTCACAAATTATGTAAACCTCCGGCAAGTCATCCAACTGCCTCCCTATCCTTGGGTCTCTCCCTCATT-----AATAAAACGAATTGTCCCAGGATAGGCAGTTATGAAA------------
q oryCun2.chr14                                              -9998999799798999975698558689989-----------------------------------69989-----------------------------------------------9999899999999-------------------9999999999999999999999999-9999999999999999--9999999999999-9999999999999999999999------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----9999999999999999999999999999999999999------------
i oryCun2.chr14                    I 3 C 0
s bosTau4.chr1                     156982851 264 + 161106243 -CCT-GTTCTTGTAAAGTGACCAATTCCCCAA-------------------TATTATTACTGGGAAAACAAA-------------------------------------------CGAAAGAATGACTTATG-------------------TGTTTGGA---ACATACCAAAAGTG-GCCTCTTGGTCTATTTTCCCCACCCTTCCCA-TCAGAATAACCTCTCCACTATTTTTGTTTTGTAATATTTGCCTGATTTTGTTTACAAATTACAT-AACCTTGGGTGATTCATGTAATTCCCACCCTGTCTCTTGGG---TCCCTTCTT-----TTGAAAGCGAAGA--CCCCTGACAGGCCATT------------------
q bosTau4.chr1                                               -999-999999999999999999999999999-------------------999999999999999999999-------------------------------------------99999999999999999-------------------99999999---99999999999999-9999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999999999--9999999999999999------------------
i bosTau4.chr1                     I 1 C 0
s canFam2.chr23                     25991591 266 -  55389570 -GCTAGTTCTTATAAACTAACCAATCCCCCAA-------------------TATTATTACCAGAAAAATAAA-------------------------------------------GGAAAAAATGACTTATC-------------------TGTTTGGAGGGACATACCAATTGTA-GCCTCTTGGTCTATTT--CTCACCCCACCCA-CCAGGATAACCTCTCTACTATTTTTGTTTTGTAAGATTTGCCTGACTTCGTTGACAAATtatgt-aaccttgggcaagtcatatgactcccaccccatctcttggg---tccattctt-----tataaaatgaaga--CCCTGGATCGGCAATT------------------
q canFam2.chr23                                              -9999999999999999999999999999990-------------------999999999999999999999-------------------------------------------99999999999999999-------------------9999999999999999999999999-9999999999999999--9999999999999-9999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999999999--9999999999999999------------------
i canFam2.chr23                    I 1 C 0
s equCab2.chr16                     22211014 266 -  87365405 -TCTAGTTCTTGTAAACTGACCAATCCCCCAA-------------------TATTATTACTAGAAAAATAAG-------------------------------------------CGAAGGAATGACTTAGT-------------------TGTTTGGCTGGACATACCGATCGTA-GCCTCTTGGTCTATTT--CTCACCCCACCCA-TCAGAGCAACCTCTCCACTATTTTTGTTTTGCAATATTTGCCTGATTTcgtttacaaattatgt-aaccttgggcaagtcatataactcccaccccatctcttggg---tccctcgtt-----tataaaatgaaga--ccctggataggcaatt------------------
q equCab2.chr16                                              -9999999999999999999999999999999-------------------999999999999999999999-------------------------------------------99999999999999999-------------------9999999999999999999999999-9999999999999999--9999999999999-9999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999999999--9999999999999999------------------
i equCab2.chr16                    I 1 C 0
s eriEur1.scaffold_377961              13300 265 +     88154 -tacagtttttATAAAGTGACCAATCTCCCAA-------------------TATTACTActagaaaaataaa-------------------------------------------caatgaaagaaCTTACC-------------------CATTTGTGGATGGCAACCGACTGAA-GCCTTTTGATCTATTT--CTCACCACACTCA-T-AGTGTAACGTCTtcactatttttcttttggaaCATCTGCCTGATTTCATATAGATATTATGC-AACTTTGGGGAAATGATATAACTCCCACCCCGTCTGCTAGA---TCCCTCAAT-----TATAAACTGAAGG--CCCTGGGCAAGCAATT------------------
q eriEur1.scaffold_377961                                    -9999999999999999995999699999999-------------------999999999999999999999-------------------------------------------99999999999999999-------------------9999999999997999999999999-9999999999999999--9999999999999-9-99999999999999999999999999999999999999999999999999999999999799-98999999999999999999999999999999999999997---999999999-----9999999999999--9986786799999999------------------
i eriEur1.scaffold_377961          I 1 C 0
s loxAfr3.scaffold_36                 512408 264 -  24123610 aaatatttCTTGTAAAGTGACCAATACTCCAA-------------------TGTTATTGTTAGAAAAATAAT-------------------------------------------CGAAAGAATTATGTATC-------------------TGTTGGGCTGGACATGCCCATT----GTCTCTCAGTCTGTTT--CTCACCCCACCCA-TAGGCATAATCTCTCCACTAGTTTTGTTTTGTAATATTTGCCTGAATTcatttacaaattatgt-aattctgggaaagtcatataactccctccccatctcgtggg---tccctcatt-----tataaaatgaagg--ccctggatgggcaatt------------------
q loxAfr3.scaffold_36                                        99999999999999999999999999999999-------------------999999999999999999999-------------------------------------------99999999999999999-------------------9999999999999999999999----9999999999999999--9999999999999-9999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999---999999999-----9999999999999--9999999999999999------------------
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737        9362 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=54154.000000
s hg19.chrY                          7653381 21 +  59373566 CTTAAAGGAGCTTTCAACTTT
s rheMac2.chr2                     158761924 18 + 189746636 ---aaaggcgctttcaacttt
q rheMac2.chr2                                              ---999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034717 18 - 202140232 ---aaaggcactttcaacttt
q ponAbe2.chr3                                              ---999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        506914 21 +  23952694 CTTAAAGGAGCTTTCAACTTT
q panTro2.chrY                                              000000000000000000000
i panTro2.chrY                     C 0 C 0
s otoGar1.scaffold_99909.1-31737       10886 21 -     31737 ctcacagcaaccccaaactct
q otoGar1.scaffold_99909.1-31737                            999999999999998999999
i otoGar1.scaffold_99909.1-31737   I 1524 n 1524
s rn4.chr9                         107346196 15 - 113440463 ------GGAATTTCCAACTCT
q rn4.chr9                                                  ------999999999999999
i rn4.chr9                         C 0 I 1
s cavPor3.scaffold_0                 8222729 15 -  88675666 ------GGAGCTTACAACTTT
q cavPor3.scaffold_0                                        ------999999999999999
i cavPor3.scaffold_0               C 0 I 1
s oryCun2.chr14                      2469734 14 + 163896628 -------AAGCTTCCAAGCTC
q oryCun2.chr14                                             -------99999999999999
i oryCun2.chr14                    C 0 I 1
s bosTau4.chr1                     156983115 20 + 161106243 CC-AAAGGAGCATCCAACTTT
q bosTau4.chr1                                              99-999999999999999999
i bosTau4.chr1                     C 0 C 0
s canFam2.chr23                     25991857 21 -  55389570 CTGATAGAAGCTTCCAACTTT
q canFam2.chr23                                             999999999999999999999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22211280 21 -  87365405 cttaaaggaactttcaacttt
q equCab2.chr16                                             999999999999999999999
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961              13565 21 +     88154 CTGAAAGGAGCTTCCAACTTT
q eriEur1.scaffold_377961                                   999999999999999999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 512672 20 -  24123610 ttgaaagaaatctcccattt-
q loxAfr3.scaffold_36                                       99999999999999999999-
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=230531.000000
s hg19.chrY                          7653402 164 +  59373566 AAAATGCAATAATTTTAATGTTTCAATTTGGAGGCTAAGGTAC-CAGT---TTCTAACTAAAAAG-TAACATTGGATAATATAACAAATGTTTT-CAAT-GTTAACTGAAAGAGTTC---CCCAAAATCAG---------------------------AGCTAAAGTTGGAAT-AAGGAACACC------------------------------------------------CACATGGCATGTGTAGGT---------------------
s rheMac2.chr2                     158761942 164 + 189746636 aaaatgcaataattttaGTATTTCAATTTGGAGGCTAAGGTAC-CAGT---TTCTAACTAAAAAG-TAACATTGGATAATATAACAAATGTTTT-CAAT-GTTAACTGAAAGAGTTC---CCCCAAACCAG---------------------------AGCTAGAATTGGAAT-ACGGAACACC------------------------------------------------CACATGGCATGTGTGGGT---------------------
q rheMac2.chr2                                               9999999999999999999999999999999999999999999-9999---99999999999999-9999999999999999999999999999-9999-99999999999999999---99999999999---------------------------999999999999999-9999999999------------------------------------------------999999999999999999---------------------
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034735 164 - 202140232 aaaatgcaataattttatcattTCAATTTGGAGGCTGAGGTAC-CAGT---TTCTAACTAAAAAG-TAATATTGGATAATATAACAATTGTTTT-CAAT-GTTAACTGAAAGAGTTC---CCCCAAACCAG---------------------------AGCTAGAATTGGAAT-AAGGAACACC------------------------------------------------CACATGGCATGTGTGGGT---------------------
q ponAbe2.chr3                                               9999999999999999999999999999999999999999999-9999---99999999999999-9999999999999999999999999999-9999-99999999999999999---99999999999---------------------------999999999999999-9999999999------------------------------------------------999999999999999999---------------------
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        506935 164 +  23952694 AAAATGCAATAATTTTAATGTTTCAATTTGGAGGCTAAGGTAC-CAGT---TTCTAACTAAAAAG-TAACATTGGATAATATAACAAATGTTTT-CAAT-GTTAACTGAAAGAGTTC---CCCAAAATCAG---------------------------AGCTAAAGTTGGAAT-AAGGAACACC------------------------------------------------CACATGGCATGTGTAAGT---------------------
q panTro2.chrY                                               0000000000000000000000000000000000000000000-0000---00000000000000-0000000000000000000000000000-0000-00000000000000000---00000000000---------------------------000000000000000-0000000000------------------------------------------------000000000000000000---------------------
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346212 149 - 113440463 ATGAAGCGATTTT---ATTATTTCAACTTGAAGACTTAGGAATCTATT---TTCTAACTAAAAAG-TAGCAAAGTATAGTAGGGTATATGTTT--CAAA-ATGAATGGAAAGACCTT---GATAAAGACAG---------------------------AGCTGACACAGGAAT-AAGGAATGGC------------------------------------------------GCTACG---------------------------------
q rn4.chr9                                                   9999999999999---99999999999999999999999999999999---99999999999999-999999999999999999999999999--9999-99999999999999999---99999999999---------------------------999999999999999-9999999999------------------------------------------------999999---------------------------------
i rn4.chr9                         I 1 C 0
s cavPor3.scaffold_0                 8222745 239 -  88675666 AAAATGCAATAAT----TTATTTTCACTTGAAGACTAAGCAAT-TGGC---TTCTGTCTAAAAAA-TGAAACTGAATAATACAATAAATGTTTTCCATG-TCAGCTAGAAGAATTTTCCAAATCAGAACAGAAACAAGGAACAATTACACATGTGTGCAGTGGATAGAAAAATGAAAGAATAGCATATTCAGGGCCAgggacatagctcagccgcacagctcctgcccagcaggcacgaggt-catgagt---------------------
q cavPor3.scaffold_0                                         9999999999999----99999999999999999999999999-9999---99999999999999-999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999---------------------
i cavPor3.scaffold_0               I 1 C 0
s oryCun2.chr14                      2469749 137 + 163896628 A-AATGCAATTGTTTCACTATTCCAAAGTGGAGACTGATGTGTCTGTCCATTTCTAACAAAAAAG-TGACCCTG---AGTACAACAGATATTCT-CAAT-GCGAATGGGAGAGC------AATTACACCTG---------------------------------TGGGTGGGT-GGGGAGCGGC---------------------------------------------------------------------------------------
q oryCun2.chr14                                              9-999999999999999999999999999999999999999999999999999999999999999-99999999---99999999999999999-9999-99999999999999------99999999999---------------------------------999999999-9999999999---------------------------------------------------------------------------------------
i oryCun2.chr14                    I 1 C 0
s bosTau4.chr1                     156983135 155 + 161106243 CAAATGCGACGATGTTAATATTTCGATCTGGAGACTAAGGTAT-AAGT---TTCTAACTAGAAAG-GGACATCGGAGAATAGAATAAATATTTC-CAGC-GTGAACTGAAAGGGTCC---TCCC-AACCAG---------------------------AGTCAAAAG-------AAGCAACAAT------------------------------------------------CACATGGCA--GGCAGGC---------------------
q bosTau4.chr1                                               9999999999999999999999999999999999999999999-9999---99999999999999-9999999999999999999999999999-9999-99999999999999999---9999-999999---------------------------999999999-------9999999999------------------------------------------------999999999--9999999---------------------
i bosTau4.chr1                     C 0 C 0
s canFam2.chr23                     25991878 154 -  55389570 AAAATGCAATTATCTCATTATTTCAATCTGAAGAGTAACAT-C-CAGT---TTCTAACTAAAAAA-TGACATTGGATAATATGATAAATGTTCG-CAAA-GTGAACTCAAAGAATTC---CCCTAAACTAG---------------------------AGCCATAATGGGAAT-AAGGAAAAAC------------------------------------------------CGCACG-----TGT-------------------------
q canFam2.chr23                                              99999999999999999999999999999999999999999-9-9999---99999999999999-9999999999999999999999999999-9999-99999999999999999---99999999999---------------------------999999999999999-9999999999------------------------------------------------999990-----999-------------------------
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22211301 160 -  87365405 aaaacgcaacaatttaatggttTCATTTTGGAGATTACGGTAC-CAAT---TTCTAACTAAAAAAGTGACATTGGATAATATAATAAATGTTTT-TGAC-ATAAACTGAAAGAGTTT---CCCCAAACCAG---------------------------AGGCAAAATGGGAAC-AGGGAACAAC------------------------------------------------CACATG-----TGCTGAT---------------------
q equCab2.chr16                                              9999999999999999999999999999999999999999999-9999---9999999999999999999999999999999999999999999-9999-99999999999999999---99999999999---------------------------999999999999999-9999999999------------------------------------------------999999-----9999999---------------------
i equCab2.chr16                    C 0 C 0
s eriEur1.scaffold_377961              13586 128 +     88154 AAAACACAGTGATTTTACTATT-----------------------------------CCACACAG-AGACACTGGGTAATAC-ATAAAAGTTTG-CAAATGGAAATggggggggTTC---CCCCAACCCAG---------------------------AGCCAAAATGGTATT-AACCaccacc------------------------------------------------cgtgtg-----tgtgtgt---------------------
q eriEur1.scaffold_377961                                    9999999999999999899697-----------------------------------99999999-9969993982532111-21244223451-1232123251222253212423---99935634113---------------------------228299622312322-3124333346------------------------------------------------322322-----3333333---------------------
i eriEur1.scaffold_377961          C 0 I 1444
s loxAfr3.scaffold_36                 512692 180 -  24123610 aaaatgcaataattttattattTCAATTTGGAGACAAAAGCAC-CAGC---TTCTGAGGAAGCAGATGATGTCATATTATCC-ATAAATGTTTT-TAAT-GGGAACTGAAAGAGTTT---CCCCAAACCAG---------------------------AGCTGAAGTAGAAAT-AAGGAACCAC------------------------------------------------CATACG-----TGCAGGTGGGTGGGGGAGACAGACAGAT
q loxAfr3.scaffold_36                                        9999999999999999999999999999999999999999999-9999---9999999999999999999999999999999-99999999999-9999-99999999999999999---99999999999---------------------------999999999999999-9999999999------------------------------------------------999999-----9999999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=-20325.000000
s hg19.chrY                          7653566 12 +  59373566 TG----------------------------------CTGGAGCAAG-
s rheMac2.chr2                     158762106 12 + 189746636 GG----------------------------------CGGCAGGGAG-
q rheMac2.chr2                                              99----------------------------------9999999999-
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034899 12 - 202140232 GG----------------------------------CTGGAGTGAG-
q ponAbe2.chr3                                              99----------------------------------9999999999-
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507099 12 +  23952694 TG----------------------------------CTGGAGCAAG-
q panTro2.chrY                                              00----------------------------------0000000000-
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346361 10 - 113440463 ------------------------------------CTGTGGGACA-
q rn4.chr9                                                  ------------------------------------9999999999-
i rn4.chr9                         C 0 I 5
s cavPor3.scaffold_0                 8222984 46 -  88675666 tgaagtcccagtaccAAGAAAAAGAGAACagctcatctgtggaaca-
q cavPor3.scaffold_0                                        9999999999999999999999999999999999999999999999-
i cavPor3.scaffold_0               C 0 I 63
s oryCun2.chr14                      2469886 10 + 163896628 ------------------------------------CAGGCGGACA-
q oryCun2.chr14                                             ------------------------------------9999999999-
i oryCun2.chr14                    C 0 I 4
s bosTau4.chr1                     156983290  9 + 161106243 -------------------------------------TGGTGGAGA-
q bosTau4.chr1                                              -------------------------------------999999999-
i bosTau4.chr1                     C 0 C 0
s canFam2.chr23                     25992032  6 -  55389570 ----------------------------------------GGGAGA-
q canFam2.chr23                                             ----------------------------------------999999-
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22211461  9 -  87365405 -------------------------------------GGGTGGAGA-
q equCab2.chr16                                             -------------------------------------999999999-
i equCab2.chr16                    C 0 C 0
s loxAfr3.scaffold_36                 512872 10 -  24123610 -------------------------------------GGGTGGAGAG
q loxAfr3.scaffold_36                                       -------------------------------------9999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=-8795.000000
s hg19.chrY                          7653578 148 +  59373566 GAACAAA----AGGCTAGAAGA-----TATCCGCTTCCAGTG-GGCAGGAGAAACACCACTGCTG--CCTGAGGG--TTCCAGCCTTCTGCCTG--CCC-AGGCACTA---GGGA---TTCT---G---GGCTAAGTGTTCC---CCAAGGGAGTGTGG----------AGAGCTGTTC-------TGG-GGAGTTCT
s rheMac2.chr2                     158762118 148 + 189746636 GAAGGAG----AGGCTGGAAGA-----TACCCGCTGCCAGTG-GGCGGGAGAAACATCACTGCTG--TCCGAGGG--TTCCGGCCTTCTGCCTG--CCC-AGGCACTA---GGGA---TTCT---G---GGTTAACTGTCCT---CCGGGGCAGTGTGG----------GGAGCTTTTC-------AGA-GGAGTTCT
q rheMac2.chr2                                               9999999----99999999999-----999999999999999-9999999999999999999999--99999999--99999999999999999--999-99999999---9999---9999---9---9999999999999---99999999999999----------9999999999-------999-99999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71034911 148 - 202140232 GAAGGAG----AGGCTGGAAGA-----TACCCGCTGCCAGTG-GGCGGGAGAAACATCACTGCTG--CCCGAGGG--TTCCAGCCTTCTTCCTG--CCC-AGGCACTA---GGGA---TTCT---G---GGCTAACTGTCCT---CTGGGGGAGTGTGG----------GGAGCTTTTC-------AGA-GGAGTTCT
q ponAbe2.chr3                                               9999999----99999999999-----999999999999999-9999999999999999999999--99999909--99999999999999999--999-99999999---9999---9909---9---9999999999999---99999999999999----------9999999999-------999-99999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507111 148 +  23952694 GAACAAG----AGGCTAGAAGA-----TACCCGCTTCCAGTG-GGCAGGAGAAACACCACTGCTG--CCTGAGGG--TTCCAGCCTTCTGCCTG--CCC-AGGCACTA---GGGA---TTCT---G---GGCTAAGTGTTCC---CCAAGGGAGTGTGG----------AGAGCTGTTC-------TGG-GGAGTTCT
q panTro2.chrY                                               0000000----00000000000-----000000000000000-0000000000000000000000--00000000--00000000000000000--000-00000000---0000---0000---0---0000000000000---00000000000000----------0000000000-------000-00000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346376 122 - 113440463 GAGGCAG-----GACAGGGAGC-----CCACTGCTCTT------------------------------CCTCTGG--TCACG--TCTCGCCCATGACCT--GGTTCTG---TGGAGACTTCT---GAAGCTCCCACTGTCAC---T--TAGGAGCACAG-----------GAGACTCCC-------AGG-GAGTCCCC
q rn4.chr9                                                   9999999-----9999999999-----99999999999------------------------------9999999--99999--999999999999999--9999999---99999999999---99999999999999999---9--99999999999-----------999999999-------999-99999999
i rn4.chr9                         I 5 C 0
s cavPor3.scaffold_0                 8223093 141 -  88675666 GAGGCAGACAGAGGCAGGATGA-----TAGCTGGTGTTAGTA-GGGGCTAGA-----AGGTGCTG--ATCTAAGG--TCTGA--TTTTTGCCAT--CCC--AGCACTA---GAGAGGATTCA---G------CAACCATCAC---G--GGGCATCATGG-----------AAGCTTTCT-------AGG-AGACTTCT
q cavPor3.scaffold_0                                         9999999999999999999999-----999999999999999-999999999-----99999999--99999999--99999--9999999999--999--9999999---99999999999---9------9999999999---9--99999999999-----------999999999-------999-99999999
i cavPor3.scaffold_0               I 63 C 0
s oryCun2.chr14                      2469900 117 + 163896628 GTGCCAG-------CAGG---------CAGCTACACCT-------------------GGGTGCTG---ACAAGGG--CCCCG--CTCCCACCTG--CCC--------------------TCT---GCTGCTCCGGCTGTCCC---C--AGGCAAGGGAGCGGGGTGCAGAGAGCCTTCC-------AGG--GATTTCT
q oryCun2.chr14                                              9999999-------9999---------99999999999-------------------99999999---9999999--99999--9999999999--999--------------------999---99999999999999999---9--9999999999999999999999999999999-------999--9999999
i oryCun2.chr14                    I 4 C 0
s bosTau4.chr1                     156983299 141 + 161106243 GACGGAA----AGGCGGGCGAAAG---AACCTGTCGCTGGTGTGGCCGGGCGAGACTCCCCGCTG-----AAgggcttccccact------------------ggctg-----ct---ggctaagg---gtcc-acgggcccatgc--aggggacacgg-----------gttccatccctgctctggg-aagatcc-
q bosTau4.chr1                                               9999999----9999999999999---99999999999999999999999999999999999999-----999999999999999------------------99999-----99---99999999---9999-999999999999--99999999999-----------9999999999999999999-9999999-
i bosTau4.chr1                     C 0 I 252
s canFam2.chr23                     25992038 147 -  55389570 GATGGAT----AG--AGGCAAG-----GACCTGCTGCCACTGTGGCAGATTAAAAGCCACTGTTGTTTTTGAGGG--TCCCAGTCTTCTACCCA--TCTCAGGCACTA---GACT---GTCC---G---CTCCGACTGTCCT---C--AGGGGGTTGGG-----------AAGCTTTCC-------GGG-GGCATTCT
q canFam2.chr23                                              9999999----99--9999999-----990999999999999999999999999999999999999999999999--99999999999999999--999999999999---0999---9999---9---9999999999999---9--99999999999-----------999999999-------999-99999999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22211470 140 -  87365405 GATGGAA----AGAAAGACAGGAGCATAACCTGTTGCTGGGAAGGCAGGATAAACACCACTGTGG--TCCGAGGG--TCCCAGCC-----------TAGAAGGGATTG------T---GCCT---G---GTCCGACTGTCCC---C--CGGGGCTGTGG-----------GAGCCTTCC-------AGG-GGAGTTCT
q equCab2.chr16                                              9999999----999999999999999999999999999999999999999999999999999999--99999999--99999999-----------999999999999------9---9999---9---9999999999999---9--99999999999-----------999999999-------999-99999999
i equCab2.chr16                    C 0 C 0
s loxAfr3.scaffold_36                 512882 146 -  24123610 ATGCAAG----AGACAAGAAAAT----AATCTGTGGCCAATACGTCAGCATGAAAATCCCCACCG--TCTGAGCG--TCCCAGCCTTCCGCCTA--CCT-GGGTGCTGGTGGGGA---TTCC---G--------AGCATCTC---C--TGGGACTGAGG-----------GGGTATTCC-------AGGGGGAGTTCT
q loxAfr3.scaffold_36                                        9999999----999999999999----99999999999999999999999999999999999999--99999999--99999999999999999--999-999999999999999---9999---9--------99999999---9--99999999999-----------999999999-------999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=46096.000000
s hg19.chrY                          7653726 51 +  59373566 AGGG-------AAGAGATGCCTGTCCAGTGGTGG-GAG--AGAAAA--CTAATGTTTTA------ACTA
s rheMac2.chr2                     158762266 51 + 189746636 AGGG-------AAGAGAGGCCTGCCCAGTGGTGG-GAG--AGAAAA--CAAGTGTTTCA------AGTA
q rheMac2.chr2                                              9999-------99999999999999999999999-999--999999--99999999999------9999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035059 51 - 202140232 AGGG-------AAGGGATGCCTGCCCAGTGGTGG-GAG--AGAAAA--CGAATGTTTTA------AGTA
q ponAbe2.chr3                                              9999-------99999999999999999999999-999--999999--99999999999------9999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507259 51 +  23952694 AGGG-------AAGAGATGCCTGTCCAGTGGTGG-GAG--AGAAAA--CTAATGTTTTA------ACTA
q panTro2.chrY                                              0000-------00000000000000000000000-000--000000--00000000000------0000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346498 48 - 113440463 AGCG-ATATGGAAGAGATAAG-----AGCAGAAC-GGG--AGAAAA--GCGGTATCTGA----------
q rn4.chr9                                                  9999-9999999999999999-----99999999-999--999999--99999999999----------
i rn4.chr9                         C 0 C 0
s cavPor3.scaffold_0                 8223234 58 -  88675666 AGGGAATGAGAAAGAGATGCGCA---AGCAGTGTAGGA--AGGAAA--GGGGTATCTCA----CGAATA
q cavPor3.scaffold_0                                        99999999999999999999999---999999999999--999999--99999999999----999999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2470017 62 + 163896628 GTGG-AACAAGAAGAGATATCCG---GGCAGGGT-GGAACAGAAAA--GGGGTGTTTAAAAAACAAATG
q oryCun2.chr14                                             9999-999999999999999999---99999999-99999999999--999999999999999999999
i oryCun2.chr14                    C 0 C 0
s equCab2.chr16                     22211610 54 -  87365405 AGGG-------AAGATCAGCCTGCACGGTGGTGG-GAG--AGAACA--GGGGCATTTTA---GGAAATA
q equCab2.chr16                                             9999-------99999999999999999999999-999--999999--99999999999---9999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992185 54 -  55389570 AGGG-------AAGAAATGCCTGCACAGTCATGG-GAG--AGAAAG--GGGATATTTTA---AGAAGCA
q canFam2.chr23                                             9999-------99999999999999999999999-999--999999--99999999999---9999999
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 513028 56 -  24123610 GGGG-------GCGAGATGCTGGCACATTGGTGA-GAG--AGTAAATGGGGGTGTGTTA---AGAAGTA
q loxAfr3.scaffold_36                                       9999-------99999999999999999999999-999--9999999999999999999---9999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e bosTau4.chr1                     156983440 252 + 161106243 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               17117 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=49333.000000
s hg19.chrY                          7653777 66 +  59373566 TTGCTGAGGATA--ATGGGTCCCCTTCATCCTAGAG-------GAGAGCTACAAGGAA-AA-GGCATGAGTTATTCT
s rheMac2.chr2                     158762317 66 + 189746636 TCACTGAGGATG--ATGGGTCTCCTTCATCCTAGAG-------GAGAGCTACAAGAAA-AC-GGCGTGGGTTATTCT
q rheMac2.chr2                                              999999999999--9999999999999999999999-------999999999999999-99-999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035110 66 - 202140232 TCACTGAGGATG--ATGGGTCTCCTTCACCCTAGAG-------GAGAGCTACAAGGAA-AC-GGCATGAGTTATTCT
q ponAbe2.chr3                                              999999999999--9999999999999999999999-------999999999999999-99-999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507310 65 +  23952694 TCGCT-AGGATA--ATGGGTCCCCTTCATCCTAGAG-------GAGAGCTACAAGGAA-AA-GGCATGAGTTATTCT
q panTro2.chrY                                              00000-000000--0000000000000000000000-------000000000000000-00-000000000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346546 45 - 113440463 -----GCAGGAC--ATGGAG------------GACA-------GACCCCACACACGTG-AG-GTTACCA----TTTT
q rn4.chr9                                                  -----9999999--999999------------9999-------999999999999999-99-9999999----9999
i rn4.chr9                         C 0 C 0
s cavPor3.scaffold_0                 8223292 65 -  88675666 TCACTGGGGGAC--ATGGGGCCCCTTCACCTTGAAG-------GAGAATAATCAGGAA-AG-GGTGCAAGTT-TTCT
q cavPor3.scaffold_0                                        999999999999--9999999999999999999999-------999999999999999-99-9999999999-9999
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2470079 69 + 163896628 CTGGGGAGGGTCAGATGGGTCCCTCCCATCCCAGAG-------GAGAGCTCCAAGGAACAT-GGTGTGGGTTATTCT
q oryCun2.chr14                                             999999999999999999999999999999999999-------999999999999999999-999999999999999
i oryCun2.chr14                    C 0 C 0
s equCab2.chr16                     22211664 46 -  87365405 TCTGTGGCAATG--ACAG---------------------------GAGCTACAAGGAAAAT-GGTATGAGTG-ATCT
q equCab2.chr16                                             999999999999--9999---------------------------9999999999999999-9999999999-9999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992239 66 -  55389570 TCCCTAGGGACG--GTGGGTTCCTCTCTTCCTAGCA-------GAGAGCTAGGAGGACAAC-AGTGTGAGTT-ATCT
q canFam2.chr23                                             999999999999--9999999999999999999999-------999999999999999999-9999999999-9999
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 513084 66 -  24123610 TTGCAGGGGAAG--ATGGGTCCCCTTCATCCTAGAG-------GAGAGCTATAAGGAA-AACGGCCTGAGTTTTTT-
q loxAfr3.scaffold_36                                       999999999999--9999999999999999999999-------999999999999999-99999999999999999-
i loxAfr3.scaffold_36              C 0 C 0
s proCap1.scaffold_51344               18457 70 -     18560 CTGCTAGGCCTG--ACAGGAATCA--CATCGTGGAGTCCCTGATATAGC-ATGAGGGA-AA-GGCATGTGCAAATCT
q proCap1.scaffold_51344                                    999999999999--9999999999--99999899999999899999999-41384899-99-999988899998969
i proCap1.scaffold_51344           I 1340 n 1340
e mm9.chr17                         50248744 1211 +  95272651 I
e bosTau4.chr1                     156983440 252 + 161106243 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=68416.000000
s hg19.chrY                          7653843 64 +  59373566 GAAGT--------------TACTTTGGCTTCCTGGCCTTT--------------GACCAGGAC-------------------CTGACTCTAAGGC-TGAACCACATGAACTG
s rheMac2.chr2                     158762383 64 + 189746636 GAAGT--------------TACTTTGGCTGCCTGGCCTTT--------------GACCAGGAC-------------------CTGACTCTAAGGC-TGAACTACATGAATCG
q rheMac2.chr2                                              99999--------------999999999999999999999--------------999999999-------------------9999999999999-9999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035176 64 - 202140232 GAAGT--------------TACTTTGGCTTCCTGGCCTTT--------------GACCAGGAC-------------------CTGACTCTAAGGC-TGAACCACATGAACCG
q ponAbe2.chr3                                              99999--------------999999999999999999999--------------999999999-------------------9999999999999-9999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507375 64 +  23952694 GAAGT--------------TACTTTGGCTTCCTGGCCTTT--------------GACCAGGAC-------------------CTGACTCTAAGGC-TGAACCACATGAACTG
q panTro2.chrY                                              00000--------------000000000000000000000--------------000000000-------------------0000000000000-0000000000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346591 46 - 113440463 GAA----------------TCCTCTGAT---CTGGACT--------------------------------------------CCCGCTCTGAAACAGGA-CCACATAAGC--
q rn4.chr9                                                  999----------------999999999---9999999--------------------------------------------99999999999999999-9999999999--
i rn4.chr9                         C 0 C 0
s cavPor3.scaffold_0                 8223357 61 -  88675666 GAAGT--------------TACTTTGGTTTCCTAGACTTT--------------CACCAGGAC-------------------CCCACTCTGGGAT-TAA-CCACATAAGC--
q cavPor3.scaffold_0                                        99999--------------999999999999999999999--------------999999999-------------------9999999999999-999-9999999999--
i cavPor3.scaffold_0               C 0 C 0
s oryCun2.chr14                      2470148 99 + 163896628 GAAGTCACCAGGCCAGACACACACTGTGTCCCTACACTGCCTTTCTCCTCCCGACACCAGGCCCTGTTCAATCGCAGGGCGGCTAGCTCTCAGGC-TGGC------------
q oryCun2.chr14                                             99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999------------
i oryCun2.chr14                    C 0 I 377
s equCab2.chr16                     22211710 62 -  87365405 GAAGT--------------TACGCAGGCTTCCTGGATTTT--------------TACTAGGAC-------------------TCTACTCCAGGGC-TGAACCACCTACGC--
q equCab2.chr16                                             99999--------------999999999999999999999--------------999999999-------------------9999999999999-99999999999999--
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992305 64 -  55389570 GCAGT--------------TACTCTGACGTCCTAGGATTT--------------TATTACGAT-------------------TCCACTCCAGGAC-TGAACTATGTACACCA
q canFam2.chr23                                             99999--------------999909999999990999999--------------999999999-------------------9999999999999-9999999999999999
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 513150 64 -  24123610 GAAAT--------------TACTTTGGCTTCCTGGGCTTT--------------TACTTGGAC-------------------CCCACTCCAGGAA-TGAACCATGTAAGCCA
q loxAfr3.scaffold_36                                       99999--------------999999999999999999999--------------999999999-------------------9999999999999-9999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e bosTau4.chr1                     156983440 252 + 161106243 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=48164.000000
s hg19.chrY                          7653907 41 +  59373566 TCTCATCATAAGTTAAAATTTCTA----ATTAT---AA--CTTCATAGTG
s rheMac2.chr2                     158762447 41 + 189746636 TCTCATCATAAGTTAAAATTTCTA----ATTAT---AA--CTTCATAGTC
q rheMac2.chr2                                              999999999999999999999999----99999---99--9999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035240 41 - 202140232 TCTCATCATAAGTTAAAATTTCTA----ATTAT---AA--CTTCATAGTC
q ponAbe2.chr3                                              999999999999999999999999----99999---99--9999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507439 41 +  23952694 TCTCATCATAAGTTAAAATTTCTA----ATTAT---AA--CTTCATAGTG
q panTro2.chrY                                              000000000000000000000000----00000---00--0000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8223418 40 -  88675666 ---CACTGCATA--ACAATTTATTTACAAATGT---GA--TTTCATACGC
q cavPor3.scaffold_0                                        ---999999999--9999999999999999999---99--9999999999
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107346637 40 - 113440463 ---CATTGTGAGGTGCAACTTTTGTGC-ACTGT---CA---TTCACATGC
q rn4.chr9                                                  ---999999999999999999999999-99999---99---999999999
i rn4.chr9                         C 0 C 0
s equCab2.chr16                     22211772 43 -  87365405 ---CATCGTAAGTTAAAACTGTTA----ATTACTAAAAGTTTTCATATCC
q equCab2.chr16                                             ---999999999999999999999----9999999999999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992369 42 -  55389570 -CTCATTGTAAGTTGAAATTTCTA----ATTAT---AAGCCTTCATGTTC
q canFam2.chr23                                             -99999999999999999999999----99999---99999999999999
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 513214 41 -  24123610 TGTCACCAGAAGTTAAAATTCCTA----ATTAT---AA--CTTCATATTT
q loxAfr3.scaffold_36                                       999999999999999999999999----99999---99--9999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e bosTau4.chr1                     156983440 252 + 161106243 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=63631.000000
s hg19.chrY                          7653948 86 +  59373566 TGAAGATGAGGTACACTGGTGAGGCTGTCTTATCCACCTTTACCCTTCAGAAAGAGAAAACACCAGCCTATTCAGAGTGGGCAGAC----
s rheMac2.chr2                     158762488 86 + 189746636 TGAAGACAAGGGACACTGGTGAGGCTGTCTTAGCCACCGTTACCCTCCAAAAAGAGAAAATGCCAGCCTACTCAGAGTGGGCTGCA----
q rheMac2.chr2                                              99999999999999999999999999999999999999999999999999999999999999999999999999999999999999----
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035281 86 - 202140232 TGAAGATAAGGGACACTGGTATGGCTGTCTTAGCCACCGTTACCTTCCAAAAAGAGAAAATGCCAGCCTACTCAGAGTGGGCTGCT----
q ponAbe2.chr3                                              99999999999999999999999999999999999999999999999999999999999999999999999999999999999999----
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507480 86 +  23952694 TGAAGATGAGGGACACGGGTGAGGCTGTCTTATCCACCTTTACCCTTCAGAAAGAGAAAACACCAGCCTATTCAGAGTGGGCAGTC----
q panTro2.chrY                                              00000000000000000000000000000000000000000000000000000000000000000000000000000000000000----
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8223458 85 -  88675666 TGAGGATAAGGGCCACTGATGATACTGTCTTTGCCACTGCTGCTCTCTAGTGAAAGAGAGTATGACCCTGCTTGTAGTGGGCAG-C----
q cavPor3.scaffold_0                                        999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9----
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107346677 80 - 113440463 TGAGGACAA--GCAACTGATAAGGC--TCTCAACCATGGCTTCTCTCCAGCAAGAGGAAATG-GTGTCGGCCCAGGGAGGGCAG-C----
q rn4.chr9                                                  999999999--99999999999999--99999999999999999999999999999999999-999999999999999999999-9----
i rn4.chr9                         C 0 C 0
s bosTau4.chr1                     156983692 66 + 161106243 TGAAGCAGAGAG--CCCGATTGGACTGTCTTGGCCAGCGTGACTCTCCAGGCTAGGGCTCGGCACCCA----------------------
q bosTau4.chr1                                              999999999999--999999999999999999999999999999999999999999999999999999----------------------
i bosTau4.chr1                     I 252 C 0
s canFam2.chr23                     25992411 82 -  55389570 TTAAGATGAGAGACACTGATGATGCTGTCTTGGTCAATGTT--TCTCCAGTCTGAGGCAATGCCAC--TGTTACGGCCCAGTATCT----
q canFam2.chr23                                             99999999999999999999999999999999999999999--99999999999999999999999--999999999999999999----
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22211815 68 -  87365405 TGAAGATGAGGGACACTGATGAGCGTGTCTTGGACAATGTTACCCTCCAGTCTGAGGAAATGCCAGCA----------------------
q equCab2.chr16                                             99999999999999999999999999999999999999999999999999999999999999999999----------------------
i equCab2.chr16                    C 0 I 23
s loxAfr3.scaffold_36                 513255 57 -  24123610 ------------------------TTTTTTATTCTGTCGTGACCCTTCAATGTGAGAAAATGGCAGCC---------TGGGTAGCCACAC
q loxAfr3.scaffold_36                                       ------------------------99999999999999999999999999999999999999999999---------9999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e echTel1.scaffold_321361             117945 6038 +    198078 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=-4062.000000
s hg19.chrY                          7654034 26 +  59373566 GCTGTGAGGGCT----------------GATCACACTTTTT----T
s rheMac2.chr2                     158762574 26 + 189746636 GCCGCGAGGGCT----------------GACCACACCTTTC----T
q rheMac2.chr2                                              999999999999----------------9999999999999----9
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035367 25 - 202140232 GCCACGAGGGCT----------------GATCACAC-TTTT----T
q ponAbe2.chr3                                              999999999999----------------99999999-9999----9
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507566 26 +  23952694 GCTTTGAGGGCT----------------GATCACACTTTTT----T
q panTro2.chrY                                              000000000000----------------0000000000000----0
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8223543 26 -  88675666 ACCATTAGTGCT----------------GATCACTCATTCC----T
q cavPor3.scaffold_0                                        999999999999----------------9999999999999----9
i cavPor3.scaffold_0               C 0 C 0
s rn4.chr9                         107346757 24 - 113440463 ACCCGGAGGAGG----------------GGCCAACC--TCC----C
q rn4.chr9                                                  999999999999----------------99999999--999----9
i rn4.chr9                         C 0 C 0
s bosTau4.chr1                     156983758 20 + 161106243 -CTCGAAGG---------------------TCACACTTTCC----T
q bosTau4.chr1                                              -99999999---------------------99999999999----9
i bosTau4.chr1                     C 0 C 0
s canFam2.chr23                     25992493 25 -  55389570 GCCTGAAG---------------------ATCACACTCTCCTCTTT
q canFam2.chr23                                             99999999---------------------99999999999999909
i canFam2.chr23                    C 0 C 0
s loxAfr3.scaffold_36                 513312 25 -  24123610 -----------------CTCCATCTGAAGATCACACTTGTC----T
q loxAfr3.scaffold_36                                       -----------------999999999999999999999999----9
i loxAfr3.scaffold_36              C 0 C 0
s echTel1.scaffold_321361             123983 42 +    198078 GCTGTGGGAGGCCAAACCTCTATTTGAAGATCTCAGGCCCC----A
q echTel1.scaffold_321361                                   99999999999999999999999999999999999999999----9
i echTel1.scaffold_321361          I 6038 N 0
s equCab2.chr16                     22211906 14 -  87365405 ----------------------------AATCACACTTTTC----T
q equCab2.chr16                                             ----------------------------9999999999999----9
i equCab2.chr16                    I 23 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=57045.000000
s hg19.chrY                          7654060 49 +  59373566 CTCCACTTTCTACTCTGTCATGTTC------TGTACTCTTA-ATTTACAGTGACCA
s rheMac2.chr2                     158762600 47 + 189746636 CTCCACTTTCTAATCCGTCAGGTTC------TATAGTCT---ATCTATAGTGATCC
q rheMac2.chr2                                              9999999999999999999999999------99999999---99999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035392 49 - 202140232 CTCCACTTTCTAATCTGTCAGGTTC------TATAGTTTTT-ATCTACAGTGATCA
q ponAbe2.chr3                                              9999999999999999999999999------9999999999-99999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507592 49 +  23952694 CTCCACTTTCTACTCTGTCATGTTC------TGTACTCTTA-ATTTACAGTGACTA
q panTro2.chrY                                              0000000000000000000000000------0000000000-00000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8223569 48 -  88675666 GTCCACTTCTGAACCGGCTACACCC------CACACTATGT-ATC-CCAGGGATTA
q cavPor3.scaffold_0                                        9999999999999999999999999------9999999999-999-9999999999
i cavPor3.scaffold_0               C 0 I 3
s rn4.chr9                         107346781 48 - 113440463 TTCCTCTTCCCAGCTTGTCTCTCTCTGTAATCACACCG--------ACAGTGATCA
q rn4.chr9                                                  99999999999999999999999999999999999999--------9999999999
i rn4.chr9                         C 0 I 3
s bosTau4.chr1                     156983778 45 + 161106243 CTCCACTTTCTCAACTGTCCTGTCT------CACAGACTTC-ACCAACAGTG----
q bosTau4.chr1                                              9999999999999999999999999------9999999999-9999999999----
i bosTau4.chr1                     C 0 I 34
s canFam2.chr23                     25992518 45 -  55389570 CTCCACTTTCCAA----TCAAGTTC------TCAAGTCTTT-ATCTACAGTGATCA
q canFam2.chr23                                             9999999999999----99999999------0999999999-99999999999999
i canFam2.chr23                    C 0 I 5
s equCab2.chr16                     22211920 49 -  87365405 CTCCACTTTCCAATCTGTCATGTTG------CCAAATCTTT-ACCCACAGTGATCA
q equCab2.chr16                                             9999999999999999999999999------9999999999-99999999999999
i equCab2.chr16                    C 0 I 57
s loxAfr3.scaffold_36                 513337 50 -  24123610 CTCTGCTTTCTAATCTGTCATAGTC------CATGGTTTTTCATCTATAGTTATCA
q loxAfr3.scaffold_36                                       9999999999999999999999999------9999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=21206.000000
s hg19.chrY                          7654109 45 +  59373566 CACTCACCTCATCTGGGAAGGACACCCA-CGTGCTCCCAC--AATACC
s canFam2.chr23                     25992568 48 -  55389570 CAAGCCCAGGGACCAGGCTGGACACCCCCTGTGCTCCTACTCAGTGGC
q canFam2.chr23                                             999999999999999999999999999999999999999999999999
i canFam2.chr23                    I 5 C 0
s rn4.chr9                         107346832 35 - 113440463 CCTAGGCCTGATCTAG----GCTGCACA-TGGACTCCTGC--------
q rn4.chr9                                                  9999999999999999----99999999-99999999999--------
i rn4.chr9                         I 3 I 28
s cavPor3.scaffold_0                 8223620 43 -  88675666 CACCCACCTTATCCCGTGTAGTTACCCACTGGCCTCCTA-----CACC
q cavPor3.scaffold_0                                        999999999999999999999999999999999999999-----9999
i cavPor3.scaffold_0               I 3 C 0
s panTro2.chrY                        507641 45 +  23952694 CACTCACCTCATCTGGGAAGGACACCCA-CGTGCTCCCAC--AATACC
q panTro2.chrY                                              0000000000000000000000000000-00000000000--000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71035441 45 - 202140232 CACTTGCCTTATCTGGGAAGGACACCCA-CGTGCTCCCAc--actgcc
q ponAbe2.chr3                                              9999999999999999999999999999-99999999999--999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158762647 45 + 189746636 CACTCGCCTTATCTGGGAAGGACACCCA-CGTGCTCCCAc--actgcc
q rheMac2.chr2                                              9999999999999999999999999999-99999999999--999999
i rheMac2.chr2                     C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e equCab2.chr16                     22211969 57 -  87365405 I
e bosTau4.chr1                     156983823 34 + 161106243 I
e loxAfr3.scaffold_36                 513387  0 -  24123610 C
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=14274.000000
s hg19.chrY                          7654154 46 +  59373566 ATA-atcttggct-cactgcaacctctgcctc--ctggattccagtgatc
s rheMac2.chr2                     158762692 46 + 189746636 aca-atcttagct-cactgaaacctccgcctt--ctggactcaagtgatc
q rheMac2.chr2                                              999-999999999-999999999999999999--9999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035486 46 - 202140232 aca-atcttggct-cacagaaacctccgcctt--ctggactcaagtgatc
q ponAbe2.chr3                                              999-999999999-999999999999999999--9999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507686 46 +  23952694 ATA-atcttggct-cactgcaacctccgcctc--ctagatcccagtgatc
q panTro2.chrY                                              000-000000000-000000000000000000--0000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8223663 49 -  88675666 GCATGTCTTCATTCCGCCCTTGCCTGTGTCTC-ACTGCAATGCAGAGACC
q cavPor3.scaffold_0                                        99999999999999999999999999999999-99999999999999999
i cavPor3.scaffold_0               C 0 I 350
s loxAfr3.scaffold_36                 513387 25 -  24123610 --------------GGCTGCAAGCTCTGCCCAGGCTGGA-----------
q loxAfr3.scaffold_36                                       --------------9999999999999999999999999-----------
i loxAfr3.scaffold_36              C 0 C 0
e rn4.chr9                         107346867 28 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e equCab2.chr16                     22211969 57 -  87365405 I
e bosTau4.chr1                     156983823 34 + 161106243 I
e canFam2.chr23                     25992616  0 -  55389570 C
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=46146.000000
s hg19.chrY                          7654200 122 +  59373566 ctcccacctcagcctcctgagcagctgggactacaggtgtgcaccaaca-tgcttagctaattcttgtacttttagtagagatcaggtttcatcacattggccaggctggtcttgaactcctg
s rheMac2.chr2                     158762738 122 + 189746636 ctcctgcctcagccccttgagtagctgggattacaggtgtgtgccaaca-tgcccagctaatttttgtatttttagtagagacagggtttcaccttgttggccaggctggtcttgaactcctg
q rheMac2.chr2                                               9999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035532 122 - 202140232 ctcctgcctcagccccctgagtagctgggactacaggtgtgcaccaaca-tgcccagctaatttttgtatttttagtggagacagggtttcaccgtgttggccaggcttttcttgaactcctg
q ponAbe2.chr3                                               9999999999999999999999999999999999999999990999999-9999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507732 122 +  23952694 ctcccacctcagcctcctcagcagctgggactacaggtgtgcaccaaca-tgcttagctaattcttgtacttttagtagagatcaggtttcgtcacattggccaggctggtcttgaactcctg
q panTro2.chrY                                               0000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s loxAfr3.scaffold_36                 513412  27 -  24123610 ----------AGTCTCC--------------------TGTGCTCCCATACTACCGAG------------------------------------------------------------------
q loxAfr3.scaffold_36                                        ----------9999999--------------------99999999999999999999------------------------------------------------------------------
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8223712 350 -  88675666 I
e rn4.chr9                         107346867  28 - 113440463 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e equCab2.chr16                     22211969  57 -  87365405 I
e bosTau4.chr1                     156983823  34 + 161106243 I
e canFam2.chr23                     25992616   0 -  55389570 C
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=62798.000000
s hg19.chrY                          7654322 82 +  59373566 CTCATCTTCATCCCGAACCAGGGCTTTGTCGTGCTGCAGTGCAAAG-GTCAGCTCTCT-CTTGGCTTCTCCC--TGACTTGGGCAG
s panTro2.chrY                        507854 82 +  23952694 CTCATCTTCATCCCAAACCAGGGCTTTGTCGTGCTGCAGTGCAAAG-GACAGCTCTCT-CTTGGCTTCTCCC--TGACCTGGGCAG
q panTro2.chrY                                              0000000000000000000000000000000000000000000000-00000000000-0000000000000--000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71035654 82 - 202140232 cccATCTTCATCCCATAACAGGGCTTTGTCCTGCTGCAGTGCCAAG-GGCAATTCTCT-CCTGGCTTCTCCC--CGACCTGGGCAG
q ponAbe2.chr3                                              9999999999999999909999999999999999999999999999-99999999999-9999999999999--999999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158762860 82 + 189746636 cccATCTTCATCCCATACCAGGGCTTTGTCCTGCTGCAGTGCAAAG-GACAGTTCTCT-CCTGGCTTCTCCC--CAACCTGGGCAG
q rheMac2.chr2                                              9999999999999999999999999999999999999999999999-99999999999-9999999999999--999999999999
i rheMac2.chr2                     C 0 C 0
s canFam2.chr23                     25992616 83 -  55389570 CGCATCTTCCTTGCTCACAGGGACTTGGACTTACAGC-GTGCAAAG-GCCAGTTCTCCAGCTGGCCTCTCCGACCACCCT-GGCAG
q canFam2.chr23                                             9999999999999999999999999999999999999-99999999-999999999999999999999999999999999-99999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22212026 81 -  87365405 ----TCTCCATCCTACGTGGGAACTTTGTCCTACTGCTGTGCAAAG-CCCTGTTCTCCAGCTGGCTTCTCCCACCAGCTTGGGCAG
q equCab2.chr16                                             ----999999999999999999999999999999999999999999-999999999999999999999999999999999999999
i equCab2.chr16                    I 57 C 0
s bosTau4.chr1                     156983857 68 + 161106243 GCCGCCTCCATCCCAAGTGGGTACTT-GTCCCGCCGCCGTGCAAAGCCCCAGTTCTCCAGCCCG-----------------AGCAG
q bosTau4.chr1                                              99999999999999999999999999-9999999999999999999999999999999999999-----------------99999
i bosTau4.chr1                     I 34 C 0
s rn4.chr9                         107346895 53 - 113440463 --------------------------CACCCTACAGCATGGCGCGG-GCTGACTC-CT-GCTGGTTTCTTCC----ACATGTACAG
q rn4.chr9                                                  --------------------------99999999999999999999-99999999-99-9999999999999----9999999999
i rn4.chr9                         I 28 C 0
s loxAfr3.scaffold_36                 513439 53 -  24123610 ----TCTTCATTGCACACCAGGACTTTGTCCCTCTGGAATGTAAAG-GCCAGTTCTTT----------------------------
q loxAfr3.scaffold_36                                       ----999999999999999999999999999999999999999999-99999999999----------------------------
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8223712 350 -  88675666 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e eriEur1.scaffold_377961              13714 1444 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=18993.000000
s hg19.chrY                          7654404 27 +  59373566 GGGCAGAGTCTCATCTCCTTATGAGAC
s rheMac2.chr2                     158762942 27 + 189746636 GGGCAGAGTCTCATCTCCTTACTGGAC
q rheMac2.chr2                                              999999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035736 27 - 202140232 GGGCAGAGTCTCATCTCCTCACTGGAC
q ponAbe2.chr3                                              999999999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507936 27 +  23952694 GGGCAGAGTCTCATCTCCTTATGAGAC
q panTro2.chrY                                              000000000000000000000000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107346948 23 - 113440463 GAGCAGAGCCTCAGCTT----TGAGAC
q rn4.chr9                                                  99999999999999999----999999
i rn4.chr9                         C 0 I 134
s bosTau4.chr1                     156983925 26 + 161106243 AGGCTAGGTCTCATCCCGTGACCT-GT
q bosTau4.chr1                                              999999999999999999999999-99
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22212107 27 -  87365405 CAGCTGGTTCTCATCTCATGACCCAGC
q equCab2.chr16                                             999999999999999999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992699 27 -  55389570 GAATTGGCTCTTACCTGGTGACCTGGT
q canFam2.chr23                                             999999999999999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              15158 27 +     88154 GGGGACAGTGTCATCTCATCATCTGGT
q eriEur1.scaffold_377961                                   999999999999999999999999999
i eriEur1.scaffold_377961          I 1444 C 0
s loxAfr3.scaffold_36                 513492 13 -  24123610 GGGTGGTTTCCCA--------------
q loxAfr3.scaffold_36                                       9999999999999--------------
i loxAfr3.scaffold_36              C 0 C 0
e cavPor3.scaffold_0                 8223712 350 -  88675666 I
e mm9.chr17                         50248744 1211 +  95272651 I
e oryCun2.chr14                      2470247 377 + 163896628 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=208554.000000
s hg19.chrY                          7654431 182 +  59373566 AGAGGGCTTGATGTGGATCCCAAGGCCAGTAACAGAGACA------TCcatgggccagggaaataaagtaaacaagaga--ta---cgagccaggggaaaagcaatgaacatcgcggcctcatcttgcccaagg---gggcagcattttgcccttcttgcctggttactgctaaaggg-gaagtgggcc-caatggtg
s rheMac2.chr2                     158762969 182 + 189746636 AGAGGGCTTGGTGCAGATCCCAACGCCAGTAACAGAGACA------TCTGCgggccagggaaataaagtaaacaagaga--ca---cgagccagggggacagcaatgaccacctaggccccatcttgcccaagg---gggcagcatcttgtccttcttgcctggttgctgctaatagg-caagtgggcc-cattgatg
q rheMac2.chr2                                               9999999999999999999999999999999999999999------999999999999999999999999999999999--99---999999999999999999999999999999999999999999999999---99999999999999999999999999999999999999999-9999999999-99999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035763 180 - 202140232 AGAGGGCTTGGTGCAGATCCCAACACCAGTAACAGAGGTA------TCTGCAggccagggaaatcaagtaaacaggaga--ca---tgagccagggggacagcaatgaacactgaggccccatcttgcccaagg---gggcagcatcttgtc--tcttgcctggttactgctaatggg-caagtgggcc-caatggtg
q ponAbe2.chr3                                               9999999999999999999999999999999999999999------999999999999999999999999999999999--99---999999999999999999999999999999999999999999999999---999999999999999--999999999999999999999999-9999999999-99999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        507963 182 +  23952694 AGAGGGCTTGATGTGGATCCCAAGGCCAGTAACAGAGACA------TCTATgggccagggaaataaagtaaacaagaga--ta---cgagccaggggaaaagcaatgaacatcgcggcctcatcctgcccaagg---gggcagcattttgcccttcttgcctggttactgctaatggg-caagtgggcc-caatggtg
q panTro2.chrY                                               0000000000000000000000000000000000000000------000000000000000000000000000000000--00---000000000000000000000000000000000000000000000000---00000000000000000000000000000000000000000-0000000000-00000000
i panTro2.chrY                     C 0 C 0
s rn4.chr9                         107347105 144 - 113440463 agatgggctcgtatagaactcaaggctGG-----GTG---------CCTTGGGGTCCAGATAGAGAAGTAAACAAAAGA--CA---CAGGCC----------------------AGGCCCACTTGAACCCAGGG----TCTGTAACCTTGTCCTTCTGGCCTGGGTACTCCCAATG-------TGGACC-CAATGGT-
q rn4.chr9                                                   99999999999999999999999999999-----999---------999999999999999999999999999999999--99---999999----------------------99999999999999999999----99999999999999999999999999999999999999-------999999-9999999-
i rn4.chr9                         I 134 I 931
s cavPor3.scaffold_0                 8224062 179 -  88675666 AGAGGACCTGGTATAGATTCCAAGGCCTA-ACCTGTGACCCCCCCCCCCCGGGGCCAAGTAGGTAAAACAAACAATAAA--CA---CAAACTAA---AGAAAGAATGAACTCTGAAGCCCCACTGACTCAAGTG----GGCAGTGTCTTGTC---CTAGCCTAGTCACTTTCAATGGT-CATTTGGGCC-CAAGGC-A
q cavPor3.scaffold_0                                         99999999999999999999999999999-9999999999999999999999999999999999999999999999999--99---99999999---9999999999999999999999999999999999999----99999999999999---99999999999999999999999-9999999999-999999-9
i cavPor3.scaffold_0               I 350 C 0
s oryCun2.chr14                      2470624 163 + 163896628 ------------GCTGTTCCCAAGGCCAG-----GAA---------CTGGGGGACCC---CAGGCCAGTAAACACGGGACCCA---CAAGCAAG-GCAATAATGAGGAAGACCGAAGCTTCACCTTGCCCAAGGCAGCGGCAGCACCCTGTCCTTCCAGCCCGAATACTCCCAATGTA-CACATGGGCT-CTGTGGTG
q oryCun2.chr14                                              ------------99999999999999999-----999---------99999999999---99999999999999999999999---99999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999-99999999
i oryCun2.chr14                    I 377 C 0
s bosTau4.chr1                     156983951 177 + 161106243 ACTGGGCCTGGGACAGACCGCAAGGCCAGGATCTGAGGCC------CC--AGGGTCCAATGGATAGGGTAAGCAAGACA--GA----GAGCCA-GGGACGGACAAGGAG-GTGGAAGCCCCACCTCACCAGGAG----AGCGGCACCCTCTCCTCCCAGTCAGATTATTACTGAGGGG-CTCGGGGGGCCCAGTAGTG
q bosTau4.chr1                                               9999999999999999999999999999999999999999------99--99999999999999999999999999999--99----999999-999999999999999-999999999999999999999999----9999999999999999999999999999999999999999-9999999999999999999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22212134 180 -  87365405 AGAAGGTCTGGTGCAGATCCCAAGGTCAGAAACCAGGgcc------ctcaggggctggatggataaagtcaacaagaga--ca----cagtcagggaaagaacaatgaacacgaaggccccaacttgccaaggg----ggtgacatctcgttcttctagcttggttattagcaatggg-cacatgggcccca-tggtg
q equCab2.chr16                                              9999999999999999999999999999999999999999------999999999999999999999999999999999--99----99999999999999999999999999999999999999999999999----9999999999999999999999999999999999999999-9999999999999-99999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992726 169 -  55389570 AGAGGGTCTGGGGCAGATCACAAAGCCAGGAACTGGGGCC------CCC-GGGACTGGAAGGATATGGT--ACAAGAGA--CA----CAGCTACGGGAAGAATAATGAATACTAAAGCCCCATCTCACCaaggg----ggcagcatcgtgttcttccagcctggtccctgtcaatggg-aacacaggcc---------
q canFam2.chr23                                              9999999999999999999999999999999999999999------909-9999999999999999999--99999999--99----99999999999999999999999999999999999999999999999----9999999999999999999999999999999999999999-9999999999---------
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              15185 167 +     88154 AGAGGGATGCGTATGGGTCCCAAGACCATGAACAGCAGCC------TGC-AGGGGTCAGGTGACAAAATAAAGAAGAGA--TGCCACCAACCAGAGCAAGTACAATGACCACAGACGCCCTGTGT----GCAGG----GGTAGCACCTGGCCCTCCGAGTCTTGTTAATGCC----GG-ACCAGAGAAG---------
q eriEur1.scaffold_377961                                    9999999899999999999999999999999999999999------999-99999999999999999999999999999--99999999999999999999999999999999999999999999----99999----9999999999999999999999999999999999----99-9999999999---------
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 513505 167 -  24123610 ----GACCTGCCACAGATCCCAGGGCCAGGAACCTGGGCC------CCTGggggccaagtaga-----tagacaagaca--ca---tgggccaggggaa-aacagtgaccactgagaccttggctgcccaaggg-------agcatcctgtc-atctggcc-agttatcacaggcaggccacatgggcc-ccatggta
q loxAfr3.scaffold_36                                        ----999999999999999999999999999999999999------99999999999999999-----99999999999--99---9999999999999-9999999999999999999999999969999999-------99999999999-99999999-999999999999999999999999999-99999999
i loxAfr3.scaffold_36              C 0 C 0
e mm9.chr17                         50248744 1211 +  95272651 I
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=194770.000000
s hg19.chrY                          7654613 154 +  59373566 ccagagcttctaactctta---ctttcaataagtcagaaatcttaatcctccta------------atctttaaatgtggcaagtaattATAATTTTAT-TTTCAATCCCATATGG------------------------------CC-AAAGCCAAGACCT---------------------------------------------------------------------------------------------------------------------------------GTCAGGTTGCAGAGTATGGATG-GGGCATTTGATAAA---AGT
s rheMac2.chr2                     158763151 155 + 189746636 ccagaacttctcactctta---ctttcaagaagtctggaatcttaatcttccta------------atcttcaaatgtggcaagtaattGTCATTTTAT-TTTCAATACCATATAG------------------------------CC-AAAGCCAAGACCT---------------------------------------------------------------------------------------------------------------------------------GGCAGCCTGCAGAGTATGGATGCGGGCATTTCATAAA---GGT
q rheMac2.chr2                                               9999999999999999999---99999999999999999999999999999999------------999999999999999999999999999999999-9999999999999999------------------------------99-9999999999999---------------------------------------------------------------------------------------------------------------------------------9999999999999999999999999999999999999---999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71035943 154 - 202140232 ccagaacttctaactctta---ctttcaagaagtccgaaatcttaatcttccta------------atctttaaatgtggcaactaattGTAATTTGAT-TTTCAGTCCCATATGG------------------------------CC-AAAGCCAAGACCT---------------------------------------------------------------------------------------------------------------------------------AGCAGCCTGCAGAGTATGGATG-GGGCATTTGATAAA---GTT
q ponAbe2.chr3                                               9999999999999999999---99999999999999999999999999999999------------999999999999999999999999999999999-9999999999999999------------------------------99-9999999999999---------------------------------------------------------------------------------------------------------------------------------9999999999999999999999-99999999999999---999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508145 154 +  23952694 ccagagcttctaactctta---ctttcaataagtcagaaatcttaatcctccta------------atctttaaatgtggcaagtaattATAATTTTAT-TTTCAATCCCATATGG------------------------------CC-AAAGCCAAGACCT---------------------------------------------------------------------------------------------------------------------------------GTCAGGTCGCAGAGTATGGATG-GGGCATTTGATAAA---AGT
q panTro2.chrY                                               0000000000000000000---00000000000000000000000000000000------------000000000000000000000000000000000-0000000000000000------------------------------00-0000000000000---------------------------------------------------------------------------------------------------------------------------------0000000000000000000000-00000000000000---000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8224241 129 -  88675666 GTAGAACTTCTAAGTCCTA---CTTTTACAATGCCCAAAATCTTAATTTCCACA------------ATCTTTGA-----------------------AT-TTTCTGCTCCTTTAGG------------------------------GC-CAATCCAAA--TT---------------------------------------------------------------------------------------------------------------------------------GCAGG---TTGCAGTCTGGATA-GGGCCCTTGATAAAGGTGGG
q cavPor3.scaffold_0                                         9999999999999999999---99999999999999999999999999999999------------99999999-----------------------99-9999999999999999------------------------------99-999999999--99---------------------------------------------------------------------------------------------------------------------------------99999---99999999999999-99999999999999999999
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50249955 124 +  95272651 CCAGAATTTCCAGTTCA-------TTTGAGAAGTCACAAATCATAATACTGAC---------------CTTTGA-----------------------AT-TTTCAACCCCTATGAC------------------------------TCAAAAGTCGAGACGT---------------------------------------------------------------------------------------------------------------------------------GATGGGCTTGAGAGTCTGGCTG-GGGCATTTGACAA----TGT
i mm9.chr17                        I 1211 C 0
s rn4.chr9                         107348180 121 - 113440463 CCAGAATTTCCAGTTCA-------TTCGAGAAGTCAGAAGTCATAATACTGAC---------------CTTTGA-----------------------AT-TTTCAACCCCTATAAC------------------------------TC-AAAGTCAAA--GT---------------------------------------------------------------------------------------------------------------------------------GTTGGGCTTCAGAGTCTGGCTA-GGGCATTTGACAG----TGT
q rn4.chr9                                                   99988888899999888-------88899999999999999999999999888---------------998878-----------------------89-8999889998899999------------------------------99-999999999--99---------------------------------------------------------------------------------------------------------------------------------9999999999999999999999-9999999999999----999
i rn4.chr9                         I 931 C 0
s oryCun2.chr14                      2470787  89 + 163896628 CCAGACCTTCTAATGTCAA---CTTTCAAGAAGTCAG-------------------------------CTTCAA-----------------------AA-TTTCAACTCC----AC------------------------------GT---------------------------------------------------------------------------------------------------------------------------------------------------GGCTGCAGAGGCTCGCT---GGCACCTGATAAA---CGT
q oryCun2.chr14                                              9999999999999999999---999999999999999-------------------------------999999-----------------------99-9999999999----99------------------------------99---------------------------------------------------------------------------------------------------------------------------------------------------99999999999999999---9999999999999---999
i oryCun2.chr14                    C 0 C 0
s bosTau4.chr1                     156984128 324 + 161106243 CCAGAACTTCTAATTCTTA---CCCCCAA-AACTCACAGTTCTTGACCCTCGTAGAAACTCCCCTAATCCTCAGCTTTGGCAAGTCAGTCCCACTTCA--TTTCAACCCcacatgggctccctggtggctcctacaatgcaggagacccaggttcaatccctgggttgggaagatctcctggagagggagatggctgcccactccagtattcctgcctggagaatcccatggatagaggagcctggtgagctacaggccatggggtcacacagtcaagacacgactCACCCGGTGGGCTGCAGAGTCTGGCTG-GGGCATTCCATAAG---TGT
q bosTau4.chr1                                               9999999999999999999---9999999-99999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999---999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22212314 167 -  87365405 ccagaacttctaattctta---gcttcaagaagtcagaaatcttgatcctcatagaaactcacctaatctttaaattcagcaagcaatttcaattttat-tttaaaccccatgtaa------------------------------cccaaaGCCAATACTT---------------------------------------------------------------------------------------------------------------------------------GGTAGGTTACAGAGTCTGCATG-GGGCTTGTGATCCA---TGT
q equCab2.chr16                                              9999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999------------------------------9999999999999999---------------------------------------------------------------------------------------------------------------------------------9999999999999999999999-99999999999999---999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25992895 167 -  55389570 caagaacttcatattctta---ccttcaagaactcagaaatcttggtcctcatggaaactctcctcatctttagatttggcaattaattcCCATTTTAT-TTTCAAGTCCATATGG------------------------------CCCAAAGCCAAGACCT----------------------------------------------------------------------------------------------------------------------------------GTAGGTTGCAGAGTCTGGATG-GGGCATTTAATTAAG--TGT
q canFam2.chr23                                              9999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999------------------------------9099999999999999----------------------------------------------------------------------------------------------------------------------------------999999999999999999999-999999999999999--999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              15352 170 +     88154 GCAGAACTTCTCACTGCTATTCCTTTCAAGAAGCCAGAAATCTTGGTTCTTATAAAAATTCTCCTAGTCTTGATAACTGACAGGCAGTTCCAACTGTATCCTCAAACCCCATGTGG------------------------------TCCCAAGCCAAGACCT---------------------------------------------------------------------------------------------------------------------------------GCTAGTTTGGAGAGTCTG-CTG-GGACATTTGATTAC---TAT
q eriEur1.scaffold_377961                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------------------------9999999999999999---------------------------------------------------------------------------------------------------------------------------------999999999999999999-999-99999999999999---999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 513672 160 -  24123610 tcagaacttctaattctta---ctttcaa-------gaaatcttgatcttcaaaggaaatctcctcatctttaactctggagaataattccaattttat-tttcaacaccatgtag------------------------------cctaacaCCAAGACCT---------------------------------------------------------------------------------------------------------------------------------GACAGGTTTGACTGTCTGAACG-GTGCCTTCAATGGC---TGT
q loxAfr3.scaffold_36                                        9999999999999999999---9999999-------999999999999999999999999999999999999999999999999999999999999999-9999999999999999------------------------------9999999999999999---------------------------------------------------------------------------------------------------------------------------------9999999999999999999999-99999999999999---999
i loxAfr3.scaffold_36              C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=-29113.000000
s hg19.chrY                          7654767 21 +  59373566 AGG-------GCACGGATG-----TCTGCCCTC
s dasNov2.scaffold_55020                1853 25 -     11008 ---GCGCTCCGGACGGGTGCCCGGCTGA-----
q dasNov2.scaffold_55020                                    ---9999999899999999999999999-----
i dasNov2.scaffold_55020           N 0 C 0
s loxAfr3.scaffold_36                 513832 23 -  24123610 ----------GGGGGGCTGGCTGCCTTATACTC
q loxAfr3.scaffold_36                                       ----------99999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s eriEur1.scaffold_377961              15522 20 +     88154 GGGG------AAGGAGGT-------CTTACCCC
q eriEur1.scaffold_377961                                   9999------99999999-------99999999
i eriEur1.scaffold_377961          C 0 C 0
s canFam2.chr23                     25993062 16 -  55389570 AGGG------AGATGGAT-----------TCTC
q canFam2.chr23                                             9999------99999999-----------9999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22212481 22 -  87365405 AGAC------GGATGGATG-----GCCCACATC
q equCab2.chr16                                             9999------999999999-----999999999
i equCab2.chr16                    C 0 C 0
s bosTau4.chr1                     156984452 24 + 161106243 GGGA------GGACAGACGC---CCCCCGCCTC
q bosTau4.chr1                                              9999------9999999999---9999999999
i bosTau4.chr1                     C 0 C 0
s oryCun2.chr14                      2470876 22 + 163896628 GGG-------GGACAGTTG----CCCCGTGCTG
q oryCun2.chr14                                             999-------999999999----9999999999
i oryCun2.chr14                    C 0 C 0
s rn4.chr9                         107348301 21 - 113440463 AGG-------CTAGGGATG-----CCCTTCCTC
q rn4.chr9                                                  999-------999999999-----999999999
i rn4.chr9                         C 0 C 0
s mm9.chr17                         50250079 21 +  95272651 AGG-------CTATGGATG-----CCCTTCCTC
i mm9.chr17                        C 0 C 0
s cavPor3.scaffold_0                 8224370 19 -  88675666 AGG-------ATACAGA-------CCCACACTT
q cavPor3.scaffold_0                                        999-------9999999-------999999999
i cavPor3.scaffold_0               C 0 C 0
s panTro2.chrY                        508299 21 +  23952694 GGG-------GCACGGATG-----TCTGCCCTC
q panTro2.chrY                                              000-------000000000-----000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71036097 22 - 202140232 GGG-------GGATGGATG----CCCCGCACTC
q ponAbe2.chr3                                              999-------999999999----9999999999
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158763306 22 + 189746636 GGG-------GGATGGATG----CCCTGCACTC
q rheMac2.chr2                                              999-------999999999----9999999999
i rheMac2.chr2                     C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276497648 4885 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=-69113.000000
s hg19.chrY                          7654788 84 +  59373566 CTTCCTATC-TCTGA-----CCCTG--GCACTGT----------------------------CCAGGCGCAGTGTGA-CC-ATCA---GTCATGCAGGG-------TGGAGGATGACATTCTGTTCATTCCC
s rheMac2.chr2                     158763328 87 + 189746636 CTTCCTATC-GCTGA-----CCCTG--GCACTGT----------------------------CCAGGCACAGTGTGA-GC-ATCAGTCATCATGCACGG-------AGGAGGATGCCATTCTGTTCATTCCC
q rheMac2.chr2                                              999999999-99999-----99999--9999999----------------------------999999999999999-99-999999999999999999-------99999999999999999999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71036119 86 - 202140232 CTTCCGATT-TCTGA-----TCCTG--GCACTGT----------------------------CCAGGCACAGTGTGA-GC-ATCACCCATCATGCAGGG-------AGGAGGATGTCGTTCTGTTCA-TCCC
q ponAbe2.chr3                                              999999999-99999-----99999--9999999----------------------------999999999999999-99-999999999999999999-------999999999999999999999-9999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508320 84 +  23952694 CTTCCTATC-TCTGA-----CCCTG--GCACTGT----------------------------CCAGGCGCAGTGTGA-CC-ATCA---GTCATGCAGGG-------TGGAGGATGACATTCTGTTCATTCCC
q panTro2.chrY                                              000000000-00000-----00000--0000000----------------------------000000000000000-00-0000---00000000000-------00000000000000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8224389 78 -  88675666 CTTGCTTGC-CTTCA-----TCTTG--ATACTGT----------------------------CAAGGGATGGCATAG-GC-ATTC---------TACTA-------AAAAGTGGGCCCAGTCAGTCATTCCC
q cavPor3.scaffold_0                                        999999999-99999-----99999--9999999----------------------------999999999999999-99-9999---------99999-------99999999999999999999999999
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50250100 99 +  95272651 CTTTCTTGC-TTCTA-----TCCCC--ACACCGCTGACACTCAGTATGCCCATCAGTGAGGACAGGGCACGGCAAGG-AT-GCC-----------------------AAGGGAAGCCTATCTGGCTACTCTC
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107348322 95 - 113440463 TACTCTTGC-CTCTG-----T-CCC--ACACTGCTGACACTCAGCAAAT---TCAGTGAGGACAGCGAAAGGCAAGG-AT-GCT-----------------------GAGGGAAGCCCATCTGGTTTCTCCC
q rn4.chr9                                                  999999999-99999-----9-999--9999997777777845555567---8998968688886667777878888-65-555-----------------------5777788899976445577566778
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2470898 62 + 163896628 TCCCCT--C-CCTGA-----TCTTG--GCGCCCC----------------------------CGGGGCACTGGACAGCAC-ACC-------------------------------CCTCTCTGTTCACCCCG
q oryCun2.chr14                                             999999--9-99999-----99999--9999999----------------------------999999999999999999-999-------------------------------99999999999999999
i oryCun2.chr14                    C 0 C 0
s bosTau4.chr1                     156984476 76 + 161106243 CTTCTCATC-CCAGA-----CGGTG--ACACTGC----------------------------CGAGGG-----GCGA-CC-GCCA---GTCGGGCGCTG-------ACGTGCTT---CCTCGGTGCCCTCTC
q bosTau4.chr1                                              999999999-99999-----99999--9999999----------------------------999999-----9999-99-9999---99999999999-------99999999---999999999999999
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22212503 84 -  87365405 CTTCCTAAC-ACTGA-----TCTTA--GCACTTT----------------------------GAAGGGTCAGCGTGA-GC-AACA---GTCACGTATTG-------GAGAGCTTGTGATTCCACTCATTTCC
q equCab2.chr16                                             999999999-99999-----99999--9999999----------------------------999999999999999-99-9999---99999999999-------99999999999999999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25993078 83 -  55389570 CTTCCTATC-TCTGA-----TC-TA--GCACTGT----------------------------CAAAGCATGGTGTGA-GC-CTCG---GTCATGTACTG-------AAGAGCTTGTGATTCTGTTCATTCTC
q canFam2.chr23                                             999999999-99999-----99-99--9999999----------------------------999999999999999-99-9999---99999999999-------99999999999999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              15542 82 +     88154 CTTTCCAGCTCCTGA-----TTCTA--GCAGCAT----------------------------CAAGGC--AGTCTGA-TC-ACCA---GTCAGTTACTG-------AAGAGTCTGAGAGT-AATTCATTCCC
q eriEur1.scaffold_377961                                   999999999999999-----99999--9999999----------------------------999999--9999999-99-9999---99999999999-------99999999999999-99999999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 513855 92 -  24123610 CTTCCTACC-CCTGATCCTTCCTTA--GCACCAG----------------------------TGAGGTGCAGTGGGG-GT-ATTAGCAATTATGTATTG-------AAGAGTTTGTGATTCCATTCATTTCC
q loxAfr3.scaffold_36                                       999999999-999999999999999--9999999----------------------------999999999999999-99-999999999999999999-------99999999999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
s dasNov2.scaffold_55020                1878 34 -     11008 --------------------CCTTA--GC-------------------------------------------TGGAG-GC-GTCGGCAGGGACCTA-CG-------AGG-----------------------
q dasNov2.scaffold_55020                                    --------------------99999--99-------------------------------------------99999-99-999799999999999-99-------999-----------------------
i dasNov2.scaffold_55020           C 0 N 0
s monDom5.chr8                     276502533 84 + 312544902 cctctcatc-tccag-----gcctgcagctctat----------------------------catgccaccatgcta-cctagca---gtccTTGAATGATCCTGAAGAAGACCGCCAC----------CCC
q monDom5.chr8                                              999999999-99999-----99999999999999----------------------------999999999999999-9999999---9999999999999999999999999999999----------999
i monDom5.chr8                     I 4885 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6808156 754 +   6934412 I

a score=83449.000000
s hg19.chrY                          7654872 87 +  59373566 A--CACCAACACAAGGTACATCAAAGGCTTCAAGGACAAATCTGCAGG---------TATTTGATACTGGC-CTCTATTTCCTAATTCTTTTTTTTT-----TT
s rheMac2.chr2                     158763415 86 + 189746636 A--CATCATCACAAGGTACATCAAAAGCTTCAAGGACACATCTGCAGG---------TGTTTGACACTGGC-CTCTATTTCCTAATTCCTCTTTTTT------T
q rheMac2.chr2                                              9--999999999999999999999999999999999999999999999---------99999999999999-9999999999999999999999999------9
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71036205 85 - 202140232 A--CATCATCACAAGGTACATCAAAAGCTTCAAGGACTCATCTGCAGG---------TATTTGATACTGGC-CTCTATTTCCTAATTCCCCTTTTTT-------
q ponAbe2.chr3                                              9--999999999999999999999999999999999999999999999---------99999999999999-9999999999999999999999999-------
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508404 85 +  23952694 A--CACCAACACAAGGTACATCAAAAGCTTCAAGGACAAATCTGCAGG---------TATTTGATACTGGC-CTCTATTTTCTAATTCTTTTTTTTT-------
q panTro2.chrY                                              0--000000000000000000000000000000000000000000000---------00000000000000-0000000000000000000000000-------
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8224467 83 -  88675666 A--GGTCACCACGGTGCATATCAAAGGCTTCAACAACACACCTGTAGA---------TATTTGAC---AGTGGCCTCTATTTTAATTCCTCCCTTTT-------
q cavPor3.scaffold_0                                        9--999999999999999999999999999999999999999999999---------99999999---99999999999999999999999999999-------
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50250199 56 +  95272651 ACGGAGCATCACGG---ACACCCGTGG---------------------------------CTGAT----AT-ACCTGTCTCTCAAGTCCTTCCTGTT-------
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107348417 80 - 113440463 ACGGAGCATCACGG---ACACCCATGGCTTTGAGGCCATGTCTGTGGA----------AACTGAT---GAT-ACCTGTCTCTTGAGTCCCTCCTCTT-------
q rn4.chr9                                                  88788876666788---7766786777766667688987777888899----------6556799---974-4556666675634444466665332-------
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2470960 74 + 163896628 TATCTGCACCACGC---CTGCCAAAGGTTCAGGGCACATGC-----------------GCACGAT--CAAC-TCCTGGCCTCTGCTTCCGCCCTCTT-------
q oryCun2.chr14                                             99999999999999---999999999999999999999999-----------------9999999--9999-9999999999999999999999999-------
i oryCun2.chr14                    C 0 C 0
s bosTau4.chr1                     156984552 85 + 161106243 C--CGTCATCGCGA--TGCATCCATGTCTGCAAGGTTACACCCACAGG---------CACTGGAAGCAGGC-CTCTGCTtgc---ttcctgtctcttgcttt--
q bosTau4.chr1                                              9--99999999999--99999999999999999999999999999999---------99999999999999-9999999999---99999999999999999--
i bosTau4.chr1                     C 0 I 522
s equCab2.chr16                     22212587 85 -  87365405 A--TATCATCACAATTTACATCAAAGTCTTCGAGGATACACTTGTAGA---------TATTTCACACAGGC-CTCGATTTCCTAATTCCTCCCTTTT-------
q equCab2.chr16                                             9--999999999999999999999999999999999999999999999---------99999999999999-9999999999999999999999999-------
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25993161 83 -  55389570 A--CATCATCACGATTTACATC--AGCATTCAAGGATACATCTGCACG---------TATTTGACACAGCC-CCCTATTTCCTAATTCTTCTCTCTT-------
q canFam2.chr23                                             9--9999999999999999999--999999999999999999999999---------99999999999999-9999999999999999999999999-------
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              15624 83 +     88154 A--CATCATCACAATTCACACC--AGTCTTCAAGGATATATCTGTGGG---------TATCTGACAAAGGT-CTCTCTATCCTAACACCTCCCTTTT-------
q eriEur1.scaffold_377961                                   9--9999999999999999999--999999999999999999999999---------99999999999999-9999999999999999999999999-------
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 513947 85 -  24123610 A--TGTCATCGCAATTTACAGCAAAGTCTTCAAGGACACATTTGCAGG---------TATGTGACACTGGC-CTCTATTTCCAAACTCCTCCCTTTT-------
q loxAfr3.scaffold_36                                       9--999999999999999999999999999999999999999999999---------99999999999999-9999999999999999999999999-------
i loxAfr3.scaffold_36              C 0 C 0
s monDom5.chr8                     276502617 85 + 312544902 A--CTTGGAGCCCCTGCCCAGTCAAGTCTGAGAGGCACCACATGCACA---------TACTTGAAACGAGG-CCTGATTTCTTCATTTGTGCTACTT-------
q monDom5.chr8                                              9--999999999999999999999999999999999999999999999---------99999999999999-9999999999999999999999999-------
i monDom5.chr8                     C 0 I 2
s ornAna1.Ultra117                   6808910 90 +   6934412 A--CAGTAAACAAATGTAAAATAAACAGTTTAAAAACTAATTGGAAAAAATAAAAGTCACTTGGCAGTGCT-ATTCTGTCTCTGGTTCAATTT-----------
q ornAna1.Ultra117                                          9--99999999999999999999999999999999999999999999999999999999099999999999-909999999999999999999-----------
i ornAna1.Ultra117                 I 754 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=372551.000000
s hg19.chrY                          7654959 263 +  59373566 --CTATATTGGCATTGAGACAAAC-----------ACAAAGTTTAGAACC------ACAT------GATTACATTTTGAATCTTTTGGAATTTTTT---GTTGTTGTTGTTCTGGACAGTATTACCAATAATCAGC------TTTTCTAAAA-----TCAAAATACAGAAACTACTGCTGAAA----AGCTG-TTTTGGGTGGTATGAGAGTCC--AAACATCTTTTTAAATA---AGTGTTTTGTTTTCC---TTTCA------------GAAAATAACTCCATATAAATAAATAAACCATTATTC-----CAAGAGG--------------T-----a---aaaaaaaggaa
s rheMac2.chr2                     158763501 264 + 189746636 --CTGTACTGGCACTGAGATGAAC-----------AAAAAGTTTAGAATC------ACAT------GATTGCATTTTGAATCTTTGGGAAATC-------TTTTTTTTATTCTGGACTCTATTACCAATAACAGAC------TTTTCTAAAA-----TCAAAATATAGAAACTACTGCTGAAA----AGGTA-TTTTGGGTGGCATGAGAGTCC--AAACGTCTTTTGAAATA---AGTGTTTTGTTTTTC---TTTCA------------GAAAATAATTCCATATAAATAAATAAACCATTATTC-----Caagaac--------------agaaaaa---aaaaaaaggaa
q rheMac2.chr2                                               --9999999999999999999999-----------999999999999999------9999------999999999999999999999999999-------999999999999999999999999999999999999------9999999999-----99999999999999999999999999----99999-999999999999999999999--99999999999999999---999999999999999---99999------------999999999999999999999999999999999999-----9999999--------------9999999---99999999999
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71036290 265 - 202140232 --CTATATTGGCACTGAGATGAAC-----------AAAAAGTTTAGAATC------AGAT------GATTGCATTTTGAATCTTTTGGAAATCTT-----TTTTTTTCATTCCAGACTCTATTACCAATAACAGGC------TTTTATAAAA-----TCAAAATATAGAAACTACTGCTGAAA----AGGTA-TTTTGGGTGGCATGGGAGTCC--AAACGTCTTTTGAAATA---AGTGTTTTGTTTTTC---TTTCA------------GAAAATAACTCCATATAAATAAATAAACCATTATTC-----CAAGAAC--------------TT-aaaa---aaaaaaaggaa
q ponAbe2.chr3                                               --9999999999999999999999-----------999999999999999------9999------99999999999999999999999999999-----999999999999999999999999999999999999------9999999999-----99999999999999999999999999----99999-999999999999999999999--99999999999999999---999999999999999---99999------------999999999999999999999999999999999999-----9999999--------------99-9999---99999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508489 263 +  23952694 --CTATATTGGCATTGAGACAAAC-----------ACAAAGTTTAGAACC------ACAT------GATTACATTTTGAATGTTTTGGAATTTTTT---GTTGTTGTTGTTCTGGACAGTATTACCAATAATCAGC------TTTTCTAAAA-----TCAAAATACAGAAACTACTGCTGAAA----AGCTG-TTTTGGGTGGTATGAGAGTCC--AAACATCTTTTTAAATA---AGTGTTTTGTTTTCC---TTTCA------------GAAAATAACTCCATATAAATAAATAAAACATTATTC-----CAAGAGG--------------T-----a---aaaaaaaggaa
q panTro2.chrY                                               --0000000000000000000000-----------000000000000000------0000------000000000000000000000000000000---0000000000000000000000000000000000000------0000000000-----00000000000000000000000000----00000-000000000000000000000--00000000000000000---000000000000000---00000------------000000000000000000000000000000000000-----0000000--------------0-----0---00000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8224550 226 -  88675666 --GCATGTTGATGTTGAGCTGAAC-----------TAAGAGTTTACAAAC------ACAT------CATTATGTTTTAAACCCCTTGGAAATCT-------------TTTTCCTGACT---TTACCAACAACAGGT------TTCTTGAAAA-----TTGAAATAT----AAAACTGTTGAAA----TA-TA-CTTTGAGTAGCATGAAAATCC--TAAGGTCT-TCCAAATAA--ATTGCTTTGCTTTT--------G------------GAAATTAACCCC----AAATAGATAAGCCAT----------TAAGAGT--------------T-----A---AAGAAA-----
q cavPor3.scaffold_0                                         --9999999999999999999999-----------999999999999999------9999------9999999999999999999999999999-------------99999999999---999999999999999------9999999999-----999999999----9999999999999----99-99-999999999999999999999--99999999-999999999--99999999999999--------9------------999999999999----999999999999999----------9999999--------------9-----9---999999-----
i cavPor3.scaffold_0               C 0 I 5
s mm9.chr17                         50250255 208 +  95272651 --CTTCACCCATAGGAAG-------------------AAAGCTTAGAACC------ACAT------AGTTATACTCAAATCCCGTTGGAAAGCCAG---------TGTTTCCCTGAGT-GATTGCCAAGATTAGTC------TTTTCTCACA-----T-----CAC----GTCTCTGATGAAA----AG-TA-TTTAGAGCTGTTCAATGGACG--GAAGGTCTCTTAAAATAAGCAATGCTTTCCTTAT-------------------------------------AAATAAATTCACCATCCTTC-----CAAGAGT--------------T--------------A-----
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107348497 211 - 113440463 --GTGCACCCGTAGGAAG-------------------AGAGCTTAGGACC------AC--------AGTTATATCCAAATCCCGTT-GAAATCCAG---------TGTTTCCCTGAGC-AACTGCCAAGATTAGTC------TTTTCTAACA-----T-----CAC----GTCTCTGCTGAAA----AG-TA-TTTCAGGCTATTCAATGGCCG--GAAGGTCTCTTAAAATAAGCAATGCTTTCCTTAT-------------------------------------AAATAAATTTACCATCATTC-----CAAGAGT--------------T-----A---AGAGAA-----
q rn4.chr9                                                   --2265889999999999-------------------9765668888777------76--------66775666667765557787-754566567---------7655442325633-23376777654478889------9999556569-----9-----999----9989998999999----99-99-999999999999999999999--9999999999999999999999999999999999-------------------------------------99999888999988888899-----9999999--------------9-----9---999989-----
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2471034 247 + 163896628 --TAACGGCGTGGAGAAG---AAC-------------AGAGCTCAGAACC------GCACA-----AACTCTATTGTGAATTCCTTGGAAATCTTA----TCGCTTTTCTCCCCAACTCAATTACCAAGAACCGGC------TTTTCCAAAA-----CCAAAATAG----GCCAC-----AAA----GG-TATTTTTGGGTGACACGAGAGTCT--GAAGGTCTCTCAAAATA---AATGTTTTCCTTCTC---TTTCA------------GAAAATAACTCCGTCTAAATAAATAAACCATTACCC-----CAAGAGC--------------T-----ACACAAAGAA-----
q oryCun2.chr14                                              --9999999999999999---999-------------9999999999999------99999-----999999999999999999999999999999----999999999999999999999999999999999999------9999999999-----999999999----99999-----999----99-999999999999999999999999--99999999999999999---999999999999999---99999------------999999999999999999999999999999999999-----9999999--------------9-----9999999999-----
i oryCun2.chr14                    C 0 C 0
s bosTau4.chr1                     156985159 273 + 161106243 --CTATACTGATGGAGATATGAAC-----------AAAGAGGTTAGGACC------ACAT------AACTACATTTCAAATCCCTTGGAAATC--------TTTGCTTTGTCCTCATTCAATTACCAATAACAGGC------TTTTTAAAAAAAA--TCAACACGCAGAAAGCACTGCTGGAA----AGGTA-TTTCGGGTAACATGAGAGTCC--AAAGGTCTTTTGAAATA---AGTGTTTTGCTCTTCAGTGTTTA------------GAAAATAATTCCGTATGAATAAATAAACCATTATTC-----CTGGAGGTTTTATTTTTTTTTT-----T---AAAGAA-----
q bosTau4.chr1                                               --9999999999999999999999-----------999999999999999------9999------999999999999999999999999999--------99999999999999999999999999999999999------9999999999999--99999999999999999999999999----99999-999999999999999999999--99999999999999999---99999999999999999999999------------999999999999999999999999999999999999-----9999999999999999999999-----9---999999-----
i bosTau4.chr1                     I 522 C 0
s equCab2.chr16                     22212672 257 -  87365405 --CTATACTGACGTAAAGATGAAC-----------AAAGAGTTTAGAACC------ACAT------AATTATATTTTGAATCCCTTGGAAATC-------TTATTTTTTTTCCTCACTTAATTACCACTAACAGAC------TTTCTAAAAA-----TCAAAATATAGAAGGTATTGCTGGAA----AGGTA-TTTTGGGTGGCATAAGAGTCC--AGAGATCTTTTGAAATA---AGTGTTTTGTTTTTC---TTTCA------------GAAAGTAACTCCATATAAATAAATAAGCCATTATTC-----CAGGAGG------------------------GAAAAAGAAAA
q equCab2.chr16                                              --9999999999999999999999-----------999999999999999------9999------999999999999999999999999999-------999999999999999999999999999999999999------9999999999-----99999999999999999999999999----99999-999999999999999999999--99999999999999999---999999999999999---99999------------999999999999999999999999999999999999-----9999999------------------------99999999999
i equCab2.chr16                    C 0 I 8
s canFam2.chr23                     25993244 265 -  55389570 --CTATGCTGATGTAGAGATGAAC-----------TACAAGTTTAGAACC------ATAT------AATTATGTTTTGAATCCTCTGGAAA----------TATTTCTTTCCTTCATTCAATCACCAATAACAGGCTTTTGATTTCTAAAAAAAAAGTCAAAATATAGAAAGTACTGCTGGAA----AGGTA-TTTTGGGTGGCATGAGAGTCC--AAAGATCTTTTAGAATA---AGGATTTTGTTTTCC---TTTCA------------GAAAATAACTCCATATAAATAACTAAGCCATTATTC-----CAGGGGT------------------------aaaaaaaaaaa
q canFam2.chr23                                              --9999999999999999999999-----------999999999999999------9999------9999999999999999999999999----------9999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999-999999999999999999999--99999999999999999---999999999999999---99999------------999999999999999999999999999999999999-----9999999------------------------99999999999
i canFam2.chr23                    C 0 I 8
s eriEur1.scaffold_377961              15707 223 +     88154 --ATACACTGGTGTGGAGAAGAAC-----------AAAGACTTTCGGGCC------ACAT------GACTATGTCTC----CCTGGGGAAA----------TATAATTTTCCCTTACTCAATTACCAGTAACAGac------tatatatatgaca--t-----------------------------------ttgTGGGTAGCATGGGAATCC--CAAGATCTTCTAAAATA---AGTG--CTATTGTTC---TCTCA------------GAAAATAACTCgatataaacaaataaaccacTATGG-----TAgaagt--------------t-----t---aaaaagaagaa
q eriEur1.scaffold_377961                                    --9999999999999999999999-----------999999999999999------9999------99999999999----9999999999----------99999999999998987999999999999999999------9999999988899--9-----------------------------------999799989979786784677--99794899977799899---9999--899869899---99988------------899989979999999999999979897897799777-----9789999--------------8-----9---97678999998
i eriEur1.scaffold_377961          C 0 I 8
s loxAfr3.scaffold_36                 514032 268 -  24123610 --CCATACTGGTGTAGAGATGAAC-----------AAAGAGTTTAGAACC------ACATGAACATAATTATATTCTGAAACCCTGGGATATCTTT--TTTTTTTTTTCCCCCTGACTCAATTACCAATAACTGGT------CTTTGAAAAA-----TCAAAATATGAAAACGCCTGCTGGAA----AGGTA-TTTTGGGCAGCTTGAAAGCCC--AACGGTCTTTCGAAATA---AAT--TTTATTTTTC---TTCTA------------GAAAATAACTGTATGTAAATAAATAAACCATTATTC-----CAAGAGC--------------C-----A---AAAAAAAAAAA
q loxAfr3.scaffold_36                                        --9999999999999999999999-----------999999999999999------9999999999999999999999999999999999999999--99999999999999999999999999999999999999------9999999999-----99999999999999999999999999----99999-999999999999999999999--99999999999999999---999--9999999999---99999------------999999999999999999999999999999999999-----9999999--------------9-----9---99999999999
i loxAfr3.scaffold_36              C 0 I 12
s monDom5.chr8                     276502704 259 + 312544902 --CTACGCTTGTGTAAAAGTCAACAGACATAAAATAAATAGTTCTGAGCTATGTGGACAT------GGTTATATTCTGAGTTAGTTAAAAATATTA------TTCTATCTCTGTGGCTCAACCACCAGCAATTTCC------TCTTTGCATC-----CTAA--------------TGCTGAGA----AGACA-CTTTTGGAGGAA-AACAATCCTAAAAGGTTTCTGAGAATC---AGCAACTT----------TTTAAAAGGGGGGAGGGAAaaagaaagcgagaaagaaagagaga---------------aagaga--------------a-----a---gaaagagagaa
q monDom5.chr8                                               --9999999999999999999999999999999999999999999999999999999999------999999999999999999999999999999------9999999999999999999999999999999999------9999999999-----9999--------------99999999----99999-999999999999-999999999999999999999999999---99999999----------99999999999999999999999999999999999999999999---------------999999--------------9-----9---99999999999
i monDom5.chr8                     I 2 I 1
s ornAna1.Ultra117                   6809000 244 +   6934412 CCAGAAATTCCTGAAAAAACAGAT---------TTGCTGAATTTTCAACT------GGAA------AAATGAGACATCAATCCTCT------CTTTCTTGGTCTCTCTCTTCTTCACTTTCTCGTTGCTAACC--C------TTTCCCACTG-----CTCTACTTCTGGGTCTGCAGCCAAAAGATGAGCTA-CTTGTTGGGGAATATGAGCCT--AAAGATCTTAGGGAATGAGCAGAGTTTT---------------------------GAAAACACTCCC-----TATAAAGATGTCCTTATTTTTTAATAGGTCT-----------------------------------
q ornAna1.Ultra117                                           999999999999999999999999---------99999999999999999------9999------99999999999999999999------99999999999999999999999999999999999999999--9------9999999999-----99999999999999999999999999999999999-999999999999999999999--9999999999999999999999999999---------------------------999999999999-----9999999999999999999999999999999-----------------------------------
i ornAna1.Ultra117                 C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=52998.000000
s hg19.chrY                          7655222 27 +  59373566 aagaa-aggaatgaaaatagagaaaa--aa
s rheMac2.chr2                     158763765 27 + 189746636 aagaa-aggaatgaaaacagagaaca--aa
q rheMac2.chr2                                              99999-99999999999999999999--99
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71036555 27 - 202140232 aagaa-aggaatgaaaacagagaaaa--aa
q ponAbe2.chr3                                              99999-99999999999999999999--99
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508752 27 +  23952694 aagaa-aggaatgaaaatagagaaaa--aa
q panTro2.chrY                                              00000-00000000000000000000--00
i panTro2.chrY                     C 0 C 0
s mm9.chr17                         50250463 27 +  95272651 AGAAA-AGGAATGAAAACATGTGCAA--TC
i mm9.chr17                        C 0 I 1
s rn4.chr9                         107348708 27 - 113440463 AGAAA-AGGAATGAAAACATGTGGAA--TC
q rn4.chr9                                                  99989-99777877788999877778--88
i rn4.chr9                         C 0 I 1
s dipOrd1.scaffold_20859                4343 27 -     25303 agaga-gagaATTAAAGTACAGGAAA--TA
q dipOrd1.scaffold_20859                                    99999-99999999999999999999--99
i dipOrd1.scaffold_20859           N 0 I 3384
s cavPor3.scaffold_0                 8224781 20 -  88675666 AAGCA-GGAAACAGAAAAACA---------
q cavPor3.scaffold_0                                        99999-999999999999999---------
i cavPor3.scaffold_0               I 5 C 0
s oryCun2.chr14                      2471281 27 + 163896628 AAGAA-AGGAATGGAAAAGTAGGGGA--AA
q oryCun2.chr14                                             99999-99999999999999999999--99
i oryCun2.chr14                    C 0 I 4
s bosTau4.chr1                     156985432 21 + 161106243 ------AGGAATG-AAACAGGGGGAA--AA
q bosTau4.chr1                                              ------9999999-999999999999--99
i bosTau4.chr1                     C 0 C 0
s equCab2.chr16                     22212937 28 -  87365405 AAGAA-AGGAATGAAAGCAAGGGGAAA-AA
q equCab2.chr16                                             99999-999999999999999999999-99
i equCab2.chr16                    I 8 C 0
s canFam2.chr23                     25993517 30 -  55389570 aaaaaGAGGAATGCAAACAGGGGGAAAGAA
q canFam2.chr23                                             999999999999999999999999999999
i canFam2.chr23                    I 8 C 0
s eriEur1.scaffold_377961              15938 19 +     88154 aagaa-atggatg--------gGGAA--AA
q eriEur1.scaffold_377961                                   99999-9889989--------99999--97
i eriEur1.scaffold_377961          I 8 C 0
s loxAfr3.scaffold_36                 514312 27 -  24123610 CAGAA-AGGAATGGAAACATGGGGGG--AA
q loxAfr3.scaffold_36                                       99999-99999999999999999999--99
i loxAfr3.scaffold_36              I 12 I 5
s monDom5.chr8                     276502964 27 + 312544902 gagaa-agaaagagagagaaagaaaa--aa
q monDom5.chr8                                              99999-99999999999999999999--99
i monDom5.chr8                     I 1 I 2823
s ornAna1.Ultra117                   6809244 17 +   6934412 ------TGATATGATAGAACAGC-------
q ornAna1.Ultra117                                          ------99999999999999999-------
i ornAna1.Ultra117                 C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=659940.000000
s hg19.chrY                          7655249 186 +  59373566 a----aaTCCACA----AAACCACACATTTCTTAACACTCCTGGGATAAAGGA---AATTTTGTTTTTGCTATGGCTATG-TTTTGTT--TAGG-A-AAAACATTCTGCAGCCCTATTTATTCCCTTGAAATAAAGCCCTTC-AGACATTTGCAAAGG-GCC-------------AAAGTGAGGTCTTTGC----TAT-TTCAGACTTTATTATTGGGAAAG
s rheMac2.chr2                     158763792 190 + 189746636 aC-ATAATCCACA----AAACCACACATTTCTTAACACTCCTGGGATAAAGTA---AATTTTGTTTTTGCTATGACTATG-TTTTGTT--TAGCAA-AAAACATTCTGCAGCCCCATTTATTCTCTGGAAACGAAGCCCTTC-AGACATTTGCAAAGG-GCC-------------AAAGTCAGGTCTTTGC----TAT-TTCAAACTTTCTTATTGGGAAAG
q rheMac2.chr2                                               99-9999999999----999999999999999999999999999999999999---999999999999999999999999-9999999--999999-999999999999999999999999999999999999999999999-999967667666767-766-------------6767776666666776----666-66666666767666776666666
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71036582 188 - 202140232 C--ATAATTCACA----AAACCACACATTTCTTAACACTCCTGGGATAAAGTA---AATTTTGTTTTTGCTATGACTATG-TTTTGTT--TAGC-A-AAAACATTCCGCAGCCCCATTTATTCCCTGGAAACGAAGCCCTTC-AGACATTTGCAAAGG-GCC-------------AAAGTGAGGTCTTTGC----TAT-TTCAAACTTTATTATTGGGAAAG
q ponAbe2.chr3                                               9--9999999999----999999999999999999999999999999999999---999999999999999999999999-9999999--9999-9-999999999999999999999999999999999999999999999-999999999999999-999-------------9999999999999999----999-99999999999999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508779 186 +  23952694 a----aaTCCACA----AAACCACACATTTCTTAACACTCCTGGGATAAAGGA---AATTTTGTTTTTGCTACGGCTATG-TTTTGTT--TAGG-A-AAAACATTCTGCAGCCCCATTTATTCCCTTGAAATAAAGCCCTTC-AGACATTTGCAAAGG-GCC-------------AAAGTGAGGTCTTTGC----TAT-TTCAGACTTTATTATTGGGAAAG
q panTro2.chrY                                               0----00000000----000000000000000000000000000000000000---000000000000000000000000-0000000--0000-0-000000000000000000000000000000000000000000000-000000000000000-000-------------0000000000000000----000-00000000000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8224801 184 -  88675666 ----TATTACCCA----AAACCAAACATTTCTCAACACTCTTGGGACAGAGAA---GAGTTTGTTTTTGTTATGACTATG-TTTTATT--TAGC-A-AAAACATTCTGCAGCCTCGTTTCTTCCCTAGCAGGTAAGCTCCTC-AGACCTCTATGTAGCAGCTATG----------TCTGCACTGTTCAGACTTGATTT-TGGGAGCACATCA----------
q cavPor3.scaffold_0                                         ----999999999----999999999999999999999999999999999999---999999999999999999999999-9999999--9999-9-999999999999999999999999999999999999999999999-9999999999999999999999----------99999999999999999999999-9999999999999----------
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50250491 178 +  95272651 ----TAACCCACA----AAACCACATATTTCTCAACACTCCTGGGACACAGTC---GACTCTGCTTTTGTTATGACTGTGTTTTTGTT--TAGC---CAAACATTCTGCAGCC-CATTTCCCCCCTGGAAATGAAGCTCTTC-AGACATCTTCAGAGGAACT-------------TAAGCAATGCCCTGGT----TGT-TCGGAACAATCCACT--------
i mm9.chr17                        I 1 C 0
s rn4.chr9                         107348736 176 - 113440463 ----TAACCCACA----AAACCACATATTTCTCAACACTCCTGGGACACAGAC---GATTCTGCTTTTGTTATGACTGTGTTTTTGTT--TAGC---CAAACGTTCTGCGGCC-CATTTCCCCCCTGGAAACGAAGCTCTTC-AG--TTCTTCAGAGGAACT-------------TAAGCAGTGCTCTGGC----TGC-TCAGAACAATTCACT--------
q rn4.chr9                                                   ----999999999----999999999999999889999999999888999888---89999999999988899887977777999888--9988---8999988999988888-9999999999999888988889999999-99--999999986769899-------------9999999877789988----877-596988888899999--------
i rn4.chr9                         I 1 C 0
s oryCun2.chr14                      2471312 175 + 163896628 ----TAATCCACC----AAACCACACATTACTTAACACCCCTGGGACCAGGCA---GGCCTTGTTTTTGCTATGACTG----TTTGTT--TAGC-A-AAAACACTCGGCAGCTCCACTTTTTCCCTGGAAAC--AACCCCTC-AG-------CAGAGGAGCC-------------AAAGCGATGTCTCTGC----TGT-TGCAAACGTCCCTGTTGGAAAAG
q oryCun2.chr14                                              ----999999999----999999999999999999999999999999999999---9999999999999999999999----999999--9999-9-99999999999999999999999999999999999--99999999-99-------9999999999-------------9999999999999999----999-99999999999999999999999
i oryCun2.chr14                    I 4 C 0
s bosTau4.chr1                     156985453 187 + 161106243 -GCATAATCCACA----AAACCACATATTTCTTAACACTCCTGGGATAAAGTA---GATT--GCTTTTGCTATGACTATG--TTTGTT--TAAC-A-AAAACATTCTGCAGCCCCGTTGACTCCCTGGAAATGAGGCCTTTC-AGACATCTGCAGAGGAGCC-------------AAAGTGATGTTGCTGC----TGC-TTCAAATTTCCTTATGGGGAAgg
q bosTau4.chr1                                               -999999999999----999999999999999999999999999999999999---9999--999999999999999999--999999--9999-9-999999999999999999999999999999999999999999999-9999999999999999999-------------9999999999999999----999-99999999999999999999999
i bosTau4.chr1                     C 0 I 137
s equCab2.chr16                     22212965 190 -  87365405 -ACACAATCCGCG----AAACCACACATTTCTTAACACTCATGGGATAAAGTG---GATTTTGTTTTTGCTATGACTATG-TTTTGTT--TAGC-A-AAAACATTCTGCAGCCCCATTTATTCCCTAGAAACAAAGCCCTTC-ACACATCTGCGAAAGAGCC-------------AAGGAGATGTCTTTGC----TAC-TTCAAACTTTATTATTGGGAAAG
q equCab2.chr16                                              -999999999999----999999999999999999999999999999999999---999999999999999999999999-9999999--9999-9-999999999999999999999999999999999999999999999-9999999999999999999-------------9999999999999999----999-99999999999999999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25993547 191 -  55389570 -ACCTCATCCACA----AAACCACACATTTCTTAACACTCCTGGGATAAAGTA---GATTTCGTTTTTGCTATGACTATG-TTTTGTT--TAGC-A-AAAACATTCTGCAGCCCCACTTATTCCCTGGAAACGAAGCCCTGC-AGACATCTGCAGAAGAGCC-------------AAAGCGACGGCTTTGC----TCCTTTCAAACTTTATTCCTGGGAAAG
q canFam2.chr23                                              -999999999999----999999999999999999999999999999999999---999999999999999999999999-9999999--9999-9-999999999999999999999999999999999999999999999-9999999999999999999-------------9999999999999999----999999909999999999999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              15957 173 +     88154 -TCGTAATTCACA----AAACCACACATTTCTTGACACCCTTGGGAGGTA--A---GATTCTGCCTTTGCTGTGACTAGG-TTTTGTT--TAGC-ATAACACATTTCACCGCCCCACGTACTCCCTGAAAGGAA-----------------GCAGAAGAACT-------------CAGGAAATGTCTTGgc----tac-tttaaattttattattgggaaAG
q eriEur1.scaffold_377961                                    -988998898889----995798878999999999999999988899999--9---999999899988999989999898-9999999--9998-698988989999989889999889899999999999989-----------------99999899999-------------9888999999999999----999-99999999999999998999999
i eriEur1.scaffold_377961          C 0 C 0
s loxAfr3.scaffold_36                 514344 186 -  24123610 ----TAATCCACA----AAACCTCACATTTCTTAATACTCTTGGGATAAAGGA---GATTTTGCTTTTGCTATGACTATG-TTTTGTT--TAGC-A-AAAACATTC-GCAGCCCAATTCATTCCCTGGAAATGAAGCCTTTC-AGACATCTGAAGAAGAGCC-------------AAAGCTATGTCTCTGC----TGT-TTCAAGCTTTACTACTGGGAAAG
q loxAfr3.scaffold_36                                        ----999999999----999999999999999999999999999999999999---999999999999999999999999-9999999--9999-9-999999999-99999999999999999999999999999999999-9999999999999999999-------------9999999999999999----999-99999999999999999999999
i loxAfr3.scaffold_36              I 5 C 0
s ornAna1.Ultra117                   6809261 200 +   6934412 ----AACTCCACCCTATAACCCAAAGATTTCTCTACCCCCATGGGGGAAAGTACCGGATTTTCCCT--------ACAATG-TCATATTACTGCC-C-AGAAAGGAATGAAATCCTCTTCATCCTCT--CACCTAAACCTTTCTAAAGGATACCAGAGAGGCCCAGAAATAGTCAACAAGCAATAGCTTTAC----TGC-TTTGAACTTTAGTATGCAGAAAG
q ornAna1.Ultra117                                           ----99999999999999999999999999999999999999999999999999999999999999--------999999-9999999999999-9-99999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999----999-99999999999999999999999
i ornAna1.Ultra117                 C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276502991 2823 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e dipOrd1.scaffold_20859                4370 3384 -     25303 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=578366.000000
s hg19.chrY                          7655435 243 +  59373566 TATCAGCCTCCAACACAAG--AAAGAAACCACT-GCATA-----------------------CAG-------------C-AACTACATAT-TT-CAC---T--CGGCTCTATAAAGCAGGAAA-CAGCAGGCTGAAATGCAAAAGTTACTATTATTTTGCCTGGAAATAATTTCTGACTTTAACTTAATCATTC-AACGTCTGACTTTGCTTTTCTAATTACATCAGCTGATGGA-TCTGTCAATATCAAGGA-GCGCAATGTGAG-AAA--GA--C--ACCATCTCCCTC----AGGTAAGTTC
s rheMac2.chr2                     158763982 243 + 189746636 TATCAGCCTCCAACACAAG--AAAGAAACCACT-GCATA-----------------------CAG-------------C-AACTGCCCAT-TT-CAC---T--CAGCTCTGTAAAGCAGGAAA-CAGCAGGCTGAACTGCAACAGCTTCTATTATTTTGCCCAGAAATCATCTGTGACTTTAACCTAATTATTC-AAAGTCCAACTTTGCTTTTCTAATTACATTCGCTAATGGA-TCTGTCAATACGAAGGA-GTGCAACATGAG-ACA--GA--C--ACCATCTCCCTC----GGGAAATTTC
q rheMac2.chr2                                               6666666666666666676--676666666666-77666-----------------------667-------------7-7666666666-66-666---6--77766766666666667676-7667676676667666676666766666676666676766766666666666766666666676766676-6766677666776677766667776667766667766666-67667666566666666-666666667666-666--66--6--666667766666----7665666666
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71036770 243 - 202140232 TATCAGCCTCCAACACAAG--AAAGAAATCACT-GCATA-----------------------CAG-------------C-AACTGCCCAT-TT-CAC---T--CAGCTCTGTAAAGCAGGAAA-CAGCAGGCTGAACTGCAACAGCTTCTATTATTTTGCCCAGAAATCATTTGTGACTTTAACCTAATTATTC-AAAGTCTGACTTTGCTTTTCTAATTACATCCGCTAATGGA-TCTGTCAATACGAAGGA-GTGCAACATGAG-ACA--GA--C--ACCAATTCCCTC----GGGAAATTTC
q ponAbe2.chr3                                               9999999999999999999--999999999999-99999-----------------------999-------------9-9999999999-99-999---9--99999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999999999-999999999999-999--99--9--999999999999----9999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        508965 243 +  23952694 TATCAGCCTCCAACACAAG--AAAGAAACCACT-GCATA-----------------------CAG-------------C-AACTACATAT-TT-CAC---T--CGGCTCTATAAAGCAGGAAA-CAGCAGGCTGAAATGCAAAAGTTTCTATTATTTTGCCTGGAAATAATTTCTGACTTTAACTTAATCATTC-AACGTCTGACTTTGCTTTTCTAATTACATCAGCTGATGGA-TCTGTCAATATCAAGGA-GTGCAATGTGAG-AAA--GA--C--ACCATCTCCCTC----AGGTAAGTTC
q panTro2.chrY                                               0000000000000000000--000000000000-00000-----------------------000-------------0-0000000000-00-000---0--00000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000-00000000000000000-000000000000-000--00--0--000000000000----0000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8224985 222 -  88675666 -----GCCTCCAACACAAG--AAGCAAA---CA-ACACA---------------------GGCGG-------------CAACCTGCAC---TG-CCA---T--CAACTCCATCGGAAG------------GCCAAGCCAGCAC---TTCTATTATTTTGTCCAAGAATCATTTGTGGCTTTAACCTAATTATTC-GAAGTCCGACTCTGCTCTTCTAATTACTTCTGCTAATGGA-TCTGTCAATACCAAGGA-ACGCAGCTTGAC-ACA--GACCA--ACCTTCCCGCCC----A--TAATTTC
q cavPor3.scaffold_0                                         -----99999999999999--9999999---99-99999---------------------99999-------------9999999999---99-999---9--999999999999999------------9999999999999---999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999999999-999999999999-999--99999--999999999999----9--9999999
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50250669 226 +  95272651 --AAGCTCTCCAACACAGA--AAGGAAATCTCG-ACACA-----------------------CAG-------------C--CCTGCTCCCTTC-CCT---TGGCCCCTTCACGCAGCA------------GCAGGAACGACAC-----CTATTATTCTGTCCAGCCATCATTTGTGACTTTAACCTAATTATTC-CAAGTCTGACTTTGCTTTTCTAATTACACTCGCTAATGGA-TCTGTCAATACCAAAGA-GCCTGGTGTGAG-GGA--GA--A--GCCACCACCCCT----A-GCAATTTC
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107348912 224 - 113440463 --AAGCTCTCCGACACAGA--AAGGAAATCTCG-GCACA-----------------------CAG-------------C--CCTGCCCCCTCC-CCC---C--CCACTCCATCGTGCA------------GCAGTAACGACAC-----CTATTATTCTGTCCAGCGATCATTTGTGACTTTAACCTAATTATTC-CAAGTCTGACTTTGCTTTTCTAATTACACTCGCTAATGGA-TCTGTCAATACCAAAGA-GCCTGGTGTGAG-GGA--GA--A--GCCACCTCCCCT----G-GTAATTTC
q rn4.chr9                                                   --98899999999998866--869777888899-88899-----------------------998-------------8--899888899999-999---9--999999999999999------------9999999999999-----9999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999999999-999999999999-999--99--9--999999999999----9-99999999
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2471487 241 + 163896628 C-GTGCGCTCCGACGCCGG--CGAGAAACCACT-GCACCTTCCAACGCTCATTTCTAGAAAGCAG-------------T--CCTG------TG-TCG---C--CCACGCC----GGCA------------GCTGAAGCGCTACAACTCCTATTATCCTGCCCAGGA--------CGACTTTAACCTAATTATTC-AACGTCCGACTTTGCTCTTCTAATTGCATCCGCTAATGGC-TCTGTCGATACCAGGGGCGAGGGGCGCGAGTGCC--GG--G--GCCACCCCCTCCCTGGA-ATCATTTC
q oryCun2.chr14                                              9-99999999999999999--999999999999-9999999999999999999999999999999-------------9--9999------99-999---9--9999999----9999------------999999999999999999999999999999999999--------99999999999999999999-9999999999999999999999999999999999999999-9999999999999999999999999999999999--99--9--99999999999999999-99999999
i oryCun2.chr14                    C 0 C 0
s bosTau4.chr1                     156985777 247 + 161106243 CACCAG-CTTCCACACAAG--AAAGAAAGCTC--ATGCA-----------------------CGACGACCAGAGACCTC-ACAT-------CT-CAC---C--CACGTCCCTGCAGCAGGCCA--GCCACGCCCAGCTGCAACAGCCCCCATGTTCGTGCCCAGCAATCGTTTCTG-CTTTAGCCCGATTACTC-AAAGTCCGACCCTGCTTTTCTAATTATATCCACTAACGGA-TCTGTCAATACCA-GGA-GCCCAACACGAG-AGACAGA--C--ACCATCTCCCGG----GGGTCAGCGT
q bosTau4.chr1                                               999999-999999999999--99999999999--99999-----------------------99999999999999999-9999-------99-999---9--99999999999999999999--999999999999999999999999999999999999999999999999999-99999999999999999-9999999999999999999999999999999999999999-9999999999999-999-999999999999-9999999--9--999999999999----9999999999
i bosTau4.chr1                     I 137 C 0
s equCab2.chr16                     22213155 233 -  87365405 CACCAGCATCCAACACAAG--AAAGAAACCCCC-GTGTA-----------------------CGG-------------C-ACAT-------GT-CAC---C--CAGCTCTCTACAGCAGGCAG-TGGC-CGCCGAATG-----AACTTCTGTTATTTTGCCCAGCAATCATTTGTGACTTTAACCTAATTATTC-AAAGTCTGACTTTGCTTTTCTAATTACATCCGCTAATGGA-TCTGTCAATACCAAGGA-GCACCACACGAG-AGAGAGA--C--ACCATCTCCCTC----GGGTAATTTC
q equCab2.chr16                                              9999999999999999999--999999999999-99999-----------------------999-------------9-9999-------99-999---9--99999999999999999999-9999-999999999-----999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999999999-999999999999-9999999--9--999999999999----9999999999
i equCab2.chr16                    C 0 C 0
s canFam2.chr23                     25993738 240 -  55389570 TGCCAG-GTTCAAGACAAG-----GAAACCCCTGGTGTA-----------------------CAG-------------C-ACCC-------GCACACTTTT--CTCCTCTGTACAGGAGACAA-CGGCGTGCTGAACTGCAACAGCTTCTATTATTTTGCTCAGCCATCATTTGTGACTTTAACCTAATTATTC-AAAGTCCGACTCCGCTTTTCTAATTACATCTGCTAATGGA-TCTGTCAATACCAGGGA-ACGAAACACGAG-AGAATGA--C--ACCATCTCCCTC----GGGTAATTTC
q canFam2.chr23                                              999999-999999999999-----999999999999999-----------------------999-------------9-9999-------9999999999--99999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999999999-999999999999-9999999--9--999999999999----9999999999
i canFam2.chr23                    C 0 C 0
s eriEur1.scaffold_377961              16130 205 +     88154 TACCAGCTTCCAACCCCAG--CAAGAACTCTTGTGTGTA-----------------------AGG----CAGAGGG--T-ACCT-------TT-CCCTGGC--TTGCTCTCTGTAGC----------------------CAACAGCTCCTGTGCTTTTGCAAGACAAGCCTTTGTGACTTTAACCTAATTATTC-AAAGTCCGACTTTGCTTTTCTAATTACACCCGCTAATGGA-TCTGTCAATACCGAGGA-GATCAACACCAG-AGA--GA--C----------------------------
q eriEur1.scaffold_377961                                    9999999999999999999--999999999999999999-----------------------999----9999999--9-9999-------99-9999999--99999898799999----------------------9999999999999999987899989999989999999999998989895357679-9998989899996989899888999998985353681265-79698996868999898-755662656999-888--76--8----------------------------
i eriEur1.scaffold_377961          C 0 I 24689
s loxAfr3.scaffold_36                 514530 246 -  24123610 TACCAGCTCCCAACACAAG--AAAGAAACCACT-GCGTA-----------------------CGG-------------C-AACCACACAC-TT-CAC---C--TCCCTCTACAAAGCAAGCAAACAGCAGGCTGAATTGCCACAGCTTCTGCCATTCTGCTCCATAATCATTTGTGACTTTAACCTAATTATTT-AAAGTCCAACTTTGCTTTTCTAATTACGTCCACTAATGGA-TCTGTCAATACCAGGGA-GCTCAACCCAAG-ACA--GA--GACACGATCTCCCTC----GGGTAATTTC
q loxAfr3.scaffold_36                                        9999999999999999999--999999999999-99999-----------------------999-------------9-9999999999-99-999---9--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999999999-999999999999-999--99--999999999999999----9999999999
i loxAfr3.scaffold_36              C 0 C 0
s ornAna1.Ultra117                   6809461 239 +   6934412 TATTGA-CTCAGGCCTAAGAAAAAGATATTACT-GCCAA-----------------------CTC-------------C-TATTGTGCA--TT-TTC---T--CAACATTACAAAAGACAGAA-CAGCCCTCTGGCCTAACAA----TGTGCTGTTTTGCCATACACTCTGTTACAAC--TAAC--AATCACTCAAAAGTTTTCCTTCATTTTTCTTACTGTGCTGGTCAATGGGTTCAGTCAATCACAGTAA-AACTCCCATAAG-AGA--AA--GATGTCATTCCCCCT----AAGTAATTTC
q ornAna1.Ultra117                                           999999-99999999999999999999999999-99999-----------------------999-------------9-999999999--99-999---9--99999999999999999999-9999999999999999999----9999999999999999999999999999999--9999--9999999999999999999999999999999999999999999999999999999999999999999-999999999999-999--99--999999999999999----9999999999
i ornAna1.Ultra117                 C 0 I 1532
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276502991 2823 + 312544902 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e dipOrd1.scaffold_20859                4370 3384 -     25303 I
e papHam1.scaffold12353                60426 8117 +     70985 I

a score=667572.000000
s hg19.chrY                          7655678 215 +  59373566 GCTCACAGGTGAAGCTAATAATGACACTGCTCAACCAAA--------------TCTCTTTCTTTTTTTA-AAAAA-------------AGT--TACTTCAAGACTGCTAGTGCTATAACATCAAT---GTGCCTGGGCTTTGCAGTAGATCCAATTTAGCAAAACATTAAAATCAATCACTTTTCAATGCAGGAC--------TTTTTATTGTATAGGTAAGAAATGGGAGTCCAA--TTTTTAAAACAATGCTTGCA
s rheMac2.chr2                     158764225 210 + 189746636 CCTCACAGGTGAAGCTGATAATGACACTGCTCAACCAAA--------------TCTCTCTTTTT------AAAAA-------------AGT--TCCTTCAAGACTGCTGGTGCTATAACATCAAT---CTGCCTGGGCTTTGCAGTAGATCCAATTTAGCAAAACACTAAAATCCATCACTTTTCGATGCGGGAC--------TTTTTATTGTATAGGTAGGAAATAGGAGCCCAA--TTTTTAAAATAATGTTTGCA
q rheMac2.chr2                                               667666666666666667766666655676667666665--------------66676766766------77766-------------655--55655665566666676666666666666666---6666666666666666666666655566666666666666676666566666676566566665555--------556665656655657666666556566667555--55677766666666556676
i rheMac2.chr2                     C 0 C 0
s ponAbe2.chr3                      71037013 210 - 202140232 CCTCACAGGTGAAGCTGATAATGACACTGCTCAACCAAA--------------TCTCTCTTTTT------AAAAA-------------AGT--TCCTTCAAGACTGCTAGTGCTATAACATCAAT---CTGCCTGGGCTTTGCAGTAGATCCAATTTAGCAAAACACTAAAATCAATCACTTTTTGATGCAGGAC--------TTTTTATTGTATAGGTAGGAAATAGGAGTCCAA--TTTTTAAAATAATGTTTGCA
q ponAbe2.chr3                                               999999999999999999999999999999999999999--------------99999999999------99999-------------999--99999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999--------999999999999999999999999999999999--99999919999999999999
i ponAbe2.chr3                     C 0 C 0
s panTro2.chrY                        509208 215 +  23952694 GCTCACAGGTGAAGCTAATAATGACACTGCTCAACCAAA--------------TCTCTTTCTTTTTTTA-AAAAA-------------AGT--TCCTTCAAGACTGCTAGTGCTATAACATCAAT---GTGCCTGGGCTTTGCAGTAGATCCAATTTAGCAAAACATTAAAATCAATCACTTTTCAATGCAGGAC--------TTTTTATTGTATAGGTAAGAAATGGGAGTCCAA--TTTTTAAAATAATGCTTGCA
q panTro2.chrY                                               000000000000000000000000000000000000000--------------0000000000000000-00000-------------000--00000000000000000000000000000000---0000000000000000000000000000000000000000000000000000000000000000000--------000000000000000000000000000000000--00000000000000000000
i panTro2.chrY                     C 0 C 0
s cavPor3.scaffold_0                 8225207 216 -  88675666 CCTCACAGGTGAAGCTGATAATGACAGTGTTCTACCAAG--------------TTGGTTTTATGAGGGGGAGGGGGAGG---------AGTGGTTCTTAAAGACTGCTTTTTATATAACATCAAT---CTGCCTGGATTTTGCATTAGATCCAATTTAGCAAAACACTAAAATCACTCATTTTTTAATGTA------------TCTTC-ATGTGTAGGTAAGGAATAGGAATTCAA--TTTTTGAAATACTGTCTGT-
q cavPor3.scaffold_0                                         999999999999999999999999999999999999999--------------99999999999999999999999999---------9999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999999999------------99999-999798358988587998588769999--9999999999999999999-
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50250895 212 +  95272651 TCTCACAGGTAAAGCTGATAATCACACTGTTCACCCGAA--------------GCCTTTTT---------AAATATATA---------AAT--TCCTTTAAGACTGCTATTTCTATAACATCAAT---CTGCCCGAGCTTTGTAGTAGATCCAATTTGGTGAAACACTAAAATCAATCATTTCTCAATGTGAAGC-------TTTTTCAATGTGCACAGAAGAAATAAGAATTCAA--TTTTTTAAACACTATTTGTG
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107349136 210 - 113440463 TCTCACAGGTAAAGTTGATAATCACACTGTTCGCCCAAA--------------GCTTTTTT---------TAATGTATA---------AGT--TCCTTGAAGACTGCTATTTCTATAACATCAAT---CTGCCTGAGCTTTGCAGTAGATCCAATTTGGTAAAATACTAAAATCAGTCATTTCTCAACGTGAAGC--------TTTTCAATGAACACAGAAGGAATAAGAATTCGA---TTTTTAAACATTGTTTGCA
q rn4.chr9                                                   999999999999999999999999999999999999999--------------99999999---------999999999---------999--99999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999--------999999999999999999999999999999999---9999999899999999999
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2471728 197 + 163896628 CCTCCCAGGTGAGACGGACG---GCGCTGTTCAAGCAAA--------------TCCTT------------AGCTTTGTCTTCCCCCCTAGC--TCCTTGAAGACTGCTATTTCTACCACTTCA--------------------GGTAGATCCAATTTAGTCAA--ACTAAAATCAATCATTTTTCACCGTGGGTT--------TTCTTGAGGTATAGGTAAGGAACAGGAATTCCCTGTGTTTAAAATCACATTCACA
q oryCun2.chr14                                              99999999999999999999---9999999999999999--------------99999------------999999999999999999999--999999999999999999999999999999--------------------99999999999999999999--999999999999999999999999999999--------9999999999999999999999999999999999999999999999999999999
i oryCun2.chr14                    C 0 C 0
s canFam2.chr23                     25993978 221 -  55389570 CCTCACAGGTAGAGCTGATAATGACACTGTTCAACCAAAtctctctctctctctctctctctctctctc-A-----------------AGT--TCCTTGAAGGCCGCTATTTCTATAACATCAGT---CGGCCTGCACTTTGCAATAGATCCAATTTAGCGAAACACTAAAATCAATCATTTTTCAATGTGGGGT--------TT---ATTGTATAGGTAAGGAACAGGAATTCAA--TTTTTTAAATAATGCTTGC-
q canFam2.chr23                                              999999999999999999999999999999999999999999999999999999999999999999999-9-----------------999--99999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999--------99---9999999999999999999999999999--9999999999999999999-
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22213388 210 -  87365405 CCTCACAGGTGAAGCTGATAATGACACTGTTCAACAAAA--------------TCTTTTTTTCTTTTTA-A-----------------AGT--TCCCTAAAGGCCACTGTTTCTATAACATAAAT---CTGCCTGGGCTTTGCAGTAGATCCAATTTACCAAAACACTAAAATCAATCATTTTTCAATGTGGCGT--------TTTTCATTGTATAGGTAAGGAATAGGAATTCCA--TTTTTAAAATAATGTTTGT-
q equCab2.chr16                                              999999999999999999999999999999999999999--------------9999999999999999-9-----------------999--99999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999--------999999999999999999999999999999999--9999999999999999999-
i equCab2.chr16                    C 0 C 0
s bosTau4.chr1                     156986024 210 + 161106243 CCACTCAGGTGAAGCTGATAACGATACTGTTCAACCAAA--------------TCCTTTTTTTTCCCTCTA-----------------AGT--CCCTTGAAGGCCACCATTTCTATAACCTCAAT---CTGCCTG-GCTTTGCCGTAGATCCAATTCAGCAAAACACAAAAGTCAATCATTGCTCGATGTGGGGT--------TTTTCACTGTGTAAGTGAAAAAAAGGAATTCGA--GCTTTAAAATAAGGTTTGC-
q bosTau4.chr1                                               999999999999999999999999999999999999999--------------999999999999999999-----------------999--99999999999999999999999999999999---9999999-99999999999999999999999999999999999999999999999999999999999--------999999999999999999999999999999999--9999999999999999999-
i bosTau4.chr1                     C 0 C 0
s loxAfr3.scaffold_36                 514776 223 -  24123610 CCTCACAGGTGAAGCTGATAATGACATTGTTCAACCACA--------------TTTTTTTTTTTTTTTT-A-----------------AGT-ATCCTTGAAGACCACTCTTTCTATAACATCAATCTGCTGCCTAGACTTTGTAGAGGATCCAATTTGACAAACCACTAAAATCGATCATTTTTTTATGTGGTTTTTTTTTTTTTTTCATTGCATAGGTAATGAGTAGGAATTCAA--TTTTTAAAATTATGTTTGTA
q loxAfr3.scaffold_36                                        999999999999999999999999999999999999999--------------9999999999999999-9-----------------999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e tupBel1.scaffold_130011.1-168288     43421 5578 -    168288 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276502991 2823 + 312544902 I
e eriEur1.scaffold_377961              16335 24689 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e dipOrd1.scaffold_20859                4370 3384 -     25303 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6809700 1532 +   6934412 I

a score=49117.000000
s hg19.chrY                          7655893 44 +  59373566 GAAGACAAAGCCT-ATTTCTTCCAC------ATGTGTCATTTCTAAATCTG
s panTro2.chrY                        509423 44 +  23952694 GAAGACAAAGCCT-ATTTCTTCCAC------ATGTGTCATTTCTAAATCTG
q panTro2.chrY                                              0000000000000-00000000000------00000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr3                      71037223 44 - 202140232 GAAGACAAAGCCC-ATGTCTTCTGT------ATGTGCCATTTCTAAATCTG
q ponAbe2.chr3                                              9999999999999-99999919999------99999756999999925869
i ponAbe2.chr3                     C 0 C 0
s rheMac2.chr2                     158764435 44 + 189746636 GAAGGCAAAGCCC-ATGTCTTCTGT------ATATGTCATTTCTAAATCTG
q rheMac2.chr2                                              6666666666666-66599999999------99999999999999999999
i rheMac2.chr2                     C 0 C 0
s tupBel1.scaffold_130011.1-168288     48999 20 -    168288 -AAAAGAAACCTC-ATTTCCCC-----------------------------
q tupBel1.scaffold_130011.1-168288                          -999999999999-99999999-----------------------------
i tupBel1.scaffold_130011.1-168288 I 5578 N 0
s cavPor3.scaffold_0                 8225423 31 -  88675666 -----------CC-ATATTTGCTAT--------GTGTCATTTCCAAACGTG
q cavPor3.scaffold_0                                        -----------99-99999999999--------999999999999999999
i cavPor3.scaffold_0               C 0 C 0
s mm9.chr17                         50251107 35 +  95272651 ---------GCCC-TTGGCTGCAAT------AGGTGTCATTTTGAAATTTC
i mm9.chr17                        C 0 C 0
s rn4.chr9                         107349346 35 - 113440463 ---------GCCC-TTGGCTGCAAT------GGGTGTCATTTTGAGATTTT
q rn4.chr9                                                  ---------9877-88899999999------99999999999999999999
i rn4.chr9                         C 0 C 0
s oryCun2.chr14                      2471925 40 + 163896628 ---------G-CC-GAGTCTTCCGTACTGACAGGCGTCATTTCTCAATCTG
q oryCun2.chr14                                             ---------9-99-9999999999999999999999999999999999999
i oryCun2.chr14                    C 0 C 0
s canFam2.chr23                     25994199 39 -  55389570 --------AGCCCAATATCTTCTGT----CTGTATGTCATTTCTAAATCTG
q canFam2.chr23                                             --------99999999999999999----9999999999999999999999
i canFam2.chr23                    C 0 C 0
s equCab2.chr16                     22213598 32 -  87365405 --------GGCCC-ACGTCTTCTG----------TGTCATTTCTAAGTCTG
q equCab2.chr16                                             --------99999-9999999999----------99999999999999999
i equCab2.chr16                    C 0 C 0
s bosTau4.chr1                     156986234 32 + 161106243 --------AGCCC-ATGTCTTTGG----------TATCATTTCTAAATCTG
q bosTau4.chr1                                              --------99999-9999999999----------99999999999999999
i bosTau4.chr1                     C 0 C 0
s loxAfr3.scaffold_36                 514999 35 -  24123610 ---------GGCT-TTGTCTTCTGT------ATGTGCCATTTCTAAATCTG
q loxAfr3.scaffold_36                                       ---------9999-99999999999------99999999999999999999
i loxAfr3.scaffold_36              C 0 C 0
e vicPac1.scaffold_6092                40542 4348 -     83534 I
e speTri1.scaffold_135460              78600 25574 -    203079 I
e micMur1.scaffold_734                270086 6625 -    418489 I
e ochPri2.scaffold_2292               101139 5426 +    188698 I
e felCat3.scaffold_206809               3730 5129 -    143945 I
e calJac1.Contig102                  1032597 7661 -   1157145 I
e monDom5.chr8                     276502991 2823 + 312544902 I
e eriEur1.scaffold_377961              16335 24689 +     88154 I
e turTru1.scaffold_111402              11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737       10907 1524 -     31737 I
e proCap1.scaffold_51344               18527 1340 -     18560 I
e dipOrd1.scaffold_20859                4370 3384 -     25303 I
e papHam1.scaffold12353                60426 8117 +     70985 I
e ornAna1.Ultra117                   6809700 1532 +   6934412 I

a score=126837.000000
s hg19.chrY                        7655937 50 +  59373566 TGGAATAAG---TGAGAATGTTTA--TTCTAGGCCTCTAAAAATTTAGACTTCTG
s panTro2.chrY                      509467 50 +  23952694 TGGAATAAG---TGAGAATGTTTA--TTCTAGGTCTCTAAAAATTTAGACTTCTG
q panTro2.chrY                                            000000000---000000000000--00000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71037267 50 - 202140232 TGGAATAAA---TTAAAATGTTGT--TCTAAGGGCTTTAAAAATTTAGACTTCTG
q ponAbe2.chr3                                            697994999---999999799996--79997996889333285695528867459
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158764479 50 + 189746636 TGGAATAAG---TTAAAATGTTTG--TTCCAGGGCTTTAAAAATTTAGACTTCTG
q rheMac2.chr2                                            999999999---999998898888--99999999999999999986666666665
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8225454 49 -  88675666 TAGAA-AAA---TTGAAATGTTTA--CTTTTGAGTTTTTAAAATTCAAGTTTCTG
q cavPor3.scaffold_0                                      99999-999---999999999999--99999999999999999999999979999
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50251142 50 +  95272651 TGGAACAAG---TTAAGACTTTCA--TTAGAAGGTTCTTTAAATTCAGATTTCCA
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107349381 50 - 113440463 TGGAACAAG---TTAAAACTTTCA--TTAGAAGGTTCTTTACATTCAGATTTCCA
q rn4.chr9                                                999999999---999999999999--99999999999999999999999999999
i rn4.chr9                       C 0 C 0
s oryCun2.chr14                    2471965 50 + 163896628 GGGAACAAG---TTAAGATGGTCA--CTTCAGGGCCTGTTAGAATCGGATTTCTg
q oryCun2.chr14                                           999999999---999999999999--99999999999999999999999999999
i oryCun2.chr14                  C 0 I 1164
s ochPri2.scaffold_135072              102 50 -      1325 GGGAACAAG---TTAAAACACTCA--TTTTACGGTCTGTTAAAATCAGATTTCTG
q ochPri2.scaffold_135072                                 387869989---984435444977--59989578555945548677579797668
i ochPri2.scaffold_135072        n 5426 C 0
s canFam2.chr23                   25994238 50 -  55389570 CGGAATAAA---TTAAAGCTTGCA--TTTTGAAGCTTTGCAAATTCAGATTTCTA
q canFam2.chr23                                           999999999---999999999999--99999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22213630 53 -  87365405 GGGGGAAAAGCTTTCAAGCATTCA--TTTTAGGGCTTTTCAAATTCAGATTTCTG
q equCab2.chr16                                           999999999999999999999999--99999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s bosTau4.chr1                   156986266 44 + 161106243 GGGCATAAC--------ACTTCCA--TCTTAGGG-TCTTCAAATTCAAATTTTTG
q bosTau4.chr1                                            999999999--------9999999--99999999-99999999999999999999
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               515034 52 -  24123610 GGGAGCAAG---CCAGAAACTTTGATTTTTAAGGCTTTTCAAAGTAAAATTTTGG
q loxAfr3.scaffold_36                                     999999999---9999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e speTri1.scaffold_135460            78600 25574 -    203079 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e turTru1.scaffold_111402            11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=69382.000000
s hg19.chrY                        7655987 30 +  59373566 TCA----TCTTTTCATTAAAC-AAATTCATGTTTC
s panTro2.chrY                      509517 30 +  23952694 TCA----TCTTTTCATTAAAC-AAATTCATGTTTC
q panTro2.chrY                                            000----00000000000000-0000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71037317 30 - 202140232 TCA----TCTTCTCGTTAAAC-AAATTCATGTATC
q ponAbe2.chr3                                            942----35223553132314-3228882885769
i ponAbe2.chr3                   C 0 I 687
s rheMac2.chr2                   158764529 30 + 189746636 TCA----TTTTCTCATTAAAC-AAATTCATGTTTC
q rheMac2.chr2                                            566----66676543235466-6666666666666
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8225503 28 -  88675666 TCA----TCTCA---TTAAATTATATTCAAGTTTC
q cavPor3.scaffold_0                                      999----99999---99999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50251192 18 +  95272651 T--------------TTAA---AAATCCAAGCTTC
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107349431 28 - 113440463 TCA----TCTTTCCATTAA---AAACCCAAGCTTC
q rn4.chr9                                                999----999999999999---9999999999999
i rn4.chr9                       C 0 C 0
s ochPri2.scaffold_135072              152 30 -      1325 CCA----TTTTCTCATTAAAC-AAGTTCACATTTT
q ochPri2.scaffold_135072                                 655----69966374454454-4475663668964
i ochPri2.scaffold_135072        C 0 C 0
s canFam2.chr23                   25994288 34 -  55389570 TCATTACTTGTCTTATCAAAT-AAATGCATGTTTT
q canFam2.chr23                                           999999999999999999999-9999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22213683 30 -  87365405 TCA----TCTTTTCATCAAAT-AAATTCATGTTTC
q equCab2.chr16                                           999----99999999999999-9999999999999
i equCab2.chr16                  C 0 C 0
s bosTau4.chr1                   156986310 29 + 161106243 TCA----ACTTTTTATC-AAC-AAATTCATGTTTC
q bosTau4.chr1                                            999----9999999999-999-9999999999999
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               515086 30 -  24123610 TCA----TCTTTTTTTCAAAT-AAATTTACATTTC
q loxAfr3.scaffold_36                                     999----99999999999999-9999999999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2472015 1164 + 163896628 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e speTri1.scaffold_135460            78600 25574 -    203079 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e turTru1.scaffold_111402            11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=18339.000000
s hg19.chrY                        7656017 21 +  59373566 TGAAACTTAAAAAAAAAA---TAA
s rheMac2.chr2                   158764559 18 + 189746636 TGAAACTTAAAAACACAC------
q rheMac2.chr2                                            666766699999999999------
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038034 20 - 202140232 TGAAACTTAAAAAACAAA----AC
q ponAbe2.chr3                                            490587995999969999----79
i ponAbe2.chr3                   I 687 C 0
s panTro2.chrY                      509547 18 +  23952694 TGAAACTTAAAAAAAAAA------
q panTro2.chrY                                            000000000000000000------
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8225531 21 -  88675666 TAAAACTTAAAAAAAAAAAAG---
q cavPor3.scaffold_0                                      999999999999999999999---
i cavPor3.scaffold_0             C 0 I 9
s mm9.chr17                       50251210 14 +  95272651 TAAAAGTgaagaaa----------
i mm9.chr17                      C 0 I 10494
s rn4.chr9                       107349459 11 - 113440463 TAAAAGTAAAA-------------
q rn4.chr9                                                99999999999-------------
i rn4.chr9                       C 0 I 12976
s ochPri2.scaffold_135072              182 18 -      1325 TGAAACTTGCAAGGAAGA------
q ochPri2.scaffold_135072                                 586368768414899999------
i ochPri2.scaffold_135072        C 0 C 0
s canFam2.chr23                   25994322 18 -  55389570 TGAAACTTACATAAATAA------
q canFam2.chr23                                           999999999999999999------
i canFam2.chr23                  C 0 I 3
s equCab2.chr16                   22213713 18 -  87365405 TGAAACTTACAAAAAAGA------
q equCab2.chr16                                           999999999999999999------
i equCab2.chr16                  C 0 I 1
s bosTau4.chr1                   156986339 18 + 161106243 TGAAACAAAACAAAACAG------
q bosTau4.chr1                                            999999999999999999------
i bosTau4.chr1                   C 0 I 1
s loxAfr3.scaffold_36               515116 17 -  24123610 TGACACTTAGAAAATGA-------
q loxAfr3.scaffold_36                                     99999999999999999-------
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2472015 1164 + 163896628 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e speTri1.scaffold_135460            78600 25574 -    203079 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e turTru1.scaffold_111402            11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=10296.000000
s hg19.chrY                        7656038 22 +  59373566 AACACATACATATCC-----AGGCTTA
s rheMac2.chr2                   158764577 21 + 189746636 -ACACACACATATCC-----AGGCTCA
q rheMac2.chr2                                            -99999999999999-----9999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038054 22 - 202140232 AAAAAACACATATAC-----AGGCTTA
q ponAbe2.chr3                                            999999999999999-----9999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509565 22 +  23952694 AACACATACATATCC-----AGGCTTA
q panTro2.chrY                                            000000000000000-----0000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8225561 15 -  88675666 AACAAA-------CT-----GGGCCTA
q cavPor3.scaffold_0                                      999999-------99-----9999999
i cavPor3.scaffold_0             I 9 I 134
s speTri1.scaffold_160574             7404 15 -    115260 GACAGA-------AT-----ACCTTTA
q speTri1.scaffold_160574                                 999999-------99-----9999999
i speTri1.scaffold_160574        n 25574 I 53
s ochPri2.scaffold_135072              200 14 -      1325 -ACACG-------CA-----TCCTCCA
q ochPri2.scaffold_135072                                 -99998-------89-----9986889
i ochPri2.scaffold_135072        C 0 I 5
s canFam2.chr23                   25994343 22 -  55389570 AAG-----CCTATCCAGGATAGGCTCA
q canFam2.chr23                                           999-----9999999999999999999
i canFam2.chr23                  I 3 C 0
s equCab2.chr16                   22213732 17 -  87365405 AAC-----CATATCC-----AGGTTCA
q equCab2.chr16                                           999-----9999999-----9999999
i equCab2.chr16                  I 1 C 0
s bosTau4.chr1                   156986358 22 + 161106243 AACACACACACATCC-----AGACTCA
q bosTau4.chr1                                            999999999999999-----9999999
i bosTau4.chr1                   I 1 C 0
s loxAfr3.scaffold_36               515133 19 -  24123610 ---AAACACATATCC-----AGGCTCA
q loxAfr3.scaffold_36                                     ---999999999999-----9999999
i loxAfr3.scaffold_36            C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e turTru1.scaffold_111402            11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=40423.000000
s hg19.chrY                        7656060 27 +  59373566 GGAGACCACACCATTAA----AACACTAttt
s rheMac2.chr2                   158764598 27 + 189746636 GGAGACCACACCACTAA----AATACTAttt
q rheMac2.chr2                                            99999999999999999----8899999499
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038076 27 - 202140232 GGAGACCACACCACTAA----AACACAAttt
q ponAbe2.chr3                                            99999999999999999----9999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509587 25 +  23952694 GGAGACCACACCATTAA----AACACt--tt
q panTro2.chrY                                            00000000000000000----000000--00
i panTro2.chrY                   C 0 C 0
s speTri1.scaffold_160574             7472 31 -    115260 gagtactctaccactgagccacaaccccagc
q speTri1.scaffold_160574                                 9999989999998999999999999999899
i speTri1.scaffold_160574        I 53 I 1792
s ochPri2.scaffold_135072              219 27 -      1325 GGCCACTCCACCATTAA----AACAGCGCTC
q ochPri2.scaffold_135072                                 99889999997567676----7777777677
i ochPri2.scaffold_135072        I 5 I 6
s canFam2.chr23                   25994365 27 -  55389570 GGAGACCACACCATTAA----AACACTATTT
q canFam2.chr23                                           99999999999999999----9999999999
i canFam2.chr23                  C 0 I 16
s equCab2.chr16                   22213749 27 -  87365405 GGAGACCACACCATTAA----AACACTATTT
q equCab2.chr16                                           99999999999999999----9999999999
i equCab2.chr16                  C 0 I 16
s bosTau4.chr1                   156986380 27 + 161106243 AGAGACCATACCATTAA----AACACTATGT
q bosTau4.chr1                                            99999999999999999----9999999999
i bosTau4.chr1                   C 0 I 16
s loxAfr3.scaffold_36               515152 16 -  24123610 CAAGACCACACTATTC---------------
q loxAfr3.scaffold_36                                     9999999999999999---------------
i loxAfr3.scaffold_36            C 0 I 598
e cavPor3.scaffold_0               8225576 134 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e turTru1.scaffold_111402            11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=99148.000000
s hg19.chrY                        7656087 58 +  59373566 ttaaaatttgaagtaaagtttccataatataaaattaatcattttaaagtgaacaatt
s rheMac2.chr2                   158764625 58 + 189746636 ttaaaatttgaagtgaaatttctataacataaaattaatcattttaaagtgaacaatt
q rheMac2.chr2                                            9999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038103 58 - 202140232 ttaaaatttgaagtgaaatttccataagataaaattaatcattttaaagtgaacaatt
q ponAbe2.chr3                                            9999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509612 58 +  23952694 taaaaatttgaagtaaagtttccataatataaaattaatcactttaaagtgaacagtt
q panTro2.chrY                                            0000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8225710 58 -  88675666 CAAAaaattgaaatggaactcctaaaacataaatttagccatcataaaatgaacaatt
q cavPor3.scaffold_0                                      9999999999999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0             I 134 C 0
s ochPri2.scaffold_135072              252 55 -      1325 ---CCAACCGAAGTGTCATttcccaaacataagatttaccattctaaagtgaacaaca
q ochPri2.scaffold_135072                                 ---7588777988684545755346686788848568878556787567666553555
i ochPri2.scaffold_135072        I 6 C 0
s canFam2.chr23                   25994408 50 -  55389570 ---ttaattgaagtgaaattc-----acatgagatcaaccattttaaagtgaacaatt
q canFam2.chr23                                           ---999999999999999999-----99999999999999999999999999999999
i canFam2.chr23                  I 16 C 0
s equCab2.chr16                   22213792 55 -  87365405 ---TTaattgaagtaaaatttacataacataaaatcaactattttaaagtgaacaatt
q equCab2.chr16                                           ---9999999999999999999999999999999999999999999999999999999
i equCab2.chr16                  I 16 C 0
s bosTau4.chr1                   156986423 54 + 161106243 ---TTaattggactgaaattcacttaacataaagtcaatca-tttaaagtgagtcagt
q bosTau4.chr1                                            ---99999999999999999999999999999999999999-9999999999999999
i bosTau4.chr1                   I 16 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e turTru1.scaffold_111402            11463 4906 -     37689 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=48440.000000
s hg19.chrY                        7656145 28 +  59373566 tggtggcattt-agtacactcatgatgtt
s rheMac2.chr2                   158764683 28 + 189746636 tggtggcattt-agtacattcatgatgtt
q rheMac2.chr2                                            99999999999-99999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038161 28 - 202140232 tggtggcattt-agtacattcatgatgtt
q ponAbe2.chr3                                            99999999999-99999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509670 28 +  23952694 tggtggcattt-agtacactcatgatgtt
q panTro2.chrY                                            00000000000-00000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8225768 27 -  88675666 tggggacattt-aatgtatt-ataatgct
q cavPor3.scaffold_0                                      99999999999-99999999-99999999
i cavPor3.scaffold_0             C 0 C 0
s ochPri2.scaffold_135072              307 17 -      1325 c-aggacactc-a----------cacgct
q ochPri2.scaffold_135072                                 7-667877866-3----------755785
i ochPri2.scaffold_135072        C 0 C 0
s turTru1.scaffold_111402            16369 26 -     37689 --gtggcattt-aatatatttgcaatgtt
q turTru1.scaffold_111402                                 --999999999-99999999999999999
i turTru1.scaffold_111402        I 4906 C 0
s bosTau4.chr1                   156986477 29 + 161106243 caggggcatttaaaaacatttacaatgtt
q bosTau4.chr1                                            99999999999999999999999999999
i bosTau4.chr1                   C 0 I 394
s equCab2.chr16                   22213847 28 -  87365405 cagcagcattt-agcacatttataatgtt
q equCab2.chr16                                           99999999999-99999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   25994458 28 -  55389570 caatggcattt-agtacattcataaggtt
q canFam2.chr23                                           99999999999-99999999999999999
i canFam2.chr23                  C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=144152.000000
s hg19.chrY                        7656173 145 +  59373566 gcaaaaccatcaactccatgtgtaggttctagaacattttcatcaacccaaaaggaaaccccacatccattaagcaattactctttccattc-------------------------------------------------------------------------------------------------ccctctctcccccag--ccctagcaaccaccaatatgctttcAC-AAAAAACTATT
s rheMac2.chr2                   158764711 146 + 189746636 gcataaccataaactctatctatacgttctgaaacattttcatccccctcaaaggaaaccccacgtccattacgcagttgctcttcccattc-------------------------------------------------------------------------------------------------ccctctctccccgag--ccctagcaatcgccaacatgctttcACAAAAGAACTATT
q rheMac2.chr2                                             99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------------------------------------------------------------------------------------------------999999999999999--999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038189 146 - 202140232 gcacaaccatcaactctatctataggttctgaaacattttcatcacccccagaggaaactccatgtccattacgcagttactcttcccattc-------------------------------------------------------------------------------------------------ccctctctccccgag--ccctagcagtcaccaacatgctttcACAAAAAAACTATT
q ponAbe2.chr3                                             99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------------------------------------------------------------------------------------------------999999999999999--999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509698 145 +  23952694 gcaaatccatcaactccatgtgtaggttctagaacattttcatcaccccaaaaggaaaccccacatccattaagcaattactctttccattc-------------------------------------------------------------------------------------------------ccctctctcccccag--ccctagcaaccaccaatatgctttcAT-AAAAAACTATT
q panTro2.chrY                                             00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-------------------------------------------------------------------------------------------------000000000000000--000000000000000000000000000-00000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8225795 241 -  88675666 gtacagtcatcaattctatcca---gatctaaaacatttttctcatcccagaaaggatcctctcattcactaagcagttattctcttctttttttcttttttgtagcagggatcaaacttataaccttgcacttagcaggcaagtgctcaagccactgagctaaatccccGGCTAAATAGTTACTTGCATCCTCTCTCCCAGAAGCTGTTGAAAACTACAAGTATGCCTTTAT-AAGACACTATT
q cavPor3.scaffold_0                                       9999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999
i cavPor3.scaffold_0             C 0 C 0
s ochPri2.scaffold_135072              324 137 -      1325 atgcaaccaacagcttcatcta---gttctgaaacatctgtattaccccaaagggaaaccccataaccactgagcaattat------------------------------------------------------------------------------------accccgg-----------------tcccttcccccccaa-ctcctggaaaccaccagcatgctttcAT-AAAACACTA--
q ochPri2.scaffold_135072                                  7664776799577777646677---63567875669766868878776534655366675555686545677656698996------------------------------------------------------------------------------------6554478-----------------677778766666589-8776773666898766578666567667-966767887--
i ochPri2.scaffold_135072        C 0 C 0
s turTru1.scaffold_111402            16395 111 -     37689 atacaaccatcacctctgtcta---gttctaaaat----------------gaggaaactgcatattcattaagcagttattc--cccattc-------------------------------------------------------------------------------------------------ctctctcccc-cagc--ccctggcaaccaccaatctgctttcA-------------
q turTru1.scaffold_111402                                  9999999999999999999999---9999999999----------------99999999999999999999999999999999--9999999-------------------------------------------------------------------------------------------------9999999999-9999--99999999999999999999999999-------------
i turTru1.scaffold_111402        C 0 N 0
s equCab2.chr16                   22213875 128 -  87365405 gtgcaatcctcatctctatcaa---gttctaaaacatcttcatcacgccaaaaggaaaccccatagccactaagcagtcattc--ccccttc-------------------------------------------------------------------------------------------------ccttctccccgtggc--ccctgggaaccaccaatccgAATTCA-------------
q equCab2.chr16                                            9999999999999999999999---9999999999999999999999999999999999999999999999999999999999--9999999-------------------------------------------------------------------------------------------------999999999999999--99999999999999999999999999-------------
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   25994486 122 -  55389570 ggacgaccatcacctctctgta---tttttaaaacatattcctca--ccacaaggaaaccccatagccattcagcagttactc--cctactc-------------------------------------------------------------------------------------------------tcttctgcttatagg--ctttggcaaccaccagtt----tTCA-------------
q canFam2.chr23                                            9999999999999999999999---99999999999999999999--999999999999999999999999999999999999--9999999-------------------------------------------------------------------------------------------------999999999999999--999999999999999999----9999-------------
i canFam2.chr23                  C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e vicPac1.scaffold_6092              40542 4348 -     83534 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=-11986.000000
s hg19.chrY                        7656318 22 +  59373566 -------CTTTTTAAA---AATTCTATTTTAA---
s rheMac2.chr2                   158764857 17 + 189746636 -------CTTTTT--------TAAAATTGTAA---
q rheMac2.chr2                                            -------999999--------99999999999---
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038335 17 - 202140232 -------CTTTTT--------TTAAATTTTAA---
q ponAbe2.chr3                                            -------999999--------99999999999---
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509843 22 +  23952694 -------CTTTTTAAA---AATTCTATTTTAA---
q panTro2.chrY                                            -------000000000---0000000000000---
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226036  8 -  88675666 -------TGGTCTGA--------------------
q cavPor3.scaffold_0                                      -------99999999--------------------
i cavPor3.scaffold_0             C 0 I 1
s ochPri2.scaffold_135072              461 18 -      1325 ---------GTCTAAT-----TTATATTTTTT---
q ochPri2.scaffold_135072                                 ---------6684888-----75656533236---
i ochPri2.scaffold_135072        C 0 n 0
s vicPac1.scaffold_6092              44890 35 -     83534 Cattccactgtatacgtgtgttactactttatcca
q vicPac1.scaffold_6092                                   99995999999999999999999999999999999
i vicPac1.scaffold_6092          I 4348 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e equCab2.chr16                   22214003  0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608  0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=14728.000000
s hg19.chrY                        7656340 46 +  59373566 TTGATTTT--ttg-tgtacatttaaggtgtacaacctgatgctttgatg
s rheMac2.chr2                   158764874 48 + 189746636 TTGATTTTTGttg-tgtatatttaaagagtacaacatgatgctttgatg
q rheMac2.chr2                                            9999999999999-99999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038352 47 - 202140232 TTGATTTTTGttg-tgtatatttaaggtgtacaacataatgc-tcgatg
q ponAbe2.chr3                                            9999999999999-9999999999999999999999999999-999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509865 46 +  23952694 TTGATTTT--ttg-tgtacatttaaggtgtacaacctgatgctttgatg
q panTro2.chrY                                            00000000--000-00000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226045 41 -  88675666 TTATTTTT-ACtg-tacatatgtaaggtatgc------atgttttgaca
q cavPor3.scaffold_0                                      99999999-9999-999999999999999999------99999999999
i cavPor3.scaffold_0             I 1 C 0
s ochPri2.scaffold_2292             106565 28 +    188698 TTAACCCT--CTG-TGC-TACATTGTGAACCC-----------------
q ochPri2.scaffold_2292                                   99999999--999-999-99999999999999-----------------
i ochPri2.scaffold_2292          I 5426 I 416
s vicPac1.scaffold_6092              44925 43 -     83534 ttcatcta--ttgatgcgcacttaggatgc----tcctatgtcttggtg
q vicPac1.scaffold_6092                                   99999999--99999999999999999998----999999999999999
i vicPac1.scaffold_6092          C 0 N 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e equCab2.chr16                   22214003  0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608  0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=83487.000000
s hg19.chrY                        7656386 177 +  59373566 tacacatacttag-tcaaatgattactacactcaagaaagccaacataacaatcacatcacaaagttagttttcttttttgtgtgtgggaagagtacctaaaatctattctcttagcagatttccagtatataatattattagctatattccccatgttgtacattagatcagtcccc
s rheMac2.chr2                   158764922 163 + 189746636 tacatatacttagctcaaatgattactacagtcaagataaccaacataaccatcatctcacatagttagttttcctttttgtgtatggtaagagtacctaaaatctattctctgagcagatttccagtatatgatgttattagctatagtccctgtgttgtac---------------
q rheMac2.chr2                                             9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038399 163 - 202140232 tacatatacttagttcaaatgattactagagtcaagaaaagcaacataaccatcatttcacatagttagttttcttttttgtgtgtggtaagagtacctaaaatctattctctgagcagatttccagtacacagtgttattcactatagtccccatgttgtac---------------
q ponAbe2.chr3                                             9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      509911 177 +  23952694 tacacatacttag-tcaaatgattactacactcaaggaagccaacataacaatcacatcacaaagttagttttctttttcgtgtgtgggaagagtacctaaaatctattcttttagcagatttccagtatataatattattagctatattccccatgttgtacattagatcagtcccc
q panTro2.chrY                                             0000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226086 161 -  88675666 tacatatgctcag------tgatctccaccctcaaaccaattaat-tgctcatcatgtcaca-----gttctgtctccttgtgtgt-acagaagaacctaaacactactcccttagcaaatcttcagcataaaatactcctaacaaatcttcctgttctatac--tagatcactgc--
q cavPor3.scaffold_0                                       9999999999999------99999999999999999999999999-9999999999999999-----9999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999--
i cavPor3.scaffold_0             C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2472015 1164 + 163896628 I
e equCab2.chr16                   22214003   0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608   0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e ochPri2.scaffold_2292             106593 416 +    188698 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=29740.000000
s hg19.chrY                        7656563 95 +  59373566 atgatgtgtattagatctctagattgacttatcatacataactgcaactttgtacctttcaccta-catctccccatctccctgaccaccgccccc
s rheMac2.chr2                   158765085 80 + 189746636 ---------attagatctctagatttacttatcatacataactgcaactttgtacctttgagcta-catctccccttctccctg------accccc
q rheMac2.chr2                                            ---------99999999999999999999999999999999999999999999999999999999-999999999999999999------999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038562 80 - 202140232 ---------attagatctctagatttacttatcatacataactgcaactttgtacctttgaccta-caaatccccatctccctg------accccc
q ponAbe2.chr3                                            ---------99999999999999999999999999999999999999999999999999999999-999999999999999999------999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      510088 93 +  23952694 atgatgtctattagatctctagattgacttatcatacataactgcaactttgtacctttcaccta-catctccccatctccctgacca--gccccc
q panTro2.chrY                                            00000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000--000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226247 69 -  88675666 ---acttatcctaggtaactgaa--actttattctctataact-cacatttcctcctccccactctcacctgccc---------------------
q cavPor3.scaffold_0                                      ---99999999999999999999--999999999999999999-9999999999999999999999999999999---------------------
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2473179 72 + 163896628 ATTATCTGTCGTGGCCCCCAGGACCGCTTCGCCCCACATCACTGCAGCTGTGGTCCTTCTGACTA-CACCATC-----------------------
q oryCun2.chr14                                           99999999999999999999999999999999999999999999999999999999999999999-9999999-----------------------
i oryCun2.chr14                  I 1164 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e equCab2.chr16                   22214003  0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608  0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e ochPri2.scaffold_2292             106593 416 +    188698 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=30551.000000
s hg19.chrY                        7656658 75 +  59373566 caaa----------ctacagttctactctctgtttctgtgtat--ttgatttttagttt--gattgcacataatatgtgagattatgta
s rheMac2.chr2                   158765165 76 + 189746636 taaa----------ctacagttctactctctgtttccgtgtat--ttgatttttagtttaagattgcacata-tatgagagattatgta
q rheMac2.chr2                                            9999----------99999999999999999999999999999--999999999999999999999999999-9999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038642 72 - 202140232 caaa----------ctacagttctactctctgtttc----tat--ttgatttttagtttaagattgcacata-tatgcgagattatgta
q ponAbe2.chr3                                            9999----------9999999999999999999999----999--999999999999999999999999999-9999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      510181 74 +  23952694 caaa----------ctacagttctactctctgtttctgtgtat--ttgatttttagttt--gattgcacata-tatgtgagattatgta
q panTro2.chrY                                            0000----------00000000000000000000000000000--00000000000000--00000000000-0000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226316 59 -  88675666 -----------------ctgcttta----tgacttatatgtagcaattttttttaa-----gattccacaaa-taagcaagatcat---
q cavPor3.scaffold_0                                      -----------------99999999----999999999999999999999999999-----99999999999-9999999999999---
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2473251 68 + 163896628 --------------CTATGGttccaccctctgtttctaggtaggattcagctttag------actctacagg-aaagcgagaccctgca
q oryCun2.chr14                                           --------------999999999999999999999999999999999999999999------9999999999-9999999999999999
i oryCun2.chr14                  C 0 I 5
s ochPri2.scaffold_2292             107009 74 +    188698 ccaaccacagccctctacaattcca----ctgcttcgaagtatgact--gttttca--------tctatgcg-aaagtgagatcctgca
q ochPri2.scaffold_2292                                   9999999999999999999999999----999999999999999999--9999999--------99999999-9999999999999999
i ochPri2.scaffold_2292          I 416 N 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e equCab2.chr16                   22214003  0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608  0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=168141.000000
s hg19.chrY                        7656733 264 +  59373566 gtatttttccttctgtgtctggcttatttcacttagcagaatgtcctctaggttcacccatgctattgaaaatggaggatcaccttcttttttaaagctgaataatattccat--tgtgtatatataccacagtttatttatccaatcatctattgatggacatgtagattgtttcc---------------------------------------------------------atatactggctattatgaataatgctgcaaataagatggagtgcagatatccctttaacatactgatttcatttcctttggagaaatac
s rheMac2.chr2                   158765241 257 + 189746636 gtatttttccttctgtgtctggcttatttcacttagcagaatatcctctaggtttacccaggctgttgtaaatggaggatcatcatcttttttaaggctgaataatattcctt--tgcgtatatataccatagtttatttatccagtcatctattaatggatatgtaagttgtttcc---------------------------------------------------------atatcctggctattgtgaataatgctga-------atggagcacagatatttcttcaacatactgatttcatttcctttggagaaatac
q rheMac2.chr2                                             99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999---------------------------------------------------------9999999999999999999999999999-------999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038714 256 - 202140232 gtatttttccttctgtgtctggcttatttcatttagcagaatgtcctctaggttcacccatgctgttgtaaatggaggatcatcttc-tttttaaggctgaataatattccat--tgcatatatataccatagtttatttatccagtcatctattgatggacatgtaggttgtttcc---------------------------------------------------------atatcccggctattgtgaataatgctgc-------atggagtgcagatatctcttcaacatactgatttcatttcctttggagaaatac
q ponAbe2.chr3                                             999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999---------------------------------------------------------9999999099999999999999999999-------999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      510255 321 +  23952694 gtatttttccttctgtgtctggcttatttcacttagcagaatgtcctctaggttcacccatgctattgaaaatggaggatcaccttcttttttaaagctgaataatattccat--tgtgtatatataccatagtttatttatccaatcatctcttgatggacatgtagattgtttccctatactggctattatgaataatgctgcaaataagatggagtgcagatattgtttccatatactggctattatgaataatgctgcaaataagatggagtgcagatatccctttaacatactgatttcatttcctttggagaaatac
q panTro2.chrY                                             00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226375 246 -  88675666 gtatatttcatcctgtgactggtttctttcactgagcacaatctcctttcagtacatccatggtgttgccaatggagga----ctgcttatctaatactaaataacattccact-tgtatataaatagtatagccccctcatccatttgtgcactgactggtccttaggttgtgtcc---------------------------------------------------------acatcttggctactatgaac---------------ttggagtgtagctatcttcataagatgtcaagtttatttcctttatgcatatac
q cavPor3.scaffold_0                                       9999999999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999---------------------------------------------------------99999999999999999999---------------999999999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0             C 0 I 3
s oryCun2.chr14                    2473324 242 + 163896628 gtattgtttgttct----ctggtttactgtattaaa-------tcctccggatttaactacgtggttgcaaatgaaggctc-tccccttgttcagggctgtataatactccactgtggatatttatgccatgacttcttcctccacagacacgtgggtctgtcct---------------------------------------------------------------------gcatcctggctgtcgtggatgacgtggcctgagcatgggagagcagacaacttcgcaaggcgctgctcccattccctgagagtccacac
q oryCun2.chr14                                            99999999999999----999999999999999999-------99999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------------------------------------------------------------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i oryCun2.chr14                  I 5 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e equCab2.chr16                   22214003   0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608   0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=191678.000000
s hg19.chrY                        7656997 351 +  59373566 ccagtaatggggttgctagatcatatggtatttctatttttc--ctttttgatgaatctccatattgtcttccataatgactgtactagtttacattcccaccaaccatgtgcaaggtttctcttattctccacattctcaccagcacttgttatctcttgtattttttatagtagccatcctaatacatgttaactcatatctcactatggttttgatttgcatttccct--gataatcagtta-gttaataagcattctttcctacatgtgtgggccactcttatatctcctttggtgatatgtctattcaggccatctgcccatttttc-aagttgtgttatttg-tggttttcc
s rheMac2.chr2                   158765498 352 + 189746636 ccagtaatgggattgctagatcatatgatatttctattttta--atttttgatgaacctccatattgttttccataatggctgtgctagtttacattcccaccaatggagtgcaagggttctcttattctccacatcctcaccagcacttcttatctcttgtatttttgatagtagccattctaacaggtgtgagctgatatctcactgtggttttgatttgcatttctct--gatgtttaatgacattaataaccattctttcctatatgcgtggaccacttttatatctccttaggagatatgtctattcaggccctctgcccatttttc-aagttgggttatttg-tattcttgc
q rheMac2.chr2                                             999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999996766-999999999999999-999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71038970 352 - 202140232 ccagtaatgggattgctagatcataggatatttctattttta--atttttgatgaacctccatattgttttccacaatggctgtactagtttacattcccaccaacggggtgcaagagttctcttactctccacatcctcaccaacacttcttatctcctgtatttttgatagtagccattctaacaggtgtgagctgatatctcactgcggttttgatttgcatttctct--gatgtttagtgatgttaataagcattctttcatatatgtgtgggccacttttatatctcctttggagatatgtctattcaagccctctgcccatttttc-aagttgggttatttg-tatttttgc
q ponAbe2.chr3                                             999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999-999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      510576 351 +  23952694 ccagtaatggggttgctagatcatatggtatttctatttttc--ctttttgatgaacctccatattgtcttccataatgactgtactagtttacattcccaccaaccgtgtgcaaggtttcttttattctccacattctcaccagcacttgttatctcttgtattttttatagtagccatcctaatacgtgttaactgatatctcactatggttttgatttgcatttccct--gataatcagtta-gttaataagcattctttcctacatgtgtgggccactgttatatctcctttggtgatatgtctattcagggcatctgcccatttttc-aagttgtgttatttg-tggttttcc
q panTro2.chrY                                             000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000-000000000
i panTro2.chrY                   C 0 C 0
s oryCun2.chr14                    2473566 309 + 163896628 ccagcagaggaatcact-ggccacatagggctgttgtttttaatctctttaaggaacctcgatgctgttttccaccgtggctgc-ccaatctgaattccca-----------------------------ccacattcgtgccgacagctgtcatctcttgtctt-----------cctttctcagaggtgtg-------acctcatcgtggttttgattggcatttcccccggcgacctagcaatgtaaactagcacccttccacacaccgacgggcggtcctgatgtcttatttggagaaacatctactcaggtccttggttcattttttaaaagggggttattcactttttttgc
q oryCun2.chr14                                            99999999999999999-999999999999999999999999999999999999999999999999999999999999999999-9999999999999999-----------------------------99999999999999999999999999999999999-----------99999999999999999-------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i oryCun2.chr14                  C 0 C 0
e cavPor3.scaffold_0               8226621   3 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e equCab2.chr16                   22214003   0 -  87365405 C
e bosTau4.chr1                   156986506 394 + 161106243 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e canFam2.chr23                   25994608   0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=130702.000000
s hg19.chrY                        7657348 79 +  59373566 tattgagctgaatgagttcTGAAACACTGTTCTTAATAATTTAATTAAACCATGGATGAACACACAGTG--GA-ATCTCAGT
s bosTau4.chr1                   156986900 61 + 161106243 -------------------TAAAACACAATTCTTAACACCTTAACTACAACACAGATAAACTCAAGAGGG-GA-ATCTCAGT
q bosTau4.chr1                                            -------------------999999999999999999999999999999999999999999999999999-99-99999999
i bosTau4.chr1                   I 394 C 0
s canFam2.chr23                   25994608 62 -  55389570 -------------------TAAAACACAGTTCTTAACACCTTATCTAAATCATGGATAAACTCAAGGGGGAAA-ATCTTGGT
q canFam2.chr23                                           -------------------999999999999999999999999999999999999999999999999999999-99999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22214003 60 -  87365405 -------------------TAAAACACGATTCTTAACACCTTAACCAAACCACAGATAAACTCAAGGGG--AA-ATCTCAGT
q equCab2.chr16                                           -------------------99999999999999999999999999999999999999999999999999--99-99999999
i equCab2.chr16                  C 0 C 0
s rheMac2.chr2                   158765850 79 + 189746636 tattgagctgaatgagttcTGAAACGCTATTCTTAATACCTTAATTAAACCATGGATGAACACACAGGG--GA-ATCTCAGT
q rheMac2.chr2                                            999999999999999999999999999999999999999999999999999999999999999999999--99-99999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71039322 79 - 202140232 tattgagctgaatgagttcTGAAACACTATTCTTAATACCTTAATTAAACCATGGATGAACACACAGGG--GA-ATCTCAGT
q ponAbe2.chr3                                            999999999999999999999999999999999999999999999999999999999999999999999--99-99999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      510927 79 +  23952694 tattgagctgagtgagttcTGAAACACTGTTCTTAATAATTTAATTAAACCATGGATGAACACACAGTG--GA-ATCTCAGT
q panTro2.chrY                                            000000000000000000000000000000000000000000000000000000000000000000000--00-00000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8226624 80 -  88675666 TGTTAAACTGTTTAAGTTCTAAAACACTATTCTTAATACCATAACTGAATCATGGATAAACACAGAGGG--GAGATCTCAGT
q cavPor3.scaffold_0                                      999999999999999999999999999999999999999999999999999999999999999999999--99999999999
i cavPor3.scaffold_0             I 3 C 0
s oryCun2.chr14                    2473875 75 + 163896628 tattgagttgcatgagttctagaagattattctgcgtactTTA----AATCACGGGTAAACACACAGGG--CA-ATCTCAGT
q oryCun2.chr14                                           9999999999999999999999999999999999999999999----9999999999999999999999--99-99999999
i oryCun2.chr14                  C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e loxAfr3.scaffold_36               515168 598 -  24123610 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=257462.000000
s hg19.chrY                        7657427 140 +  59373566 AAGATTAAAATAATTTCTTTAAGCTTATATAAACCTAAGATTC-TGCAGGTCAGTCAGAGAGTAACTGGCAAAGCAACAGATG---CCTGATCAAATGAAT---TAAGTTGC----AGGCTGTCGGACCACAAATGACTGTTAA-ACATCAG
s oryCun2.chr14                    2473950 134 + 163896628 AATGCT------GTTTCTTTCAGCTCAGAGAGACCAGGGATTCCCTAGGGTCCATCAGCAAATAACTGGCGAAGCAGCGGATG---CCTCGTGGAGTGTGTTC-TGAGGTGC----AGGTCGCCAGATCTTC----ACTGTGGAGGCATCAG
q oryCun2.chr14                                            999999------99999999999999999999999999999999999999999999999999999999999999999999999---99999999999999999-99999999----9999999999999999----9999999999999999
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8226704 142 -  88675666 AAGACTAA---AAGCACTTTCAGCTTCTGTAAAACAAGGATTTGTGCAGGTCAATCAGGGAGTAATTGGCAAAGCAACAGATG---CCTCATCAAATGAGTTCTTAAAAGGC----ACTGTAGCAGATCATAGAAGACTGTTAGAAGGGCAG
q cavPor3.scaffold_0                                       99999999---999999999999999999999999999999999999999999999999999999999999999999999999---99999999999999999999999999----999999999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s panTro2.chrY                      511006 140 +  23952694 AAGATTAAAATAATTTCTTTAAGCTTATATAAACCTAAGATTC-TGCAGGTCAGTCAGAGAGTAACTGGCAAAGCAACAGATG---CCTGATCAAATGAGT---TAAGTTGC----AGGCTGTCGGACCACAAGTGACTGTTAA-GCATCAG
q panTro2.chrY                                             0000000000000000000000000000000000000000000-000000000000000000000000000000000000000---000000000000000---00000000----0000000000000000000000000000-0000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71039401 141 - 202140232 AAGACTAAAAGAACTTCTTTAAGCTTATATAAACCTAAGATTC-TGCAGGTCAATTAGGGAGTAACTGGCAAAGCAACAGATG---CCTCATCAAATGAAT---TAAGTTGC----TGGCCGCCAGACCACAAATGACTGTTAATGCATCAG
q ponAbe2.chr3                                             9999999999999999999999999999999999999999999-999999999999999999999999999999999999999---999999999999999---99999999----999999999999999999999999999909999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158765929 138 + 189746636 AAGACTAAAAGAACTTCTTCAAGTTTGTATAAACCTAAGATTC-TGCAGGTCAATTAGGGAGTAACTGGCAAAGTGACAGATG---CCTCACCAAATGAAT---TAAGTTGC-------CAGCCAGACCACAAATGACTGTTAAAGCATCAG
q rheMac2.chr2                                             9999999999999999999999999999999999999999999-999999999999999999999999999999999999999---999999999999999---99999999-------999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s equCab2.chr16                   22214063 142 -  87365405 AAGACTAAAAGCACTTCTTCAAACTTATATAAACCTAGGA-CC-TACAGGTCACTCAGTGGGTAACTGTAAATGCAACAGATG---CCTCATTGAATGAGTTCTTAAGATGC----AGGCCTCCAGACCACAAACGATGGCTAA-GCATCAG
q equCab2.chr16                                            9999999999999999999999999999999999999999-99-999999999999999999999999999999999999999---99999999999999999999999999----9999999999999999999999999999-9999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   25994670 149 -  55389570 AAGTCTAAAAGCATTTCTTTAAACTTATATAAACCTAGGATTC-TACA-TTCAATCATGGAGTAATTGGCAAAGCAACAGACGACACCTCATCAAATGAGTTCTTAAGATTTTTTGTGGCCACCAGACCACAAATGACTGGGAA-GCATCAG
q canFam2.chr23                                            9999999999999999999999999999999999999999999-9999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156986961 139 + 161106243 AGGACTAAAAGCACTTCCTCAAGCTTCCACGAACCTAGGATTC-TACAGGTCAGCCAGC-AATAACTGACGAAACAACCCATG----CTCATCAAATGAG-TCCTGAGATGG----GGGTCGCCAGTCcac-agtggctatgaa-tcccccg
q bosTau4.chr1                                             9999999999999999999999999999999999999999999-999999999999999-99999999999999999999999----9999999999999-99999999999----999999999999999-999999999999-9999999
i bosTau4.chr1                   C 0 I 149
s loxAfr3.scaffold_36               515766 143 -  24123610 AGGACTAAAAGAGGTTCTGTAAATGCGTATAAACCCAGGATTC-TGCAGGTGAAACAGGGAGTAATTGGCAAAGCAATAGATG---CCTCACCAAATGAGTTCTTAAGATGC----AAACCACCTGACCACAAATGATGACTGA-GCTTCTA
q loxAfr3.scaffold_36                                      9999999999999999999999999999999999999999999-999999999999999999999999999999999999999---99999999999999999999999999----9999999999999999999999999999-9999999
i loxAfr3.scaffold_36            I 598 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=151064.000000
s hg19.chrY                        7657567 175 +  59373566 ACTGCCATGACA-------------------------------------------------------------ATGGGAGAG-GGGGAAAGGTAAATTGTTATTGCTTTGCTTGTCATTTCAGAGAATCACACATAGTCAGTAAATTacacacacacaca----catgcacacacacacacacCCCACTGTGCTGTAAAAATTCAGTGTCCAG-------------GTATT-TGTAATGAGACTGCCTCAATAAT
s loxAfr3.scaffold_36               515909 147 -  24123610 ATAGTCATGACA-------------------------------------------------------------AGCAGAGGG-GAGG-------------------TTTGCTTGGC-TTTCAAAGGGTCACACAGAGTCACTGAATTATGCACCTTTGTA--------CACTCACACACACACCATACCGT----TAGAAACTCAGTGTCTGG-------------ATATT-TGAAAGGAGAATACCTGAATTAT
q loxAfr3.scaffold_36                                      999999999999-------------------------------------------------------------999999999-9999-------------------9999999999-9999999999999999999999999999999999999999999--------99999999999999999999999----999999999999999999-------------99999-99999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s equCab2.chr16                   22214205 206 -  87365405 ACAACCACAACAATGCG---------gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgAAG---GGGACGGGG-AGGGGAAGTCAAGTTCTCATTGGTTTGCTTGTCATTTCAAAGGGTCACACACAGTCACAGAATTACACACACACACA-------------------ATATGGTACTGTA---AAAAAATTCAGCGTCTAG-------------GTGTT-TGTAAGGAGAGTGCCTGAATAAT
q equCab2.chr16                                            99999999999999999---------99999999999999999999999999999999999999999999---999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999-------------------9999999999999---999999999999999999-------------99999-99999999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   25994819 212 -  55389570 ATGATCAAAGTGCTAGGATAACAGgtgtgtgtgtctctgtgtgtacatgtttgtgtgtgtgtgGGTAAAGCAAAGGGTGGAG-GGAGACAGGAAACTTGTTATTGG-TTGCTGGTCATTTCAAAGAGTCACGCATAGTCACTGAATT--ATGCACACACA-------------------ACATCATACTGT----AAAAAATTCAGTGTCTAG-------------AAG-T-TGTAAGGAGAGTG-CTGAGTAAT
q canFam2.chr23                                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999-9999999999999999999999999999999999999999--99999999999-------------------999999999999----999999999999999999-------------999-9-9999999999999-999999999
i canFam2.chr23                  C 0 C 0
s oryCun2.chr14                    2474084 142 + 163896628 ACTGCCCTGACA-------------------------------------------------------------GCGGAGA---GAGGGGAGCCACGTTGTTATGTG----CTTATCCTTTCAATGGGTCACGCAAAGCCACTGAACTGTGCGCACACATACACA-------------GCGCACCCTAA---------AAACGTTAGTGTCCAG-------------GTGTTCAGGAGGGAAA----------AAC
q oryCun2.chr14                                            999999999999-------------------------------------------------------------9999999---99999999999999999999999----999999999999999999999999999999999999999999999999999999-------------99999999999---------9999999999999999-------------9999999999999999----------999
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8226846 192 -  88675666 ACTGCCATGGCAACAGG----------------------------------------------GGTGG-----GTGGAGG---AAGGAGGGTCAAGGTACTATTGGTTTTCTTGTCAATTCAAAAGGTCATATAAAGCTACTGAATTATacacacacacacacacacacacacacacacacacacaac---------acacaacacCGTGCTGAATAAACTTCATTGTGTGCTGAAAGGAGCCGACCTGAGTAAC
q cavPor3.scaffold_0                                       99999999999999999----------------------------------------------99999-----9999999---999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------9999999999999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s panTro2.chrY                      511146 173 +  23952694 ACTGCCATGACA-------------------------------------------------------------ATGAGAGAG-GGGGAAAGGTAAGTTGTTATTGCTTTGCTTCTCATTTCAGAGAATCACACATAGTCAGTAAATTacacacacacaca------tgcacacatacacacacCCCACTCTGCTGTAAAAATTCAGTGTCCAG-------------GTATT-TGTAATGACGCTGCCTCAATAAT
q panTro2.chrY                                             000000000000-------------------------------------------------------------000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000------00000000000000000000000000000000000000000000000-------------00000-00000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71039542 173 - 202140232 GCTGTCGTGACA-------------------------------------------------------------ATGGGAGCC-GGGGAGAGTTAAGTTGTTATTGGTTTGCTCGTCATTTCAGAGAATCACACATAGTCAATGAATTacacacacacaca------cacacacacacacacacCCCACTGTACTGTAAAAATTCAGTGTCCAG-------------GTATT-TGTAAGGAGACTGCCTCAACAAT
q ponAbe2.chr3                                             999999999999-------------------------------------------------------------999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999-------------99999-99999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158766067 180 + 189746636 GCTGTGGTGACA-------------------------------------------------------------GTGGGAGGGCAGGGAGAGTTAAGTTGTTATTGGTTTGCTTGTCATTTCAGAGAATCACGCATAGTCAATGAATcacacacacacacacacacacacacacacacacacacacCACTGTACCATAAAAATTCAGTGTCCAA-------------GTATT-TGTAAGGAGACTGCCTCAACAAT
q rheMac2.chr2                                             999676765666-------------------------------------------------------------67677666666666766666776666666666676666677666666676666666666667667766676766666676766666776666667667666666676666667665666667767766766777656666-------------66666-76666766666667666766666
i rheMac2.chr2                   C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e bosTau4.chr1                   156987100 149 + 161106243 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             3730 5129 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276502991 2823 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ornAna1.Ultra117                 6809700 1532 +   6934412 I

a score=111827.000000
s hg19.chrY                        7657742 62 +  59373566 TTCTATTGACTGTATCTATTAATAAAACTCAGAAGATGGCATTATTGCTCACCTCACCAGTC
s monDom5.chr8                   276505814 55 + 312544902 TGCCATCAACTGTGAATACTGATC-------AAAGCTGTAAGCCTGCCCCAGTTCTCTAGTT
q monDom5.chr8                                            999999999999999999999999-------9999999999999999999999999999999
i monDom5.chr8                   I 2823 C 0
s loxAfr3.scaffold_36               516056 62 -  24123610 TCCCATTGACTGTGCCCAGTGATCACACCAAAACAATGGCATTGTTGCTCAACTCACCAGTC
q loxAfr3.scaffold_36                                     99999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s equCab2.chr16                   22214411 62 -  87365405 TCCCCAAGATTGTACCCATTGATCAAACCCAAAAGATGGCATTATTGCTCATCTCACCAGTC
q equCab2.chr16                                           99999999999999999999999999999999999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   25995031 62 -  55389570 TCCCATTGACTGTACCCATTAATCAAACCCAAAGGACGGCATTACTGCTCATCTCACTGGTC
q canFam2.chr23                                           99999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s oryCun2.chr14                    2474226 38 + 163896628 TCCCATTGGCTGTACCCACTGCTCTGACCC--AAG-TGACG---------------------
q oryCun2.chr14                                           999999999999999999999999999999--999-99999---------------------
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8227038 59 -  88675666 TCCCA-TGATGGTACTCACTGATCAAAACC--AAGATGACATTCTAGCTCATCTCCCTAGTC
q cavPor3.scaffold_0                                      99999-999999999999999999999999--999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s panTro2.chrY                      511319 62 +  23952694 TTCTATTGACAGTATCTATTAATAAAACTCAGAAGATGGCATTATTGCTCACCTCACTAGTC
q panTro2.chrY                                            00000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71039715 62 - 202140232 TTCCATTGACTGTATCCATTAACAAAACTCAGAAGATGGCATTATTGCTCACCTCACCAGTC
q ponAbe2.chr3                                            99999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158766247 62 + 189746636 TTCCATTGACTGTATCCATTAATAAAACCCAGAAGATAGCGTTATTGCTCATCTCACTAGTC
q rheMac2.chr2                                            66666666676666666666666666666666666666666676676676677666667667
i rheMac2.chr2                   C 0 C 0
s ornAna1.Ultra117                 6811232 53 +   6934412 ----ATTGGCTCTCTATACTGATTAGAATC-----ATCAAGTAATTGCTCAACTCTACATTT
q ornAna1.Ultra117                                        ----99999999999999999999999999-----999999999999999999999999999
i ornAna1.Ultra117               I 1532 C 0
s felCat3.scaffold_206809             8859 38 -    143945 ------------------------GAACCCAAAAGACGGCGTTCCCGCTCATCTCACTGGTC
q felCat3.scaffold_206809                                 ------------------------99999999999979989999988998975999479999
i felCat3.scaffold_206809        I 5129 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e bosTau4.chr1                   156987100 149 + 161106243 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=89292.000000
s hg19.chrY                        7657804 30 +  59373566 CATTTTGTCAGAGAAGACACAGATTAAGAT
s rheMac2.chr2                   158766309 30 + 189746636 CATTTTGTCAGAGAAGACACAGGCTAAGAT
q rheMac2.chr2                                            667666676667666667666666776666
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71039777 30 - 202140232 CATTTTGTCCGAGAAGACACAGGCTAAGAT
q ponAbe2.chr3                                            999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      511381 30 +  23952694 CATTTTGTCAGAGAAGACACAGGTTAAGAT
q panTro2.chrY                                            000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8227097 30 -  88675666 CATTTTGTCACAAAACAAACAGGCTAAGGT
q cavPor3.scaffold_0                                      999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2474264 26 + 163896628 ----TTGCCAGAGAAAACGCAGGCTCGAGT
q oryCun2.chr14                                           ----99999999999999999999999999
i oryCun2.chr14                  C 0 C 0
s canFam2.chr23                   25995093 30 -  55389570 CATTTTGACAGAGAAGACACAGGCAAAGAT
q canFam2.chr23                                           999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_206809             8897 30 -    143945 CATTTTGTCAGAGAAGACACAGGCTAAGAT
q felCat3.scaffold_206809                                 999996899999999999999996999999
i felCat3.scaffold_206809        C 0 C 0
s equCab2.chr16                   22214473 28 -  87365405 CGTGTTGTTGGAGGAG--ACAGGCCAAGAT
q equCab2.chr16                                           9999999999999999--999999999999
i equCab2.chr16                  C 0 C 0
s bosTau4.chr1                   156987249 30 + 161106243 CACTCTAACATAAAATAAATAATTAAAAAC
q bosTau4.chr1                                            999999999999999999999999999999
i bosTau4.chr1                   I 149 C 0
s loxAfr3.scaffold_36               516118 29 -  24123610 CAT-TGGTCAGAGGAAAGACACGCTAAGAT
q loxAfr3.scaffold_36                                     999-99999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s monDom5.chr8                   276505869 29 + 312544902 AACTTCCATTGAGAAAACACAA-CCAAGAT
q monDom5.chr8                                            9999999999999999999999-9999999
i monDom5.chr8                   C 0 C 0
s ornAna1.Ultra117                 6811285 30 +   6934412 CACTTTGACTGTGAACACCCAACCCAAGAT
q ornAna1.Ultra117                                        999999999999999999999999999999
i ornAna1.Ultra117               C 0 N 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=291171.000000
s hg19.chrY                        7657834 164 +  59373566 ATATCAA-GAAC-CCTTTTTAA-GAAACACCAAGTGCCCTGATGCTTAGATTTAGTAGT----GGGTACTCAAATATT-AAAA--------------GCAACCAG------CTAGAAA------------TGGAA-CCTGGAGTATTAATAAAGTATTTCA--------TACATTTAAAAGTACTTC-------------------------------------T-------GTCAGAGAAGACACAAAG-GATC--------ACC--
s rheMac2.chr2                   158766339 164 + 189746636 ACATCAA-GAAG-CCTTTTTAA-GAAACACCAGGTCTCCTGATGCTTAGATTTACTAGT----GGGTACTCAAATATT-AAAA--------------GCAACCAG------CTAGAAA------------TGGAG-CCTCGAGTATTAACAAAATATTTCA--------TACATTTAAAAGTACTTT-------------------------------------T-------GTTAGAGAAGACACAAAG-GATC--------ACC--
q rheMac2.chr2                                             6666676-6676-666766666-666676666666666666666667766667666666----679999999999999-9999--------------99999999------9999999------------99999-9999999999999999999999999--------999999999999999999-------------------------------------9-------999999999999999999-9999--------999--
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71039807 164 - 202140232 ACATCAA-GAAG-ACTTTTTAA-GAAACACCAGGTCCCCTGATGATTAGATTTAGTAGT----GGGTACTCAAATATT-AAAA--------------GCAACCCA------CTAGAAA------------TGGAA-CCTGGAGTATTAATAAAATATTTCA--------TACATTTAAAAGTACTTT-------------------------------------T-------GTTAGTGAAGACACAAAG-GATC--------ACC--
q ponAbe2.chr3                                             9999999-9999-999999999-999999999999999999999999999999999999----999999999999999-9999--------------99999999------9999999------------99999-9999999999999999999999999--------999999999999999999-------------------------------------9-------999999999999999999-9999--------999--
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      511411 164 +  23952694 ATATCAA-GAAC-ACTTTTTAA-GAAACACCAGGTGCCCTGATGCTTAGATTTAGTAGT----GGGTACTCAAATATT-AAAA--------------GCAACCAG------CTAGAAA------------TGGAA-CCTGGAGTATTAATAAAGTATTTCA--------TACATTTAAAAGTACTTC-------------------------------------T-------GTCAGAAAAGACACAAAG-GATC--------ACC--
q panTro2.chrY                                             0000000-0000-000000000-000000000000000000000000000000000000----000000000000000-0000--------------00000000------0000000------------00000-0000000000000000000000000--------000000000000000000-------------------------------------0-------000000000000000000-0000--------000--
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8227127 217 -  88675666 TCTTTAAGAACA-TTTTTAAGA-GAGAAGT------CCCTATTGTTTAGATTTAGTGAT----GAGTACTCAAATATT-AAAA-----------ACTGAAACCGAACATTTATAGAAATAATTTTGAAACTGaaa-attt--------ataaaaaattttatctacttttgaattttgaaacatttataaaaaaatttGTATCTACTTGGTAATATATCTAATAG-------AGAAAGGAGGACACAGAG-GATC--------ACC--
q cavPor3.scaffold_0                                       999999999999-999999999-9999999------99999999999999999999999----999999999999999-9999-----------99999999999999999999999999999999999999999-9999--------99999999999999999999999999999999999999999999999999999999999999999999999999999-------999999999999999999-9999--------999--
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2474290 146 + 163896628 TCTTCTC-AACG-GCTTTGCAA-GAAACACCAGGAACCCTTCTGCTCAGATTCACACGC----GGGTACTCAAATAAT-GAGA---------------TAACCGG-----CACAGAAA------------TGAAA-CCCC--------AGAGCA---------------CGCGCTTCAACGCAT----------------------------------------G-------GGGACGGGAGACACTGAG-GATC--------ACC--
q oryCun2.chr14                                            9999999-9999-999999999-999999999999999999999999999999999999----999999999999999-9999---------------9999999-----99999999------------99999-9999--------999999---------------999999999999999----------------------------------------9-------999999999999999999-9999--------999--
i oryCun2.chr14                  C 0 C 0
s canFam2.chr23                   25995123 170 -  55389570 ---TCAA-GAAA-GCTCTTCCA-GCAACACCAGGCCTCACGCTGCTTAGATTTCACAGT---GGGGTATTGAAATATTAAAAA--------------GCAACTGG------CTAGAAA------------CTGAA-CTCAGAGTATTAATAAAATATTTCA--------CACACTTAAAAATACTTC-------------------------------------TTATATAGTGAAGAGAAGATGTAAAG-GATC--------ACC--
q canFam2.chr23                                            ---9999-9999-999999999-999999999999999999999999999999999999---999999999999999999999--------------99999999------9999999------------99999-9999999999999999999999999--------999999999999999999-------------------------------------99999999999999999999999999-9999--------999--
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_206809             8927 170 -    143945 TCATCAA-GAAA-GCTTTTCCA-GAAACACCAGGCCTCAAGCTGCTTGGACTTCGCAGT---GGGGTATTCAAATATT-AAAA--------------GCAACCGG------CTAGAAA------------CTGAA-GTTGGAGTATTAATAAAATATATCA--------CACGCTTAAAAATACTTT-------------------------------------T--TATGGTGAAGGGGAGAAGCAAAG-GATC--------ACC--
q felCat3.scaffold_206809                                  9999999-9999-999999999-676899899999899999799999999999579879---9999999999999999-9999--------------99999899------6779999------------85999-6446999999966879999999997--------977934599999966679-------------------------------------7--99599999999999888999979-7239--------696--
i felCat3.scaffold_206809        C 0 n 0
s equCab2.chr16                   22214501 169 -  87365405 TCATCGA-GAAA-GCTTTTCAA-GAAACTCCAGGCCCCATGCTGC-TAGATTTCACAGT---GGGGTACTCAAATATT-AAAA--------------ACAACTAG------CTGGAAA------------CTGAA-CTCAGAGTATTAATAAAATATTTCA--------CACCCTTAAAAGTACTTT-------------------------------------T--TATAGAGAAGGGAAGATGCAAAG-GATC--------ACC--
q equCab2.chr16                                            9999999-9999-999999999-9999999999999999999999-9999999999999---9999999999999999-9999--------------99999999------9999999------------99999-9999999999999999999999999--------999999999999999999-------------------------------------9--99999999999999999999999-9999--------999--
i equCab2.chr16                  C 0 C 0
s bosTau4.chr1                   156987279 144 + 161106243 ---------AAA-AC----------AATACCAGGCACCGTGAAGCTCAGATTTCACAGT---GGGGTACTCAAATATT-AAAA--------------GCAACCAG------CTAGAAA------------CTGAA-CCCAGAGTATTAATAAAATATTTCA--------CACGCTTAAATGTACTCT-------------------------------------T--TAT---------AAGACACGAAG-GATT--------ACC--
q bosTau4.chr1                                             ---------999-99----------9999999999999999999999999999999999---9999999999999999-9999--------------99999999------9999999------------99999-9999999999999999999999999--------999999999999999999-------------------------------------9--999---------99999999999-9999--------999--
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               516147 152 -  24123610 TCATCAA-GAAG-GCTTTTCAA-GAAACACCAGGCCCCATACTGCTTAGATTTCAAAGC---GGTGTACTCAAATATT-AAAA--------------GCATTCAG------AGAGAAG------------CTGAACCCTAGAGTATTAATAAAATATTTCA--------TACACTTCAAAGCACCAT-------------------------------------T-------TAGAGAGAAGG-------------------------
q loxAfr3.scaffold_36                                      9999999-9999-999999999-999999999999999999999999999999999999---9999999999999999-9999--------------99999999------9999999------------9999999999999999999999999999999--------999999999999999999-------------------------------------9-------99999999999-------------------------
i loxAfr3.scaffold_36            C 0 C 0
s monDom5.chr8                   276505898 195 + 312544902 TCATAAA-AAGGCACTTTTTAATGATATATTAAAGACTCTGCTGTCTGGGAAAAGCAACATGATAATACATGAATATT-AAAAAAAAAAAAACAACCACCACCGG------CTCCGAA------------GAGAC-CCGGGGATCGTGACAGAACGCTTCA--------TTAACTTAAAAGCTTTTC-------------------------------------T-------GGGGCACGAGACAGGGGGAGATCTGCCAAGAACCCT
q monDom5.chr8                                             9999999-9999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999------9999999------------99999-9999999999999999999999999--------999999999999999999-------------------------------------9-------999999999999999999999999999999999999
i monDom5.chr8                   C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=500489.000000
s hg19.chrY                        7657998 220 +  59373566 AGTTATTCAGAACTGGTAACCAAACTCACCCATA---------------CCAAATCCAAGA-GGAGCTTT-----TTGTGACTCAGAAG-AAAGGATATTGTGAATGTTTTAAGCCA-TTTTCC---TAAGG---------AGTATGATAGCTGACATTCTTGGTAGTTCTTCT--CATTTT----GAGAGTACATTGCACTGATGGCATCAAAGAC-AGCCATTAATGAATATGTACAAATAATATAAAAATTAAACTACT
s rheMac2.chr2                   158766503 221 + 189746636 AATTACTCAGAATCGGTAACCAAACTCATCCATA---------------CCAAATCCAAGA-AGAGCTTT-----TTGTGAGTCAGAAG-AAAGCAAATTATGAATGTTTTAAGCCA-TTTTCC---TAATG---------AGTATGATAGCTGACATTCTTGGTAGTTCTCCT--GATTTT----GAGAGTACATTATGCTGATGGCATCAAAGACTAACCACTAATGAATATGTACAAACAATATAAAAATTAAACTACT
q rheMac2.chr2                                             9999999999999999999999999999999999---------------999999999999-99999999-----99999999999999-999999999999999999999999999-999999---99999---------999999999999999999999999999999999--999999----9999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71039971 221 - 202140232 AATTATTCAGAATCGGTAATGAAACTCATCCATA---------------CCAAATCCAAGA-AGTGCTTT-----TTGTGAGTCAGAAG-AAAGCAAATTATGAATGTTTTAAGCCA-TTTTCC---TAATG---------AGTATGATAGCTGACATTCTTGGTAGTTCTCTT--GATTTT----GAGAGTACATTATGCTGATGGCATCAAAGACTAGCCACTAATGAATATGTACAAACAATATAAAAATTAAACTACT
q ponAbe2.chr3                                             9999999999999999999999999999999999---------------999999999999-99999999-----99999999999999-999999999999999999999999999-999999---99999---------999999999999999999999999999999999--999999----9999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      511575 220 +  23952694 AGTTATTCAGAACTGGTAACCAATCTCACCCATA---------------CCAAATCCAAGA-GGAGCTTT-----TTGTGACTCAGAAG-AAAGGATATTATGAATGTTTTAAGCCA-TTTTCC---TAATG---------AGTATGATAGCTGACATTCTTGGTAGTTCTTCT--CATTTT----GAGAGTACATTGCACTGATGGCATCAAAGAC-AGCCACTAATGAATATGTACAAATAATATAAAAATTAAACTACT
q panTro2.chrY                                             0000000000000000000000000000000000---------------000000000000-00000000-----00000000000000-000000000000000000000000000-000000---00000---------000000000000000000000000000000000--000000----0000000000000000000000000000000-00000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8227344 243 -  88675666 ATGTCTTCTTAATTACTAACCAAATCTATCCACACCAAATCTATCCACACCAAATCTAAGA-AGAGT--------TTACAAGTCAAAGA-GAAGCTAGTTATCAATATTTTATGCTG-TTTTTC---AAATTGTGTATGACAGCACCATAGCTGACACTCCTGGTAATTCTCTTTTGATTTT----GAGAGTACATTAAACTGATTGCATCAAAGACTAGCCACTAATGAATATGTACAAACAATATGGGAATTAAACAAT-
q cavPor3.scaffold_0                                       9999999999999999999999999999999999999999999999999999999999999-99999--------99999999999999-999999999999999999999999999-999999---9999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999-
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2474436 198 + 163896628 GCGTCTTCAGAACT-----------------------------------CCCAATCCGGGA-AGAGTGGC-----TCCTGGGTCAGGAG-GAAGCCAGTTCTCAGCG--TGAGGCCG-TTTTCC---AAATGCAGGATGACAGCACAACAGCGGACCCTCCGCGCCTGTCTCTTTCAATTCT----CAGAGTGC----CACCCCTC--------GACCAGCCACTACCGATGATGCACAAGCTACAAGGAAAGTACACTGTC
q oryCun2.chr14                                            99999999999999-----------------------------------999999999999-99999999-----99999999999999-99999999999999999--99999999-999999---9999999999999999999999999999999999999999999999999999999----99999999----99999999--------999999999999999999999999999999999999999999999999
i oryCun2.chr14                  C 0 C 0
s equCab2.chr16                   22214670 229 -  87365405 AAGTCTTCAGAATTTCTATCCAGACTCATCCACG---------------CCAAATCCAAGA-AGAGCTGA-----GCATGAGTCAGAAGGGAAGCTAGTTATCAATATTTTATGCCA-TTTTCC---TAATTGAGCGTGATAGCATGATAGCTGATAGTCCTGGT---TTTCTTTTGATTTT----GAGAGTACAATAAACAGACTGCATCAAAGACCAGCCACTAATGAATATGTACAAACAATATGGAAATAAAACTGT-
q equCab2.chr16                                            9999999999999999999999999999999999---------------999999999999-99999999-----999999999999999999999999999999999999999999-999999---99999999999999999999999999999999999999---99999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999-
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   25995293 231 -  55389570 AAGTCTTTAGAATTTCTATTCCAACTGGTCCATA---------------CCAAATCCAAGG-AGAGCTTA-----GCATGAGTCAGAAGAAAAGTTAGTTATCAATATTTTATGCCA-CTTTCC---TAATTGAGCATGATATCATGATAGCTGACACTCTGAGCAG-TTCTCTTTGATTTT----GAGAGTACAATAAACTGATTGCATCCAAGACCAGCTACTAATGAATATGTGCAAACAATATGGAAATGAAACTGT-
q canFam2.chr23                                            9999999999999999999999999999999999---------------999999999999-99999999-----999999999999999999999999999999999999999999-999999---9999999999999999999999999999999999999999-99999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999-
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156987423 232 + 161106243 AAGTCTTCA-AACTTTTAACCAAACTCATTCACA---------------CCAGACCCAAAA-ACAGCTTA-----GCGTGAGTCAGAAGGGAACCTGATTATCAGTATTTTATGCCCTTTTTCC---TAATTGAGCGTGATAGCTCTCTAGCTGACACTCCTGGAAGTTCTCTTTTGATTCT----GAGACTACAATAAACTGATTGCATCAAAGACCAGCCTCTAATGAATATGTACAAACAATATGGAAATGAAACTAT-
q bosTau4.chr1                                             999999999-999999999999999999999999---------------999999999999-99999999-----9999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999-
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               516299 217 -  24123610 -------GAAGACTTCTAACCAAACTCTTCCACA---------------CCAAACCCAAGA-AGGGCTTTACTCAGCATGAGTCAGAAG-GGAGCT-ATTATCAACATTTTATACCA-TTTCCC---TAA-----------ACTATCACAGATGACACTCTCAGTAGTTCTCTTTTGATTTG----GAGAGTACAATAAACTGACCATATCAAAGACAAGTCACTACTGAATATGTACAAACAATATCAAAATTAAACTAT-
q loxAfr3.scaffold_36                                      -------999999999999999999999999999---------------999999999999-999999999999999999999999999-999999-99999999999999999999-999999---999-----------99999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999-
i loxAfr3.scaffold_36            C 0 C 0
s monDom5.chr8                   276506093 233 + 312544902 GATTCTTTAGAACTTCTAACCAAACTGTCTCAAA---------------GTAAAACTAAGGCACAGCTTA-----GAATGAGTCAGACGAAAGGCTAGTTATTAATATTTTATGTCA-TTTTCCCCTTAATTG--------ATTACAGTAACTGACACTCTCAATAGTTTTCCTTTGACTTTGAAAGAGAGCATAATAAACTGTTTCCATCAAAGGGGAGTCACTAATGAATATGTAAGAATAATATGGAAATTAAGCCATT
q monDom5.chr8                                             9999999999999999999999999999999999---------------999999999999999999999-----999999999999999999999999999999999999999999-999999999999999--------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i monDom5.chr8                   C 0 I 15915
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097   0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=104310.000000
s hg19.chrY                        7658218 75 +  59373566 GTATTTACAATGCAAAATGATTTGTCATATAAATCCTGTCCGGATTTTCAATTAT-AAAGTCTCAAGACTTAAttt
s rheMac2.chr2                   158766724 75 + 189746636 GTATTTACAATGTAAAATGATTTGTCATAGAAATCCTGTATGGATTTTCTATTAT-AAAATCTCAAGACTTAAttt
q rheMac2.chr2                                            9999999999999999999999999999999999999999999999999999999-99999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71040192 75 - 202140232 GGGTTTACAATGTAACATGATTTGTCATAAAAATCCTGTATGGATTTTCTATTAC-AAAATCTCAAGACTTAAttt
q ponAbe2.chr3                                            9999999999999999999999999999999999999999999999999999999-99999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      511795 75 +  23952694 GTATTTACAATGCAAAATGATTTGTCATATAAATCCTGTCTGGATTTTCAATTAT-AAAGTCTCAAGACTTAAttt
q panTro2.chrY                                            0000000000000000000000000000000000000000000000000000000-00000000000000000000
i panTro2.chrY                   C 0 C 0
s cavPor3.scaffold_0               8227587 53 -  88675666 ----TTAGAATGT-AAATG-----------AGACCCTATATGGA-TTTCTATGAC-AAAGTCTCAAGACTT-----
q cavPor3.scaffold_0                                      ----999999999-99999-----------99999999999999-9999999999-999999999999999-----
i cavPor3.scaffold_0             C 0 I 52
s oryCun2.chr14                    2474634 59 + 163896628 ---CCCAGAACGT-ACATG-----------GGGCCCTATAAGGG-TTTCTATGAT-AAAGTCTCAAGACTTTGTTT
q oryCun2.chr14                                           ---9999999999-99999-----------99999999999999-9999999999-99999999999999999999
i oryCun2.chr14                  C 0 I 9929
s equCab2.chr16                   22214899 51 -  87365405 ----TTAGAATGC-AAATG-----------GGACTCTGTATGAA-TTTCTATAAT-AAAGTCTCAAGAC-------
q equCab2.chr16                                           ----999999999-99999-----------99999999999999-9999999999-9999999999999-------
i equCab2.chr16                  C 0 I 3
s canFam2.chr23                   25995524 53 -  55389570 ----TTAGAATGT-AAATG-----------GGATCTTATATAGA-TTTCTATGCT-AAAGTCTAAAGATTT-----
q canFam2.chr23                                           ----999999999-99999-----------99999999999999-9999999999-999999999999999-----
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156987655 57 + 161106243 ----TTAGAATGT-AAATG-----------AGACCCTATATGGA-TTTCTACGATAAAAGTCTCAAGACCTGGT--
q bosTau4.chr1                                            ----999999999-99999-----------99999999999999-99999999999999999999999999999--
i bosTau4.chr1                   C 0 I 6415
s loxAfr3.scaffold_36               516516 57 -  24123610 ----TTAGAATGT-AAATG-----------GAACGCTATATGGGATTTCTATGAC-AAAGTCTCAAGACTTGGT--
q loxAfr3.scaffold_36                                     ----999999999-99999-----------9999999999999999999999999-999999999999999999--
i loxAfr3.scaffold_36            C 0 I 9
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097  0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=240357.000000
s hg19.chrY                        7658293 521 +  59373566 cttcatgtccttatgggtttttt-ccaggcactccagcttcctgccacatcccaaaggtgtccacgttaggttaacaggcatgtctacattgtcccagtctgagggagtgtgagagtgtgtgagagactactcctgcaattgaatgacatcctgtccagggctggtgcctgccttgcatcctaaccttctggcacagcctccagccatccaagaagctgaactggaatacatcagttggaaaatgaatgaaggaatgaatacaaataattgtaaaataaaaatgtgtacagtccatgataatcacacagatgcgcaaccattaacaatgtgggatgaaagcacctggtgagcccaccggatttgttattgttttttaacttcctggtggggggaagtgcttcttacgaatttcactttgtaaacatttattccctgatttcacccactaccgctacaaccactatcactcactgttttacaaaaaattgggcaagtcattatcttatttgtttttattaatc
s rheMac2.chr2                   158766799 520 + 189746636 ctccatgtccttatgggtttttt-ccaggcactgcggcttcctcccacatcccaaagatgtgcacgttaggtaaacaggcatgtctacagtgtcccagtttgagtgagtgtgagtgtgtctatgagagtagtcctgcaatagaatgacatcctgtctagggctggtgcctgccttgcatcctgagctgctgggacaggctccggccacccaagaccccgaactggaataagcgagttggaaaatgaatgaaggaatgaatacaaataattgtaaaataaaaatgtgtaaagtctgtgataatcacacagatgcacaacaataaacaatgtggaatgaaagaacttggcgagcccaccaaatttgttattgtttttgaacttcgtgttggaaagaagtgctccttacaagtttcactttgcagacatttattccttgatttaacccaccaccactacaaccaccatcactcactgttttaccaaaaattgggtaagtcattaccttacttg-ttttattaata
q rheMac2.chr2                                             99999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999899999999999999996666666676666766666776677667676777767766666766767766667767666667667666-66666666666
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71040267 505 - 202140232 cttcatgtccttatgggtttttt-ccaggcactccagcttcctcccacatcccaaagatgtgcacgttaggtaaacaggcatgtctacattgtcccagtctgagcgagtgtgagtgtgtgtgtgagagtactcctgcaatggaatgacatcctgtctagggctggtgcctgccttgcatcctgagctgctgggacagactctggccacccaagaccctgaactgcaataagcgagttggaaaatgaatgaaggaatgaatacaaataattgtaaaataaaaatgtgtac---------------caca-atataccacaataaacaatgtgggatgaaagcacttggtgagcccaccaaatttgttattgtttttgaacttcgtgatgggaggaagtgctctttacgagtttcactttgcaaacatttattccttgatttaacccaccaccactacaaccaccatcactcgccgttttaccaaaaactgggtaagtcattatcttatttgtttttattaatc
q ponAbe2.chr3                                             99999999999999999999999-9999999999999999999999999999999999999999099999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------9999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 M 437
s panTro2.chrY                      511870 522 +  23952694 cttcatgtccttacgggtttttttccaggcactccagcttcctcccacatcccaaaggtgtccacgttaggttaacaggcatgtctacattgtcccagtctgagggagtgtgagagtgtgtgagagactactcctgcaattaaatgacatcctgtccagggctggtgcctgccttgcatcctaaccttctggcacagcctccagccatccaagaagctgaactggaatacatcagttggaaaatgaatgaaggaatgaatacaaataattgtaaaataaaaatgtgtacagtccatgataatcacacagatgcacaaccattaacaatgtgggatgaaagcacttggtgagcccatcggatttgttattgttttttaacttcctggtggggggaagtgcttcttacgaatttcactttgcaaacatttattccctgatttcacccactaccgctacaaccactatcactcactgttttacaaaaaattgggtaagtcattatcttatttgtttttattaatc
q panTro2.chrY                                             000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
e cavPor3.scaffold_0               8227640  52 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e equCab2.chr16                   22214950   3 -  87365405 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e loxAfr3.scaffold_36               516573   9 -  24123610 I
e canFam2.chr23                   25995577   0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097   0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=44230.000000
s hg19.chrY                        7658814 173 +  59373566 tttctttactgtatgtacagctcacatttatttccatgtttagtattagaaatattttggcctttatggagaagtttggtaatgtttttgtgaacagaaatatgccataggaatttaagtcttgattttctcaattagcctatggtaaaattggtttcatgatacattgtttc
s panTro2.chrY                      512392 173 +  23952694 tttctttactatatgtacagctcacatttatttccatgtttagtactagaaacattttggcctttatggagaagtttggtaatgtttttgtgaacagaaatatgccataggaatttaagtcttgattttcttaattagcctatggtaaaattggtttcatgatacattgtttc
q panTro2.chrY                                             00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s rheMac2.chr2                   158767319 173 + 189746636 tttcttaactgtatgtacagctcacatttatttccatgtttagtattagaaatgttttggtcttcatggagaagttgggtaatgtttttgtggccagaaatatgccataggaatttaactcttgattttctcaattagcctatggtaaaattggtttcattatacactgtttc
q rheMac2.chr2                                             66776666666766666667666667668666666676666566666666667766666667776766766676666666566665676655656666666655666666566666666676549797999999987889999999999999998889899999999999999
i rheMac2.chr2                   C 0 C 0
e cavPor3.scaffold_0               8227640  52 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e equCab2.chr16                   22214950   3 -  87365405 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e loxAfr3.scaffold_36               516573   9 -  24123610 I
e canFam2.chr23                   25995577   0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097   0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I
e ponAbe2.chr3                    71040772 437 - 202140232 M

a score=29259.000000
s hg19.chrY                        7658987 53 +  59373566 atttacagttgcagtttccaagaacctactgacaatgttaagtgaggacttac
s rheMac2.chr2                   158767492 53 + 189746636 acttacagttgcagtttccaagaacctactgacaatgttaagtgaggacttac
q rheMac2.chr2                                            99999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71041209 53 - 202140232 atttacagttgcagtttccaagaacctattgacaatgttaagtgaggacttac
q ponAbe2.chr3                                            76965777656755799575677582756575769668779968788558965
i ponAbe2.chr3                   M 437 C 0
s panTro2.chrY                      512565 53 +  23952694 atttacagttgcagtttccaagaacctactgacaatgttaagtgaggacttac
q panTro2.chrY                                            00000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
e cavPor3.scaffold_0               8227640 52 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e equCab2.chr16                   22214950  3 -  87365405 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e loxAfr3.scaffold_36               516573  9 -  24123610 I
e canFam2.chr23                   25995577  0 -  55389570 C
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097  0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e dipOrd1.scaffold_20859              4370 3384 -     25303 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=73242.000000
s hg19.chrY                        7659040 64 +  59373566 tATGCAGAAATAAACAGTACCAAAA--ACAATGCTG-CTGCAGCCAAGCTCTTAGAGAAAACATATA
s canFam2.chr23                   25995577 66 -  55389570 -TTATAAAAATAATCAGTACTGAAAAAATAATGTCAACTGTGGCCAAGTCCTCAGAGAAGGCGTATC
q canFam2.chr23                                           -999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22214953 63 -  87365405 --TATAAAAGTAATCAGTACTGAAAATATAATGCCA--TGTGGCCAAGTTCTTAGAGAAGGCATAGC
q equCab2.chr16                                           --9999999999999999999999999999999999--99999999999999999999999999999
i equCab2.chr16                  I 3 C 0
s panTro2.chrY                      512618 64 +  23952694 tATGCAGAAATAAACAGTACCAAAA--ACAATGCTG-CTACAGCCAAGCTCTTAGAGAAAACATATA
q panTro2.chrY                                            0000000000000000000000000--000000000-000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71041262 64 - 202140232 tATGCAGAGGTAAACAGTACCAAAA--ACAATGCTG-TTGCAGCCAAGCTCTTAGAGAAAACATATA
q ponAbe2.chr3                                            9746689886778898996899999--689989789-948998799996969989999997899898
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158767545 64 + 189746636 tATGCAGAGGTAAACAGTACCGAAA--ACAATGCTG-TTGCAGCCAAGCTCTTAGAGAAAACATATA
q rheMac2.chr2                                            9999999999999999999999999--999999999-999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s dipOrd1.scaffold_20859              7754 51 -     25303 TGTGTAGAAATAATCAGCACTAAGAATATAATGCTA-CTGTGGC---------------ACTGTGTC
q dipOrd1.scaffold_20859                                  999999999999999989999999999999999999-9999999---------------99999999
i dipOrd1.scaffold_20859         I 3384 C 0
s loxAfr3.scaffold_36               516582 58 -  24123610 -----AAAAGTAATCACTACTGAGT--ATATAGTCA-TTGTGGCCAAGTTCTTAG-GAAAATATATC
q loxAfr3.scaffold_36                                     -----99999999999999999999--999999999-999999999999999999-99999999999
i loxAfr3.scaffold_36            I 9 C 0
e cavPor3.scaffold_0               8227640 52 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097  0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=121442.000000
s hg19.chrY                        7659104 77 +  59373566 AGAAAAATAATGCGTCTTTA-AAGGC------ACTTTTGAGG-AGTCTCAGTT-TCAACTAAG-AGTATGATTGCTCTGATATCTTC
s panTro2.chrY                      512682 77 +  23952694 AGAAAAATAACGCGTCTTTA-AAGGC------ACTTTTGAGG-AGTCTCAGTT-TCAACTAAG-AGTATGATTGCTCTGATATCTTC
q panTro2.chrY                                            00000000000000000000-00000------0000000000-0000000000-000000000-00000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71041326 78 - 202140232 AGAAAAATAATGCATCTTTACAAGGC------ACTTTTGAGG-AGTCTCAGTT-TCATCTAAG-AGTATGATTGCTCTGATACCTTC
q ponAbe2.chr3                                            99999989998996989998898999------9999979999-9993999999-999979999-99999998999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158767609 78 + 189746636 AGAAAAATAATGCATCTTTACAAGGC------ACTTTTGAGG-AGTCTCAGAT-TCAATGAAG-AGTATGATTGCTCTGACACCTTC
q rheMac2.chr2                                            99999999999999999999999999------9999999999-9999999999-999999999-99999999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8227692 73 -  88675666 agaaaaataatttattttGC--ATGT------GTTTTCGAGG-AGTCTCAGTT-TCACT---A-AGTGTGATGGCTCTGATACCTTC
q cavPor3.scaffold_0                                      99999999999999999999--9999------9999999999-9999999999-99999---9-99999999999999999999999
i cavPor3.scaffold_0             I 52 C 0
s dipOrd1.scaffold_20859              7805 77 -     25303 AGAGAAGGAATACCTCTTCCCAAGGA------TCTGCCCAGA-AGCATCCGTTGTCAGG--AA-AGTATAATCATTCTGACACCTTT
q dipOrd1.scaffold_20859                                  99999999999999999999999999------9999999799-9999999999999999--99-99999967999999999999999
i dipOrd1.scaffold_20859         C 0 C 0
s canFam2.chr23                   25995643 69 -  55389570 AGAAAAATAATGCACCTTTACAAGGA------GCTGTAGGAA------------TCAACTAAGAAGTGTGATTGCTCTAATGCCTTC
q canFam2.chr23                                           99999999999999999999999999------9999999999------------999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22215016 79 -  87365405 AGAACAATAACGCCTCTTTACAAGGA------GCTTTTGGGGGAGTCTCCATT-TCAACTAAG-AGTCTGATTGTTCTGATACCTTC
q equCab2.chr16                                           99999999999999999999999999------999999999999999999999-999999999-99999999999999999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               516640 84 -  24123610 AGAAAAAGAATGCATTTTTACAAGGATGGAGTATGCTTGGGG-AATCTCAATT-TCACCTAAG-AGTGTGATTTCCCTAATACCGTC
q loxAfr3.scaffold_36                                     999999999999999999999999999999999999999999-9999999999-999999999-99999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e speTri1.scaffold_160574             7503 1792 -    115260 I
e micMur1.scaffold_734              270086 6625 -    418489 I
e felCat3.scaffold_206809             9097  0 -    143945 I
e calJac1.Contig102                1032597 7661 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e papHam1.scaffold12353              60426 8117 +     70985 I

a score=135098.000000
s hg19.chrY                        7659181 52 +  59373566 TCAG---AAAAG--TGTCTTGAAGGCACAGGATCC-CACTAAAGGAGAACCT----TTGATG
s rheMac2.chr2                   158767687 52 + 189746636 TCAG---ACAGG--TGTGTTGAAGGCAGAGGATCC-CACTGAAGGAGCGCCT----TTGATG
q rheMac2.chr2                                            9999---99999--999999999999999999999-9999999999999999----999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71041404 52 - 202140232 TCAG---ACAGG--TGTGTTAAAGGCAGAGGATCC-CACTAAAGGAGTGTCT----TTGATG
q ponAbe2.chr3                                            9999---99999--999997999999999999999-9989999999999999----999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      512759 52 +  23952694 TCAG---AAAAG--TGTCTTGAAGGCACAGGATCC-CACTAAAGGAGAACCT----TTGATG
q panTro2.chrY                                            0000---00000--000000000000000000000-0000000000000000----000000
i panTro2.chrY                   C 0 C 0
s micMur1.scaffold_734              276711 51 -    418489 TCCG---ACAGG--TGTGTTGAAAGCAGAAGATCC-CAGTAAAGGAG-GCCT----CCAGTG
q micMur1.scaffold_734                                    9999---99999--999999999999999999999-99999999999-9999----999999
i micMur1.scaffold_734           I 6625 C 0
s calJac1.Contig102                1040258 49 -   1157145 ---G---ACAGG--TGTGTTGAAGACAGAGGGTCC-CACTAAAGGAGTGCCC----TTGATG
q calJac1.Contig102                                       ---9---99999--999999999999999999999-9999999999999999----999999
i calJac1.Contig102              I 7661 C 0
s papHam1.scaffold12353              68543 49 +     70985 ---G---ACAGG--TGTGTTAAAGGCAGAGGATCC-CACTAAAGGAGCGCCT----TTGATG
q papHam1.scaffold12353                                   ---7---77778--777779589787777787758-9777589787777685----897775
i papHam1.scaffold12353          I 8117 C 0
s dipOrd1.scaffold_20859              7882 51 -     25303 TCAC---ACAGG--TGTG-GCAAAGCAAAGGGTCC-CAATGAAGGAGTGCTG----TCCATG
q dipOrd1.scaffold_20859                                  9969---89999--9999-9999999999998698-9699999799699999----899799
i dipOrd1.scaffold_20859         C 0 C 0
s cavPor3.scaffold_0               8227765 44 -  88675666 TCAG---GCAGG--TGTG-GGAAAGTTGTGGATCC-TGCTGATGAAGCGCT-----------
q cavPor3.scaffold_0                                      9999---99999--9999-9999999999999999-999999999999999-----------
i cavPor3.scaffold_0             C 0 C 0
s speTri1.scaffold_160574             9295 57 -    115260 TCAG---ACAGGCATGTG-AAAAAGCTAAGGATCC-CACTCAAGGAGTGCCACACCTCCCTG
q speTri1.scaffold_160574                                 9999---99776997848-9999699999996988-99999968889999969999968677
i speTri1.scaffold_160574        I 1792 C 0
s canFam2.chr23                   25995712 36 -  55389570 --AG----------------AGAAGCCAAAGG----AACCGAAGAAGCACCT----GAAATG
q canFam2.chr23                                           --99----------------999999999999----9999999999999999----999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22215095 53 -  87365405 --TCATTTTAGG--TGTGTTGAAAGCAGAGAATCC-CGCTAAAAGAGCACCT----CAAACA
q equCab2.chr16                                           --9999999999--999999999999999999999-9999999999999999----999999
i equCab2.chr16                  C 0 C 0
s felCat3.scaffold_217554           345406 49 -    369131 -------TCAGG--TGTGCTGAAAGCCAAGAGGCTAAAGCAAAGGGGCACCT----TAAATG
q felCat3.scaffold_217554                                 -------99999--99999999999999999999999999999999999999----999999
i felCat3.scaffold_217554        I 37100 C 0
s loxAfr3.scaffold_36               516724 52 -  24123610 TCAG---ACAGA--CGTGTCAAAAGCAGAGAATCC-AGCTAACAAAGAACCT----CAAATG
q loxAfr3.scaffold_36                                     9999---99999--999999999999999999999-9999999999999999----999999
i loxAfr3.scaffold_36            C 0 C 0
s choHof1.scaffold_17232             11681 51 -     19280 ACTG---ACAGT--TGTGTTAAAAGCAGA-AACAC-ACTGAAAGGAGTGCCT----CCAATG
q choHof1.scaffold_17232                                  5348---45643--392835574644526-72237-4357371515138245----921111
i choHof1.scaffold_17232         N 0 N 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I

a score=94110.000000
s hg19.chrY                        7659233 36 +  59373566 GGTATCAGGTGCTGAGTCTGCAAACACTCTCTGACC
s rheMac2.chr2                   158767739 36 + 189746636 GGTAGCAGGTGCTGAGGCTGCACACACACTCTGACC
q rheMac2.chr2                                            999999999999999999999999999999999999
i rheMac2.chr2                   C 0 I 9147
s ponAbe2.chr3                    71041456 36 - 202140232 GGTATCAGGTGCTGAGGTTGCAAATATACTCTGACC
q ponAbe2.chr3                                            999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 I 9293
s panTro2.chrY                      512811 36 +  23952694 GGTATCAGGTGCTGAGTCTGCAAACACACTCTGACC
q panTro2.chrY                                            000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s micMur1.scaffold_734              276762 36 -    418489 TGCGGCAGGTACCAAGCCCACAAACACTCTCTGACC
q micMur1.scaffold_734                                    999999999999999999999999999999999999
i micMur1.scaffold_734           C 0 I 10943
s calJac1.Contig102                1040307 10 -   1157145 GGTATCAGGT--------------------------
q calJac1.Contig102                                       9999999999--------------------------
i calJac1.Contig102              C 0 I 16226
s papHam1.scaffold12353              68592 36 +     70985 GGTAGCAGGTGCTGAAGCTGCACACACACTGTGACC
q papHam1.scaffold12353                                   897777779777779999999999999999999999
i papHam1.scaffold12353          C 0 N 0
s dipOrd1.scaffold_20859              7933 36 -     25303 AGAAGCAGATACTAAGCCCACAAATCTGTTCTGACC
q dipOrd1.scaffold_20859                                  979969969699999898659899999959989968
i dipOrd1.scaffold_20859         C 0 N 0
s cavPor3.scaffold_0               8227809 31 -  88675666 ----GCAGACACAGGGTCC-CAAACGCACTGTGACC
q cavPor3.scaffold_0                                      ----999999999999999-9999999999999999
i cavPor3.scaffold_0             C 0 I 6617
s speTri1.scaffold_160574             9352 35 -    115260 GGCAGCTGGTACCTAGCCCACAAACCCATCCTGAC-
q speTri1.scaffold_160574                                 76999979799979786997999999999998989-
i speTri1.scaffold_160574        C 0 n 0
s canFam2.chr23                   25995748 34 -  55389570 GGTAGCAT--AGTGAGCCAGCATATACATTCTGAAC
q canFam2.chr23                                           99999999--99999999999999999999999999
i canFam2.chr23                  C 0 I 6138
s equCab2.chr16                   22215148 36 -  87365405 GGTAACACGTACGGAGCCTGCGAACACATTGTGACC
q equCab2.chr16                                           999999999999999999999999999999999999
i equCab2.chr16                  C 0 I 8538
s felCat3.scaffold_217554           345455 34 -    369131 GGTAGCAC--ACTGAGCCGGCAAACACATTCTGACT
q felCat3.scaffold_217554                                 99999999--99999999999999999999999999
i felCat3.scaffold_217554        C 0 T 2781
s loxAfr3.scaffold_36               516776 29 -  24123610 -------GGTACCAAGCCTACAAACTCACTCTGACC
q loxAfr3.scaffold_36                                     -------99999999999999999999999999999
i loxAfr3.scaffold_36            C 0 I 11020
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2474693 9929 + 163896628 I
e bosTau4.chr1                   156987712 6415 + 161106243 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I

a score=182534.000000
s hg19.chrY                        7659269 103 +  59373566 CACAGTGATTATAAATATCCAGTATAAGCCAGACATGCTTAATTTCAGGGTACGATGA-AAGAAAATAACCAAAGTAAATA----TTTGAAAAGCAAATTCAACTTTT
s panTro2.chrY                      512847 103 +  23952694 CACAGTGATTATAAATATCCAGTATAAGCCAGACATGCTTAATTTCAGGGTACGATGA-AAGAAAATAACCAAAGTAAATA----TTTGAAAAGCAAATTCAACTTTT
q panTro2.chrY                                             0000000000000000000000000000000000000000000000000000000000-0000000000000000000000----00000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71050785 102 - 202140232 CACAGTGGTCACAAATATCCAGCATAAACCAGACATGCTTAATTTCAGGGTATGATAC-AAGAAAATAAATGAAGCAAATA----TTT-AAAAGCAAATTCAACTTTC
q ponAbe2.chr3                                             9999999999999999999999999999999999999999999999999999999999-9999999999999999999999----999-9999999999999999999
i ponAbe2.chr3                   I 9293 C 0
s rheMac2.chr2                   158776922 102 + 189746636 CACAGTGATTACAAATATCCAGCATAAACCAGACATGCTTAATTTCAGGGTATGATGC-AAGAAAATAAACAAAGCAAATA----TTT-AAAAGCAAATTCACCTTTC
q rheMac2.chr2                                             9999999999999999999999999999999999999999999999999999999999-9999999999999999999999----999-9999999999999999999
i rheMac2.chr2                   I 9147 C 0
s cavPor3.scaffold_0               8234457  62 -  88675666 CAAAGTGATTATAAATAACCATCACAAACTAAATATGCTTAATCCCAGGGTGTGACAC-AAGG---------------------------------------------
q cavPor3.scaffold_0                                       9999999999999999999999999999999999999999999999999999999999-9999---------------------------------------------
i cavPor3.scaffold_0             I 6617 C 0
s oryCun2.chr14                    2484622  89 + 163896628 CACAGCCATCAAAAATAAGCAGCAGAGACCAGACACGCTTACTGCTAGGGTGCAACAC-AACA-------CAAATCCAATG----CTC-------AAAtttaaatttt
q oryCun2.chr14                                            9999999999999999999999999999999999999999999999999999999999-9999-------99999999999----999-------9999999999999
i oryCun2.chr14                  I 9929 I 255
s bosTau4.chr1                   156994127  95 + 161106243 ---AGTGCTTATAAATAACCATTAGAAACCAGACTTGCCTCATTTCGGGGTATGGCAA-GCAA----AAATAAAGCAACTG----TTT-AAAAGCAAATCCAGTTTGC
q bosTau4.chr1                                             ---9999999999999999999999999999999999999999999999999999999-9999----99999999999999----999-9999999999999999999
i bosTau4.chr1                   I 6415 C 0
s canFam2.chr23                   26001920 101 -  55389570 -ATAATGATTATAAATAACCACCCGAAACCAGACTTGTTTAATTTCAGGGTATGACAC-AAGAAAATAAATAAAGCAAATG----TTT-AAAAGAGAATCCACTTTTC
q canFam2.chr23                                            -999999999999999999999999999999999999999999999999999999999-9999999999999999999999----999-9999999999999999999
i canFam2.chr23                  I 6138 C 0
s equCab2.chr16                   22223722  97 -  87365405 -AGAGACATTATAAATAATCACCGTAAACCAGACTTCCTTAATTTCAGGGTGTGACAC-ACAA----AAATAAAGGAACTA----TCT-TAAAGCAAATCCGATCCTC
q equCab2.chr16                                            -999999999999999999999999999999999999999999999999999999999-9999----99999999999999----999-9999999999999999999
i equCab2.chr16                  I 8538 C 0
s loxAfr3.scaffold_36               527825  98 -  24123610 ----GTGATGATAAATAACCACCACAAGCCAGACAGGCTTAATTTCAGAGTATGACAC-AAGAAAATAAACAATGCCAATA----TTT-AAAGACAAATTAGATTTTC
q loxAfr3.scaffold_36                                      ----999999999999999999999999999999999999999999999999999999-9999999999999999999999----999-9999999999999999999
i loxAfr3.scaffold_36            I 11020 C 0
s macEug1.Scaffold7817               22771 105 -     41428 CAAATTGACAATAAATTTCTGTAATAAACCAGCAAACCTTAATTTCTGGGGAGAACGCTAAGAGATCCAACaaaataaatggtttttt-aaaggcccatcacattt--
q macEug1.Scaffold7817                                     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999--
i macEug1.Scaffold7817           N 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I

a score=92530.000000
s hg19.chrY                        7659372  81 +  59373566 CAGTTTAAATTTTAAAAATGTTATTC-AAAGACATTTATAAAGAGA-G-AGTGACATAATTAAGGAAA-------------------------GCAAAATGCAAAT--AAC
s macEug1.Scaffold7817               22876  74 -     41428 ----taaaatgtgagtATTGTTCTTA-AGATGCTTTTAGCTGATGA-C-GCTATT----TTCAGGCAG-------------------------GC-AAATACAAATCTAAC
q macEug1.Scaffold7817                                     ----9999999999999999999999-9999999999999999999-9-999999----999899999-------------------------99-999999999999999
i macEug1.Scaffold7817           C 0 C 0
s loxAfr3.scaffold_36               527923  81 -  24123610 AAATTTAAATTTTAATAGTGCTATTC-AAAGACATTTATAAAGAGGTG-GCTGATGTAATTCAGGCAA-------------------------GT-AAATGCAAAT--AAC
q loxAfr3.scaffold_36                                      99999999999999999999999999-999999999999999999999-9999999999999999999-------------------------99-9999999999--999
i loxAfr3.scaffold_36            C 0 C 0
s bosTau4.chr1                   156994222  71 + 161106243 AAAGTTAAATTTCCACAG-----TTC-AAAGACATTTATAGAGTGA-G-----AACTGATTCAGGTGA-------------------------GG-AAATGCAAAT--AAC
q bosTau4.chr1                                             999999999999999999-----999-9999999999999999999-9-----999999999999999-------------------------99-9999999999--999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26002021  81 -  55389570 AAATTGAAATTTTAATAGTGATCTTC-AAAGACATCAATAATGTGG-GGGCCGAGGCATTTCAGTTGG-------------------------GC-AAATCCAAAC--AAC
q canFam2.chr23                                            99999999999999999999999999-9999999999999999999-999999999999999999999-------------------------99-9999999999--999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22223819  82 -  87365405 AAATTTAAATTTTAATAGTGATATTCAAAAGACATTTATAAAGTGA-GGGCCCAACTAATTCAGGTGG-------------------------GA-AACTGCAAAT--AAC
q equCab2.chr16                                            9999999999999999999999999999999999999999999999-999999999999999999999-------------------------99-9999999999--999
i equCab2.chr16                  C 0 C 0
s oryCun2.chr14                    2484966  71 + 163896628 CGGTTTGCCTTTTAGCAGTGCTACAC-G-----GTTCACAAAGAGG-G-ATTGATAGAATGCACGC-A-------------------------GC-CAATGCAAAC-----
q oryCun2.chr14                                            99999999999999999999999999-9-----9999999999999-9-99999999999999999-9-------------------------99-9999999999-----
i oryCun2.chr14                  I 255 C 0
s cavPor3.scaffold_0               8234519  35 -  88675666 -----------------------------------------------G-ACAGATGTAATTCAGGTGA-------------------------GC-AAATACAAAT--AAT
q cavPor3.scaffold_0                                       -----------------------------------------------9-9999999999999999999-------------------------99-9999999999--999
i cavPor3.scaffold_0             C 0 C 0
s rheMac2.chr2                   158777024  81 + 189746636 TAATTTTAATTTTAAAAGTGTTATTC-AAAGACATTTATAAAGAGA-G-AGTGACCTAATTAAGGCAA-------------------------GCAAAATGCAAAT--AAC
q rheMac2.chr2                                             99999999999999999999999999-9999999999999999999-9-9999999999999999999-------------------------9999999999999--999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71050887 106 - 202140232 CAATTTTAATTTTAAAAGTGTTATTC-AAAGACATTTATAAAGAGA-G-AGTGATATAATTAAGGCAAGCAAaatgcaaataatgcaaataatgcaaaatgcaaat--aaC
q ponAbe2.chr3                                             99999999999999999999999999-9999999999999999999-9-999999999999999999999999999999999999999999999999999999999--999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      512950  81 +  23952694 CAGTTTAAATTTTAAAAATGTTATTC-AAAGACATTTATAAAGAGA-G-AGTGACATAATTAAGGAAA-------------------------GCAAAATGCAAAT--AAC
q panTro2.chrY                                             00000000000000000000000000-0000000000000000000-0-0000000000000000000-------------------------0000000000000--000
i panTro2.chrY                   C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I

a score=179053.000000
s hg19.chrY                        7659453 93 +  59373566 ATGTTACTGACCTTCTCC-ATGTCCCAGGACTTCCTGCCCACAG---TGCAGAAATAGAAGGCAGAGG--ACAGAAGT-CTAAGGTAG-AGGT--GAACAAGG
s panTro2.chrY                      513031 93 +  23952694 ATGTTACTGACCTTCTCC-ATGTCCCAGGACTTCCTGCCCACAG---TGCAGAAATAGAAGGCAGAGG--ACAGAAGT-CTAAGGTAG-AGGT--GAACAAGG
q panTro2.chrY                                            000000000000000000-0000000000000000000000000---000000000000000000000--00000000-000000000-0000--00000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71050993 93 - 202140232 ATGTTATTGACCTTCTCC-GTGTCCCAGGACTTCCTTCCCACAG---TGCAGAAATGGAAGGCAGAAG--ACAAAAGT-CAAAGCCAG-GGGT--GAACAGGG
q ponAbe2.chr3                                            999999999999999999-9999999999999999999999999---999999999999999999999--99999999-999999999-9999--99999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158777105 93 + 189746636 ATGTTATTGACTTTCTCC-GTGTCCCAGGACTTCCTTCCCACAG---TGCAGAAATGGAAGGCAGAAG--ACAAAAGT-CAAAGCCGG-GGGT--GAACAGGG
q rheMac2.chr2                                            999999999999999999-9999999999999999999999999---999999999999999999999--99999999-999999999-9999--99999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8234554 95 -  88675666 ACAATATTGACCTGCTCT-ATGTTCCTGGACTTCCTGTCTACAG---TGCAGAAATAGGAGGTAGAAA--ACAAATGC-GACAGCCAA-AAATATGAACAAGG
q cavPor3.scaffold_0                                      999999999999999999-9999999999999999999999999---999999999999999999999--99999999-999999999-99999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2485037 85 + 163896628 ---ATCTCCACCTTCTCC-CTGTCCATGAACCTCTTGCCCACAACCTTGCAGAAATGAGAG---------ACAAAAGT-AACAGCCAG-AGGTTAG---CAGG
q oryCun2.chr14                                           ---999999999999999-999999999999999999999999999999999999999999---------99999999-999999999-9999999---9999
i oryCun2.chr14                  C 0 C 0
s equCab2.chr16                   22223901 94 -  87365405 ATGTTATTGACCTTCTCC-GTGTCTCTGGACTTCCTGCCCACAG---TGCGGAGGTGGGAGGCAGAGG--ACAAAAGT-CACAGCCAGGAGGT--GAGCAGGG
q equCab2.chr16                                           999999999999999999-9999999999999999999999999---999999999999999999999--99999999-99999999999999--99999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26002102 91 -  55389570 ACGTTATCAACCTTCCCC-GTGTCTCTGGACTTCCTGCCCACAG---TGCAGAAGTGGGAGGCAGATG--ATAAACGT-CTAAGCC---AGAT--TAACGGTA
q canFam2.chr23                                           999999999999999999-9999999999999999999999999---999999999999999999999--99999999-9999999---9999--99999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156994293 91 + 161106243 ACACTGCTGACCTTCTCC-ATGTCCCTGGAC-TCCTGCCCACAG---TGCAGAAGGCGGGGGCACAGG--GCAAAGGT-CACAGCCAGGAAGT--GACAGG--
q bosTau4.chr1                                            999999999999999999-999999999999-999999999999---999999999999999999999--99999999-99999999999999--999999--
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               528004 81 -  24123610 ATGTTATTGACCTTCTCC-------CTGGGCTTCCTGCCCACAG---CACAGAA--GGGATGTAAAGG--ACCGAAGT-C--AGTC---AGGT--TAAGAGAG
q loxAfr3.scaffold_36                                     999999999999999999-------9999999999999999999---9999999--999999999999--99999999-9--9999---9999--99999999
i loxAfr3.scaffold_36            C 0 C 0
s macEug1.Scaffold7817               22950 88 -     41428 ACTTT----ACCCTCTAG-TCCCTTTCAGACTTCCTGCCCAAAG-----CAGAAATGGGAGGCCGAGG--GTAGAAATGTAAAGTTGG-AGGG--TAACCAGG
q macEug1.Scaffold7817                                    99999----999999999-9999999988999999999997999-----9999999999999899999--999999999999989999-9999--99999999
i macEug1.Scaffold7817           C 0 I 2177
s xenTro2.scaffold_1099             293279 81 -    315732 ATGTTCCAAACCCTCCCCCAGGCCCTGGGACTCTCTGCCCATCA---ACCAGAGCCTGGAGGGGGAGGGAGTAGGAGG-GGGCGC------------------
i xenTro2.scaffold_1099          N 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I

a score=41917.000000
s hg19.chrY                        7659546 77 +  59373566 CATTATGCCAG-------AACTCTCTGAGGAATATGAGCTCCATC-----TGATCTGTGCTTCCTT---------GGATGAAAAG---GCT-GCCACTGTAA
s panTro2.chrY                      513124 77 +  23952694 CATTATGCCAG-------ACCTCTCTGAGGAGTATGAGCTCCATC-----TGATCTGTGCTTCCTT---------GGATGAAAAG---ACT-GCCACTGCAA
q panTro2.chrY                                            00000000000-------000000000000000000000000000-----0000000000000000---------0000000000---000-0000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71051086 77 - 202140232 CATGATGCCAG-------ACCTCTACAAGGAGTATGAGCTCCACC-----AGATCTGAGCTTCTCT---------AGATGACAAG---GCT-GCCACTGTAA
q ponAbe2.chr3                                            99999099999-------999999999999999999999999999-----9999999999999999---------9999999999---999-9999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158777198 77 + 189746636 CATCATGCCAG-------ACCTCTACGAGGAGTATGAGCTCCACC-----TGATCTCAGCTTCCCT---------AGATGACAAG---GCT-GCCACTGTAA
q rheMac2.chr2                                            99999999999-------999999999999999999999999999-----9999999999999999---------9999999999---999-9999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8234649 77 -  88675666 TGTTAGGCCAA-------ACCTG--CACAGAGTATGCACACTATC-----TGGCCTGCCTTCCCCTT--------AGAGGAGATG---GGGTACCACAGTGA
q cavPor3.scaffold_0                                      99999999999-------99999--99999999999999999999-----99999999999999999--------9999999999---99999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2485122 88 + 163896628 TGCCCTGTCAGTGCCCCCGCCCC--CAGAGGGTGTACAGTTCATATCCCGTGGTCTGGGCCTCCCCA--------GGATGAGGAG---GGG-GCCACAGGAG
q oryCun2.chr14                                           99999999999999999999999--999999999999999999999999999999999999999999--------9999999999---999-9999999999
i oryCun2.chr14                  C 0 C 0
s equCab2.chr16                   22223995 67 -  87365405 GGTCATGGCAG-------ACCTCTGCAAATA-CCTGATCAAT-CC-----TGGCGTGAGCTTCCCCGGGT-----AGGAGA--GG---GGT-----------
q equCab2.chr16                                           99999999999-------9999999999999-9999999999-99-----99999999999999999999-----999999--99---999-----------
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26002193 81 -  55389570 TGTCGTGGCAG-------ACCTCTGTAATGAGTATGAACAATATC-----TGGTGTGTGCCTCCCCTGGT-----GGGAGATGGG---GGT-GCCACCCTAA
q canFam2.chr23                                           99999999999-------999999999999999999999999999-----99999999999999999999-----9999999999---999-9999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156994384 89 + 161106243 CGCCTTGGTGG-------ACTTCCACAAAGAGTTTGACCCGTATC-----TGGTTTGAGCATCCCCAGGTACTGGGGGGGACAGGACAGGT-GGCTCTGGAA
q bosTau4.chr1                                            99999999999-------999999999999999999999999999-----99999999999999999999999999999999999999999-9999999999
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               528085 80 -  24123610 TGTTATGGCAG-------GACTCTACAAAGAACATGAATGATACC-----TAGCCTGAACTTCTTCTA-------GTATGAGAAG---GGGAGCCACTCTAA
q loxAfr3.scaffold_36                                     99999999999-------999999999999999999999999999-----999999999999999999-------9999999999---99999999999999
i loxAfr3.scaffold_36            C 0 C 0
s xenTro2.scaffold_1099             293360 67 -    315732 CGCTCAGCCAC-------AAGTGCCCA----------TTTTCACA-----TGAACAGGTCTAACTT---------AAATGACACA---GCA-TCTTCTATAA
i xenTro2.scaffold_1099          C 0 I 3628
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I

a score=54933.000000
s hg19.chrY                        7659623 49 +  59373566 CCAGGTCTCCTTAGTCACCTCTCTGCTTTCCTAATGAGAATCATTTCCA
s panTro2.chrY                      513201 49 +  23952694 CCAGGTCTCCTTAGTCACCTCTCTGCTTTCCTAATGAGAATCATTTCCA
q panTro2.chrY                                            0000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71051163 49 - 202140232 CCAGGTCTCCTTAGTCACATCTCTGCTCTCCTGATGACAGTCATTTCCG
q ponAbe2.chr3                                            9999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158777275 49 + 189746636 CCAGGTGTCCTTAGTCACCTCTCTGCTCTCCTAATGAGAATCATTTCCA
q rheMac2.chr2                                            9999999949999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8234726 49 -  88675666 CCAGGTCTCCTCAATAACCAAGCTGCTCTCTCAGTGGTAATCATTTCTG
q cavPor3.scaffold_0                                      9999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2485210 37 + 163896628 --AGGTTTCCTCGACCACC-TTCTGCACCCTAAAGG---------TCTG
q oryCun2.chr14                                           --99999999999999999-9999999999999999---------9999
i oryCun2.chr14                  C 0 C 0
s equCab2.chr16                   22224062 39 -  87365405 -----TTTCCTCCTCCACC--TCTGCTCTCCTAAGGGTAATCATTC---
q equCab2.chr16                                           -----99999999999999--9999999999999999999999999---
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26002274 37 -  55389570 CAAAGCTTCCTCCTTCAC---------CTCCTGATGGTAATAATTT---
q canFam2.chr23                                           999999999999999999---------9999999999999999999---
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156994473 40 + 161106243 CAACGTTTCTTCATTCACC--TCTACTCTTCTTGTG----TCATTA---
q bosTau4.chr1                                            9999999999999999999--999999999999999----999999---
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               528165 49 -  24123610 CAATGTTTCCTCATTTGCCTCTCGGTTCCCCTCATGACAATCATTcaca
q loxAfr3.scaffold_36                                     9999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 I 111
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=59553.000000
s hg19.chrY                        7659672 63 +  59373566 TAGTTCCTAATA----------GTTTCTATCACGATG---CTTTTCTAAAATCCCACTCTTATATATCTTTACAGG
s panTro2.chrY                      513250 66 +  23952694 TAGATCCTAATA----------GTTTCTATCACAATGATACTTTTCTAAAATCCCACTCTTATATATCTTTACAGG
q panTro2.chrY                                            000000000000----------000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71051212 66 - 202140232 TAGTTTCTAATA----------GTTTCTATCACGATGATGCTTTTCTAAAAACCCACTCTTATATATCTTTACAGG
q ponAbe2.chr3                                            999999999999----------999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158777324 64 + 189746636 TAGTTTCCAATA----------GTTTCCATCACAATGATGCTTTTCTAAAAACCCACTC--ATATATCTTTACAGG
q rheMac2.chr2                                            999999999999----------9999999999999999999999999999999999999--999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8234775 74 -  88675666 TAGTAACTGGCATAACAGTTACTTTTCCAGCACAACAGT--TTTTCTAAACACCTATGACCATGTATCTTTACAGA
q cavPor3.scaffold_0                                      999999999999999999999999999999999999999--99999999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2485247 40 + 163896628 TCACATCCAGCA----------TTTCCCATCCTGACGATGACTTTCTAAA--------------------------
q oryCun2.chr14                                           999999999999----------9999999999999999999999999999--------------------------
i oryCun2.chr14                  C 0 I 2281
s equCab2.chr16                   22224101 41 -  87365405 ------TTAGCG----------------------------CTTTTCTAAAA-CCCGGGTTCATAAATCTTCATAGG
q equCab2.chr16                                           ------999999----------------------------99999999999-999999999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26002311 42 -  55389570 ------TTAATG----------------------------CTTTTCTAGAACCCCATGTTCATACGTCTTCATAGG
q canFam2.chr23                                           ------999999----------------------------999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156994513 42 + 161106243 ------TTAACA----------------------------CATTCCCAAACACCCATGTTCAAATATCTTTACAGG
q bosTau4.chr1                                            ------999999----------------------------999999999999999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               528325 66 -  24123610 tggtttCCAATG----------TTTTCTATCACAATCATGCTTTTCTAAAAACCTGAGTTCATATATCCTTTCAGG
q loxAfr3.scaffold_36                                     999999999999----------999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            I 111 I 1946
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=66066.000000
s hg19.chrY                        7659735 68 +  59373566 GGC-------------AATTGCCAAATTGCCC--CACATTGC-TCTTATCAATTCATAAT-CCATCTATGGAATGAGACCATGCC
s bosTau4.chr1                   156994555 68 + 161106243 CTCAAGATTTGATAGGAGTCCCCAAATTGCCCTAGGCATCAG-TCTGACCA-TTCACAGTCCAGCCTATG---------------
q bosTau4.chr1                                            999999999999999999999999999999999999999999-99999999-999999999999999999---------------
i bosTau4.chr1                   C 0 I 4841
s canFam2.chr23                   26002353 70 -  55389570 CAGGGGATTTAATAGCAATTACCAAATTGCCC--TACCACTG-TCTTACTG------------ATCTGTGGAGTGAGACCATGCC
q canFam2.chr23                                           99999999999999999999999999999999--99999999-99999999------------9999999999999999999999
i canFam2.chr23                  C 0 I 2714
s equCab2.chr16                   22224142 80 -  87365405 CTCAAGATTTCATAGGAATTGCCAAATTGCCCTATACATCTG-TCTTCCCAATTCACAGTCCCATCTATGGGGTGAGACCA----
q equCab2.chr16                                           999999999999999999999999999999999999999999-99999999999999999999999999999999999999----
i equCab2.chr16                  C 0 I 1738
s cavPor3.scaffold_0               8234849 80 -  88675666 TTAAAGATCTGACAGAAACTGACAAATTTACC--TACTTTGGATCTCACTACTCCACAGTGAAATCTATGGTGTAA---CATGCC
q cavPor3.scaffold_0                                      99999999999999999999999999999999--999999999999999999999999999999999999999999---999999
i cavPor3.scaffold_0             C 0 I 16167
s rheMac2.chr2                   158777388 81 + 189746636 GTCAAAATTTAATTGGAATTGCCAAATTGCCC--CACATTGG-TCTTATCAATTCACGGT-CCATCTATGGAGTGAGACCATGCC
q rheMac2.chr2                                            99999999999999999999999999999999--99999999-99999999999999999-999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051278 81 - 202140232 GTCAAAATTTAATAGGAATTGCCAAATTGCCC--CACATTGG-TCTTATCAATTCACAGT-CCATCTATGGAGTGAGACCATGCC
q ponAbe2.chr3                                            99999999999999999999999999999999--99999999-99999999999999999-999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      513316 68 +  23952694 GGC-------------AATTGCCAAATTGCCC--CACATTGC-TCTTATCAATTCATAAT-CCATCTATGGAATGAGACCATGCC
q panTro2.chrY                                            000-------------0000000000000000--00000000-00000000000000000-000000000000000000000000
i panTro2.chrY                   C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2485287 2281 + 163896628 I
e loxAfr3.scaffold_36               528391 1946 -  24123610 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e felCat3.scaffold_217554           345489 2781 -    369131 T
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=25579.000000
s hg19.chrY                        7659803 42 +  59373566 A---TATTGACTTCTCAGCAAAGTGGCAGCTGCTGAGCAcaactg
s felCat3.scaffold_217554           342708 31 -    369131 --------GATTTCTCAATA------CTGTTGCTGAGCACATCTG
q felCat3.scaffold_217554                                 --------999999999999------9999999999999999999
i felCat3.scaffold_217554        T 2781 C 0
s equCab2.chr16                   22225960 38 -  87365405 AGACAACT-GATTCTCGACA------CGGTTGCTGAGCACACCTg
q equCab2.chr16                                           99999999-99999999999------9999999999999999999
i equCab2.chr16                  I 1738 C 0
s rheMac2.chr2                   158777469 42 + 189746636 G---TGCTGACTTCTCAGCAAAGTAGCAGCTGCTGAGCACACTTg
q rheMac2.chr2                                            9---99999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051359 42 - 202140232 A---TGTTGATTTCTCAGCAAAGTGGCAGCTGCTGAGCACACCTg
q ponAbe2.chr3                                            9---99999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      513384 42 +  23952694 A---TATTGACTTCTCAGCAAAGTGGCAGCTGCTGAGCACACCTg
q panTro2.chrY                                            0---00000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s loxAfr3.scaffold_36               530337 17 -  24123610 ----------------------------GTTGCTGAGAACACCTA
q loxAfr3.scaffold_36                                     ----------------------------99999999999999999
i loxAfr3.scaffold_36            I 1946 C 0
s canFam2.chr23                   26005137 16 -  55389570 -----------------------------CTGTCCAGCACATCTG
q canFam2.chr23                                           -----------------------------9999999999999999
i canFam2.chr23                  I 2714 C 0
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2485287 2281 + 163896628 I
e bosTau4.chr1                   156994623 4841 + 161106243 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=56015.000000
s hg19.chrY                        7659845 62 +  59373566 catcaggatcacctgggg------------------gt-gggaagaatgtgttcacattaggaatgagcat-cccagg-------ctgt-----
s rheMac2.chr2                   158777511 62 + 189746636 catcaggatcatcgaggg------------------gt-gggaagagtgtgtttacattaggaatgcgggt-cccagg-------ctat-----
q rheMac2.chr2                                            999999999999999999------------------99-99999999999999999999999999999999-999999-------9999-----
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051401 62 - 202140232 catcaggatcatctaggg------------------gt-gggaagagtgtgtttacattaggaatgcaggt-cccagg-------ctgt-----
q ponAbe2.chr3                                            999999999999999999------------------99-99999999999999999999999999999999-999999-------9999-----
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      513426 62 +  23952694 catcaggatcacctgggg------------------gt-gggaagaatgtgttcatattaggaatgagcat-cccagg-------ctgt-----
q panTro2.chrY                                            000000000000000000------------------00-00000000000000000000000000000000-000000-------0000-----
i panTro2.chrY                   C 0 C 0
s bosTau4.chr1                   156999464 48 + 161106243 CAGCAGAATCGCCCCGGG------------------GGTGGG-----------------------GTAGATCCCCAGGTCCCACCCCAA-----
q bosTau4.chr1                                            999999999999999999------------------999999-----------------------999999999999999999999999-----
i bosTau4.chr1                   I 4841 C 0
s felCat3.scaffold_217554           342739 62 -    369131 TATCAGGGCCGCCTGGGG------------------GTAGGGTAGAGCAGGTCTGCTT--Aaaatggatatccccagg-------ctat-----
q felCat3.scaffold_217554                                 999999999999999999------------------9999999999999999999999--999999999999999999-------9999-----
i felCat3.scaffold_217554        C 0 C 0
s canFam2.chr23                   26005153 80 -  55389570 CACCAGGGTCACCTGGGGCGGGGATGGGGGGTGGGTGGATGGGAGAGCATGTCTGCTT--AGAATGCGTATCCCTGGG-------CTAA-----
q canFam2.chr23                                           9999999999999999999999999999999999999999999999999999999999--999999999999999999-------9999-----
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22225998 63 -  87365405 catcaggatcacctgggg------------------gccggggtgagcacgtttgctt-aaaaatgcagattcccagg-------ctac-----
q equCab2.chr16                                           999999999999999999------------------9999999999999999999999-9999999999999999999-------8999-----
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               530354 67 -  24123610 CATTGGGAGCACCTGGGG------------------GAGGGAAGGAATGTATttacta--aaaatgcagattactaag-------ctaagctat
q loxAfr3.scaffold_36                                     999999999999999999------------------9999999999999999999999--999999999999999999-------999999999
i loxAfr3.scaffold_36            C 0 C 0
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2485287 2281 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              276798 10943 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=15045.000000
s hg19.chrY                        7659907 32 +  59373566 accacaga-------cctactcaatcagaccagcatttc
s ponAbe2.chr3                    71051463 31 - 202140232 -ccccaga-------tctactaaatcagacctgcacttc
q ponAbe2.chr3                                            -9999999-------999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158777573 31 + 189746636 -ccccgga-------tctactacatcagacctgcatttc
q rheMac2.chr2                                            -9999999-------999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s panTro2.chrY                      513488 32 +  23952694 accacaga-------cctactcaatcagaccagcatttc
q panTro2.chrY                                            00000000-------000000000000000000000000
i panTro2.chrY                   C 0 C 0
s micMur1.scaffold_734              287741 36 -    418489 gcaacagagtgagactctgtctcaacaaagcaaaac---
q micMur1.scaffold_734                                    999999999999999999999999999999999999---
i micMur1.scaffold_734           I 10943 I 4711
s oryCun2.chr14                    2487568 28 + 163896628 ----CACA-------CCCACTACGGCAGCTCTGTATTTC
q oryCun2.chr14                                           ----9999-------999999999999999999999999
i oryCun2.chr14                  I 2281 C 0
s bosTau4.chr1                   156999512 23 + 161106243 GCACCGGG-------TCA---------GAGCTGCATCTC
q bosTau4.chr1                                            99999999-------999---------999999999999
i bosTau4.chr1                   C 0 C 0
s felCat3.scaffold_217554           342801 32 -    369131 gtcccaga-------tctacaaaatcagatctgcagggg
q felCat3.scaffold_217554                                 99999999-------999999999999999999999999
i felCat3.scaffold_217554        C 0 C 0
s canFam2.chr23                   26005233 30 -  55389570 GTCCCAGA-------TCTATAAGTT--GATCTGCAGGGC
q canFam2.chr23                                           99999999-------9999999999--999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22226061 20 -  87365405 gtcccaga-------tct---------gcttttcag---
q equCab2.chr16                                           99999876-------375---------645996556---
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               530421 32 -  24123610 atccccaa-------tatattgaatcagatctgcatttc
q loxAfr3.scaffold_36                                     99999999-------999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=256947.000000
s hg19.chrY                        7659939 186 +  59373566 aacaaccatgcttattgacttgttt-gctcactcaagtctgaAGATGATTCTGTGAGAGGCAGTCTAGAGCCATGTTTAAAAAAAAAAAAAACACTGTGAAGCCAAGGGTGAGCTCACTGAGAAACAGTTCCCAATCAATTCATAAGGTCTG-CAAGGTGGCA-----------GGAGTGG---------------------------------------------GAGAATCA----GGGTAG-------------------------------------------------------------------------ATGG
s panTro2.chrY                      513520 185 +  23952694 aacaaCCATGCTTATTGACTTGTTT-GCTCACTCAAGTCTGAAGATGATTCTGTGAGAGGCAGTCTAGAGCCACGTTTAAAAAAAAAAAAA-CACTGTGAAGCCAAGGGTGAGCTCACTGAGAAACAGTTCCCAATCAATTCATAAGGTCTG-CAAGGTGGCA-----------GGAGTGG---------------------------------------------GGGAATCA----GGGTAG-------------------------------------------------------------------------ATGG
q panTro2.chrY                                             0000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000-0000000000-----------0000000---------------------------------------------00000000----000000-------------------------------------------------------------------------0000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71051494 178 - 202140232 aataaccagggccattgacttgttt-gctcactcaagtctgaggacgattgtgtgagaggctgcctggagccacgtctggagaaa-------gactgtggagctaagggtgagctcactgggaaacagttcccaatcaattcataatgcctg-catggtggca-----------ggaatgg---------------------------------------------gggaaTC-----GGGTAG-------------------------------------------------------------------------ATGG
q ponAbe2.chr3                                             9999999999999999999999999-99999999999999999999999999999999999999999999999999999999999-------999999999999999999999999999999999999999999999999999999999999-9909999999-----------9999999---------------------------------------------9999999-----999999-------------------------------------------------------------------------9999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158777604 178 + 189746636 aataaccagggccattgatttgttt-gctcactcaagtctgaggaTGATTGTGTGAGAGGCTGTCTGGAGCCAAGTCTGGAACAA-------GACTGTGAAGCCAAGGGTGAGCTCACTAGGAAACAGTTCCCGATCAATTCATAATGCCTG-CATGGTGGCA-----------GGAATGG---------------------------------------------CGGAATC-----GGGTAG-------------------------------------------------------------------------ATGG
q rheMac2.chr2                                             9999999999999999999999999-99999999999999999999999999999999999999999999999999999999999-------999999999999999999999999999999999999999999999999999999999999-9999999999-----------9999999---------------------------------------------9999999-----999999-------------------------------------------------------------------------9999
i rheMac2.chr2                   C 0 C 0
s oryCun2.chr14                    2487596 162 + 163896628 AGAGGCCAGAGCCTCTGGCT-----------------TCTCAGAACGACTGTGTGCAAGGCCGTGTGGACCCAGGTTCTGAGAAA-------GAC-GTTAGGCCAACGGTGAGCTCGCCTGGCAAGAGTTCCCAGTCGGTTACTAGTGTCGC-CATGGTGGCA-----------GGAACGG---------------------------------------------GAAAACAG----GTACAG-------------------------------------------------------------------------Acag
q oryCun2.chr14                                            99999999999999999999-----------------999999999999999999999999999999999999999999999999-------999-99999999999999999999999999999999999999999999999999999999-9999999999-----------9999999---------------------------------------------99999999----999999-------------------------------------------------------------------------9999
i oryCun2.chr14                  C 0 I 1180
s bosTau4.chr1                   156999535 174 + 161106243 AACAGCTTAGGCCACTGGCTTCCCTGGCTCCCTC-TGCTCGAGAAGGATTCTTTATGAGGCT-TCAGGAGTCGTGTTCTGGAAAG-------GACTGTGGGGCCAAGACTGAGCTCAC-AGGAAACAGCTCCTGGTCGATGGGTGATGTCTA-TGCGGTGGCA-----------GAAC------------------------------------------------GCGAATCC----ATGCAG-------------------------------------------------------------------------GCGG
q bosTau4.chr1                                             9999999999999999999999999999999999-999999999999999999999999999-9999999999999999999999-------99999999999999999999999999-999999999999999999999999999999999-9999999999-----------9999------------------------------------------------99999999----999999-------------------------------------------------------------------------9999
i bosTau4.chr1                   C 0 C 0
s felCat3.scaffold_217554           342833 171 -    369131 aacaaccagggccgtttacttcttttgctcattcaagtttgagGTGGATTGTGAGAGAGGCTGTTGGGAGCCATGTTCTGAAAAA-------GACTGTTAGGCTGAGGGTGAGCTCACCACGAAATAGTTCCCAACTGATTAGTAATGCCTG-CATGGCAGCA-----------GGAACGG---------------------------------------------AGGAATAC----T----------------------------------------------------------------------------------
q felCat3.scaffold_217554                                  9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------999999999999999999999999999999999999999999999999999999999999-9999999999-----------9999999---------------------------------------------99999999----9----------------------------------------------------------------------------------
i felCat3.scaffold_217554        C 0 C 0
s canFam2.chr23                   26005263 171 -  55389570 AACGAATAGGGTCATTTACTTCTTTTGCTCACTCAAGTTTGAGGCAGATTGTGTGAGAGGCTGTCGGGAGCTGCATTCTGAAAAA-------GACCGTCAGGCCCAGGACAAGCTCACCAGGAAACAGTTCGCAGTTGATTAGTAATGCCTG-TATGGTGGCA-----------AGAATGG---------------------------------------------GTGAATAC----A----------------------------------------------------------------------------------
q canFam2.chr23                                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------999999999999999999999999999999999999999999999999999999999999-9999999999-----------9999999---------------------------------------------99999999----9----------------------------------------------------------------------------------
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22226081 175 -  87365405 --caaccagggccactgacttcttttgctcactcaagtttgagaaCAATTGTGTGAGA-GCTGTAGGGAAGCATGTTCTGAAAAA-------GACTGT-GGGCCAAGGGTGAGCTCACAGGGAAATAG-TCCTGACTGATTAGTAATACCTG-CATGGTGGCA-----------GGAAGAG---------------------------------------------GGGAACAG----ATGCAG-------------------------------------------------------------------------ATAC
q equCab2.chr16                                            --56666578646537573635478653363456344485431255425352544314-31544457455345453465649783-------342322-36335356923232234342693261223-46835426454343552217422-3336233573-----------1262345---------------------------------------------54222335----455667-------------------------------------------------------------------------5523
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               530453 303 -  24123610 ggcaaccagggccacttacttcttttgcctattcaagtttgaaaatgactgTGTGAGATGTTGTGTGCAGTCATGGTCTGGAAA--------GACTGTT----------CCTGTTCACCAGGAAATAGTTCCTGATCAATTAATAATGCCTGTCAtggtggcacagtggttaagagcatggctgctaaccaaaagatcagcagtttaaatccaccagccactccttggaaatgctatggggcagttctactctgtcctacagggttgccataagttggaattgtcttgacagcaacaggtttttttatttttttGCCATGG
q loxAfr3.scaffold_36                                      999999999999999999999999999999999999999999999999999999999999999999999999999999999999--------9999999----------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 I 14
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=70849.000000
s hg19.chrY                        7660125 62 +  59373566 ATATTTAAGACACCAATCTttcc-ttctcctcccctcctcattcccagactgcctagagaact
s rheMac2.chr2                   158777782 63 + 189746636 ATACATAAGACACCAATCTCTACTTTCTCCTCTCCTCCTCATCCCCTGACTGCTTGGAGAACT
q rheMac2.chr2                                            999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051672 63 - 202140232 ATACATAAGACACAAATCTCTCCTTTCTCCTCTCCTCCTCATTCCCTAACTGCTTAGAGAATT
q ponAbe2.chr3                                            999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      513705 62 +  23952694 ATATTTAAGACACCAATCTTTCC-TTCTTCTcccctcctcattcccagactgcctagagaact
q panTro2.chrY                                            00000000000000000000000-000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s bosTau4.chr1                   156999709 56 + 161106243 -----ACAAGGCCCTGCTTCCCGCCCTTCGCCTCC--CCAGTTCCCTGTCTGCCCCGAGAATC
q bosTau4.chr1                                            -----999999999999999999999999999999--99999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s felCat3.scaffold_217554           343004 56 -    369131 -------GGGTCCTGACCTCTCCTTCTTCCCCTCCTGCTCCTTCCCTGTCTGCTTAGAAAATC
q felCat3.scaffold_217554                                 -------99999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_217554        C 0 I 239
s canFam2.chr23                   26005434 49 -  55389570 -------AGATCCCAAGCTCTCCTTCCTCCTCTCCTGCTCACTCCCTACCTGTTCA-------
q canFam2.chr23                                           -------9999999999999999999999999999999999999999999999999-------
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22226256 57 -  87365405 -----ACAAGTGCCAATCTCTGCTTCTCCCCTTCCT-CTCATTCTCTGTCTGCTTAGAGAATC
q equCab2.chr16                                           -----1534731177111745283634267792638-44747545424682753156688127
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               530770 59 -  24123610 ATACATAAGATCCCAACCTGTCATTTCTCCTCTCCTC----TTTCCTGTCTACTTAGAAAATT
q loxAfr3.scaffold_36                                     9999999999999999999999999999999999999----9999999999999999999999
i loxAfr3.scaffold_36            I 14 C 0
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2487758 1180 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=231198.000000
s hg19.chrY                        7660187 169 +  59373566 cctactcatccttcataactctttctagaagag----acttcttcaacccacaagccaaggc---ctccctccttgtgtcaaggcactatctagatctagtactcact-------atcacagttttctagaatgtctttcagtga-agccagggactttttcttgttcattttgttctcctcac
s rheMac2.chr2                   158777845 155 + 189746636 CCTTCTCATCCTTCACAACTCTTCCTAGCAGAG----ACTTCTTCAACCTACACACCAAGGC---CTCCCTCCTTGTGTCAAGGCACC------ATCTAGCACTCACC-------A-------TTTCTGGCATGTCTCCCAGGGA-AGGCAGGG-CTTTGTCTTGTTCATTTTGTTCTCCTCAC
q rheMac2.chr2                                             999999999999999999999999999999999----9999999999999999999999999---99999999999999999999999------99999999999999-------9-------9999999999999999999999-99999999-99999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051735 163 - 202140232 CCTACTCATCCTTCACAACTCTTTCTAGAAGAG----ACTCCTTCAACCTATACACCAAGGC---CTCCCTCCTTGTGTCAAGGCACC------ATCTAGCACTCACC-------ATCACAGTTTTCTGGTGTGTCTCCCAGGga-aggcagggactttgtcttcttcattttgttctcctcac
q ponAbe2.chr3                                             999999999999999999999999999999999----9999999999999999999999999---99999999999999999999999------99999999999999-------999999999999999999999999999999-99999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      513767 169 +  23952694 cctactcatccttcataaccctttctagaagag----acttcttcaacccacaagccaaggc---ctccctccttgtgtcaaggcactatctagatctagtactcact-------atcacagttttctagaatgtctttcagtga-agtcagagactttttcttgttcattttgttctcctcac
q panTro2.chrY                                             000000000000000000000000000000000----0000000000000000000000000---0000000000000000000000000000000000000000000-------000000000000000000000000000000-00000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s equCab2.chr16                   22226313 169 -  87365405 CCTACTCACCCTTCACAACTCCTTCTAGAAGAG----ACATCTTCAACCCACCC-CCAAGGC---CTCCTTCCATGTCTGAAGGCCCC------ATGTAGCGCCCTCATGTTAACATAACAGTTTTCTCCTGTGTCTctcccggg-aggcagggacctggtcttgctcattttgttctcctcac
q equCab2.chr16                                            999999979999997999999999999999999----99999999999999999-9999999---99999999999999999999999------999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s felCat3.scaffold_217554           343299 157 -    369131 CCTACTCATCCTCCACAACGCTTTCTAGAAGAG-------------GCCTGCC---GAAGGC---CTCCCTCCATATCTGAAGGCACC------ATCTAGCACTCTCC--TTAATGTAACAGTTTACTGGTGCGTCTCTCCTGGGCAGGCAGGGACTTCGTCTTGCTTGTTTTGTTCTCCTCAC
q felCat3.scaffold_217554                                  999999999999999999999999999999999-------------9999999---999999---99999999999999999999999------99999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_217554        I 239 C 0
s canFam2.chr23                   26005483 172 -  55389570 -TTCCTCATCCTCCATGACTCTTTCTAGAAGAGTCTTTCTTCTTCAGCCTGCC--TGAAGGC---CTCTCTCCATATCTCCAGGCACT------ATCTAGCACTCTTTTGTTCAAATAATAGTTTACTAGTGTGTCTCTCTCAGGCAggcagggactttgtcttgctcactttcatgtcctcac
q canFam2.chr23                                            -9999999999999999999999999999999999999999999999999999--9999999---99999999999999999999999------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156999765 147 + 161106243 --CTCCGGGCCCTCACGGCTCTTTCTGGAAGAC----GCTTCCTCAGCCTCCC--CCATGGCTGTCTCCCTCC--------AGACACC------ACCTGGAGCACCCG-----------CAGCTT-CCAGGGCGTCTCTGAGAG--CGGCCGGGACCTCATCTTGCCCA-TTTGGTCCCTCTGC
q bosTau4.chr1                                             --9999999999999999999999999999999----9999999999999999--999999999999999999--------9999999------99999999999999-----------999999-999999999999999999--99999999999999999999999-99999999999999
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               530829 163 -  24123610 CCGACTCATCCTTCA---CTCTCTCTAGAAAAG----ACTTTTTCCACCTACCCACCCAACG---CTCCCTCCTTATTTCAAGGTACC------ATCTAGAACTCTCA---TATGTGAACAGCTTCCTAGTGTGTCTCCCTTGGGAAGGCAGATGCTTTGTC--GTTATTTTTGTCCCCCTAAC
q loxAfr3.scaffold_36                                      999999999999999---999999999999999----9999999999999999999999999---99999999999999999999999------99999999999999---999999999999999999999999999999999999999999999999999--99999999999999999999
i loxAfr3.scaffold_36            C 0 I 190
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2487758 1180 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=105823.000000
s hg19.chrY                        7660356  97 +  59373566 -----------------------------------aactag----ttttttgcctagtacataactagaagtcaataaatccttatcaaattaatacatGATTGAGAAAACAA---------------------------------------------------------------------------------------------------------------------------------AAACAAAGGATAGAGCAAATACA
s rheMac2.chr2                   158778000  97 + 189746636 -----------------------------------AACTAG----TTTTTTGCCTAGTCCATAACTAGAATTCAACAAATCCTTAGCAAATGACTACGTGATTGAAAAAACAA---------------------------------------------------------------------------------------------------------------------------------AAACAAAGGATAGAGCAAATACA
q rheMac2.chr2                                             -----------------------------------999999----99999999999999999999999999999999999999999999999999999999999999999999---------------------------------------------------------------------------------------------------------------------------------99999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051898  97 - 202140232 -----------------------------------aactag----ctttttgcctagtccataactagaattcaataaatccttagcaaatgaCTACGTGATTGAAAAAACAA---------------------------------------------------------------------------------------------------------------------------------AAACAAAGGATAGAGCAAATACA
q ponAbe2.chr3                                             -----------------------------------999999----99999999999999999999999999999999999999999999999999999999999999999999---------------------------------------------------------------------------------------------------------------------------------99999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      513936  96 +  23952694 -----------------------------------aactag----ttttttgcctagtacataactagaagtcaataaatccttatcaaattaatacatGATTGAGAAA-CAA---------------------------------------------------------------------------------------------------------------------------------AAACAAAGGATAGAGCAAATACA
q panTro2.chrY                                             -----------------------------------000000----0000000000000000000000000000000000000000000000000000000000000000-000---------------------------------------------------------------------------------------------------------------------------------00000000000000000000000
i panTro2.chrY                   C 0 C 0
s equCab2.chr16                   22226482  94 -  87365405 -----------------------------------aactagcctcctctttgcctagctgataaccagaattcaataaatacttagcaaatgaataaaCGATAAAA----------------------------------------------------------------------------------------------------------------------------------------AAAAAAAGGACAGAGCAAACACA
q equCab2.chr16                                            -----------------------------------99999999999999999999999999999999999999999999999999999999999999999999999----------------------------------------------------------------------------------------------------------------------------------------99999999999999999999999
i equCab2.chr16                  C 0 C 0
s felCat3.scaffold_217554           343456  96 -    369131 -----------------------------------AACTGGCCTCCTCTTTGCCTGGCTAATTATCAGAATTCAATAACTACTTCACAAATGAATAAATGATTAAAGA--------------------------------------------------------------------------------------------------------------------------------------AAAAAAAGGACAGAGTAACTACA
q felCat3.scaffold_217554                                  -----------------------------------9999999999999999999999999999999999999999999999999999999999999999999999999--------------------------------------------------------------------------------------------------------------------------------------99999999999999999999999
i felCat3.scaffold_217554        C 0 C 0
s canFam2.chr23                   26005655 227 -  55389570 -----------------------------------aactag---tctctttgcctagctaataatgagaattcaagagctactttgcaaatgaataaatGATAAAAGAggaggaagggagggagggagggagggagggagggaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggagggagggagggagggagggagggagggagggaggggagggaaggaaggaaggagCAAATACA
q canFam2.chr23                                            -----------------------------------999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999099909999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   156999912  86 + 161106243 -----------------------------------ATCCGG-CTCTCCTCTGCCCAGCTAATAACCAGAACTCAACAAGTACTCAGCAGACAAAC--ATGATGAAT---------------------------------------------------------------------------------------------------------------------------------------------CAGGACCCAGCGAGCACA
q bosTau4.chr1                                             -----------------------------------999999-99999999999999999999999999999999999999999999999999999--999999999---------------------------------------------------------------------------------------------------------------------------------------------999999999999999999
i bosTau4.chr1                   C 0 C 0
s loxAfr3.scaffold_36               531182 126 -  24123610 aactggtctccatgagttgatggcaattggttAACAACTAG------CTCTGCCTAACTCATCACCAGGATTTAATAAATGTTTACCAAATGAATAAATGATTAAAAAG-------------------------------------------------------------------------------------------------------------------------------------AAAAAAAGCATGTTGTGAATACA
q loxAfr3.scaffold_36                                      99999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999-------------------------------------------------------------------------------------------------------------------------------------99999999999999999999999
i loxAfr3.scaffold_36            I 190 C 0
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2487758 1180 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e eriEur1.scaffold_377961            16335 24689 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=119284.000000
s hg19.chrY                        7660453 78 +  59373566 -GAACCAGTTACTAAGAAGGACAAGACAGC-AAAACCCAGCCTCCTACTCTCCACCATGCTGTCTCCCATAAAGATCTCA
s rheMac2.chr2                   158778097 77 + 189746636 -GAACCAGTTACTGGGTAGGAGAAGACGG--AAAACCCGGCCTCCTCCTCTCCACCATGCTGTCTCCCGTGAAGATTCCA
q rheMac2.chr2                                            -9999999999999999999999999999--9999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71051995 78 - 202140232 -GAACCAGTTACTGGGAAGGACAAGACAGC-AAAACCCGGCCTCCTCCTCTCCACCATGCTGTCTCCCATGAAGATCCCA
q ponAbe2.chr3                                            -99999999999999999999999999999-9999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      514032 78 +  23952694 -GAACCAGTTACTAAGAAGGACAAGACAGC-AAAACCCAGCCTCCTACTCTCCACCATGCTGTCTCCCATAAAGATCTCA
q panTro2.chrY                                            -00000000000000000000000000000-0000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s bosTau4.chr1                   156999998 73 + 161106243 -GAATCCATCACTGCGAAGGACAGATGGGT-GAAA--CCGCCTCTTCCTCTGCAGCACGCCGCCTCCC---GAGACCCTG
q bosTau4.chr1                                            -99999999999999999999999999999-9999--9999999999999999999999999999999---999999999
i bosTau4.chr1                   C 0 I 1
s canFam2.chr23                   26005882 76 -  55389570 -TAGCCAGTTACTGGGAAGGATAAGACAGG-AAAC--CTGTGTCTTTCTCTACACCATGTAGCTTCGCAGCATGATCCCT
q canFam2.chr23                                           -99999999999999999999999999999-9999--9999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 I 1
s felCat3.scaffold_217554           343552 71 -    369131 -----CAGTTACTGGGAAGGACAAGACCGC-AAAA--CCGTCTCTTCCTCTACACCTTGTAG-TTCCCATCAGGATCCCT
q felCat3.scaffold_217554                                 -----9999999999999999999999999-9999--9999999999999999999999999-99999999999999999
i felCat3.scaffold_217554        C 0 I 1
s equCab2.chr16                   22226576 75 -  87365405 -GAGCCAGTTACTGGGAAGGTCAAGATGGT-AAA---CAGTCTCTCCCTCTAAACCATGCCGCCTCCCCTTAAGACCCCT
q equCab2.chr16                                           -99999999999999999999999999999-999---9999999999999999999999999999999999999999999
i equCab2.chr16                  C 0 I 1
s eriEur1.scaffold_371855             3735 77 -     87482 -GAAATagctacaaacaacaacaaaaagttcagAG--CGGTTTCCTCCTTAATACCGCGTTCTCACCCAGGAAGTTCCCT
q eriEur1.scaffold_371855                                 -9999999999999999999999999999999999--9999999999999999999999999999999999999999999
i eriEur1.scaffold_371855        n 24689 C 0
s loxAfr3.scaffold_36               531308 76 -  24123610 GGGCTAAGTTACTGATAAAGACAAGACTGC-ATAACCTAGTCTC---CTCTACACCACATTGCCTCCCACTAAGAGCCCC
q loxAfr3.scaffold_36                                     999999999999999999999999999999-9999999999999---999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e cavPor3.scaffold_0               8234929 16167 -  88675666 I
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2487758 1180 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=-6523.000000
s hg19.chrY                        7660531  95 +  59373566 GGTCTTCCAAGGGTAAGGAAAAAAAAGCTGATAAATG-AGGAC-------TGGTGG-CCAGCAACCTCC-------TCACTGCAGC----CAGGCT---TTATA---------------------------------------------TCTAGGCCATAAAC
s panTro2.chrY                      514110  95 +  23952694 GGTCTTCCAAGGGTAAGGAAAAAAAAGCTGATAAATG-AGGAC-------TGGTGG-CCAGCAACCTCC-------TCACTGCAGC----CAGGCT---TTATA---------------------------------------------TCTAGGCCAAAAAC
q panTro2.chrY                                             0000000000000000000000000000000000000-00000-------000000-000000000000-------0000000000----000000---00000---------------------------------------------00000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71052073  95 - 202140232 AGTCTTCCAAGGGTAAGGAAAAACAGGCTGATATATG-AGGGC-------TGGCGG-CCAGCAACCCTC-------CCACTGCAGC----CAGGCT---TTGTC---------------------------------------------TCCAGGCCATTAAC
q ponAbe2.chr3                                             9999999999999999999999999999999999999-99999-------999999-999999999999-------9999999999----999999---99999---------------------------------------------99999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158778174  95 + 189746636 GGTCTTCCAAGGGTAAGGGAAAACAGGCTGATAAATG-AGGTC-------TGGCAG-CCAGCAACCGTC-------CCACTGCAGC----CAGGCT---TTGTC---------------------------------------------TCCAGGCCATAAAC
q rheMac2.chr2                                             9999999999999999999999999999999999999-99999-------999999-999999999999-------9999999999----999999---99999---------------------------------------------99999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8251096  99 -  88675666 ggTTCTTCAGTGGCA--GATAAGCAGGCTGATCAAAG-AAG---------CAGCAC-CCAGAGGCCTCC------------ACAGT----CAGGTC---TTCTCCAGTC------------------------ACATGCAA--------TGGAGACCGTAGGG
q cavPor3.scaffold_0                                       999999999999999--99999999999999999999-999---------999999-999999999999------------99999----999999---9999999999------------------------99999999--------99999999999999
i cavPor3.scaffold_0             I 16167 C 0
s bosTau4.chr1                   157000072 129 + 161106243 G--CCTCCAGGGA-------------------TGAGGCAAGAC-------TGCCTGACAAACCAAGGCTGCTGGGCACAGTCCTGCCTCCAGGACCACCTCGTCTGGACGAGTGATGGAGCCCCCAGGCGGGGAC------CGGGTACCACCAGGCTTGGGGA
q bosTau4.chr1                                             9--9999999999-------------------99999999999-------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999------9999999999999999999999
i bosTau4.chr1                   I 1 C 0
s canFam2.chr23                   26005959 101 -  55389570 GCTCCTCTGAAGA-------------------TGATG-AAGAC-------TAGTGC-CCAGCAAAGCCT------CCCACTCCAGC--CCCAGATT--CTTGTCTGGGC------------------------ACTCATGACGGGGACCTCCAGACCATCAAG
q canFam2.chr23                                            9999999999999-------------------99999-99999-------999999-999999999999------99999999999--99999999--99999999999------------------------999999999999999999999999999999
i canFam2.chr23                  I 1 C 0
s felCat3.scaffold_217554           343624  98 -    369131 GCTCCTCTGAAGA-------------------TGAAG-AAGAC-------TGGCAG-CCAGCAAAGCCT------CCCACTCTAGC--CCCAGACT---TTGTCTGCAC-------------------------CCCGTGACGGGAGCCTCCAGGCCATCAA-
q felCat3.scaffold_217554                                  9999999999999-------------------99999-99999-------999999-999999999999------99999999999--99999999---9999999999-------------------------9999999999999999999999999999-
i felCat3.scaffold_217554        I 1 C 0
s equCab2.chr16                   22226652 112 -  87365405 GGTCCTCCAAGAG-AAGGAACGACAGGCTGACGGATG-AAGCC-------TGGCCG--CGTCAGAGCCT-------CCACTGCGGC--CCAGG------CTGTCCGGGC-------------------------GTCTGGGAGGGCGCCCTGGGGCCATCACC
q equCab2.chr16                                            9999999999999-99999999999999999999999-99999-------999999--99999999999-------9999999999--99999------9999999999-------------------------99999999999999999999999999999
i equCab2.chr16                  I 1 C 0
s eriEur1.scaffold_371855             3812 100 -     87482 ---CCCCCCAAAA-------------------TGAGGAAAGACAGGAAGATGGCAG-CTAGCAAAGTCC------CCCACTGCAAC--ACTGGTCT-------TTGGGT------------------------ATCTGTCACGACAACCTCCAGGCCCACAC-
q eriEur1.scaffold_371855                                  ---9999999999-------------------999999999999999999999999-999999999999------99999999999--99999999-------999999------------------------99999999999999999999999999999-
i eriEur1.scaffold_371855        C 0 C 0
s loxAfr3.scaffold_36               531384 117 -  24123610 AGTCTTCCCAGCATAAAGAGAGAT-GGCTGATCAATG-AAGAC-------TGGCAG-TCAGAAAGCCCT------CCCATTCCAGC--ACCAG-CT---CTGGCTGGGC------------------------ATCTGGACTGGAGCCCTCCAGGCCACAGAT
q loxAfr3.scaffold_36                                      999999999999999999999999-999999999999-99999-------999999-999999999999------99999999999--99999-99---9999999999------------------------999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e rn4.chr9                       107349470 12976 - 113440463 I
e mm9.chr17                       50251224 10494 +  95272651 I
e oryCun2.chr14                    2487758 1180 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=692239.000000
s hg19.chrY                        7660626 235 +  59373566 ACCT----CCTTGCTCACAGGAGC---TAGA------CCCTGT---GATCAGCAAACAGCT--GCAACAACAGCAGCGTGTGGCCTGCCCAGCTTGTTTAG---------GTGGTGTGTGTTTGTTAGAAAAACTTGCTCTGTGGTGTTTCTTTATAACGACTACTTGGAGAAATGATGTTATTTTTA--GGGGGTGGGGAATATCAAAGAGGC------TTATTTGGCAAAAG-CCACAATCTGCTCACTTCCACTTTGTGTGAGTATGT
s panTro2.chrY                      514205 235 +  23952694 ACCT----CCTTGCTCACAGGAGC---TAGA------CCCTGT---GATCAGCAAACAGCT--GCAACAGCAGCAGCATGTGGCCTGCCCAGCTTGTTTAG---------ATGGTGTGTGTTTGTTAGAAAAACTTGCTCTGTGGTGTTTCTTTATAACGATTACTTGGAGAAATGATGTTATTTTTA--GGGGGTGGGGAATATCAAAGAGGC------TTATTTGGCAAAAG-CCACAATCTGCTCACTTCCACTTTGTGTGAGTATGT
q panTro2.chrY                                             0000----0000000000000000---0000------000000---000000000000000--00000000000000000000000000000000000000---------000000000000000000000000000000000000000000000000000000000000000000000000000000--000000000000000000000000------00000000000000-000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71052168 237 - 202140232 ACCT----CCTTGCTCACAAGAGT---TGGA------CCCTGTTGGGATCAGCAAACAGCT--GCAGCAACAGGAGCACATGACCCACCCAGTTTGTTTAG---------GTGGCGTGTGTTTGTGAGGAGAACTTGCTCTGTGGTGTTTTTCTATAA-GATTACTTGGAGAAATGATGTTATTTTCA--GGGGGTGAGGAATACCAAAGAGGC------TTATTTGGCAAAAG-CCACAATCTGTTCACTTCTACTTTGTGTGCGTATGT
q ponAbe2.chr3                                             9999----9999999999999999---9999------999999999999999999999999--99999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999-99999999999999999999999999999--999999999999999999999999------99999999999999-999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158778269 238 + 189746636 ACCT----TCTTGCTCACAGGAGT---TGGA------CCCTGTTGGGATCAGCAAACAGCT--GCAGAAACAGCAGCGCATGACCCGTGCAGTTTGTTTAG---------GTGGCGTGTGTCTGTGAGGAAAACTTGCTCTGTGGTGTTTTTCTATAACGATTACTTGGAGAAATGATGTTATTTTCA--GGGGGTGAGGAATACCAAAGAGGC------TTATTTGGCAAAAG-TCATAATCTGTTCACTTCCACTTTGTGTGCATATGT
q rheMac2.chr2                                             9999----9999999999999999---9999------999999999999999999999999--99999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999------99999999999999-999999999999999998899999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8251195 243 -  88675666 CCCTAAACTCTTATTCACAGATGT---CTGA------TACTATTGGGATCAGCAAATAGCT--GCAGCAACAGCCGCACATTACAATCCTCGTGTGTTTAG---------TTGGTGTGGGTTTGTGAGAAAAACTTGCCTTCTGGTGTTTTCTCTTAACTATCACTTGGAAGAATGATGTTATTTTTA--GGGGGCAGAAAACACCAAAGAGGC------TTACTTGGCAAAGGAACACAATCTGTTCACCTCTACTTCACACGTGTATGT
q cavPor3.scaffold_0                                       999999999999999999999999---9999------999999999999999999999999--99999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999------999999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2488938 219 + 163896628 ACCT-------CCCTGGGACCTGG---G------------CACTGGGGTTAGCCAGCCTCT--GCAG-------CACACAGGACTGCCCCGATATGGTTAG---------ATAGCAGATGTTTGTGAGAAAGACTCGCTCT---GTGTTTTTCTTCAACCATCACTTGGAG-AGTGAGGTTATCTGCA--GGGAGCTGGGGACACCGAGCAGGC------TCATTTGGCCAACGGACACAATCTGTTCACCTCCGCTTTGCATGCAGGTGT
q oryCun2.chr14                                            9999-------9999999999999---9------------999999999999999999999--9999-------999999999999999999999999999---------9999999999999999999999999999999---999999999999999999999999999-9999999999999999--999999999999999999999999------999999999999999999999999999999999999999999999999999
i oryCun2.chr14                  I 1180 C 0
s rn4.chr9                       107362446 227 - 113440463 --------CCTCCCTCGCAGCCAA---GGTT------ATATATTGGCATCATGGAACAGCCAAGCAG-GACGGCTGCCTAAGACCCTCCTAGTTCATTCAG----------AGGTGTCTGTCTGTCTGAATACCTCGCTCTGTGGTGTTTCTCTTTAGCTCTTACTTGGAGAAATGGTG------TTA--GGAGGAGTCAGGTAGCAAGAAC--------TTCCATAGCAAGTGAAGTCAATCTACTCCCTTCTACTTTGCAGAAGTGTGT
q rn4.chr9                                                 --------9999999999999999---9999------999999999999999999999999999999-999999999999999999999999999999999----------99999999999999999999999999999999999999999999999999999999999999999999------999--9999999999999999999999--------999999999999999999999999999999999999999999999999999
i rn4.chr9                       I 12976 C 0
s mm9.chr17                       50261718 205 +  95272651 -----------------------------------------------ATCAGTGAGCAGCCAGGCGG-GACAGCTGCCTAGGCTGCTCCCAGTTTACTCAG----------TGGTGTCTGTCTGTCAGAATACCTTGTTCTGCGGTGTTTCTCTTTAAGTCTTACTTGGAGAAATGATG------TTA--GGAGGAGTCGGGTAGCAAGAACGCAAGAAAGTCCATAGCAAGCGAACCCAATCTACTCCCTTCCACTTCTCAGAACTGTGT
i mm9.chr17                      I 10494 C 0
s bosTau4.chr1                   157000201 233 + 161106243 --------GCAGGCGCAGAAGCGTCCACGGGAGCCACCCCTG--TGGCTTGGT-----------TTGGTTTGGCTCCGTTTGGTCACCCAGGTTTGCTCGG---------CTACAGAGGGGCCGTGAGGCGAACTTGCCCTGTGATGACTTCCTGCGACTCTCACTTGCAGGAGTGATGTTATTTTTA--GGGGGCGGGGGACGCCAAAGAGGC------TTATTTGGCAAACGAACACCATTTGGTCGCCTGAGCTCTGCGTGCGGGTGT
q bosTau4.chr1                                             --------9999999999999999999999999999999999--999999999-----------9999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999------999999999999999999999999999999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26006060 236 -  55389570 --------GCCTCTTTGCTCACGTACCTGGG------CACTG--GGGATCAACCACCAGCT--GCAGAAACAGCCGCACACCAGCATCCCCATTTGTTTAG---------GTGGTGCTTGTTTGTAAAAAGAGCTTGCTCTGTGGTGATTCTCTTTAACTATGACTTGGAGGACTGCTGTTATTTTTA--GAGGCCAGGGGACACTAAAGAGGC------TTATCTGGCAAAGAAACACAATTTGTTCGCCTGAGCTTTGCGTGTGTATGT
q canFam2.chr23                                            --------99999999999999999999999------99999--99999999999999999--99999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999------999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           343722 236 -    369131 --------GCCTTCCCGTGCACGTACTTGGG------CACCG--GGGATTAGCGAACAGCT--GCAGAAACAGCCGCACGGAACCATCCCAGTTTGCTTAG---------GTGGTGTGCATTTGTGAGAAAAGCTTGCTCTGTGGTGATTCTCTTTAACTACCACTCGGAGGACGGATGTTATTTTTA--GGGGCTGGGGGACACCAAAGAGGC------TTATTTGGCGAATGAACGCAATTTGTCCGCCTGAGCTTTGCGTGTGTATGT
q felCat3.scaffold_217554                                  --------99999999999999999999999------99999--99999999999999999--99999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999------999999999999999999999999999999999999999999999999999
i felCat3.scaffold_217554        C 0 C 0
s equCab2.chr16                   22226764 236 -  87365405 --------GCCTCCTCGCTCATGT-CGTGGA------CACTGCCTGGATCGGAGAACAGCT--GCAGAAACAGCTGCCCAGAACTGTCCC-ATTTGTTTAG---------GTGGCGCGTGTTGGTGAGAAAAACTTGCTCCGTGGTGTTTTTCTTGAACGATCACTTGGAGGAACAATGTTATTTTTA--GGGGGTGGGGGTCACCAAAGAGGC------TTACTTGGCAAATGGACACAATTTGTTCGCCTGAGCTTTGTGTGTGTATGT
q equCab2.chr16                                            --------9999999999999999-999999------999999999999999999999999--999999999999999999999999999-9999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999------999999999999999999999999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_371855             3912 223 -     87482 -----------------------TCCTTGGA------CACTGCTGGGATCAGCTGACAGCT--GCAGAAGCAGCCGCACAGGGCAATCCCAGTTTGTTTAG---------ATGGTGTGTGCCTGGGAGGGAGACATGTTCAGTGGTGATTTCCTCCAGCTATCACTTGGAGGAATGATGTTATTCTTAGTGGGGGCAGGGGAC-CCAAAGTGAC------TTGTTTGGCAAATGAATGCAATTTGTTCACCTCAGCTTTCTGAGTGTATG-
q eriEur1.scaffold_371855                                  -----------------------99999999------999999999999999999999999--99999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999------99999999999999999999999999999999999999999999999999-
i eriEur1.scaffold_371855        C 0 C 0
s loxAfr3.scaffold_36               531501 247 -  24123610 GCCT----CCTTGCTCACAGTAGT--TGGGA------CACTGTTGGGATCAGCGAACAGCT--GCAGAAACAGCCTCGTATAATCTTCCC-GTTTACTTGGTGGGGGGGATGGGAGGGTGTTTGTGAGAAAAACTTGCATTGGGGTGTTTTTCTTTAACTATCACTTGGAGGAATGATGTTATTTTTA--GGGGG-AGGGGACACCAAAGAGGC------TCATTTGGCAAACGAACACAATATGTTCATCTCAGCTTTGCATGTGCCTGT
q loxAfr3.scaffold_36                                      9999----9999999999999999--99999------999999999999999999999999--999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999-999999999999999999------999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e monDom5.chr8                   276506326 15915 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=2412404.000000
s hg19.chrY                        7660861 654 +  59373566 GAAAATCC-----TCACTCTAGT--AGCCAGGAGTTTTC--AAATCCACTGGGA-AGAGACTCCAAAAACAG-G-----------------TTGGTGGCAGGAAAAC--------ACAACCCTAGG-A----TGACAAGTG--------------------TGCAAATTAA------------CACTGAAA--CCATGCAAATGACC---AGTGCTGACAGATGAAAA-CACTGAGGTCAGCTA-TATGTAAGGATTAAGAAAATTCTAAA-TAGGGAAGCA----TTCTGC-CCACAAATGTCATT-ATGAGAGGACATTAACACCAGTCTTTTATGGTTCTCAAAGC---CCAGTA----TA-TTGGTGTTG---GGGGTGTAGTTGTCTGCAG---TGTTCAAAGGA-CAGTGGCACTGAAAACTTAGGACTCAGAGCCG----------------CTCTCCTCTTAAC----TCTTAA----AGCTCTCAGATAATCAACTAGTAG-AGTC-AAAATAAACTAATTGCGGACTACT-AATGCACATGGCAAAAACTCAACGGATA-TGCTA-GTCAACA-AATTCTTCATCTGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAATCTGTG----AGAACATGATGCCAAGAGGAAGAAATACAAATTGGGCTCCTATATTCCTTATGAAAATTAGAAGATTCTAAACTAATCAATTAGCTTTACATCCCCCACCACCTC-----------CC-------CCA-ATCTCTGC---ATAATCATTTCACTTCATGAAATTTCTTAG
s monDom5.chr8                   276522241 603 + 312544902 gaaaatcc-----caactggggt--agcaaaaag-------taggccacgatga-aaatgactaaaaaacaa-Gagtccaacacctttgccttgcagataaggaatc-------tgaggcccaggg-aggttTTACAGGCGGGAGACCCAAGTCCCTTCCGTTCAAATTCAGAGCTTTTTCCactctggaggtctactccaatgacttcatttttttacagctgaaga-aactgaggctcagTA-AA----------AAAAAAATGCAGAA-CTGGAAGGCAGATTCCCCGA-CTCCACAATCCA---AAATGAAATAATTAACACCCGTCAAATAA-------AAAGCACTCCGTTATTATTA-TTATTAATG---GAGA-------GCCGTTGG---TGTTCTGGGGA--------------------------TGGGAGA-------GCCG-----------GCTGCGCTCGCCCTCCA----AGTCCTCAGATAATCAGCTA-CAG-AGTC-AGAATAATCTAATCATCCTATACTAAATGCATATAG------------------CCGTG-TTCCACAGAATTCTAAACCTGCCGTCCTGGGAGGATGAGAAAGAAACGTTAGA---CAGTCTGGG----GGAACGTCCGGC-------------------TCCGGCCCCACCATTCCTCACGGAAATGAGGCCGCTCGGAACTCATCATTCAGTGGAAAGGCTCCCGGCGC--------------CC-------CCC-TTCCCTAC---A-----------------------------
q monDom5.chr8                                             99999999-----9999999999--999999999-------9999999999999-99999999999999999-9999999999999999999999999999999999-------999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999-99----------99999999999999-99999999999999999999-999999999999---99999999999999999999999999999-------99999999999999999999-999999999---9999-------99999999---99999999999--------------------------9999999-------9999-----------99999999999999999----99999999999999999999-999-9999-999999999999999999999999999999999999------------------99999-99999999999999999999999999999999999999999999999999999---999999999----999999999999-------------------99999999999999999999999999999999999999999999999999999999999999999999999--------------99-------999-99999999---9-----------------------------
i monDom5.chr8                   I 15915 C 0
s loxAfr3.scaffold_36               531748 677 -  24123610 GAAAATCC-----TCACACCCGGTAGGCAGGCAGTTTTC--AAGCCCACTGGGA-ATAGGCTCCATAAACAGAG-----------------GTTGGGGCAAGACAAC-------AAAAGCCCCAGG-A----TGACAAGCT--------------------TGCAAATTAA------------CCCTGGA---CCAGGCAAAGAACC---AGCACTGAAGGATAGAAAACAACGAAGCCGGCTG-TATGTACAAATTAGGAAAATCCTGAA-TAAGGGAGCA----TTCTTC-CCAAAAGTTTTATT-A----AAGACATTAACACCGGTAATTTATAGGCCCCAGAAC---CCAGAA----GA-TCTGCACTG---GGGGAGGAGGCATCCACTG---TGTTCAAAGAACCAGTGGCACAGAAATTTCTGGACACAGAAAGG-------TACA-----TCCTCCCCTGAGCTCACTCCTCA----AGCCCTCAGATAATCAACTAATAG-AGTT-GAAATAATCTAATCACAAAGTAATAAATGCACATGGACAAAACACAACGGATA-TCCTC-TTCAACAGAATTATACATCGGCTGCTCTGTCGAGATGATAATGAAACGTCAGA---CAATCTGTG----AGAATACGATGCCAAGGAGAAGC---ACAAATTGGGCTCCTCCACTGCTCATGGAAATTAGAAGATTCTAAACTAATCAATTAGCTCAGCACCCCCCTCCCCGGCCCCCACACACACA-------CTCTATCTCTGCATTATTATCATTCCTTTTCATGAAATTTCCCCG
q loxAfr3.scaffold_36                                      99999999-----99999999999999999999999999--9999999999999-9999999999999999999-----------------9999999999999999-------999999999999-9----999999999--------------------9999999999------------9999999---99999999999999---9999999999999999999999999999999999-99999999999999999999999999-9999999999----999999-99999999999999-9----999999999999999999999999999999999999---999999----99-999999999---9999999999999999999---99999999999999999999999999999999999999999999-------9999-----99999999999999999999999----999999999999999999999999-9999-99999999999999999999999999999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---999999999----99999999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s eriEur1.scaffold_371855             4135 682 -     87482 -AAATTCC-----TCACGCT-----AGTCAGTGGCTTGTAAAAATCCATTGGGA-AGACACtccataaacag-g-----------------ctgggggcaagaaaacaacaacaaaaaccctcaaG-A----TGATAAGTG--------------------TGCAAATTAA-------------CCTGGAG--CCAGGGAAAGAACC---AGTGATGACAGACAGA----GATAAAGCCACTCA-CAGGCCAGGGTTAGGAGTACTCTGAA-CAAGGACACA----TTCTGCCTCAAGAGTTTTATTAAAAAGAGGACGTTGACACCAGTCACTCATGATCCCCAAAGC---CCAATA----TA-GCAAcatggggaggggatgagatgtccATTG---TGCTCAATGGATCAGTGACACCGAAAATTCAGGACTCACAGAGG-------TATG---CTTTATGCCCGGGGCTTACTCCTAC----AGCTCTCAGATAATCAACTCATAG-AGTCAAAAATAATCTAATCATGAAGTAataaatgcacatggcaaaaaCACAGCGGAGA-TTCTG-TTCAACAGAATTACATATCAGCTGTTCTGTTAAAATGATAATGAAACCTCAGA---CAATCCGGGAGCAAGAATGCCACGCCAAGGAGGAGTCATACAAATTGGGCTACCCCATTCTTCATGGAAATGAGAAGATT-----CTAATCAATTAGCTCAATGTCCCCCACTACCTC-----------CACTCGCGCCCCCATCTCTGC---ATTATCATTCCTCTTCATGACATTTCCTGG
q eriEur1.scaffold_371855                                  -9999999-----9999999-----99999999999999999999999999999-99999999999999999-9-----------------99999999999999999999999999999999999-9----999999999--------------------9999999999-------------9999999--99999999999999---9999999999999999----99999999999999-99999999999999999999999999-9999999999----999999999999999999999999999999999999999999999999999999999999999---999999----99-9999999999999999999999999999999---99999999999999999999999999999999999999999999-------9999---9999999999999999999999999----999999999999999999999999-9999999999999999999999999999999999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999999999999999999-----------999999999999999999999---999999899999999999999999999999
i eriEur1.scaffold_371855        C 0 C 0
s equCab2.chr16                   22227000 671 -  87365405 GAAAATCC-----TCACGCTGGG--AGCCGGGAGTTTTC--AAATCCACTGGGA-AAGGACTTCATAAACAG-A-----------------TTGGGGGCAAAAAAAT-------AAAAACCCAAGG-A----TGACAAGCA--------------------TGCAAATTAA------------CCCTGGAA--CCAGGCGCAGAACC---AGTGTTGACAGACAGAAAACAATGAAGCCGGCCA-TATGTAAGGATTAGGAAAATTCTGAA-TAAGGGAGCA----TTCTGC-CTAAAAGTTTTATT-AGGAGAGGACATTAACACCAGTCATTTAT-GTCCCCAAAGC---CCAACA----TA-TCAACATTG---GGGAAGGAGATGTCCACTG---TGTTCCAAGGACCAGTGGCACTGAAAATTCAGGACCCAGAGAGG-------TACAGTACACTCTCCTCTGA-CTCATTCCTCC----AGCTCTCAGATAATCAACTAATAG-AGTC-AAAATAATCTAATCATGAAGTAATAAATGCACATGGCAAAAACACAACGGATA-TCCTA-TTCAACAGAATTATACATCAGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAATCTGCG----AGAATACCATGCCAAAGAGGAGAAACACAAATTGGGCTCCTCCATTCCTCATGGAAATGAGAAGATTCTAAACTAATCAATTAGCTCAACATCCCCCACGACCTC-----------CA-------CCCCCTCTCGGC---ATTATCATCCCTCTTCATGAAATTTCCTGG
q equCab2.chr16                                            99999999-----9999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999-------999999999999-9----999999999--------------------9999999999------------99999999--99999999999999---9999999999999999999999999999999999-99999999999999999999999999-9999999999----999999-99999999999999-99999999999999999999999999999-99999999999---999999----99-999999999---9999999999999999999---99999999999999999999999999999999999999999999-------99999999999999999999-99999999999----999999999999999999999999-9999-99999999999999999999999999999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99-------999999999999---999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s felCat3.scaffold_217554           343958 672 -    369131 TAAAATCCTCACATCACACTCCT--AGCCTGCAGTTCTC--AAATCCACTGAGA-AGAGGCTCCATAAACAG-G-----------------TTGGGAGCAGGGGAAC-------AAAAACCCCAGG-A----TGACAAGCG--------------------TGCAAATTAA------------CCCTGGAA--CCAGATGAAGAAGC---AGTGTTGACAGACAGAAAGCAATGAAGCTGGCCG-TATGTAAGGATTAGGGAAATTCTGAA-TAAGAGAACA----TTCTGCAACAAAAGTTTTATT-AGCAGAAGACATTAACACCAGTCATTTATGGTCCCCAAAGC---CCAGTA----TA-TTATCATCA---GGGAAGGAGGTATCCGCTG---TGTTCAAAGGGCCAGAGGCACTGAAAATTCAGGACCCAGAGATG-------TACA-------CTCCTCTGAGCTCACTCCTCC----AGCTCTCAGATAATCAACTAATAG-AGAC-AAAATAATCTAATCATGAAGTAATAAATGCACATGGCAAAAACACAACGGATA-TACTA-CTCAACAGAATTATATATCAGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAATCTGTG----AGAATAACATGCCAAGGAGGAGAAATACAAATTGGGCTCCTCCATTCCTCATGGAAATTAGAAGATTCTAAACTAATCAATTAGCTCAACATCCCCCACTACCTC-----------CA-------CCCCATCTCTGC---ATTATCATTGCTCTTCATGAAATTTCCTGG
q felCat3.scaffold_217554                                  99999999999999999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999-------999999999999-9----999999999--------------------9999999999------------99999999--99999999999999---9999999999999999999999999999999999-99999999999999999999999999-9999999999----999999999999999999999-99999999999999999999999999999999999999999---999999----99-999999999---9999999999999999999---99999999999999999999999999999999999999999999-------9999-------999999999999999999999----999999999999999999999999-9999-99999999999999999999999999999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99-------999999999999---999999999999999999999999999999
i felCat3.scaffold_217554        C 0 I 4429
s canFam2.chr23                   26006296 667 -  55389570 GAAAATCC-----TCACGCTCCC--GGCCGGCAGTTCTC--AAATCCACT---A-AGAGACTCCATAAACAG-G-----------------ATGGGGGCAGGAAAAC-------AAAAACCCCAGG-A----TGACAAGCG--------------------TGGAAATTAA------------CCCTGGAA--CCAGGCAAAGAACT---GGTGTTGACAGACAGAAGGCAATGAAGTTGGCCA-TATGTAAGGATTAGGGACATTTTGAA-TAAGAGAACA----TTTTGC-ACAAAAGTTTTATT-AGGAGAAGACATTAACACTAGTCATTTATGGTCCCCGAAGC---CCAATA----TA-TTATCATCG---GGGGAGGAGATGTCCACTG---TGTTCAAAGGACCAGGGGCCCTGAAAATTCAAGACCCAGAGATG-------TTCA-------TTCCTCTGAGCTCACTCCTCCAGCTAGCTCTCAGATAATCAGCTAATAG-AGAC-AAAATAATCTAATCATGAAGTAATAAATGCACATGGCAAAAACACAACGGATA-TACTA-TTCAACAGAATTATACATCAGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAATCTGTG----AGAATAACATGCCAAGGAGGAGAAATACAAATTGGGCTCCTCCATTCCTCATGGAAATTAGAAGATTCTAAACTAATCAATTAGCTCAACATCCCCCACTACCTC-----------CA-------CCCCATCTCTGC---ATTATCATTGCTCTTCATGAAATTTCCTGG
q canFam2.chr23                                            99999999-----9999999999--99999999999999--999999999---9-99999999999999999-9-----------------9999999999999999-------999999999999-9----999999999--------------------9999999999------------99999999--99999999999999---9999999999999999999999999999999999-99999999999999999999999999-9999999999----999999-99999999999999-99999999999999999999999999999999999999999---999999----99-999999999---9999999999999999999---99999999999999999999999999999999999999999999-------9999-------9999999999999999999999999999999999999999999999999-9999-99999999999999999999999999999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99-------999999999999---999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   157000434 667 + 161106243 GAAGGTCC-----TCACACTAGA--AGCTAGTGGTTTTC--AAATCCACCGGAA-AGAGTCTCCATACACAG-G-----------------TCAGGGGCAGGAAAAT-------AAAAACCCCAGG-A----TGACAAGCG--------------------TGCAAATTAA------------CCCTGGAA--CCAGGCGAGGAACC---AGGGATGATGGACAGGAAACAATGAAGCTGACCA-CACGTCAGGACGAGGAAAATTCTGAG-GAAGGGAGCA----TTCTGC-CCAAAAGTTTCATT-AGGAGAGGGCATTCACACCAGGCATTTATGGCCCCCAAAGT---CCAGTC----TG-TTAGCACCG---GGGCAGGAGCTGTCCACTG---TGTTCAAAAGACCAGTGACACTGAAAATTTAGGACCCCAAGAGG-------TCTT-----CTCCCCTCTGAGTTCACTCCCC-----AGCTCTCAGACAATCAGCTAATCG-AGTC-CAAATAATCTAATCATGAAGTAATAAATGCACATGGCAAAAACACAATGGATATTCCTA-CTCAACAGAATTAGACATCAGCTGTGGTGTCGAGATGCTAATGAAACATCAGA---CAATCTGTG----AGAGTGCCATGCCAAGGAAAAGAAAGACAAATTGGGCTCCTCCACTCCTCATGGAAATTAGAAGATTCTAAACTAATCAATTAGCTCCACAT-CCCCACAATCTC-----------CA-------CCCCGTCTCTGC---ATTATTATTCCTCTTCATGAAATTTCCTCG
q bosTau4.chr1                                             99999999-----9999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999-------999999999999-9----999999999--------------------9999999999------------99999999--99999999999999---9999999999999999999999999999999999-99999999999999999999999999-9999999999----999999-99999999999999-99999999999999999999999999999999999999999---999999----99-999999999---9999999999999999999---99999999999999999999999999999999999999999999-------9999-----9999999999999999999999-----999999999999999999999999-9999-99999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999---999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999-----------99-------999999999999---999999999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s mm9.chr17                       50261923 576 +  95272651 GAAAAGCT-----TCACCTCAGA--TACTCAGAGTTCTC--AAACT--GTGGCATAGAGCCTCCACAAAGGT-A-----------------CTGGGGCCAGGAAAAC--------AAAGACCACTG-A----TAACAAGTG-------------------ATACACATTAA------------CCCCGGAG--GCAAGAAAGGA--------------------------AGTGAAACGGGCCA-CA-GTAGAGGTTAGGAATCTTGTGAA-CACTGGCACACA--CTGTGA-CTC----TCTTTGT-AGCAGAGAACACGAACTCCA-TCATTTGTGGTTCTCAAAGC---CCAGGA----GGGTTAGCACTG---GGGA-----GGGTCCGGCG-------CAAAGGA-CATTGGCACG-GAAATTCAAAACTCACAGAGG-------GCTC-----TT---------AC--------------AGCTCTCAAATAATCAACTA--AG-AGTG-AAGATCATCTCATCGTGGAGTAATGAGTGCTCACGGCAAGAGCA----------CCCTGGTTCAATAGTATCAGACATTAGCTGGTCTGTCAGGACGATAATAAA-------A---CAATTTGAG----AGACTACGATGCCAAGAAGGAGCGATACAGATTGGGCT-CTCCAACCCTCACGGAAATGATAAGATT-----TTAATCAATTAACCCAGCA-CCCCCTGTCCCTG-----------CA-------CCC--------C---CTAATCTGCCCTCTTCAC---AGTTCCTGG
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107362673 608 - 113440463 GAAAATCT-----TCACCTTAGG--CACTCAGAGTCCTC--GAACCCACTGGGA-AGAGACTCCACAAACAT-A-----------------CTGGGGACAGGAAAAG--------AAAGACCACTG-A----TCACAAGTG--------------------TACAAATTAA------------CCCTGGAG--GCAGGAAAGGAAGG---AATATCAACAGACAGGAAACAGTGAAAGGGGCCA-CATGTGGAGGTTAGGAACCTTGTGAA-CACGGGCACACACTCTGTGA-CAC----ACTTTAT-AGCAGAGAACACGAACTCCA-TCATTTGCGGTCCTCAAAGC---CCAGGA----GAGTTAGCACTG---GGGA----GGGGTCCAGTG-------CAAAGGA-CACTGGCACT-AAAATTCAAAACTCCCTGAGG-------ACTC-----TTCTCATCCTAAC--------------AGCTCTCAAATAATCAACCG--AG-AGTC-AAAATAATCTCATCATGGAGTAATGAGTGCCCACAGCATG-GCA----------------TTCAATACTATTAGATATTAGCCGTTCTGTCAGGATGATAA-AAA-------A---CAATTTGAG----AGACTATGATGCCAAGGGGGAGCGATACAGATTGGGCT-CTCCAACCCTCATGGAAATGATAAGATT-----CTAATCAATTAGCCCAGCATCCCCCAGTCCCTG-----------CA-------CCC--------C---CTTATCTGCCCTCTTCACAGAAGTTCCTGG
q rn4.chr9                                                 99999999-----9999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999--------99999999999-9----999999999--------------------9999999999------------99999999--99999999999999---9999999999999999999999999999999999-99999999999999999999999999-99999999999999999999-999----9999999-99999999999999999999-99999999999999999999---999999----999999999999---9999----99999999999-------9999999-9999999999-999999999999999999999-------9999-----9999999999999--------------99999999999999999999--99-9999-9999999999999999999999999999999999999999-999----------------99999999999999999999999999999999999999999-999-------9---999999999----99999999999999999999999999999999999999-9999999999999999999999999999-----999999999999999999999999999999999-----------99-------999--------9---999999999999999999999999999999
i rn4.chr9                       C 0 C 0
s oryCun2.chr14                    2489157 588 + 163896628 GAAAACCC-----ACACAGTTGT--AGCTGGGAGTTTGG--GGACCCGCTGGCA-AGAG--------------A-----------------CTGAGAACAGGAAAAC--------AGAACCCAGGG-G----TAACA--TG--------------------TATGAATTAA------------CCCCGGGA--CCA-GCAGAGAACT---AGTG-AGACAGACAGAAAGCAATGGAGTCGAATATTATGTAAGGACTAGGAAGACACTGAATTACAGGTGCA----TTCTAC-CCA----CAAGTGT-CATCAAGAACA-----------------GGTCCCCCAAAGC---CCAGGA----CAG--AGGCCTC---AGGC--------TCCATTG---TCTTCAAGACA-CAGCAGCACTGAAAATGCAGGACACACAGAGAGGGACACGCTC-----CCCGTGGCTCAGC------CTCC----AGCGCTCGGATAATCAACTA--AGCAGAC-AAACTAATCTCGTTCTCAAGTAATCAACGCACCCGGCAGAAGCGGC---GGCT-CGCCCACTCCACAGAACTGTCCCTCGGCCGAGCTGTCGGGAGCACGAGGAA-------ATGCCAATCTGGG----AACGTGCGAGGCCAAGGAGGAGGCGCACAAATTGGGCTCCTCCGCTCCTCG-GGAAATCACAAGATTCTAAACTAATCAATTAGCTCCGAG--------------------------G-------CCC--------------TATCTCTGCTCGTCACGAAATTCCCTGG
q oryCun2.chr14                                            99999999-----9999999999--99999999999999--9999999999999-9999--------------9-----------------9999999999999999--------99999999999-9----99999--99--------------------9999999999------------99999999--999-9999999999---9999-9999999999999999999999999999999999999999999999999999999999999999999----999999-999----9999999-99999999999-----------------9999999999999---999999----999--9999999---9999--------9999999---99999999999-9999999999999999999999999999999999999999999-----9999999999999------9999----99999999999999999999--9999999-9999999999999999999999999999999999999999999999---9999-999999999999999999999999999999999999999999999999999-------9999999999999----999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999--------------------------9-------999--------------9999999999999999999999999999
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8251438 650 -  88675666 GAAAATCC-----TCAAGCTAGT--AGCTGGGAATTTTC--AAAACTATGGGGA-GGAAACTCCATAAACAG-A-----------------CTTAGGGCAAGAAAAC--------AAAAACCCCAGAA----TGACATATG--------------------TGCAAATTAA------------CCCTAGAG--CTAGGTAAAGAATT---AGTGCTGACAGAAGAAAA--AGTCAAG-----CA-TATGCAAGGATCAGAAAAGTGTCAAA-TAGGGAGAG-----TTCTAC-CCC-AAGTTTTCTT-AGGAAAGCATACCAAACCAA-TCATTTTGTGTCCTCAAAGC---CTATCA----CA-TTAGCACTG---GGAA----GGTGGCATTTGCTGCACTCAAAGGA-CAGTGGCACTCAAAATTCAGGACTCAGAGCAG-------GGCA-----ATGTCAATTGAACACACTCCTCA----AGCTCTCAGATAATCAACTAATAG-AGTC-AAAATAATCTCATCACAAAGGAATAAATGTACACAGCAAAACCACA---GATA-CCCTACTCAAAAAGAATTGCGCATTGCCTGTGCTTTCAAGATCATAATAAAACATCAGA---CAATCTGTG----AGAATACGATGCCAAGGAGAAAC---ACAAATTGGACTCCTCCATTCCTCATGGAAATGAGAAGATTCTAAACTAATCAATTAGCTCAGCATTCCCCACTCCCTC-----------CA-------CCC-ACCTCTGC---ATTATCACTGCTTTTTATGAAATTTCCTGG
q cavPor3.scaffold_0                                       99999999-----9999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999--------9999999999999----999999999--------------------9999999999------------99999999--99999999999999---999999999999999999--9999999-----99-99999999999999999999999999-999999999-----999999-999-9999999999-99999999999999999999-99999999999999999999---999999----99-999999999---9999----9999999999999999999999999-99999999999999999999999999999999-------9999-----99999999999999999999999----999999999999999999999999-9999-9999999999999999999999999999999999999999999999---9999-99999999999999999999999999999999999999999999999999999999999---999999999----99999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99-------999-99999999---999999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s rheMac2.chr2                   158778507 655 + 189746636 GAAAAGCC-----TCACACTAGT--AGCCAGGAGTTTTC--GAATCCACTGGGA-AGAGACTCTAAAAACAG-G-----------------TTGGAGGCAGGAAAAC--------AAAACCCTAGG-A----TGCCAAGCG--------------------TGCAAATTAA------------CACTGAAA--CCAGGCAAAGGACT---AGTGCTGACAGATGAAAA-CACTCAAGCCAGCTC-TACGTAAGGATTAGGACAATTCTAAA-TAGGGGAGCA----TTCTGC-CCACAAGTTTTGTT-AGGAGAGGACATTAACATCAGTCATTTATGGTCCTCAAAGC---CCAGTA----TA-TTCGTATTG---GGGGTGGAAGTGTCTGCTG---TGTTCAGAGGA-CAGTGGCACTGAAAACTCAGGACTCAGAGACA----------------CTCTCCTCTTAAC----TCCTCA----AACTCTCAGATAATCAACTAGTAG-AGTC-AAAATAATCTAATCATGGACTATT-AATGCACATGGCAAAAACTCAACTGATA-TCCTA-GTCAACAGAATTCTACATTGGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAATCTGTG----AGAACACGATGCCAAGAAGAAGAAATACAAATTGGGCTCCTCCATTCCTCATGGAAATTAGAAGATTCTAAACTAATCAATTAGCTTCACATCCCCCGCCACCTA-----------CC-------CCC-GTCTCTGC---ATTATCATTCCACTTCATGAAATTTCCTGG
q rheMac2.chr2                                             99999999-----9999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999--------99999999999-9----999999999--------------------9999999999------------99999999--99999999999999---999999999999999999-999999999999999-99999999999999999999999999-9999999999----999999-99999999999999-99999999999999999999999999999999999999999---999999----99-999999999---9999999999999999999---99999999999-99999999999999999999999999999999----------------9999999999999----999999----999999999999999999999999-9999-999999999999999999999999-9999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99-------999-99999999---999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71052405 665 - 202140232 GAAAATCC-----TCACACTAGT--AGCCAGGATTTTTT--GAATCCACTGGGA-AGAGACTCCAAAAACAG-G-----------------TTGGGGGCAGGAAAAC--------AAAACCCTAGG-A----TGACAAGCA--------------------TGCAAATTAG------------CACTGAAA--CCAGGCAAAGGACT---AGTCCTGACAGATGAAAA-CACTCAAGCCAGCTG-TAGGTAAGGATTAGGAAAATTCTAAA-TAGGGAAGCA----TTCTGT-CCACAAGTTTTGTT-AGGAGAGGACATTAACACCAGTCATTTATGGTCCTCAAAGC---CCAGTA----TG-TTGGTGTTG---GGGGTAGAGGTGTCTGCTG---TGTTCAAAGGA-CAGTGGCACTGAAAACTCAGGACTCAGAGACA----------------CTCTCCTGTTAAC----TCCTCA----AGCTCTCAGATAATCAACTAGTAG-AGTC-AAAATAATCTAATCATGGACTATT-AATGCACATGGCAAAAACTCAACGGATA-TCCTA-GTCAACAGAATTCTACATCGGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAATCTGTG----AGAACACGATGCCAAGAAGAAGAAATACAAATTGGGCTCCTCCATTCCTCATGGAAATTGGAAGATTCTAAACTAATCCATTAGCTTCACATCCCCTGACACCTCACCCCCAC-CACC-------CCC-ATCTCTGC---ATTATCATTCCACTTCATGAAATTTCCTGG
q ponAbe2.chr3                                             99999999-----9999999999--99999999999999--9999999999999-99999999999999999-9-----------------9999999999999999--------99999999999-9----999999999--------------------9999999999------------99999999--99999999999999---999999999999999999-999999999999999-99999999999999999999999999-9999999999----999999-99999999999999-99999999999999999999999999999999999999999---999999----99-999999999---9999999999999999999---99999999999-99999999999999999999999999999999----------------9999999999999----999999----999999999999999999999999-9999-999999999999999999999999-9999999999999999999999999999-99999-99999999999999999999999999999999999999999999999999999---999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999-------999-99999999---999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      514440 654 +  23952694 GAAAATCC-----TCACTCTAGT--AGCCAGGAGTTTTC--AAATCCACTGGGA-AGAGACTCCAAAAACAG-G-----------------TTGGTGGCAGGAAAAC--------ACAACCCTAGG-A----TGACAAGTG--------------------TACAAATTAA------------CACTGAAA--CCATGCAAATGACC---AGTGCTGACAGATGAAAA-CACTGAGGTCAGCCA-TATGTAACGATTAGGAAAATTCTAAA-TAGGGAAGCA----TTCTGC-CCACAAATGTCATT-ATGAGAGGACATTAACACCAGTCTTTTATGGTTCTCAAAGC---CCAGTA----TA-TTGGTGTTG---GGGGTGTAGTTGTCTGCAG---TGTTCAAAGGA-CAGTGGAACTGAAAACTTAGGACTCAGAGCCG----------------CTCTCCTCTTAAC----TCTTCA----AGCTCTCAGATAATCAACTAGTAG-AGTC-AAAATAAACTAATTGCGGACTACT-GATGCACATGGCAAAAACTCAACGGATA-TGCTA-GTCAACA-AATTCTTCATCTGCTGTTCTGTCAAGATGATAATGAAACATCAGA---CAAGCTGTG----AGAACATGATGCCAAGAGGAAGAAATACAAATTGGGCTCCTATATTCCTTACGAAAATTAGAAGATTCTAAACTAATCAATTAGCTTTACATCCCCCACCACCTC-----------CC-------CCC-ATCTCTGC---ATAATCATTTCACTTCATGAAATTTCTTAG
q panTro2.chrY                                             00000000-----0000000000--00000000000000--0000000000000-00000000000000000-0-----------------0000000000000000--------00000000000-0----000000000--------------------0000000000------------00000000--00000000000000---000000000000000000-000000000000000-00000000000000000000000000-0000000000----000000-00000000000000-00000000000000000000000000000000000000000---000000----00-000000000---0000000000000000000---00000000000-00000000000000000000000000000000----------------0000000000000----000000----000000000000000000000000-0000-000000000000000000000000-0000000000000000000000000000-00000-0000000-000000000000000000000000000000000000000000000---000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-----------00-------000-00000000---000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=1147259.000000
s hg19.chrY                        7661515 316 +  59373566 GAATCCACTTACTATTC-TGTGATCATAGACAGCAAAT-GAAAATT-----AAGTTCTCTGTAGAACAGGA--GAAACTTTGCATTGTAATGTAAAACGAGCTGATTAAGGGCACTT-AATCCAAGAACAGCTAATTCTTAAGA-C-CTCAAAGCAGAGTGGATTAAACATAAGGAAG-----GACGTATGCAGCCCGCTTCTGATCACACA-GAAG--AAT-GGATTCTGAGA--CTTGACAGGCTGCCTTATTAACAATTACAGTAAC---TAGGACTGTTCTTTTCAAA------------------------------------------------AGAATGCCTTGCAAGTTAGAATAAATACCCCA--TCTTTGGATATCTGAGGT
s loxAfr3.scaffold_36               532425 316 -  24123610 GAATCCACTTACTATTC-TGTGATGGCAGATATCAAAT-GAAAATC-----AAGTTCTCTGAAGAACATGAGAGAAACTTTACATTGTAATGTAAAACGCACTGATTAAGGGTACTTAAATCTACCAACAGCTAATTCTTAAAA-C-CTCGAAGCGGAGTGGATAAAATGTCAGGAAG-----GAAGAATTGAGTCTAGTTTTGATCGCACA-GAAA--AAT-GGATTCAGGCA--CTCGGCAGGCTGCCTTGTTTACAATTGTAGTAAC---CAGGGCTGTTCTT---AAA------------------------------------------------ATAATGTCCTACAACTTAGTACCAAGACCCAG--TCTTTGGAGAGCCAAGGT
q loxAfr3.scaffold_36                                      99999999999999999-99999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9-9999999999999999999999999999999-----99999999999999999999999999999-9999--999-99999999999--9999999999999999999999999999999999---9999999999999---999------------------------------------------------99999999999999999999999999999999--999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s eriEur1.scaffold_371855             4817 307 -     87482 GAATCCACTTACTAGTC-CGGGACCACGGCTATCAAGT-GAAAATC-----ACGTTCTTGGCTGAACACGagagaaactttacatcagaatGTAAGATGAACTGATTAAGGGCACTT-AATCTGTGAACAGCTAATTCTTAAAA-AGCTTGAAGCAGAGTGGATGACATGTCAGGAAA-----GAGAAATGCAGCTTAG------------a-aaaa--aaT-GGATTCTGGCA--CTCAGCAGGCTGCCTTATTAACAATTACAGTAAC---TGGGGCTGTTCTTTCCAAA------------------------------------------------ATGGTGTTCTGCAAGTTAGAATACAGACCCAA--TCTTGCAAGAaacaagga
q eriEur1.scaffold_371855                                  99999999999999999-99999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-999999999999999999999999999999999-----9999999999999999------------9-9999--999-99999999999--9999999999999999999999999999999999---9999999999999999999------------------------------------------------99999999999999999999999999999999--999999999999999999
i eriEur1.scaffold_371855        C 0 C 0
s equCab2.chr16                   22227671 316 -  87365405 GAATCCACTTACTATTC-TGTGATCGCAGAGAGCAAAC-GAAAATC-----AAGTTCTCTGCTGAACATGAGAGAAACTTTACATTGTAATGTAAGATGAACTGATTAAGGGCACTT-AATCTACGAAAAGCTAATTCTTAAAA-C-CTCGAAGCGGAATGGATGAAA--TCAGAAAG-----GAGAAATGCAGCTTAGTTTTGATCGCACA-GAAA--AAT-GAATTCTGGCA--CTCAGCGGGCTGTCTTATTAACAATTACAGTAAC---TAGGGCTGTTCTTTCCAAA------------------------------------------------ATAACGCTCTGCAAGTTAGAATGAAGACCCAG--TCTTCAGAGAATCAAAGT
q equCab2.chr16                                            99999999999999999-99999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-999999999999999999999--99999999-----99999999999999999999999999999-9999--999-99999999999--9999999999999999999999999999999999---9999999999999999999------------------------------------------------99999999999999999999999999999999--999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26006963 319 -  55389570 GAATCCACTTACTATTC-TGTGATCGCAGATATCAAAT-GAAAATC-----AAGTTCTCTGCTGAACACAAGAGAAACTTTACATTGTAATGTAAGATGAACTGATTAAGAGCACTT-AATCTGTGAGCAGCTAATTCTTAAAA-C-CTCCTAGCAGAGTGGATGAAATGTCAGAAAA-----GAGAAATGCAGCTTAGTTTTGATCACATAGGAAA--AAT-GGATTCTGGCA--CTCAGCAGGCTGCCTTATTACCAAGTACAGTAAC---GGGGGCTGTTCTTTCTCAA------------------------------------------------ATAAGGCTCTGGAGGTTAGAATGAAGAGCCAA--TCTCTGGAGAACCAAGGT
q canFam2.chr23                                            99999999999999999-99999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-9999999999999999999999999999999-----9999999999999999999999999999999999--999-99999999999--9999999999999999999999999999999999---9999999999999999999------------------------------------------------99999999999999999999999999999999--999999999999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   157001101 306 + 161106243 GAATCCACTTACTATTCTTATGATCGCAGATATCAAAT-GAAAATC-----AAGCCCTCTGCAGAACAGGAGAGAAACTTCACGTTGTAATGTAAGATGAACTGATTAAGGGCACTT-AATCTACGAGCAGCTAATTCTCAAAG-C-CTCCAAGTGGAGTGGAGGAGAGGTCAGGAAG-----GAGGGATGCCGCTTAGTTTCGATCACACA-GAAA--AAT-GGGTTCTGGCG--CTCAGCAGGCTGCCTTGTTAACAATCACAGTAAC---GAGGGTCG-------------------------------------------------------------GGCACGCTGCAAGTTAGAAAGAGGACCCAA--TCATCAGAGAACCAAGGG
q bosTau4.chr1                                             99999999999999999999999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-9999999999999999999999999999999-----99999999999999999999999999999-9999--999-99999999999--9999999999999999999999999999999999---99999999-------------------------------------------------------------999999999999999999999999999999--999999999999999999
i bosTau4.chr1                   C 0 C 0
s mm9.chr17                       50262499 280 +  95272651 GAAGCCACTTACTATTC-TGTGATCACAGACAGGAAATGGAAAATCA----AAGAAGTCTGTGGAATGTGGCAGAAGCTTCACATTGTAATTCAAGATAGCCTGATTAAGGACACTT-AATCTGCACACAGCTAATTCGTAAGA-C-CGAGAAGCAGAGTGGGTGTAACGCAAAAGACT----GGAGAACTCAGT-----TCTAATCACACA-GAAA--AACCTGATCCCAGCATCCTTCTTAAGAAGCCTCCTTCACAATTGCAGGAAC---GGAGCCTGCTCTATTCAAA------------------------------------------------TGGATGCTCTA-----------------------------------------
i mm9.chr17                      C 0 I 374
s rn4.chr9                       107363281 269 - 113440463 GAAGCCACTTACTATTC-TGTAATCGCAGACAGGAAATGGAAAATCA----AAGTCCTCTGTGGAACGTGGCAGAAACCTCACATTGTAATTCAAGATAGTCTGATTAAGGACACTT-AATCTTCACACAACTAATTCTTAAGA-C-TGAGAAGTAGAGTGGGTGTGATGCCAAAAAGT----GGAGGGCTCAGT-----TCTAATCACACA-GAAA--GAT------------------------GGATCCCTTCTTAATCACAGGGAC----GAGGCTGCTGTGTTCAAA------------------------------------------------TGGATGC---------------------------TCTATGGATACTCAAAGG
q rn4.chr9                                                 99999999999999999-99999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-99999999999999999999999999999999----999999999999-----999999999999-9999--999------------------------999999999999999999999999----999999999999999999------------------------------------------------9999999---------------------------999999999999999999
i rn4.chr9                       C 0 C 0
s oryCun2.chr14                    2489745 318 + 163896628 GAATCCACTTACCACTC-TGTGATCACAGCCAGCAAAT-GAACATC-----AAATTCTCTGCGGAACACGAGGGAGACTGCACCTTGTAATGGCAGCGGAACTGATTAAGGGCACTT-AATCTGCCAACGGCTAATTCTTAGGG-C-CACGAAGCAGAGTGGATGGAACGTTAGCAAGGAGCAGAGTCATTCATT-----TCTGATAACACA-GAAA--AAT-GGATCCCGGCA--CTCGGCAGGCTGCCTTGCCGACAATTACAGTAAG---CAGGGCTGCTCTTGTCACA------------------------------------------------CCGATGCCTTGCGAGTATGAACGCAGAGCCAG--TCTTGGTAGGTCTCAGGC
q oryCun2.chr14                                            99999999999999999-99999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-999999999999999999999999999999999999999999999999-----999999999999-9999--999-99999999999--9999999999999999999999999999999999---9999999999999999999------------------------------------------------99999999999999999999999999999999--999999999999999999
i oryCun2.chr14                  C 0 I 2
s cavPor3.scaffold_0               8252088 353 -  88675666 GCGCCCAATTACTATTC-TGTGATCACGAATAGTAAAT-GAAAATCAAATCAAGTTCTCTGCAGAACATAAGAGAAACTCTACAGTGTAATGTAAAATGAATTGATTAAGAGCACTT-AATCCACACATAGCTAATTCTTAAAA-C-TATGAAGCAGTGTAGATGAAATGTCAGGAAG-----GAAGAACTTAGC----------TCACACA-GAAA--AAT-GGGTCCCAGCA--CTCAGCAGGCTGCCTTATTAACAACTACTGTAAC---CAATGCTGTTATTGTCAGAAAACCAAAACcaaacaaacaaacaaacaaaAAACCCCCTCCACAAACCTAG--------CTTGTTAGAATGAAGAAGCAA--TCTTTAGGAAACCGAACT
q cavPor3.scaffold_0                                       99999999999999999-99999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-9999999999999999999999999999999-----999999999999----------9999999-9999--999-99999999999--9999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999999--------999999999999999999999--999999999999999999
i cavPor3.scaffold_0             C 0 I 6061
s rheMac2.chr2                   158779162 318 + 189746636 GAATCCACTTACTATTC-TGTGATCATGGACAGCAAAT-GAAAATC-----AAGTTCTCTGCAGAACATGAGAGAAACTTTACATTGTAATGTAAAACGAGCTGATTAAGGGCACTT-AATCCAAGAACAGCTAATTCTTAAGA-C-CTCGAAGCAGAGTGGATGAAATGTCAGGAAG-----GAGGAATGCAGCCGGGTTCTGATCACACA-GAAA--AAT-GGATTCCGGCA--TTCGACAGGCTGCCTTATTAACAATTACAGTAAC---TAGGGCTGTTCTTTTCAAA------------------------------------------------AGAATGCTTTGCACGTTAGGATAAAGACCCCA--TCTTTGGAGATCTGTGGT
q rheMac2.chr2                                             99999999999999999-99999999999999999999-9999999-----999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9-9999999999999999999999999999999-----99999999999999999999999999999-9999--999-99999999999--9999999999999999999999999999999999---9999999999999999999------------------------------------------------99999999999999999999999999999999--999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71053070 318 - 202140232 GAATCCACTTACTATTC-TGTGATCATGGACAGCAAAT-GAAAATC-----AAGTTCTCTGCAGAACATGAGCGAAACTTTACATTATAATGTAAAACGAGCTGATTAAGGGCACTT-AATCCAAGAACAGCTAATTCTTAAGA-C-CTCGAAGCAGAGTGGATGAAATGTCAGGAAG-----GAGGAATGCAGCCGGGTTCTAATCACACA-GAAA--AAT-GGATTCCAGCA--CTCGACAGGCTGCCTTATTAACAATTACAGTAAC---TAGGGCTGTTCTTTTCGAA------------------------------------------------AGAATGCCTAGCAAGTTAGAATAAAGACCCCA--TCTTTGGAGATCTGTGGT
q ponAbe2.chr3                                             99999999999999999-99999999999999999999-9999999-----999999999999999999999099999999999999999999999999999999999999999999-99999999999999999999999999-9-9999999999999999999999999999999-----99999999999999999999999999999-9999--999-99999999999--9999999999999999999999999999999999---9999999999999999999------------------------------------------------99999999999999999999999999999999--999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      515094 315 +  23952694 GAATCCACTTACTATTC-TGTGATCATGGACAGCAAAT-GAAAATT-----AAGTTCTCTGTAGAAAAGGA--GAAACTTTGCATTGTAATGTAAAACGAGCTGATTAAGGGCACTT-CATCCAAGAACAGCTAATTCTTAAGA-C-CTCAAAGCAGAGTGGATTAAACATAAGGAAG-----GAGGTATGCAGCCAGCTTCTGATCACACA-GAAG--AAT-GGATTCTGAGA--CTTGACAGGCTGCCTTATTAACAATTACAGTAAC---TAGGACAGTTCTTTTCAAA------------------------------------------------AGAATGCCTTGCAAGTTAGAAT-AATACCCCA--TCTTTGGATATCTGAGGT
q panTro2.chrY                                             00000000000000000-00000000000000000000-0000000-----00000000000000000000--00000000000000000000000000000000000000000000-00000000000000000000000000-0-0000000000000000000000000000000-----00000000000000000000000000000-0000--000-00000000000--0000000000000000000000000000000000---0000000000000000000------------------------------------------------0000000000000000000000-000000000--000000000000000000
i panTro2.chrY                   C 0 C 0
s monDom5.chr8                   276522844 277 + 312544902 -------------------GTGACC--------------GCACCCC-----GAGTT--------AACGT----GGAACCCTACATTGTAATGTAAGATGAGCGGATGAAGAGCACTT-CA-CTAGAAAAAGATCATTTTAAATATC-CCTGAGACTGAATGGAGGGAATATTGGGGGG-----GGGG---GCAGCCAACTCTGGATCTCCCA-GAAAATAAC-CCATTCTGATC--CCTGGCAGACTCCCTTATTAGCAGTTATAGGGAGGAGCAGGGCTG-CCTCTTCAAA------------------------------------------------ACACAGTCCTG-GGGCTGGATGGAGGCTCCCAACACGCAGGGCACCCAAGGA
q monDom5.chr8                                             -------------------999999--------------9999999-----99999--------99999----99999999999999999999999999999999999999999999-99-9999999999999999999999999-9999999999999999999999999999999-----9999---9999999999999999999999-999999999-99999999999--999999999999999999999999999999999999999999999-9999999999------------------------------------------------99999999999-9999999999999999999999999999999999999999
i monDom5.chr8                   C 0 C 0
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e felCat3.scaffold_217554           344630 4429 -    369131 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               23038 2177 -     41428 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=25917.000000
s hg19.chrY                        7661831 14 +  59373566 AGAAAGAATA---------------CCCC
s panTro2.chrY                      515409 14 +  23952694 AGAAAGAATA---------------CCCC
q panTro2.chrY                                            0000000000---------------0000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053388 14 - 202140232 AGAAAGAATA---------------CCCC
q ponAbe2.chr3                                            9999999999---------------9999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779480 14 + 189746636 AGAAAGAACA---------------CCCC
q rheMac2.chr2                                            9999999999---------------9999
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107363550  5 - 113440463 ---------A---------------GTCT
q rn4.chr9                                                ---------9---------------9999
i rn4.chr9                       C 0 C 0
s cavPor3.scaffold_0               8258502 14 -  88675666 AAAAAGAATA---------------TACT
q cavPor3.scaffold_0                                      9999999999---------------9999
i cavPor3.scaffold_0             I 6061 C 0
s oryCun2.chr14                    2490065 14 + 163896628 AAAGGGCACC---------------CCCT
q oryCun2.chr14                                           9999999999---------------9999
i oryCun2.chr14                  I 2 C 0
s bosTau4.chr1                   157001407 14 + 161106243 AGAAAGAGCA---------------CCCT
q bosTau4.chr1                                            9999999999---------------9999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26007282 14 -  55389570 AGGAAAAATA---------------CCTT
q canFam2.chr23                                           9999999999---------------9999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22227987 14 -  87365405 AGAAAGGATA---------------CCCT
q equCab2.chr16                                           9999999999---------------9999
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_371855             5124 29 -     87482 agaagaaaaaaaaatttttttaaagccct
q eriEur1.scaffold_371855                                 99999999999999999999999999999
i eriEur1.scaffold_371855        C 0 C 0
s loxAfr3.scaffold_36               532741 14 -  24123610 AGAGAGACTA---------------TCCT
q loxAfr3.scaffold_36                                     9999999999---------------9999
i loxAfr3.scaffold_36            C 0 C 0
s macEug1.Scaffold7817               25215 13 -     41428 AGGAGAAACT---------------CCC-
q macEug1.Scaffold7817                                    9999999999---------------999-
i macEug1.Scaffold7817           I 2177 I 4878
s monDom5.chr8                   276523121 14 + 312544902 GAACGGAAGA---------------GTCT
q monDom5.chr8                                            9999999999---------------9999
i monDom5.chr8                   C 0 C 0
e mm9.chr17                       50262779 374 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e felCat3.scaffold_217554           344630 4429 -    369131 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=112839.000000
s hg19.chrY                        7661845 50 +  59373566 TTCTTTTAGAAAATAAGTTACTC-TGGGCTTTGGGAG-CATCCTGAAAGAAG
s panTro2.chrY                      515423 50 +  23952694 TCCTTTTAGAAAATAAGTTACTC-TGGGCTTTGGGAG-CATCCTGAAAGATG
q panTro2.chrY                                            00000000000000000000000-0000000000000-00000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053402 50 - 202140232 TCTTTTTAGAAAATAAGTTACTC-CGGCCTTTGGGAG-CATCCTAAAAGATG
q ponAbe2.chr3                                            99999999999999999999999-9999999999999-99999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779494 50 + 189746636 TCTTTTTAGAAAATAAGTTACTC-CGGGCTGCGGGAG-CATCCTAAAAGATG
q rheMac2.chr2                                            99999999999999999999999-9999999999999-99999999999999
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107363555 51 - 113440463 CCACAGTTAGGGCCCATGACCTC-GGGGTCTTGGGAACCACCCTAAAAGATG
q rn4.chr9                                                99999999999999999999999-9999999999999999999999999999
i rn4.chr9                       C 0 I 266
s cavPor3.scaffold_0               8258516 50 -  88675666 TCCTTTTAAAAACTAACTTGCTC-AGAGCTTTGGGAG-CACCTTACAAGATG
q cavPor3.scaffold_0                                      99999999999999999999999-9999999999999-99999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2490079 50 + 163896628 TCCTTTCAGAAAGGAAGCTGCTCAGGGGCTCCGGGAG-CACC-TGCAAGATG
q oryCun2.chr14                                           9999999999999999999999999999999999999-9999-999999999
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157001421 49 + 161106243 TTCTTTTAGGAAATACGTTGCTC-AGGGCTTAGGGAT-TCTTCTA-AAGATG
q bosTau4.chr1                                            99999999999999999999999-9999999999999-9999999-999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26007296 50 -  55389570 TTCTTTTAGGAGATGAGCTGCTC-AGGGCTTTGAGAG-GACCCTAAAAGATG
q canFam2.chr23                                           99999999999999999999999-9999999999999-99999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22228001 43 -  87365405 TTCTTTTAGGAAGTTAGT--------GGCTTTGAGAG-CACCCTAAAAGATT
q equCab2.chr16                                           999999999999999999--------99999999999-99999999999999
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_371855             5153 47 -     87482 TCCTTTTAGAAAATAAATGGCTC-AGAGCTTTGAAAG-TAACTTAA---ATG
q eriEur1.scaffold_371855                                 99999999999999999999999-9999999999999-99999999---999
i eriEur1.scaffold_371855        C 0 n 0
s loxAfr3.scaffold_36               532755 43 -  24123610 TCCTTTTAGGAAATAAGTAGCTT--------TGAGAG-CACCTTAAAAGATG
q loxAfr3.scaffold_36                                     99999999999999999999999--------999999-99999999999999
i loxAfr3.scaffold_36            C 0 C 0
s monDom5.chr8                   276523135 40 + 312544902 --CCCTTGGGG---CAGCGACTC-CTGGATTCTGGAG-CTCCCCATG-----
q monDom5.chr8                                            --999999999---999999999-9999999999999-999999999-----
i monDom5.chr8                   C 0 C 0
e mm9.chr17                       50262779 374 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e felCat3.scaffold_217554           344630 4429 -    369131 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=56647.000000
s hg19.chrY                        7661895 31 +  59373566 -AGAGGAAGCTCA---AGGAGAATGG-TTTAT--------CTTT
s panTro2.chrY                      515473 31 +  23952694 -AGAGGAAGCTCA---AGGAGAATGG-TTTAT--------CTTT
q panTro2.chrY                                            -000000000000---0000000000-00000--------0000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053452 31 - 202140232 -AGAGGAAACTCA---AGGAGAATGG-TTTAT--------CTTT
q ponAbe2.chr3                                            -999999999999---9999999999-99999--------9999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779544 31 + 189746636 -AGAGGAAACTCA---AGGAGAATGG-TTTAT--------CTTT
q rheMac2.chr2                                            -999999999999---9999999999-99999--------9999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258566 41 -  88675666 -CCAAGTAGCTCAAA-AAGAGAATGG-TTTGTGCAAGACACATT
q cavPor3.scaffold_0                                      -99999999999999-9999999999-99999999999999999
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2490129 34 + 163896628 -CGAGGTGGCTCAGATCGGAGACAGG-CTTGT--------CTTT
q oryCun2.chr14                                           -9999999999999999999999999-99999--------9999
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157001470 35 + 161106243 -CAAGCAACTCAAAAGGGAAGAATGGTTTTGT--------CTTC
q bosTau4.chr1                                            -9999999999999999999999999999999--------9999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26007346 34 -  55389570 -CAAGGTAGCTCAAAGAGAAGAACGG-TTTAC--------CTTT
q canFam2.chr23                                           -9999999999999999999999999-99999--------9999
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           349059 33 -    369131 -CAAGGCAGCTCAAAAAGAAGAAT-G-TTTAT--------CTTT
q felCat3.scaffold_217554                                 -32133322231465502223130-0-16213--------1362
i felCat3.scaffold_217554        I 4429 C 0
s equCab2.chr16                   22228044 34 -  87365405 -CCAGGTGGCTCAAAGAGAAGGAGTG-TTTAT--------CTTT
q equCab2.chr16                                           -9999999999999999999999999-99999--------9999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               532798 34 -  24123610 -CTATGTGGCTCAAAAAGGAGAGCTG-TTAAT--------TTTT
q loxAfr3.scaffold_36                                     -9999999999999999999999999-99999--------9999
i loxAfr3.scaffold_36            C 0 C 0
s monDom5.chr8                   276523175 33 + 312544902 TGAGGCTGGTCCAAAGGCATGAATGG-CTTAC--------TT--
q monDom5.chr8                                            99999999999999999999999999-99999--------99--
i monDom5.chr8                   C 0 I 4661
e rn4.chr9                       107363606 266 - 113440463 I
e mm9.chr17                       50262779 374 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_51344             18527 1340 -     18560 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=-49076.000000
s hg19.chrY                        7661926 21 +  59373566 CTGAATGGTTTGTCTTTCTA----A
s panTro2.chrY                      515504 21 +  23952694 CTGAATGGTTTGTCTTTCTA----A
q panTro2.chrY                                            00000000000000000000----0
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053483 21 - 202140232 CTGAATGGTTTATCTTTCTA----A
q ponAbe2.chr3                                            99999999999999999999----9
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779575 21 + 189746636 CTGAATGTTTTATCTTTATA----A
q rheMac2.chr2                                            99999999999999999999----9
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258607  1 -  88675666 T------------------------
q cavPor3.scaffold_0                                      9------------------------
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2490163  1 + 163896628 C------------------------
q oryCun2.chr14                                           9------------------------
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157001505 10 + 161106243 CGAAG-----------ACAA----A
q bosTau4.chr1                                            99999-----------9999----9
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26007380 10 -  55389570 TTAAG-----------GCAA----A
q canFam2.chr23                                           99999-----------9999----9
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           349092  9 -    369131 CTAA------------GCAA----A
q felCat3.scaffold_217554                                 1312------------4335----1
i felCat3.scaffold_217554        C 0 C 0
s equCab2.chr16                   22228078 10 -  87365405 CTAAG-----------ACAA----A
q equCab2.chr16                                           99999-----------9999----9
i equCab2.chr16                  C 0 C 0
s proCap1.scaffold_15753             25062 21 -     39409 CCAAAAGGTTGGCAGTTCAA----A
q proCap1.scaffold_15753                                  99999999999999999999----9
i proCap1.scaffold_15753         I 23823 I 2700
s loxAfr3.scaffold_36               532832 15 -  24123610 CTA------TGGCAGATTTC----A
q loxAfr3.scaffold_36                                     999------99999999999----9
i loxAfr3.scaffold_36            C 0 I 10
s echTel1.scaffold_271453             2262 23 -      6854 --TGACTCTATGCACCCCAGAACCT
q echTel1.scaffold_271453                                 --99999999999899999799799
i echTel1.scaffold_271453        N 0 I 2207
e rn4.chr9                       107363606 266 - 113440463 I
e mm9.chr17                       50262779 374 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=150600.000000
s hg19.chrY                        7661947 141 +  59373566 ----------------------------------------------------------------TTTCATCTCACT-----------------------------------------------------------------------------------------CAACTCCTTACATATTGGAAGGTGATTGCAAACTCTGGTATGTTAG-GAATAAATTT-CTATT---------AAAAAG-------CAATAAACACCCTCCACTGACCAAACTCTTAGAAAAG--G-------------ATTAcagaac------------------------------------cactttccacttt-g
s panTro2.chrY                      515525 141 +  23952694 ----------------------------------------------------------------TTTCATCTCACT-----------------------------------------------------------------------------------------CAACTCCTTACATATTGGAAGGTGATTGCAAACTCTGGTATGTTAG-GAATAAATTT-CTATT---------AAAAAG-------CAATAAACACCCTCCACTGACCAAACTCTTAGAAAAG--G-------------ATTAcagaac------------------------------------cactttccacttt-g
q panTro2.chrY                                             ----------------------------------------------------------------000000000000-----------------------------------------------------------------------------------------0000000000000000000000000000000000000000000000-0000000000-00000---------000000-------0000000000000000000000000000000000000--0-------------0000000000------------------------------------0000000000000-0
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053504 142 - 202140232 ----------------------------------------------------------------TTTCATCTCATT-----------------------------------------------------------------------------------------CAACTTCTCACACATTGGAAGGTGATTGTAAACTCAGGTATGTTAG-GAATAAGTCTATTATT---------AAAAAG-------TAATAAACACCCTCCGCTGACCAAACTCTTAGAAAAG--G-------------ATTAcagaac------------------------------------cacttttcacttt-g
q ponAbe2.chr3                                             ----------------------------------------------------------------999999999999-----------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999-9999999999999999---------999999-------9999999999999999999999999999999999999--9-------------9999999999------------------------------------9999999999999-9
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779596 142 + 189746636 ----------------------------------------------------------------TTTCATCTCATT-----------------------------------------------------------------------------------------CAACTTCTTACACATTGGAAGGTGATTGTAAACTCAGGTATGTTAG-GAATAAGTTTATTATT---------AAAAAG-------TAATAAACAACTTCCACTGACCAAACTCTTAGAAAAG--G-------------ATGAcagaac------------------------------------cacttttcactta-g
q rheMac2.chr2                                             ----------------------------------------------------------------999999999999-----------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999-9999999999999999---------999999-------9999999999999999999999999999999999999--9-------------9999999999------------------------------------9999999999999-9
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258608 140 -  88675666 -------------------------------------------------------------------CATCTCACC-----------------------------------------------------------------------------------------CAACTTTTCACATGGTGGAAAATGATTGTAAATTCGGGTATAGTAAGGAATAAACTCACTG-T---------AAAAAA-------CAGTGAATACCTTCCACTGGCCAAGCTCTTACAAAAG-Gg-------------gtctcaaaac------------------------------------tacttataactct-t
q cavPor3.scaffold_0                                       -------------------------------------------------------------------999999999-----------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999999999999999999-9---------999999-------9999999999999999999999999999999999999-99-------------9999999999------------------------------------9999999999999-9
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2490164 103 + 163896628 -------------------------------------------------------------------TAATGCA--------------------------------------------------------------------------------------------GATTTCTTGCATGTTAGAAGGCAGTTGCAAACTCAGGTCTAGCTA-GAATAAATTTATTA-T---------AATAAA-------C-------ACCCTCTGCTGAGCCAACTCTTAGGAAAG-----------------------------------------------------------------------------
q oryCun2.chr14                                            -------------------------------------------------------------------9999999--------------------------------------------------------------------------------------------999999999999999999999999999999999999999999999-99999999999999-9---------999999-------9-------99999999999999999999999999999-----------------------------------------------------------------------------
i oryCun2.chr14                  C 0 I 979
s bosTau4.chr1                   157001515 186 + 161106243 ----------------------------------------------------------------TCTCATTTTGCC-----------------------------------------------------------------------------------------GAACTGCTAACACCCTGGAAAAGGATTGCAGACTCAG----ATTTG-GAATACGTTTATTA-C---------AAAAAA-------CAATAACCACCCTCCACTGA--GAACTCTAAGAAAAAAGGAATCATTTTTTCAGTCTTAAAATTTCTGGGAGGGACTtcccaggtggtccagtgcttaagaatttaccttcca-
q bosTau4.chr1                                             ----------------------------------------------------------------999999999999-----------------------------------------------------------------------------------------9999999999999999999999999999999999999----99999-99999999999999-9---------999999-------99999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-
i bosTau4.chr1                   C 0 I 140
s canFam2.chr23                   26007390 142 -  55389570 ----------------------------------------------------------------TTTCATCTTACC-----------------------------------------------------------------------------------------CAACCTCTTACACGTTGTAAAGGAATTACAAACTCGGGCATATTTG-GAACAAATTAATTG-T---------AAAAAA-------TAGTAAACACTGTCTATTGAACAAACTC-CAAGAAAAAGg-------------gtctcagaat------------------------------------ggcttttccttctt-
q canFam2.chr23                                            ----------------------------------------------------------------999999999999-----------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999-99999999999999-9---------999999-------9999999999999999999999999999-99999999999-------------9999999999------------------------------------99999999999999-
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           349101 151 -    369131 -----------------------------------------------------------------TTCATC-TACC-----------------------------------------------------------------------------------------CAACTTC-TGCACATGGAAAGGGA--TACAAACTCAGGTGTATTTG-GGATACAGttatta-ttattaaaaaaaaaaaCAACAACCAGTAAACACCATCTATTGAACAAACT--CAGAAAAAAGg-------------gtctcagaat------------------------------------ggcttttcacg-ga-
q felCat3.scaffold_217554                                  -----------------------------------------------------------------131130-3145-----------------------------------------------------------------------------------------1130300-1021400004514420--10306504435412335635-85443533423433-54342577777777746535316734457463774645342552656526--44568876367-------------3636544853------------------------------------52477747546-47-
i felCat3.scaffold_217554        C 0 C 0
s equCab2.chr16                   22228088 147 -  87365405 ----------------------------------------------------------------TTTCATCTTACC-----------------------------------------------------------------------------------------CAACTTCTTACACATTGGAAAGGGATTGCAAACTCAGGTACATTTG-TAATAAATTTATTA-CTATA-----AAAAAA-------TACTAAACACCCTCCCTTGACCAAACTCTGAGAAAAAAAg-------------gtctcaggat------------------------------------cacttttcactctt-
q equCab2.chr16                                            ----------------------------------------------------------------999999999999-----------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999-99999999999999-99999-----999999-------9999999999999999999999999999999999999999-------------9999999999------------------------------------99999999999999-
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               532857 297 -  24123610 TTTCTTATggagccctggtgggtgcagtggttaagagcttggctgctaaccaaaaggtcggcagtttgaatctaccagccactctctggaaaccctacggggtggttctactctgcctattgggtcaccgtgagtcggaatcaacttgacggcaCACAGCAACAATAACATCTTACACATTGGAAGAGAATTGCAAACTCTTATATATTTG-GGGTGAATTTATTA-T---------AAATCA--------AATATACACCCTCCACTGACCTAACTCTGAGAGTGGTGG-------------TTCTCAGAAA----------------------------------AGGGATTCTcactctt-
q loxAfr3.scaffold_36                                      9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999-9---------999999--------999999999999999999999999999999999999999-------------9999999999----------------------------------9999999999999999-
i loxAfr3.scaffold_36            I 10 C 0
e rn4.chr9                       107363606 266 - 113440463 I
e mm9.chr17                       50262779 374 +  95272651 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=121195.000000
s hg19.chrY                        7662088 68 +  59373566 aaaaattcctgaggtcgcccctaagaacttttgtttatgtg--ggttacatctatt-------tatattcatc----------aaat
s panTro2.chrY                      515666 68 +  23952694 aaaaattcctgaggtcgcccctaagaacttttgtttatgtg--ggttacatctatt-------tatattcatc----------aaat
q panTro2.chrY                                            00000000000000000000000000000000000000000--0000000000000-------0000000000----------0000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053646 67 - 202140232 aaaaattcttgaggat-cccctaagaacttttgtttatgtg--ggttacatctatc-------tatattcatc----------acat
q ponAbe2.chr3                                            9999999999999999-999999999999999999999999--9999999999999-------9999999999----------9999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779738 68 + 189746636 aaaaattcttgaggacgtccctaagaacttttgtgtaggtg--ggttacatctatc-------tatattcatc----------acac
q rheMac2.chr2                                            99999999999999999999999999999999999999999--9999999999999-------9999999999----------9999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258748 67 -  88675666 aaaaatgcttgaggca-tccctaagagctttcctttatgt---agtt------tttctttataagtatttatt----------atat
q cavPor3.scaffold_0                                      9999999999999999-99999999999999999999999---9999------99999999999999999999----------9999
i cavPor3.scaffold_0             C 0 C 0
s rn4.chr9                       107363872 41 - 113440463 AAGAGTTCGTGTGTCTG--------------------------GGCCAGAACTTTT-------GGTATGTATT-------------T
q rn4.chr9                                                99999999999999999--------------------------9999999999999-------9999999999-------------9
i rn4.chr9                       I 266 C 0
s mm9.chr17                       50263153 49 +  95272651 -----------------CCCCCACGAGTTTGTGTGTGTGTCGGGGCTAGAAC-TTT-------GGTATGCatt-------------t
i mm9.chr17                      I 374 C 0
s bosTau4.chr1                   157001841 67 + 161106243 attaattctgggagag-tccctaagagtttttgtttatatg--aattatatctagt-------gatatttata----------atat
q bosTau4.chr1                                            9999999999999999-999999999999999999999999--9999999999999-------9999999999----------9999
i bosTau4.chr1                   I 140 C 0
s canFam2.chr23                   26007532 67 -  55389570 aaaaattcttgagggt-tccttaagaacttttgtgtacatg--tgttacatcggtc-------aatatttatt----------atat
q canFam2.chr23                                           9999999999999999-999999999999999999999999--9999999999999-------9999999999----------9999
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           349252 66 -    369131 agaaattgttgaggac-tccctaagag-gtttgtttatgtg--ggttatatctatt-------gatatttatt----------ttat
q felCat3.scaffold_217554                                 4478554442657444-5772565678-7571389785748--9687655857783-------6768788688----------8778
i felCat3.scaffold_217554        C 0 C 0
s equCab2.chr16                   22228235 67 -  87365405 aaaaattcttgagtcc-tccctaagagcctttgtttatatg--ggtcatatctatc-------aatgtttatt----------atac
q equCab2.chr16                                           9999999999999999-999999999999999999999999--9999999999999-------9999999999----------9999
i equCab2.chr16                  C 0 I 910
s loxAfr3.scaffold_36               533154 77 -  24123610 aaaaattaatgaaggc-tccctaagagctttcgtttatgtg--ggttgtatctatt-------agtatctatcagtatttttcatat
q loxAfr3.scaffold_36                                     9999999999999999-999999999999999999999999--9999999999999-------999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=41513.000000
s hg19.chrY                        7662156 28 +  59373566 tagaacacttaaaactaagacattttaa
s panTro2.chrY                      515734 28 +  23952694 tagaacacttaaaactaagacattttaa
q panTro2.chrY                                            0000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053713 28 - 202140232 tagaacatttaaaactaagacattttaa
q ponAbe2.chr3                                            9999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779806 28 + 189746636 tagaatgtttaaaactaagacattttaa
q rheMac2.chr2                                            9999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258815 21 -  88675666 ttggaaatttaaaactaaggc-------
q cavPor3.scaffold_0                                      999999999999999999999-------
i cavPor3.scaffold_0             C 0 C 0
s rn4.chr9                       107363913 21 - 113440463 GAGAAAGTTTTAAACTTTTTC-------
q rn4.chr9                                                999999999999999999999-------
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50263202 21 +  95272651 tagaaaattttaaactttttc-------
i mm9.chr17                      C 0 C 0
s bosTau4.chr1                   157001908 13 + 161106243 tagaaaaattcaa---------------
q bosTau4.chr1                                            9999999999999---------------
i bosTau4.chr1                   C 0 C 0
s equCab2.chr16                   22229212 28 -  87365405 aagaaaatttaaaaCTAAGACATTTTTa
q equCab2.chr16                                           9999999999999999999999999999
i equCab2.chr16                  I 910 C 0
s felCat3.scaffold_217554           349318 28 -    369131 tggaaaacttaaaactaagaCAttttta
q felCat3.scaffold_217554                                 2748998676896627733376899987
i felCat3.scaffold_217554        C 0 I 244
s canFam2.chr23                   26007599 24 -  55389570 tggaaaat----aacgaaggcattttct
q canFam2.chr23                                           99999999----9999999999999999
i canFam2.chr23                  C 0 C 0
s loxAfr3.scaffold_36               533231 27 -  24123610 tagaaaa-ttgaaatgaagacattttta
q loxAfr3.scaffold_36                                     9999999-99999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=249190.000000
s hg19.chrY                        7662184 117 +  59373566 aaataagaatatccaagcacacatg-ttaattagtgatgatgccattatgtgtcatgtaaccaatggaaa---actccattgcacacttgtcagaggagaagag---tgaaaaaggcgaacaaa
s panTro2.chrY                      515762 117 +  23952694 aaataagaatatccaagcacacatg-ttaattcgtgatgatgccattatgtgtcatgtaaccaatggaaa---actccattgtgcacttgtcagagaagaagag---tgaaaaaggcgaacaaa
q panTro2.chrY                                             0000000000000000000000000-00000000000000000000000000000000000000000000---0000000000000000000000000000000---00000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053741 115 - 202140232 aaataagaatacccaag--cacata-ttaattagtgatgataccatcatgtgtcatgtagccacaggaaa---actccattgcacgcttgtcaaagaataagag---tgaaaaaggtgaacaaa
q ponAbe2.chr3                                             99999999999999999--999999-99999999999999999999999999999999999999999999---9999999999999999999999999999999---99999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779834 115 + 189746636 aaataagaatatccaag--cacata-ttaattagtgatgatgccattatgtgtcatgtagccactggaaa---actccattgcaggcctgtcagagaataagag---tagaaaaggcgaacaaa
q rheMac2.chr2                                             99999999999999999--999999-99999999999999999999999999999999999999999999---9999999999999999999999999999999---99999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258836 108 -  88675666 agacatgaatatccaag--caggaa-ttc-tcggtgatgacaccatcagaagtcacttaatctctggaaa---atttcactatgtgtttg--agagagtaagag---tgaaaaaag----ccaa
q cavPor3.scaffold_0                                       99999999999999999--999999-999-9999999999999999999999999999999999999999---99999999999999999--999999999999---999999999----9999
i cavPor3.scaffold_0             C 0 C 0
s rn4.chr9                       107363934  98 - 113440463 CAACAAGAATACTCGAG--CAGTGG-TTAGTCAGTGGTAAAGCAGTCATATGTCACAAATCATCTGGAGA---AGTCC----TGAGT------GGGAATGAAAG---AGGAAACAG-------A
q rn4.chr9                                                 99999999999999999--999999-99999999999999999999999999999999999999999999---99999----99999------99999999999---999999999-------9
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50263223  98 +  95272651 agacaagaatgtccaag--cggtgg-ttaaacagcggcaaagcagtcatatgccgtgaatcttctggaga---agtcc----cgcgt------gagaatgaaag---aggaaacag-------a
i mm9.chr17                      C 0 C 0
s bosTau4.chr1                   157001921 112 + 161106243 aaacaagggtatctgag--cacaca-ttaactagtgatgatgtcatcacacatcacgtaacctgtggaaa---atcccaccaggagctcgt--aaaagagtggg---aaaaaaaggtaagaga-
q bosTau4.chr1                                             99999999999999999--999999-99999999999999999999999999999999999999999999---999999999999999999--99999999999---9999999999999999-
i bosTau4.chr1                   C 0 C 0
s equCab2.chr16                   22229240 113 -  87365405 aaacaagaatatccaag--cacaca-ttaattggcaatgatgccgttatacatcacgcagcctctggaaa---actccactgggtggctga--gagaataagag---tgaaaaaggcaaataaa
q equCab2.chr16                                            99999999999999999--999999-99999999999999999999999999999999999999999999---999999999999999999--99999999999---99999999999999999
i equCab2.chr16                  C 0 C 0
s felCat3.scaffold_217554           349590 111 -    369131 aaaccagtatatccaag--cacaca--taattagtgata----catcatacatcacgtagcctctggaaa---accccattgtgcgcttat--gagagaataagactgaaaaaaagcaaaaaaa
q felCat3.scaffold_217554                                  99789999976999776--968689--999968698875----659886575897699967486389999---999999999997989986--7586588997764369999976579999999
i felCat3.scaffold_217554        I 244 I 12
s canFam2.chr23                   26007623 116 -  55389570 aaacaagagtatccaag--cacaca-ttaattagtgacgatgccatcatccgccatgcagcccctggaaaaagactccactgtgtgcttgt--gagtgaatgaa---tgaaaaatgcaaataaa
q canFam2.chr23                                            99999999999999999--999999-99999999999999999999999999999999999999999999999999999999999999999--99999999999---99999999999999999
i canFam2.chr23                  C 0 I 201
s loxAfr3.scaffold_36               533258 116 -  24123610 aaataagaatacccaag--cacacaatctattagccatagggccatcccatgtcccacagactctggaga---actccactgtgtacctgtgagagaataagag---tgaaagaggcaaataaa
q loxAfr3.scaffold_36                                      99999999999999999--999999999999999999999999999999999999999999999999999---9999999999999999999999999999999---99999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=191020.000000
s hg19.chrY                        7662301 130 +  59373566 gatcttagtatcattttgaaaatatttgggac--------ctcccaggggtccccagatcac----------actctgagaaccactgGACTAGAGTCATGTCTGGTTGACACAGAAGTGTGTTAGAGTTCTAGAGATGT-AACTCTTT
s panTro2.chrY                      515879 130 +  23952694 gatcttagtatcattttgaaaatatttgtgac--------ctcccaggggtccccagatcac----------actctgagaaccactgGACCAGCGTCATGTCTGGTTGACACAGAAGTGTGTTAGAGTTCTAGAGATGT-AACTCTTT
q panTro2.chrY                                             00000000000000000000000000000000--------0000000000000000000000----------00000000000000000000000000000000000000000000000000000000000000000000-00000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053856 137 - 202140232 ggtcttagtatcattttgaaaatagttgggaccttaagaactcccaggggtccccagac--c----------actctgagaaccattgACCTAGAGTCATGTCTGGTTGACATAGAAATGTGTTAGAGTTATAGAGAGGTCAACTCTTT
q ponAbe2.chr3                                             99999999999999999999999999999999999999999999999999999999999--9----------99999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158779949 137 + 189746636 ggtcttagtatcattctgaaaatagttgggaccttaagaactcccagggatccccagac--c----------actctgagaaccactgACCTAGAGTCATGTCTGGTTGACATAGAAATGTGTGAGAGTTATAGAGATGTCAACTCTTT
q rheMac2.chr2                                             99999999999999999999999999999999999999999999999999999999999--9----------99999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8258944 117 -  88675666 gatcttagtattgtttttaaaacaatctggacccttggaactcccAGTGG------AGACACTGGCCTGGAGAC-------ACCTCTAAATGACAGAGATGTGTTAGCAATACAGAGATG------------------TT-AACTCTGC
q cavPor3.scaffold_0                                       99999999999999999999999999999999999999999999999999------999999999999999999-------999999999999999999999999999999999999999------------------99-99999999
i cavPor3.scaffold_0             C 0 C 0
s rn4.chr9                       107364032 116 - 113440463 TATTTCAGGATTATTTTGAAAATGACTTGGATCTTGGGTGCTTTTGGCTGTCCCTAAACCACAGG---GAGAACCC----AACCTCAGGTCTAAAGATATGGCTGGTGGTCACAGAA---------------------GT-GAGT----
q rn4.chr9                                                 99999999999999999999999999999999999999999999999999999999999999999---99999999----9999999999999999999999999999999999999---------------------99-9999----
i rn4.chr9                       C 0 I 481
s mm9.chr17                       50263321 119 +  95272651 tatcttaggatgattttgaaaacaacttgggtcttgGGTGCTTCTGGGTATCCCCAAACCACACG---GAAAAC--------CCTCAGGTTTAAAGATGTGGATGGTGGTCGCTGAAAGG------------------GT-GAGTCTGC
i mm9.chr17                      C 0 I 257
s bosTau4.chr1                   157002033 100 + 161106243 ggtctcagtattattttgaaaacagctctgtcctccaggactcccGGG--------GACCAC----------ACTTGGAG--CTGCT-----GGG-----CTCTGGCTGACGCAGAGATG------------------AC-AACCGCTT
q bosTau4.chr1                                             999999999999999999999999999999999999999999999999--------999999----------99999999--99999-----999-----99999999999999999999------------------99-99999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26007940 115 -  55389570 gaccttactattattttgaaaaaagttttgcccttaggaactcctggagggcttcagaccac----------actctgagagctgct-----AGAGTCATGTCTGGCTGACACAGAGATG------------------TT-GTCTGTCT
q canFam2.chr23                                            99999999999999999999999999999999999999999999999999999999999999----------999999999999999-----9999999999999999999999999999------------------99-99999999
i canFam2.chr23                  I 201 C 0
s felCat3.scaffold_217554           349713 115 -    369131 aatcttaatattactttgaaaagagttttgcccttaggagctccccggggtccacagaccac----------actctgagaactgcC-----AGAGTCATGTCTGGCTGACACAGAGATG------------------TC-GACTGTTT
q felCat3.scaffold_217554                                  99999999999999999999999999999999999999999999999999999999999999----------999999999999999-----9999999999999999999999999999------------------99-99999999
i felCat3.scaffold_217554        I 12 C 0
s equCab2.chr16                   22229353 120 -  87365405 gatcttagtaggattgtggcgagagttttgcccttaggaactcccagggctccccggaccac----------agtgggagaagtgctgGCCGAGAGTCATGTCTGGCTGACACAGAGACG------------------TC-AACTGTTT
q equCab2.chr16                                            99999999999999999999999999999999999999999999999999999999999999----------999999999999999999999999999999999999999999999999------------------99-99999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               533374 132 -  24123610 gatcttagcattattttaaaaatagttttgagcttagagatttccaagggtcccc-gaccac----------actctgagaaccactgGCCTAGCGTCACGTCTTGGTGACATAGAAATGTCTCAGTGATGGG-----TC-TACTGTTT
q loxAfr3.scaffold_36                                      9999999999999999999999999999999999999999999999999999999-999999----------9999999999999999999999999999999999999999999999999999999999999-----99-99999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=50334.000000
s hg19.chrY                        7662431 52 +  59373566 CAAGAACTACTTCTG-------TCATAAAAAGAAA---CATTCTGTTTATTACATGTCAGTA
s panTro2.chrY                      516009 52 +  23952694 CAAGAACTACTTCTG-------TCATAAAAACAAA---CATTCTGTTTATTACATGTCAGTG
q panTro2.chrY                                            000000000000000-------0000000000000---000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71053993 52 - 202140232 CAAGAACCACTTCTG-------TTATAAAAACAAA---CACTTTGTGTATTACGTGTCAATA
q ponAbe2.chr3                                            999999999999999-------9999999999999---999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780086 48 + 189746636 CAAGAACCACTTCTG-------TCAGAA----AAA---CACTCTGTGTATTATGTGTCAATA
q rheMac2.chr2                                            999999999999999-------999999----999---999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s mm9.chr17                       50263697 26 +  95272651 CCAGAACCATTTCTG-------TTATTAAAAAC-----------------------------
i mm9.chr17                      I 257 I 237
s rn4.chr9                       107364629 29 - 113440463 CCAGAACCATTTCTG-------TTATTAGAAACCA---C-----------------------
q rn4.chr9                                                998889999999999-------9999777787899---9-----------------------
i rn4.chr9                       I 481 I 261
s cavPor3.scaffold_0               8259061 32 -  88675666 CAAAAGCCCTCCACA------------------------------TGTATTATGTAGCAATA
q cavPor3.scaffold_0                                      999999999999999------------------------------99999999999999999
i cavPor3.scaffold_0             C 0 I 2
s bosTau4.chr1                   157002133 54 + 161106243 CCAGAGTCACTTCCG-------CCATAAAATCCAAACGCCCGCTGTGTTCAACACGTCCAT-
q bosTau4.chr1                                            999999999999999-------999999999999999999999999999999999999999-
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008055 62 -  55389570 CAAGCACCATTTCCCTTTGTATTTGTAAAAACAAAATACTCCATGCATCTTATGAGTCAATA
q canFam2.chr23                                           99999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           349828 55 -    369131 CAAGCACCACTTCCC-------TCATAAAAACAAAACACTCTATGTGTATTATGAGTCAATA
q felCat3.scaffold_217554                                 999999999999999-------9999999999999999999999999999999999999999
i felCat3.scaffold_217554        C 0 C 0
s equCab2.chr16                   22229473 55 -  87365405 CAAGAACCACTTCTA-------TCGTAAAAACAAAACACTCTATTCGTATTACGCATCAATA
q equCab2.chr16                                           999999999999999-------9999999999999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               533506 49 -  24123610 CAGAAGCCATTCCCA-------TTGTCATAAAAA----CACTCTGTGT--TATATGTCAATA
q loxAfr3.scaffold_36                                     999999999999999-------999999999999----9999999999--999999999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=254761.000000
s hg19.chrY                        7662483 104 +  59373566 AAAAG-TTTTTTTT-TAAATAATAGATG-CCAGC-ACTATAAGAACTTTAATAAGTATATGTAAAGCTTTCTGGTAG-CTGGCAGGAAAACTGGCTCTTTAATCTTTTA
s panTro2.chrY                      516061 104 +  23952694 AAAAG-TTTTTTTT-AAACTAATAGGTG-CCAGC-ACTATAAGAACTTTAATAAGTATATGTAAAGCTTTCTGGTAG-CTGGCAGGAAAACTGGCTCTTTAATCTTTTA
q panTro2.chrY                                             00000-00000000-0000000000000-00000-000000000000000000000000000000000000000000-0000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054045 104 - 202140232 AAAAG-TTTTTTTT-TAAATGACAGATG-CCACT-GCTATAAGAACTTTAATAAGTATATGTGAAACTTTCTGGTAG-CTGGCAGGAAAACTGGCTCTTTAATCTTTTA
q ponAbe2.chr3                                             99999-99999999-9999999999999-99999-990999999999999999999999999999999999999999-9999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780134 105 + 189746636 AAAAGTTTTTTTTT-TTAACGACAGATG-CCATT-GCTATAAGAACTTTAATAAGTGTATGTGAAACTTTCTGGTAG-CTGGCAGGAAAACTGGCTCTTTAATCTTTTA
q rheMac2.chr2                                             99999999999999-9999999999999-99999-999999999999999999999999999999999999999999-9999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8259095 104 -  88675666 AAGGG-TTTTTTTT-TTAATGACACATG-CCAGC-TTTATAAGAATTTCAACCAGTGTATGAGAATGTTCCTAGTAG-TTGACAGTAAGAGTGGTTCCTTAATGTTTTA
q cavPor3.scaffold_0                                       99999-99999999-9999999999999-99999-999999999999999999999999999999999999999999-9999999999999999999999999999999
i cavPor3.scaffold_0             I 2 C 0
s rn4.chr9                       107364919  76 - 113440463 ------------------ATGGCAGATG-CCAGC-GCTGTAACAGCTTTAACAAGTGTATGTAAACCTTGC-----------CAGGAAAACTGGCTCC--AACCTTCCA
q rn4.chr9                                                 ------------------9998767779-88999-999999999999999999999999999999999999-----------9999999999999999--999999999
i rn4.chr9                       I 261 C 0
s mm9.chr17                       50263960  93 +  95272651 AGGAA-TTCTACAT-GCATTAATTGATA-ACAGCAGATCTAACAGCTTCAAGAAGTGAATGTAAAACTTTC-----------CAGGAAAATTGGCTCC--GATCTGTTA
i mm9.chr17                      I 237 C 0
s bosTau4.chr1                   157002187  93 + 161106243 GAATG----TTTAC-AAGCTAAC--ATG-CCAGC-TCTAGGAGAACTTCAGAAAGTATGCATGCAATTTTC-------ATGACAAGAAAACGGGCTCTTGAGTCTCCTA
q bosTau4.chr1                                             99999----99999-99999999--999-99999-999999999999999999999999999999999999-------9999999999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008117 102 -  55389570 AAAAG----TTTAC-AAAATGGCAGATG-CCAGC-TCTATAAGAACTCTAACATGTATGTGTGAAACTTTTTGGGAGAATGACAGGAACACTGGCTCTTTCATCTTTTA
q canFam2.chr23                                            99999----99999-9999999999999-99999-99999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s felCat3.scaffold_217554           349883 102 -    369131 AAAAG----TTTAC-AAATTGGCAGATG-CCAGC-TCTATAAGAACTTTGACAAGTACGTGTGAAACTTTCTGGGAGAATGACAGGAAAACTAGCTCTTTAATCTTTTA
q felCat3.scaffold_217554                                  99999----99999-9999999999999-99999-99999999999999999999999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_217554        C 0 N 0
s equCab2.chr16                   22229528 100 -  87365405 AAAAG----TTTAC-GAAATGACAGATG-CCAGC-TCCACAAGAACTTCAACAAGTATATGTGAGACTTTCTGGTAG-ATGA-AGGAAAACTGGCTCTTTAATCTTTTA
q equCab2.chr16                                            99999----99999-9999999999999-99999-999999999999999999999999999999999999999999-9999-99999999999999999999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               533555 103 -  24123610 AAAAG----TTTACAAAAATGGCAGACACCCAGT-TGTATAAGAATTCCTTCAAGTATATGTGAAACTTTCTGATCG-CTGACAGGAGAGCTCACTCTTTAATCGTTTA
q loxAfr3.scaffold_36                                      99999----9999999999999999999999999-999999999999999999999999999999999999999999-9999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=336005.000000
s hg19.chrY                        7662587 284 +  59373566 CAGTTCACCACATTTGTTTTACAGCCTCTGCAAGTACAGATGAGTCACTGCTTCTACACCGAGCTGTGCAGTGTTT-----CTACCAAGGGCCAGGCCT-GTCT-----GGGT-AAATCCATTCCCTTCAGCAAACAC--TGCAGGCAGGCAAGTCACCTTA-A--GAAGcagtttaactcagtggttaagggcccaggctctggatttagac-ttcctgggttcaaatcctggcttgtgttcttgccaaatgaccttggg-----tgagttctta-a---------------tcttcctccaa-----gtataaaaagggacaataa
s panTro2.chrY                      516165 284 +  23952694 CAGTTCACCACATTTGTTTTACAGCCTCTGCAAGTACAGATGACTCACTGCTTCTACACCGAGCTGTCCAGTGTTT-----CTACCAAGGGCCAGGCCT-GTCT-----GGGT-AAATCCATTCCCTTCAGCAAACAC--TGCAGGCAGGCAAGTCACCTTA-A--GAAGcagtttaactcagtggttaagggcccaggctctggatttagac-ttcctgggttcaaatcctgacttgtgttcttgccaaatgaccttggg-----tgagttctta-a---------------tcttcctccaa-----gtataaaaagggacaataa
q panTro2.chrY                                             0000000000000000000000000000000000000000000000000000000000000000000000000000-----000000000000000000-0000-----0000-000000000000000000000000--0000000000000000000000-0--00000000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000-----0000000000-0---------------00000000000-----0000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054149 285 - 202140232 CAGTTCACCACATTTGTTTTACGGCCTCTGCAAGTACAGATGACTAACTGCTTCTACGCAGAGCTGTGCAGCGTTT-----CTGCCAATGGCCAGGCCT-GTTT-----GGGTAAAATCCATTCCGTTCAGTAAACAC--TGCAGGGAGGCAAGTCACATTA-A--GAAGcagtttaactcagtggttaagagcccaggctctggatttagac-ttcctgggttcaaatcctggcttggcctcttgccaagtgaccttgcg-----tgagttctta-a---------------tcttcttccaa-----gtataaaaaggaagaataa
q ponAbe2.chr3                                             9999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999-9999-----99999999999999999999999999999--9999999999999999999999-9--99999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999-----9999999999-9---------------99999999999-----9999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780239 283 + 189746636 CAGTTCACCACATTTGTTTTACGGCTTCTGCAAGTACAGATGACTAACTGCCTCTACGCAGAGCTGTGCAGTGTTT-----CTACCAAGGGCCAGGCCT-CTCT-----GGGT-AAATCCACTCGCTTCAGTAAACAC---GCAGGGAGGCAAGTCACCTTA-A--GAAGcagtttaacccagtggttaagagcccaggctctagatttagac-ttcctgggttcaaatcctggcttggcctcttgccaagtgaccttggg-----tgagttctta-a---------------ttttcctccaa-----gtataaaaagggagaataa
q rheMac2.chr2                                             9999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999-9999-----9999-999999999999999999999999---999999999999999999999-9--99999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999-----9999999999-9---------------99999999999-----9999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8259199 223 -  88675666 CTGCCTATTACATTTGTTTCATGACCTCTGCAAGTGCTGATGCCTCGCTGTTCCCA----------------------------GCAAGGGC--AGCCT-GTGTTTTGGGGGC-AAGCGCACTCCTTCCCATGAGCAC--GGCACACAGG-------CTGTG-GCTGAGGCACTTTAGACTAACAGCTCAGAACACAG---ATGATC----AC-TTTGCAAGT----GCTCTGGC-TGGGCT---ACCTAATATCTCAG-------TATCTCA---------------------CTTTCTTCCTAGGAT-------------------
q cavPor3.scaffold_0                                       99999999999999999999999999999999999999999999999999999999----------------------------99999999--99999-9999999999999-999999999999999999999999--9999999999-------99999-99999999999999999999999999999999999---999999----99-999999999----99999999-999999---99999999999999-------9999999---------------------999999999999999-------------------
i cavPor3.scaffold_0             C 0 I 507
s rn4.chr9                       107364995 235 - 113440463 CAGCTCCCTCCACTTGCTTTACGGCCTCAGCAAGTGCCCA--------------------------------------------CTGAGGAC--AGGATGGTCT-----GGGC-AGATGAGTTCTCTTCCACGGGGGT--TGCAGGCCCC-------CTCCA-A--GATGcagcttagcttagtggctccgagtacagtccctggttttaggc-tttccaggttcaagccctgga-tgatctcacacacactggctttggggaggttgcctcatct-g---------------tcatccttcac-----------cagaaaaaaataa
q rn4.chr9                                                 9999999999999999999999999999999999999999--------------------------------------------99999999--9999999999-----9999-999999999999999999999999--9999999999-------99999-9--99999999999999999999999999999999999999999999999-999999999999999999999-9999999999999999999999999999999999999999-9---------------99999999999-----------9999999999999
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50264053 258 +  95272651 CAGATCCCTCCACTTGCTTTAGAGCCTCAGCAAGTGCACGTG-TGAACAGAGCACATACAAG-------------------CTTCCGAGGAT--AGGGT-GTCT-----GGAC-AGATGTGTTCCCTTCCACAGATGT--TGCAGGCCAC-------CTCCA-A--GATGcagtttggcttagtgactcagggtacagtctccggttttaggc-tttccaggctcaagccctgga-tgacctcatacacactagctttggagaggctgcctcatca-g---------------tcatccttcac-----------aggaagagaataa
i mm9.chr17                      C 0 C 0
s bosTau4.chr1                   157002280 291 + 161106243 CAGCTCACCACGTTTGATTTATGGCCTCTGCTGATACAGACGACTTGCCACTTCTACACGGGGCTATGCAATGTCT-----TCAGTAAGGGACGGGCCT-GCCA-----GGGT-ACATGC-GATCCATCAACAAATACC-T-CCTTCAAGCCAGTCATTCCC-A--GAGGCAG--CACCCTTAGGGTCAGAGGTGCAGCCTC----GAcagat-atcccgggttcgaatcctggctcggccatgtgccggctggcggtggg-----cgagttactt-accctatcagtgcttttgcctccccag-----atataaaaa-ggacaataa
q bosTau4.chr1                                             9999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999-9999-----9999-999999-999999999999999999-9-99999999999999999999-9--9999999--999999999999999999999999999----9999999-99999999999999999999999999999999999999999999999-----9999999999-999999999999999999999999999-----999999999-999999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008219 306 -  55389570 TAGTTCACCACATTTGTTTGATGGCCTCTGCCAGTACAGATGACTTATTGCTTCTACACAGGGTCATGAGATGCCTCTACCACACCAAGGGATGGGCTT-GTCC-----CGGT-AAATTCAGTTCCTCCAATAAA-ACC-TGCATGTAAGTCAGCCACTCCCTA--AAGGCTgtgtaccctagaggctaggaacgcactctatggagggagac-tccttgggctcaaaccctggcttggccacttgctgaatgatgttggg-----tgagttctttcaatctatttgtgcctctatttccccaa-----gcctaaaaagggacaataa
q canFam2.chr23                                            999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999-----9999-999999999999999999999-999-999999999999999999999999--99999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999-----99999999999999999999999999999999999999-----9999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22229628 290 -  87365405 CAGTTCACAGCGTTTGTTTTATAGTCTCTGCGAGGACAGACGACTTA---CTCCTTCACAGGGCTGTG-------------CCGCCAAGGGAAGGGACT-CTCT-----GGGT-GAATTTAGACCCTTCAAGAAACACCGTGTGTGCAGGCTAGTCACTCCCAG--GAGacagtttagcttagtggttagaagtgcaggctctggagtgggat-ttcctgggttcaaa-cctggcttggtcacttgctgggtgtcatttgc-----taagttactt-aatctcttggtgcctttgtttcctcaa-----acataaaaacggacaataa
q equCab2.chr16                                            99999999999999999999999999999999999999999999999---999999999999999999-------------999999999999999999-9999-----9999-99999999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999-99999999999999-99999999999999999999999999999999-----9999999999-999999999999999999999999999-----9999999999999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               533658 300 -  24123610 CAGTTCACCACATTTGTTTACTGGCCTCTGCTAGTAGAGATGACCTACTGTTTCCACCTGGTGTTGAGCCATGTTT-----CCACCAATGGAAGGGCCT-GTCT-----GAGT-AAAGTCATTCCCATGGACAAACAC--TGCTTGCAGACAGGTTGCTCCCAA--GAGGcagttcagcttagtggataaggatatagactctggcctaagactttcctgagtacaaatcctgtccctgtcacttgtt-agtgaccttgga-----tgagttactt-aacctctcagtgccttcatttgcccac-----ctataaaaAAGTACACTGA
q loxAfr3.scaffold_36                                      9999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999-9999-----9999-999999999999999999999999--999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999-----9999999999-999999999999999999999999999-----9999999999999999999
i loxAfr3.scaffold_36            C 0 I 856
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=82419.000000
s hg19.chrY                        7662871  90 +  59373566 caatatttacctggtaggatcttcacaggaaacctatgaaggcttacatttctaggaca------------------------------------------------------------------tagt--agtattcaa-----taaatgcc------agttatcatt
s equCab2.chr16                   22229918  93 -  87365405 cagtatttacctgacaggatctttatagaaatca---aaaggcttagatgcct-agata------------------------------------------------------------------tagt-cagtactcaa-----caaatACCTTTTGAAGGTATTATC
q equCab2.chr16                                            9999999999999999999999999999999999---9999999999999999-99999------------------------------------------------------------------9999-9999999999-----999999999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26008525  87 -  55389570 tca-aattgcctcacgggagcttgatagaaagca---aaaggattaaatgcctaagaca------------------------------------------------------------------tcat-aaatgcccaa-----caaaaacc------agttgttatt
q canFam2.chr23                                            999-999999999999999999999999999999---9999999999999999999999------------------------------------------------------------------9999-9999999999-----99999999------9999999999
i canFam2.chr23                  C 0 C 0
s bosTau4.chr1                   157002571  88 + 161106243 cagtatttacccgtcaggatctttatagaaacca---agagggttagccacctaagaca------------------------------------------------------------------tagt-aagtacttaa-----taaacatc------agctgttaGG
q bosTau4.chr1                                             9999999999999999999999999999999999---9999999999999999999999------------------------------------------------------------------9999-9999999999-----99999999------9999999999
i bosTau4.chr1                   C 0 C 0
s cavPor3.scaffold_0               8259929  84 -  88675666 CGGTATTTATCTGGTAGGATCTTTCTA-GAAACC---AAAA---GCGATTGCTAAGACA------------------------------------------------------------------TGGT-CACTACACAA-----CAAATGGC------AGTTGTCATC
q cavPor3.scaffold_0                                       999999999999999999999999999-999999---9999---999999999999999------------------------------------------------------------------9999-9999999999-----99999999------9999999999
i cavPor3.scaffold_0             I 507 C 0
s rn4.chr9                       107365230 156 - 113440463 caatacttatctgacagCCCCTTTCT---AAGCCTGGAGAA---TAGATGTCTAGGACAAGCTGAGTCCCCAGAAAAGGGCAATTATTATCACAAAGTGTTCGCAGTGTGCTACGATGTTTCAACAGTT-TTAGGTCCAGATTTCAGAATAGT------CACTATTGTT
q rn4.chr9                                                 99999999999999999999999999---999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999------9999999999
i rn4.chr9                       C 0 I 1497
s mm9.chr17                       50264311  85 +  95272651 caatacatatctGGCAGCTCCTTTCC---AAGCCTGGGGAA---TAGATGGCTAGGACA------------------------------------------------------------------AGCT-GTGGCCCCAG-----AAAAGGGC------AACTATTAGC
i mm9.chr17                      C 0 C 0
s rheMac2.chr2                   158780522  90 + 189746636 caatatttacctggtaggatattcataggaatcctatgaagggttacatttctaggaca------------------------------------------------------------------cagt--attactcaa-----taaatgcc------agctatcatt
q rheMac2.chr2                                             99999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------9999--999999999-----99999999------9999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71054434  90 - 202140232 cgatatttacctggtaggatcttcataggaatcttatgaagggttacatttctaggaca------------------------------------------------------------------tagt--agtactcaa-----taaatgcc------agttatcatt
q ponAbe2.chr3                                             99999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------9999--999999999-----99999999------9999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      516449  90 +  23952694 caatatttacctggtaggatcttcacaggaaacctatgaaggcttacatttctaggaca------------------------------------------------------------------tagt--agtattcaa-----taaatgcc------agttatcatt
q panTro2.chrY                                             00000000000000000000000000000000000000000000000000000000000------------------------------------------------------------------0000--000000000-----00000000------0000000000
i panTro2.chrY                   C 0 C 0
s loxAfr3.scaffold_36               534814  62 -  24123610 ------------------------ATAGGAACCA---TAAGGATTAGGTTTTTAGGCCA------------------------------------------------------------------CAGTTAAGTATTCAG-----TAAATGCC------AGGTATT---
q loxAfr3.scaffold_36                                      ------------------------9999999999---9999999999999999999999------------------------------------------------------------------999999999999999-----99999999------9999999---
i loxAfr3.scaffold_36            I 856 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=78274.000000
s hg19.chrY                        7662961 42 +  59373566 ATACCTTCTTTTACGAT--ATACAAAGCATCCC-AAAAGTCTCAA
s panTro2.chrY                      516539 42 +  23952694 ATACCTTCTTTTACGAT--ATACAAGGCATCCC-AAAAGTCTCAA
q panTro2.chrY                                            00000000000000000--00000000000000-00000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054524 42 - 202140232 ATACCTTCTTTTACGAT--ATACAAGGCATCCC-AAAAGTCTCAA
q ponAbe2.chr3                                            99999999999999999--99999999999999-99999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780612 42 + 189746636 ATACCTTCTTTTACGAT--AAACAAGGCATCCC-AAAAGTCTCAA
q rheMac2.chr2                                            99999999999999999--99999999999999-99999999999
i rheMac2.chr2                   C 0 C 0
s mm9.chr17                       50264396 41 +  95272651 ATA-CTTTGTTCATAGT--GTACTACAATGTAG-CCAAGTCTCAC
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8260013 42 -  88675666 ATATCTTCTTTTGTGAT--GTACAAGATATTCT-CCAAGTTTCAA
q cavPor3.scaffold_0                                      99999999999999999--99999999999999-99999999999
i cavPor3.scaffold_0             C 0 C 0
s bosTau4.chr1                   157002659 42 + 161106243 GTACCTTCTTTGACAAT--ATACAAGGTACCCC-AAACGTATCAA
q bosTau4.chr1                                            99999999999999999--99999999999999-99999999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008612 45 -  55389570 ATACCTTCTTTTACAATATACACACAGTTGCCTAAAAAGTCTCAA
q canFam2.chr23                                           999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230011 42 -  87365405 ATACCTTCTTTTACAGTA-ATACAAGGTACCCC--AAAGTCTCAA
q equCab2.chr16                                           999999999999999999-99999999999999--9999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               534876 44 -  24123610 ATACGTTCATTTACTTTTCATTCAGGGTATCTC-AAAAGTCTTAA
q loxAfr3.scaffold_36                                     999999999999999999999999999999999-99999999999
i loxAfr3.scaffold_36            C 0 C 0
e rn4.chr9                       107365386 1497 - 113440463 I
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             2285 2207 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=78000.000000
s hg19.chrY                        7663003 27 +  59373566 TACAGTTTTATGCTGAAATTTCAGAAC
s panTro2.chrY                      516581 27 +  23952694 TACAGTTTTATGCTGAAATTTCAGAAC
q panTro2.chrY                                            000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054566 27 - 202140232 TACAGTTTTATGCTGAAATTTCAGAAA
q ponAbe2.chr3                                            999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780654 27 + 189746636 TATGGTTTTATGCTGAAATTTCAGAAA
q rheMac2.chr2                                            999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s mm9.chr17                       50264437 27 +  95272651 CACAGTTTTATGCTCAGATTTCAGAAC
i mm9.chr17                      C 0 I 502
s cavPor3.scaffold_0               8260055 27 -  88675666 TACAGCTGTACACTCAGACTTCAAAAG
q cavPor3.scaffold_0                                      999999999999999999999999999
i cavPor3.scaffold_0             C 0 C 0
s bosTau4.chr1                   157002701 27 + 161106243 CACAGTTTTAAGCTCAAACTTCAGAAG
q bosTau4.chr1                                            999999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008657 27 -  55389570 GGCAGTTTTAAGCTCAAATTTCAGAAG
q canFam2.chr23                                           999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230053 27 -  87365405 GGCAGTTTTAAGCTCAAACTTCAGAAG
q equCab2.chr16                                           999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               534920 27 -  24123610 TGCACTTTTCAGCTTTAACTTAAGAAG
q loxAfr3.scaffold_36                                     999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s echTel1.scaffold_271453             4492 27 -      6854 TGCAGTTCTCAGCTCTATCTTCATAAG
q echTel1.scaffold_271453                                 679987969989899968999999999
i echTel1.scaffold_271453        I 2207 C 0
e rn4.chr9                       107365386 1497 - 113440463 I
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=32494.000000
s hg19.chrY                        7663030 30 +  59373566 TATAAGCATTAC------------------AAACTTACCTAAAAT-ACC
s panTro2.chrY                      516608 30 +  23952694 TATAAGCATTAC------------------AAACTTACCTAAAAT-ACC
q panTro2.chrY                                            000000000000------------------000000000000000-000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054593 30 - 202140232 TATAAGCATTAC------------------AAACTTACCTCAAAT-ACC
q ponAbe2.chr3                                            999999999999------------------999999999999999-999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780681 30 + 189746636 TATAAGCATTAC------------------AAACTTACCTCAAAT-ACC
q rheMac2.chr2                                            999999999999------------------999999999999999-999
i rheMac2.chr2                   C 0 C 0
s mm9.chr17                       50264966 49 +  95272651 TAAAAGCAAGATGCCACTTTGACACTCAGCAAACTCAGCTCATGCAATC
i mm9.chr17                      I 502 C 0
s cavPor3.scaffold_0               8260082 29 -  88675666 TATTAGCAATAT------------------AATCTTACCCAAAG--ACT
q cavPor3.scaffold_0                                      999999999999------------------99999999999999--999
i cavPor3.scaffold_0             C 0 C 0
s bosTau4.chr1                   157002728 27 + 161106243 TATAAGCATCAC------------------AAACTTACCAAACAA----
q bosTau4.chr1                                            999999999999------------------999999999999999----
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008684 30 -  55389570 TGTGAGCTCTAT------------------AAACTTACCAGAAAA-TAC
q canFam2.chr23                                           999999999999------------------999999999999999-999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230080 27 -  87365405 TATAAGCACTAC------------------AAACTTACCCCCCAA----
q equCab2.chr16                                           999999999999------------------999999999999999----
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               534947 30 -  24123610 TATAAATGCTGC------------------AAACCAACAAAAGCC-ATC
q loxAfr3.scaffold_36                                     999999999999------------------999999999999999-999
i loxAfr3.scaffold_36            C 0 I 31
s echTel1.scaffold_271453             4519 30 -      6854 TATCACGGCTGC------------------AAACCAGCATAAGTC-ACC
q echTel1.scaffold_271453                                 979999999999------------------898999999999999-999
i echTel1.scaffold_271453        C 0 I 116
e rn4.chr9                       107365386 1497 - 113440463 I
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=30301.000000
s hg19.chrY                        7663060 26 +  59373566 ATTCATGTAGATCt------ataaattttaag
s panTro2.chrY                      516638 26 +  23952694 ATTCATGTAGATCt------ataaattttaag
q panTro2.chrY                                            00000000000000------000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054623 26 - 202140232 ACTTATTTAGTTCT------GTAAATTTTAAG
q ponAbe2.chr3                                            99999999999999------999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780711 26 + 189746636 ATTTATTTAGTTCT------GTAAATTTTAAG
q rheMac2.chr2                                            99999999999999------999999999999
i rheMac2.chr2                   C 0 C 0
s mm9.chr17                       50265015 32 +  95272651 CTCTATCCACTACCCTGTTGACCAATCACTAA
i mm9.chr17                      C 0 I 17
s cavPor3.scaffold_0               8260111 26 -  88675666 ATTTATTTAGTGCT------GCAAATTTCAAA
q cavPor3.scaffold_0                                      99999999999999------999999999999
i cavPor3.scaffold_0             C 0 I 144
s bosTau4.chr1                   157002755 25 + 161106243 -CTTGTTGAATTCT------GTGAATTTTAAA
q bosTau4.chr1                                            -9999999999999------999999999999
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26008714 16 -  55389570 CATTATTTAATTCT------GT----------
q canFam2.chr23                                           99999999999999------99----------
i canFam2.chr23                  C 0 I 211
s equCab2.chr16                   22230107 26 -  87365405 AATTATTTAATTCT------GTGAATTCTGaa
q equCab2.chr16                                           99999999999999------999999999999
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               535008 26 -  24123610 ACTTACTTAGTTGA------Gtaaatttttga
q loxAfr3.scaffold_36                                     99999999999999------999999999999
i loxAfr3.scaffold_36            I 31 C 0
e rn4.chr9                       107365386 1497 - 113440463 I
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             4549 116 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=98791.000000
s hg19.chrY                        7663086 60 +  59373566 taataa---------------------------aatttttattt-tttGT---TTCAGTCCTGCTGATTCAAAGTGGCTACTGCTGACT---GA
s panTro2.chrY                      516664 60 +  23952694 taataa---------------------------aatttttattt-tttGT---TTCAGTCCTGCTGATTCAAAGTGGCTACTGCTGACT---GA
q panTro2.chrY                                            000000---------------------------00000000000-00000---000000000000000000000000000000000000---00
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054649 60 - 202140232 TAATAA---------------------------AATTTTAGTTT-TTTGT---TTCGGTGCCTCTAATTGAAAGTGACAAGTGCTGCCT---GA
q ponAbe2.chr3                                            999999---------------------------99999999999-99999---999999999999999999999999999999999999---99
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780737 60 + 189746636 TCATAA---------------------------AATTTTAGTTT-TTTGT---TTCAGTGCCTCTGATTGAAAGTGGCAAGTACTGCCT---GA
q rheMac2.chr2                                            999999---------------------------99999999999-99999---999999999999999999999999966777766759---99
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8260281 84 -  88675666 TAATGACTGAAATGTCATTACATGGCACATGACAAATTTTAATT-TTGGT---TTCAGCCCTC---ACTGAAAATGGTAAATGGTCCCT---GA
q cavPor3.scaffold_0                                      99999999999999999999999999999999999999999999-99999---9999999999---99999999999999999999999---99
i cavPor3.scaffold_0             I 144 C 0
s mm9.chr17                       50265064 59 +  95272651 TAATAA---------------------------AATTGTTAGTT-TTGG----TTCTGTCCTT---ACTGAACACACTACATACCATCTGGGGA
i mm9.chr17                      I 17 C 0
s bosTau4.chr1                   157002780 60 + 161106243 TAATAA---------------------------AATTTCCATTT-TTTGT---TTCAGTTCCTCTAAGCGAAAATGGAGAATGCTATCT---GA
q bosTau4.chr1                                            999999---------------------------99999999999-99999---999999999999999999999999999999999999---99
i bosTau4.chr1                   C 0 C 0
s equCab2.chr16                   22230133 60 -  87365405 taataa---------------------------aattttaatat-tttGT---TTCAGTCTCTCAGATTGAAAATGGCAAATGCTGCCC---GA
q equCab2.chr16                                           999999---------------------------99999999999-99999---999999999999999999999999999999999999---99
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26008941 59 -  55389570 AAATAA---------------------------AATCTTACTTT-TTTCT---TTCAGTCT-TCTGACTTAAAATGGTAAATGCTACCT---AA
q canFam2.chr23                                           999999---------------------------99999999999-99999---99999999-999999999999999999999999999---99
i canFam2.chr23                  I 211 C 0
s loxAfr3.scaffold_36               535034 64 -  24123610 taataa---------------------------aattttaatttCTTTGTTTGTTTAGTCCCTCTGATTAAAAATGATACATACTGCCT---GA
q loxAfr3.scaffold_36                                     999999---------------------------99999999999999999999999999999999999999999999999999999999---99
i loxAfr3.scaffold_36            C 0 C 0
e rn4.chr9                       107365386 1497 - 113440463 I
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e echTel1.scaffold_271453             4549 116 -      6854 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=56074.000000
s hg19.chrY                        7663146 44 +  59373566 AACAAAAATTACAT---TATTAATCTTATGGGGGTGTGG-GGAATAA------T-----
s panTro2.chrY                      516724 44 +  23952694 AACAAAAATTACAT---TATTAATCTTATGGGGGTGTGG-GGAATAA------T-----
q panTro2.chrY                                            00000000000000---0000000000000000000000-0000000------0-----
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054709 44 - 202140232 AACAAAAATTACAT---TACTAATTTCATAGTGGAGCAG-AGAATAA------G-----
q ponAbe2.chr3                                            99999999999999---9999999999999999999999-9999999------9-----
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780797 44 + 189746636 AACAAAAATTACAT---TATTAATCTCATAGTGGAGCAG-GGAATAA------G-----
q rheMac2.chr2                                            99999999999999---9999999999999999999999-9999999------9-----
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8260365 44 -  88675666 AACAAAAATTAAAT---GAATAATCTTGTAGTGATACGG-AGAATGA------G-----
q cavPor3.scaffold_0                                      99999999999999---9999999999999999999999-9999999------9-----
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50265123 37 +  95272651 AACCAGATTCCAAT------CAATTGCACATCAATGTGG-GTAA---------------
i mm9.chr17                      C 0 I 772
s bosTau4.chr1                   157002840 49 + 161106243 AACAAAAATTTAAC---TACAACGGTCATTGTGAGGTGG-GGAATAAGATGAA------
q bosTau4.chr1                                            99999999999999---9999999999999999999999-9999999999999------
i bosTau4.chr1                   C 0 C 0
s equCab2.chr16                   22230193 52 -  87365405 AACAAAAATTAAACTAGTGCACACCTCACAGTCCAGTGG-AGAATAAGATGAA------
q equCab2.chr16                                           999999999999999999999999999999999999999-9999999999999------
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26009000 43 -  55389570 AACAAAAACTAAAC---TGCTAATCTCATAGTGGGATGG-GGAATAA------------
q canFam2.chr23                                           99999999999999---9999999999999999999999-9999999------------
i canFam2.chr23                  C 0 I 141
s loxAfr3.scaffold_36               535098 45 -  24123610 AACAAAAATTACAT---TACTAACCTCATAGTGGAGAGGAGGAATAG-----------G
q loxAfr3.scaffold_36                                     99999999999999---999999999999999999999999999999-----------9
i loxAfr3.scaffold_36            C 0 C 0
s echTel1.scaffold_271453             4665 50 -      6854 AACAAAAATTGAAC---TACTAATCGCTGAGTGAAAAGGGAGAATAA------GATATG
q echTel1.scaffold_271453                                 89999999999999---999999999999999999999999999999------999999
i echTel1.scaffold_271453        I 116 C 0
e rn4.chr9                       107365386 1497 - 113440463 I
e oryCun2.chr14                    2490267 979 + 163896628 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=17737.000000
s hg19.chrY                        7663190 62 +  59373566 TGTACACACAACT-GTT-------AGACAAAGA-----------------------------AGATATTTTACCATTAAGAC---TTAATTCGATAGACATt
s panTro2.chrY                      516768 62 +  23952694 TGTACACACAACT-GTT-------AGACAAAGA-----------------------------AGATATTTTACCATTAAGAC---TTAATTCGATAGACATt
q panTro2.chrY                                            0000000000000-000-------000000000-----------------------------00000000000000000000---00000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054753 62 - 202140232 TGTACACACAACT-GTT-------AGACAAAGG-----------------------------AGACTTTTTACCATTAAGAC---TTAATTCGATAGACATG
q ponAbe2.chr3                                            9999999999999-999-------999999909-----------------------------99999999999999999999---99999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780841 62 + 189746636 TGTGCACACAACT-ATT-------AGACAAAGG-----------------------------AGACTTTTTACCATTAAGAC---TTAATTTGATAGACATG
q rheMac2.chr2                                            9999999999999-999-------999999999-----------------------------99999999999999999999---99999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8260409 58 -  88675666 ----TATATAGCA-ATTCTTATA-AGCCAAAAC-----------------------------ATATGCGTTACCATTAAGAT---------TAGGAAACAAG
q cavPor3.scaffold_0                                      ----999999999-999999999-999999999-----------------------------99999999999999999999---------99999999999
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50265932 62 +  95272651 --AGCACACAACTAATTCTTACACAG---AACC-----------------------------ATATTTGCTGCCATGGAGAC-----AATTCAATAAGCA-A
i mm9.chr17                      I 772 C 0
s rn4.chr9                       107366883 54 - 113440463 --------------ATTCTTACTCAG--AAAAA-----------------------------ATACCTGCTGCCATGGAGAC---TTAAATCAATAAGCACA
q rn4.chr9                                                --------------999999999999--99999-----------------------------99999999999999999999---99999999999999999
i rn4.chr9                       I 1497 C 0
s bosTau4.chr1                   157002889 64 + 161106243 TATATAAATGATC-CTT-------ACAAAAAG------------------------------ATTTTTTTTGCCATTAAGACATATTAATGTAATAGACATT
q bosTau4.chr1                                            9999999999999-999-------99999999------------------------------9999999999999999999999999999999999999999
i bosTau4.chr1                   C 0 I 2013
s equCab2.chr16                   22230245 54 -  87365405 TATATAAATAATT-CTG-------AAAAAAAGA-----------------------------AGATTTTTTATCATCAAGACAattcatta-----------
q equCab2.chr16                                           9999999999999-999-------999999999-----------------------------99999999999999999999999999999-----------
i equCab2.chr16                  C 0 C 0
s loxAfr3.scaffold_36               535143 37 -  24123610 TATACAAGTAATT-CTT-------ATACAAAGA-----------------------------ATTTTTTTTTCT----------------------------
q loxAfr3.scaffold_36                                     9999999999999-999-------999999999-----------------------------999999999999----------------------------
i loxAfr3.scaffold_36            C 0 I 276
s echTel1.scaffold_271453             4715 83 -      6854 TATACAAACAGTT-CGT-------AGACAAAGAAGAATACatatatattatgtatattatatatatatttaCCATTAAGAGC---ttaattcag--------
q echTel1.scaffold_271453                                 9999999999999-999-------9999999999999999999999999999999999999999999999999999999999---999999999--------
i echTel1.scaffold_271453        C 0 N 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e canFam2.chr23                   26009043 141 -  55389570 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=15629.000000
s hg19.chrY                        7663252 22 +  59373566 gctgtggtctgagtatgtctcc
s myoLuc1.scaffold_7336              36501 16 -    312611 --tat----taagcacctcccc
q myoLuc1.scaffold_7336                                   --999----9999999999999
i myoLuc1.scaffold_7336          N 0 I 345
s rn4.chr9                       107366937 21 - 113440463 GCCACAGTCCAAGCGTGG-Gcc
q rn4.chr9                                                999999999999999999-999
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50265994 21 +  95272651 GGCatggtccaaacatgg-gcc
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8260467 21 -  88675666 gttatgatctgaacatgt-acc
q cavPor3.scaffold_0                                      999999999999999999-999
i cavPor3.scaffold_0             C 0 C 0
s rheMac2.chr2                   158780903 22 + 189746636 gctgtggtccgaatgtgtctcc
q rheMac2.chr2                                            9999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71054815 22 - 202140232 gctgtggtctgaatgtggctcc
q ponAbe2.chr3                                            9999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      516830 22 +  23952694 gctgtggtctgagtatgtctcc
q panTro2.chrY                                            0000000000000000000000
i panTro2.chrY                   C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e equCab2.chr16                   22230299  0 -  87365405 C
e bosTau4.chr1                   157002953 2013 + 161106243 I
e loxAfr3.scaffold_36               535180 276 -  24123610 I
e canFam2.chr23                   26009043 141 -  55389570 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=130852.000000
s hg19.chrY                        7663274 127 +  59373566 ccaaaattcatgtgttggaaactaaatcctcaatgcaacagtgttgggtggtgggtccttttcagaggtgcttaggtcaggagggctcagcctttatatgtggattaatatcattat-aaatggtttc
s panTro2.chrY                      516852 127 +  23952694 tcaaaattcatgtgttgggaactaaatcctcaatgcaatagtgttgagtggtgggtccttttcagaggtgcttaggtcaggagggctcagcctttatatgtggattaatatcattat-aaatggtttc
q panTro2.chrY                                             000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71054837 128 - 202140232 cccaaatttatgtgttggaaacttaatcctcaacgcaacagtgaagggaggtgggtccttttgagaggtgcttaggtcatgagggctcagcccttatgagtggattaatatcattataaaagggtttc
q ponAbe2.chr3                                             99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158780925 128 + 189746636 cccaaatttatgtgttggaaacttaatcctcaatgcaacagtgaagggaggtgggtccttttgagagatgtttaggtcatgagggctcagcccttatgagtggattaatatcattataaaagggtttc
q rheMac2.chr2                                             99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s cavPor3.scaffold_0               8260488 116 -  88675666 ctaaaactcct--gttggaagcttaatccctaatgcaacagtactgagtgataaggccgtctcagaattattta---------ggctcagtcttcatatgcagattaatacaattataaaagg-tctt
q cavPor3.scaffold_0                                       99999999999--9999999999999999999999999999999999999999999999999999999999999---------9999999999999999999999999999999999999999-9999
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50266015 128 +  95272651 cccaaattcacaggatggaaactgaaccatgaacgtggcagtgttaagaggccgagttttttcagaagtgattaagccctgagggcttagcctttatgagggagtttatgccattacaaaaggagctt
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107366958 128 - 113440463 tccaaatccacaggctggaaacgcaaccgtacacgtaacagtgttgggaggacaaatctttacagaggtgattaggtcatgagggctcagccttcacgagtgagttaatgccattacgaaaggggctt
q rn4.chr9                                                 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999988
i rn4.chr9                       C 0 C 0
e oryCun2.chr14                    2490267 979 + 163896628 I
e equCab2.chr16                   22230299   0 -  87365405 C
e bosTau4.chr1                   157002953 2013 + 161106243 I
e loxAfr3.scaffold_36               535180 276 -  24123610 I
e canFam2.chr23                   26009043 141 -  55389570 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              36517 345 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=140162.000000
s hg19.chrY                        7663401 165 +  59373566 acagacagagtttgg----tcccttttgccttctgccttccaccatgtgaggacacagcattcctctcctctggaggacacagaaacaaggcaccatcttggaagtggagatcagccc-ttaccagacaacaaacctgtcagcaacttgatctttgact-tcttagcctcc
s oryCun2.chr14                    2491246 130 + 163896628 aTAAAAGgagtctggt---ccctttcaccctgctgccttctgccacgtgaggacacacca-cacgtccc-caggtgggcgctacaac-aggtgccatctgggaagccaacatcaggcc-tcacc-----------------TT-----------------GCTCCACCTCC
q oryCun2.chr14                                            9999999999999999---99999999999999999999999999999999999999999-99999999-99999999999999999-999999999999999999999999999999-99999-----------------99-----------------99999999999
i oryCun2.chr14                  I 979 C 0
s cavPor3.scaffold_0               8260604 163 -  88675666 gacggaggagctcag----tctttttgcaggtctgccttttgccagtttggcatacagtattccctccctcaagaggatgcagtaagacaatgccatcatggagacaaagaccaggcc-tcatcaaatat-caaacttgtagtgtcttgttctcgattt--tctagcctcc
q cavPor3.scaffold_0                                       999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999-9999999999999999999999999999--9999999999
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50266143 161 +  95272651 tttggagaggcattgggcctctgtttactcttctgtcttttgtccattgaagacacagtgatccttctc-tagggagatacagcaactagacaccatcttgcagacacagaccagaccactatc-------cagttttagatt-cttcgttcttggact-gcccagcctcc
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107367086 168 - 113440463 gaagaagatgtacagtgcctctgtttacccttctgtcagttgtccactgagggtgcagcattccttccc-cagggagatagagcaactagacaccatcatggagacacagaccagaccaccatccaacacacagtcttatatt--tttgttcttggactggtccaggttcc
q rn4.chr9                                                 888999999999999999999999999999999877787676663336577999998755544442311-1457577999998767878777766677777677877787778897656777877776778888889999999--99999999999999999999999999
i rn4.chr9                       C 0 C 0
s rheMac2.chr2                   158781053 165 + 189746636 acagacagagtttgg----tcctttttgccttctgccttccaccatgtgatgacacagcattcctcctctctggaggatgtagaaacaaggtgccatcttggaagtggagatcagccc-tcaccagacaccaaacctgccagcaacttgatcttggact-tcccagcctcc
q rheMac2.chr2                                             999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71054965 165 - 202140232 acagacagagtttgg----tcctttttgccttctgccttccaccatgtgaggacacagcattccacccctctggaggatgcaaaaacaagacaccatcttggaagtggagatcagccc-tcaccagacaccaaacctgccagcaacttgatcttggact-tcccagcctcc
q ponAbe2.chr3                                             999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999-99999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      516979 165 +  23952694 acagacagagtttgg----tcccttttgccttctgccttccaccatgtgaggacacagcattcctctcctctggaggacacagaaacaaggcaccatcttggaagtggagatcagccc-ttaccagacaacaaacctgtcagcaacttgatctttgact-tcttagcctcc
q panTro2.chrY                                             000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000-00000000000
i panTro2.chrY                   C 0 C 0
e equCab2.chr16                   22230299   0 -  87365405 C
e bosTau4.chr1                   157002953 2013 + 161106243 I
e loxAfr3.scaffold_36               535180 276 -  24123610 I
e canFam2.chr23                   26009043 141 -  55389570 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200   0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              36517 345 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=-17584.000000
s hg19.chrY                        7663566 38 +  59373566 agaact----gca---agcaagc--aagcaaacaaacaaactaacaa
s panTro2.chrY                      517144 42 +  23952694 agaactgcaagca---agcaagc--aagcaagcaaacaaacaaacaa
q panTro2.chrY                                            0000000000000---0000000--0000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055130 17 - 202140232 agaact----gtg---agcaaa-----------------------aa
q ponAbe2.chr3                                            999999----999---999999-----------------------99
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158781218 16 + 189746636 agaact----gtg---agcaa------------------------aa
q rheMac2.chr2                                            999999----999---99999------------------------99
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107367254 18 - 113440463 agaacc----agaaccagaa-------------------------at
q rn4.chr9                                                999999----9999999999-------------------------99
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50266304 18 +  95272651 agaatc----agaacaagaa-------------------------at
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8260767 15 -  88675666 agaact----gta---agaa-------------------------at
q cavPor3.scaffold_0                                      999999----999---9999-------------------------99
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2491376 14 + 163896628 TAATCC----TG----AGGA-------------------------AT
q oryCun2.chr14                                           999999----99----9999-------------------------99
i oryCun2.chr14                  C 0 C 0
s myoLuc1.scaffold_7336              36862 40 -    312611 ataatt----ata---agcaaacaaaagcaaaaaaaaaaaacaacac
q myoLuc1.scaffold_7336                                   554446----456---5453855278743479879999994533535
i myoLuc1.scaffold_7336          I 345 I 25
e equCab2.chr16                   22230299  0 -  87365405 C
e bosTau4.chr1                   157002953 2013 + 161106243 I
e loxAfr3.scaffold_36               535180 276 -  24123610 I
e canFam2.chr23                   26009043 141 -  55389570 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=24500.000000
s hg19.chrY                        7663604 53 +  59373566 aaaactct-gttctttataaattacccagtcttgggta-ttttgtttcaacaaca
s canFam2.chr23                   26009184 16 -  55389570 AAGACtta-attcatta--------------------------------------
q canFam2.chr23                                           99999999-99999999--------------------------------------
i canFam2.chr23                  I 141 C 0
s myoLuc1.scaffold_7336              36927 22 -    312611 GAGATTTT-ATCAGTGGTAAACT--------------------------------
q myoLuc1.scaffold_7336                                   44263884-54644335149522--------------------------------
i myoLuc1.scaffold_7336          I 25 C 0
s oryCun2.chr14                    2491390 52 + 163896628 GAGCACCG-GCTCTTCACGAACTCCCCAGGCTTGGGAA--CTGGTCACGGCTGCA
q oryCun2.chr14                                           99999999-99999999999999999999999999999--999999999999999
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8260782 49 -  88675666 g----tct-attttttgtaaacaacctagtctccagaa-tgttactgtatcagca
q cavPor3.scaffold_0                                      9----999-99999999999999999999999999999-9999999999999999
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50266322 54 +  95272651 gaatctct-gctatttacaaactacctcgcctctgatatttttgataaaacatcg
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107367272 54 - 113440463 gcatccctggctctttacaaaccacctcacctctgata-gcttggtatagcttca
q rn4.chr9                                                99999999999999999989999998999899999999-9999999999999999
i rn4.chr9                       C 0 C 0
s rheMac2.chr2                   158781234 53 + 189746636 aaatctct-gttctttgtaaactacccaggcttgggta-ttttgtttcaacaaca
q rheMac2.chr2                                            99999999-99999999999999999999999999999-9999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71055147 53 - 202140232 aaatcttt-gttctttataaactacccagtcttgggta-ttttgtttcaacaaca
q ponAbe2.chr3                                            99999999-99999999999999999999999999999-9999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      517186 53 +  23952694 aaaactct-gttctttataaattacccagtcttgggta-ttttgtttcaacaaca
q panTro2.chrY                                            00000000-00000000000000000000000000000-0000000000000000
i panTro2.chrY                   C 0 C 0
e equCab2.chr16                   22230299  0 -  87365405 C
e bosTau4.chr1                   157002953 2013 + 161106243 I
e loxAfr3.scaffold_36               535180 276 -  24123610 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=56362.000000
s hg19.chrY                        7663657 66 +  59373566 gacagtggactaagacaGacatttactgagcac--------------------ctactatgtgccatg-cttgtgctaggtaccagg
s panTro2.chrY                      517239 66 +  23952694 caaagtggactaaggcaGacatttactgagcac--------------------ctactatgtgccatg-cttgtgctaggtaccagg
q panTro2.chrY                                            000000000000000000000000000000000--------------------000000000000000-000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055200 66 - 202140232 caaagtggactaagacaGacattctttgagcac--------------------ctactatgtgccatg-cttgtgttaggtaccagg
q ponAbe2.chr3                                            999999999999999999999999999999999--------------------999999999999999-999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158781287 66 + 189746636 caaagtggactaagacaGacattcactgagcac--------------------ctactatgtgccatg-cttgtgctaggtaccagg
q rheMac2.chr2                                            999999999999999999999999999999999--------------------999999999999999-999999999999999999
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107367326 61 - 113440463 caaCACAGa-----aaaaacatttattgagcac--------------------ctactatgtgctagg-ctaataccatgctgttgg
q rn4.chr9                                                999999999-----9999999999999999999--------------------999999999999999-999999999999999999
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50266376 60 +  95272651 caacacag------aaagacatttattgagcac--------------------ctactatgtgccagg-ctagtgccatgctgttgg
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8260831 48 -  88675666 caaaatgaaccaagacatacatttattgagtac--------------------atactatgttccagg-------------------
q cavPor3.scaffold_0                                      999999999999999999999999999999999--------------------999999999999999-------------------
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2491442 56 + 163896628 CGGGTC--------AGAGACGTTT-CTGGGCAC--------------------CCACCCCGCGCCGCG--CAGTAGCAGGTACGAGG
q oryCun2.chr14                                           999999--------9999999999-99999999--------------------999999999999999--99999999999999999
i oryCun2.chr14                  C 0 C 0
s loxAfr3.scaffold_36               535456 49 -  24123610 ggcactgggttAAGAAT----------------------------------GGTAGctatgtgccaagaactgtgctaaatgc----
q loxAfr3.scaffold_36                                     99999999999999999----------------------------------99999999999999999999999999999999----
i loxAfr3.scaffold_36            I 276 I 134
s bosTau4.chr1                   157004966 43 + 161106243 ------------------------actgaGCACT-------------------TCACTATGTGTCCCG-TTTGTACTAGGTGCCAAG
q bosTau4.chr1                                            ------------------------9999999999-------------------999999999999999-999999999999999999
i bosTau4.chr1                   I 2013 C 0
s equCab2.chr16                   22230299 49 -  87365405 -----------------gacacttattgagcat--------------------ctaacacatgccagg-cttgttccaggtgccagg
q equCab2.chr16                                           -----------------9999999999999999--------------------999999999999999-999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26009200 49 -  55389570 -----------------gacacttattgagcac--------------------ctgccatgtgccagg-cttgtatgaggcgccagg
q canFam2.chr23                                           -----------------9999999999999999--------------------999999999999999-999999999999999999
i canFam2.chr23                  C 0 I 10
s myoLuc1.scaffold_7336              36949 56 -    312611 -----------------GATTCATATTTGGCACCTTCTCTCCTTTGTTTGTCACTGAGAGATGCGTGA-CTGAT-------------
q myoLuc1.scaffold_7336                                   -----------------452343353651141334152510318232715121113315231222243-33331-------------
i myoLuc1.scaffold_7336          C 0 I 624
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_371855             5200  0 -     87482 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=3537.000000
s hg19.chrY                        7663723 152 +  59373566 aag---ataaaagga----aacaagacaagatgatta--acca------------atggaggtttacaaag---ccagcaggggaaaGTGTGGAAACACATTGATATA----GAATGTGTTCTGCTGTATTACTCAGGTCCTGGTATGCTCAGCA-TG----CTGGGGTTTCAGGTAAT-GGGTGA
s eriEur1.scaffold_377961            41024 138 +     88154 --a---agagaaaga----gaaaaaggaaggaaggaa--acca------------gTGAAAGGGTAT---GT--TTA-------CAAAGATGGAAGCAGG--AGTACA----GCACACGCTATGCTGTCTC-CTTGGATCCAGTGATGCTCAGAG-C-----CCTGAGCCTCAGACATCCAAGTCC
q eriEur1.scaffold_377961                                  --9---999999999----999999999999999999--9999------------999999999999---99--999-------9999999999999999--999999----9999999999999999999-99999999999999999999999-9-----999999999999999999999999
i eriEur1.scaffold_377961        I 24689 C 0
s equCab2.chr16                   22230348 158 -  87365405 gag---ataaaaaga----aaccagacaaggtgtcca--gcca------------atagaggcttacacagc--ctaatgggggcaagcaTGGAAATAGGTGGAAATA----GCACGTGTCCTGCTGTATCATTAAAGTCTGATTATGTTCAGGG-TGCTGACTGGTGCCTCAGGTAGTTGAGTCC
q equCab2.chr16                                            999---999999999----999999999999999999--9999------------99999999999999999--9999999999999999999999999999999999----9999999999999999999999999999999999999999999-999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26009259 147 -  55389570 aaa---aaaaaaaga----aaagaaaaaaagcagc-----cca------------actggggcttacacagt--ctagtgggggcaggcatggaaacaATTCAATATAGCATGCATGCATCCTGCTGTATTACTAAAGTCTAGTTCTGCTCAGGG-TG----TTGGGGCCTCAGGTAG--------
q canFam2.chr23                                            999---999999999----9999999999999999-----999------------99999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999-99----9999999999999999--------
i canFam2.chr23                  I 10 C 0
s bosTau4.chr1                   157005009 138 + 161106243 GAG---ATACAACGA----AACCAGACAAGGTGTCTA--GCCA------------GT----------GCAGT--CCA------GCAGGC-TAGAAATGGGTCAGGAGA----GCATGT---CTGTGGTACCACCATGGTCCAGTTAAGCTCAGGC-TGGGTCCTGGGGCCTCAGGTAGAAGAGTCC
q bosTau4.chr1                                             999---999999999----999999999999999999--9999------------99----------99999--999------999999-999999999999999999----999999---9999999999999999999999999999999999-999999999999999999999999999999
i bosTau4.chr1                   C 0 C 0
s oryCun2.chr14                    2491498 119 + 163896628 ATG---ATAAAGAGA----AACCAGGTAAGACAGCCA--GCCGACAGGCGCTTACAAGGAGGTCCACAGAGCACCTGTCCTCCTGCATCAAGGTCAC----------------------------------------------ACGAGCTCAGGG-GG----CTGGCGCCTCAGGTAGT-------
q oryCun2.chr14                                            999---999999999----999999999999999999--9999999999999999999999999999999999999999999999999999999999----------------------------------------------999999999999-99----99999999999999999-------
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8260879  78 -  88675666 ------AAGATTAAA----AAACACACAGTATGTCTA--GCCA--------------AGAGGAC-ACCAAGT--CTAGCACGGAAAGACAAGGGC---------------------------------------CAGGTTG--ACACA--------------------------------------
q cavPor3.scaffold_0                                       ------999999999----999999999999999999--9999--------------9999999-9999999--999999999999999999999---------------------------------------9999999--99999--------------------------------------
i cavPor3.scaffold_0             C 0 C 0
s mm9.chr17                       50266436 130 +  95272651 atgctaaacaacaaaacaaaaacaaaaAACAAAACAAACACCA-------------GAGAAGGCAATTAAGTGCTTAGCTAAGAGCCATAGGGACAC-----------------------------------TTAAAGT----GCACATTTGGGATTC----TCGGGGCCTCAGGCAGCAATGTCC
i mm9.chr17                      C 0 C 0
s rn4.chr9                       107367387 126 - 113440463 atg---aaaaacaaaac--aaacaaaCAAACATGCAA--ACCA-------------GAGAAGGCAATTAGGTAATTAGCCAAGAGTCACAGGGGCAC-----------------------------------TTAAAGCTGAGGTACACTTGGTA-TC----TTGGGGCCGCAGGCAGCGATGTCC
q rn4.chr9                                                 999---99999999999--999999999999999999--9999-------------99999999999999999999999999999999999999999-----------------------------------99999999999999999999999-99----999999999999999999999999
i rn4.chr9                       C 0 C 0
s rheMac2.chr2                   158781353 153 + 189746636 aag---ataaaagga----aacaagatgAGATGATTA--GCCA------------ATAGAGGTGTACAAAG---CCAGCAGGGGCAAGTGTGGAAATAGATTGTCACA----GCATGTGTTCTGCTGTATTATTCAGGTCCAGGTACACTAGGGG-TG----CTGGGGTTTTAGGCAGTAGGGTGC
q rheMac2.chr2                                             999---999999999----999999999999999999--9999------------9999999999999999---9999999999999999999999999999999999----9999999999999999999999999999999999999999999-99----999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s ponAbe2.chr3                    71055266 151 - 202140232 aag---ataaaagga----aacaagatgAGATGATTA--GACA------------ATAGAGGTGTACAAAG---CCAGCAGGGGCAAGCATGGAAATAGATTGCTACA----GCA--TGTTCTGCTGTATTATTCAGGTCCAGGTATGCTCGGGG-TG----CTGGGGTTTCAGGTAGTGGGGTGC
q ponAbe2.chr3                                             999---999999999----999999999999999999--9999------------9999999999999999---9999999999999999999999999999999999----999--99999999999999999999999999999999999999-99----999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      517305 152 +  23952694 aag---ataaaagga----aacaagacaagatcatta--acca------------atggaggtttacaaag---ccagcaggggaaaGTGTGGAAACACATTGATATA----GAATGTGTACTGCTGTATTACTCAGGTCCTGGTATGCTCAGCA-TG----CTGGGGTTTCAGGTAAT-GGGTGA
q panTro2.chrY                                             000---000000000----000000000000000000--0000------------0000000000000000---0000000000000000000000000000000000----0000000000000000000000000000000000000000000-00----00000000000000000-000000
i panTro2.chrY                   C 0 C 0
e loxAfr3.scaffold_36               535505 134 -  24123610 I
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37005 624 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=478133.000000
s hg19.chrY                        7663875 252 +  59373566 TATTCCCAGGATACAGCCTAAAGGAAAAG--------------GAATAGTGTTCCCCTCACTGAC---ATCTGGAAGACATTTTCCCTCTTTGTGATGTGAATTTTTCC-TTCACTTGTCATTAATTCTGTTCACCTTCAAGAAGCCCATCTAT----------------------------------------CTATAG-CTTTGCCTTTGCAGTATC-TTTTCTATAGTAGATCTTTATTGAGCTTTTCCATCTTTGTAAATTG--TAAATTGTCC-TTTCAACATGCATAATG----------------ACACACTCTATTTACATAT
s panTro2.chrY                      517457 252 +  23952694 TATTCCCAGGATACAGCCTAAAGGAAAAG--------------GAATAGTGTTCCCCTCACTGAC---ATCTGGAAGACATTTTCCCTCCTTGTGATGTGAATTTTTCC-TTCACTTGTCATTAATTCTGTTCACCTTCAAGAAGCCCATCTAT----------------------------------------CTATAG-CTTTGCCTTTGCAGTATC-TTTTCAATAGTAGATCTTTATTGAGCTTTTCCATCTTTGTAAATTG--TAAATTGTCC-TTTCAACATGCATAATG----------------ACACACTCTATTTACATAT
q panTro2.chrY                                             00000000000000000000000000000--------------0000000000000000000000---00000000000000000000000000000000000000000-00000000000000000000000000000000000000000000----------------------------------------000000-000000000000000000-0000000000000000000000000000000000000000000000--0000000000-00000000000000000----------------0000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055417 269 - 202140232 TATGCCCAGGATACAGTAGAAAGGAAAAG--------------GAAAAGTGTTTCTCTCACTGAC---ATTTGGAAGACATTTTCCCTCCTCATGATGTGAATTTTTCCTTTCACTTGTCATTAATTCTGTTCATCTGCAAGAAGCCCATCTAT----------------------------------------CTATAG-CTTTCCTTTTGCAGTAGC-TTTTCAATAGTGGATCTTTATTGAGCTTTTCCATCTTTGTAAACCG--TAAATTGTCC-TTTCAACATGCATAATGACAAGCATTTCGACCCACACACTCTATTTACATAT
q ponAbe2.chr3                                             99999999999999999999999999999--------------9999999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------------------------999999-999999999999999999-9999999999999999999999999999999999999999999999--9999999999-9999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158781506 269 + 189746636 TATGCCCAGGATACAGCAGAAAGGAAAAG--------------GAAAAGTGATCCCCTCACTGAC---ATTTGGAAGACATTTTCCCTCCTCATCATGTGAATTTTTCCTTTCACTTGTCATTAATTCTGTTCATCTGCAAGAAGCCCATCTAT----------------------------------------CTATAG-CTTTCCTTTCACAGTAGC-TTTTCAATAGTGGATCTTTATTGAGCTTTTCCATCTTTGTAAATCG--TAAATTGTCC-TTTCAACATGCATAATGACAAGCATTTCGACCCACACACTCTATTTACATAT
q rheMac2.chr2                                             99999999999999999999999999999--------------9999999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------------------------999999-999999999999999999-9999999999999999999999999999999999999999999999--9999993999-9999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107367513 270 - 113440463 CATCCATGGGCTCTAGCAGTTGGAAATGGGGGCGGGGAGTGGTGGGAAGTAATGTATTTGTTGTC---G-GAGAGAAATATTTCCCCTAATGGCAAAGCCAAGTTTTCTTCTCCCT-TCCACTGATTTCGGTTCCCACAAGAGAAGCCCCCTTT---------------------------------------------G-CTCTGCCTC--CTTTGGCATTCTCCCCATGGGTTCTTCATTGAGC--TCCCGTCTCTGTAAATCA--TAAATGGCCC-CTTCAA---CCACAATGACAAGCATTTCAATGAGTATGCTCTATGTGCACAT
q rn4.chr9                                                 99999999999999999999999999999999999999999999999999999999999999999---9-9999999999999999999999999999999999999999999999-9999999999999999999999999999999999999---------------------------------------------9-999999999--9999999999999999999999999999999999--999999999999999999--9999999999-999999---9999999999999999999999999999999999999999999
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50266566 261 +  95272651 TGGTAACAGGCTCTAGCAGTCAGAAAAGGAGTTG---------GGGGAGCAATGTGTTTGTTGTCATGG-GGGAAAAATACTATGCCTAACGGCAAAGCCAAGTTTTCTCCTCCCT-TCCACTAGCTTCGGTTCTCACGAGAGAAG--CCCTTT---------------------------------------------A-CTTTGCTTC--CCTTGGCATTCTCAGCGAGGGCTCTTCACTGAGCTGTCCTGTCTCTGTACATCA--TAAATGGCCC-TTCCAA---CC---ATGACAAGCATTGCAATGAGCACACTCTCTGTGCACAT
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8260957 229 -  88675666 -----------------------------------------------------GTGTGTACTGCT---A-GGGTAAAGTATTCTTCCTGACTGTGAAGTGAACTGTTCCAATCCCTAGTCATTAATTCTGTTCATCAGCAAAAAGTTCATCTAT----------------------------------------CTACAG-CTCTGCTTTTGCACTAGC-TCTTCAATACTGGGTATCTATTAGGTTTTTCTGTCTTGGTAAATTA--TAAATTGTCC-TTTCAACATCCATAATGACAAGCATTTCAACCCACATGCTCTATTTACATAT
q cavPor3.scaffold_0                                       -----------------------------------------------------999999999999---9-999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------------------------999999-999999999999999999-9999999999999779696999989476448755969865996589--5897656556-6996465586768557855676765975458855555865748598555885
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2491617 241 + 163896628 -----------------------------------------------------ATCCTTGTCCAC---A-CTGGAAGGCATTTGCCACCAGAGCGAAGTGGATTTTTCCTCTCCCTTGCCATCCAT--------------GGGAAGCTGCACATGCACGCGCGTGCGCGcacacacacacacacacgcacacacacacaG-CTTTCCTGCTGCACCAGC-TCTTCAACA---GATCTGGGCTGGAC--GCCTGTC------AATCAATGAGATGATCC-TTTCGGGATGCACCATGG-AAGTGTCTGACCGCACA----CTGTTTACCTAG
q oryCun2.chr14                                            -----------------------------------------------------999999999999---9-99999999999999999999999999999999999999999999999999999999--------------999999999999999999999999999999999999999999999999999999999999-999999999999999999-999999999---99999999999999--9999999------99999999999999999-999999999999999999-99999999999999999----999999999999
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157005147 242 + 161106243 TTAGCCTCC-TGAGGGCAGAGGAAAGGCA----------------ACAACATTGTCCTTGCTGAC---ATTTGGAAAACATCTTCC-TACCAG-GAAGTCAATTTTCCCCT---CATGTCATTGATTCTGTTCATTTGCATGAAGCCTGTGTAT----------------------------------------CTATAG-CTTTC-TATTGCACCAGC-TCTTCAATA-TAGATCTTTATTGAGCTTTTCCGTCTTTGTAAATCA--TAAACTGTCC-TTTCACCATCCACAAAGGCAAGCA-TTCGACCCACA----------------
q bosTau4.chr1                                             999999999-9999999999999999999----------------99999999999999999999---999999999999999999-999996-99999999999999999---9999999999999999999999999999999999999999----------------------------------------999999-99999-999999999999-999999999-999999999999999999999999999999999999--9999999999-999999999999999999889799-99999999999----------------
i bosTau4.chr1                   C 0 I 208
s canFam2.chr23                   26009406 267 -  55389570 TTAGCCCAAGTGAGGACAGAGGGAAGGAA---------------GAAAATATTGGCCTTGCTGAC---ATCTGGAAAACATTTTCCCTACCAGTGAAGTGAACTTTTCCTTTCACTTGTCATTGATTCTGTTCATCCACAAGAAGCCCATCTAT----------------------------------------CTACAG-CACTCTTATCGCACCAGC-TCTTTAATA-CAGATCTTTATTGAGCTTTTCCGTCTTTGTAAATCG--TAAATTGTCC-TTTCAACATCCATAATGACAAGCATTTCGACCCATACGTTCTATTTACATAT
q canFam2.chr23                                            99999999999999999999999999999---------------999999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------------------------999999-999999999999999999-999999999-999999999999999999999999999999999999--9999999999-9999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230506 259 -  87365405 TTAGCCCAGGCTAGGGCAGAGGGAAGGGA---------------AAAAGCA-TGTCCTTGCTGAC---AGATGGAAAACATCTTCCGTACCAGAGAAGTGAACTTTCCCTTTCACTT---ACTAATTCTGATCATCTGC-CGAAGCCCATCTAT----------------------------------------CTACAG-CTTTCCTATTGCACCAGC-TCTTCAACA-TGGATC-GTATTGAGCTTCTCCGCCTTTGCAAATCA--TAAATTGTCC-TTTTAACATACATAAGGACAAGCATTTTGACCCATACATTCTATTTACAT--
q equCab2.chr16                                            99999999999999999999999999999---------------9999999-9999999999999---9999999999999999999999999999999999999999999999999---9999999999999999999-99999999999999----------------------------------------999999-999999999999999999-999999999-999999-99999999999999999999999999999--9999999999-99999999999999999999999999999999999999999999999999--
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_377961            41162 252 +     88154 CCAGctcactctggggaagaaggtcaAAG---------------GAAGCTATTGTCCTCACAGAC---ATTTGGAAAGCATTCCACCCACTAG-------AATttgtcctctctctttccattaatTCTGTTCACCCACTAGAAACTCGTCTGT----------------------------------------GT-----CTCACCCATTACACCAGT-ACTCCAATA-TGGATCGTGATTGAACTTGTCCACCTCTGTATATCA--TCAAGCGTCCGTTCCATTGTGCACAATGACAAGCG-TTCCACTCATG----CTATTTACATGT
q eriEur1.scaffold_377961                                  99999999999999999999999999999---------------999999999999999999999---9999999999999999999999999-------999999999999999999999999999999999999999999999999999999----------------------------------------99-----999999999999999999-999999999-999999999999999999999999999999999999--99999999999999999999999999999999999-99999999999----999999999999
i eriEur1.scaffold_377961        C 0 C 0
s loxAfr3.scaffold_36               535639 265 -  24123610 TTTGCCCAGGCTAAGGTAGAAGGAAAGGA--------------AGAATATACTGTCCTGGCTGAC---ATTTGAAAAGCATTTTCCCTACCAGTTAGGTGA----TTGCTTTGCTTTGTCATTAAT-CTGTCCGTCTGGAAGAGGTCTATCTAT----------------------------------------CTACCGTTTTTCCCCTTGCGCCAGC-TCTTCAATAACAGATCTTGATTGAGCTTTTCTGTCTCTGTAAATCT--TAAATTGTCC-TTTCAACGTTCCTAATGACAAGCATTTTGACCCACATACTCTTTTTACATAT
q loxAfr3.scaffold_36                                      99999999999999999999999999999--------------9999999999999999999999---999999999999999999999999999999999----999999999999999999999-999999999999999999999999999----------------------------------------9999999999999999999999999-9999999999999999999999999999999999999999999999--9999999999-9999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            I 134 C 0
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37005 624 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=246639.000000
s hg19.chrY                        7664127 67 +  59373566 CATAGCAACAGCCTCTTATTTAGATGTCAAATTCCAGCAACT-AAAAACTCAGATCCACA----------AAACAT----CA
s panTro2.chrY                      517709 67 +  23952694 CATAGCAACAGCCTCTTATTTAGATGTCGAATTCCAGCAACT-AAAAACTCAGATCCACA----------AAACAT----CA
q panTro2.chrY                                            000000000000000000000000000000000000000000-00000000000000000----------000000----00
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055686 67 - 202140232 CATAGCAACAGCCTCTTATTTAGATGTCAAATTCCAGCAACT-AAAAACTCAGATCCACA----------AAACAG----CA
q ponAbe2.chr3                                            999999999999999999999999999999999999999999-99999999999999999----------999999----99
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158781775 67 + 189746636 CATAGCAACAGCCTCTTATTTAGATGTCAAATTCCAGCAACT-AAAAACTCAGATCCACA----------AAACAG----CA
q rheMac2.chr2                                            999999999999999999999999999999999999999999-99999999999999999----------999999----99
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107367783 65 - 113440463 CATAGCAACGGCCTCTAATTTAGATGTCAAATTCCAGAAACT-GTGATCTCGGACCCACA------------GGAA----CT
q rn4.chr9                                                999999999999999999999999999999999999999999-99999999999999999------------9999----99
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50266827 65 +  95272651 CATACCAACAACCTCTTATTTAGATGTTAAATTCCAGAAACT-GTGATCTCGGATCCACA------------AGAA----TG
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8261186 68 -  88675666 CATACTAATAGCCTCTTATTTAGATGTCAGATTCCAGCTACT-CAAAACTCAGACCTATAC---------ACACAA----CA
q cavPor3.scaffold_0                                      555865764855656448495666454653846255556646-749965764363465455---------343445----54
i cavPor3.scaffold_0             C 0 C 0
s oryCun2.chr14                    2491858 64 + 163896628 CACAGAAACAGCCT-TTGTCTGGCTGGCAACTGCGGGCAGCT-GAAAGCTCGGATCCAGG------------CAGA----CA
q oryCun2.chr14                                           99999999999999-999999999999999999999999999-99999999999999999------------9999----99
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157005597 80 + 161106243 caCAGTAACAGCCTCTTATATAGATGCCAAATTTCAGCAACT-AAAAACTCAAATGCATACAAAGCAAACGCAAAGCAC-AA
q bosTau4.chr1                                            999997999987999978359999999999635999999999-998997999989999999999999999998777789-74
i bosTau4.chr1                   I 208 C 0
s canFam2.chr23                   26009673 77 -  55389570 CATAGTAACAGCCTCTTATTTAGATGTCAAATTCCAGTAACTAAAAAACTCAGATGCATACAAAG-----AAAAAGCACAAA
q canFam2.chr23                                           99999999999999999999999999999999999999999999999999999999999999999-----999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230765 79 -  87365405 -ATAATAACAGCCTCTTATTTAGATGTCAAATTCCATTAACT-AAAAACTCAGACGCACACAAAACAAACAAAAAGCAC-AA
q equCab2.chr16                                           -99999999999999999999999999999999999999999-999999999999999999999999999999999999-99
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_377961            41414 75 +     88154 CAGAGGAACAGCTTCTTATTTAGATGTCAAATTCCAGTAACT-AAAAACTCaa--gcatacaaaaaaaaaaaaaaa----aa
q eriEur1.scaffold_377961                                 999999999999999999999999999999999999999999-9999999999--999999999999999999999----99
i eriEur1.scaffold_377961        C 0 C 0
s loxAfr3.scaffold_36               535904 76 -  24123610 CATAGTAACAGCCTcttatgtagacgtcaaattccggcaact-aaaaactcagatgcacacaaaacaaa-caaaag----ca
q loxAfr3.scaffold_36                                     999999999999999999999999999999999999999999-99999999999999999999999999-999999----99
i loxAfr3.scaffold_36            C 0 I 4
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37005 624 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=217818.000000
s hg19.chrY                        7664194 72 +  59373566 AGAAGCC--AAATAATTCTCAAAACCATGA-TACTTTCAATAAACTT-CAGTCCCCT---TTGTG-CAGTCCTTCAGGCC
s panTro2.chrY                      517776 72 +  23952694 AGAAGCC--AAATAATTCTCAAAACCATAA-TACTTTCAATAAACTT-CAGTCCCCT---TTGTG-CAGTCCTTCAGGCC
q panTro2.chrY                                            0000000--000000000000000000000-0000000000000000-000000000---00000-00000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055753 72 - 202140232 AAAAGCC--AAATAATTCTCAAAACCATAA-TGCTTTCCATAAACTT-CAGTTCCCT---TTGGG-CAGTCCTTCAGGCC
q ponAbe2.chr3                                            9999999--999999999999999999999-9999999999999999-999999999---99999-99999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158781842 72 + 189746636 AGAAGCC--AAATAATTCTCAAAGCCATGA-TACTTTCCATAAACTT-CAGTTCCCT---TTGGC-CAGTCCTTCAGGCC
q rheMac2.chr2                                            9999999--999999999999999999999-9999999999999999-999999999---99999-99999999999999
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107367848 74 - 113440463 AAAGGCCAAAAAGAATTCTCAAAACCCAAA-TACTTTTTATAAACTC-CAGTCCCCT---CCCAA-GAGTCCCTTGGGCC
q rn4.chr9                                                999999999999999999999999999999-9999999999999999-999999999---99999-99999999999999
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50266892 72 +  95272651 AAAGGTC-AAAAGAATTCTCAAAACCCACA-TACTTTTTATAAACTT-CAGTCCCCT---CCCAA--AGTCCCTAGGGCC
i mm9.chr17                      C 0 C 0
s cavPor3.scaffold_0               8261254 75 -  88675666 ACAAGCC-AAAATAATTGTCAAAATCATAA-TACTTTACATAAATTT-CAGTTTCTTTGACCCTT--AGCCCCTTAGACC
q cavPor3.scaffold_0                                      4624735-5785541524465885563315-1225943226493295-34537221532005212--5456642342444
i cavPor3.scaffold_0             C 0 I 207
s oryCun2.chr14                    2491922 70 + 163896628 AGAAGTC-CCGGGAA--CTCCAAACCACAG-GGCTTCCCACCGACTTCCGGTCTCCC---CACAG--ACTCCCTTGGGC-
q oryCun2.chr14                                           9999999-9999999--9999999999999-99999999999999999999999999---99999--999999999999-
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157005677 73 + 161106243 AGAAGTC--AAATAATTCTCAAAACCACAGCCACTTTCCATAAACTT-CAGCCCCTT---TTGAA-GAGTGTCTCAAGCT
q bosTau4.chr1                                            2289899--33378536997799999599779999999837798999-953788668---88899-39599597848987
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26009750 74 -  55389570 AGATGCC-GAAATAATTCTCAAAACCATGGCTACTTTCCATAAACTT-CAGTTCTCT---TTGGA-GAGTGTCTCAGGCT
q canFam2.chr23                                           9999999-999999999999999999999999999999999999999-999999999---99999-99999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230844 74 -  87365405 AGAAGCC-AAAATAATTCTCAAAACCATGGCTACTTTCCATAAACAT-CAGTCCACT---CTGGA-GAATGTCTCAGGTC
q equCab2.chr16                                           9999999-999999999999999999999999999999999999999-999999999---99999-99999999999999
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_377961            41489 72 +     88154 agaagtg--aaatagtAATC-AGACCACAGATACTTCCCAGAAACTT-CAGTTCCAT---TTGGA-GAGTGTCCCCAGTC
q eriEur1.scaffold_377961                                 9999999--99999999999-99999999999999999999999999-999999999---99999-99999999999999
i eriEur1.scaffold_377961        C 0 C 0
s loxAfr3.scaffold_36               535984 75 -  24123610 agaagcc-aaaataattctgaaagccatggctactttccacatactt-cagcccccc---ctgaaagagtccctcaggcc
q loxAfr3.scaffold_36                                     9999999-999999999999999999999999999999999999999-999999999---99999999999999999999
i loxAfr3.scaffold_36            I 4 C 0
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37005 624 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=48954.000000
s hg19.chrY                        7664266 71 +  59373566 ATATAG------CTGTTCTTTTTAAATACACAT----T----TATAA---------------------TGAGTCTGCTCA-TCTG--TTTTTCTAGCAGATTAGAAGTA
s panTro2.chrY                      517848 71 +  23952694 ATATAG------CTGTTCTTTTTAAATACACAT----T----TATAA---------------------TGAGTCTGCTCA-TCTG--TTTTTCTAGCAGATTAGAAGTA
q panTro2.chrY                                            000000------000000000000000000000----0----00000---------------------000000000000-0000--0000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055825 71 - 202140232 ATATAG------CTGTTCTTTTTAAATACACAT----T----TATAA---------------------TGAACCTGTTCG-TCTG--TTTTTCTAGCAGGTTAGAAGTA
q ponAbe2.chr3                                            999999------999999999999999999999----9----99999---------------------999999999999-9999--9999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s rheMac2.chr2                   158781914 71 + 189746636 ATATAG------CTGTTATTTTTAAATACACAT----T----TATAA---------------------TGAGTCTGTTCA-TCTG--TTTTTCTAGCAGATTAGACGTA
q rheMac2.chr2                                            999999------999999999999999999999----9----99999---------------------999999999999-9999--9999999999999999999999
i rheMac2.chr2                   C 0 C 0
s rn4.chr9                       107367922 61 - 113440463 --ATAG------CTGTTC----TGAACACATA-----A----TAAAA---------------------TGAGT---CTTG-ACTG--TTTTCCCAGCAGATTAGCAGCA
q rn4.chr9                                                --9999------999999----9999999999-----9----99999---------------------99999---9999-9999--9999999999999999999999
i rn4.chr9                       C 0 C 0
s mm9.chr17                       50266964 71 +  95272651 --ATCGCTGTTCCTGTTC----TGAACACACAT---CA----TAAAA---------------------AGAGT---TCGG-TCTGTTTTTTTCCAGCAGATTAGCAGCA
i mm9.chr17                      C 0 C 0
s oryCun2.chr14                    2491992 62 + 163896628 -GACGG------CTGCTC----TGATTTCACACCCGCA----CGTAA---------------------GGAGTGTGCTCG-TCTATTTTTT------GTATTAG----A
q oryCun2.chr14                                           -99999------999999----9999999999999999----99999---------------------999999999999-9999999999------9999999----9
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157005750 60 + 161106243 --ATAG-------TACTC----TTATCTTATAC----A----CATAA----------------------GAGCCTGT----TATC--TTTTTTCTACCGATTGAAAGTA
q bosTau4.chr1                                            --9663-------58999----59969599688----5----85969----------------------88395574----9759--8999993237869599676446
i bosTau4.chr1                   C 0 C 0
s canFam2.chr23                   26009824 70 -  55389570 --ATAC------TTACTC----TTCTTTTACAC----AAAGGTATAG---------------------TGAGTTTGTACACTTTT--TTTTTCTAACACATTGGAAATA
q canFam2.chr23                                           --9999------999999----99999999999----9999999999---------------------99999999999999999--9999999999999999999999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22230918 57 -  87365405 --ATAG------TTACTC----TTATTTTA------------TATAG---------------------TGAGTTTA-----CCTT--TTTTTCTAGCAGAGTGGAAGTA
q equCab2.chr16                                           --9999------999999----99999999------------99999---------------------99999999-----9999--9999999999999999999999
i equCab2.chr16                  C 0 C 0
s eriEur1.scaffold_377961            41561 80 +     88154 ----AG------CTACTC----TAGTTTTGCCC----A----CATATGTACTGTTTGTGCATATGCCCTGAACTTA-----TTTA--AATTTCTAGTAGCCTGTAAGTA
q eriEur1.scaffold_377961                                 ----99------999999----99999999999----9----9999999999999999999999899999999999-----9999--9999999998999999999997
i eriEur1.scaffold_377961        C 0 C 0
s loxAfr3.scaffold_36               536059 69 -  24123610 --agag------ctgcttgtattttacacacag----a----tacag---------------------caagcttgctca-tctg--ttcttctagcagattggaagcg
q loxAfr3.scaffold_36                                     --9999------999999999999999999999----9----99999---------------------999999999999-9999--9999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37005 624 -    312611 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=135979.000000
s hg19.chrY                        7664337 81 +  59373566 CAAAAATCAGGGGAGGCATTTGAAAACATGGTGCTCAGCTTGATGAATTCCCTAAAAGTTACAACCCAGCACT-----AGTAGATT
s panTro2.chrY                      517919 81 +  23952694 CAAAAATCAGGGGAGGCATTTGAAAACATGGTGCTCAGCTTGATGAATTCCCTAAAAGTTACAACCCAGCACT-----AGTAGATT
q panTro2.chrY                                            0000000000000000000000000000000000000000000000000000000000000000000000000-----00000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055896 69 - 202140232 CAAAAACCAGGGGAGTCATTTGAAAACATGGTGCTTAGCTTCATGAATTCCCTAAAAGGTATAACCCAG-----------------
q ponAbe2.chr3                                            999999999999999999999999999999999999999999999999999999999999999999999-----------------
i ponAbe2.chr3                   C 0 I 19
s rheMac2.chr2                   158781985 68 + 189746636 CAAAAATCA-GGGAGTCATTTGAAAACATGGTGCTTAGCTTCATGAATTCCCTAAAAGTTACAACCCAG-----------------
q rheMac2.chr2                                            999999999-99999999999999999999999999999999999999999999999999999999999-----------------
i rheMac2.chr2                   C 0 I 19
s rn4.chr9                       107367983 70 - 113440463 TAATAATCAGAAAGATGTTTTGAAAGCACAACCCTTGGCTTCATAACGTTCTTTAGAGTCACACACCAG-------------A---
q rn4.chr9                                                999999999999999999999999999999999999999999999999999999999999999999999-------------9---
i rn4.chr9                       C 0 I 8
s mm9.chr17                       50267035 62 +  95272651 TAATCATCAGAAAGATGCTTTGAAAGTGCAACCCTTGGC-CCACAACATCCTTTCAAGTCACA-----------------------
i mm9.chr17                      C 0 I 1
s oryCun2.chr14                    2492054 67 + 163896628 TAAAAATCCAAAGAA---TCTGAAAATACCATACTCGGCTTCGTGAATCCTCTCAAAGCTACAAACCAG-------------G---
q oryCun2.chr14                                           999999999999999---999999999999999999999999999999999999999999999999999-------------9---
i oryCun2.chr14                  C 0 C 0
s bosTau4.chr1                   157005810 69 + 161106243 TAAAAATCTGAGAG-TAAATT-AAAATATGATACCCGGCCTCAGGAGTTCTCT-AAAGTTACAAACCAGTAC--------------
q bosTau4.chr1                                            68999456678395-599869-9999786995689999999999999999999-999999999999999999--------------
i bosTau4.chr1                   C 0 I 6
s equCab2.chr16                   22230975 80 -  87365405 TAAAAATCTGAAGAGTCAGTTGAAAATATGATACTCAGCTTCATGAATTCTCT-AAAGTTATAAACCAGTATTACTTG-----GTT
q equCab2.chr16                                           99999999999999999999999999999999999999999999999999999-999999999999999999999999-----999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26009894 71 -  55389570 CAGAAATCTGAAGA-TCAATTGAAAATACGATGCTCAGCTCCAGAAGTTCTTT-AAAGTTACCAACCAGGACT-------------
q canFam2.chr23                                           99999999999999-99999999999999999999999999999999999999-9999999999999999999-------------
i canFam2.chr23                  C 0 C 0
s myoLuc1.scaffold_7336              37629 69 -    312611 CAAAAATCTGAAAAGTAAACTGAAAATATAATGCTTGGCTTCATGAATTCTCT-AAAGTCACAAGCCAGT----------------
q myoLuc1.scaffold_7336                                   89999999699999999999799999999999999699999998996999999-9999998999999999----------------
i myoLuc1.scaffold_7336          I 624 I 5478
s eriEur1.scaffold_377961            41641 66 +     88154 CAAAAATATGAAGCATAAAC--AAAATATCATGCTCAGTTTCATGAACTCTCA-AAGATTGCAAACCAG-----------------
q eriEur1.scaffold_377961                                 95999999999999899999--9999999989989977999978999999889-998999878998989-----------------
i eriEur1.scaffold_377961        C 0 I 1282
s loxAfr3.scaffold_36               536128 74 -  24123610 tgaacatcagaagagTAATTTGAAAATAAGATGGTCGGTTTCATGAAGTTTCTTAAAGTTTCAAGCTTGTATTA------------
q loxAfr3.scaffold_36                                     99999999999999999999999999999999999999999999999999999999999999999999999999------------
i loxAfr3.scaffold_36            C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=2450.000000
s hg19.chrY                        7664418 72 +  59373566 TTCctccctttccctttccctttccctttccctttccctttccctttccctttccctttccctttccctttc
s panTro2.chrY                      518000 41 +  23952694 TTCctccctttccctttccctttctctttccctttcccttt-------------------------------
q panTro2.chrY                                            00000000000000000000000000000000000000000-------------------------------
i panTro2.chrY                   C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e rn4.chr9                       107368053  8 - 113440463 I
e mm9.chr17                       50267097  1 +  95272651 I
e oryCun2.chr14                    2492121  0 + 163896628 C
e equCab2.chr16                   22231055  0 -  87365405 C
e bosTau4.chr1                   157005879  6 + 161106243 I
e loxAfr3.scaffold_36               536202  0 -  24123610 C
e canFam2.chr23                   26009965  0 -  55389570 C
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e rheMac2.chr2                   158782053 19 + 189746636 I
e calJac1.Contig102                1040317 16226 -   1157145 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I
e ponAbe2.chr3                    71055965 19 - 202140232 I
e xenTro2.scaffold_1099             293427 3628 -    315732 I

a score=4723.000000
s hg19.chrY                        7664490 36 +  59373566 cctcccctcccctcccctcccctctcctttcctttc
s calJac1.Contig102                1056543 36 -   1157145 cccccccTCCTTTCTTCTCttcttttattccctttt
q calJac1.Contig102                                       399900999999999999999999999999999999
i calJac1.Contig102              I 16226 N 0
s panTro2.chrY                      518041 31 +  23952694 -----cctcccctcccctcccctctcctttcctttt
q panTro2.chrY                                            -----0000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s xenTro2.scaffold_1099             271975 12 +    315732 ------------------------TTTTTTAATTTT
i xenTro2.scaffold_1099          n 3628 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e rn4.chr9                       107368053  8 - 113440463 I
e mm9.chr17                       50267097  1 +  95272651 I
e oryCun2.chr14                    2492121  0 + 163896628 C
e equCab2.chr16                   22231055  0 -  87365405 C
e bosTau4.chr1                   157005879  6 + 161106243 I
e loxAfr3.scaffold_36               536202  0 -  24123610 C
e canFam2.chr23                   26009965  0 -  55389570 C
e speTri1.scaffold_160574             9387  0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e rheMac2.chr2                   158782053 19 + 189746636 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I
e ponAbe2.chr3                    71055965 19 - 202140232 I

a score=95727.000000
s hg19.chrY                        7664526 165 +  59373566 cttttcttttctttctaacagggtctcactctgtcaccaggctggagtgcagtgatgccatcacagatcactgcggccttcatctcccaggctcaggtgattccccctctctagcctcctgagtagctgggaccacaggtgtgcaccaccacatccagctgtttt
s rheMac2.chr2                   158782072 164 + 189746636 -ttttcttttctttgagacagtgtctcactctgtcaccaggctggagtgcagtgatgccatcacaggtcactgcagccttgacctctcagactcaggtgattctcccacctcagcctcctgagtagctgggaccacaggtgtgcgccaccatgcccagctaattt
q rheMac2.chr2                                             -99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   I 19 C 0
s panTro2.chrY                      518072 165 +  23952694 cttttcttttctttctaacagggtcttactgtgtcaccaggctggagtgcagtgatgccatcacagatcactgcagccttcatctcccaggctcaggtgattccccctctctagcctcctgagtagctgggaccacaggcgtgcaccaccacatccagctgtttt
q panTro2.chrY                                             000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71055984 165 - 202140232 cttttcgtttctttcagacagcatctcactctgtcaccaggctggagtatagtgatgccatcacaggtcactgcagcctcgacctcccagactcgggtgattctcccacctcagcctcccgagtagctgggaccacaggtgtgtgccaccatgcccagctaattt
q ponAbe2.chr3                                             999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   I 19 C 0
s xenTro2.scaffold_1099             271987 151 +    315732 TTGTTATTATTTTTGAGATGGAGTCTTGCTCTGTCCCCAGACTGGAGTGCAGTGGCGTGATCTTGGCTCACTGAAACCTTCGCCTCCTGCGTTCAAGCAGTTCTCCTGCATT-------CAAGCAGTT-------CTCCTGCCTGCCACCACACCTGGCTGATTT
i xenTro2.scaffold_1099          C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e rn4.chr9                       107368053   8 - 113440463 I
e mm9.chr17                       50267097   1 +  95272651 I
e oryCun2.chr14                    2492121   0 + 163896628 C
e equCab2.chr16                   22231055   0 -  87365405 C
e bosTau4.chr1                   157005879   6 + 161106243 I
e loxAfr3.scaffold_36               536202   0 -  24123610 C
e canFam2.chr23                   26009965   0 -  55389570 C
e speTri1.scaffold_160574             9387   0 -    115260 I
e micMur1.scaffold_734              287777 4711 -    418489 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I

a score=-12233.000000
s hg19.chrY                        7664691 19 +  59373566 t------tttgttttgtt-------ttgtttt
s ponAbe2.chr3                    71056149  1 - 202140232 t-------------------------------
q ponAbe2.chr3                                            9-------------------------------
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      518237 25 +  23952694 ttttttgtttgttttttt-------ttttttt
q panTro2.chrY                                            000000000000000000-------0000000
i panTro2.chrY                   C 0 C 0
s rheMac2.chr2                   158782236  1 + 189746636 t-------------------------------
q rheMac2.chr2                                            9-------------------------------
i rheMac2.chr2                   C 0 C 0
s micMur1.scaffold_734              292488 31 -    418489 -tttctatatatattagttggccaattaattt
q micMur1.scaffold_734                                    -9999999999999999999999999999999
i micMur1.scaffold_734           I 4711 N 0
s xenTro2.scaffold_1099             272138  2 +    315732 ------------------------------TT
i xenTro2.scaffold_1099          C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e rn4.chr9                       107368053  8 - 113440463 I
e mm9.chr17                       50267097  1 +  95272651 I
e oryCun2.chr14                    2492121  0 + 163896628 C
e equCab2.chr16                   22231055  0 -  87365405 C
e bosTau4.chr1                   157005879  6 + 161106243 I
e loxAfr3.scaffold_36               536202  0 -  24123610 C
e canFam2.chr23                   26009965  0 -  55389570 C
e speTri1.scaffold_160574             9387  0 -    115260 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I

a score=88074.000000
s hg19.chrY                        7664710 131 +  59373566 tttgtatttattgtagagatgaggtttcgccatgttgcttcggctagtcttgaacccttgggctcagacaatccactttccttagcatcacaaagtgctggaattacaggtatgagccactgtgcctagcc
s rheMac2.chr2                   158782237 129 + 189746636 tttgtattttttgtagagatgaggtttcac--tgttgctcaggctagtctcgaacccccaggctcaagcaatccacttgccttaacctcccaaagtgctggaattacaggtatgagccactgttcctgacc
q rheMac2.chr2                                             999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s panTro2.chrY                      518262 131 +  23952694 tttgtatttattgtagagacaaggtttcgccatgttgcttcggctagtcttgaacccctgggctcagacaatccactctccttagcgtcacaaagtgctggaattacaggtatgagccactgtgcctagcc
q panTro2.chrY                                             00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71056150 128 - 202140232 -ttgtattttttgtagagatgaggtttcgc--tgttgctcaggctagtcttgaacccctgggctcaagcaatccacttgccttagcctcccaaagtgctggaattacaggtatgagccactgtgcctggcc
q ponAbe2.chr3                                             -99999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s xenTro2.scaffold_1099             272140 127 +    315732 ---GAATTTTTAGTAGAGTTGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATGTACCTG-CTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCCCGGCC
i xenTro2.scaffold_1099          C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e rn4.chr9                       107368053   8 - 113440463 I
e mm9.chr17                       50267097   1 +  95272651 I
e oryCun2.chr14                    2492121   0 + 163896628 C
e equCab2.chr16                   22231055   0 -  87365405 C
e bosTau4.chr1                   157005879   6 + 161106243 I
e loxAfr3.scaffold_36               536202   0 -  24123610 C
e canFam2.chr23                   26009965   0 -  55389570 C
e speTri1.scaffold_160574             9387   0 -    115260 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             25083 2700 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I

a score=206127.000000
s hg19.chrY                        7664841 80 +  59373566 ACTGCTGTGTTTTCTGAAGGAAATTAGTTTTAACAAAACCAGAAAGGACTAAGTAATATCCACAAAGTATATCAGACACC
s ponAbe2.chr3                    71056278 80 - 202140232 ACTACTGTGTTTTCTGAAGGAAATTAGTTTTAACAGAACCAGAAAGGACTAAGTAATATCCACAAAGTATAACAGACACC
q ponAbe2.chr3                                            99999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                   C 0 C 0
s panTro2.chrY                      518393 80 +  23952694 ACTGCTGTGTTTTCTGAAGGAAATTAGTTTTAACAAAACCAGAAAGGACTAAGTAATATCCACAAAGTATATCAGACACC
q panTro2.chrY                                            00000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s rheMac2.chr2                   158782366 80 + 189746636 ACTACTGTGTTTTCTGAAGGAAATTAGTTTTAACAGAACCAGAAAGGACTAAGTAGTATCCACAAAGTATATCAGACACC
q rheMac2.chr2                                            99999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                   C 0 C 0
s mm9.chr17                       50267098 80 +  95272651 ACTCCAAGGTTTTCTCAGTGAAATTAACCTTAACAAAACCATAGAAGGTTAAGTTATAGGCAGAAAGTATTCCCAGCACC
i mm9.chr17                      I 1 C 0
s oryCun2.chr14                    2492121 73 + 163896628 ACTGCTGGATTTCCTGAATGAAACGAAGTCT-------TCAGAAAGGTCTACGTAAAGCCCACAGAGGATTTCCAACAGC
q oryCun2.chr14                                           9999999999999999999999999999999-------999999999999999999999999999999999999999999
i oryCun2.chr14                  C 0 C 0
s proCap1.scaffold_15753             27783 58 -     39409 --------------------AAATTAGTCTTAAC--AACCAGACAGAGCTACGGAATGTCCACGAAACATTTCTAGGATC
q proCap1.scaffold_15753                                  --------------------99999999999999--99999999999999999999999999999999999999999999
i proCap1.scaffold_15753         I 2700 I 2540
s loxAfr3.scaffold_36               536202 74 -  24123610 ----CTTGGCTTTCTGAATAAAATTAGTCTTAAC--AACCAGAGAGGGCTAAGAAATGTCCACAAAACATTTCCGGCATC
q loxAfr3.scaffold_36                                     ----999999999999999999999999999999--99999999999999999999999999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s rn4.chr9                       107368061 72 - 113440463 --------GTTTTCTCAATGAAATTAACCTTAAGAAAACCAGAAAAGGTTAAGTTATAGACAGAAAGTATTTCCAACATC
q rn4.chr9                                                --------999999999999999999999999999999999999999999999999999999999999999999999999
i rn4.chr9                       I 8 C 0
s bosTau4.chr1                   157005885 74 + 161106243 ------GTTTTTGCTGAATGAAATTAGTCTTAACAGAACCAAAAAGGACTAAGTAATGTTCACAAAGTATTTCAGATATC
q bosTau4.chr1                                            ------99999999999999999999999999999999999999999999999999999999999999999999999999
i bosTau4.chr1                   I 6 C 0
s equCab2.chr16                   22231055 71 -  87365405 ---------TTTACTGAATGAAATCAGTCTTAACAGAACCAGAAAGGACTAAGTAACATCCACAAAGGATTTCAGACATC
q equCab2.chr16                                           ---------99999999999999999999999999999999999999999999999999999999999999999999999
i equCab2.chr16                  C 0 C 0
s canFam2.chr23                   26009965 71 -  55389570 ---------TTAACCAAATGAAATTAGTCTTCATGGGACCAGAAAAGACTAAGTAACGTCCACAATGTATTTCAGACATC
q canFam2.chr23                                           ---------99999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                  C 0 C 0
s xenTro2.scaffold_1099             272267 38 +    315732 -----------TCTCCAATATTTTTATTATT-----------AAAATGCTAAATACTGCC--------------------
i xenTro2.scaffold_1099          C 0 C 0
e cavPor3.scaffold_0               8261329 207 -  88675666 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I

a score=48053.000000
s hg19.chrY                        7664921 21 +  59373566 TAAACTCTTACATGAAGA---GTT
s loxAfr3.scaffold_36               536276 20 -  24123610 TAGCCTCTTACA-GAAGA---GTC
q loxAfr3.scaffold_36                                     999999999999-99999---999
i loxAfr3.scaffold_36            C 0 C 0
s canFam2.chr23                   26010036 21 -  55389570 TAAACTCTCACAGGAGGA---AAG
q canFam2.chr23                                           999999999999999999---999
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22231126 21 -  87365405 TAAATTCTTACATGAAGA---CTC
q equCab2.chr16                                           999999999999999999---999
i equCab2.chr16                  C 0 C 0
s bosTau4.chr1                   157005959 21 + 161106243 TAAACTCAGACATGGGAA---GTC
q bosTau4.chr1                                            999999999999999999---999
i bosTau4.chr1                   C 0 C 0
s oryCun2.chr14                    2492194 20 + 163896628 TAAACTCTCGCACAAAGA---GT-
q oryCun2.chr14                                           999999999999999999---99-
i oryCun2.chr14                  C 0 C 0
s cavPor3.scaffold_0               8261536 21 -  88675666 TGATCTCCTCCATGAAAA---GTT
q cavPor3.scaffold_0                                      255115113264243662---254
i cavPor3.scaffold_0             I 207 C 0
s rn4.chr9                       107368133 18 - 113440463 GTAACCCTTACACAAGGA------
q rn4.chr9                                                999999999999999999------
i rn4.chr9                       C 0 I 113
s mm9.chr17                       50267178 24 +  95272651 TTAACCCTTACACAAGGAAAAGTT
i mm9.chr17                      C 0 I 245
s rheMac2.chr2                   158782446 21 + 189746636 TAAACTCTTACATGAAGA---GTT
q rheMac2.chr2                                            999999999999999999---999
i rheMac2.chr2                   C 0 C 0
s panTro2.chrY                      518473 21 +  23952694 TAAACTCTTACATGAAGA---GTT
q panTro2.chrY                                            000000000000000000---000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71056358 21 - 202140232 TAAACTCTCACCTGAAGA---GTT
q ponAbe2.chr3                                            999999993999999999---999
i ponAbe2.chr3                   C 0 C 0
e speTri1.scaffold_160574             9387  0 -    115260 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             27841 2540 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I
e xenTro2.scaffold_1099             272305  0 +    315732 C

a score=109222.000000
s hg19.chrY                        7664942 64 +  59373566 ACATGACCTAGTGAAAAACTATTTTTAATTTTCTCC-TATCT-CAAAACATTGAAAATTACAAATC
s xenTro2.scaffold_1099             272305 26 +    315732 ---GGGCCCAGTGG------------------CTCA-CACCT-GTAATC-----------------
i xenTro2.scaffold_1099          C 0 C 0
s loxAfr3.scaffold_36               536296 64 -  24123610 CTTAGCCCCAGGAAAAGGCTATTTTTCATTTTCTCA-TATCT-CAAAAGATTGGAAGTTAAAAATC
q loxAfr3.scaffold_36                                     999999999999999999999999999999999999-99999-99999999999999999999999
i loxAfr3.scaffold_36            C 0 C 0
s canFam2.chr23                   26010057 59 -  55389570 ATTTATTCTTATGAAAGACTGATTTCTATTTTCCCATTATGT-CAAAAGACTGAAAATTA------
q canFam2.chr23                                           999999999999999999999999999999999999999999-99999999999999999------
i canFam2.chr23                  C 0 C 0
s equCab2.chr16                   22231147 64 -  87365405 CTTTGCCCCAGTGCAAGACTGTTTTTTATATTCCCG-TATGT-CAAAAGACTGCACATTAAAAATC
q equCab2.chr16                                           999999999999999999999999999999999999-99999-99999999999999999999999
i equCab2.chr16                  C 0 C 0
s bosTau4.chr1                   157005980 63 + 161106243 CTTTGCCTTAGTGAAAGACAATTTTTCAT-TTCCCA-TATGT-CAAAAGACTGAAAACTAAAAACC
q bosTau4.chr1                                            99999999999999999999999999999-999999-99999-99999999999999999999999
i bosTau4.chr1                   C 0 C 0
s oryCun2.chr14                    2492214 64 + 163896628 ACTTTACCTAAAGAGAGGCCGTGGTCCATTTTCTCC-TGTCT-CAAAAGGCTGAAAATTAAAAATC
q oryCun2.chr14                                           999999999999999999999999999999999999-99999-99999999999999999999999
i oryCun2.chr14                  C 0 I 8
s cavPor3.scaffold_0               8261557 55 -  88675666 -TTTGGCCTAGTGAAAGACCATTTTTCATCTTCTTA-TTACTGCAAAAGACTGAAAA---------
q cavPor3.scaffold_0                                      -44563714454699999999999999999999999-99999999999999962222---------
i cavPor3.scaffold_0             C 0 I 3
s rheMac2.chr2                   158782467 64 + 189746636 ATGTGCCCTAGTGAAAAACGATTTTCCATTTTCTCA-TATCT-CAAAAGACTGAAAATTACAAATC
q rheMac2.chr2                                            999999999999999999999999999999999999-99999-99999999999999999999999
i rheMac2.chr2                   C 0 C 0
s panTro2.chrY                      518494 64 +  23952694 ACATGACCTAGTGAAAAACTATTTTTAATTTTCTCC-TATCT-CAAAACATTGAAAATTACAAATC
q panTro2.chrY                                            000000000000000000000000000000000000-00000-00000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr3                    71056379 64 - 202140232 ATGTGCCCTAGTAGAAAACTATTTTTCATTTCCTCA-TATCT-CAAAAGATTGAAAATTACAaatc
q ponAbe2.chr3                                            999999999999999999999999999999996772-58787-73266292999999999999999
i ponAbe2.chr3                   C 0 C 0
e rn4.chr9                       107368151 113 - 113440463 I
e mm9.chr17                       50267202 245 +  95272651 I
e speTri1.scaffold_160574             9387  0 -    115260 I
e macEug1.Scaffold7817               25228 4878 -     41428 I
e monDom5.chr8                   276523208 4661 + 312544902 I
e eriEur1.scaffold_377961            41707 1282 +     88154 I
e otoGar1.scaffold_99909.1-31737     10907 1524 -     31737 I
e proCap1.scaffold_15753             27841 2540 -     39409 I
e myoLuc1.scaffold_7336              37698 5478 -    312611 I

a score=14085.000000
s hg19.chrY                         7665006 11 +  59373566 CTAGCACTT--------------TA
s oryCun2.chr14                     2492286 11 + 163896628 TTTGCACTT--------------TA
q oryCun2.chr14                                            999999999--------------99
i oryCun2.chr14                   I 8 I 721
s otoGar1.scaffold_99906.1-214988    103026 25 -    214988 TCGGCGCCTATAGCTCAACCGGCTA
q otoGar1.scaffold_99906.1-214988                          7256234354558366987443067
i otoGar1.scaffold_99906.1-214988 I 40550 C 0
s rheMac2.chr2                    158782531 11 + 189746636 CTAGCACTT--------------TG
q rheMac2.chr2                                             999999999--------------99
i rheMac2.chr2                    C 0 C 0
s panTro2.chrY                       518558 11 +  23952694 CTAGCACTT--------------TA
q panTro2.chrY                                             000000000--------------00
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71056443 11 - 202140232 ctagcactt--------------tg
q ponAbe2.chr3                                             999999999--------------99
i ponAbe2.chr3                    C 0 C 0
s xenTro2.scaffold_1099              272331 11 +    315732 CCAGCACTT--------------TG
i xenTro2.scaffold_1099           C 0 C 0
s danRer6.Zv8_NA1725                  17362 11 -     49906 CCAGCACTT--------------TG
i danRer6.Zv8_NA1725              N 0 C 0
e cavPor3.scaffold_0                8261612  3 -  88675666 I
e rn4.chr9                        107368151 113 - 113440463 I
e mm9.chr17                        50267202 245 +  95272651 I
e equCab2.chr16                    22231211  0 -  87365405 C
e bosTau4.chr1                    157006043  0 + 161106243 C
e loxAfr3.scaffold_36                536360  0 -  24123610 C
e canFam2.chr23                    26010116  0 -  55389570 C
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=4406.000000
s hg19.chrY                         7665017 46 +  59373566 GGAGG--------------CTGAAGCAGTAGCTTC----------------------------------------------------TCCTTTAAACATT-----TAAAA---TTTAgtc
s ponAbe2.chr3                     71056454 46 - 202140232 ggagg--------------ctgaagcgggagtctc----------------------------------------------------tactttaaaaatt-----taaaa---atgagcc
q ponAbe2.chr3                                             99999--------------9999999999999999----------------------------------------------------9999999999999-----99999---9999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       518569 46 +  23952694 GGAGG--------------CTGAAGCAGTAGCTTC----------------------------------------------------TCCTTTaaaaatt-----taaaa---tttagtc
q panTro2.chrY                                             00000--------------0000000000000000----------------------------------------------------0000000000000-----00000---0000000
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158782542 46 + 189746636 GGAGG--------------CTGAagcgggagtctc----------------------------------------------------tactttaaaaatt-----taaaa---attagcc
q rheMac2.chr2                                             99999--------------9999999999999999----------------------------------------------------9999999999999-----99999---9999999
i rheMac2.chr2                    C 0 C 0
s otoGar1.scaffold_99906.1-214988    103051 64 -    214988 GGGCGCCAGCCACGTACACCTAAGGTGGTAGGTTC------------GAATCC----CCAGCCCGGA--------------------CCCGCCAAACAAC--------------------
q otoGar1.scaffold_99906.1-214988                          66453773557655657674976766588787884------------652457----7988875883--------------------6776798857969--------------------
i otoGar1.scaffold_99906.1-214988 C 0 I 309
s loxAfr3.scaffold_36                536360 52 -  24123610 --AAA--------------CTCAAATCTTAAGTTT----------------------------------------------------TTTTCTTAAAATTTTTCTTAAAAAATTCTAGTC
q loxAfr3.scaffold_36                                      --999--------------9999999999999999----------------------------------------------------999999999999999999999999999999999
i loxAfr3.scaffold_36             C 0 I 493
s xenTro2.scaffold_1099              272342 99 +    315732 GGAGG--------------CTGAAGCGGGTGGATCACCTGAGGTCAGGAGTTCGCGACCAGCCTGGGCCACATGGTGAAACCCTGTCTCTTCTAAAAATA-----CAAAAA--ATTAGCT
i xenTro2.scaffold_1099           C 0 C 0
s danRer6.Zv8_NA1725                  17373 96 -     49906 GGAGG--------------CTGAGGCAGGCGGATC--ACGAGGTCAGGAGTTCAACACCAGCCTGGTCAACATGGTGAAACCCCGTCTCTACTAAAAACA-----CAAAA---ATTAGCA
i danRer6.Zv8_NA1725              C 0 C 0
e cavPor3.scaffold_0                8261612  3 -  88675666 I
e rn4.chr9                        107368151 113 - 113440463 I
e mm9.chr17                        50267202 245 +  95272651 I
e oryCun2.chr14                     2492297 721 + 163896628 I
e equCab2.chr16                    22231211  0 -  87365405 C
e bosTau4.chr1                    157006043  0 + 161106243 C
e canFam2.chr23                    26010116  0 -  55389570 C
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=35891.000000
s hg19.chrY                         7665063 48 +  59373566 agatacggacgtgtgtgcctgt-atcccagctgcttgggaggcttaggt
s rheMac2.chr2                    158782588 48 + 189746636 aggaatagcagtgtgtgccttt-atcccagctacctgggaggctgaggt
q rheMac2.chr2                                             9999999999999999999999-99999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s panTro2.chrY                       518615 48 +  23952694 agatacggacgtgtgtgcctgt-atcccagctgcttgggaggcttaggt
q panTro2.chrY                                             0000000000000000000000-00000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71056500 47 - 202140232 aggaatagcagtgtgtgccttt-atcccagctactt-ggagactgaggt
q ponAbe2.chr3                                             9999999999999999999999-9999999999999-999999999999
i ponAbe2.chr3                    C 0 C 0
s xenTro2.scaffold_1099              272441 49 +    315732 GGGCGTGGTGGCAGGCGCCTGTAATCTCAGCTACTCGGGAGGGTGAGGC
i xenTro2.scaffold_1099           C 0 C 0
s danRer6.Zv8_NA1725                  17469 49 -     49906 GGGCCTGGTGGCTCACGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGC
i danRer6.Zv8_NA1725              C 0 C 0
e cavPor3.scaffold_0                8261612  3 -  88675666 I
e rn4.chr9                        107368151 113 - 113440463 I
e mm9.chr17                        50267202 245 +  95272651 I
e oryCun2.chr14                     2492297 721 + 163896628 I
e equCab2.chr16                    22231211  0 -  87365405 C
e bosTau4.chr1                    157006043  0 + 161106243 C
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e canFam2.chr23                    26010116  0 -  55389570 C
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103115 309 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=25718.000000
s hg19.chrY                         7665111 34 +  59373566 gggggcattgcttaagctcaagggttcaaggcta
s ponAbe2.chr3                     71056547 33 - 202140232 -ggggcattgcttaagctcaagagttcaaggcta
q ponAbe2.chr3                                             -999999999999999999996999999999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       518663 34 +  23952694 gggggcattgctgaagctcaagggttcaaggcta
q panTro2.chrY                                             0000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158782636 33 + 189746636 -tgggcattgcttaagctcaggagttcaaggcta
q rheMac2.chr2                                             -999999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s dipOrd1.scaffold_8112                1277 23 -     49748 ----------ctgaggatcgtg-gttcaaagcca
q dipOrd1.scaffold_8112                                    ----------999999999999-99999999999
i dipOrd1.scaffold_8112           N 0 I 3553
s xenTro2.scaffold_1099              272490 34 +    315732 AGGAGAATCGGTTGAACCCAGGAGGTGGAGGTTG
i xenTro2.scaffold_1099           C 0 C 0
s danRer6.Zv8_NA1725                  17518 34 -     49906 AGGAGAATCGTTTGATCCCGGGAGGTGGAGGTTG
i danRer6.Zv8_NA1725              C 0 C 0
e cavPor3.scaffold_0                8261612  3 -  88675666 I
e rn4.chr9                        107368151 113 - 113440463 I
e mm9.chr17                        50267202 245 +  95272651 I
e oryCun2.chr14                     2492297 721 + 163896628 I
e equCab2.chr16                    22231211  0 -  87365405 C
e bosTau4.chr1                    157006043  0 + 161106243 C
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e canFam2.chr23                    26010116  0 -  55389570 C
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103115 309 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=62053.000000
s hg19.chrY                         7665145 80 +  59373566 cagtgagctgtgattgtgccact--gcact-cagtctgggtgacagagcgacaccct-gtttctaaaataataat------aagtaaata
s rheMac2.chr2                    158782669 84 + 189746636 cactgagctg----agtaccagtaggcact-cagcctaggtgacagagcgagaccct-gtttctaaaataataataataataaataaata
q rheMac2.chr2                                             9999999999----9999999999999999-99999999999999999999999999-99999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s panTro2.chrY                       518697 80 +  23952694 cagtgagctgtgatcgtgccact--gcact-cagtctgggtgacagagcgacaccct-gtttctaaaaTAATAAT------AAGTAAATA
q panTro2.chrY                                             00000000000000000000000--00000-00000000000000000000000000-00000000000000000------000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71056580 86 - 202140232 cagtgagctgtgatcgtgccact--gcact-cagcctgggtgacagagtgagaccct-gtttctaaaataataataataaaaagtaaata
q ponAbe2.chr3                                             99999999999999999999999--99999-99999999999999999999999999-99999999999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s xenTro2.scaffold_1099              272524 81 +    315732 CAGTGAGCCAGAATCGCACCACT--GCACTCCAGCCTGGGTGACAGAGTGAGACGCC-ATCTCAGAGAGAAAAAA------AAGAAATTA
i xenTro2.scaffold_1099           C 0 n 0
s danRer6.Zv8_NA1725                  17552 82 -     49906 CAGTGAGCCAAGATCATGCCATT--GCACTCCAGCCTGGGCTACAGGGCGAGACTCCAGTCTCaaataaataaat------acataaata
i danRer6.Zv8_NA1725              C 0 C 0
e cavPor3.scaffold_0                8261612  3 -  88675666 I
e rn4.chr9                        107368151 113 - 113440463 I
e mm9.chr17                        50267202 245 +  95272651 I
e oryCun2.chr14                     2492297 721 + 163896628 I
e equCab2.chr16                    22231211  0 -  87365405 C
e bosTau4.chr1                    157006043  0 + 161106243 C
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e canFam2.chr23                    26010116  0 -  55389570 C
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103115 309 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=-11853.000000
s hg19.chrY                         7665225 21 +  59373566 aataaaTGTTTAA------AATGAAAC
s rheMac2.chr2                    158782753 21 + 189746636 aaTGAAAATTAAA------AATAAAAC
q rheMac2.chr2                                             9999999999999------99999999
i rheMac2.chr2                    C 0 C 0
s panTro2.chrY                       518777 21 +  23952694 AATAAATGTTTAA------AATGAAAC
q panTro2.chrY                                             0000000000000------00000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71056666 20 - 202140232 aaTGAAAATTAAA------AATAAAA-
q ponAbe2.chr3                                             9999999999999------9999999-
i ponAbe2.chr3                    C 0 C 0
s xenTro2.scaffold_1099              297055 18 -    315732 aaaaaa---agaa------aaTGCAGC
i xenTro2.scaffold_1099           I 3628 I 315
s mm9.chr17                        50267447 15 +  95272651 ------CCATTAA------CATCAAAT
i mm9.chr17                       I 245 C 0
s cavPor3.scaffold_0                8261615 10 -  88675666 -----------AA------AACCACAC
q cavPor3.scaffold_0                                       -----------25------99999999
i cavPor3.scaffold_0              I 3 C 0
s canFam2.chr23                    26010116  9 -  55389570 ------------A------AATCAAAC
q canFam2.chr23                                            ------------9------99999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22231211  4 -  87365405 -----------------------AAAC
q equCab2.chr16                                            -----------------------9999
i equCab2.chr16                   C 0 C 0
s bosTau4.chr1                    157006043  4 + 161106243 -----------------------AAAC
q bosTau4.chr1                                             -----------------------9999
i bosTau4.chr1                    C 0 C 0
s danRer6.Zv8_NA1725                  17634 27 -     49906 aataaaATTCCCACTAGTCAGTGGAAC
i danRer6.Zv8_NA1725              C 0 C 0
e rn4.chr9                        107368151 113 - 113440463 I
e oryCun2.chr14                     2492297 721 + 163896628 I
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103115 309 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=31565.000000
s hg19.chrY                         7665246 33 +  59373566 -----TCAACTCTACattaaaaattttt------aatttttctt------
s bosTau4.chr1                    157006047 25 + 161106243 -----TCAAATCTACACTCAAAAT--------------TTTCTT------
q bosTau4.chr1                                             -----9999999999999999999--------------999999------
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22231215 25 -  87365405 -----TCAAATCGACACTCAAAAT--------------TTTCTT------
q equCab2.chr16                                            -----9999999999999999999--------------999999------
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26010125 37 -  55389570 -----TTAAATCTACACTCAAAATTCTCCT--AAAATGTTTCTT------
q canFam2.chr23                                            -----9999999999999999999999999--999999999999------
i canFam2.chr23                   C 0 C 0
s ponAbe2.chr3                     71056686 36 - 202140232 ------CAACTCTACATTCAAAATTTTCTT--AAAATTTTTCTT------
q ponAbe2.chr3                                             ------999999999999999999999999--999999999999------
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       518798 33 +  23952694 -----TCAACTCTACattaaaaattttt------aatttttctt------
q panTro2.chrY                                             -----00000000000000000000000------0000000000------
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158782774 37 + 189746636 -----TCAACTCTACATTCAGAATTTTCTT--AAAATTTTCCTT------
q rheMac2.chr2                                             -----9999999999999999999999999--999999999999------
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8261625 37 -  88675666 -----TGAATTCTATACTTGAAATTTTCTT--TCAATTTTTCTC------
q cavPor3.scaffold_0                                       -----9999999999999999999998767--655599989999------
i cavPor3.scaffold_0              C 0 C 0
s mm9.chr17                        50267462 39 +  95272651 -----TCACCTCTATACTTGAAATTTACTCGATTTATTTTTCTT------
i mm9.chr17                       C 0 C 0
s danRer6.Zv8_NA1725                  17661 46 -     49906 TGTTCTCAATCTTAAAGCCACCACCCCCTT----GTTCTTGCTTTGTTTC
i danRer6.Zv8_NA1725              C 0 C 0
e rn4.chr9                        107368151 113 - 113440463 I
e oryCun2.chr14                     2492297 721 + 163896628 I
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103115 309 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=58648.000000
s hg19.chrY                         7665279 33 +  59373566 aaaaattCTAGTCCATGTGCAAAACTCACTGGC-
s ponAbe2.chr3                     71056722 33 - 202140232 AAAAATTCTAGTCCATGTGCAGAATTCACTTGC-
q ponAbe2.chr3                                             999999999999999999999999999999999-
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       518831 33 +  23952694 aaaaattCTAGTCCATGTGCAAAACTCACTGGC-
q panTro2.chrY                                             000000000000000000000000000000000-
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158782811 33 + 189746636 AAAAATTCTAGTCCATGTGCAGAATTCACTTGC-
q rheMac2.chr2                                             999999999999999999999999999999999-
i rheMac2.chr2                    C 0 C 0
s mm9.chr17                        50267501 32 +  95272651 GCAAATTGCAGT-TAGACTCAGAGCTTACATGT-
i mm9.chr17                       C 0 C 0
s cavPor3.scaffold_0                8261662 33 -  88675666 AACAATTCTAATCTATGCTCAGAACTCACTTGT-
q cavPor3.scaffold_0                                       999999999999999999999999999999999-
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2493018 33 + 163896628 aaaaaaTCTAGTCTATGCTGAGAATTCACTTGC-
q oryCun2.chr14                                            999999999999999999999999999999999-
i oryCun2.chr14                   I 721 C 0
s otoGar1.scaffold_99906.1-214988    103424 14 -    214988 -------------------caaatctgcctgga-
q otoGar1.scaffold_99906.1-214988                          -------------------56845545655774-
i otoGar1.scaffold_99906.1-214988 I 309 C 0
s bosTau4.chr1                    157006072 31 + 161106243 AAAAATTCTAGTT--TTACTAGAATACACTTGC-
q bosTau4.chr1                                             9999999999999--999999999999999999-
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22231240 33 -  87365405 AAAAATTCTAGTCTATGATCAGAATTCACTTGC-
q equCab2.chr16                                            999999999999999999999999999999999-
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26010162 33 -  55389570 GAAAATACTAGTCCATGCTCAAAATTCCCTTTC-
q canFam2.chr23                                            999999999999999999999999999999999-
i canFam2.chr23                   C 0 C 0
s danRer6.Zv8_NA1725                  17707 33 -     49906 -ACAATCCTAAATCAACAAATAAATCTTTTTGTC
i danRer6.Zv8_NA1725              C 0 N 0
e rn4.chr9                        107368151 113 - 113440463 I
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=6904.000000
s hg19.chrY                         7665312 22 +  59373566 TTT---------------------AAATAAG---CTGTCACTTATA
s ponAbe2.chr3                     71056755 21 - 202140232 -TT---------------------AAATAAG---CTATCACTTATA
q ponAbe2.chr3                                             -99---------------------9999999---999999999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       518864 22 +  23952694 TTT---------------------AAATAAG---CTGTCACTTATA
q panTro2.chrY                                             000---------------------0000000---000000000000
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158782844 21 + 189746636 -TT---------------------AAATAAG---CTATCACTTATA
q rheMac2.chr2                                             -99---------------------9999999---999999999999
i rheMac2.chr2                    C 0 C 0
s mm9.chr17                        50267533 20 +  95272651 -TC---------------------CTGTCA----TAGTCGCATACA
i mm9.chr17                       C 0 I 5
s cavPor3.scaffold_0                8261695 19 -  88675666 -AT---------------------GTGTAA----TAATGGAAGCC-
q cavPor3.scaffold_0                                       -99---------------------999999----99999999999-
i cavPor3.scaffold_0              C 0 I 3
s oryCun2.chr14                     2493051 20 + 163896628 -TT---------------------AAATAG----CTATCACTTTTA
q oryCun2.chr14                                            -99---------------------999999----999999999999
i oryCun2.chr14                   C 0 I 10
s otoGar1.scaffold_99906.1-214988    103438 46 -    214988 cttcccatcttccagaattatgagaaataaatctctgttgtttcta
q otoGar1.scaffold_99906.1-214988                          5652852656599579557445577969786549799767586799
i otoGar1.scaffold_99906.1-214988 C 0 I 3726
s bosTau4.chr1                    157006103 20 + 161106243 -TT---------------------AACTAG----CTATCACTCATA
q bosTau4.chr1                                             -99---------------------999999----999999999999
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22231273 20 -  87365405 -CT---------------------GAATAG----CTATCGCTTACA
q equCab2.chr16                                            -99---------------------999999----999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26010195 20 -  55389570 -CT---------------------GAGTAG----CTGTCCCATATC
q canFam2.chr23                                            -99---------------------999999----999999999999
i canFam2.chr23                   C 0 C 0
e rn4.chr9                        107368151 113 - 113440463 I
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=134527.000000
s hg19.chrY                         7665334 121 +  59373566 ----------TCTAGTCAATATC------ATTATGCTATAGAAAAAAAGTTGAAAA-AGGAACATAT-------------------------------------------------AGAATTATTATCCATTGTTGTTTATTTAAATGCTAGAAAAAAAA----CTCTAAGATTTAT--GTACAATAAGTTTT
s canFam2.chr23                    26010215 136 -  55389570 TCTATAGTGACTTAGTCAATATC------ATGATGGCATAA-AAAAAGGATGAAGA-GTGAGTATATTACTCT-------------------------------------------AGAAATGTTGGCCAT---TGTTTGTTTAAATGCTAG-AGAAAAGTAAGCTCTGAGATTTAT--GGATAATAGGTTTT
q canFam2.chr23                                             99999999999999999999999------999999999999-99999999999999-9999999999999999-------------------------------------------999999999999999---999999999999999999-999999999999999999999999--99999999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22231293 139 -  87365405 TCTATAATGACCTAGTCAATATC------ATCATGATATAG-AAAAAAGAAGAAAA-ATGAACATATTATTAT-------------------------------------------AGAAAGGTGGGCCATTACTATTTGTTTAAATAACAG-AAAAAAGGAAACTCTAAGACTTAT--ACACAATAGGCTTT
q equCab2.chr16                                             99999999999999999999999------999999999999-99999999999999-9999999999999999-------------------------------------------999999999999999999999999999999999999-999999999999999999999999--99999999999999
i equCab2.chr16                   C 0 C 0
s bosTau4.chr1                    157006123 132 + 161106243 TCTTTAAGGACCTAGTCAGTGTC------ATCATGATATAG-AAAAA-GATCAAAG-ATGAACATGTTATTAT-------------------------------------------AG-AATCTTGACCATGACTATTTGTTTAAATGTTAG-A-AAAAGTAAACTCTCATATTTAT--ATACATTATG----
q bosTau4.chr1                                              99999999999999999999999------999999999999-99999-99999999-9999999999999999-------------------------------------------99-999999999999999999999999999999999-9-9999999999999999999999--9999999999----
i bosTau4.chr1                    C 0 C 0
s oryCun2.chr14                     2493081 109 + 163896628 ----------TTTAGTCAATATC--------------------ACCATGATGAAAA-ATTAACACATTAT----------------------------------------------AGAA---TTGGTCATTATGTTGCATTTCAATGCTAG-GAAAAAGTAAACTCTAAGattttttaataaaataaat---
q oryCun2.chr14                                             ----------9999999999999--------------------9999999999999-9999999999999----------------------------------------------9999---99999999999999999999999999999-9999999999999999999999999999999999999---
i oryCun2.chr14                   I 10 I 713
s cavPor3.scaffold_0                8261717 110 -  88675666 ----------GCTAACACATATA----------------GG-GAAAAAGATGAAAA-ATGAACTCATTAC----------------------------------------------AAGATTGTTAGTGATTGTTATTTGTTGAAATGCTAG-AAAAAAT------CTAAAATTTAT--ATATACCAGGTTTT
q cavPor3.scaffold_0                                        ----------9999999999999----------------99-99999999999999-9999999999999----------------------------------------------999999999999999999999999999999999999-9999999------99999999999--99999999999999
i cavPor3.scaffold_0              I 3 C 0
s mm9.chr17                        50267558 128 +  95272651 ----------ACTGATCTATACCTGCTACCTCAGG---TGG-GAATAAGGTGACAATGTGCCCCTGTTAC----------------------------------------------GGTACGGCTGGCT-TTATCATTTGTTGCTGTACCAG-AGAAAATGATCCCTCGGGAGTTAC--ACGCACCGGGTTT-
i mm9.chr17                       I 5 C 0
s rheMac2.chr2                    158782865 122 + 189746636 ----------TCTAGTCAATATC------ATCATGTTATAG-AAAAAAGTTGAAAA-AGGAACATATTAC----------------------------------------------AGAATTATTGGCCATTGTTGTTTATTTAAATGCTAG-AAAAAGG----CTCTAAGATTTAT--ATACAATAAGTTTT
q rheMac2.chr2                                              ----------9999999999999------999999999999-99999999999999-9999999999999----------------------------------------------999999999999999999999999999999999999-9999999----9999999999999--99999999999999
i rheMac2.chr2                    C 0 C 0
s panTro2.chrY                       518886 121 +  23952694 ----------TCTAGTCAATATC------ATCATGCTATAGAAAAAAAGTTGAAAA-AGGAACATAT-------------------------------------------------AGAGTTATTATGCATTGTTGTTTATTTAAATGCTAGAAAAAAAA----CTCTAAGATTTAT--GTACAATAACTTTT
q panTro2.chrY                                              ----------0000000000000------000000000000000000000000000-0000000000-------------------------------------------------00000000000000000000000000000000000000000000----0000000000000--00000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71056776 168 - 202140232 ----------TCTAGTCAATATC------ATCATGTTATAG-AAAAAAGTTGAAAA-AGGAACATATTATAGAATTACTAAATTATGTGCCAAAAAAATGTGCCAAAAAAAAAAAAAGAATTACTGGCCATTGTTATTTATTTAAATGCTAG-AAAAAAA----CTCTAAGATTTAT--ATACAACAAGTTTT
q ponAbe2.chr3                                              ----------9999999999999------999999999999-99999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999----9999999999999--99999999999999
i ponAbe2.chr3                    C 0 C 0
e rn4.chr9                        107368151 113 - 113440463 I
e loxAfr3.scaffold_36                536412 493 -  24123610 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=191341.000000
s hg19.chrY                         7665455  94 +  59373566 GAGAGAA---GTTTATCATT-T---TTGGTTCCTGTAACTTTTAGTTATTTGACATTTGTAAACT-AAACTAGAAAACTAAGAAAATTAAATGT-------------------GATAACTG
s ponAbe2.chr3                     71056944 113 - 202140232 GAGAGAA---GTTTATCATTTT---TTGGCTCCTGTAACTTCTAGTTATTTGACATTTGCAAACT-AAATTGGAAAACTAAGAAAATTAAATGTGATTTTTTTTTCTTTTC-AGATAACTG
q ponAbe2.chr3                                              9999999---999999999999---9999499999999999999999999999999999999999-999909999999999999999999999999999999999999999-999999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519007  95 +  23952694 GAGAGAA---GTTTATCATTCT---TTGGTTCCTATAACTTTTAGTTATTTGACATTTGTAAACT-AAACTAGAAAACTAAGAAAATTAAATGT-------------------GGTAACTG
q panTro2.chrY                                              0000000---000000000000---0000000000000000000000000000000000000000-0000000000000000000000000000-------------------00000000
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158782987 113 + 189746636 GAGAGAA---GTTTATCATTTT---TTGGTTCCTATAACTTTTAGTTATTTGACATTTGCAAACT-AAGCTGGAAAACTGAGAAAATTAAATGTGATTTTTTTTTCTTCTC-AGATAACTG
q rheMac2.chr2                                              9999999---999999999999---9999999999999999999999999999999999999999-999999999999999999999999999999999999999999999-999999999
i rheMac2.chr2                    C 0 C 0
s mm9.chr17                        50267686 104 +  95272651 -GGACCA---GGTTACTGG--T---TTGGTTCCTATAACTTTTAGTTATGTGGCTGCTACAGACT-AAAAAGAGAAATTAGGAAA---AAATTT----TTTTTTTCTTCTCAAAATGAATG
i mm9.chr17                       C 0 C 0
s cavPor3.scaffold_0                8261827  90 -  88675666 AGAAGTG---TTTTATCAT--T---TTTGCTTCTGTAACTTTTAGACATTTG-------TAGACT-AAAAAGGAAAATT----------AAATT----CAGTTTTCTTCTC-AAGTAACTG
q cavPor3.scaffold_0                                        9999999---999999999--9---999999999999999999999999999-------999999-9999999999999----------99999----9999999999999-999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2493903 110 + 163896628 --GAGCGAGCTTTCATCTT--T---TTTGTTGCTGTAACTTTGAGCTGTTTGACATTTGCAGACTAAAAAAAGAAAACTAGGAAAATTAAATGT----GAATTTTTTTTTTCAAATAGCAG
q oryCun2.chr14                                             --99999999999999999--9---999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999
i oryCun2.chr14                   I 713 C 0
s bosTau4.chr1                    157006255 100 + 161106243 -----------TTTATC--TTT---TTTGTTTCTATAACTTGGAGCTGTTTGACATTTGCAGACT-AAAACAAAAAACTAAGAAAATTAAATGTG---ATATTTTCTTCTC-AGATAACCA
q bosTau4.chr1                                              -----------999999--999---9999999999999999999999999999999999999999-99999999999999999999999999999---9999999999999-999999999
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22231432 108 -  87365405 TAAAGAG---CTTTATCGTTTT---TTTGGTTCTATAACTTCCA----TTTCACATTTGCAGACT-AAAATAGAAAACTAAGAAAATTAAACGTG-CCTTTTTTTCTTCTC-AGATAACTA
q equCab2.chr16                                             9999999---999999999999---9999999999999999999----99999999999999999-99999999999999999999999999999-999999999999999-999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26010351 102 -  55389570 GAGAGAG---GTTTATT------------ATTCTGTAACTTTTAGTTGTTTGACATTTGCAGACT-AAAATAGAAAACTCAGAAAATTCAATGTG--ATCTTTTTCTTCTC-AGATAACCA
q canFam2.chr23                                             9999999---9999999------------999999999999999999999999999999999999-99999999999999999999999999999--99999999999999-999999999
i canFam2.chr23                   C 0 C 0
s loxAfr3.scaffold_36                536905 113 -  24123610 GTAAGAG---GTTTGCCATTTTTTGTTGGTTTCTATAACTTT-AGCCATTTGGCACTTACAGACT-AAAATAGAAAACTATAAAAATGAAATGC--AATTTTTTTCTCCTC-AGATAACTG
q loxAfr3.scaffold_36                                       9999999---99999999999999999999999999999999-9999999999999999999999-9999999999999999999999999999--999999999999999-999999999
i loxAfr3.scaffold_36             I 493 C 0
e rn4.chr9                        107368151 113 - 113440463 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=194027.000000
s hg19.chrY                         7665549 52 +  59373566 AAGCCAAGGCATTTTTAAGAACATGAATTTTCCATA----TTATTGACTTATTTCA
s ponAbe2.chr3                     71057057 52 - 202140232 AAGCCAAGACATTTTTGAGAACATGAATTTTCCATA----TGATTGACTTATTTCA
q ponAbe2.chr3                                             999999999999999999999999999999999999----9999999999999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519102 52 +  23952694 AAGCCAAGGCATTTTTAAGAACATGAATTTTCCATA----TTATTTACTTATTTCA
q panTro2.chrY                                             000000000000000000000000000000000000----0000000000000000
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158783100 52 + 189746636 AAGCCAAGACATTTTTGAGAACATGAATTTTCCATA----TGATTGACTTATTTCA
q rheMac2.chr2                                             999999999999999999999999999999999999----9999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8261917 52 -  88675666 AAGCCAAGATGTTTTTGAGACCATCAATTTTCCAAA----TGATTGACTTATTTCA
q cavPor3.scaffold_0                                       999999999999999999999999999999999999----9999999999999999
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107368264 52 - 113440463 AAGTCAAGAGGCTTTTGAGAACATCAATTTCCCAAA----TGACTGACTTAGTTCC
q rn4.chr9                                                 999999999999999999999999999999999999----9999999999999999
i rn4.chr9                        I 113 C 0
s mm9.chr17                        50267790 56 +  95272651 AAGTCAAGAGGCTTTTGAGAACATCAGTTTCCCAAATGACTGACTGACTTAGTTCT
i mm9.chr17                       C 0 C 0
s oryCun2.chr14                     2494013 49 + 163896628 AAGCCAA---GTTTTTGAAAGCCTGACTTTTCCAAA----TGATTGACGGACTTCA
q oryCun2.chr14                                            9999999---99999999999999999999999999----9999999999999999
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157006355 47 + 161106243 AAG-----ATGCTTTTGAAAGCATGAATTTTTCAGG----TGATTGGCTGATTTCA
q bosTau4.chr1                                             999-----9999999999999999999999999999----9999999999999999
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22231540 52 -  87365405 AAGCCAATATGTTTTTGAGAGCATGAATTTTCCAAA----GGATTGGCTCACTTCA
q equCab2.chr16                                            999999999999999999999999999999999999----9999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26010453 52 -  55389570 CAGCCAAGATATTTTTAAGAGCATGAACTTTCCAAA----TGATTGGCTCATTTCA
q canFam2.chr23                                            999999999999999999999999999999999999----9999999999999999
i canFam2.chr23                   C 0 C 0
s loxAfr3.scaffold_36                537018 52 -  24123610 AAGCCAAGATGCTTTCGCGAGCATGAATTTTCCATA----TGATTGGCTTCTTTCA
q loxAfr3.scaffold_36                                      999999999999999999999999999999999999----9999999999999999
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             41707 1282 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=162255.000000
s hg19.chrY                         7665601 129 +  59373566 ACACTTTGAGTGGACATAGC-TTT------ATTGCAAATTTTTATGAA-TTTTAGAGTTGATTCAGAAATTACAATGTAAGTAT-----------------TATGTGAAATCAGATAATAAGGTAATA---TGTAA-----AATATGCC------------------------------------------------------------------------------------TGGTGGAAGGAGT
s ponAbe2.chr3                     71057109 129 - 202140232 ATGCTTTGAGTGGGCATAGC-TTT------ATTCTAAATTTTTATGAA-TTTTAGAGTTGATTCAGAAATTACAATGTGAATAT-----------------TATATAAAATCAGATAATAATGTAGTA---TGTAA-----AATATGTA------------------------------------------------------------------------------------TGATGGAAGGAGT
q ponAbe2.chr3                                              99999999999999999999-999------999999999999999999-99999999999999999999999999999999999-----------------999999999999999999999999999---99999-----99999999------------------------------------------------------------------------------------9999999999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519154 129 +  23952694 ACACTTTGAGTGGACATAGC-TTT------ATTGCAAATTTTTATGAA-TTTTAGAGTTGATTCAGAAATCACAATGTAAGTAT-----------------TATGTGAAATCAGATAATAAGGTAATA---TGTAA-----AATATGCC------------------------------------------------------------------------------------TGGTGGAAGGAGT
q panTro2.chrY                                              00000000000000000000-000------000000000000000000-00000000000000000000000000000000000-----------------000000000000000000000000000---00000-----00000000------------------------------------------------------------------------------------0000000000000
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158783152 129 + 189746636 ATGCTTTGAGTGGGCATAGC-TTT------ATTCTAAATTTTTATGAA-TTTTAGAGTTGATTCAGAACTTACAATGTGAATAT-----------------TATATAAAATCAGATAATAATGTAGTA---TGTAA-----AATACGCA------------------------------------------------------------------------------------CGGTGGAAGGAGT
q rheMac2.chr2                                              99999999999999999999-999------999999999999999999-99999999999999999999999999999999999-----------------999999999999999999999999999---99999-----99999999------------------------------------------------------------------------------------9999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8261969 110 -  88675666 ACACTTTGAGTGAATAC-ACATTT------GTTCTGGATTTTTATGAG-TTTTAG-----------AAATTAT-ACACGAATAT-----------------TATGCAAAGTCAGACAGT------GTAGTACATAA-----AATAAACA----------------------------------------------------------------------------------------TGACAGAAC
q cavPor3.scaffold_0                                        99999999999999999-999999------999999999999999999-999999-----------9999999-9999999999-----------------999999999999999999------99999999999-----99999999----------------------------------------------------------------------------------------999999999
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107368316 120 - 113440463 ACATTTTGTGGAGACAT-GT-TTT------GTTCTGGATTCTGGTAAG-TTTCAA-GTGGGCCCC-AAGTGAA-CTGGAAACAT-----------------GATGTAAGGTCAGATCAT------TTAG---ACAGAACAAAATACAAT----------------------------------------------------------------------------------------GAAAGGTGT
q rn4.chr9                                                  99999999999999999-99-999------999999999999999999-999999-999999999-9999999-9999999999-----------------999999999999999999------9999---99999999999999999----------------------------------------------------------------------------------------999999999
i rn4.chr9                        C 0 C 0
s mm9.chr17                        50267846 116 +  95272651 CCATTTTGTAGTGACAT-AT-TTT------GTTCTGGATTCTGGTGAGTTTTCAA-GCAGGTCCC-AAGTGAC-CTGAAAACAT-----------------GATGTAAGATCAGATCAT------TTAG---ACAG-----AATACAAC----------------------------------------------------------------------------------------GGAAGGAGA
i mm9.chr17                       C 0 C 0
s oryCun2.chr14                     2494062 119 + 163896628 ACACTGTGTGGACACA--GT-TCT------GTTCTGAATATCTATTAG-CTGCAGAGCTGATCCAGAAACGAC-ATGTGACTGT-----------------TATGTGAAATCAAATAGT------GCCACCTGTGC-----AATACGCA----------------------------------------------------------------------------------------CGGTGGAGC
q oryCun2.chr14                                             9999999999999999--99-999------999999999999999999-999999999999999999999999-9999999999-----------------999999999999999999------99999999999-----99999999----------------------------------------------------------------------------------------999999999
i oryCun2.chr14                   C 0 C 0
s canFam2.chr23                    26010505 124 -  55389570 ACACTGTATGTGGACATAGC-CTT------GGTCTGAATGTTTGTGAG-TTTTCAAGATGATCCAGATATATT-ACATGAGTAT-----------------TATATAAAATCAGATAAT------GTAGTTTGTAA-----AATATAC-------------------------------------------------------------------------------------TTGTAGAAGGAGT
q canFam2.chr23                                             99999999999999999999-999------999999999999999999-999999999999999999999999-9999999999-----------------999999999999999999------99999999999-----9999999-------------------------------------------------------------------------------------9999999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22231592 125 -  87365405 ACACTGCATGTGGACATAGC-TTT------GGTCTGAATTTTTATGAA-TTATAGAGATGATCCAGAAATCAC-ACATGAATAT-----------------TACATAAAATCAGATAAT------GCAGTACGTAA-----AGTTTACA------------------------------------------------------------------------------------CTGAAGAAGGAGT
q equCab2.chr16                                             99999999999999999999-999------999999999999999999-999999999999999999999999-9999999999-----------------999999999999999999------99999999999-----99999999------------------------------------------------------------------------------------9999999999999
i equCab2.chr16                   C 0 C 0
s bosTau4.chr1                    157006402 197 + 161106243 ACAATGCATGTGGACATAGC-TTG------GGT-TGAATTTTTCTGAA-C------AGTGATCCAGA---CCC-ACATGAATAT-----------------TAGACACAATCAGGTA--------GTAGTATGCAA-----AATGTAcactgggattctaggtggctcagtggtgaagaatccacctgccaatgcaggagacccaggttccatccctgggtcaggaagaccccctggaggaggaaa
q bosTau4.chr1                                              99999999999999999999-999------999-99999999999999-9------99999999999---999-9999999999-----------------9999999999999999--------99999999999-----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i bosTau4.chr1                    C 0 I 140
s eriEur1.scaffold_377961             42989 137 +     88154 ---ATGCTTTGAGACAGAAT-TTTCTAAAAGAT-TGA---TTTGTATG-TGTTAGAGGTGATCCAGAAAT-----TGTGAATATTATAGAAATTGTGAATATATAGAAAACCAGATAAC------ACATTATGCAA-----AATATACA------------------------------------------------------------------------------------TTGCAGAAGGAGC
q eriEur1.scaffold_377961                                   ---23325522224212233-763135962422-333---36133212-111424241132345242734-----12114131532424374523225331215354762765634315------26364342238-----86325274------------------------------------------------------------------------------------4545335282444
i eriEur1.scaffold_377961         I 1282 I 2
s loxAfr3.scaffold_36                537070 122 -  24123610 ACACCCTGTGTAGACACAGC-GTT------GGTCTGAATTTTTATGAG-TTCTAGACTTGGTCTAGAAATTAC-ACATGAATAT-----------------TATATTAAATCGGATAAT------CTGGTATATAA-----ACTACACA---------------------------------------------------------------------------------------TAGAAGCAGT
q loxAfr3.scaffold_36                                       99999999999999999999-999------999999999999999999-999999999999999999999999-9999999999-----------------999999999999999999------99999999999-----99999999---------------------------------------------------------------------------------------9999999999
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=1014903.000000
s hg19.chrY                         7665730 384 +  59373566 AA---ATTGTGTGGATTATTCTGGCCCTGCAAAAT-----A-CA--GAAGTGTCTCAATTTCTCTTTT--TCCACTGTGATTTTTATCTGTTGTGT--TATTTTGATATTTGTACATTTATTGGGAGCTGGCA----GGGTGAGTTGCACATTGGTAGCA---TTTATATT---AACTAAATTTTGTTTTCATTTTAGAAACAAA----------TTTCTCCTC-TCTTCATTTTTTCTGCTGCCCAAGC-CCAGCAGGCTTATAAATAAATACACAGCCCACAGGGAAGACTTGAGGAGG----TTCAAGTAGACATTTCATTTGAATTTCCTGAGCCTGGTTTTATCTTAA-----CAGCCCT-ATACTCTTTGGACCACATCTGGGCAAGC----GAAGTGAAGTGGGAGATAAAATAATTGGATCAATGA---T
s ponAbe2.chr3                     71057238 385 - 202140232 AA---AGTGTGTGGATTATTCTGGCCCTGCAAAAC-----A-CA--GAAGTGTCTCAATTTCTCTTTT--TCCACTGTGATTTTTATCTATTGTGT--TATTTTGATATTTGCACATTTACTGGGAGCTGGCA----GGATGAGTTGCACATGGGTAGCA---TTTATATT---AACTAAATTTGGTTTTCATTTTAGAAACAAA----------TTCCTCCTC-TCTTCTTTTTTTCTGCTGCCAAAGC-CCAATAGGCTTATAAATAAATACACAGCCCACAGGAAAGACTTGAGGAGG----TTCAGGTAGACATTTCATTTGAATTTCCTGAGCCTGGTTTTATCTTAA-----CAGCCCTCATACTCTTTGGACCACATCTGGGCAAGC----AAAGTGAAGTGGGAAATAAAATAGTTGGATCAATGA---C
q ponAbe2.chr3                                              99---999999999999999999999999999999-----9-99--9999999999999999999999--99999999999999999999999999--99999999999999999999999999999999999----99999999999999999999999---99999999---9999999999999999999999999999999----------999999999-9999999999999999999999999-99999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999----999999999999999999999999999999999999---9
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519283 382 +  23952694 AA---ATTGTGTGGATTATTCTGGCCCTGCAAAAT-----A-CA--GAAGTGTCTCAATT--TCTTTT--TCCACTGTGATTTTTATCTGTTGTGT--TATTTTGATATTTGTACATTTATTGGGAGCTGGCA----GGGTGAGTTGCACATTGGTAGCA---TTTAAATT---AACTAAATTTCATTTTCATTTTAGAAACAAA----------TTTCTCCTC-TCTTCATTTTTTCTGCTGCCGAAGC-CCAGCAGGCTTATAAATAAATACACAGCCCACGGGGAAGACTTGAGGAGG----TTCAAGTAGACATTTCATTTGAATTTCCTGAGCCTGGTTTTATCTTAA-----CAGCCCT-ATACTCTTTGGACCACATCTGGGCAAGT----GAAGTGAAGTGGGAAATAAAATAATTGGATCAATGA---T
q panTro2.chrY                                              00---000000000000000000000000000000-----0-00--00000000000000--000000--00000000000000000000000000--00000000000000000000000000000000000----00000000000000000000000---00000000---0000000000000000000000000000000----------000000000-0000000000000000000000000-00000000000000000000000000000000000000000000000000----000000000000000000000000000000000000000000000000-----0000000-0000000000000000000000000000----000000000000000000000000000000000000---0
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158783281 385 + 189746636 AA---ACTGTGTGGATGATTCTGGCCCTGCAAAAC-----A-CA--GAAATGTCTCAATTTCTCTTTT--TCCACTGTGATTTTTATCTATTGTGC--TATTCTGACATTTGTACATTTACTGGGAGCTGGCA----GGATGAGTTGCACATGGGTAACA---TTTATATT---AACTAAATTTGGTTTTCATTTTAGAAACAAA----------TTCCTCCTC-TCTTCTTTTTTTCTGCTGCCAAAGC-CCAATAGGCTTATAAATAAATACACAGCCCACAGGAAAGACTTGAGGAGG----TTCAGGTAGACATTTCATTTGAATTTCCTAACCCTGGTTTTATCTCAA-----CAGCCCTCATACTCTTTGGACCACATCTGGGCAAGC----AAAGTGAAGTGGGAAATAAAATAGTTGTATCAATGA---C
q rheMac2.chr2                                              99---999999999999999999999999999999-----9-99--9999999999999999999999--99999999999999999999999999--99999999999999999999999999999999999----99999999999999999999999---99999999---9999999999999999999999999999999----------999999999-9999999999999999999999999-99999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999----999999999999999999999999999999999999---9
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8262079 349 -  88675666 AG---ACTCTGTGGATAATTCTAGCCCTCGGAA-------A-CA--GGATTCTCTAAATTTCTCTTTT--CT-GACACAACTTTTGTTTATTGTGT--TATTTTTTTGCTTGTATATTTATTGGGGGCTGGCA------------------------------TTTATATT---AATTAAATTTGGCTTTCATTTTAGGAACAAA----------TTCCTCTTT-----------TCCTTCTCCTAAGGC-CCAATAGGCTTATAAATAAATCCACATCCCAGAGAGGAGACTTGAGAAGA----TTTAGGCAGATATTTCAGCTGAATTTGCTGAGCCTGGTTTTATCTTAA-----CAACCTTTATTCTCTTGGGACCACATCTGGGCAAGC----AAAGTGAAGCGGGAAATAGAATAATTAGATCAACGA---A
q cavPor3.scaffold_0                                        99---9999999999999999999999999999-------9-99--9999999999999999999999--99-99999999999999999999999--99999999999999999999999999999999999------------------------------99999999---9999999999999999999999999999999----------999999999-----------999999999999999-99999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999----999999999999999999999999999999999999---9
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107368436 382 - 113440463 TA---ATTCTGTGGATAATTCAGGCCTGTAAAATG-----G-CC--ACACTGTCTG---CTCTCTTTT--TT--AGGAAGCTTTTATTTACAGTGT--TATTCTGGTGTTTGTACACTTCTT-GGGGCTGGCA----GAAGGAGCTGCCAGTGGG-AGGG---TGTCTATC---AATTGAACTTGGCTTTCTTTTTAAGAACAAG----------TCCCTCTTTCCCTTGTTCCTTCCTTCCCCTGAGGCACCATGAGGTTTATAAGTAAACCCAGAAGCTGGAAAAAGAACTAAGGACAA----TGGAAGTCCATGGGCCATCCGAGTCTCCCAAGCCTGGTTTTATCTGCG-----CATACTTCATCCTCTCTGAACCACATCTGGACAAGCTTGGAAAGTGGA-----GAACGAAGAAATCGGATGAATAACGTC
q rn4.chr9                                                  99---999999999999999999999999999999-----9-99--9999999999---999999999--99--9999999999999999999999--999999999999999999999999-9999999999----999999999999999999-9999---99999999---9999999999999999999999999999999----------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999999999999999-----999999999999999999999999999
i rn4.chr9                        C 0 C 0
s mm9.chr17                        50267962 376 +  95272651 TA---ATTCTGTAAATGATCCAGGCTTGTAAAATG-----G-CC--ACATTGTCTTCTCCTCTCTTTT--TC--ACGGAGCTTTTATTTACAGTAT--TATTCTGGTGTTTGTACACTTCTT-GGGGCTGGCA----GGAGGCGCTGCCAGGGGG-GGAGGTATGTCTAGC---AACTGGCTTTGGCTTTCTTTTTAAGAACAAA----------TCCCTCTTT--CTTGTGTCTTCCTTTCCCTGAGGC-CCATGAGGCTTATAAATAAACCCAGAACCCGGAGAAAAGACTGAGGAAAA----TGGAAGT-------CCATCCGAGTCCCCCAAGCCTGGTTTTATCTGAG-----CATCCTTCACGCTCTCTGGACCACATCTGGACAAGCTTGGAAAGTGGA----GGAATGGAGAAATCAGACGAATAA---T
i mm9.chr17                       C 0 C 0
s oryCun2.chr14                     2494181 327 + 163896628 AGTGCATCTGGTGAGCCCTCTGGGCCTACAGAACC-----T-CA--GCACGCTCTGAACTTCTCGTCC--CG--GCGTGATTCGTATCT-CTGCCG--GATTCTGCTATTTGGACTCC-----ATCAACGGCA----GGAGGAGCCGTGCAGGGG-AGCT---TTCCTGTT---AACTGCACTTGCTCTTCATCCAAGGAGCCAA----------TTCCTCCTC-TCCCCTCTTTCCCTTCCCCCGAGGC-CCGTCAGG--------------------------------CTGCGGAAGA------------------CCACCCA-----CCTGAACCAGGCTTTCCCGGGA-----GAGCCCTCACAGGCTGTGCACC-CATCTGAAGGTGC----AGGGTGAAGAGCGAGACGGGGCAACTGGATCAGTGA---C
q oryCun2.chr14                                             99999999999999999999999999999999999-----9-99--9999999999999999999999--99--999999999999999-999999--99999999999999999999-----9999999999----999999999999999999-9999---99999999---9999999999999999999999999999999----------999999999-9999999999999999999999999-99999999--------------------------------9999999999------------------9999999-----9999999999999999999999-----9999999999999999999999-9999999999999----999999999999999999999999999999999999---9
i oryCun2.chr14                   C 0 I 407
s bosTau4.chr1                    157006739 367 + 161106243 AA---ATCATGCGGAATCTTCTCACCCAGTGAAAC-----ACCA--AAACTGTCTCAA-TTCCCTTTT--CGCAATGTGATTTTTTTTTATTATGTG-CATTTTGATATTTGCAGGTTTATTGGAGGCTAGT------GGTGAGTTGCACATGGGGAGAT---TTAAGT-----AACCATATTTGGTTTTC----TAGAAACAAT----------CTCCTCC---------TTTCTCCTTCACCCAAGGC-CCATCATG-TTATAAATAAACCCACAGCCCAGAGGGAAGGCCTCAGGGAG----CCCAGGTGGGCATCATGTCAGAATGTGCTGAGCCCA-TTTTGTCTGAA-----AAGCCCTCTTAATGCCT-GACCACACCTGAGCAAGC----AAATCGAAGCAGGAAACAGAATATTCAGATCAGCGG---G
q bosTau4.chr1                                              99---999999999999999999999999999999-----9999--999999999999-999999999--999999999999999999999999999-9999999999999999999999999999999989------9999999999999999999999---999999-----99999999999999999----9999999999----------9999999---------9999999999999999999-99999999-99999999999999999999999999999999999999999----999999999999999999999999999999999999-99999999999-----99999999999999999-999999999999999999----999999999999999999999999999999999999---9
i bosTau4.chr1                    I 140 C 0
s equCab2.chr16                    22231717 386 -  87365405 AA---ATTAGGAGGATTGTTCTGGCCCTGCAAAAC-----ACCA--CAATTCTTGCAATTTCTCTTTT--TCCAATGTGATTTTTATCCACTGTGTGTTATTTTGATAGTTGTACATTTATTGGAGGCTAACA----AGACGAGTCGCACAGAGGGAGCT---TTTATATT---AACCAAATTTAGTTTTCATTTTAGGAACAAA----------TTCCTCCTC-TCCTT-TTTTTTCTCCTCCCAAGGC-CCACTGGGCTTATAAATAAACCCTCAGCCCAGAGGGAAGACTTCAGGAGG----CACAGGTGGACATTTCCTCTGAATTTGCTGAGCCCAGTTTGGTCTCAA-----CAGCGCTCATACTCTTT-GACCACATCTGGGCAAGC----AAAGTGAAACAGGAAATAGAATAATCGGATCGATGA---T
q equCab2.chr16                                             99---999999999999999999999999999999-----9999--9999999999999999999999--999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999---99999999---9999999999999999999999999999999----------999999999-99999-9999999999999999999-99999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999-----99999999999999999-999999999999999999----999999999999999999999999999999999999---9
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26010629 395 -  55389570 AA---ATTATGTGGATTCTTCTGGCCCTGCAAAAC-----ATCA--GAATTGTCTCAATTTCTCTTTT--TCCAGTGTGATTTTTATCTACTGTATGTTGTTTTGATATGTGTACTTTTATTGGAGGCTGGTG----GGATAAGCTGTACATAGGGAGCT---TTTTTTTTTTAAACCATATTTGGTTTTCATTTTAGGAACAAA----------TTCCTCCTC-TCCTCATTTTTTCTTCCCCCGAGGT-CCATTAGGTTTATAAATAAACTCAAAGCCCAGAGGGAAAACTTCAGGAGGCACACACAGGTGGACCTTTCATCTGAATTCGCTGAGCCCACTTCTGTCTGAA-----CAGCTCTCATCCTCTTCGGACCACATCTGGGCAAGC----AAAGTGAAGCAGTAAATATAAGAAGTGGATCAGTGA---T
q canFam2.chr23                                             99---999999999999999999999999999999-----9999--9999999999999999999999--999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999---999999999999999999999999999999999999999999----------999999999-9999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999----999999999999999999999999999999999999---9
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             43128 365 +     88154 AT---TTTATCTAGAGAATTCTGATCCTGCAGAACGTTCTACCC--AGACTGTCTCAATTTCACTTTTCCTCCAATA-GACTGTTATCTACCAAGTGTTTCTCTGAAATTTATACACTTATTGGATGCTGGT-----------------------GAGAT---CATATATT---AATCATATTTGGTTTTCACT-TAGGAAcaga----------ttcttc----------ttttttcttcctccaaggC-CCAACAGGGTTACAAATAAACACACAGCCCAGAGGGGAGATGTCGGGAGG----CCCAGGTGGACCTGTCATCTCAATTTGCTGAGTCCAGTGTTTCTTTAA-----CAAGTCTCACAGTCTTCAGAGCACATCTGGCAAAGC----AAAGTGAGGCAGGAAACAGAATAATCATATCAGTGG---T
q eriEur1.scaffold_377961                                   45---983254445356657456367644555765575373287--6676546385679945558995457577555-755556757695576555659969346999596675776897968776773896-----------------------77968---77969698---87996889997769979979-9679797995----------496996----------9999998999996999997-99979999979789999999989599899999999999998999999999----999999699999999999999999999999999999999999999999-----999999999997999999999999999999999999----999999999999999999999999999999999999---9
i eriEur1.scaffold_377961         I 2 C 0
s loxAfr3.scaffold_36                537192 399 -  24123610 AA---ATTACGTGGATAATTATGGCCCTCCAAAAC-----A-TAAGAAATTGTCTCAGTTTCTCTCTT--TCCAAGGTGATTTTTATCTATCATGT--TATTTTGATATTTGTACATTTATTGGGGGCTGGCACACTGGATGCATTG------GGGAGCT---TTCATATG---AACCAAATTTGGTTTTCATTTTAGGAAAAAAAAAAACGCCTTCTCTCTTC-TTTTTTGTTTTTCTTCCCCCAAGGC-CCAAAAGACTTATAAATAAACACTTGGGCCAGAGGGAAGACTTGAG-AGG----CGCTGGCAGACATCTCATTTGAATTTGCTGAGCCCCATTTTGTCTGAATTTGCTTGCCCTCATGCTCTTCGAATCACTTTTGGGCAAGC----AAAGCCAAGCAGGTAAAAGGATAATCGGATCAATGA---C
q loxAfr3.scaffold_36                                       99---999999999999999999999999999999-----9-99999999999999999999999999--99999999999999999999999999--9999999999999999999999999999999999999999999999999------9999999---99999999---99999999999999999999999999999999999999999999999999-9999999999999999999999999-9999999999999999999999999999999999999999999999-999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999---9
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=163797.000000
s hg19.chrY                         7666114 72 +  59373566 GTCAACAATGAATGCTG-CTGTCCCAAACCAAAACCACACATTTCAGACAGAGGCTAGGTGGGGAatatatat------
s ponAbe2.chr3                     71057623 64 - 202140232 GTCAACAACTAACGCCA-CTGTCCAAAACCAAAACCTCACATTTCAAGCAGAGGCTGGGTGGGGA--------------
q ponAbe2.chr3                                             99999999999999999-99999999999999999999999999999999999999999999999--------------
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519665 64 +  23952694 GTCAACAATGAATGCTG-CTGTCCCAAACCAAAACCAAACATTTCAGACAGAGGCTAGGTGGGGA--------------
q panTro2.chrY                                             00000000000000000-00000000000000000000000000000000000000000000000--------------
i panTro2.chrY                    C 0 C 0
s rheMac2.chr2                    158783666 72 + 189746636 GTCAACAACCAACGCTG-CTGTCCAAAACCAAAACCTCACATTTCAAGCAGAGGCTGGGTGGGGAATATGTAT------
q rheMac2.chr2                                             99999999999999999-9999999999999999999999999999999999999999999999999999999------
i rheMac2.chr2                    C 0 I 8
s mm9.chr17                        50268338 64 +  95272651 GTCAATGATCTCTCCCA-TGATCTTCAGCCAAAGCTCTGCATTGTAGCCAGGGTCTGGGCTGGGA--------------
i mm9.chr17                       C 0 I 5
s rn4.chr9                        107368818 64 - 113440463 GTCAAAGGTCTCTCCCA-CAGTCCTCAGCCAAAGCTCTCTATTGGAGCCAGGGCCTGGGCTGGGA--------------
q rn4.chr9                                                 99999999999999999-99999999999999999999999999999999999999999999999--------------
i rn4.chr9                        C 0 I 5
s cavPor3.scaffold_0                8262428 59 -  88675666 ATCAACAACCCATACCA-CTGTACAAGACCAAAACCTCACATTTCAGTCAG-----AGGTAGGGA--------------
q cavPor3.scaffold_0                                       99999999999999999-999999999999999999999999999999999-----999999999--------------
i cavPor3.scaffold_0              C 0 I 7
s bosTau4.chr1                    157007106 64 + 161106243 GTCAACCACCCACACCA-ACAGCCAGGACCAGAGCCACACATTTCAATCAGAGGTGGGGTGGGGA--------------
q bosTau4.chr1                                             99999999999999999-99999999999999999999999999999999999999999999999--------------
i bosTau4.chr1                    C 0 I 8
s equCab2.chr16                    22232103 59 -  87365405 GTCAACAAGTAACACCA-CTGGCCAAGACCAAAACC-----TTTCAATCAGAGGTTGGGTGGGGA--------------
q equCab2.chr16                                            99999999999999999-999999999999999999-----999999999999999999999999--------------
i equCab2.chr16                   C 0 I 8
s canFam2.chr23                    26011024 64 -  55389570 GTCAACCACCAACATCA-CTGGCCAAGATCGAAACCTCACATTTCAATCAGAGGCTGGATAGGGA--------------
q canFam2.chr23                                            99999999999999999-99999999999999999999999999999999999999999999999--------------
i canFam2.chr23                   C 0 I 8
s eriEur1.scaffold_377961             43493 63 +     88154 GTCAATAACCAACACCA-CTGGCCAAGACAAAAACCTCATATTTCAATCAGAGGTTGTGCA-GGa--------------
q eriEur1.scaffold_377961                                  99999999999999999-9999999999999999999999999999999999999999999-999--------------
i eriEur1.scaffold_377961         C 0 I 35
s loxAfr3.scaffold_36                537591 71 -  24123610 GTCAACAACCAACAAGAGCCGTCCAAGACCAAAGCCTCATATTTCAATCAAAGGTTGGGTGGAGA--------GTATGT
q loxAfr3.scaffold_36                                      99999999999999999999999999999999999999999999999999999999999999999--------999999
i loxAfr3.scaffold_36             C 0 C 0
e oryCun2.chr14                     2494508 407 + 163896628 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=-37737.000000
s hg19.chrY                         7666186 52 +  59373566 atatat-atatatgtgtgtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtgt
s ponAbe2.chr3                     71057687 15 - 202140232 ATATAT-ATTTTTTTA-------------------------------------
q ponAbe2.chr3                                             999999-999999999-------------------------------------
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519729 48 +  23952694 ATATAT-ATATAtgtgtgtgtg----tgtgcgtgtgtgtgtgtgtgtgtgtgt
q panTro2.chrY                                             000000-000000000000000----000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s mm9.chr17                        50268407  9 +  95272651 -------ATTTTCTTA-------------------------------------
i mm9.chr17                       I 5 C 0
s rn4.chr9                        107368887  9 - 113440463 -------ATTTTCTTA-------------------------------------
q rn4.chr9                                                 -------999999999-------------------------------------
i rn4.chr9                        I 5 C 0
s cavPor3.scaffold_0                8262494 15 -  88675666 -TGTTTATTTTTTTTA-------------------------------------
q cavPor3.scaffold_0                                       -999999999999999-------------------------------------
i cavPor3.scaffold_0              I 7 C 0
s bosTau4.chr1                    157007178  5 + 161106243 -----------CCTTA-------------------------------------
q bosTau4.chr1                                             -----------99999-------------------------------------
i bosTau4.chr1                    I 8 C 0
s equCab2.chr16                    22232170  4 -  87365405 -----------TTTC--------------------------------------
q equCab2.chr16                                            -----------9999--------------------------------------
i equCab2.chr16                   I 8 C 0
s canFam2.chr23                    26011096  5 -  55389570 -----------TTTTA-------------------------------------
q canFam2.chr23                                            -----------99999-------------------------------------
i canFam2.chr23                   I 8 C 0
s loxAfr3.scaffold_36                537662  5 -  24123610 ----------TTTTT--------------------------------------
q loxAfr3.scaffold_36                                      ----------99999--------------------------------------
i loxAfr3.scaffold_36             C 0 C 0
e oryCun2.chr14                     2494508 407 + 163896628 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e rheMac2.chr2                    158783738  8 + 189746636 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             43556 35 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=110084.000000
s hg19.chrY                         7666238 38 +  59373566 -ACCTAAA---TCTTCTCA----------TTTTCT--CCTTTTTTGTTAAGGGT
s panTro2.chrY                       519777 38 +  23952694 -ACCTAAA---TCTTCTCA----------TTTTCT--CCTTTTTTGTTAAGGGT
q panTro2.chrY                                             -0000000---00000000----------000000--00000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71057702 41 - 202140232 -ACCTAAATCTTCTTCTCA----------TTTTCT--CCTGTTTTGGTTAGGGT
q ponAbe2.chr3                                             -999999999999999999----------999999--99999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158783746 41 + 189746636 -ACCTAAATCTTCTTCTCA----------TTTTCT--CCTTTTTTGGTGAGGGT
q rheMac2.chr2                                             -999999999999999999----------999999--99999999999999999
i rheMac2.chr2                    I 8 C 0
s mm9.chr17                        50268416 43 +  95272651 -ACCTGAATTATCTCCCCA----------ATCCCCCACCCTTTTTGGCTAGGGG
i mm9.chr17                       C 0 C 0
s rn4.chr9                        107368896 43 - 113440463 -ACCTGAGTTATCTCCTCA----------ATTTCCCCCCTTTTTTGGCTAGGGG
q rn4.chr9                                                 -999999999999999999----------9999999999999999999999999
i rn4.chr9                        C 0 C 0
s cavPor3.scaffold_0                8262509 41 -  88675666 -ACCTGAATTATCTTCCCA----------GTTTTC--TCCTTTTTGACTAGTGT
q cavPor3.scaffold_0                                       -999999999999999999----------999999--99999999999999999
i cavPor3.scaffold_0              C 0 C 0
s bosTau4.chr1                    157007183 41 + 161106243 -ACTGACATTTTCTTCCTAG---------TTTTCT--CCTTTTTT-GCTAAGGT
q bosTau4.chr1                                             -9999999999999999999---------999999--99999999-99999999
i bosTau4.chr1                    C 0 I 2556
s equCab2.chr16                    22232174 42 -  87365405 -ACTGAAATTTTCTTCCCAG---------TTTTCT--CCTTTTTTGGCTAGGGT
q equCab2.chr16                                            -9999999999999999999---------999999--99999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011101 42 -  55389570 -ACTGAAATGTTCTTCCCAG---------TTTTCT--CCTTTTTTGGCTAGGGT
q canFam2.chr23                                            -9999999999999999999---------999999--99999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             43591 41 +     88154 -----------tcttcccagttttttttttttttt--ccttttttggctaGGAT
q eriEur1.scaffold_377961                                  -----------999999999999999999999999--99999999999999999
i eriEur1.scaffold_377961         I 35 C 0
s loxAfr3.scaffold_36                537667 43 -  24123610 AACTGGAATTTTCTTCTCAG---------CTTTCT--CCTTTTTTGTCTAGGGT
q loxAfr3.scaffold_36                                      99999999999999999999---------999999--99999999999999999
i loxAfr3.scaffold_36             C 0 C 0
e oryCun2.chr14                     2494508 407 + 163896628 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=223212.000000
s hg19.chrY                         7666276 71 +  59373566 ------------------AGAAATATCATGTAAGAGGCCTGTTACACATACAATTAATGTGAGAGACACATGAGCAGA-TGTCACTTGAG
s loxAfr3.scaffold_36                537710 89 -  24123610 AGAATTTTTTTTTTTTTTAGAATTACCATGTAAGAAGCCTGTTACACAAATAGCTAATATGAGAGACATGTGAGCAGA-TGTCACTTGAG
q loxAfr3.scaffold_36                                      999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999
i loxAfr3.scaffold_36             C 0 C 0
s eriEur1.scaffold_377961             43632 72 +     88154 ------------------GGAACTATCCTATCAGAGGCCTGCTACACAAATAACTAGTGTGAGAGACATCTGAGCACATCATCACTTGAG
q eriEur1.scaffold_377961                                  ------------------999999999999999999999999999999999999999999999999999999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s canFam2.chr23                    26011143 71 -  55389570 ------------------AGAAGTATCATATCAAAGGGCTGTTACACAAATAACGGATGTGAGAGACAAATGAGCAGA-CATCACTTTAG
q canFam2.chr23                                            ------------------999999999999999999999999999999999999999999999999999999999999-99999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22232216 71 -  87365405 ------------------AGAAATATCATATCGGAGGTCCGTTACACAAATAACTAATGTGAGAGACATATAAGCAGA-CATCGCTTGAG
q equCab2.chr16                                            ------------------999999999999999999999999999999999999999999999999999999999999-99999999999
i equCab2.chr16                   C 0 C 0
s bosTau4.chr1                    157009780 52 + 161106243 ------------------agaAGTATCATATCAGAGACCTGTGATGCAAACAAGAGATATGA------------------ATCA--TAAG
q bosTau4.chr1                                             ------------------99999999999999999999999999999999999999999999------------------9999--9999
i bosTau4.chr1                    I 2556 C 0
s cavPor3.scaffold_0                8262550 69 -  88675666 ------------------AGAAATATCACAAAAGAGCCTTGTTACACAGATAATTCATG--AGAGACATGTAAGCCCA-GATCTCGTGGG
q cavPor3.scaffold_0                                       ------------------99999999999999999999999999999999999999999--99999999999999999-99999999999
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107368939 68 - 113440463 ------------------AGGAATAT---GGAAGAGGCCTATTACACAGACAACTGATGTTAGAGACATGTGAGCACG-CGTCTCCTGAG
q rn4.chr9                                                 ------------------99999999---9999999999999999999999999999999999999999999999999-99999999999
i rn4.chr9                        C 0 C 0
s mm9.chr17                        50268459 68 +  95272651 ------------------AGAAATAT---GGAAGAGGCCTATTATACAGATAACTAATGCTAGAGACATGTGAGCACG-CATCTCCTGAG
i mm9.chr17                       C 0 C 0
s rheMac2.chr2                    158783787 71 + 189746636 ------------------AGAAATATCATGGAAGAGGCGTGTTATACAGATAACTAATGTGAGAGACACGTGATCAGA-TGTCACTTGAG
q rheMac2.chr2                                             ------------------999999999999999999999999999999999999999999999999999999999999-99999999999
i rheMac2.chr2                    C 0 C 0
s ponAbe2.chr3                     71057743 71 - 202140232 ------------------AGAAATACCATGTAAGAGGCCTGTTACACAGACAACTAATGCGAGAGACACGTGAGCAGA-CGTCACTTGAG
q ponAbe2.chr3                                             ------------------999999999999999999999999999999999999999999999999999999999999-99999999999
i ponAbe2.chr3                    C 0 C 0
s panTro2.chrY                       519815 71 +  23952694 ------------------AGAAATATCATGTAAGAGGCCTGTTACACAGACAACTAATGTGAGAGACACATGAGCAGA-TGTCACTTGAG
q panTro2.chrY                                             ------------------000000000000000000000000000000000000000000000000000000000000-00000000000
i panTro2.chrY                    C 0 C 0
e oryCun2.chr14                     2494508 407 + 163896628 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I
e xenTro2.scaffold_1099              297073 315 -    315732 I

a score=334195.000000
s hg19.chrY                         7666347 101 +  59373566 CCTCATTTTCCATGCAAAAATTCAGGATTTATGGTCTAAAA-CCATAGAGGATATTTTAAAGCCAGATGATTCCAGAAAATCTGAGACATGTGTCCAT--CAGC
s panTro2.chrY                       519886 101 +  23952694 CCTCATTTTCCATGCAAAAATTCAGGATTTATGGTCTAAAA-CCATAGAGGATATTTTAAAGCCAGATGATTCCAGAAAATCTGAGACATGTGTCCAT--TAGC
q panTro2.chrY                                              00000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000--0000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71057814 103 - 202140232 CCTCATTTTCCATGCCAAAATTCAGGATTTAAGGTCTAAAA-CCATAGAGAATATTTTAGAGCCAGATGGTTCCAGAAAATCTGAGACATGTGGCCACCACAGC
q ponAbe2.chr3                                              99999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158783858 103 + 189746636 CCTCATTTTCCATGCCAAAATTCAGGATTTAAGGTCTAAAA-CCATAGAGAATATTTTAGAGCCAGATGGTTCCAGAAAATCTGAGACATGTGGCCACCACAGC
q rheMac2.chr2                                              99999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s mm9.chr17                        50268527  98 +  95272651 CCTCATTTTCCAAGCTGAAATTCAGAATTTAAGGTCTAAAA-CCATGAAGAGCATTTTAGAGCCAGGTGTTTCCAGAGGACCTGAGACATGTGGC-----TGGC
i mm9.chr17                       C 0 C 0
s rn4.chr9                        107369007  99 - 113440463 CCTCGTTTTCTAAGCCGAAAGTCAGACTTTAAGGTCTAAAACCCATGAAGAGCACTTCAGAGCCAGGTGTTTCCAGAGGATCTGAGACATAAGGC-----TGGC
q rn4.chr9                                                  99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----9999
i rn4.chr9                        C 0 C 0
s cavPor3.scaffold_0                8262619 101 -  88675666 CCTCACTGTCCAAGCCAACATTCCAGATTTAAGGTCTAATA-CTGTAAAGAATATTTTAGAGCCAGGTGCTACCAGAAAA--TGAGACATGTGGTCACCACAGC
q cavPor3.scaffold_0                                        99999999999999999999999999999999999999999-99999999999999999999999999999999999999--9999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s bosTau4.chr1                    157009832 100 + 161106243 CCTCATTTTTCAAGCCAAAGTTCAGAGTGGAAGGTCTAAAA-CCAGGAAGAATCCTTTAGACTCTGATGATGTCAGAACCTTTGAGCAGTGT---CTCTGCAGC
q bosTau4.chr1                                              99999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999---999999999
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22232287  91 -  87365405 CCTCATTTTCCAAGCCACAATTC--TATGTGAGTTCTAAAA-GAAGAAAGAGTATTTTAGAAC----------CGGAACATCTGAGACATGTGGCCTCCACAGC
q equCab2.chr16                                             99999999999999999999999--9999999999999999-999999999999999999999----------9999999999999999999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011214 103 -  55389570 CCTCATTTTCCAAGCCAAAATTCAGGATGTAAGATCTAAAA-CCAGAAAGAATATTTTAGAACCAGAAAGTTTCAGAACATCTGAGACATGTGGCCTCTGCAGC
q canFam2.chr23                                             99999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             43704 103 +     88154 CTTCATTTTCTACGCCAAACTTCAGGATGGAAGGTCTAAAA-CCAGAAGGAAGACTGAAGAGCCAGATGGTTTCAGAACCTACGAGAAACGTGGTCCCTGCAGC
q eriEur1.scaffold_377961                                   99999999999999999999999999999999999999999-99999999999998999999999999999999999999999999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                537799 101 -  24123610 CCTCATGTTCCAAGTCAAAATTCAGGATGTAAGGTCTAAAA-CTGGAAAGAATATTTTAGAAAGAGATGGTTCCAGAAAATTGGAGATATGTGGCCACCACA--
q loxAfr3.scaffold_36                                       99999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999--
i loxAfr3.scaffold_36             C 0 C 0
s xenTro2.scaffold_1099              297388  87 -    315732 CCTCTATTTCCAAGGAAAGAATTCAGTCATATGAAAGAAAG-CAGTCAGGTGTATTTTAAAGTGGCCTGACTCCAGGCGA-CTGAGATA---------------
i xenTro2.scaffold_1099           I 315 N 0
e oryCun2.chr14                     2494508 407 + 163896628 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=24465.000000
s hg19.chrY                         7666448 35 +  59373566 TGTGATGT-GGCC----CACTCTCT---CCCACCTACCCACC-----G
s panTro2.chrY                       519987 35 +  23952694 TGTGATGT-GGCC----CACTCTCT---CCCACCTACCCACC-----G
q panTro2.chrY                                             00000000-0000----00000000---00000000000000-----0
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71057917 35 - 202140232 TGTGATGT-GGCC----CACTCTGT---CCCACCTACCCACC-----C
q ponAbe2.chr3                                             99999999-9999----99999999---99999999999999-----9
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158783961 35 + 189746636 TGTGATGT-GGCC----CATTCTCT---CCTACCTACCCACC-----C
q rheMac2.chr2                                             99999999-9999----99999999---99999999999999-----9
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8262720 34 -  88675666 TGCGACAC-AGCC----TA-TTTTT---CCCACTCACTTACC-----C
q cavPor3.scaffold_0                                       99999999-9999----99-99999---99999999999999-----9
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107369106 26 - 113440463 TGCTAAGC-------------CTTT---CCCACC-ACTCCCC-----C
q rn4.chr9                                                 99999999-------------9999---999999-9999999-----9
i rn4.chr9                        C 0 I 114
s mm9.chr17                        50268625 18 +  95272651 TGTTATGC-------------CTCC---CCCACC--------------
i mm9.chr17                       C 0 I 122
s oryCun2.chr14                     2494915 18 + 163896628 cgcggccc-------------cTTC---CCTGCC--------------
q oryCun2.chr14                                            99999999-------------9999---999999--------------
i oryCun2.chr14                   I 407 C 0
s bosTau4.chr1                    157009932 45 + 161106243 TGTGACGT-GACCCACTCACTCCCTC--TCCACCTGCTCCCCCTCCTC
q bosTau4.chr1                                             99999999-99999999999999999--99999999999999999999
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22232378 36 -  87365405 TGTGACAT-GGCC----CACTTCCTC--CCCACCCTTGCACC-----C
q equCab2.chr16                                            99999999-9999----999999999--99999999999999-----9
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011317 35 -  55389570 TATGACAT-GGTC----CACTCCCT---CCCACCCACTCACC-----C
q canFam2.chr23                                            99999999-9999----99999999---99999999999999-----9
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             43807 38 +     88154 TGTGACAC-GACC----AGCTCCCTTGAACCACCCACTCGCC-----C
q eriEur1.scaffold_377961                                  99999999-9999----9999999999999999999999999-----9
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                537900 36 -  24123610 GCTGAAGCAGGCG----TGCTCCCT---CCCACCCACTCACC-----C
q loxAfr3.scaffold_36                                      9999999999999----99999999---99999999999999-----9
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=279877.000000
s hg19.chrY                         7666483 232 +  59373566 CAGAATTTCTT-GCCCTTCATAATGTAATCTCCCTACTTGAGGCTAGCCAGACTTCTTCAAC-AAACGGCAGACAAAGCAGGCTTGGTCCCAATGT-----AAAATGGAG---TCTCAGAA--TGCACTACTCAGCCATTTTGGAGAGTGAATTGAAAAGGCCATGCCACAGACACCCTTGGG-CAGCACAGCTTCTGTGACAATATGGGCCAGTGCCAGGA--------A----TAGGAAG-GATCAAGTTAAATGT
s panTro2.chrY                       520022 232 +  23952694 CAGAATTTCTT-GCCCTTCATAATGTAATCTCCCTACTTGAGGCTAGCCAGACTTCTTCAAC-AAACGGCAGACAAAACAGGCTTGGTCCCAATGT-----AAAATGGAG---TCTCAGAA--TGCACTACTCAGCCATTTTGGAGAGTGAATTGAAAAGGCCATGCCACAGACACCCTTGGG-CAGCACAGCTTCTGTGACAATATGGGCCAGTGACAGGA--------A----TAGGAAG-GATCAAGTTAAATGT
q panTro2.chrY                                              00000000000-00000000000000000000000000000000000000000000000000-000000000000000000000000000000000-----000000000---00000000--000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000000--------0----0000000-000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71057952 230 - 202140232 CAGAATTTCTT-ACCCTTCATAAGGCAG--CCCCTATTCGAGGCTGGCCAGACTTCTTCAAC-AAATGACAGACAAAGCAGGCTTGGTCCCAATGT-----AAAATGAAG---TCTGAGAA--CCCACTGCTCAGCCATTTTGGAGAGTGAGATGAGGAGGCCACGCCACAGAGGCCCTCGGG-CAGCACAGCTGCCATGACAATATGGGCCGGTGCCAGGA--------A----TAGGAAG-GATCAAGTTAAATGT
q ponAbe2.chr3                                              99999999999-9999999999999999--99999909999999999999999999999999-999999999999999999999999999999999-----999999999---99999999--999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999--------9----9999999-999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158783996 230 + 189746636 CAGAATTTCTT-ACCCTTAATAAGGCAG--CCCCTACTCGAGGCTGGCCAGATTTCTTCAAC-AAATGAGAGACAAAGCAGGCTTGGTCCCAGTGT-----AAAATGAAG---TCTCAGAA--CCCACTGCTCAGCCATTTTGGAGAGTGAGATGAGGAGGCCACACCACAGAGGCCCTCGGG-CAGCACAGCTGCCGTGACAATATGGGCCAGTGCCAGGA--------A----TAGGAAG-GATCAAGTTAAATGT
q rheMac2.chr2                                              99999999999-9999999999999999--99999999999999999999999999999999-999999999999999999999999999999999-----999999999---99999999--999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999--------9----9999999-999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8262754 168 -  88675666 --CAGCTCAT--ACCCTACACTAAACAG--AC----TTT----------------------T-AAACAACAGAAAAAGCAGGCTTGACCCCAGGATC----ATGAAGGAG---TCTTGGAACTCGCTCTAC----CCATTTGGGAACATGGGATGCAGGGGCTG---CAGAGGTAATCTGGG-----------------------------------CAGGA--------CCCAGTGTAGAGAGGTCAAGCCGGACAT
q cavPor3.scaffold_0                                        --99999999--9999999999999999--99----999----------------------9-9999999999999999999999999999999999----999999999---999999999999999999----99999999999999999999999999999---999999999999999-----------------------------------99999--------9999999999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2494933 174 + 163896628 CAGAGCTTCTTAACCCTTCCCACGGCAG--CCCATGCTC----------------------T-GGACGGGCCGCAAAGCAGGCTTGGGCTCAACGTCAAAAATACAGGCG---TC-GGAAAAACACACTGCTGGGCCCTTTGGGGACGGGAGAGCAGGAGGCCGTGTCTCTGGAGCTCCCGC-----------------------------------CAAGA--------C----TACAAAG-GGTCAAGT-------
q oryCun2.chr14                                             9999999999999999999999999999--999999999----------------------9-99999999999999999999999999999999999999999999999---99-999999999999999999999999999999999999999999999999999999999999999999-----------------------------------99999--------9----9999999-99999999-------
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157009977 205 + 161106243 CAGAAAT--TT-ATCCTTCATAAGGCAG--CCCCTACCCTCGACTGGCCAGACTTCTGAAACGAAATGACAGGCAAAGGAGGATCAGCCCCAGAGT-----CAAATGGAGAGATCTCAGAA--GACAC----CAGTCATTCTGGAAAGTGAGATGGAAAAGCC----CACAGAGGCCCCTGAGGCAG--------------------GGGCCAGTGCCAGGC--------T----CAGGAAG-GATGCAGAGAAACGT
q bosTau4.chr1                                              9999999--99-9999999999999999--999999999999999999999999999999999999999999999999999999999999999999-----99999999999999999999--99999----9999999999999999999999999999999----99999999999999999999--------------------999999999999999--------9----9999999-999999999999999
i bosTau4.chr1                    C 0 I 132
s equCab2.chr16                    22232414 221 -  87365405 CCAAATTTCTC-ACCCTTCATAAGGCAG--CCCTC-CTCTTGAATAGCCAGACTTCTTAAACAAAATGACAGACAAAGCAGGTTTGGCCCCAATAT--------------GTGTCTCAGAA--CACGCTATTCAGTCATTTTGGAAAGTGCAAGGGAAAGGTC----CAGGGAGGCCCTGGAGGTGGCCCAGCTACAGTGACAACATGGGCCTGGGCTAGAA--------A----TACGAAG-GATCAAGTAAAATGT
q equCab2.chr16                                             99999999999-9999999999999999--99999-999999999999999999999999999999999999999999999999999999999999--------------99999999999--9999999999999999999999999999999999999999----9999999999999999999999999999999999999999999999999999999--------9----9999999-999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011352 238 -  55389570 CAGAATTTCTT-ACCCTTTGCAAGGCAG--CCCCCACCCTAAAAGAGCCAGACTTCTCAAACAAAATGACAGACAAAGCAGACTTGGCCCCCATAT-----AAATCCGAGAAATCTCAAAA--CACATTACTCAGTCG-TTTGAAAAGTGAGCTGGAAAGGCC----CATGGAGGCACTTCAGACAGCCTAGGCTGAGGGACAACACGAGCCTGTGCAAGCACATGAGTGC----TGTGCAA-GCACAAGTCAAATGT
q canFam2.chr23                                             99999999999-9999999999999999--999999999999999999999999999999999999999999999999999999999999999999-----99999999999999999999--999999999999999-999999999999999999999999----9999999999999999999999999999999999999999999999999999999999999999----9999999-999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             43845 181 +     88154 CC--------------------AGGCA-------------------GGCAGACTTCTTAAACTAAATAAAAGGGAAAGCCAGCTCAGCACCCACAC-----AGAATGGAGAGAGCACAGAA--CACACTACCTGGTCATTCTGGAAAGTGAGATGCAAAGGCC----CTA------CCTAGAGGCAGTCCAGCTGCAGCGACCGCAAGGGACAGAACCCAGG--------A----TATGCAG-CATCCAG--------
q eriEur1.scaffold_377961                                   99--------------------99999-------------------99999999999999999999999999999999999999999999999999-----99999999999999999999--9999999999999999999999999999999999999999----999------9999999999999999999999999999999999999999999999--------9----9999999-9999999--------
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                537936 226 -  24123610 GAGAATTTCTT-AACCTTCATAAGACCA--CCTCTACACTAGAATGGCCAGA-----GAAGCAAAATGACAGGCAAAGCAGGCTTAGTCGCAACAT-----AAAATGAAGAAATCTCAGAA--TATACTGTTCAGCCATTTTGGAACGTGAATTGGAGAGGTC----CATGGAGACCCTCAAGGCAGCACAGCTGCAGTGACCACATGGGCCAGTGCCAGGA--------A----CATGAAG-GATCAAGGTAAATAT
q loxAfr3.scaffold_36                                       99999999999-9999999999999999--9999999999999999999999-----999999999999999999999999999999999999999-----99999999999999999999--9999999999999999999999999999999999999999----9999999999999999999999999999999999999999999999999999999--------9----9999999-999999999999999
i loxAfr3.scaffold_36             C 0 C 0
e rn4.chr9                        107369132 114 - 113440463 I
e mm9.chr17                        50268643 122 +  95272651 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=207566.000000
s hg19.chrY                         7666715 172 +  59373566 TTGTGATCCAA---------------------------------------------------------------------------------------------TAACAAAACTACA-------------------------------------------------------------------------------------ACATGGGCCCCTTTAAGTAAGACTTAG------GTAGAAGCTAAT----AAACTGAATCTAATTTTCTGTTGACCATCTTTGACAAGGAATAAGCTCTGCTATAA---TAAGT---------TTCCTAGGCAATTCAAATATAGACATTACAGTGG-----------------------------------------------------AGCttaat--------------------------------------------------------------------------------------------------taaaaa
s panTro2.chrY                       520254 172 +  23952694 TTGTGATCCAG---------------------------------------------------------------------------------------------TAACAAAACCACA-------------------------------------------------------------------------------------ACATGGGCCCCTTTAAGTAAGGCTTAG------GTAGAAGCTAAT----AAACTGAATCTAATTTTCTGTTGACCATCTTTGACAAGGAATAAGGTCTGCTATAA---TGAGT---------TTCCTAGGCAATTCAAATATAGACATTACAGTGG-----------------------------------------------------AGCttaat--------------------------------------------------------------------------------------------------taaaaa
q panTro2.chrY                                              00000000000---------------------------------------------------------------------------------------------0000000000000-------------------------------------------------------------------------------------000000000000000000000000000------000000000000----00000000000000000000000000000000000000000000000000000000---00000---------0000000000000000000000000000000000-----------------------------------------------------00000000--------------------------------------------------------------------------------------------------000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058182 167 - 202140232 TTGTGATCCAA---------------------------------------------------------------------------------------------TAACAAAACCACA-------------------------------------------------------------------------------------ACACGGGCCCCATTAAGCAAGGTTTAG------GTAGAAGCTAAT----GAACTGAATCTAATTTTCTTTTGACCATCTTTGACAAGGAATAAGCTCTGCTATAA---TGAGT---------TTCCTAGGCAATTCAAATATAGACATTACAGTGG-----------------------------------------------------GGCTCAAT-------------------------------------------------------------------------------------------------------A
q ponAbe2.chr3                                              99999999999---------------------------------------------------------------------------------------------9999999999999-------------------------------------------------------------------------------------999999999999999999999999999------999999999999----99999999999999999999999999999999999999999999999999999999---99999---------9999999999999999999999999999999999-----------------------------------------------------99999999-------------------------------------------------------------------------------------------------------9
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784226 169 + 189746636 TTGTGATCCAA---------------------------------------------------------------------------------------------TAACAAGACCACA-------------------------------------------------------------------------------------ACACGGGCCCCATTAAGCAAGGTTTAG------GTAGAAGCTAAT----GAACTGAATCTGATTTTCTTTTGACCATCTTTGACAAGGAATAAACTCTGCTATAA---TGAGT---------TTCCTAGGCAATTCAAATATAGACATTACAGTGG-----------------------------------------------------GGCTCAAT-----------------------------------------------------------------------------------------------------AAA
q rheMac2.chr2                                              99999999999---------------------------------------------------------------------------------------------9999999999999-------------------------------------------------------------------------------------999999999999999999999999999------999999999999----99999999999999999999999999999999999999999999999999999999---99999---------9999999999999999999999999999999999-----------------------------------------------------99999999-----------------------------------------------------------------------------------------------------999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8262922 158 -  88675666 GTGTGAACCAA---------------------------------------------------------------------------------------------CAGCACAACCACA-------------------------------------------------------------------------------------ACACGGGCCCCATTAGGCGAGGCACAG------GGAGAAGCTTAT----GAACTGAACCAATTTT--------CCATCTTGGATAAGTAATACATTGTGCTGTAA---TGTGT---------CTCTTAGGCAATTCAAGTACAGACACTAAGGCAG-----------------------------------------------------GGCTCAAT--------------------------------------------------------------------------------------------------------
q cavPor3.scaffold_0                                        99999999999---------------------------------------------------------------------------------------------9999999999999-------------------------------------------------------------------------------------999999999999999999999999999------999999999999----9999999999999999--------99999999999999999999999999999999---99999---------9999999999999999999999999999999999-----------------------------------------------------99999999--------------------------------------------------------------------------------------------------------
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495107 153 + 163896628 -------TCAA---------------------------------------------------------------------------------------------AGGT----CCACA-------------------------------------------------------------------------------------ACACGGGCTCCACGGAGCAAGGGCTCG------GGA-CAGCTACC----GAGCTGCACCTGCTCCTGCCCCGACCATCGCCTTTGAGGAGTAGATGCAGCTCTAA---TGAGT---------TTCCTAGGAGCGGCAAAGAC-GACCTTCCAGAAG-----------------------------------------------------GGCTCCAT--------------------------------------------------------------------------------------------------------
q oryCun2.chr14                                             -------9999---------------------------------------------------------------------------------------------9999----99999-------------------------------------------------------------------------------------999999999999999999999999999------999-99999999----99999999999999999999999999999999999999999999999999999999---99999---------99999999999999999999-9999999999999-----------------------------------------------------99999999--------------------------------------------------------------------------------------------------------
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010314 253 + 161106243 ttgtggcctggagaattccatggacagaggagcctggcaggatacagtccatgggattgcagagagtcagacgacgaACACCTTACTTTCACCTTTTCTTTCAACATCAAAACCACA-------------------------------------------------------------------------------------ACACAGACCTCGTTAGGTAAAGATCAG------GTCGCAGCTAAC----AAACCTAACCTAATTTTCCTCTGACCATCTTTGACGAGGAATAATCTCTGC--TAC---------------------------ATTCGAATACAGACTTTCTGGTAG---GGGGTGGGGG---------------------------------------TGGGTCAAT--------------------------------------------------------------------------------------------------------
q bosTau4.chr1                                              999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------------------------------------------------------------------------------------999999999999999999999999999------999999999999----999999999999999999999999999999999999999999999999999--999---------------------------999999999999999999999999---9999999999---------------------------------------999999999--------------------------------------------------------------------------------------------------------
i bosTau4.chr1                    I 132 C 0
s equCab2.chr16                    22232635 152 -  87365405 ATGTGATCCAA---------------------------------------------------------------------------------------------CAGCAAACCCACA-------------------------------------------------------------------------------------ACATGGACCTCAA------------AG------GCAGAGGCTAAT----GAACTGAGCCTGACTTTCCTTTGACCATCTTTAACGAGGAATAAGCTCTCC--TAA---TAAGT---------TTCCTGGACAATTTAAATACAGACATTACAGTAG-----------------------------------------------------GCGTCAAT--------------------------------------------------------------------------------------------------------
q equCab2.chr16                                             99999999999---------------------------------------------------------------------------------------------9999999999999-------------------------------------------------------------------------------------9999999999999------------99------999999999999----999999999999999999999999999999999999999999999999999--999---99999---------9999999999999999999999999999999999-----------------------------------------------------99999999--------------------------------------------------------------------------------------------------------
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011590 167 -  55389570 CTGTGATCTAG----------------------------------------------------------------------------------------------AGCAAAATCACA-------------------------------------------------------------------------------------ACATAGATCCCACTAGGCAATACTTAG------GAAGAAGCTAAT----GAACTGAACCAAATTTTCCTTTGACCATTTTTGATGAGAAACAAGCTCTGCTATAA---TAACT---------TTCTTGGAAGATTTAAATATAGACATGACAGTAG-----------------------------------------------------AGTTCAAT----------------------------------------------------------------------------------------------------AA--
q canFam2.chr23                                             99999999999----------------------------------------------------------------------------------------------999999999999-------------------------------------------------------------------------------------999999999999999999999999999------999999999999----99999999999999999999999999999999999999999999999999999999---99999---------9999999999999999999999999999999999-----------------------------------------------------99999999----------------------------------------------------------------------------------------------------99--
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             44026 415 +     88154 ----------------------------------------------------------------------------------------------------CCAACAGCAGGACCACAGAGTGTGACAGGCTGGGGGTGCTCTCAAGTCTTACTCTTGAGCACCTGCTTTGTCTGGCCTGCCCTGGCTACAGTTTGCGACATTACTAAAGACCCATTATGTGAGGTTTGA------GTAGAAGCGAATGAAAGAAATGACCCTAGCTTTCCTTTGATAAATTTTGATGGGGATTAAGTTCTGC--TATGAGTAACCCTTTGGTTACTTCTGCAAGATTTACATCTAGAGATTGTTgcagtctggggtggggggtaggtgtGGTAGCAGAAAACATGCACTCCTATGGtgatgagttcaatccctggcagtgcgAGTGCCAGAGTGATAGCTCTGGTTTACTTTCTCTCTCGCTAGCAAATaatacattaataaattaaaaagtacataTACAGTTTATGAAAGG
q eriEur1.scaffold_377961                                   ----------------------------------------------------------------------------------------------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                538162 178 -  24123610 ACATAATACAA---------------------------------------------------------------------------------------------TAGCAAAACTACC-------------------------------------------------------------------------------------ATATGGACCTCTTTAGGCCAGGCTTAACCTAATGTTTAGACAAAG----GAACTGACCCTGGTTTTCCTTTGACCATCTTTGATGAGGAATAATCTTTGCTATAA---TGAGT---------TTCCTGGGTGACTCAAATATAGACGTTATGACAG-----------------------------------------------------GGCTCAAT--------------------------------------------------------------------------------------------------GGAAAA
q loxAfr3.scaffold_36                                       99999999999---------------------------------------------------------------------------------------------9999999999999-------------------------------------------------------------------------------------999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999---99999---------9999999999999999999999999999999999-----------------------------------------------------99999999--------------------------------------------------------------------------------------------------999999
i loxAfr3.scaffold_36             C 0 I 1
e rn4.chr9                        107369132 114 - 113440463 I
e mm9.chr17                        50268643 122 +  95272651 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=-31037.000000
s hg19.chrY                         7666887 21 +  59373566 taaaaataaaaaaaC------------------TTTTC------A
s panTro2.chrY                       520426 21 +  23952694 taaaaataaaaaaaC------------------TTTTC------A
q panTro2.chrY                                             000000000000000------------------00000------0
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058349 21 - 202140232 AAAAAAAAAAAAAAA------------------CTCTC------A
q ponAbe2.chr3                                             999999999999998------------------99999------9
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784395 21 + 189746636 AAACAAACAAAAAAA------------------CTCTC------A
q rheMac2.chr2                                             999999999999999------------------99999------9
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263080 12 -  88675666 ------GAATGAAAC------------------TT---------A
q cavPor3.scaffold_0                                       ------999999999------------------99---------9
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495260 15 + 163896628 ------GAAGACAAC------------------CTCTG------A
q oryCun2.chr14                                            ------999999999------------------99999------9
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010567 15 + 161106243 --------GAAAATC------------------CTCTTAT----A
q bosTau4.chr1                                             --------9999999------------------9999999----9
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22232787 17 -  87365405 ------GAAAAACAC------------------TTCTAAT----A
q equCab2.chr16                                            ------999999999------------------9999999----9
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011757 19 -  55389570 ----AAAAAAAAAAA------------------CTCTTAT----A
q canFam2.chr23                                            ----99999999999------------------9999999----9
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             44441 27 +     88154 ACTCAAAAAAGTAGC------------------GTCTTATATAGA
q eriEur1.scaffold_377961                                  999999999999999------------------999999999999
i eriEur1.scaffold_377961         C 0 C 0
s echTel1.scaffold_309969              1549 35 -     41825 --TGAGGATGGTACAGGACTGTGTGGTGTTCTGTTCT--------
q echTel1.scaffold_309969                                  --99999959899999999999999999999999999--------
i echTel1.scaffold_309969         N 0 N 0
s loxAfr3.scaffold_36                538341 21 -  24123610 --AAAAAAAGGAAAA--------------CCTATTTT--------
q loxAfr3.scaffold_36                                      --9999999999999--------------99999999--------
i loxAfr3.scaffold_36             I 1 I 1
e rn4.chr9                        107369132 114 - 113440463 I
e mm9.chr17                        50268643 122 +  95272651 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=112338.000000
s hg19.chrY                         7666908 63 +  59373566 CAAAGGAGTCTGTCTCCTC--AAATAGACTCTGAGGTGGTTTAAGTTGGAAGCACATAGTTCTTT
s panTro2.chrY                       520447 63 +  23952694 CAAAGGAGTCTGTCTCCTC--AAATAGATTCTGAGGTGGTTTAAGTTGGAAGCACATAGTTCTTT
q panTro2.chrY                                             0000000000000000000--00000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058370 63 - 202140232 CAAAGGAGCTGATCTCCTC--AAATAGACTCTAAGGTGGTTTAACTTGGAAGCATGTATTTCTTT
q ponAbe2.chr3                                             9999999999999999999--99999999999999999999999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784416 63 + 189746636 CAAAGGAGCCGATCTCCTC--AAATAGACTCTAAGGTGGTTTAACTTGGAAGCATATATTTCTCT
q rheMac2.chr2                                             9999999999999999999--99999999999999999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263092 63 -  88675666 CAAAGGAGCCAACCTCCTT--ATGCAGACTCTCCAGCAATTTAAATGGGACATACACAGTCCCTT
q cavPor3.scaffold_0                                       9999999999999999999--99999999999999999999999999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495275 53 + 163896628 CACAGGTGCCAATCCCCTCCAAGGCGATTTCACCTGC----------GGGCGTGTAT--TTCTTT
q oryCun2.chr14                                            9999999999999999999999999999999999999----------9999999999--999999
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010582 60 + 161106243 AAGAGGGGTCAAT---CTC--AAATAGACGCGAAGGTGGCTTGCCTTGGAGGCAAACACTACTTT
q bosTau4.chr1                                             9999999999999---999--99999999999999999999999999999999999999999999
i bosTau4.chr1                    C 0 C 0
s equCab2.chr16                    22232804 51 -  87365405 AAGGGGGGCCAATAGCCTC--AAATCGGCTCTAAGCTGGTTTACCTTGGAGGC------------
q equCab2.chr16                                            9999999999999999999--99999999999999999999999999999999------------
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26011776 63 -  55389570 AAGGGGAAACCATCTCCTC--AAATAGACTCTAAGGTGATTTACCTTGGAGGCACATTTTTCTGT
q canFam2.chr23                                            9999999999999999999--99999999999999999999999999999999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             44468 61 +     88154 CAGAGGAGCCAATCTCTTT----ATTGACTCTAAGGTGGCTTATGTTGGAGTAATATTTTACTTT
q eriEur1.scaffold_377961                                  9999999999999999999----999999999999999999999999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                538363 63 -  24123610 ATGAGGAGCTGATCTCTTC--AAATAGCTTCTAAGGTGGTTCAACTTGGAAATACAAATTTCTTT
q loxAfr3.scaffold_36                                      9999999999999999999--99999999999999999999999999999999999999999999
i loxAfr3.scaffold_36             I 1 C 0
e rn4.chr9                        107369132 114 - 113440463 I
e mm9.chr17                        50268643 122 +  95272651 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              27841 2540 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=59275.000000
s hg19.chrY                         7666971  42 +  59373566 AAAACTCT-------------------------------------------------------------TACATGAAT--------------------AATCAAGAATAATCATACa-ttaaaa-
s panTro2.chrY                       520510  42 +  23952694 AAAACTCT-------------------------------------------------------------TACATGAAT--------------------AATCAAGAATAATCATACa-ttaaaa-
q panTro2.chrY                                              00000000-------------------------------------------------------------000000000--------------------0000000000000000000-000000-
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058433  43 - 202140232 AAAACTCT-------------------------------------------------------------TCCGTGAAT--------------------AATCAGGAATGATCATCCATTTTAAA-
q ponAbe2.chr3                                              99999999-------------------------------------------------------------999999999--------------------99999999999999999999999999-
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784479  43 + 189746636 AAAACTCT-------------------------------------------------------------TACATGAAT--------------------AATCAGGAATAATCATCCATTTAAAA-
q rheMac2.chr2                                              99999999-------------------------------------------------------------999999999--------------------99999999999999999999999999-
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263155  41 -  88675666 AAAACTCT-------------------------------------------------------------TACACAAAT--------------------TAGCAGCAGTAATGAAAC--TTTAAA-
q cavPor3.scaffold_0                                        99999999-------------------------------------------------------------999999999--------------------999999999999999999--999999-
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495328  39 + 163896628 AAAACTCT-------------------------------------------------------------TACATGAA---------------------TATCAGCGACAAC-AAAC--TTTGAA-
q oryCun2.chr14                                             99999999-------------------------------------------------------------99999999---------------------9999999999999-9999--999999-
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010642  41 + 161106243 AAAACTCT-------------------------------------------------------------TACACGAAT--------------------TATCAGCAATAATCAAAC--TTTAAA-
q bosTau4.chr1                                              99999999-------------------------------------------------------------999999999--------------------999999999999999999--999999-
i bosTau4.chr1                    C 0 I 1
s equCab2.chr16                    22232855  37 -  87365405 ---ACTCT-------------------------------------------------------------TACATAAAT--------------------TATCAGCAATAATCAAAC--TTGAA--
q equCab2.chr16                                             ---99999-------------------------------------------------------------999999999--------------------999999999999999999--99999--
i equCab2.chr16                   C 0 I 1
s canFam2.chr23                    26011839  41 -  55389570 AAAACTCT-------------------------------------------------------------TACATGAAT--------------------TATCAGAAATAATCAACC--TTTAAA-
q canFam2.chr23                                             99999999-------------------------------------------------------------999999999--------------------999999999999999999--999999-
i canFam2.chr23                   C 0 I 305
s eriEur1.scaffold_377961             44529  41 +     88154 GAGACCCT-------------------------------------------------------------TTTATGAGT--------------------TATAAGCAACAATTAGAC--TTCAGA-
q eriEur1.scaffold_377961                                   99999999-------------------------------------------------------------999999999--------------------999999999999999999--999999-
i eriEur1.scaffold_377961         C 0 I 7
s loxAfr3.scaffold_36                538426  42 -  24123610 AAAATCCT-------------------------------------------------------------TACATGAGT--------------------TATCAACAATAATCAAAC--TTTAAAA
q loxAfr3.scaffold_36                                       99999999-------------------------------------------------------------999999999--------------------999999999999999999--9999999
i loxAfr3.scaffold_36             C 0 C 0
s proCap1.scaffold_15753              30381 101 -     39409 AAAATCCCAGTTTTGATTTAAAAACATATCCTGTGTGTGTGTGTACACAGACACAGAAAATACATTCTGtatgtgtgtatatatacaaacactgtatatat------------------------
q proCap1.scaffold_15753                                    69934396335883535745888575425121536353646465497989999989999999999999966354756666666648694999999999999------------------------
i proCap1.scaffold_15753          I 2540 I 133
e rn4.chr9                        107369132 114 - 113440463 I
e mm9.chr17                        50268643 122 +  95272651 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=-447.000000
s hg19.chrY                         7667013  51 +  59373566 atacttt-ttataattccatttttaatt-------aaa----------------------------------------------atatatG----------------------------CACATACAT----AAATA
s panTro2.chrY                       520552  51 +  23952694 atacttt-ttataattccatttttaatt-------aaa----------------------------------------------atatatG----------------------------CACATACAT----AAATA
q panTro2.chrY                                              0000000-00000000000000000000-------000----------------------------------------------0000000----------------------------000000000----00000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058476  58 - 202140232 ATACTTT-TTATATTTCCATTTTTAATT-------AAAAatata---------------------------------------tacacata----------------------------cacgtacat----aaata
q ponAbe2.chr3                                              9999999-99999999999999999999-------999999999---------------------------------------99999999----------------------------999999999----99999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784522  51 + 189746636 ATACTTT-TTATATTTCCATTTTTAATT-------AAA----------------------------------------------atataca----------------------------catatacat----aaata
q rheMac2.chr2                                              9999999-99999999999999999999-------999----------------------------------------------9999999----------------------------999999999----99999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263196  50 -  88675666 ATACTCC-TG-CACTTCCATTTTTAAT---------------------------------------------------------ATATATA----------------------------CACAGTCACACAAAAATA
q cavPor3.scaffold_0                                        9999999-99-9999999999999999---------------------------------------------------------9999999----------------------------999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495367  52 + 163896628 ATCCTTC-CGACACTCCCATTTCCCATTA------AAA----------------------------------------------ACATATC----------------------------CACAGACAC----ACACA
q oryCun2.chr14                                             9999999-999999999999999999999------999----------------------------------------------9999999----------------------------999999999----99999
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010684  62 + 161106243 -TACCCCTCtatatttttgtttttaatta------aaa----------------------------------------------atataCACACAA------------------CTCCACACCTGTAT----ATACA
q bosTau4.chr1                                              -9999999999999999999999999999------999----------------------------------------------999999999999------------------99999999999999----99999
i bosTau4.chr1                    I 1 C 0
s canFam2.chr23                    26012185  68 -  55389570 aTACTCC-CTATATTACCATTTTCAGTTCtatatatac----------------------------------------------acatacatgtgt------------------gcacacacacacac----acata
q canFam2.chr23                                             9999999-999999999999999999999999999999----------------------------------------------999999999999------------------99999999999999----99999
i canFam2.chr23                   I 305 C 0
s equCab2.chr16                    22232893  63 -  87365405 ATACTCC-CTATATTCCCATTGTTAATTTT-----TAA----------------------------------------------AAatacatatat------------------acacacacatacct----aaata
q equCab2.chr16                                             9999999-9999999999999999999999-----999----------------------------------------------999999999999------------------99999999999999----99999
i equCab2.chr16                   I 1 C 0
s eriEur1.scaffold_377961             44577  55 +     88154 TTACGTC-CTATATTTCCATTA-------------TAA----------------------------------------------CCAaaagtgtgt------------------tctctctctctcac----acaca
q eriEur1.scaffold_377961                                   9999999-99999999999999-------------999----------------------------------------------999999999999------------------99999999999999----99999
i eriEur1.scaffold_377961         I 7 C 0
s rn4.chr9                        107369246  31 - 113440463 --------------------TTTGAATT--------AA----------------------------------------------AAGTATG----------------------------CACAGGGAC----AAGTT
q rn4.chr9                                                  --------------------99999999--------99----------------------------------------------9999999----------------------------999999999----99999
i rn4.chr9                        I 114 C 0
s mm9.chr17                        50268765  32 +  95272651 -------------------TTTTGAATT--------AA----------------------------------------------AAGTACG----------------------------CACATGCAC----AAATT
i mm9.chr17                       I 122 C 0
s loxAfr3.scaffold_36                538468 124 -  24123610 -TGTCCC-CTATATTCCCatttttaatt-------aaaaatacattaaattaaaaGATATGTTCtatatgtatatatattatctatatatgtacataaaaataacacattttcaacacacacatacaa----aaatc
q loxAfr3.scaffold_36                                       -999999-99999999999999999999-------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e proCap1.scaffold_15753              30482 133 -     39409 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=-29547.000000
s hg19.chrY                         7667064 22 +  59373566 CACACACATA--TATGTATGA----------------------------------------AT-T-
s panTro2.chrY                       520603 22 +  23952694 CACACACATA--TATGTATGA----------------------------------------AT-T-
q panTro2.chrY                                             0000000000--000000000----------------------------------------00-0-
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058534 22 - 202140232 catacacata--tatgtatGA----------------------------------------AT-T-
q ponAbe2.chr3                                             9999999999--999999999----------------------------------------99-9-
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784573 22 + 189746636 catacacata--catgtaTGA----------------------------------------AT-T-
q rheMac2.chr2                                             9999999999--999999999----------------------------------------99-9-
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263246 22 -  88675666 CATATACATG--TCTGTGTGT----------------------------------------AT-T-
q cavPor3.scaffold_0                                       9999999999--999999999----------------------------------------99-9-
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495419 15 + 163896628 CACGTGCATG--CAGGT-------------------------------------------------
q oryCun2.chr14                                            9999999999--99999-------------------------------------------------
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010746 23 + 161106243 CATGTGCACA--TACATGCAT----------------------------------------GTAC-
q bosTau4.chr1                                             9999999999--999999999----------------------------------------9999-
i bosTau4.chr1                    C 0 I 1
s canFam2.chr23                    26012253 25 -  55389570 aatacatacatTTATCTGTAT----------------------------------------GTAT-
q canFam2.chr23                                            999999999999999999999----------------------------------------9999-
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22232956 23 -  87365405 catacacacg--taTGTGTGT----------------------------------------ATTT-
q equCab2.chr16                                            9999999999--999999999----------------------------------------9999-
i equCab2.chr16                   C 0 C 0
s eriEur1.scaffold_377961             44632 19 +     88154 cacacacac---tctctctct-------------------------------------------c-
q eriEur1.scaffold_377961                                  999999999---999999999-------------------------------------------9-
i eriEur1.scaffold_377961         C 0 C 0
s rn4.chr9                        107369277 15 - 113440463 CTCATATATG--TATCT-------------------------------------------------
q rn4.chr9                                                 9999999999--99999-------------------------------------------------
i rn4.chr9                        C 0 C 0
s mm9.chr17                        50268797 19 +  95272651 CCCATGTAAG--TATGTAC-------------------------------------------T-T-
i mm9.chr17                       C 0 C 0
s loxAfr3.scaffold_36                538592 23 -  24123610 catacacata--tatgtacgc----------------------------------------aG-CT
q loxAfr3.scaffold_36                                      9999999999--999999999----------------------------------------99-99
i loxAfr3.scaffold_36             C 0 C 0
s proCap1.scaffold_15753              30615 63 -     39409 catacacaaa--tataGACACGCACATATAGAATGTACTTTTTATATATTTTATTTATGAGAG-CC
q proCap1.scaffold_15753                                   9999999999--999999999999999999999999999999999999999999999999999-99
i proCap1.scaffold_15753          I 133 N 0
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=1859864.000000
s hg19.chrY                         7667086 440 +  59373566 TTCCGCTAGGAAACCCACACCAAGAACTTAGGGTTTGTCTGTAACAACTGAACACACTATCACACTACAACCC-AATGGCCTGGCCACAGACAATAGTAGATGCTTCAAGGGAAAGAATAGAGCCCTTTCAGCCAATTATACAATTACATGATATGACCATGTTCACATTATC-AAAGGGAGGTAGACCAAATGACCTAGCTACTTCAAATCAATAACCCCATTTACCTCAATTATATGGTAGACAGAGTCCAAATAATCTGAGTAATTATTTC-AATTCATTCAGATGCTGTAGTTTTGGCCTGTGTGTGCACAACTAATTTTTCCTTCTGGTATACACACCCTTAAACCATCAGCAAATACCAAAATGCACAACAGCAAACTCCTATCAGTTTTATCTATTAGCAG----------------TGTAAAC-AAATTCT-CTCCACTATCTGGCAGATTAA
s panTro2.chrY                       520625 440 +  23952694 TTCCGCTAGGAAACCCACACCAAGAACTTAGGGTTTGTCCATAACAATTGAACACACTATCACACTATAACCC-AATGGCCTGGCCACAGACAATAGTAGATGCTTCAAGAGAAAGAATAGAGCCCTTTCAGCCAATTATACAATTACATGATATGACCATGTTCACATTATC-AAAGGGAGGTAGACCAAATTACCTAGCTACTTCAAATCAATAACCCCATTTACCTCAATTATATGGTAGGCAGAGTCCAAATAATCTGAGTAATTATTTC-AATTCATTCAGATGCTGTAGTTTTGGCCTGTGTGTCCACAACTAATTTTTCCTTCTGGTATACACACCCTTAAACCATCAGCAAATACCAAAATGCACAACAGCAAACTCCTATCGGTTTTATCTATAAGCAG----------------TGTAAGC-AAATTCT-CTCCACTATCTGGCAGATTAA
q panTro2.chrY                                              0000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----------------0000000-0000000-000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058556 439 - 202140232 TTCCACCAGGAAACCCACACTAAGTACTTAGGGTTTTTCTGTACTAATTGAACACACTATCACACTATAACCC-AAAGGCCTGGCCACAGACAATAGCAGATGCTTCAAGAGAAAGAATAGAGCCCTTTCAGCCAATTATACAATTACACGATATGACCATGTTTACATTATC-AAAGGGAGGCAGACCGAATTACCTAGCTACTTCAAATTAATAACCCCATTTACCTCAATTATCTGGCAGGCAGGGTCTAAATAACCTGAGTAATTACTTC-AATTCATTCAGATGGTATAGATTTGGCCTGTGTGTCCACAAGAAATTTTTCCTTCCAGTACACACA-CCTTAAACCATCAGCAAATATCAAAATGCACAATAGCAAACTCCTATCAGTTTCGTCTATAAGCAG----------------TGTAAGC-AAATTCT-CTCCATTATCTGGCAGATTAA
q ponAbe2.chr3                                              9999999999999999999999999999999999999999999999999999999999999999999999999-999999999999990399999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158784595 438 + 189746636 TTCCACTAGGAAACTCACACTAAGTATCTAGGGTTTGTCTATAATAATTGAACACACTAACATACTATAACCC--ATGGCCTGGCCACAGACAATAGCAGCCGCTTTAAGAGAAAGAATAGAGCCCTTTCAGCCAATTTTACAATTACACGATATGACCATGTTTACATTATC-AACGGGAGGCAGACCAAATTACCTAGCTACTTCAAATTAATAACCCCATTTACCTCAATTATCTGGCAGGCAGGGTCTAAATAACCTGAGTAATTACTTC-AATTCATTCATATGGTATACATTTGGCCTGTGTGTCCACAAGTAATTTTTCCTTCCAGTACACACA-CCTTAAACTATCAGCAAATATCAAAATGCACAATGGCAAACTCCTATCAGTTTCATCTCTAAGCAG----------------TGTCAGC-ACATTCT-CTCCATTATCCGGCAGATTAA
q rheMac2.chr2                                              9999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263268 433 -  88675666 TTCCACTGGGAAACTCA-GGCTAGTACCTATGGTTTGTCTATAATAATCTATCACACTATGACACTATAACCC-AATGGCCAGACCCTAGACAACAGCAGATGCTTCAAGAGAAAGAATTGAGCCCTTTCAGCCAATTATACAATTACACAATATGACCATGTTTACATTATC-AAAGGGAAGCAGACCAAATTACCTAGCTACTTCAAATTAATAACCCCATTTACCTCAATTATCTGGCAGGCAGGGTCTAAATAATCTGAGCAATTACTTC-AATTCATTCAGACAGTATAGATTTGGCCTGTGCATCCAGAAGTAATTCTTCCTTCCAGAACA------CTTCTACCGTCAGCAAATATCAAAATGCACAACAGCAAACTCACATCAGCTTTGTCTACAAGCAG----------------TGTAAGC-AAATTTT-CTCCATTATCTAGCAGATTAA
q cavPor3.scaffold_0                                        99999999999999999-9999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495434 419 + 163896628 -TCCACTCGGAAGCCAA-GCTAAGTACCTAGG-TTTGCCCATAATAACCTAATAGACTAGCACGCTGTAACCC-ACTGGCCAGGCCTCAGACAACAGCAGAGACTTCAAGAGAAAGAATTGAGCCCTTTCAGCCAATTATACAATTACACAATATGACCATGTTTACATTATC-AAAGAGAGGCAGACCAAATTACCTAGCTACTTCAAATTAATAACCCCATTTACTGCAATTATCTTGCAGGCAGGGTTTAAATAATCTGAGTAATTACCGC-AACGCATTCAGACACTATAGATTGGGCCTGTGTGTCCACAAGTCATTTTTCC------------------TCTAACATCAGCAAACATCAAAACGCACAACGGCAAATTCATAGCAGCTTTGTTCAGCAGCAG----------------TGTAAGC-AAATTTC-CCCCATTATCTGGCAGATTAA
q oryCun2.chr14                                             -9999999999999999-99999999999999-9999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999------------------999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157010770 426 + 161106243 TCTCACTAGGAAAGCCAAGCTAAGTA-CTGGAGTTTATCTGTAATAAC--------CTCATGTGCTATAACCC-AGGGGCCAGAGCACAGGCAGTAACAGACGACTCGAGAGAAAGAATAGGGCCCTGTCAGGCAATTACACAATTATACACGATGACCATGTTTACATTATC-AAAGGGAGGCAGACCCAATTACCTAGCTACTTCAAATGAATAACCCCATTTTCCTCCATTATCTGGCAGGCAGGGTCTCAATAATCTGAGTCATTACCTCAAATTTACTCAGACGGTACAGGTTTGGCCAGTGAACCCAGAAGCAGTTTTTCCTTCCAGAACG------CCTCCACCATCAGCAAATACCAAAATGCGCCGCAGTAAGCCCCCGTCAGCCTTGTCTGTAAGCAG----------------CGTAAGC-GAATTCT-CTCCCTCGCCTGGCAGATCAA
q bosTau4.chr1                                              99999999999999999999999999-999999999999999999999--------99999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999879999999999999999999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i bosTau4.chr1                    I 1 I 150
s canFam2.chr23                    26012278 425 -  55389570 TTTCACTAGGCAACCCAAGCCAAGTA-CTGGGGTTTGTCTGAAATAAT--------CTAATACACTAAAACCC-AATGGCCAAGCTACAGACAATAGCAGGTGCATCAAGAGAAAGAATAGAGCCTTTTCAACCAATTATAGAATTATACAATGTGACCATGTTTACATTATC-GAAGGGAGGCAGACCCAATTACCTAGCTACTTCAAATTAATAACCCCATTTACCTCAATTATCTGGCAGGCAGGGTCTAAGTAATCTAAGCAATTACCTT-GATTCACTCAGATGGTATAGATTTGGCCTGTGAGTCCAGAA-TAATTTTTCCTTCCAGAATG------CCTCCACCATCAGCAAATATCAAAATGCACAACAGCAAATTCACATCAGCTTCTTCCATAAGGAT----------------TAAAAAAGAAATTCT-TTCCACTGTCTGCCAGATTAA
q canFam2.chr23                                             99999999999999999999999999-999999999999999999999--------99999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999-99999999999999999999------99999999999999999999999999999999999999999999999999999999999999999----------------999999999999999-999999999999999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22232979 425 -  87365405 TTTCACTAGGAAACCC-AGCTACGTAGCCAGGGTTTGTCTGTAATAAC--------CTGACAAACTATAACCC-AATGGCCAGGCCACAGACAACAGCAGATGCGTCAAGAGAAAGAATAGAGCCCTTTCAGCCAATTATACAATTACACAATATGACCATGTTTACATTATC-AAAGGAAGGCAGACCCAATTACCTAGCTACTTCAAATTAATAACCCCATTTACCTCAATTATCTGGCAGGCAGGGTCTAAATAATCTGAGTAATTACCTC-AATTCACTCAGACAGTATAGATCGGGCCTCTGAGTCCAGAAGTGATCTTCCCTTCCAGGACA------CCTCCACCGTCAGCAAATATCAAAATGCATGACAGCAAACTCACACCAGCTTCCTCGAAAAGCAG----------------CGTGAGC-AAATTCT-CTCCATGATCTGGCAGGTTAA
q equCab2.chr16                                             9999999999999999-9999999999999999999999999999999--------99999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i equCab2.chr16                   C 0 C 0
s eriEur1.scaffold_377961             44651 427 +     88154 tttcactaggaAACCAAAGCTAGGTACCCAGAATTTGTCTATAATAGT--------CTAATATACTATAACCC-AATGGCCAGGCCAGAGACGAAAGCAGATGCTTCAAGAGAAAGAATCAAGCACTTTCAGTCAATTATACAATTACATAATATGACCATGTTTACATTATC-AAAGGGAGGCAGGCCCAATTACCTAGCTACTTCAAATTAATAACTCCATTTACCTCAATTATCTGGCAGGCAGGCTCTAAATAACCCAAGTAATTACCTC-AACTCACTCACATGGTATAGATTTGGCCTGTGGGTCCAGGAGGGATTTTTCCTTCCAGAACA------CTCCCACCTCCAGCAAATAGTGAAACTAGCCACAGCAAACTCACATCAGCTGCCTCTGTAAGTAG----------------AACAAGC-AAATTCTCCCCCACTCTCTGGCTTATCTA
q eriEur1.scaffold_377961                                   999999999999999999999999999999999999999999999999--------99999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999999----------------9999999-99999999999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s rn4.chr9                        107369292 412 - 113440463 -CCCCCTCTAAAACCGA-AGCCAGAGTCAGAG---------TGACAATCCATCATACTGTCATAATATCACCC-AGTGTCCAGGCCCCAGAC-ATAGGAGAGGCTTGAAGAGAGAAGGCAGACCCCTTCCAGCCAATTAT--------ACAATGCGGCCATGTTTACATTATC-AAAGGGAGGCAGCCCAAATTACCTAGCTACTTCAAGTTAATAACCCCATTTATGTCAATTACCTGGCAGGCGGGATCCAAACAATCTGAGTAATTACCTC-AACTCTTTCAGTCAGGATGAAGCCGGCCTACATGTCCAGCTGCAATTTTTCCTTCTACCACA------CTTCTATCCTCAGCAA--ATCAAGATGGGCAACAGCAGGACCACATCAGTCTCCTCGATAAGCAG----------------TGTAAGC-AAGTCCT-CTCCACTGCCTAGACGAGTGA
q rn4.chr9                                                  -9999999999999999-99999999999999---------99999999999999999999999999999999-999999999999999999-99999999999999999999999999999999999999999999999--------9999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999------9999999999999999--99999999999999999999999999999999999999999999999----------------9999999-9999999-999999999999999999999
i rn4.chr9                        C 0 C 0
s mm9.chr17                        50268816 432 +  95272651 CCACCCTCTAAGACCCA-AGCCAGAGTCTGAG---------TGACAATCTATCATGCTGTCACAATATCACCCAAATGTCCAGGCCCCAGAC-ACAGGAGAGGCTTGAAGAGAGAGGACAGAGCCTTTCCAGCCAATTAG--------ACAATACGGTCATGTTTACATTATCAAAAGAGAGGGGGCCCAAATTACCTAGCTACTTCAAGTTAATAACGCCATTTATGTCAATTACCTGGCAGGCAGGATCTACACAATCTGAGCAATTACCTC-AACTCTTTCAGACAGGACGAACCTGGCCTGCATGGCCAGCTGTAATTTTTCCGTCCACAACA------CTTCTATCCTCAGCAG-TATCAAGATGAGCAACAGCAGGACCACATCAGTCTCTTCGATAAGCAGCGTAAGCAAACCCTCACGTAAGC-AAATCCT-CTCCACTGCTTGGCAGATTAA
i mm9.chr17                       C 0 C 0
s loxAfr3.scaffold_36                538615 406 -  24123610 TTTCACTAGGAAACCCAAGCTAAGTACCTGGTGTTTG----TAATAAT--------CTAACACATTATAACCC-AATGTTCAGGCCACAGACAATAGCAGATGCTCCAAGAGAAAGAAAGGAGCCCTTTTAGCCAATTATACAATTACATAATACAACCATGTTTACATTATC-AAAGGGGGGCAGACCCAATTACCTAGCTACTTCAAATTAATAACCCCATTTCCCTCAATTATCTGGCATGCAGGGCCTAAATAATCTGAGTAATTACCTC-AATTCATTCAGATGGTATAGATTCGGCTTGTGAGTCCAAAAGTAATTTTTCCTTCTAGAACG------TATCCATTATCAGCAAATATCAAAATGCACAAGAGAAAACTCATATCAGCTTTGTCTATAAGCAG----------------TTTAAGC-AAACTTT-----------------ATTAA
q loxAfr3.scaffold_36                                       9999999999999999999999999999999999999----9999999--------99999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999999----------------9999999-9999999-----------------99999
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=276040.000000
s hg19.chrY                         7667526 114 +  59373566 AATTTGTTAT-ACTC-TTAATAATCCAGG-TTGAGA--------TTT-------------------TCTTTTGTGACAACAACTC-ACTGGACCATGGAACTTTAGAGCTAGGAAGTACCATCCAGGGCCAACAGTCT-----AAAAGCC
s panTro2.chrY                       521065 114 +  23952694 AATTTGTTAT-ACTC-TCAATAATCCAGG-TTGAGG--------TTT-------------------TCTTTTGTGACAACAACTT-ACTGGACCATGGAACTTTAGAGCTAGGAAGTACCATCCAAGGCCAACAGTCT-----AAAAGCC
q panTro2.chrY                                              0000000000-0000-0000000000000-000000--------000-------------------0000000000000000000-0000000000000000000000000000000000000000000000000000-----0000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71058995 114 - 202140232 AATTTGTTAT-ACTC-TTAATAATCCAGG-TTGAGG--------TTT-------------------TCTTTTCTGACAAAAACTC-ACTGGACCATAGAATTTTAGAGCTAGGAAGTACCATCCAGGGCCCACAGTCT-----AAAAGCC
q ponAbe2.chr3                                              9999999999-9999-9999999999999-999999--------999-------------------9999999999999999999-9999999999999999999999999999999999999999999999999999-----9999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785033 114 + 189746636 AATTTGTTAT-ACTC-TTAATAATCCAGG-TTGAGG--------TTT-------------------TCTTTTCTGACAAAAACTC-ACTGGACCACAGAATTTCAGAGCTAGGAAGTACCATCCAGGGCCCACAGTCT-----ACAAGCC
q rheMac2.chr2                                              9999999999-9999-9999999999999-999999--------999-------------------9999999999999999999-9999999999999999999999999999999999999999999999999999-----9999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263701 127 -  88675666 AATTTGCTAATATTC-TTAATCATCCAGTTTTGAAG--------TTTTTGGTGTTTTT--------TCTTTCTTGATAAAAACTC-ATGTGGCCACAGGATTTTTAAGTTAGAAAGTATCGAACAGGACCCCAAATTT-----GAAAGCT
q cavPor3.scaffold_0                                        999999999999999-99999999999999999999--------99999999999999--------9999999999999999999-9999999999999999999999999999999999999999999999999999-----9999999
i cavPor3.scaffold_0              C 0 C 0
s mm9.chr17                        50269248 135 +  95272651 GATGTATCGG-ACTC-TCAATAATCCGGGTTTAAAG--------TTAGGAGGTTTTTGTTTTTAAATTCGTTCTAACAAAATCCCGTTAAGACCATACCATTAACAAGCTAGCAAGTACTGACCAAGGGCTAAAAGTC-----AATAGAA
i mm9.chr17                       C 0 I 1454
s rn4.chr9                        107369704 114 - 113440463 GAAGTATCAG-ACTC-TTAATAACCCAGGCTTAAAG--------TTGGGAGCTTTTAA---AGAAATTGTTTCTAACAAAAACTC-CTAAGCCCATGGCATTTACAAGCTGGCATGTACTGACCAAGG----------------------
q rn4.chr9                                                  9999999999-9999-99999999999999999999--------99999999999999---999999999999999999999999-999999999999999999999999999999999999999999----------------------
i rn4.chr9                        C 0 I 414
s oryCun2.chr14                     2495853 117 + 163896628 AATTTGTTAC-ACTC-TTCATAATCCAGGATTGATG--------GTATC-----------------TTTTTCCTGACAAAAACTC-ACTGGGCCACAGAATTGTAGAGCTAGAAAGTGGCATCCAAGACCCCAAGGTC-----TAAAAAA
q oryCun2.chr14                                             9999999999-9999-99999999999999999999--------99999-----------------9999999999999999999-9999999999999999999999999999999999999999999999999999-----9999999
i oryCun2.chr14                   C 0 I 3
s bosTau4.chr1                    157011346 101 + 161106243 AGCGTGTCAT-A-TC-CTAATAATCCAGGCTTGAAGG-GTTTTTTTT-------------------TTCTCCCTGATAAAAACTC-ACAGGGCCACAGGACTTCAGGGC--------------------CCAAGGTCT-----AAAAGCC
q bosTau4.chr1                                              9999999999-9-99-999999999999999999999-999999999-------------------9999999999999999999-99999999999999999999999--------------------999999999-----9999999
i bosTau4.chr1                    I 150 C 0
s canFam2.chr23                    26012703 106 -  55389570 AATTTGCTAT-ACTT-TAAATAACACAGGTTTGAGG-------TTTT-------------------TTTTTTCTGACAAAAACTC-ATAGGACTATAGGATTTTACAGCTGGAAAGTAC----------CCCAGGTTT-----AAAAGCC
q canFam2.chr23                                             9999999999-9999-99999999999999999999-------9999-------------------9999999999999999999-999999999999999999999999999999999----------999999999-----9999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22233404 120 -  87365405 AATGTGTTCT-ACTC-TTAATAATCCAGGTTTGAAG--TTGATTTTT-------------------CTTTTTCTGACAAAAATtc-ataggatcctagaattttagagctagaaagcaccATCCAGGG-CCAAAGTCT-----AAAAGCC
q equCab2.chr16                                             9999999999-9999-99999999999999999999--999999999-------------------9999999999999999999-999999999999999999999999999999999999999999-999999999-----9999999
i equCab2.chr16                   C 0 C 0
s eriEur1.scaffold_377961             45078 128 +     88154 AATTTGTTAT-GCTCTTTAATAATCTAGGTTtgagagcacttttttt-------------------ttttgactagcaAAAGTTC-ACAGGGCCATGGAACTTTAGAGTTAAGCAGTACCATCTATGG-CTCAAGAGTTAAACAAAAGAC
q eriEur1.scaffold_377961                                   9999999999-999999999999999999999999999999999999-------------------9999999999999999999-999999999999999999999999999999999999999999-999999999999999999999
i eriEur1.scaffold_377961         C 0 I 3144
s loxAfr3.scaffold_36                539021 112 -  24123610 AATTTGTTAT-ACTC-TTAATAACCTAGGCTTGAAG--------AT--------------------TTTTTTCTGACAAAAACCC-ACAGGGCCATAGAATTTTAGAGGTAGAAAGTACCA-CTAGGGGCCAAAGTCT-----AAAGCC-
q loxAfr3.scaffold_36                                       9999999999-9999-99999999999999999999--------99--------------------9999999999999999999-99999999999999999999999999999999999-9999999999999999-----999999-
i loxAfr3.scaffold_36             C 0 C 0
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                1300 3553 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=52998.000000
s hg19.chrY                         7667640 28 +  59373566 AGCTCCT-------------GGAAGC--A-----GTCC-AACC--------AGAAAT
s panTro2.chrY                       521179 28 +  23952694 AGCTCCT-------------GGAAGC--A-----GTCC-AACC--------AGAAAT
q panTro2.chrY                                             0000000-------------000000--0-----0000-0000--------000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059109 28 - 202140232 AGCTCCT-------------GGAAGC--A-----GTCC-AACC--------AGAAAT
q ponAbe2.chr3                                             9999999-------------999999--9-----9999-9999--------999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785147 28 + 189746636 AGCTCCT-------------GGAAGC--A-----GTCC-AACC--------AGAAAT
q rheMac2.chr2                                             9999999-------------999999--9-----9999-9999--------999999
i rheMac2.chr2                    C 0 C 0
s dipOrd1.scaffold_8112                4853 54 -     49748 AGCTCTTTAGTAAAAGACAAAGCAGC--AAGCTGACCC-AGGCCTGTCATTAGAAGC
q dipOrd1.scaffold_8112                                    99999999999999999999999999--9999999999-999999999999999999
i dipOrd1.scaffold_8112           I 3553 I 1176
s cavPor3.scaffold_0                8263828 28 -  88675666 AGCTACT-------------GTCAGC--A-----GCCC-AAGC--------AGAAAT
q cavPor3.scaffold_0                                       9999999-------------999999--9-----9999-9999--------999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2495973 27 + 163896628 AGTCCCT-------------GGCA-C--A-----CTCC-AAAC--------AGAAAT
q oryCun2.chr14                                            9999999-------------9999-9--9-----9999-9999--------999999
i oryCun2.chr14                   I 3 C 0
s bosTau4.chr1                    157011447 28 + 161106243 AGCTGCC-------------AGCAGC--A-----GTCC-GACC--------AGAAGC
q bosTau4.chr1                                             9999999-------------999999--9-----9999-9999--------999999
i bosTau4.chr1                    C 0 C 0
s canFam2.chr23                    26012809 30 -  55389570 ACTTACT-------------AGTGGCAGT-----ATCC-AACG--------GGAAAT
q canFam2.chr23                                            9999999-------------999999999-----9999-9999--------999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22233524 28 -  87365405 AGCTGCC-------------GGCAGC--C-----ATCC-AAAC--------AGAAAC
q equCab2.chr16                                            9999999-------------999999--9-----9999-9999--------999999
i equCab2.chr16                   C 0 C 0
s loxAfr3.scaffold_36                539133 29 -  24123610 AGCTACT-------------GGCAGC--A-----GTCCAAACC--------AGAAAG
q loxAfr3.scaffold_36                                      9999999-------------999999--9-----999999999--------999999
i loxAfr3.scaffold_36             C 0 C 0
e rn4.chr9                        107369818 414 - 113440463 I
e mm9.chr17                        50269383 1454 +  95272651 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             45206 3144 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=66154.000000
s hg19.chrY                         7667668 48 +  59373566 CCAGCCTGCTCACTcatagcacgtaaggcaaggaggtctgaagctcag-------
s panTro2.chrY                       521207 48 +  23952694 CCAGCCTGCTCACTcatagcacgtaaggcaaggaggtctgaatctcag-------
q panTro2.chrY                                             000000000000000000000000000000000000000000000000-------
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059137 48 - 202140232 CCAGCCTGCTCACTcatagcacgtaaggcaaggaggtctgaagcccaa-------
q ponAbe2.chr3                                             999999999999999999999999999999999999999999999999-------
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785175 48 + 189746636 CTAGCCTGCTCACTcatagcacataaggcaaggaggtctgaagtccaa-------
q rheMac2.chr2                                             999999999999999999999999999999999999999999999999-------
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263856 37 -  88675666 CCTgcctattgactca-----------gcatcatggtccaaagcccga-------
q cavPor3.scaffold_0                                       9999999999999999-----------999999999999999999999-------
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2496000 48 + 163896628 GCAGCCTACTGACCGATGgcagtgaagggaaggcgggccagagccggg-------
q oryCun2.chr14                                            999999999999999999999999999999999999999999999999-------
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157011475 46 + 161106243 CCAG-CCACTGACTCGCagcagttcaggg-aggggctccaaagcccca-------
q bosTau4.chr1                                             9999-999999999999999999999999-999999999999999999-------
i bosTau4.chr1                    C 0 C 0
s canFam2.chr23                    26012839 47 -  55389570 CCAG-CTACTGACTcagagaaacaaagtaaaggagcgctaaagcccaa-------
q canFam2.chr23                                            9999-9999999999999999999999999999999999999999999-------
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22233552 48 -  87365405 GCAGCCTACTGACTCCCagcagctgagggaaggggctgcaaagcccag-------
q equCab2.chr16                                            999999999999999999999999999999999999999999999999-------
i equCab2.chr16                   C 0 C 0
s loxAfr3.scaffold_36                539162 55 -  24123610 CCAGCCTCCTGACTcaaagtggttaagggtatgagcttcaaagtctgaaggcctg
q loxAfr3.scaffold_36                                      9999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36             C 0 I 133
e rn4.chr9                        107369818 414 - 113440463 I
e mm9.chr17                        50269383 1454 +  95272651 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             45206 3144 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=242257.000000
s hg19.chrY                         7667716 149 +  59373566 atgcttgggttccaatcctggctctgccacttactagttgagcgac---cttggcaagtccctaaacctcaccaagcctcacagccctcttctgtacaactgtggtaataagggaatctgatttatagagaca-gtacaaggattaaatgaga
s panTro2.chrY                       521255 149 +  23952694 atgcttgggttccaatcctggctctgccacttactagttgagtgac---cttggcaagtccctaaacctcaccaagcctcacagtcctcttctgtacaactgtggtaataagggaatctgatttatagagaca-gtacaaggattaaatgaga
q panTro2.chrY                                              0000000000000000000000000000000000000000000000---000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059185 147 - 202140232 atgcttgggttcaaatcctggctctgccacttactagctgaatggc---cttggcaagttcctaaaccttgccaagcct--gagtcctcttctgtacaatggtggtaataagggaacctgatttatagagtca-gaacaaggattaaatgaga
q ponAbe2.chr3                                              9999999999999999999999999999999999999989999999---994899999999999999999999999999--9999999999999999999999999999999999999999999999999999-9999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785223 149 + 189746636 atgcttgggttcaaatcctggctctgccacttactagctgaatggt---cttggcaagttcctaaacctcgccaagcctcagagtcctcttctgtacgatggtggtaataaaggaacctgatttatagagtca-gaacaaggattaagtgaga
q rheMac2.chr2                                              9999999999999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8263893 143 -  88675666 aaccatgggttcaaatcttagctctgccacttacccactgcaagac---ctcaacaagtttcttaacttgg---agcctcagagacctca-ctgcatgatggtggtaaagatggaacctcact--tagagtca-acacactaattaaatgaga
q cavPor3.scaffold_0                                        9999999999999999999999999999999999999999999999---9999999999999999999999---9999999999999999-99999999999999999999999999999999--99999999-9999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2496048 137 + 163896628 tgcc-tggggccaaatcctggctccaccccttagcaggtgcatgat---cttggcaagttccttaacctgtac-aacctcagggctctcatccatacaatggtggtaacaacagaaccc---------agtga-gtacaaagactcagt-cgc
q oryCun2.chr14                                             9999-99999999999999999999999999999999999999999---999999999999999999999999-999999999999999999999999999999999999999999999---------99999-999999999999999-999
i oryCun2.chr14                   C 0 C 0
s bosTau4.chr1                    157011521 145 + 161106243 aggcttgtatcc-gatgctgcctctgc--ctcacgagctgcacggtgg-ctcggcaagtgctg--acctctctggacctgagaggttccatctggacgaaggtgggaataacggcacgtgtct--tagagaggtgtccgaggactaaacgaga
q bosTau4.chr1                                              999999999999-99999999999999--9999999999999999999-99999999999999--9999999999999999999999999999999999999999999999999999999999--9999999999999999999999999999
i bosTau4.chr1                    C 0 I 727
s canFam2.chr23                    26012886 148 -  55389570 acacttaggttcaaattttggctctcccacttaatagctgcaaggtgaccttagcaagtactt--acctctctgagcctaagagttctcatctgtacaaaggtggtaatgatggcacctacct--tatacttg-gtactagtgccaaacgaaa
q canFam2.chr23                                             999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999--99999999-9999999999999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22233600 150 -  87365405 atgcttgggttcaaatcctggctccaccgctcagcagctgcaaggtgacctcagcaagtacttc-agctctcgga-cctgagcatcttcctctgtgcaatcgtgctaatgatggcacccatccgatagagttg-gtactaggaccaaatgaga
q equCab2.chr16                                             9999999999999999999999999999999999999999999999999999999999999999-9999999999-999999999999999999999999999999999999999999999999999999999-9999999999999999999
i equCab2.chr16                   C 0 C 0
s loxAfr3.scaffold_36                539350 148 -  24123610 aggcctgggttcaaatcctgactccaccacttactagctgcattac---atcagcaagttccctgacctttctgagcctgagagttctcatctgcacaatggcaat-ataatggcacctaatttagaaagtat-gtatgaggattaaacgaga
q loxAfr3.scaffold_36                                       9999999999999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999-99999999999999999999999999-9999999999999999999
i loxAfr3.scaffold_36             I 133 C 0
e rn4.chr9                        107369818 414 - 113440463 I
e mm9.chr17                        50269383 1454 +  95272651 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             45206 3144 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=74342.000000
s hg19.chrY                         7667865  81 +  59373566 caattaacagaatgaacttagcatgcttcttggcacata---A--CTACTGTTGTT---------AAGTCCTTACTATTATTATTTTAA--------------------------------------------------CAGCAG
s panTro2.chrY                       521404  81 +  23952694 caattaacagaatgaacttagcatgcttcttggcacata---a--ctactgttgtt---------aagtccttactattattattTTAA--------------------------------------------------CAGCAG
q panTro2.chrY                                              000000000000000000000000000000000000000---0--00000000000---------000000000000000000000000--------------------------------------------------000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059332  81 - 202140232 caatccacataatgcacttagtatgcttcttggcacata---A--CTACCATTGTT---------AAGCCCGTACTATTATTATTCTTA--------------------------------------------------TAGCAG
q ponAbe2.chr3                                              999999999999999999999999999999999999999---9--99999999999---------999999999999999999999999--------------------------------------------------999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785372  81 + 189746636 caatccacataatgtacttagcatgcttcttggcacgta---a--ctactattgtt---------aaacccgtactattattaCTCTTA--------------------------------------------------CAGCAG
q rheMac2.chr2                                              999999999999999999999999999999999999999---9--99999999999---------999999999999999999999999--------------------------------------------------999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264036  80 -  88675666 taatccgtttggtgtccttagcatagttcttggcacata---aagcTACTGTGTTT---------AAGCACT---TATTTTAACTCCTA--------------------------------------------------AAGATT
q cavPor3.scaffold_0                                        999999999999999999999999999999999999999---99999999999999---------9999999---99999999999999--------------------------------------------------999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2496185  62 + 163896628 tgatgcctgcagtgcacttggcacagttcttggcacata---A--CTACTACTTTT---------AAATAC---------------------------------------------------------------------AGAAT
q oryCun2.chr14                                             999999999999999999999999999999999999999---9--99999999999---------999999---------------------------------------------------------------------99999
i oryCun2.chr14                   C 0 C 0
s canFam2.chr23                    26013034  88 -  55389570 taatgcatttaatgcacttggca-agttcttggaacata------ctaCCATTTTTAAGAAGCTAAAGCACTCAATATTATCATTGCTA--------------------------------------------------TAACAT
q canFam2.chr23                                             99999999999999999999999-999999999999999------99999999999999999999999999999999999999999999--------------------------------------------------999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22233750  77 -  87365405 taatgcgtgcaatgcacttagcacagttcttggcactta------gtaCCATTTTT---------AAGCACTTACTATTATTATTAC-----------------------------------------------------AACAT
q equCab2.chr16                                             999999999999999999999999999999999999999------99999999999---------9999999999999999999999-----------------------------------------------------99999
i equCab2.chr16                   C 0 C 0
s loxAfr3.scaffold_36                539498 116 -  24123610 ---------caatgc---------aGTTCTTGGTACATAGCTA--TTACCATTTTT---------AAGCACTTACTAACACTATTACtggaaaccctggtggtgtagtggttaagtgctaagattgctaaccaaaaggtcagcag
q loxAfr3.scaffold_36                                       ---------999999---------9999999999999999999--99999999999---------99999999999999999999999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36             C 0 I 109
e rn4.chr9                        107369818 414 - 113440463 I
e mm9.chr17                        50269383 1454 +  95272651 I
e bosTau4.chr1                    157011666 727 + 161106243 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             45206 3144 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=223853.000000
s hg19.chrY                         7667946 226 +  59373566 CATCACCT---------Ttaataggttc--------cccc-a---------------aaggatgtgtcc--atgtcctaatccct----agatcctgtgaatattacctt--atataacaaagga------------------tgtgattaag-----------ttaaagaccttgggaagaggtgcttatcctgttttatacaagtggtccctaaatgc--agtcacagggatccttataacagagaggcaca-gagagttttgagacagacacacaggagacgacataggcatatgg
s panTro2.chrY                       521485 226 +  23952694 CATCACCT---------TTAATAGGTTc--------cccc-a---------------aaggatgtgtcc--atgtcctaatccct----agatcctgtgaatattacctt--atataacaaagga------------------tgtgattaag-----------ttaaagaccttgggaagaggtgcttatcctgttttatacaagtggtccctaaatgc--agtcacagggatccttataacagagaggcaca-gagagttttgagacagacacacaggagacgacataggcatatgg
q panTro2.chrY                                              00000000---------00000000000--------0000-0---------------000000000000--00000000000000----000000000000000000000--0000000000000------------------0000000000-----------00000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000-00000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059413 226 - 202140232 CACCACCC---------TTAACAGGTTc--------cccc-a---------------aaggatgtgtcc--atgtcctaatccct----agaacctgtgaatattacctt--atataacaaagga------------------tgtgattaag-----------ttaaggaccttgggaagaggtgcttatcctgttttatacaagtggtccctaaatgc--agtcacatggatccttataacagacaggcaca-gagagttttgagacagacacacaggagaagacataggcacatgg
q ponAbe2.chr3                                              99999999---------99999999999--------9999-9---------------999999999999--99999999999999----999999999999999999999--9999999999999------------------9999999999-----------99999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999-99999999999999999999999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785453 222 + 189746636 CACCGCCT---------TTAATAGGTTT--------cccc-a---------------aaggatgtgtcc--atgtcctaatccct----agaacctatgaatattacctt--atataacaaagga------------------tgtgattaag-----------ttaaggaccttgggaaaaggtgcttatcctgttttatacaagtagtccctaaatgc--agtctcatagatccttataat----aggcaca-gagagttttgagacagacacacaggacaggacataggcacatgg
q rheMac2.chr2                                              99999999---------99999999999--------9999-9---------------999999999999--99999999999999----999999999999999999999--9999999999999------------------9999999999-----------99999999999999999999999999999999999999999999999999999999--999999999999999999999----9999999-99999999999999999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264116 212 -  88675666 CATAACCT---------TCaatggttgc--------cctc-a--------------aaaggatatgcccttgtgttccctccctccactagaacctgtgaatatcactaa--atacggcaaatga------------------tggtgctgaa-----------ttaaagaccttgggaagaggagaacatcttgagttacctaagtggaccctaaatgc--aatcacacgtaacc--gtaacagaaagg---a-cggagagtttag--ag----ACTGCAGAACACAA----------
q cavPor3.scaffold_0                                        99999999---------99999999999--------9999-9--------------999999999999999999999999999999999999999999999999999999--9999999999999------------------9999999999-----------99999999999999999999999999999999999999999999999999999999--99999999999999--999999999999---9-999999999999--99----99999999999999----------
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2496247 194 + 163896628 CATCACCT---------Tgaatgg--gc--------cccc-a--------------tgaaggtatgtcc--acatcctaatcctc----aaatcctgtgcatgtcagctt--acttggccaaagg------------------tg-----cag-----------ttaaggatcttgggaagcagag-----cctggatcatccaggtgggccctaaatgt-------cctgtgaac--acaacagca--g---a-gGGAGTTCTGAGGCAG----ACGGAAAAGGACAGACACA-----
q oryCun2.chr14                                             99999999---------9999999--99--------9999-9--------------9999999999999--99999999999999----999999999999999999999--9999999999999------------------99-----999-----------9999999999999999999999-----99999999999999999999999999999-------999999999--999999999--9---9-9999999999999999----9999999999999999999-----
i oryCun2.chr14                   C 0 I 12
s canFam2.chr23                    26013122 238 -  55389570 CACCACCT---------GCAATGAgctcagtgatggcccc-a--------------aaatgataagtcc--acatcataatcccc----atgacctgtgtatagtacctt--atatggagaaaga------------------tgcaa--aagtga--------ttaaggatcctgagagaaggagtttattctggattatccaggtaggccctaaaaatgcaatcacatatatccttataagagagaagcaga-aaaagttttaagacagacacaaagaaaataacacagacatacaa
q canFam2.chr23                                             99999999---------99999999999999999999999-9--------------9999999999999--99999999999999----999999999999999999999--9999999999999------------------99999--999999--------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22233827 231 -  87365405 CACCACCT---------TTCAtgggctcgacagtggccccga--------------aaaagatacatcc--acatcctaacgccc----agaacctgtgaatattaccttacatatggtaaaagagtgaatatcaccttatatggcaa--aagacaggaagaagttacagatcctgag---aggagtttaccctggattatccagatgggccctaaatgt------------------------------caga-gggagtttggagacagacacacagaagatgacacagacac---g
q equCab2.chr16                                             99999999---------9999999999999999999999999--------------9999999999999--99999999999999----99999999999999999999999999999999999999999999999999999999999--9999999999999999999999999999---999999999999999999999999999999999999999------------------------------9999-9999999999999999999999999999999999999999---9
i equCab2.chr16                   C 0 C 0
s loxAfr3.scaffold_36                539723 182 -  24123610 CACTATCTGGAGCAGGATGAATGGTAGC--------CCCC-ATTCCATTCTGGCAATTAGaatatgccc--gtgttctaatccct----ggaatctgcgactattacttt--atatggcaaaata----------------------------------------------------------------------------------------taaacat------------atccttataaaagagaggcagataggaggtttgacgcagacagacagaggacgtcacagacatacag
q loxAfr3.scaffold_36                                       9999999999999999999999999999--------9999-9999999999999999999999999999--99999999999999----999999999999999999999--9999999999999----------------------------------------------------------------------------------------9999999------------9999999999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36             I 109 C 0
e rn4.chr9                        107369818 414 - 113440463 I
e mm9.chr17                        50269383 1454 +  95272651 I
e bosTau4.chr1                    157011666 727 + 161106243 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e eriEur1.scaffold_377961             45206 3144 +     88154 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=370308.000000
s hg19.chrY                         7668172 342 +  59373566 agcagaaggtgatatgaagacagagcagagagctg--aggctatgagccaatgaatgcagatggttatcagatgctggaagaagcaaggaa-----tatattttccctttagagcctcg--agatggggtgagactgtgttgacaccttgatttcagacttctggcctcaaatgctcccaaagactacatatctattgcttt----------------------aa-accaccacatgt-----------------------------------------------------gtgat------------------------------------------------------------------a-tttgttacagacagcagcctcaggaaatgaatataCTACCTCAATGGGTGAAGCTCTTGTTTGACCTTTAAACTGCAACTTG-----------------------------------CAGATGTTAACAGTAAC-ATGATAAGGCCAAAGATAAAGGTGACTAAA
s panTro2.chrY                       521711 343 +  23952694 agcagaaggtgatatgaagacagagcagagagctg--aggctatgagccaatgaatgcagatggttatcagatgctggaagaagcaaggaa-----tatattttccctttagagcctcg--agagggggtgagactgtgttgacaccttgatttcagacttctggcctcaaatgctcccaaagactacatatctattgcttt----------------------aa-accaccacatgt-----------------------------------------------------gtggt------------------------------------------------------------------a-tttgttacagacagcagcctcaggaaatgaatataCTACCTCAATGGGTGAAGCTCTTGTTTGACCTTTAAACTGCAACTTG-----------------------------------CAGATGTTAACAGTAACAATGATAAGGCCAAAGATAAAGGTGACTAAA
q panTro2.chrY                                              00000000000000000000000000000000000--000000000000000000000000000000000000000000000000000000-----00000000000000000000000--000000000000000000000000000000000000000000000000000000000000000000000000000000000----------------------00-000000000000-----------------------------------------------------00000------------------------------------------------------------------0-0000000000000000000000000000000000000000000000000000000000000000000000000000000000-----------------------------------000000000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059639 344 - 202140232 agcagaaggcaatatgaagacagagcagagagctg--cagctacaagccaatgaatgcagacagctgccagatgctggaagaagcaaggaa-----tagattttccctctagagcctca--agaaggggtgcgactctgttgacaccttgatttcagacttctggcctccagagctccaagagactatatatctattgcttt----------------------aa-accaccacatgt-----------------------------------------------------gtggt-----------------------------------------------------------------aa-tttgtcatagacagcagccccaggagactaatacaCTACCTCAATGGGTGCAGCTCTTGTTTGACCTTTAAACTACAACTTG-----------------------------------CAGATGTTAACAGTGACAATGATAAGGCCAAAGATAAAGGTGCCTAAA
q ponAbe2.chr3                                              99999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999-----99999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------99-999999999999-----------------------------------------------------99999-----------------------------------------------------------------99-9999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------------------------------999999999999999999999999999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158785675 344 + 189746636 agcagaaggcaacatgaagacagagcagagagctg--cagctacaagccaatgaatgcagacagctgccagatgctggaagaagcaaggga-----tagattttccctctcgagcctca--agaaggggtgcgactctgttgacaccttgatttcagacttctgacctccagagatccaagagactacatatctattgcttt----------------------aa-accaccacatgt-----------------------------------------------------gtggt-----------------------------------------------------------------aa-tttgttacagacagcagccccaggaaactaatacaCTACCTCAATGGGTGCAGCTCTTGTTTAACCTTTAAACTACAACTTG-----------------------------------CAGATGTTAACAATGACAATGATAAGGCCAAAGGTAAAGGTGCCTAAG
q rheMac2.chr2                                              99999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999-----99999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------99-999999999999-----------------------------------------------------99999-----------------------------------------------------------------99-9999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------------------------------999999999999999999999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264328 457 -  88675666 GGCAGAAGACAATGTACAGAGCAAGCACAga--tg--cagctacaggccaagcagtcctgc--acttccagaagctggaagaaacaagaacaactttacttttgccctctaggccctcc--aaacagtgtgtg---gtcccgatatcctgatttccaacttctggcctcgagaactgtgacagac---atttctgttgcttcacgtggttttgtttttaagacaag-atctcaatatgtagttcagattggccttgaactcactgtgcagcacaactggcctcgagctctcagtgattctcctgcctcagccttccaagtgttgggatggaaggcctgcactactgcatccaccattctgttcc-tttgttactg-cagcag----aggaaactaatac---TGCTTAATGGATGCAACTGTCATTGAACCCCTCATTTGTGTTCTG-----------------------------------ATGGTGTTAAC-------------AGGCCCAAAAGGAGAGCGCCTGG-
q cavPor3.scaffold_0                                        9999999999999999999999999999999--99--999999999999999999999999--99999999999999999999999999999999999999999999999999999999--999999999999---9999999999999999999999999999999999999999999999999---99999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999-999999----9999999999999---999999999999999999999999999999999999999999999-----------------------------------99999999999-------------99999999999999999999999-
i cavPor3.scaffold_0              C 0 C 0
s equCab2.chr16                    22234058 311 -  87365405 agcggaaggcag---------agcacagagagatg--cggctacaagccaaggaatgctgacagccaggagaagccggaagaggtaaggaa-----c------------------ctct---gacggagtgtggccctgctgacaccttgatttcagactaatggcctccggagctgtgagagaataagttgctgttgcttt----------------------aa-gctgctatgttt-----------------------------------------------------agggt-----------------------------------------------------------------gg-tttgtta----cagcagccccaggaaacgaacataCCACCTTAAAGGACAGAGCTCTTGTTTGACCTTTCAACTGTGTCTTG-----------------------------------ATGATGTTAACAATGACAATGGTAAGGCCGAAGGTAAGGGGGCCTAA-
q equCab2.chr16                                             999999999999---------99999999999999--999999999999999999999999999999999999999999999999999999-----9------------------9999---99999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------99-999999999999-----------------------------------------------------99999-----------------------------------------------------------------99-9999999----99999999999999999999999999999999999999999999999999999999999999999999999-----------------------------------99999999999999999999999999999999999999999999999-
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26013360 348 -  55389570 agcagaaggcaatgtgaagacagagcagagagatg--cagctacaaaccaaggggtgctgagagctgccagaagct-gaagaggtaagaaa-----cagattctcccactaaggactccagagagagagtatggcactgt---caccatgttttcagatttctggcctccgg--------------aaatttctgctgcttt----------------------aaggttaccatatgc-----------------------------------------------------agggt-----------------------------------------------------------------ag-tttctta----tagcagccctagta----aCTACGTCACCTAAACAGATGCGTCTCTTGTCTGGCCTTTAAACTGTGTCGAGATAATGCCTCTCCCTCCGCCTAAGCCTGTTAGCCCATAATGCTAACAATGACAATGAC-------AAGGTAAGGATGCCTGG-
q canFam2.chr23                                             99999999999999999999999999999999999--999999999999999999999999999999999999999-99999999999999-----99999999999999999999999999999999999999999999---99999999999999999999999999999--------------9999999999999999----------------------999999999999999-----------------------------------------------------99999-----------------------------------------------------------------99-9999999----99999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------99999999999999999-
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             48350 328 +     88154 AGCAGGAGATAGAGTGCAGACAGACCACAGCAGTGTCCAGCTGTAAGCCAAGGAATGTGGACAGTCACC-GAAGCCAGTAGAGAT-----A-----CTGATACTCCTCACAAAGCCCCCAGAAGGAATGTGTTTCCCTGA---CATCCTGACTGCAGAATTCTAGGCCCCAGAGCCATGAGAAGACACATTTCTCTTGCTTT----------------------GA-GCTACCATTTTG-----------------------------------------------------TTTGT-----------------------------------------------------------------AGTTTTGTTG----TATCAATTCCCAGAGACCAATATGCCAACTTAGTGGATATGGTTCTGGCGAGGCCTGTTGAGTGTATCTTG-----------------------------------ATGATGTTAGCAATG-------TAAGGTAAAAGGTAACGGGGTCTGC-
q eriEur1.scaffold_377961                                   999999999199999999999999999999999219999999999999999999999999999999999-999999999999999-----9-----99999999999999999999999999999999999999999999---99999999999999999999999999999999999999999999999999999999999----------------------99-999999999999-----------------------------------------------------99999-----------------------------------------------------------------9999999999----99999999999999999999999999999999999999999999999999999999999999999999999-----------------------------------999999999999999-------9999999999999999999999999-
i eriEur1.scaffold_377961         I 3144 C 0
s loxAfr3.scaffold_36                539905 320 -  24123610 aagagaaggcaacat--------------gagatg--cagccacaagccaaggaatgccaatagctgccagaagctgcc--aagtaaagaa-----tggattctctc-ctagatccttc--agagggagtgtggtcctgctgactaattgatttcatgtttctggcctccaggattatgagggaataaacttctgttgtttt----------------------aa-accaccatgatt-----------------------------------------------------gtaat-----------------------------------------------------------------aa-tttgtta----tggcagctctaagaaactaatacaCCACCTTGGTGGACAGAGCTCATGTTCCACCTTT-AACTAGAGCTTG-----------------------------------ATGATGTTAACAATGAC-AGGATTAACCCAAAGGTAAGGCTGCCTGG-
q loxAfr3.scaffold_36                                       999999999999999--------------999999--999999999999999999999999999999999999999999--9999999999-----99999999999-99999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------99-999999999999-----------------------------------------------------99999-----------------------------------------------------------------99-9999999----9999999999999999999999999999999999999999999999999999999999-999999999999-----------------------------------99999999999999999-99999999999999999999999999999-
i loxAfr3.scaffold_36             C 0 C 0
e rn4.chr9                        107369818 414 - 113440463 I
e mm9.chr17                        50269383 1454 +  95272651 I
e oryCun2.chr14                     2496441  12 + 163896628 I
e bosTau4.chr1                    157011666 727 + 161106243 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=77461.000000
s hg19.chrY                         7668514 47 +  59373566 AAACGAGAAACACCAAGGTCTGGTGTTA-TGAA-TTGAGCTTAACAAAA
s panTro2.chrY                       522054 47 +  23952694 AAACGAGAAACACCAAGGGCTGGTGTTA-TGAA-TTGAGCTTAACAAAA
q panTro2.chrY                                             0000000000000000000000000000-0000-000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71059983 46 - 202140232 AAACG-GAAACACCAAGGGCTGGTGTTA-TGAA-TTGAGCTTAACAAAA
q ponAbe2.chr3                                             99999-9999999999999999999999-9999-999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158786019 47 + 189746636 AAACGAGAAACACCAAGGGCTGGTGTTA-TGAA-TTGAGCTTAACAAAA
q rheMac2.chr2                                             9999999999999999999999999999-9999-999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264785 37 -  88675666 A---------AA--TGGAAATCACTTTGTCAAA-CTAAACTGGGCAAAA
q cavPor3.scaffold_0                                       9---------99--9999999999999999999-999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2496453 48 + 163896628 AAACAGGAAACACCAAGGGCTGGTGTCCGTGAG-TGGAGCTCGGCCGAA
q oryCun2.chr14                                            999999999999999999999999999999999-999999999999999
i oryCun2.chr14                   I 12 C 0
s rn4.chr9                        107370232 46 - 113440463 -aAGGGAAGGAATCTGGAAATGGTAATACCAAT-TTGAACTTGA-AAAA
q rn4.chr9                                                 -99999999999999999999999999999999-9999999999-9999
i rn4.chr9                        I 414 C 0
s equCab2.chr16                    22234369 45 -  87365405 --GTGGGAAATGCCAAGGGCTGATGTTA-CAGG-CTGATCTTGACAAAA
q equCab2.chr16                                            --99999999999999999999999999-9999-999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26013708 47 -  55389570 -CACTGGAAATGCCAGGGGCTGGTGTTA-CGGGACTGAGCTTGACAAAA
q canFam2.chr23                                            -999999999999999999999999999-99999999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             48678 47 +     88154 ACACAGGGAAAGCCAGGGGCTAATGTCA-CCGA-GTGAGTGTGGCAAAA
q eriEur1.scaffold_377961                                  9999999999999999999999999999-9999-999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                540225 47 -  24123610 AAGTGGAAAATGTCAAGGGCTGGTGTTA-TGAG-TTGAGCCTGACAAAA
q loxAfr3.scaffold_36                                      9999999999999999999999999999-9999-999999999999999
i loxAfr3.scaffold_36             C 0 I 641
e mm9.chr17                        50269383 1454 +  95272651 I
e bosTau4.chr1                    157011666 727 + 161106243 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=68223.000000
s hg19.chrY                         7668561 23 +  59373566 GTAAAGAAGCAGAAGAATGCAAG
s panTro2.chrY                       522101 23 +  23952694 GTAAAGAAGCAGAAGAATGCAAG
q panTro2.chrY                                             00000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71060029 23 - 202140232 GTAAAGAAGCAGAAGAATGCAAG
q ponAbe2.chr3                                             99999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158786066 23 + 189746636 GTAAAGAAGCAGAAGAATGCAAG
q rheMac2.chr2                                             99999999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264822 23 -  88675666 GTAAAGAAGCAAGAACATGCAGG
q cavPor3.scaffold_0                                       99999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s oryCun2.chr14                     2496501 23 + 163896628 GCAGAGAAGCAGGGAGAGGCAGG
q oryCun2.chr14                                            99999999999999999999999
i oryCun2.chr14                   C 0 I 1100
s rn4.chr9                        107370278 21 - 113440463 CTCAAGAGGCA--GACACAGAAG
q rn4.chr9                                                 99999999999--9999999999
i rn4.chr9                        C 0 C 0
s equCab2.chr16                    22234414 23 -  87365405 CTAGAGGAGCAGGAACAAGTAAG
q equCab2.chr16                                            99999999999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26013755 23 -  55389570 GCAGAGAAGCAGGAAAATGCAAG
q canFam2.chr23                                            99999999999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             48725 23 +     88154 ATAAAGAAGCAGGAAATTGCAAG
q eriEur1.scaffold_377961                                  99999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                540913 23 -  24123610 GTAGAGAAGCAGGAAAATGCAAG
q loxAfr3.scaffold_36                                      99999999999999999999999
i loxAfr3.scaffold_36             I 641 C 0
e mm9.chr17                        50269383 1454 +  95272651 I
e bosTau4.chr1                    157011666 727 + 161106243 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=86101.000000
s hg19.chrY                         7668584  84 +  59373566 AGACAGCGAGCAAAGAG--TTACGGTTGAAGTATACACAAGGG-TTCAGGGAAG-----------------------GAAACCCA-AGAAGCATGAAGCTAGAGCCTCACA
s panTro2.chrY                       522124  84 +  23952694 AGACAGCGAGCAAAGAG--TTACGGTTGAAGTATACACAAGGG-TTCAGGGAAG-----------------------GAAACCCA-AGAAGCATGAAGCTAGAGCCTCACA
q panTro2.chrY                                              00000000000000000--000000000000000000000000-0000000000-----------------------00000000-0000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71060052  84 - 202140232 AGACAATGAGCAAAGAG--GTTTGGTTGAAGGATACACAAGGG-TTCGGGGAAG-----------------------GAAACACA-GGAAGCATGAGGCTAGAGCCTGATC
q ponAbe2.chr3                                              99999999999999999--999999999999999999999999-9999999999-----------------------99999999-9999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158786089  85 + 189746636 AGACAATGAGCAAAGAG--GCTTGGTTGAAGGATACACAAGGG-TTCGGGGAAG-----------------------GAAACACAGGGAAGCATGAAGCTAGAACCTCATC
q rheMac2.chr2                                              99999999999999999--999999999999999999999999-9999999999-----------------------9999999999999999999999999999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264845  66 -  88675666 -------TGGCAAAAA--------------GATTTGAAAAAGGATTCAGGGAAC-----------------------TTAATAAA-TTAAGCATGAAGCTGAAGGCTGACG
q cavPor3.scaffold_0                                        -------999999999--------------999999999999999999999999-----------------------99999999-9999999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107370299  74 - 113440463 -------TGACAAGGAG--CT--GACTGGGGATCAGAGAAAG--TTCGTGGCAG-----------------------ACAGTCCT-GGGAGCCTGAGGCTAGAGGCTCATC
q rn4.chr9                                                  -------9999999999--99--9999999999999999999--9999999999-----------------------99999999-9999999999999999999999999
i rn4.chr9                        C 0 C 0
s equCab2.chr16                    22234437  79 -  87365405 ACACAATAAGTTAACAG--GTTGGGTTGGAGGA-----GACAG-CTCAGGGAAG-----------------------GAAACACA-TTAAGCATGAAGCTGGAGACTCACC
q equCab2.chr16                                             99999999999999999--99999999999999-----99999-9999999999-----------------------99999999-9999999999999999999999999
i equCab2.chr16                   C 0 C 0
s canFam2.chr23                    26013778  79 -  55389570 AGACAAGAGGTAAACAG--GTTTTGTTTGAGAA-----CAGGG-GTCTGGGAAG-----------------------TAAATGCA-TTAAGCCTGAGGCTGGAGGCCCACC
q canFam2.chr23                                             99999999999999999--99999999999999-----99999-9999999999-----------------------99999999-9999999999999999999999999
i canFam2.chr23                   C 0 C 0
s eriEur1.scaffold_377961             48748 104 +     88154 AGGCAGTGAGTGAACAGATATCTGGCTAGAGGA-----GAAGC-CTCAGGGAAAATGTCTTTCACTGAACATTTAACATAATGTA-AAAAGCATGAAGTTGGAGGTTAGGC
q eriEur1.scaffold_377961                                   999999999999999999999999999999999-----99999-99999999999999999999999999999999999999999-9999999999999999999999999
i eriEur1.scaffold_377961         C 0 C 0
s loxAfr3.scaffold_36                540936  79 -  24123610 AGACAATGAGCCAAGAG--GTCTGGCTGGAGGA-----AAGGG-CTCAAGAAAG-----------------------TGAAAACA-TAAGGAACGTGGCTGGGCGCTCACC
q loxAfr3.scaffold_36                                       99999999999999999--99999999999999-----99999-9999999999-----------------------99999999-9999999999999999999999999
i loxAfr3.scaffold_36             C 0 C 0
e mm9.chr17                        50269383 1454 +  95272651 I
e oryCun2.chr14                     2496524 1100 + 163896628 I
e bosTau4.chr1                    157011666 727 + 161106243 I
e speTri1.scaffold_160574              9387   0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=131647.000000
s hg19.chrY                         7668668 65 +  59373566 CTGT-AATGGGTCTTATCCACTAGAGACAGAAATCTACAATGCCAGTGCATTGTTTGTTTCTGAAT
s panTro2.chrY                       522208 65 +  23952694 CTGT-AATGGGTCTTATCCACTAGAGACAGAAATCTACAATGCCAGTGCATTGTTTGTTTCTGAAT
q panTro2.chrY                                             0000-0000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71060136 65 - 202140232 CTGT-AATGGTTCTCATTCACTAGAGACAGAAATCTACAATGCCAGTGCATTGTTTGTTTCTAAAT
q ponAbe2.chr3                                             9999-9999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158786174 65 + 189746636 CTGT-AATGGGTCTCGTCCACTAGAGACAGAAATCTACAATGCCAGTGCATTGTTTGTTTCTAAAT
q rheMac2.chr2                                             9999-9997666666676666666666677666666676666666666776666666666776667
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264911 65 -  88675666 CTGA-AATAGATATTAACAACCAGCTATGGAAACTTACAATGCCAAGCTACTGGTTGTTTCCATGT
q cavPor3.scaffold_0                                       9999-9999999999999999999999999999999999999999999999999999999999999
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107370373 49 - 113440463 CTGA-AATGGCTCTTGGCCAATAGCAACAGGAGTCCAT----------------CTGTTCTCAAAT
q rn4.chr9                                                 9999-999999999999999999999999999999999----------------999999999999
i rn4.chr9                        C 0 C 0
s bosTau4.chr1                    157012393 64 + 161106243 ctGT-GATGGGTCTCACCCACTGGTAGCAGAAGTCTAAAGCGCCAGCGTGGTGTGTGCTTCT-GAT
q bosTau4.chr1                                             9999-999999999999999999999999999999999999999999999999999999999-999
i bosTau4.chr1                    I 727 C 0
s canFam2.chr23                    26013857 66 -  55389570 CTGTAAATGGGTCTAATCCACCAGTAACAGTAACCTCAAATGTCAGTGAATCATTTGTTTTTAAAT
q canFam2.chr23                                            999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22234516 65 -  87365405 CTGT-AATGGGTCTTACCCACCAGTAACAGTAACCTGAAACGCCAGTGTACTGTTGGTTTTTAAAT
q equCab2.chr16                                            9999-9999999999999999999999999999999999999999999999999999999999999
i equCab2.chr16                   C 0 C 0
s eriEur1.scaffold_377961             48852 36 +     88154 TTAC-AATGGGCCTTAT---------ATTGTGATCTAAAATGTCAG--------------------
q eriEur1.scaffold_377961                                  9999-999999999999---------99999999999999999999--------------------
i eriEur1.scaffold_377961         C 0 N 0
s loxAfr3.scaffold_36                541015 65 -  24123610 CTGT-AGTGGGTCTTACATGCCAGCTACAGAAATCTAAAATGCCAGTGCACTGTTTGTTTTTAAAT
q loxAfr3.scaffold_36                                      9999-9999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36             C 0 C 0
e mm9.chr17                        50269383 1454 +  95272651 I
e oryCun2.chr14                     2496524 1100 + 163896628 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e otoGar1.scaffold_99906.1-214988    103484 3726 -    214988 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=28319.000000
s hg19.chrY                         7668733 38 +  59373566 -AACATGTTTACCCATTCACTA-----------------------CTCTGTGCATTTTCTtt
s panTro2.chrY                       522273 38 +  23952694 -AACATGTTTACCCATTCACTA-----------------------CTCTGTGCAttttcttt
q panTro2.chrY                                             -000000000000000000000-----------------------00000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr3                     71060201 38 - 202140232 -AACATGTTTATCCATTCAGTA-----------------------CTCTATGCTttttcttt
q ponAbe2.chr3                                             -999999999999999999999-----------------------99999999999999999
i ponAbe2.chr3                    C 0 C 0
s rheMac2.chr2                    158786239 38 + 189746636 -AACATGTTTATCCATTCAGTA-----------------------CTCTATGCTttttcttt
q rheMac2.chr2                                             -667666666656666666667-----------------------67776667999999999
i rheMac2.chr2                    C 0 C 0
s cavPor3.scaffold_0                8264976 38 -  88675666 -AACATTTTTAACCATTCAGCA-----------------------TTGTACGCCttttattt
q cavPor3.scaffold_0                                       -999999999999999999999-----------------------99999999999999999
i cavPor3.scaffold_0              C 0 C 0
s rn4.chr9                        107370422 35 - 113440463 -AACA---CCAACTACCCAGCA-----------------------CTTGGTGGTTtttctct
q rn4.chr9                                                 -9999---99999999999999-----------------------99999999999999999
i rn4.chr9                        C 0 C 0
s bosTau4.chr1                    157012457 28 + 161106243 -AGCATCTTCATCCATCCGGCA-----------------------CCCTACG----------
q bosTau4.chr1                                             -999999999999999999999-----------------------9999999----------
i bosTau4.chr1                    C 0 C 0
s canFam2.chr23                    26013923 33 -  55389570 -GACATCCATATCCACTCAACA-----------------------CCCTGTGT-----TTTT
q canFam2.chr23                                            -999999999999999999999-----------------------99999999-----9999
i canFam2.chr23                   C 0 C 0
s equCab2.chr16                    22234581 33 -  87365405 -AACACCTTTATCCATTCCACA-----------------------CCCTGCAT-----Tttt
q equCab2.chr16                                            -999999999999999999999-----------------------99999999-----9999
i equCab2.chr16                   C 0 C 0
s sorAra1.scaffold_253821             82113 57 +     83218 -aataattttatttgttaattaataTTATACAAAGTGAATAATGTCTCTGCATATTTT----
q sorAra1.scaffold_253821                                  -999999999999999999999999999999999999999999999999999999999----
i sorAra1.scaffold_253821         N 0 N 0
s otoGar1.scaffold_99906.1-214988    107210 19 -    214988 ---------------TTTGGCT-----------------------CTCTATGCTttc-----
q otoGar1.scaffold_99906.1-214988                          ---------------9999779-----------------------999999999789-----
i otoGar1.scaffold_99906.1-214988 I 3726 N 0
s loxAfr3.scaffold_36                541080 36 -  24123610 AAGATTTTTTATCCAGTCAGCA-----------------------CTCAATGCTttttc---
q loxAfr3.scaffold_36                                      9999999999999999999999-----------------------99999999999999---
i loxAfr3.scaffold_36             C 0 C 0
e mm9.chr17                        50269383 1454 +  95272651 I
e oryCun2.chr14                     2496524 1100 + 163896628 I
e speTri1.scaffold_160574              9387  0 -    115260 I
e macEug1.Scaffold7817                25228 4878 -     41428 I
e monDom5.chr8                    276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112                4907 1176 -     49748 I
e myoLuc1.scaffold_7336               37698 5478 -    312611 I

a score=151147.000000
s hg19.chrY                 7668771 86 +  59373566 ttcttttatttattatgcttggagtatgtacaacttcttgaatctatgggttgatctctcttacaaatctggg-gaaattcttagcc
s panTro2.chrY               522311 82 +  23952694 ttct----tttattatgcttggagtatgtacaacttcttgaatctatggattgatctctcttacaaatctggg-gaaattcttagcc
q panTro2.chrY                                     0000----00000000000000000000000000000000000000000000000000000000000000000-0000000000000
i panTro2.chrY            C 0 C 0
s ponAbe2.chr3             71060239 81 - 202140232 tta-----tttattatgcttggagtttgtacgacttcttgaatctatgggttgatctctcttacaaatctgga-gaaattcttagcc
q ponAbe2.chr3                                     999-----99999999999999999999999999999999999999999999999999999999999999999-9999999999999
i ponAbe2.chr3            C 0 C 0
s rheMac2.chr2            158786277 81 + 189746636 tta-----tttattatgcttggagtttgtacaacttcttgaatgtatgggttgatctctcttacaaatctggg-gaaattcttagcc
q rheMac2.chr2                                     999-----99999999999999999999999999999999999999999999999999999999999999999-9999999999999
i rheMac2.chr2            C 0 C 0
s cavPor3.scaffold_0        8265014 80 -  88675666 -----gccttcagtatgcttggaatttgtacaactttttaaatctaggggttgatatgtcttataaatttgg--ggaatgcttagcc
q cavPor3.scaffold_0                               -----9999999999999999999999999999999999999999999999999999999999999999999--9999999999999
i cavPor3.scaffold_0      C 0 I 6
s rn4.chr9                107370457 71 - 113440463 -----gtact--------tcgtagcttgcacaacttctt-ggtctgtgggttaatgcttttgtaagttttgg--gaaattcttaagc
q rn4.chr9                                         -----99999--------999999999999999999999-99999999999999999999999999999999--9999999999999
i rn4.chr9                C 0 I 10
s equCab2.chr16            22234614 86 -  87365405 tctttgtatccattatgcttggagtttgcatagcttcttgaatctgtgggatgatatctcttatatgtttggg-gaaattcttagcc
q equCab2.chr16                                    9999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999
i equCab2.chr16           C 0 I 9
s canFam2.chr23            26013956 68 -  55389570 TCATTGTA----------------TTTTCACA---tcttgaatctgtgggtggatctctctaataaatttgggtaaaatttttagcc
q canFam2.chr23                                    99999999----------------99999999---9999999999999999999999999999999999999999999999999999
i canFam2.chr23           C 0 I 9
s bosTau4.chr1            157012485 84 + 161106243 ---Ctgtgtttattatgcttggagttggcaaagcttcttgactctctgggctgatgtggctcacaagtgtgggggaaactcttagcc
q bosTau4.chr1                                     ---999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i bosTau4.chr1            C 0 I 9
s loxAfr3.scaffold_36        541116 84 -  24123610 --ctcatatttattgtgcttggggtttgcacagcttcccaaacctacgggctgatgtctctcatcagtttggg-ataattcttagcc
q loxAfr3.scaffold_36                              --99999999999999999999999999999999999999999999999999999999999999999999999-9999999999999
i loxAfr3.scaffold_36     C 0 I 229
e mm9.chr17                50269383 1454 +  95272651 I
e oryCun2.chr14             2496524 1100 + 163896628 I
e speTri1.scaffold_160574      9387  0 -    115260 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I

a score=55829.000000
s hg19.chrY                 7668857 30 +  59373566 taaaacattgcttttgtctcactccctccc
s panTro2.chrY               522393 30 +  23952694 taaaacattgcttttgtctcactgcctccc
q panTro2.chrY                                     000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s ponAbe2.chr3             71060320 30 - 202140232 tcaaacactgcttctgtctcattccctccc
q ponAbe2.chr3                                     999999999999099999999999999999
i ponAbe2.chr3            C 0 I 1533
s rheMac2.chr2            158786358 30 + 189746636 tcaaacactgcttctgtctcattcccttcc
q rheMac2.chr2                                     999999999999999999999999999999
i rheMac2.chr2            C 0 C 0
s cavPor3.scaffold_0        8265100 26 -  88675666 ttaaatactgcttcaa----attacctcct
q cavPor3.scaffold_0                               9999999999999999----9999999999
i cavPor3.scaffold_0      I 6 I 1
s rn4.chr9                107370538 26 - 113440463 tcaaattccactctaa----gtcccttcct
q rn4.chr9                                         9999999999999999----9999999999
i rn4.chr9                I 10 C 0
s equCab2.chr16            22234709 30 -  87365405 acaaatactgcttttgtcccattctgtccc
q equCab2.chr16                                    999999999999999999999999999999
i equCab2.chr16           I 9 C 0
s canFam2.chr23            26014033 30 -  55389570 tcaaatattgcttctgtcccatcccctcct
q canFam2.chr23                                    999999999999999999999999999999
i canFam2.chr23           I 9 C 0
s bosTau4.chr1            157012578 29 + 161106243 tcaaatactgcttctatccca-cctgtccc
q bosTau4.chr1                                     999999999999999999999-99999999
i bosTau4.chr1            I 9 C 0
s loxAfr3.scaffold_36        541429 30 -  24123610 tcaaatactgtttcttccccgttctctccc
q loxAfr3.scaffold_36                              999999999999999999999999999999
i loxAfr3.scaffold_36     I 229 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e oryCun2.chr14             2496524 1100 + 163896628 I
e speTri1.scaffold_160574      9387  0 -    115260 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I

a score=132107.000000
s hg19.chrY                 7668887 141 +  59373566 actctgctc---cttctgagactccaattacacata---ttttagac-ttttcattgtgtcccacttgtctcttatgc-tttttctatatgttcaatttttc----tctctgtgcacttcagcataaatcatttctattaacctttcttccag
s rheMac2.chr2            158786388 146 + 189746636 tctctgctc---cttctgagactccagttatacata---tcttagac-ttttcattgtgccccacttgtctcttatgcttttttctatatgttccattttccattttccctctgcagttcagcttaaatcatttctattaacctttcttccag
q rheMac2.chr2                                      999999999---999999999999999999999999---99999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522423 141 +  23952694 actctgctc---cttctgagactccaattacacata---ttttagac-ttttcattgtgtctcacatgtctcttatgc-tttttctatatgttcaatttttc----tctctgtgcacttcagcataaatcgtttctattaacctttcatccag
q panTro2.chrY                                      000000000---000000000000000000000000---00000000-000000000000000000000000000000-00000000000000000000000----00000000000000000000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s cavPor3.scaffold_0        8265127 120 -  88675666 ----ttctt---ctcctgataatccaattatacatattttactagat-tactcattgtgtaccatttgtcttctaggttttttcctgtatgttctattttt-----------------tCA------ATGGTCTCCATCAACTCTtctcct--
q cavPor3.scaffold_0                                ----99999---99999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999-----------------999------999999999999999999999999--
i cavPor3.scaffold_0      I 1 C 0
s rn4.chr9                107370564 124 - 113440463 -------ct---cttctGATAACCCAGTAAGGTGTA---AATTAGAG-GACTGACTGGGT-CCATCTGTCCCTTATGATCTTCTCTGTGTGCTTTCTCCTCC----ACCCCCAGAAGGTCA--------GGTCTCCATCAACCCTTCTCCC--
q rn4.chr9                                          -------99---999999999999999999999999---99999999-999999999999-99999999999999999999999999999999999999999----999999999999999--------9999999999999999999999--
i rn4.chr9                C 0 C 0
s equCab2.chr16            22234739 125 -  87365405 ---tctcttctccttctgagaattcaattatacaga---tcttaagc-ttttcattgttt--cacttgtctc--atgttcttttctgtatgttccatttcta----actctctgcacttcagtttgaataatttc-------------tccaa
q equCab2.chr16                                     ---999999999999999999999999999999999---99999999-999999999999--9999999999--9999999999999999999999999999----99999999999999999999999999999-------------99999
i equCab2.chr16           C 0 C 0
s canFam2.chr23            26014063 137 -  55389570 ---tgtctt---cttctgagaatccaattcgaccta---tcacagac-tactcgttgtatcccacttctctt--atgctctgtttggaatgttccactttct----cctctctgcacttcagtttgaataatttctattaaccttccttccaa
q canFam2.chr23                                     ---999999---999999999999999999999999---99999999-999999999999999999999999--9999999999999999999999999999----99999999999999999999999999999999999999999999999
i canFam2.chr23           C 0 C 0
s bosTau4.chr1            157012607 131 + 161106243 ---catctt---ctcccgagactccagtcacacata---ccttagactttctcattgtgacccacttgtc--------tcttttctctttgttccactgtta----actctctgcccttcagtttgaataacttccactaatctttc-cccag
q bosTau4.chr1                                      ---999999---999999999999999999999999---9999999999999999999999999999999--------999999999999999999999999----99999999999999999999999999999999999999999-99999
i bosTau4.chr1            C 0 C 0
s loxAfr3.scaffold_36        541459 128 -  24123610 tctcttctc---cttgtgagacttcaatgacatgta---tcttaaat-ttttcactg----------acatcttatgctctttt----attttccatttttt----cttctctgtactttggtttgaagaatttccatggtcctttcttctaa
q loxAfr3.scaffold_36                               999999999---999999999999999999999999---99999999-999999999----------99999999999999999----99999999999999----99999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e oryCun2.chr14             2496524 1100 + 163896628 I
e speTri1.scaffold_160574      9387   0 -    115260 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=-19406.000000
s hg19.chrY                 7669028 35 +  59373566 gtcactatg-cttgtttcctgct--tatat----------------------gatctgtt---
s rheMac2.chr2            158786534 37 + 189746636 atcgctatt-cttgtcttctgctg-tatatc---------------------tttctgtt---
q rheMac2.chr2                                     999999999-99999999999999-999999---------------------99999999---
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522564 35 +  23952694 gtcactatg-cttgtttcctgct--tatat----------------------gatctgtt---
q panTro2.chrY                                     000000000-0000000000000--00000----------------------00000000---
i panTro2.chrY            C 0 C 0
s rn4.chr9                107370688  4 - 113440463 ----------------------------------------------------TGCC-------
q rn4.chr9                                         ----------------------------------------------------9999-------
i rn4.chr9                C 0 C 0
s cavPor3.scaffold_0        8265247 18 -  88675666 ------------------cttctactatat--------------------aatgtc-------
q cavPor3.scaffold_0                               ------------------999999999999--------------------999999-------
i cavPor3.scaffold_0      C 0 C 0
s speTri1.scaffold_135460    104174 55 -    203079 GGCACTGGG-TTTGATTCCTAGTACCACATATAAATAAGCAAATACAATAAAGGCC-------
q speTri1.scaffold_135460                          999999999-9999999999999999999999999999999999999999999999-------
i speTri1.scaffold_135460 I 25574 I 295
s equCab2.chr16            22234864 37 -  87365405 ttcattattctttgtcttctgcta-tatgt----------------------gatcttct---
q equCab2.chr16                                    999999999999999999999999-99999----------------------99999999---
i equCab2.chr16           C 0 I 3
s canFam2.chr23            26014200 33 -  55389570 ttccct----tttttcttctgttc-tgtag----------------------ggtcttct---
q canFam2.chr23                                    999999----99999999999999-99999----------------------99999999---
i canFam2.chr23           C 0 I 3
s bosTau4.chr1            157012738 37 + 161106243 ttcactcctccttgtcttccgcta-catct----------------------gatcttct---
q bosTau4.chr1                                     999999999999999999999999-99999----------------------99999999---
i bosTau4.chr1            C 0 I 3
s loxAfr3.scaffold_36        541587 38 -  24123610 ttcactatt-tttgtcttctgct--tacat----------------------gatctgctatt
q loxAfr3.scaffold_36                              999999999-9999999999999--99999----------------------99999999999
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e oryCun2.chr14             2496524 1100 + 163896628 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=70858.000000
s hg19.chrY                 7669063 134 +  59373566 aaaaccgtatccattgagttc--ttaattgcagatatattttccaagtaatagaaa--------------------------gcctatt----tgatta---actatagattccaattctctgtttaaatttttcatattttcat------------------------------------------------------------------------------------------------ctaattcct------------ccattaaaaattta---t
s rheMac2.chr2            158786571 133 + 189746636 aaaaccccatccaatgagttc--ttaattgcagatatcttttccaagtaatagaaa--------------------------ttccatt----tgattc---tttatacattccaattctttgtttaaatttttcata-tttcat------------------------------------------------------------------------------------------------ctattttat------------ccattaaaaattta---t
q rheMac2.chr2                                      999999999999999999999--999999999999999999999999999999999--------------------------9999999----999999---999999999999999999999999999999999999-999999------------------------------------------------------------------------------------------------999999999------------99999999999999---9
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522599 133 +  23952694 aaaaccatatccattgagttc--ttaattgcagatatcttttccaagtaaca-aaa--------------------------gcctatt----tgatta---tctatagattccaattctctgtttaaatttttcatattttcat------------------------------------------------------------------------------------------------ctaattcct------------ccattaaaaattta---t
q panTro2.chrY                                      000000000000000000000--00000000000000000000000000000-000--------------------------0000000----000000---0000000000000000000000000000000000000000000------------------------------------------------------------------------------------------------000000000------------00000000000000---0
i panTro2.chrY            C 0 C 0
s rn4.chr9                107370692 105 - 113440463 CTCCCTCCACCTATGAAACTC--TTAATGTCAGGT----------------------------------------------------------TCTTTC---TCT---CATTTGAATTCCCTTTTGAAATTCCTCATGTTTGTAT------------------------------------------------------------------------------------------------CTGTGTTCT----------CTTCTTCTACATTTTA---T
q rn4.chr9                                          999999999999999999999--999999999999----------------------------------------------------------999999---999---9999999999999999999999999999999999999------------------------------------------------------------------------------------------------999999999----------9999999999999999---9
i rn4.chr9                C 0 C 0
s cavPor3.scaffold_0        8265265 238 -  88675666 aaacccccatctatg---cgg--ttaatctcagata---ttccataataacagaat--------------------------gcctctgtaagttattc---tctatacattccaattctctgttgaaattttctatttttatctatttttaacttccttcttaagcatattaatcatagttTGTTACTGATATTCTGCATGGTACTGGGGAAATGACCCCAGGGACTAAGTACTCTACCACTGTGCTATATCCCTG--GCCTCttttatttttta---t
q cavPor3.scaffold_0                                999999999999999---999--9999999999999---99999999999999999--------------------------99999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999999---9
i cavPor3.scaffold_0      C 0 C 0
s equCab2.chr16            22234904 133 -  87365405 aaaccccattctattgagttc--ttaatttcacatatttttttccactaatagaat--------------------------gcccatt----tgattc---tttatagattccaattttctgttgaaattttccaacttttcat------------------------------------------------------------------------------------------------ctattttct------------ccacttaaaaagtt----
q equCab2.chr16                                     999999999999999999999--999999999999999999999999999999999--------------------------9999999----999999---9999999999999999999999999999999999999999999------------------------------------------------------------------------------------------------999999999------------99999999999999----
i equCab2.chr16           I 3 C 0
s canFam2.chr23            26014236 132 -  55389570 aaaccccgctctactgagttc--ttactt---cagatattttcacactaatagaat--------------------------gcccg-t----tgagtc---tttatagattccgattctctgttgaaattttccatcttttCAT------------------------------------------------------------------------------------------------CTATTTTCC------------CCATTCAAAAAATTTCT-
q canFam2.chr23                                     999999999999999999999--999999---999999999999999999999999--------------------------99999-9----999999---9999999999999999999999999999999999999999999------------------------------------------------------------------------------------------------999999999------------99999999999999999-
i canFam2.chr23           I 3 I 197
s bosTau4.chr1            157012778 158 + 161106243 attccgcatgctgtccagttcttttattt---caggtactttcccacaaacagattctttatagatttgtttgatcctctgattccact----cggttc---tttacaggttccaattctcttatgaagttttccatctttcccc------------------------------------------------------------------------------------------------ctattttct------------ccattaaaactttt----
q bosTau4.chr1                                      99999999999999999999999999999---999999999999999999999999999999999999999999999999999999999----999999---9999999999999999999999999999999999999999999------------------------------------------------------------------------------------------------999999999------------99999999999999----
i bosTau4.chr1            I 3 C 0
s loxAfr3.scaffold_36        541625 138 -  24123610 aaatctctatctattgtgctt--ct-----------tactttccctgtaatagaat--------------------------gtcaact----tgattcctatttatagattccaattctctgttgaaattttccatcttttcat------------------------------------------------------------------------------------------------ctatcttctgtcttttcctttactctcaatattaa---t
q loxAfr3.scaffold_36                               999999999999999999999--99-----------99999999999999999999--------------------------9999999----9999999999999999999999999999999999999999999999999999------------------------------------------------------------------------------------------------99999999999999999999999999999999999---9
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e oryCun2.chr14             2496524 1100 + 163896628 I
e speTri1.scaffold_135460    104229 295 -    203079 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=18999.000000
s hg19.chrY                 7669197 151 +  59373566 -----tttcttgaac---------atattaat---------------------------tcattatttt-----------------------------------aaaatcccc-------------------------------c-t----tttttttgctaaat--ttaattctattcactctggatcatctgtggatc--tgtttctatcatttgtttttctct-catttttgggggatggtcacattgacacactgagtaatttt
s rheMac2.chr2            158786704 142 + 189746636 -----tttcttgaac---------atattaat---------------------------tagttatttt-----------------------------------taaatccct-------------------------------c---------tttcactaaat--acaattctattcactctggatcatctgtgaatt--tatttctgtcatttg-ttttctct-catttctaggggatggtcacattgacacacctaataa----
q rheMac2.chr2                                      -----9999999999---------99999999---------------------------9999999999-----------------------------------999999999-------------------------------9---------99999999999--999999999999999999999999999999999--999999999999999-99999999-9999999999999999999999999999999999999----
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522732 152 +  23952694 -----tttcttgaac---------atattaat---------------------------tcgttatttt-----------------------------------aaaatcccc-------------------------------ctt----tttttttgctaaat--ttaattctattcactctggatcatctgtggatc--tgtttctatcatttgtttttctct-cattttgggGGGATGGTCACATTGACACACTGAGTAATTTT
q panTro2.chrY                                      -----0000000000---------00000000---------------------------0000000000-----------------------------------000000000-------------------------------000----00000000000000--000000000000000000000000000000000--000000000000000000000000-00000000000000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s cavPor3.scaffold_0        8265503 232 -  88675666 -------ttcatgat---------gaggttttgtcaaatcacataggctgggcttaaacttgcaatcttcttgcctcagtctcctggggagctgagatcataggtgtgtcccctatactcagttAAATCACAGTTATTTAAGAATTC----TTTTATGGTTAAAT--CCAATTCTGTTAATTCTAGATCATCTATGAATC--TGTTTTTC------GTTTTTCTTT-TATTTTTTTGGGGGGGGTCACATTAGA-AGTTAAGaa----
q cavPor3.scaffold_0                                -------99999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999--999999999999999999999999999999999--99999999------9999999999-999999999999999999999999999-999999999----
i cavPor3.scaffold_0      C 0 C 0
s rn4.chr9                107370797 143 - 113440463 -------TCTTAAAT---------ATAATCTT----AATCATA------------------GCTATTTT-------------------------------TAGATCCCCCCCC-------------------------------TTT----TTTTTTTGCTAAAT--TGATTCTTTCTAG--CTGGATCACCTATAAGTC--TGTTTATA------TTTTTTCTTT-TACTGT----AGCAGGACCCAATGACACATCTAGTAA----
q rn4.chr9                                          -------99999999---------99999999----9999999------------------99999999-------------------------------9999999999999-------------------------------999----99999999999999--9999999999999--999999999999999999--99999999------9999999999-999999----999999999999999999999999999----
i rn4.chr9                C 0 C 0
s oryCun2.chr14             2497624 118 + 163896628 -----TTTTTTAAAC---------AAAATCTT---------------------------------TTTT-----------------------------------TTTTTTTTT-------------------------------TCT----CTGTTTTGCTAAAT--C-AATGGTATTAATTCTAGACCA-CTGTGAGTCTGTGTCtatg------gttgttctgt-----------gggcatccctaatg----atttc--------
q oryCun2.chr14                                     -----5898936935---------39972516---------------------------------6545-----------------------------------464346566-------------------------------001----11013533534911--1-154235542334446551433-8456999999999999999------9999999999-----------99999999999999----99999--------
i oryCun2.chr14           I 1100 C 0
s equCab2.chr16            22235037 144 -  87365405 -----tttcttgaac---------acattaat-------------------------catagttatttt-----------------------------------aaaatat----------------------------------------tttttttgccatat--ctagtta-gttaattctgaatca-ctgtgagtc--tgtttctattatctgtttttctctggggttttttt----tgtcacgttggcatgcctaataatttt
q equCab2.chr16                                     -----9999999999---------99999999-------------------------999999999999-----------------------------------9999999----------------------------------------99999999999999--9999999-999999999999999-999999999--99999999999999999999999999999999999----999999999999999999999999999
i equCab2.chr16           C 0 C 0
s canFam2.chr23            26014565 153 -  55389570 -----TTTCTTGAAT---------ATATTAAT-------------------------CACATCTAAATC-----------------------------------TAATTAGTA-------------------------------AATTAGATTTTTTTACTAAAT--CTAATTA-GTAAATTCTAGATCACCTGTAAGTC--TGTTTATATTATCTGTTTCTCTCT-TGTTTTTCTA----GGTGACACTGGCATGCCTAATAAATTT
q canFam2.chr23                                     -----9999999999---------99999999-------------------------999999999999-----------------------------------999999999-------------------------------999999999999999999999--9999999-9999999999999999999999999--999999999999999999999999-9999999999----999999999999999999999999999
i canFam2.chr23           I 197 C 0
s bosTau4.chr1            157012936 150 + 161106243 -----tctcttgagc---------gtatgaat-------------------------catagttttttg-----------------------------------taaactttt-------------------------------tttc---tttttccactatatcacacatca-gttaattatggttcacctgtgagtc--tgtctctattatctgtcttcctct-tgtttttTTA-----GTTGCAATGGCATGAC-AATAACTTC
q bosTau4.chr1                                      -----9999999999---------99999999-------------------------999999999999-----------------------------------999999999-------------------------------9999---99999999999999999999999-9999999999999999999999999--999999999999999999999999-9999999999-----9999999999999999-999999999
i bosTau4.chr1            C 0 C 0
s loxAfr3.scaffold_36        541763 140 -  24123610 tatattataattaattaatattcaatattaat-------------------------catagtaattga-----------------------------------aaaatc-----------------------------------------cttttctgctacat--ccaattctgctaattc-------------------tgtttctattatctgtttttcctt-aatttttttt-----atcacattggcatgcctaataatgtt
q loxAfr3.scaffold_36                               99999999999999999999999999999999-------------------------999999999999-----------------------------------999999-----------------------------------------99999999999999--9999999999999999-------------------999999999999999999999999-9999999999-----99999999999999999999999999
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e speTri1.scaffold_135460    104229 295 -    203079 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=-5571.000000
s hg19.chrY                 7669348 22 +  59373566 tttttta--------ttgaa-----------taccagacat
s rheMac2.chr2            158786846 20 + 189746636 tttttga--------ttgaa-----------taccagac--
q rheMac2.chr2                                     9999999--------99999-----------99999999--
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522884 22 +  23952694 TTTTTTA--------TTGAA-----------TACCAGACAT
q panTro2.chrY                                     0000000--------00000-----------0000000000
i panTro2.chrY            C 0 C 0
s rn4.chr9                107370940 20 - 113440463 TTTCTGA--------TTGAA-----------TATTTGAg--
q rn4.chr9                                         9999999--------99999-----------99999999--
i rn4.chr9                C 0 I 2
s cavPor3.scaffold_0        8265735 20 -  88675666 tttctga--------ttgaa-----------tattacat--
q cavPor3.scaffold_0                               9999999--------99999-----------99999999--
i cavPor3.scaffold_0      C 0 I 2
s speTri1.scaffold_135460    104524 39 -    203079 TTTTTAAAGTCATAGTTGGACATACACACGGTATTTTAT--
q speTri1.scaffold_135460                          767636431432352426432523112131232368421--
i speTri1.scaffold_135460 I 295 I 299
s oryCun2.chr14             2497742 16 + 163896628 ----tga--------atgaa-----------tactgaca--
q oryCun2.chr14                                    ----999--------99999-----------99999999--
i oryCun2.chr14           C 0 I 1
s equCab2.chr16            22235181 15 -  87365405 ----tga--------tt-aa-----------tactagac--
q equCab2.chr16                                    ----999--------99-99-----------99999999--
i equCab2.chr16           C 0 I 2
s canFam2.chr23            26014718 15 -  55389570 ----TTA--------TT-CA-----------TACTAGAC--
q canFam2.chr23                                    ----999--------99-99-----------99999999--
i canFam2.chr23           C 0 I 2
s bosTau4.chr1            157013086 14 + 161106243 ----TGA--------CT-AA-----------TACAAG-C--
q bosTau4.chr1                                     ----999--------99-99-----------999999-9--
i bosTau4.chr1            C 0 I 2
s loxAfr3.scaffold_36        541903 17 -  24123610 ttactga--------atata-----------gacta-----
q loxAfr3.scaffold_36                              9999999--------99999-----------99999-----
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=-21942.000000
s hg19.chrY                 7669370 44 +  59373566 catgtatttcta----------------------atcatgtatt-agaaagttgaaaagattttgat
s rheMac2.chr2            158786866 28 + 189746636 ----------------------------------atcatgtatt-AGAAAG----ATAACTTCTGAT
q rheMac2.chr2                                     ----------------------------------9999999999-999999----999999999999
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522906 44 +  23952694 CAGGTATTTCTA----------------------ATCATGTATT-AGAAAGTTGAAAAGATTTTGAT
q panTro2.chrY                                     000000000000----------------------0000000000-0000000000000000000000
i panTro2.chrY            C 0 C 0
s rn4.chr9                107370962 62 - 113440463 ----tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg-tgtAGCTAGAGAGATTTCTGAT
q rn4.chr9                                         ----9999999999999999999999999999999999999999-9999999999999999999999
i rn4.chr9                I 2 C 0
s cavPor3.scaffold_0        8265757 35 -  88675666 ----tgtatata---------------------------aaaaa-aaaacctaaaaagatttctaat
q cavPor3.scaffold_0                               ----99999999---------------------------99999-9998999999999999999999
i cavPor3.scaffold_0      I 2 C 0
s speTri1.scaffold_135460    104862 32 -    203079 ----------------------------------atcatgaata-aaaaacttcagagatttctggt
q speTri1.scaffold_135460                          ----------------------------------6799689795-9999599999999989999998
i speTri1.scaffold_135460 I 299 I 446
s oryCun2.chr14             2497759 39 + 163896628 --------------------------catacatcgtcatgacat-catgac-ggagagccttctgat
q oryCun2.chr14                                    --------------------------999999999999999999-999999-999999999999999
i oryCun2.chr14           I 1 C 0
s equCab2.chr16            22235198 29 -  87365405 ------------------------------------catgtacaaaaacattga--agactcctaat
q equCab2.chr16                                    ------------------------------------999999999999999999--99999999999
i equCab2.chr16           I 2 C 0
s canFam2.chr23            26014735 31 -  55389570 ------------------------------------CATGTATGAAACAAATAAAGAGACTTTCAAT
q canFam2.chr23                                    ------------------------------------9999999999999999999999999999999
i canFam2.chr23           I 2 C 0
s bosTau4.chr1            157013102 30 + 161106243 ------------------------------------CACGTACT-AACAGTTGAGGGGACCTGTGAT
q bosTau4.chr1                                     ------------------------------------99999999-9999999999999999999999
i bosTau4.chr1            I 2 C 0
s loxAfr3.scaffold_36        541920 24 -  24123610 ------------------------------------------ta-aaaaattgaagagacttctgag
q loxAfr3.scaffold_36                              ------------------------------------------99-9999999999999999999999
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=140979.000000
s hg19.chrY                 7669414 249 +  59373566 gaagttttcttcctcaaaagtttgct---ct--cctttcttct-gccaggaagatagagttggggatgggggtgctggctaatgatctaaaccaatcaggaactcttac--------------------------aagactc-----aggctgctcctagcttatgtccttggctaggacttagctgtcc-tggccttc--attgagagcctggtgtgtctg--tgatgaccccac----cccttgcaacctccaaaagcaagtcctaaactgt-aatccttattttctcagcacc
s rheMac2.chr2            158786894 250 + 189746636 GAAGCTGTCTTCCTGAAGAGATGGCT---CT--CCTTTCTTCT-CTCAGGAAAACAGAGTTGGGGATGGGGGCGCAGGCTGATGACCTAAACCAATCAGGCACTATTAC--------------------------AAGACTC-----AGATTGCTCCTGGCTTACACCCTTTGCCAGGACTTAGCCCTCC-TGGACTTC--ACTGAGAGCCTGGTGTGTTCA--CCATGCTCCCAC----CCCTCCCAACCTCCAAAAGCCGGTCCTAAACTGTAAATCCTTATTGTCTCAGCACC
q rheMac2.chr2                                      99999999999999999999999999---99--9999999999-99999999999999999999999999999999999999999999999999999999999999999--------------------------9999999-----9999999999999999999999999999999999999999999-99999999--999999999999999999999--999999999999----99999999999999999999999999999999999999999999999999999999
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               522950 249 +  23952694 GAAGTTTTCTTCCCCAAAAGTTTGCT---CT--CCTTTCTTCT-GCCAGGAAGATAGAGTTGGGGAGGGGGGTGCTGGCTGATGATCTAAACCAATCAGGAACTCTTAC--------------------------AAGACTC-----AGGCTGCTCCTAGCTTATGCCCTTGGCTAGGACTTAGCTGTCC-TGGCCTTC--ATTGAGAGCCTGGTGTGTCTG--TGATGCCCCCAC----CCCTTGCAACCTCCAAAAGCAAGTCCTAAACTGT-AATCCTTATTTTCTCAGCACC
q panTro2.chrY                                      00000000000000000000000000---00--0000000000-00000000000000000000000000000000000000000000000000000000000000000--------------------------0000000-----0000000000000000000000000000000000000000000-00000000--000000000000000000000--000000000000----0000000000000000000000000000000000-000000000000000000000
i panTro2.chrY            C 0 C 0
s cavPor3.scaffold_0        8265792 228 -  88675666 ------g--------aagaaatggct---ct-ccctttctttc-tccagacaagcagaggagggtttgagggttagggctgatcacctaagccaattagggacCTGTGC--------------------------AAGACTC-----AGA---CTTTAGGTTTAC-CCCTTTTCTAGAACTTTGGTCCCT-TAGGATT---ATCAAAAACCCAGCGTGCTCA--CCATTCCCCA------CCCTCCCACCCTCC-ATAGAAGTTCCAGAGCTCT-AAtccttatcaccgcaacacc
q cavPor3.scaffold_0                                ------9--------99999999999---99-99999999999-99999999999999999999999999999999999999999999999999999999999999999--------------------------9999999-----999---999999999999-999999999999999999999999-9999999---999999999999999999999--9999999999------99999999999999-9999999999999999999-999999999999999999999
i cavPor3.scaffold_0      C 0 C 0
s rn4.chr9                107371024 240 - 113440463 ------GTTGACTTCAAGAAATGGCT---TT-TCCTCCCTTTCTTCCAGGCAAGTGGAGTTGTGGCTGGGGG-AAGGACTGGTTACCTAGGCCCACTGGGTCCTGTTTC--------------------------AAGA--C-----AGG---CTCCTGGTACAC-CTACAGCTAGGACTCTTTGTCTCTCTGGAACT---TTGAGCTTTCTGGTGTGGTCA--CCACCCTACAGCCACTCCCTGCCTACCTCC-TGGGAAGATCCTAAATTCA-AGTCCTTATCCTATCAA-GCA
q rn4.chr9                                          ------99999999999999999999---99-9999999999999999999999999999999999999999-999999999999999999999999999999999999--------------------------9999--9-----999---999999999999-99999999999999999999999999999999---999999999999999999999--999999999999999999999999999999-9999999999999999999-99999999999999999-999
i rn4.chr9                C 0 C 0
s oryCun2.chr14             2497798 209 + 163896628 gacgctgtcttcctcaacagatggct---gc-ctcctccttcc-actgggcagatacagtcggcgatggggacagggtctgaccacctacaccaac-agagactgctgc--------------------------aaggccccca--gga---gtcctggctcac-cctgtcgctaagacgtggccctcc---------------------------gttca--ctgggccccg------cc-------cctcc-acagcaccacctgaattct-aagcc-cgcccccgcac----
q oryCun2.chr14                                     99999999999999999999999999---99-99999999999-9999999999999999999999999999999999999999999999999999-999999999999--------------------------9999999999--999---999999999999-999999999999999999999999---------------------------99999--9999999999------99-------99999-9999999999999999999-99999-99999999999----
i oryCun2.chr14           C 0 C 0
s equCab2.chr16            22235227 251 -  87365405 gaagtcatcttcctcaagagatggct---ct-ccctttgttct-gcaaggcagatggagtgggggcgggggatg-gggtggatcacctgaaccagtgaggggctggccc--------------------------cagactc-----aaactgctgctggtttaccccccttcctaggcctgggcccacg-aaggctttcaactgagagcccggtgggttca--ccatgcccctac----ccctcccaacctcccgaagcagctccttaactct-aatctttatcttctcagcacc
q equCab2.chr16                                     99999999999999999999999999---99-99999999999-999999999999999999999999999999-9999999999999999999999999999999999--------------------------9999999-----9999999999999999999999999999999999999999999-9999999999999999999999999999999--999999999999----9999999999999999999999999999999999-999999999999999999999
i equCab2.chr16           C 0 C 0
s canFam2.chr23            26014766 244 -  55389570 GAAGTTACCTTCCTCAGGAGATGCCT---CTGCCTTTTGCT-------GGCAGATGGAGCTGGGTGGAGGAAC---AGTTGAATACCTGAACCAGCAAGGGGCTGGTAC--------------------------AGGACT------AAACTTCCCCTGGGTCACTCCTGTTCCCAGGACATGGTCCATC-AAGGCTTTCACCTGAGAGCCTGGTATATTCACTCCAT-TCCCTAC----CTCTTCTCACCTCCCAAAGCAGGTCCTGTCTGCT-CATCTTTATCTTCCCAGCACC
q canFam2.chr23                                     99999999999999999999999999---999999999999-------9999999999999999999999999---999999999999999999999999999999999--------------------------999999------9999999999999999999999999999999999999999999-9999999999999999999999999999999999999-9999999----9999999999999999999999999999999999-999999999999999999999
i canFam2.chr23           C 0 I 10
s bosTau4.chr1            157013132 207 + 161106243 GAGGGTGCC-TCCTCAGGAGACGGCTGTCCT-CCCCTCGCGCT-G---AGCAGACGGAGCAGGTGTGGGAG-----GGCCCGGCGCCCTGATCTGGAGCGAGCTGGTCC---------------------------------------------------------CCCTCTCTGAG-----GGCCCA------GCTCTCAGCTGGAGGACTCCTGCGTCCT--CTGT--GCCTGC----ATCCTCCAATCCCCC-AAGCAGGCCCTGCACCCC-Agtctttacctcctcagcacc
q bosTau4.chr1                                      999999999-999999999999999999999-99999999999-9---99999999999999999999999-----999999999999999999999999999999999---------------------------------------------------------99999999999-----999999------9999999999999999999999999999--9999--999999----999999999999999-999999999999999999-999999999999999999999
i bosTau4.chr1            C 0 I 644
s loxAfr3.scaffold_36        541944 246 -  24123610 aaagttatgtttctcaggggatggct---ct-ccctctcttct-gctaggcacaaagagctgggaa----------ctttcatcacctaagccaatcaggggctgttactagttgacagtgacttaagttgtggtaaggctcaaattagactactcctagttta--cctgtttctag-----ggctctca-----------gttgaggacttggtgtgttca--ccatgccgccac--------------ctcccaaagtaggtcctgaacact-aatctctatcttctcagcacc
q loxAfr3.scaffold_36                               99999999999999999999999999---99-99999999999-9999999999999999999999----------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999-----99999999-----------999999999999999999999--999999999999--------------999999999999999999999999-999999999999999999999
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e speTri1.scaffold_135460    104894 446 -    203079 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=58517.000000
s hg19.chrY                 7669663 150 +  59373566 agaagattactgaac--accact--------tctgctttccagagggattctggttatcttttgaa------cttctcatcccatgcag-tccagaattgggcaactgtct-tgaagggaaagccaactgtgaatttcaggttcctc----gagtctccaa-ttttgtctctc
s rheMac2.chr2            158787144 150 + 189746636 AGAAGATTACTCAAC--ACCCCT--------TTAGATTTCCAGAGAGATTCTGCTTATCTTTTGAA------CCTCTCATCCCACGCAG-TCCAGAATTTAGCAACTATCT-TGAAGGGAAAGCCAACTGTGCACTTCCGGCTCCTC----AAGTCTCCAA-TTTTGTCTCTC
q rheMac2.chr2                                      999999999999999--999999--------99999999999999999999999999999999999------99999999999999999-966666666666776666666-99999999999999999999999999999999999----9999999999-99999999999
i rheMac2.chr2            C 0 C 0
s panTro2.chrY               523199 150 +  23952694 AGAAGATTACTGAAC--ACCACT--------TCTGCTTTCCAGAGGGATTCTGGTTATCTTTTGAA------CTTCTCATCCCATGTAG-TCCAGAATTGGGCAACTGTCT-TGAAGGGAAAGCCAACTGTGAATTTCAGGTTCCTC----GAGTCTCCAA-TTTTGTCTCTC
q panTro2.chrY                                      000000000000000--000000--------00000000000000000000000000000000000------00000000000000000-000000000000000000000-00000000000000000000000000000000000----0000000000-00000000000
i panTro2.chrY            C 0 C 0
s cavPor3.scaffold_0        8266020 144 -  88675666 ataagcctgaacact--cctgct--------ttttat-----gtgttttctacttaagattctgaa------ctccatgtctcttgtagtttcagaatttagtgactgcct-cagggaaaaacccaactgta------tagctgggctccaaagactccaa-tattgtctccg
q cavPor3.scaffold_0                                999999999999999--999999--------999999-----999999999999999999999999------999999999999999999999999999999999999999-99999999999999999999------99999999999999999999999-99999599579
i cavPor3.scaffold_0      C 0 C 0
s rn4.chr9                107371264 117 - 113440463 AGGTCCCTGATAAATGGGCTGCA--------TTTCA--------GGGTTTTACCTGAGACACCGAATCTCTGCTCTAATGCGCTGGCACTTTCTG--------TACCGTCT-----------------TGTA------TAATTTTAC--------CTCTTA-TCCTGTCTCTA
q rn4.chr9                                          99999999999999999999999--------99999--------999999999999999999999999999999999999999999999999999--------99999999-----------------9999------999999999--------999999-99999999999
i rn4.chr9                C 0 C 0
s oryCun2.chr14             2498007 128 + 163896628 -----cttgactggtgggccactcccagggctctga--------ggctctccgctgagcccgcgat------ctccca-tctcgcccagcttcag-----------tgtctgcaggaggaagggacggtgtg-----ctggaggctc--------ctccag-gtctcgctcca
q oryCun2.chr14                                     -----9999999999999999999999999999999--------9999999999999999999999------999999-9999999999999999-----------99999999999999999999999999-----9999999999--------999999-99999999999
i oryCun2.chr14           C 0 C 0
s canFam2.chr23            26015020 133 -  55389570 AGAAGACTGCTGAAC--TTCTCT--------TCTGTTGTCCACAGGCCTTCTGATAAGCCTTT-AT------CTTCCCAGCCCACACAACTTCAGGATTTAGCAACTGTTT-TGAGAGGAAAAC-------ATAATTGA--CTCTCC----AA---------TTTTGTCTCTC
q canFam2.chr23                                     999999999999999--999999--------99999999999999999999999999999999-99------999999999999999999999999999999999999999-999999999999-------99999999--999999----99---------99999999999
i canFam2.chr23           I 10 C 0
s equCab2.chr16            22235478 150 -  87365405 --aagacagctgagc--tttcct--------tctgcttttcggaggctttctgattagtctttgaa------cctctcagcccacgcagcttcagaatttagcaacagcct-tgacagggaaactacctgtgaatttgagcctcctc----aagtctccagtttttgtctctc
q equCab2.chr16                                     --9999999999999--999999--------99999999999999999999999999999999999------999999999999999999999999999999999999999-99999999999999999999999999999999999----9999999999999999999999
i equCab2.chr16           C 0 C 0
s loxAfr3.scaffold_36        542190 150 -  24123610 acaagactgctgata--actccc--------gctgc-tttcagagacttcctgctcagctttccag------cctcctgtcccatgcagctttggaattcagcaactgcct-tgaggggaaaaccaactatgtgtttgaggtccctc----aagtccccag-ttttgtctctc
q loxAfr3.scaffold_36                               999999999999999--999999--------99999-99999999999999999999999999999------999999999999999999999999999999999999999-99999999999999999999999999999999999----9999999999-99999999999
i loxAfr3.scaffold_36     C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e bosTau4.chr1            157013339 644 + 161106243 I
e speTri1.scaffold_135460    104894 446 -    203079 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=26852.000000
s hg19.chrY                 7669813 68 +  59373566 aaccccagtcccaagagaatac-----------taggtttatttttct--cagagctgcaacactccatctaaacaaa---gc-c
s equCab2.chr16            22235628 79 -  87365405 cagtccagtcccatgagaccaccaaaagctctgctggtttctctttcc--cagagcagcatcgctccatccaggcaaagcc----
q equCab2.chr16                                    999999999999999999999999999999999999999999999999--9999999999999999999999999999999----
i equCab2.chr16           C 0 C 0
s canFam2.chr23            26015153 76 -  55389570 CAGTCCAGTCCTATGAAGTCACCAAAACTTCTGCTGGTTTCTCCTTCC--CAGAGCGGCAAGGCTCCAGCCAGGCAAA-------
q canFam2.chr23                                    999999999999999999999999999999999999999999999999--9999999999999999999999999999-------
i canFam2.chr23           C 0 C 0
s oryCun2.chr14             2498135 56 + 163896628 gtccag--tcccaagagaccaccgcgcac-------gtttctcttccc--cag--------------agccaggaaaa---gcc-
q oryCun2.chr14                                    999999--999999999999999999999-------999999999999--999--------------99999999999---999-
i oryCun2.chr14           C 0 C 0
s rn4.chr9                107371381 76 - 113440463 ATGAAC--TCTTGTGAGACCCATGACAGCTTTCCAGGGTTTCTTTCCT--CAGAACATCAGTGATCTGGCCAGGCCAA---GC--
q rn4.chr9                                         999999--9999999999999999999999999999999999999999--9999999999999999999999999999---99--
i rn4.chr9                C 0 C 0
s cavPor3.scaffold_0        8266164 79 -  88675666 tagtcca-tcccaggaaaccaccaaaaactctattggtttctatttcttacaggaaaaaaaaaaaaaaaacaaaacaa---ga--
q cavPor3.scaffold_0                               7995857-9986448585374495598859966666436566999999999999999999999999999999999999---99--
i cavPor3.scaffold_0      C 0 C 0
s panTro2.chrY               523349 68 +  23952694 AACCCCAGTCCCAAGAGAATAC-----------TAGGTTTATTTTTCT--CAGAGCTGCAACACTCCATCTAAACAAA---GC-C
q panTro2.chrY                                     0000000000000000000000-----------000000000000000--0000000000000000000000000000---00-0
i panTro2.chrY            C 0 C 0
s rheMac2.chr2            158787294 79 + 189746636 CACTCCAGTCCCAAGAAAACACCAAAAGCTCTGCAGGTTTATTTTTCC--CAGAGCAGCAACATTCCATCCAAGCAAA---GC-C
q rheMac2.chr2                                     999999999999999999999999999999999999999999999999--9999999999999999999999999999---99-9
i rheMac2.chr2            C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e bosTau4.chr1            157013339 644 + 161106243 I
e loxAfr3.scaffold_36        542340  0 -  24123610 C
e speTri1.scaffold_135460    104894 446 -    203079 I
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=-17006.000000
s hg19.chrY                 7669881 45 +  59373566 caggtcc----acattattttg-----------------tcaccacccagaattagaaatccccc-a--
s equCab2.chr16            22235707 46 -  87365405 tggattt----ccagtccctta-----------------tcagcactcagaaccagaactacccc--ca
q equCab2.chr16                                    9999999----99999999999-----------------99999999999999999999999999--99
i equCab2.chr16           C 0 C 0
s canFam2.chr23            26015229 44 -  55389570 --GATTT----CCGGTCCTTTG-----------------CCAGAACTCTGAACCAACAATGTCCC--TA
q canFam2.chr23                                    --99999----99999999999-----------------99999999999999999999999999--99
i canFam2.chr23           C 0 C 0
s oryCun2.chr14             2498191 55 + 163896628 -----------tggatcttgcgccccctccacacctctcccagcacccagaatccagagcgcccca---
q oryCun2.chr14                                    -----------9999999999999999999999999999999999999999999999999999999---
i oryCun2.chr14           C 0 C 0
s speTri1.scaffold_135460    105340 31 -    203079 -agcttccagaataacaccgca-----------------cccaccccaa--------------------
q speTri1.scaffold_135460                          -999999999999999999999-----------------9998999769--------------------
i speTri1.scaffold_135460 I 446 N 0
s cavPor3.scaffold_0        8266243 38 -  88675666 ---attc------gatgtcctg-----------------ccagcactcaa-aatcaaagcccccc----
q cavPor3.scaffold_0                               ---9999------999999999-----------------99999999999-99999999999999----
i cavPor3.scaffold_0      C 0 C 0
s rn4.chr9                107371457 30 - 113440463 -----------------TTGTG-----------------CCAACGCTGAG-CTCAGAAGCCCTTG----
q rn4.chr9                                         -----------------99999-----------------99999999999-99999999999999----
i rn4.chr9                C 0 C 0
s panTro2.chrY               523417 45 +  23952694 CAGGTCC----ACATTATTTTG-----------------TCACCACCCAGAATTAGAAATCCCCC-A--
q panTro2.chrY                                     0000000----00000000000-----------------00000000000000000000000000-0--
i panTro2.chrY            C 0 C 0
s rheMac2.chr2            158787373 45 + 189746636 TAGGTCC----CCATTATTTTG-----------------TCAGCACTCAGAATTAGAAATCTCCC-A--
q rheMac2.chr2                                     9999999----99999999999-----------------99999999999999999999999999-9--
i rheMac2.chr2            C 0 C 0
e mm9.chr17                50269383 1454 +  95272651 I
e bosTau4.chr1            157013339 644 + 161106243 I
e loxAfr3.scaffold_36        542340  0 -  24123610 C
e macEug1.Scaffold7817        25228 4878 -     41428 I
e monDom5.chr8            276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112        4907 1176 -     49748 I
e myoLuc1.scaffold_7336       37698 5478 -    312611 I
e ponAbe2.chr3             71060350 1533 - 202140232 I

a score=25658.000000
s hg19.chrY               7669926 101 +  59373566 taaataaagtagctacagaccatcagctcatctctcctcag-----ctctcttctttt--tgatattttag-----cccccctactcctca-tgttccaacatgtc-----tttaaaca
s equCab2.chr16          22235753  89 -  87365405 gggataaagtagctgcagaccatcagcttacctcctcgtcatgc--tccccttc---c--tgacatctccg------ccccccagtcctcattgcttcaacg-----------------
q equCab2.chr16                                   99999999999999999999999999999999999999999999--99999999---9--99999999999------9999999999999999999999999-----------------
i equCab2.chr16         C 0 I 21
s canFam2.chr23          26015273  87 -  55389570 GGGGTAGAGTAGAT-----CTGTCAGCTTATCTCCTACTCA-----CCTCCCTT---C--TGACACCTCAGCATCTCCTACCCAGTCCTCATTGTTTTAACA-----------------
q canFam2.chr23                                   99999999999999-----9999999999999999999999-----99999999---9--999999999999999999999999999999999999999999-----------------
i canFam2.chr23         C 0 I 261
s oryCun2.chr14           2498246  95 + 163896628 gggacgacgcggctgcagac---ccagcaccctcacgactg-----tccccttc---cggggacccccacc-----gt---ccactcctcactgccgcaacttttc-----agatggct
q oryCun2.chr14                                   99999999999999999999---999999999999999999-----99999999---99999979999999-----99---9999999999999999999999999-----99999999
i oryCun2.chr14         C 0 I 7
s cavPor3.scaffold_0      8266281  98 -  88675666 agaataaagtagccaatcat---ctgctcaccttgccacagttccttccccttc---c--tgattctcagt-----gtcccccacttcttactgttgcaaggtttc-----ttaaa---
q cavPor3.scaffold_0                              99999999999999999999---9999996699999999999999999999999---9--99999999989-----899999979999999999999999999999-----99999---
i cavPor3.scaffold_0    C 0 I 11
s panTro2.chrY             523462 101 +  23952694 TAAATAAAGTAGCTACAGACCATCAGCTCATCTCTCCTCAG-----CTCTCTTCTTTT--TGATATTTTAG-----CCCCCCTACTCCTCA-TGTTCCAACATGTC-----TTTAAACA
q panTro2.chrY                                    00000000000000000000000000000000000000000-----000000000000--00000000000-----000000000000000-00000000000000-----00000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158787418 104 + 189746636 AAAATAAAGTAGCTACAGATCGTCAGCTCACCTCTCCACAG-----TTCTCTTC---T--TGATATTTTAA-----CCCCCCTACTCCTCATTGTTTCAGCACTTCCCAGATTTAAACA
q rheMac2.chr2                                    99999999999999999999999999999999999999999-----99999999---9--99999999999-----9999999999999999999999999999999999999999999
i rheMac2.chr2          C 0 C 0
e rn4.chr9              107371487   0 - 113440463 C
e mm9.chr17              50269383 1454 +  95272651 I
e bosTau4.chr1          157013339 644 + 161106243 I
e loxAfr3.scaffold_36      542340   0 -  24123610 C
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=63310.000000
s hg19.chrY               7670027 105 +  59373566 gaatggtgctt-tctgtattt-------------------tatatggta---------cttcttgg-gatcgttagtttgcctcagactacccaatcctagctagaaac--aaaTCTCTG-CTTTATATTTTTCAAAG
s rheMac2.chr2          158787522 116 + 189746636 GAATGTTGCTT-TCTGCAGTC-------------------TATACGGTTTCTGTTGTTCTTCTTGG-GATCGTTAGTTTGCCTCAAACTACCCAATCCTAGCCAGAAACAGAAATCGCTT-ATTTATATTTTTCAAAG
q rheMac2.chr2                                    99999999999-999999999-------------------99999999999999999999999999-99999999999999999999999999999999999999999999999999999-99999999999999999
i rheMac2.chr2          C 0 C 0
s panTro2.chrY             523563 108 +  23952694 GAATGGTGCTT-TCTGTAATT-------------------TATATGGTAC------TTCTTCTTGG-GATCGTTAGTTTGCCTCAGACTACCCAATCCTAGCTAGAAAC--AAATCTCTG-CTTTATATTTTTCAAAG
q panTro2.chrY                                    00000000000-000000000-------------------0000000000------0000000000-000000000000000000000000000000000000000000--000000000-00000000000000000
i panTro2.chrY          C 0 C 0
s rn4.chr9              107371487  29 - 113440463 -----------------------------------------GGATGGC-------------TTGTGAGGTCACTAGTTCACCT-------------------------------------------------------
q rn4.chr9                                        -----------------------------------------9999999-------------9999999999999999999999-------------------------------------------------------
i rn4.chr9              C 0 C 0
s cavPor3.scaffold_0      8266390 112 -  88675666 aaacctaaaa------aattt-------------------tatacggcctttctcattcttttgggagatcactaatttgccttgatctacccaat-ctaaccaaaagcagaaattcCTCGTCTAATATTTTTCAAAG
q cavPor3.scaffold_0                              9966988999------95768-------------------97968945985999989999979999999999999999987999979998999999-99838999999999999999999999999999999999999
i cavPor3.scaffold_0    I 11 C 0
s oryCun2.chr14           2498348 116 + 163896628 gaattttccat-ttcctattt-------------------tatatggattttcttgttcttctggg-gatcactcatttgcctcacgccatccaatcctaaccagaagtggaaACCTCTC-TCATACATTTTTCAAAG
q oryCun2.chr14                                   99979999999-999999999-------------------99999999999999896999999999-99999999999999999999999999999999989999999899999999999-99999999999999999
i oryCun2.chr14         I 7 C 0
s equCab2.chr16          22235863 117 -  87365405 gaatgatttttgtgtgtattt-------------------tacatggcttttcttgttcttctaaa-gatcacgagtttgtctcaaacaactcaatcttacccagaagcaaaaatccCTC-ctttatatgtttcaaag
q equCab2.chr16                                   999999899999999999999-------------------99999999999999999999999999-99999999999999999999999999999999999999999999999999999-99999999999999999
i equCab2.chr16         I 21 C 0
s canFam2.chr23          26015621 136 -  55389570 GAATGGTGTGTGTGTGTGTCTGTGTCTGTACAGTGTACTGTATATGGCTTTTCTTGCTGTTCTTGG-GATCATCAGTATGCCTCAAACTCCTCAATATTACCGAGAAGCAGAAATCCCTC-CTTTATATTTTTCCAAG
q canFam2.chr23                                   999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999-99999999999999999
i canFam2.chr23         I 261 C 0
e mm9.chr17              50269383 1454 +  95272651 I
e bosTau4.chr1          157013339 644 + 161106243 I
e loxAfr3.scaffold_36      542340   0 -  24123610 C
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=13517.000000
s hg19.chrY               7670132 25 +  59373566 TGCTTTCATTGTCATAATTAA-TTTC
s rheMac2.chr2          158787638 25 + 189746636 TGCTTTCATAGTCATAATTAA-TTTC
q rheMac2.chr2                                   999999999999999999999-9999
i rheMac2.chr2          C 0 I 37
s panTro2.chrY             523671 25 +  23952694 TGCTTTCATTGTCATAATTAA-TTTC
q panTro2.chrY                                   000000000000000000000-0000
i panTro2.chrY          C 0 C 0
s mm9.chr17              50270837 25 +  95272651 TGCCTTCATTATAATATTTAA-TTTC
i mm9.chr17             I 1454 C 0
s rn4.chr9              107371516 20 - 113440463 -----TCATTATAATATTTAA-TTTC
q rn4.chr9                                       -----9999999999999999-9999
i rn4.chr9              C 0 C 0
s cavPor3.scaffold_0      8266502 20 -  88675666 CAGTTTATTTACAGT-----A-TTTT
q cavPor3.scaffold_0                             999999999999999-----9-9999
i cavPor3.scaffold_0    C 0 C 0
s oryCun2.chr14           2498464  6 + 163896628 -------------------CA-TTTG
q oryCun2.chr14                                  -------------------99-9997
i oryCun2.chr14         C 0 C 0
s equCab2.chr16          22235980 25 -  87365405 tgctttcactacgagatttcatttt-
q equCab2.chr16                                  9999999999999999999999999-
i equCab2.chr16         C 0 C 0
s canFam2.chr23          26015757 24 -  55389570 TGATTTCGCTACAATACTTAA-TTT-
q canFam2.chr23                                  999999999999999999999-999-
i canFam2.chr23         C 0 C 0
e bosTau4.chr1          157013339 644 + 161106243 I
e loxAfr3.scaffold_36      542340  0 -  24123610 C
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=-10807.000000
s hg19.chrY               7670157 33 +  59373566 TGCCATATAAACTGAT--AAGAAAA---AGATGGCAGg-
s panTro2.chrY             523696 33 +  23952694 CACCACATAAACTGAT--AAGAAAA---AGATGGCAGg-
q panTro2.chrY                                   0000000000000000--0000000---0000000000-
i panTro2.chrY          C 0 C 0
s mm9.chr17              50270862 35 +  95272651 -CACTTTTAAACCTAT--AGGAAAAGAGGAAAAGCAAG-
i mm9.chr17             C 0 C 0
s rn4.chr9              107371536 32 - 113440463 -CACTTTTAAACCTAT--AGGAAAA---GCAAGGCAGG-
q rn4.chr9                                       -999999999999999--9999999---9999999999-
i rn4.chr9              C 0 C 0
s cavPor3.scaffold_0      8266522 11 -  88675666 -CCTTTTTAAAC---------------------------
q cavPor3.scaffold_0                             -99999999999---------------------------
i cavPor3.scaffold_0    C 0 I 19
s oryCun2.chr14           2498470  4 + 163896628 -CATT----------------------------------
q oryCun2.chr14                                  -9999----------------------------------
i oryCun2.chr14         C 0 I 15
s equCab2.chr16          22236005 32 -  87365405 ccccttacaaacctac--aggaaaa---aacaggcag--
q equCab2.chr16                                  9999999999999999--9999999---999999999--
i equCab2.chr16         C 0 I 6
s canFam2.chr23          26015781 31 -  55389570 CCTCTTATAAACCTATGGGGGGAAA---AACAG-----G
q canFam2.chr23                                  9999999999999999999999999---99999-----9
i canFam2.chr23         C 0 C 0
e bosTau4.chr1          157013339 644 + 161106243 I
e loxAfr3.scaffold_36      542340  0 -  24123610 C
e rheMac2.chr2          158787663 37 + 189746636 I
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=7586.000000
s hg19.chrY               7670190 85 +  59373566 gccaggcacagtggctcatgcctgtaatcctagtactttgggaggccaaggcaggtggatcacgaggtaaggagatggagaccat
s panTro2.chrY             523729 85 +  23952694 gccaggcacactgggtcacgcctgtaatcctagtactttgggaggccaaggcaggtggatcacgaggtaaggagatggagaccat
q panTro2.chrY                                   0000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
e cavPor3.scaffold_0      8266533 19 -  88675666 I
e rn4.chr9              107371568  0 - 113440463 C
e mm9.chr17              50270897  0 +  95272651 C
e oryCun2.chr14           2498474 15 + 163896628 I
e equCab2.chr16          22236037  6 -  87365405 I
e bosTau4.chr1          157013339 644 + 161106243 I
e loxAfr3.scaffold_36      542340  0 -  24123610 C
e canFam2.chr23          26015812  0 -  55389570 C
e rheMac2.chr2          158787663 37 + 189746636 I
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=4722.000000
s hg19.chrY               7670275 90 +  59373566 cctggctaacatggtaaaaccccatctctactaaaaatacaaagaaattagccagatatggtggcagacacctgtagtaccagctacttg
s oryCun2.chr14           2498489 19 + 163896628 -------------------CCCCTT---------------------------------------CAGAAACCTACAG-------------
q oryCun2.chr14                                  -------------------999899---------------------------------------9999977988966-------------
i oryCun2.chr14         I 15 C 0
s panTro2.chrY             523814 90 +  23952694 cctggctaacatggtgaaaccccatctctactaaaaatacaaagaaattagccagatatggtggcagacacctgtagtaccagctactcg
q panTro2.chrY                                   000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
e cavPor3.scaffold_0      8266533 19 -  88675666 I
e rn4.chr9              107371568  0 - 113440463 C
e mm9.chr17              50270897  0 +  95272651 C
e equCab2.chr16          22236037  6 -  87365405 I
e bosTau4.chr1          157013339 644 + 161106243 I
e loxAfr3.scaffold_36      542340  0 -  24123610 C
e canFam2.chr23          26015812  0 -  55389570 C
e rheMac2.chr2          158787663 37 + 189746636 I
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=6611.000000
s hg19.chrY               7670365 111 +  59373566 ggaggctgaggcagga----gaatggagtgaacttgggaggtggagcttgtagtgagatgagatcgtgcctctgcactccagcctgggcaatgcagcaagactctgtctcaag-aa
s panTro2.chrY             523904 112 +  23952694 ggaggctgaggcagga----gaatggagtgaacttgggaggtggagcttgcagtgagatgagatcatgcctctgcactccagcctgggcaatgcagcaagactctgtctcaagaaa
q panTro2.chrY                                    0000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s bosTau4.chr1          157013983  56 + 161106243 accacctgatacaaaaagctgactgaactgaaCT---------GAACTTATAAACCCATAAGA---------------------------------------------------AA
q bosTau4.chr1                                    9999999999999999999999999999999999---------99999999999999999999---------------------------------------------------99
i bosTau4.chr1          I 644 C 0
e cavPor3.scaffold_0      8266533  19 -  88675666 I
e rn4.chr9              107371568   0 - 113440463 C
e mm9.chr17              50270897   0 +  95272651 C
e oryCun2.chr14           2498508   0 + 163896628 C
e equCab2.chr16          22236037   6 -  87365405 I
e loxAfr3.scaffold_36      542340   0 -  24123610 C
e canFam2.chr23          26015812   0 -  55389570 C
e rheMac2.chr2          158787663  37 + 189746636 I
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I
e ponAbe2.chr3           71060350 1533 - 202140232 I

a score=171412.000000
s hg19.chrY               7670476 174 +  59373566 aaaaaaaaGCAATATG---TTTTACTCTGATCTTTTAGAACACAGTTTGTCAGCATTGgac-aaactatgggccacaggccaagtc-cagcccagtgcctggttttgtaaataaagttttattggaatatagccatgcccactatattgtgcatattgtccatggctgctttggc----------act-a
s cavPor3.scaffold_0      8266552 147 -  88675666 ---------------TTTTTCTTACGTTGATCATTTAGACcacagg----------tgggc-aaacagttgtgagccaact-atacgcagtccactgcctt---ttttaaataaagttttattggaacacagccacattcat--tcatccccctactgtgtatggctgctttggc----------act-a
q cavPor3.scaffold_0                              ---------------9999999999999999999999999999999----------99999-9999999999999999999-9999999999999999999---99999999999999999999999999999999999999--9999999999999999999999999999999----------999-9
i cavPor3.scaffold_0    I 19 C 0
s rn4.chr9              107371568 147 - 113440463 -------------AGTAGTTTTCACTCTGATCATTGAGATcagggg----------tggga-aaactacagtgag-cagcc-agtc-tggcccactgccgtg-cttttaaataaagttttattagaacccagcgatctt--t--tcatttctatattgaccatggctgtgttggc----------act-a
q rn4.chr9                                        -------------999999999988777777888999899999999----------99999-9999999999999-99999-8888-889999999999999-999999646457999999999999999989999999--9--9999999999999999999999999999999----------999-9
i rn4.chr9              C 0 C 0
s mm9.chr17              50270897 153 +  95272651 --------GCAGGAGTATTTTTCACTCTGATCATTGAGATcagggg----------tgggc-aaaccacagtgaaccagcc-agtc-tggcccactaccgtg-cttatatataaagttttattagaacacggtgacctt--t--tcatttctatattgaccatggctgtgtaggc----------act-a
i mm9.chr17             C 0 C 0
s ponAbe2.chr3           71061883 152 - 202140232 -----------------------actctgatattttagagcacagttcgccagtgctgggc-aaactatggcccacaggccaagtc-cagcccactgcctggttttgtaaataaagttttattggaatacagccatgtccac--taacgtgcatattgtctatggctgctttgac----------act-a
q ponAbe2.chr3                                    -----------------------99999999999999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999989989989999979--9999989999999999999999889998999----------449-6
i ponAbe2.chr3          I 1533 C 0
s rheMac2.chr2          158787700 156 + 189746636 -------------------TTTTACTCTAATCTTTTAGACCACAGTTTGCCAGTCTTGgac-aaactatggcccacaggccaagtc-cagcccactgcctggttttgtaaataaagttttattggaatacagccatgtccac--tgatgtgcatattgtctatggctgctttggc----------act-a
q rheMac2.chr2                                    -------------------999999999999999999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999999--9999999999999999999999999999999----------999-9
i rheMac2.chr2          I 37 C 0
s canFam2.chr23          26015812 151 -  55389570 -----------GCAGTATTTATCATTCGGGTCTTTTAGATGagggg----------ttgg--caactatggcctacaaggcaagcc-cagcctgttgcctgtcggggtgaat----ttttactggattgcagccacacacat--tcatttacatattgtctggggttacttttgca--------aatg-a
q canFam2.chr23                                   -----------99999999999999999999999999999999999----------9999--999999999999999999999999-9999999999999999999999999----99999999999999999999999999--99999999999999999999999999999999--------9999-9
i canFam2.chr23         C 0 C 0
s equCab2.chr16          22236043 140 -  87365405 ---------------------tttctctgattttttagactaggag----------tggga-aaactatggaccccaggccaagtc-catcccattgcctgtttttgtcaat----ttttattggaacacagccacacccag--ttacttacatattgtctatagctgctcttcc----------acc-a
q equCab2.chr16                                   ---------------------9999999999999999999999999----------99999-999999999999999999999999-9999999999999999999999999----99999999999999999999999999--9999999999999999999999999999999----------999-9
i equCab2.chr16         I 6 C 0
s bosTau4.chr1          157014039 144 + 161106243 AAAACGGA---GCAATGTTCGTCACACGGATATCTGAAACCAGAGG----------TTTC-------ATGGCCCACAGGTTAGGTC-CAGCACGTGGCCAGGT-CTGCACAT----TGTCATTG-----------------C--TCTCttacatattgtggggggctgcttttgcattttgcagccct-a
q bosTau4.chr1                                    99999999---99999999999999999999999999999999999----------9999-------9999999999999999999-9999999999999999-99999999----99999999-----------------9--99999999999999999999999999999999999999998999-9
i bosTau4.chr1          C 0 C 0
s oryCun2.chr14           2498508 136 + 163896628 AAAAAATA-------------------GGATCTCTTGGATCTTGAG----------CGGGCAaaaccacagccca------------caggccacagctggt-ttcgtaaataaagttttgttggaacacagccacatccac--tcatgcgcatagtggccgtggctgctccggc----------tctca
q oryCun2.chr14                                   99999586-------------------6769799767437683685----------6774469977949963798------------999249899996732-113779989999799937977689989945977799999--9999888899999835999999999999998----------99999
i oryCun2.chr14         C 0 C 0
s panTro2.chrY             524016 174 +  23952694 aaaaaaaaGCAATATG---TTTTACTCTGATCTTTTAGAACACAGTTTGTCAGCATTGgac-aaactatgggccacaggccaagac-cagcccagtgcctggttttgtaaataaagttttattggaatatagccatgcccactatattgtgcatattgtccatggctgctttggc----------act-a
q panTro2.chrY                                    0000000000000000---000000000000000000000000000000000000000000-000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----------000-0
i panTro2.chrY          C 0 C 0
e loxAfr3.scaffold_36      542340   0 -  24123610 C
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=159429.000000
s hg19.chrY               7670650 94 +  59373566 caaaagcttttgcagatttgagtagttataacagagaccacatcaccagcaaagcccaaaatattcaccatctttccctttacagaaagtttgt---
s panTro2.chrY             524190 94 +  23952694 caaaagcttttgcagatttgagtagttataacagagaccacatcaccagcaaagcccaaaatattcaccatctttccctttacagaaagtttgt---
q panTro2.chrY                                   0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000---
i panTro2.chrY          C 0 C 0
s oryCun2.chr14           2498644 91 + 163896628 caaaagctttggcaaagtcggccagctgtggcacagagcgtatcagctgtcaaggccaggacat---ctgctatctTTCCCAAGCAGGAGTCTC---
q oryCun2.chr14                                  9999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999---
i oryCun2.chr14         C 0 I 1
s bosTau4.chr1          157014183 80 + 161106243 caagggc------agagctgaagagctgtgagagaga--------ctccccaaaccctcactacctagtgtcttccccttcacagaaaaagttt---
q bosTau4.chr1                                   9999999------999999999999999999999999--------9999999999999999999999999999999999999999999999999---
i bosTau4.chr1          C 0 I 2
s equCab2.chr16          22236183 88 -  87365405 cagtggg------agaggtgagtaggtgtgagagagagtatactacctgcaaagcccaaaatatttactatctctccttttacacaaaaagttt---
q equCab2.chr16                                  9999999------999999999999999999999999999999999999999999999999999999999999999999999999999999999---
i equCab2.chr16         C 0 I 2
s canFam2.chr23          26015963 88 -  55389570 caacggc------agagttgagtagttgtgagagagaccacagtgcctccaaagcaccaaatatttactatctgtctcttcacagaaaaagtca---
q canFam2.chr23                                  9999999------999999999999999999999999999999999999999999999999999999999999999999999999999999999---
i canFam2.chr23         C 0 I 2
s rheMac2.chr2          158787856 94 + 189746636 cagaagcttttgcagatttcagtagttgtaacagagaccacatcacccacaaagcccaaaatatttaccacctttgcctttacagaaagtttgc---
q rheMac2.chr2                                   9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062035 94 - 202140232 caaaagcttttgcagatttaagtagttgtaacagagaccacatcacccacaaagcccaaaatatttaccatctttccctttacagaaagtttgc---
q ponAbe2.chr3                                   9989999998899999899999999989998999999998999999999999999999999999999999999999999999999999999999---
i ponAbe2.chr3          C 0 C 0
s mm9.chr17              50271050 89 +  95272651 gggaagcttttacac-----agtagttgttagaaagatcatattgctcaggaaagccacagttttccttttctttctctccacaggaaaaTAGC---
i mm9.chr17             C 0 I 12
s rn4.chr9              107371715 78 - 113440463 ggagagcttt----------agtaattgttagagagatcatattgctcatgaagcccacag------ttttctttctctccacaggaaaaCGGC---
q rn4.chr9                                       9999999999----------99999999999999999999999999999999999999999------999999999999999999999999999---
i rn4.chr9              C 0 I 12
s cavPor3.scaffold_0      8266699 91 -  88675666 caaaggattctgaacagctgaataattgtaacagggaccacatagtccacaaagcccacaattt---ctctcatcttcttcatggaataaagct---
q cavPor3.scaffold_0                             9999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999---
i cavPor3.scaffold_0    C 0 I 6
s loxAfr3.scaffold_36      542340 97 -  24123610 tagcTGGTCTCgcagaattgagtagctgcgacagagaccatattgactgcaaaacccaaaatatctgctgccttgatcttcatggaaaaatgtttgc
q loxAfr3.scaffold_36                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36   C 0 C 0
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e dipOrd1.scaffold_8112      4907 1176 -     49748 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=-33800.000000
s hg19.chrY               7670744 19 +  59373566 cagcccctgCTTCAT----------------------------------------------------------------------TTG--A
s loxAfr3.scaffold_36      542437 19 -  24123610 caactcctgTTTTAG----------------------------------------------------------------------ATG--G
q loxAfr3.scaffold_36                            999999999999999----------------------------------------------------------------------999--9
i loxAfr3.scaffold_36   C 0 C 0
s bosTau4.chr1          157014265 87 + 161106243 cagc--cTATTTTATACAGGTCCGGGGAcctttggagaaggaaatggcaacccacttcagtattcttgcccgggaaattccaccgaca--g
q bosTau4.chr1                                   9999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999--9
i bosTau4.chr1          I 2 C 0
s equCab2.chr16          22236273 19 -  87365405 cagccgctattttat----------------------------------------------------------------------atg--g
q equCab2.chr16                                  999999999999999----------------------------------------------------------------------999--9
i equCab2.chr16         I 2 C 0
s canFam2.chr23          26016053 16 -  55389570 cagtccc---tTTAT----------------------------------------------------------------------ATA--G
q canFam2.chr23                                  9999999---99999----------------------------------------------------------------------999--9
i canFam2.chr23         I 2 C 0
s oryCun2.chr14           2498736  7 + 163896628 ------------AAG----------------------------------------------------------------------CTG--A
q oryCun2.chr14                                  ------------999----------------------------------------------------------------------999--9
i oryCun2.chr14         I 1 C 0
s cavPor3.scaffold_0      8266796 18 -  88675666 CTGCTC-TGTCTCCA----------------------------------------------------------------------GTG--G
q cavPor3.scaffold_0                             999999-99999999----------------------------------------------------------------------999--9
i cavPor3.scaffold_0    I 6 C 0
s dipOrd1.scaffold_8112      6083  4 -     49748 -------------------------------------------------------------------------------------CTG--A
q dipOrd1.scaffold_8112                          -------------------------------------------------------------------------------------312--2
i dipOrd1.scaffold_8112 I 1176 C 0
s rn4.chr9              107371805 10 - 113440463 CAGCTC-------------------------------------------------------------------------------TTG--A
q rn4.chr9                                       999999-------------------------------------------------------------------------------999--9
i rn4.chr9              I 12 C 0
s mm9.chr17              50271151 13 +  95272651 CAGCTC--------G----------------------------------------------------------------------TTGGCA
i mm9.chr17             I 12 C 0
s ponAbe2.chr3           71062129 19 - 202140232 cagcccctgcttcat----------------------------------------------------------------------ttg--a
q ponAbe2.chr3                                   999999999999999----------------------------------------------------------------------999--9
i ponAbe2.chr3          C 0 C 0
s rheMac2.chr2          158787950 22 + 189746636 cagcccctgCTTCAT-------------------------------------------------------------------CAGTTA--A
q rheMac2.chr2                                   999999999999999-------------------------------------------------------------------999999--9
i rheMac2.chr2          C 0 C 0
s panTro2.chrY             524284 19 +  23952694 cagcccctgCTTCAT----------------------------------------------------------------------TTG--A
q panTro2.chrY                                   000000000000000----------------------------------------------------------------------000--0
i panTro2.chrY          C 0 C 0
e macEug1.Scaffold7817      25228 4878 -     41428 I
e monDom5.chr8          276523208 4661 + 312544902 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=-57947.000000
s hg19.chrY               7670763  69 +  59373566 ag------gaaactg------------------------aagctcagacac---------------------------------------att--cagtgact---------------------------------------GA---CAAG----------------------------TTAACTTTGGAGAGAAGAC--------------TGTGTGTCAGTC
s panTro2.chrY             524303  69 +  23952694 ag------gaaactg------------------------aagctcagacat---------------------------------------att--cagtgact---------------------------------------GA---CAAA----------------------------TTAACTTTGGAGAGAAAAC--------------TGTGTGCCAGTC
q panTro2.chrY                                    00------0000000------------------------000000000000---------------------------------------000--00000000---------------------------------------00---0000----------------------------0000000000000000000--------------000000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158787972  75 + 189746636 AGCTCATTGAAACTG------------------------AAGCTCAGACAC---------------------------------------ATT--CAGTGACT---------------------------------------CG---CAAG----------------------------TTAACTTTGGAGCGAAGAT--------------TGCATGTAAGGT
q rheMac2.chr2                                    999999999999999------------------------999999999999---------------------------------------999--99999999---------------------------------------99---9999----------------------------9999999999999999999--------------999999999999
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062148  69 - 202140232 ag------gaaactg------------------------aagttcagacac---------------------------------------att--cagtgact---------------------------------------cg---caag----------------------------ttaactttggagagaagat--------------tgcacgtaaggt
q ponAbe2.chr3                                    99------9999999------------------------999999999999---------------------------------------999--99999999---------------------------------------99---9999----------------------------9999999999999999999--------------999999999999
i ponAbe2.chr3          C 0 C 0
s mm9.chr17              50271164  56 +  95272651 CA------TAAACTA------------------------AAGCCAGGACAC---------------------------------------AGT--CAGTCAGC---------------------------------------TG---CAC-----------------------------AGAACTCTGGGAAGACGAC--------------------------
i mm9.chr17             C 0 I 15
s rn4.chr9              107371815 137 - 113440463 CA------TAAACTA------------------------AAGCCAGGGCAC---------------------------------------AGT--CAGTAAGTGTACAAGAA-------------CTCTACAAAGTAGTAAGTG---TACAAGAATGCTATATAGTCAGTAAGTGTACAAGAACTCTATGCAGTCAGTAAGTGTACAAGAACTCTATACAGTCA
q rn4.chr9                                        99------9999999------------------------999999999999---------------------------------------999--99999999999999999-------------9999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999
i rn4.chr9              C 0 I 125
s dipOrd1.scaffold_8112      6087 126 -     49748 CC------TTGATTC------------------------CCACTAGGTGAT---------------------------------------CTG--CAAGCACTGCACCAGTGGCCTCTTCTTCCtttttaga----------ta---cagggtctcacgctttagtcctcactggcat-cgaagtccaaatgcccagc-------------ctctacctcttca
q dipOrd1.scaffold_8112                           02------0131004------------------------420211230131---------------------------------------113--2203000000022000000999999999999999999----------99---9999999999999999999999999999999-9999999999999999999-------------9999999999999
i dipOrd1.scaffold_8112 C 0 N 0
s cavPor3.scaffold_0      8266814  65 -  88675666 AA------TAAACTG------------------------AGGCTGAGACAC---------------------------------------ATT--CAGGTGACT--------------------------------------TG---CAAA----------------------------GTAACTTTGGAGTGACAAC--------------TGCATCC-----
q cavPor3.scaffold_0                              99------9999999------------------------999999999999---------------------------------------999--999999999--------------------------------------99---9999----------------------------9999999999999999999--------------9999999-----
i cavPor3.scaffold_0    C 0 I 9
s oryCun2.chr14           2498743  53 + 163896628 ---------AGGCTG------------------------AGGCTCAGACAC---------------------------------------GGG--CAGGGAC-----------------------------------------------------------------------------TTAACCTTGGGAGCAAGGC--------------TGCATC------
q oryCun2.chr14                                   ---------999999------------------------999999999999---------------------------------------999--9999999-----------------------------------------------------------------------------9999999999999999999--------------999999------
i oryCun2.chr14         C 0 C 0
s canFam2.chr23          26016069  69 -  55389570 AG------GAAGCTG------------------------AGGCTCAGATAC---------------------------------------TTT--CAGAGACC---------------------------------------TT---TAAG----------------------------TTAACTCGAGACAGAACAT--------------TGCATCTAAGGT
q canFam2.chr23                                   99------9999999------------------------999999999999---------------------------------------999--99999999---------------------------------------99---9999----------------------------9999999999999999999--------------999999999999
i canFam2.chr23         C 0 C 0
s equCab2.chr16          22236292  69 -  87365405 ag------gaaactg------------------------agcttcagacta---------------------------------------att--cagtgact---------------------------------------tg---caag----------------------------ttaactgtagagagaagat--------------tccacctaaggt
q equCab2.chr16                                   99------9999999------------------------999999999999---------------------------------------999--99999999---------------------------------------99---9999----------------------------9999999999999999999--------------999999999999
i equCab2.chr16         C 0 C 0
s bosTau4.chr1          157014352 128 + 161106243 ag------gagcctggctgactacagtctaaagggtcgcagagtcgggcacgaccgagcACAGCACGGAGCACCCAGGGAGCGGGCATCGGTT--TCGTGACT---------------------------------------TA---CAAG----------------------------CAGCTTCC---GAGAAGAC--------------CACACCCAAGG-
q bosTau4.chr1                                    99------9999999999999999999999999999999999999999999977999999999999999999999999999999999999999--99999999---------------------------------------99---9999----------------------------99999999---99999999--------------99999999999-
i bosTau4.chr1          C 0 C 0
s loxAfr3.scaffold_36      542456  68 -  24123610 AA------GAAGATG------------------------AGGCTCAGGGAC---------------------------------------A-T--CAGTGATT---------------------------------------TG---CAAG----------------------------TTAACTTTAGAGACAAGAT--------------CCCATCTAAGGT
q loxAfr3.scaffold_36                             99------9999999------------------------999999999999---------------------------------------9-9--99999999---------------------------------------99---9999----------------------------9999999999999999999--------------999999999999
i loxAfr3.scaffold_36   C 0 C 0
s monDom5.chr8          276527869  67 + 312544902 AA------GAGACAG------------------------GAGTTTGGGCTG---------------------------------------AGTCCCAGTGACT---------------------------------------TGGCCTACA----------------------------CTTACATCAGGGCTAGGAA--------------TAACT-------
q monDom5.chr8                                    99------9999999------------------------999999999999---------------------------------------9999999999999---------------------------------------999999999----------------------------9999999999999999999--------------99999-------
i monDom5.chr8          I 4661 C 0
e macEug1.Scaffold7817      25228 4878 -     41428 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=96946.000000
s hg19.chrY               7670832 52 +  59373566 CCCACGATTCTTA---TTCCAGCCATCTCCCCACT-CTT--CTAATTTGCTTCCCATC------
s loxAfr3.scaffold_36      542524 52 -  24123610 TTCCAGATTCTCA---TTCAAGCCATTCTGCCACA-GTT--CTAATTTGCTTCCCATC------
q loxAfr3.scaffold_36                            9999999999999---9999999999999999999-999--99999999999999999------
i loxAfr3.scaffold_36   C 0 C 0
s bosTau4.chr1          157014480 53 + 161106243 CCCCTGGTTTCTA---GTCCAGCTGCCTCCCCACTAGTC--ACGAGGTGCTTCCTACT------
q bosTau4.chr1                                   9999999999999---99999999999999999999999--99999999999999999------
i bosTau4.chr1          C 0 C 0
s equCab2.chr16          22236361 52 -  87365405 ctcctgattttca---gtccagccacctcgccact-CTC--CTAGTTTGTTCCCCATC------
q equCab2.chr16                                  9999999999999---9999999999999999999-999--99999999999999999------
i equCab2.chr16         C 0 C 0
s canFam2.chr23          26016138 52 -  55389570 CCCCTGATGTTTA---TTCTAGCCACCTTGCCACT-GTT--CTAATTCTCTTCCCATC------
q canFam2.chr23                                  9999999999999---9999999999999999999-999--99999999999999999------
i canFam2.chr23         C 0 C 0
s oryCun2.chr14           2498796 53 + 163896628 -CCCAGGCCCCTGGTATTCGGGCCACCTCCCCACT-TTC--TTGCTT-GCTCCCCATC------
q oryCun2.chr14                                  -9999999999999999999999999999999999-999--999999-9999999999------
i oryCun2.chr14         C 0 C 0
s rn4.chr9              107372077 41 - 113440463 CTCCTGGTTCTTAGC-GTCCTCCCATCTC-------------TAATT---TTCTTATC------
q rn4.chr9                                       999999999999999-9999999999999-------------99999---99999999------
i rn4.chr9              I 125 C 0
s mm9.chr17              50271235 41 +  95272651 CCCCAGATTCTTAGC-TCCCTCCCATCTC-------------TAATT---TTCTTATC------
i mm9.chr17             I 15 C 0
s cavPor3.scaffold_0      8266888 49 -  88675666 CTCTCAGTTCTTA---CTCCAACCACCTCGCTACC-CTT--TTAATT---TTCTTATC------
q cavPor3.scaffold_0                             9999999999999---9999999999999999999-999--999999---99999999------
i cavPor3.scaffold_0    I 9 C 0
s ponAbe2.chr3           71062217 52 - 202140232 cctctgattctta---ttccagccatctccccact-ctt--ctaatttgcttcccATC------
q ponAbe2.chr3                                   9999999999999---9999999999999999999-999--99999999999999999------
i ponAbe2.chr3          C 0 C 0
s rheMac2.chr2          158788047 52 + 189746636 CCCCTGATTCTTA---TTCCAGCCATCTCCCCACT-CTT--CTAATTTGCTTCCCATC------
q rheMac2.chr2                                   9999999999999---9999999999999999999-999--99999999999999999------
i rheMac2.chr2          C 0 C 0
s panTro2.chrY             524372 52 +  23952694 CCCACGATTCTTA---TTCCAGCCATCTCCCCACT-CTT--CTAATTTGCTTCCCATC------
q panTro2.chrY                                   0000000000000---0000000000000000000-000--00000000000000000------
i panTro2.chrY          C 0 C 0
s monDom5.chr8          276527936 60 + 312544902 CCCAGGACTCTTG---ATCCTGTCATCAGCATCCT-CTTCACTAGGTCACATCCCTCATGAAAC
q monDom5.chr8                                   9999999999999---9999999999999999999-9999999999999999999999999999
i monDom5.chr8          C 0 C 0
e macEug1.Scaffold7817      25228 4878 -     41428 I
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=71098.000000
s hg19.chrY               7670884 23 +  59373566 ACAATGATTCATTACAA--------------TAAAAC
s panTro2.chrY             524424 23 +  23952694 ACAATGATTCATTATAA--------------TAAAAC
q panTro2.chrY                                   00000000000000000--------------000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788099 37 + 189746636 GAAATGATTTATTATAATCATTTTTTAAGATTAACAC
q rheMac2.chr2                                   9999999999999999999999999999999999999
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062269 37 - 202140232 ACAATGATTTATTATAATCATTTTTTAAGATTAACAC
q ponAbe2.chr3                                   9999999999999999999999999999999999999
i ponAbe2.chr3          C 0 C 0
s cavPor3.scaffold_0      8266937 31 -  88675666 ACAATGATTTATTACAATCATTTTCTGAGAT------
q cavPor3.scaffold_0                             9999999999999999999999999999999------
i cavPor3.scaffold_0    C 0 C 0
s mm9.chr17              50271276 37 +  95272651 ACAATGATTTATTAGAATCATTTTTTAAGATTAACAC
i mm9.chr17             C 0 C 0
s rn4.chr9              107372118 37 - 113440463 ACAATGATTTATTAGAATCATTTTTTAAGATTAACAC
q rn4.chr9                                       9999999999999999999999999999999999999
i rn4.chr9              C 0 C 0
s oryCun2.chr14           2498849 37 + 163896628 ACGATGGCTTCTTATCTCCACTGTTAAAGATCAACAC
q oryCun2.chr14                                  9999999999999999999999999999999999999
i oryCun2.chr14         C 0 C 0
s canFam2.chr23          26016190 33 -  55389570 ACAAGA--TTATAATAAT--TTTTTAAAGATTAACAC
q canFam2.chr23                                  999999--9999999999--99999999999999999
i canFam2.chr23         C 0 C 0
s equCab2.chr16          22236413 37 -  87365405 ACAATGATTTATTACAATCATTTTTAAAGATTAACAC
q equCab2.chr16                                  9999999999999999999999999999999999999
i equCab2.chr16         C 0 C 0
s bosTau4.chr1          157014533 37 + 161106243 GCAGTGATGCATTATAAACATTTTTAAAGATGGACAA
q bosTau4.chr1                                   9999999999999999999999999999999999999
i bosTau4.chr1          C 0 C 0
s loxAfr3.scaffold_36      542576 37 -  24123610 GCCATGATGTATTACAACCATTTTTAAAAATTAAAGC
q loxAfr3.scaffold_36                            9999999999999999999999999999999999999
i loxAfr3.scaffold_36   C 0 C 0
s macEug1.Scaffold7817      30106 25 -     41428 ACAAAGAGCTATT------------TGACAGCAGAAC
q macEug1.Scaffold7817                           9999999999999------------999999999999
i macEug1.Scaffold7817  I 4878 N 0
s monDom5.chr8          276527996 23 + 312544902 --AAAGAGCTATT----TCACGGTTGAAC--------
q monDom5.chr8                                   --99999999999----999999999999--------
i monDom5.chr8          C 0 C 0
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=819745.000000
s hg19.chrY               7670907 400 +  59373566 A---------------------------------------------------------ACAAGGAGAGAGACAGAGCGGAATGAA-TTTGAAGCAGACAGTCCCAGTAAG-GAAAAGGGAGGTCTCTCAGTGAACACAATTAAGGGTCTTTCTCT----------------TTTTT----------------------GAAACACTTGGGGAA-------TTTTGGCAGTCACCTTTG------AAATCTGCTAAAACAAATA--A----TGTAAGGCAACTA---TTCAAGGATGCCACTTCAAGGT-------TTTAAA-AAAAGCCTTAATATTTCAT-----------------------AGGGTTTTT---------T-TGTTGTTGTTGTTCAGAAAATGAACATGTAAGGAAGAACA--------ATGAAAAATATCCTGAAGTATGTG-------TTC-AATTCTT-ATCCATTCGATTGCTGAGTGCTTTCATCAAGGCCATTCTCTAAGCA--GAGGAAAAAAATATTCCCAACAGATGATGGCAGCTAAGAGGGacacacacacactt
s monDom5.chr8          276528019 387 + 312544902 ----------------------------------------------------------ATGGAGAAAGA--------AGGCTAGC-TTTGAA-----TGGACTTGTCATA-GAGTAGGGAGCTCTC-CAGTTAAATTGGTGATGGG--TTTCTA-----------------TCTTA----------------------GGAATGCTCAAGGAG---GTTGTTCCAGGAGTCATTTCAGTACCTAAGATTTGCTAAAACCAAGAGCA----CAGAATTCTGCTAGATTCTAAGGGTTTTTCTTTAAGGA-------GATTTA-AAAAATCTTACTATTTCAG-----------------------AGTAGTTT----------TGTTTTTTTTTTTTTCAGCCAGTG----TGTGAGGAAGAACA--------ATGAAAACAATCCAGAAGAATGTG-------TTC-AATTTGGAATCTATTTCATTACTGAAAGGCTTCATCAAGACAGTCAACCCAGCT----GGGTAAAAAAGTCGACAAGAAGAG-----GACTTGGAGAGAAAAACAGATGCTA
q monDom5.chr8                                    ----------------------------------------------------------99999999999--------99999999-999999-----9999999999999-999999999999999-9999999999999999999--999999-----------------99999----------------------999999999999999---99999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999-------999999-9999999999999999999-----------------------99999999----------999999999999999999999999----99999999999999--------999999999999999999999999-------999-999999999999999999999999999999999999999999999999999999----999999999999999999999999-----9999999999999999999999999
i monDom5.chr8          C 0 C 0
s panTro2.chrY             524447 407 +  23952694 A---------------------------------------------------------ACAAGGAGAGAGACAGAGGGGAATGAA-TTTGAAGCAGACAGTCCCAGTAAG-GAAAAGGGAGGTATCTCAGTGAACACAATTAAGGTTCTTTCTAT----------------TTTTT----------------------GAAACACTTGGGGAA-------TTTTGGCAGTCACCTTTG------AAATCTGCTCAAACAAATA--A----TGTAAGGCAACTA---TTCAAGGATGCCACTTCAAGGT-------TTAAAA-AAAAGCCTTAATATTTCAT-----------------------AGGGTTTTTttgttgttgt-tgttgttgttgttCAGAAAATGAACATGTAAGGAAGAACA--------ATGAAAAATATCCTGAAGTATGCG-------TTC-AATTTTT-ATCCATTTGATTGCTGAGTGCTTTCATCAAGGCCATTCTCTAAGCA--GAGGAAAAAAATATTCTCAACAGATGATGGCAGCTAAGAGGG--acacacacactt
q panTro2.chrY                                    0---------------------------------------------------------000000000000000000000000000-000000000000000000000000-00000000000000000000000000000000000000000000----------------00000----------------------000000000000000-------000000000000000000------0000000000000000000--0----0000000000000---0000000000000000000000-------000000-0000000000000000000-----------------------0000000000000000000-0000000000000000000000000000000000000000--------000000000000000000000000-------000-0000000-0000000000000000000000000000000000000000000000--000000000000000000000000000000000000000000--000000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788136 400 + 189746636 A---------------------------------------------------------ACAAGGAGAGAGATAGAGGGGAATGAG-TTTGAAGCAGACAGTCCCCGTAAG-GAAAAGGGAGGTGTCTCAGCGAACACAATTAAGAGTCTTTCTA-----------------TTTTT----------------------GGAATATTTGGGGAA-------TTTTGGCAGTCACCTTGG------AAATCTGCTAACACAAATA--A----TGGAAGGCAACTA---TTCAAGGATGCCACATCAAGGT-----AAAAACAA-AAAAGCCTTAATATTTCGT-----------------------AGAGGTTT----------T-TGTTGTTGTTGTTCAGAAAATGTACATGTAAGGAAGAACA--------ATGAAAAGGATCCTGAAGAATGTG-------TTC-GATTTTT-ATCCATTTGATTGCTGAACGCTTTCATCAAGGCAATTCTCTGAGCA--GAGGAAAAAAATATCCCCAACAGAGGATGGCAGCTCAGAGGGacacacacacacac
q rheMac2.chr2                                    9---------------------------------------------------------999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999-----------------99999----------------------999999999999999-------999999999999999999------9999999999999999999--9----9999999999999---9999999999999999999999-----99999999-9999999999999999999-----------------------99999999----------9-9999999999999999999999999999999999999999--------999999999999999999999999-------999-9999999-9999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062306 405 - 202140232 A---------------------------------------------------------ACAAGGATAGAGACAGAGGGGAATGAG-TTTGAAGCAGACAGTCCCAGTAAG-GAAAAGGGAGGTGTCTCAGCGAACACAATTAAGGGTCTTTCTA-----------------TTTTT----------------------GGAATATTTGGGGAA-------TTTTGGCAGTCACCTTGG------AAATCTGCTAAAACAAATA--A----TGGAAGGCAACTA---TTCAAGGATGCCACTTCAAGGTAAAAAAAAAAAAA-AAAAGCCTTAATATTTCAT-----------------------AGAGGTTT----------T-TGTTGTTGTTGTTCAGAAAATGAACATGTAAGGAAGAAAA--------ATGAGAAGTATCCTGAAGAATGTG-------TTC-AATTTTT-ATCCATTTGATTGCTGAACGCTTTCATCAAGGCAATTCTCTGAGCA--GAGGAAAAAAATATCCCCAACAGAGTATGGCAGCTCAGAGGGacacacacacacac
q ponAbe2.chr3                                    9---------------------------------------------------------999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999-----------------99999----------------------999999999999999-------999999999999999999------9999999999999999999--9----9999999999999---99999999999999999999999999999999999-9999999999999999999-----------------------99999999----------9-9999999999999999999999999999999999999999--------999999999999999999999999-------999-9999999-9999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999
i ponAbe2.chr3          C 0 C 0
s cavPor3.scaffold_0      8266968 365 -  88675666 -----------------------------------------------------------CAGGATGA----------GGGGTGAG-TTTGAACAAGACAGTCAAAAGAAGCAAAACGGGAAGTGTCCCAGAAAACA----------------------------CAAT---ACTTT----------------------GGAATACTAGGGGAA------TTTTTGATAGTTACCTTGG------AAATATGCTAAAACAAATA--A----CAGAAGGCAATGA---TTCAAGGATGCCACTCTGAGGT-----------AA-GAATACCTTTATATTTCAT-----------------------AGGAGTTT------------TGTTACTGATGTTCAGAAAATGAACATGTAAAGCAGAACA--------ATGAAAAGAATCCTGAAGAATGTG-------TTC-AATTTTT-GCCCATTTGATAGCTGAAAGCTTTCATCAAGGCAATTCTTTGAGC----TGAGAGGAAACATTCCCAACAGAGTATGACAGTT--CAGGGacacacacacacac
q cavPor3.scaffold_0                              -----------------------------------------------------------99999999----------99999999-99999999999999999999999999999999999999999999999999----------------------------9999---99999----------------------999999999999999------9999999999999999999------9999999999999999999--9----9999999999999---9999999999999999999999-----------99-9999999999999999999-----------------------99999999------------9999999999999999999999999999999999999999--------999999999999999999999999-------999-9999999-999999999999999999999999999999999999999999999----9999999999999999999999999999999999--9999999999999999999
i cavPor3.scaffold_0    C 0 C 0
s mm9.chr17              50271313 354 +  95272651 A---------------------------------------------------------GCAGGAAGA----------GGGAGGCGAACTGAAGCAGACAGTCTTGGTAAG-AGAGGAGGAGGCAGCTCAGGCCACAGCTA--AGGGCCTTTCATTGTGTGCTTGTAAT---TTTTTTCTTTTTGGGGTGAGTAAGGAGGGAGGATTGGGGGAA-------TTTTAATATTCACCTTGG------AGATCTGCTAAAAT-CGTA--A----CAGAA---AACTA---CTCAAGGATG-AACTTTGGGCT-----------AAGAGAAGTCTTAATATTTCAT------------------GGGGTGGGGGTGG---------------------TGTTCCAAAACTGAGCCTGTAAGGAAGAACA--------ATGAAAAGAATCCT-AAGAGCGTG-------CTT-AATTTTC-ATCCATCTG--AACAGAA---------------------------------CGGAAAAATAGCCACAAAAGGG-ACAACAGTG---------------------
i mm9.chr17             C 0 I 86
s rn4.chr9              107372155 369 - 113440463 A---------------------------------------------------------GCAGGAAGA----------AGGAAGCGAACTGAA----ACAGTCTTGGTAAG-AGAGGAGGAGGCAGCTCAGGCCGCAGCTG--AGGGCCTTTCATTGTGTGCTTGTAATTTATTTTTTCTTTTTCGG--------GGTGGGAGGATT-GGGGAA-------TCTTAACATTCACCGTGG------AAATCTGCTAAAAT-AGTA--A----CAGAA---AACTC---CTCAAGGATG-AACTCTGGGCT-----------AA-AACAGTCTTAATATTTCATGGGGGTGGAGTGGGATGAGGGGTGGGAGTGG------------GGTTGTTGTTGTTCCAAAAATGAGCCTGTAAGGAAGGACA--------ATGGAAAGAATCCT-AAGAGCATG-------TTT-AATTTCC-ATCCATCCA--AGCTGAG----------------------------------GGGAAAAGAGCCACAAAAGGG-ACAACAGTG---------------------
q rn4.chr9                                        9---------------------------------------------------------999999999----------999999999999999----99999999999999-99999999999999999999999999999--99999999999999999999999999999999999999999999--------999999999999-999999-------999999999999999999------99999999999999-9999--9----99999---99999---9999999999-99999999999-----------99-99999999999999999999999999999999999999999999999999------------9999999999999999999999999999999999999999--------99999999999999-999999999-------999-9999999-999999999--9999999----------------------------------999999999999999999999-999999999---------------------
i rn4.chr9              C 0 I 25
s oryCun2.chr14           2498886 383 + 163896628 A----------------------------------------------------------AGGAGGGA----------GGGAGGTG-TCTGAGGCAGCCGCTCCCGGGAAG-GAAGAGGGAGGAGCCCCAGGGAGCACCGGGAAGGGCCCTTCCGTTTGTGCTC--------CGTTT-------------------------------GGGGACTTTTTTTTTTTGGCAGTCACCTTGG------AAATCTGCTAAAATAAATA--A----CAGAAGGCGACTG---TTCGGGGATGCCACTTAGAGGT-----------AA---GAGTCTTCACAGTTCAT-----------------------GGGGCT----------------TTGTTGTTGTTCAGAAAGTGAACATGTAAGGAAAAACA------------AAAGAATCCTGACGAATGCGTTCTTATTTT-TTTTTTT-ACCTACTCTCTTGCTGAAAGCTTTTATAAAGGCAATGCTCTTAGC----TAGGGATGAACACCTCCAACAAGG-AGGGCAGCTCAGAGGGacacacacacacac
q oryCun2.chr14                                   9----------------------------------------------------------99999999----------99999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999--------99999-------------------------------9999999999999999999999999999999------9999999999999999999--9----9999999999999---9999999999999999999999-----------99---99999999999999999-----------------------999999----------------99999999999999999999999999999999999999------------999999999999999999999999999999-9999999-999999999999999999999999999999999999999999999----999999999999999999999999-999999999999999999999999999999
i oryCun2.chr14         C 0 C 0
s canFam2.chr23          26016223 443 -  55389570 AACTCTACATCTGAAAATAATGACTAATTGAATTTAGATTTTTAAAAAAAGGATTAACACAAGCAGAGG--------GAGATGAG-TCTGAATCAGACAGGCCCAGTACA-GAAAGAGGAAGAGTCCCAGAAAACACAATTAAAAGCCCCTCTA-----------------TCTTT----------------------GGAATATTTAGGGAG-------TTTCAGCAGTCACCTTGG------AAATCTGCTGAAACAAATA--AATACAAGAAGGCAAGCA---TTCAAAGATGCCACTCTGAGCA-----------AA-GAAAGTCTTACCATCTCAT----------------------GGGGGGTTT----------T-GGTGGTGGTTGTTCAGAAAATGAACATGTAAGGCAGAACA--------ATGAAAAGAATCCTGGAGAGTATA-------TTC-AATTTTC-ATCCACTTGATTGCTAAAAGCTATCATCCTGGCAGTCC-CTGAGCTGGAGGGAAAAAAAGTTCTCCAAAAGAGGATGGCAGCTCAGACAGACAGACAT------
q canFam2.chr23                                   999999999999999999999999999999999999999999999999999999999999999999999--------99999999-999999999999999999999999-9999999999999999999999999999999999999999999-----------------99999----------------------999999999999999-------999999999999999999------9999999999999999999--999999999999999999---9999999999999999999999-----------99-9999999999999999999----------------------999999999----------9-9999999999999999999999999999999999999999--------999999999999999999999999-------999-9999999-99999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999------
i canFam2.chr23         C 0 I 15
s equCab2.chr16          22236450 371 -  87365405 A---------------------------------------------------------ACAAGGAGAGA--------AGGATGAG-TTTGAACCAGACAGTCCCAGTACG-GAAAAAGGAGAAGTCCCAGCAAACACAGTGAAGGG-CCTTCTA-----------------GCACT----------------------GGAATATTCGGGGAA--------TTCAGCAGTCACCTTGG------AAATCTGCTGAAACAAATA--A----CAGAAGGCAAATG---TTCAAGGATGCCGCTCTGAGGA-----------AA-GAAAGTCTCAATATTGTAT----------------------AAGGATTCT--------------TCGTCGTCGTTCAGAAAATGGACATGTAAGGCAGAACA--------ATGAAAATAATCCTGAAGAACGTG-------TTC-GATTTTT-ACCCATTTGATTGCTGAAAGCCTTCATCAAGACAGTC-----AGTT--AGAGAAACAATTGTCCCCAGAAGAAGATGGCAGCTCAGAGGGacaaacat------
q equCab2.chr16                                   9---------------------------------------------------------99999999999--------99999999-999999999999999999999999-99999999999999999999999999999999999-9999999-----------------99999----------------------999999999999999--------99999999999999999------9999999999999999999--9----9999999999999---9999999999999999999999-----------99-9999999999999999999----------------------999999999--------------99999999999999999999999999999999999999--------999999999999999999999999-------999-9999999-9999999999999999999999999999999999999-----9999--99999999999999999999999999999999999999999999999999------
i equCab2.chr16         C 0 C 0
s bosTau4.chr1          157014570 355 + 161106243 A---------------------------------------------------------ACAACGAGAGA--------GCGATGGT-TTTCAACCCGACAGTCCCAAGATG-GAAAAAGAAGGAGTCCCAGCAAACACAGGGAAGGACTTGTCTA-----------------TCTTT----------------------GGAATATTTGGGGAA-------CTTCAGCAGTCACCTTGG------AAATCTGCTGAAACAAATA--A----CGGGCGGCAAGTA---GTCAAGGATGCCACTCTGAGGT-----------AG-GAAAGGCTT--------------------------------------CTT----------T-TACTGTTGCTGTTCAGAAAACAAACATGTAAGGCAGAACA--------ATGAAAGGAATCCTGT-GAATGTG-------TTC-AATCTGT-ATCCATCTGATTGCTGAGCGCTTTCATCAAGGCAGTCC-CTGAGCA--GGGGGAAGAAATGTCCCCAACAGAGGCCGGCAACTCAGAAGG--------------
q bosTau4.chr1                                    9---------------------------------------------------------99999999999--------99999999-999999999999999999999999-9999999999999999999999999999999999999999999-----------------99999----------------------999999999999999-------999999999999999999------9999999999999999999--9----9999999999999---9999999999999999999999-----------99-999999999--------------------------------------999----------9-9999999999999999999999999999999999999999--------9999999999999999-9999999-------999-9999999-99999999999999999999999999999999999999-9999999--999999999999999999999999999999999999999999--------------
i bosTau4.chr1          C 0 C 0
s loxAfr3.scaffold_36      542613 385 -  24123610 A---------------------------------------------------------ACAGGGAGAGA--------GGGATGAG-TTTGAACTAGACCATTCTGCAAAG-GAAAAA--AGGAGTTTCAGCTGACACAATTAAGGACTTTTCTC-----------------TCTTT----------------------GGAATATTCAGGGAG-------TTTTAGAAGCCACCTCAG------AAATCTGCTAAAACAAATA--A----TAGAAGACAAGTA---TTCAAGGATGCCACTTTGAGGT-----------AA-GAAAGTCTTAATATTTCAC-----------------------AGGGCTTT-------------TTTGTTGTTGTTAAGAAAATGAACATCCCAGGAAGAATAATGAAATAATGAAAAGAATACTTAAGAATATG-------TTCAAATCTTT-ATCCCTTTGATTACTGAAAGCTTTCACAAAGGCAGCTCCCCCAGCT----GGGGTAAAAAGTTCCCAATAGGGGAAGGCAACTCAGAGGGAAACGCACAT----
q loxAfr3.scaffold_36                             9---------------------------------------------------------99999999999--------99999999-999999999999999999999999-999999--99999999999999999999999999999999999-----------------99999----------------------999999999999999-------999999999999999999------9999999999999999999--9----9999999999999---9999999999999999999999-----------99-9999999999999999999-----------------------99999999-------------99999999999999999999999999999999999999999999999999999999999999999999999-------99999999999-9999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999----
i loxAfr3.scaffold_36   C 0 C 0
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=-3281.000000
s hg19.chrY               7671307 66 +  59373566 ------acacacacacacacac------------------------acacacacacacacacacaACATGC----ATGATTAAACAAAATAATTTTTA-------AA
s oryCun2.chr14           2499269 44 + 163896628 --------------acacgcac------------------------atacacaca------------ATGC----CTGATTAAACAAAACAATAAAA---------A
q oryCun2.chr14                                  --------------99999999------------------------999999999------------9999----9999999999999999999999---------9
i oryCun2.chr14         C 0 C 0
s equCab2.chr16          22236821 58 -  87365405 ----------acacacacacac------------------------acacacacagacacgcacGCTATAC----ATGACTAAAGAAAACAATAAA-----------
q equCab2.chr16                                  ----------999999999999------------------------9999999999999999999999999----999999999999999999999-----------
i equCab2.chr16         C 0 I 5
s loxAfr3.scaffold_36      542998 65 -  24123610 ------ACACACACACA-AAATGCCTGCATTTTTCTTTCCCTGATGAAACACACAAA------------------ACAAACAAACAAAAA-----------------
q loxAfr3.scaffold_36                            ------99999999999-999999999999999999999999999999999999999------------------999999999999999-----------------
i loxAfr3.scaffold_36   C 0 C 0
s rn4.chr9              107372549 65 - 113440463 ---------TGCGAGCGCGCAA------------------------ATGCACGCATGCACATCCTCTATGCATCATTAATTAAACACAGCCATTTTT---------A
q rn4.chr9                                       ---------9999999999999------------------------999999999999999999999999999999999999999999999999999---------9
i rn4.chr9              I 25 C 0
s mm9.chr17              50271753 68 +  95272651 ------acacacacacacacac------------------------acacacacatgcacaTCCTCAATGCTTGATTAATTAAACAAAGCCATTTTT---------A
i mm9.chr17             I 86 C 0
s cavPor3.scaffold_0      8267333 66 -  88675666 ------acacacacacacacac------------------------acactcgcacgcaaacaTGCCATGC----CTGATTAAATAAAACAATTTTTA-------AA
q cavPor3.scaffold_0                             ------9999999999999999------------------------9999999999999999999999999----99999999999999999999999-------99
i cavPor3.scaffold_0    C 0 C 0
s ponAbe2.chr3           71062711 73 - 202140232 ------acacacacacacacac------------------------acacacacacacacacacacCATGC----CTGATTAAACAAAAGAATTTTTAAAAATCCAA
q ponAbe2.chr3                                   ------9999999999999999------------------------9999999999999999999999999----99999999999999999999999999999999
i ponAbe2.chr3          C 0 C 0
s rheMac2.chr2          158788536 53 + 189746636 ------acacacacacacacac------------------------acacacC-------------CATGC----CTGATTAAACAAAAGAATTTTTA-------AA
q rheMac2.chr2                                   ------9999999999999999------------------------9999999-------------99999----99999999999999999999999-------99
i rheMac2.chr2          C 0 C 0
s panTro2.chrY             524854 58 +  23952694 ------acacacacacacacac------------------------acacacacacac--------CATGC----ATGATTAAACAAAATAATTTTTA-------AA
q panTro2.chrY                                   ------0000000000000000------------------------000000000000--------00000----00000000000000000000000-------00
i panTro2.chrY          C 0 C 0
s canFam2.chr23          26016681 43 -  55389570 ----------------------------------------------acacacacacacacacacacTATAT----AT---TAACCAAAACAATAAA-----------
q canFam2.chr23                                  ----------------------------------------------9999999999999999999999999----99---9999999999999999-----------
i canFam2.chr23         I 15 I 5
s bosTau4.chr1          157014925 46 + 161106243 ----------------------------------------------ACACGAATGCATGCGCACACAATAT----GTGACTAAACAGCAGAAAAAA-----------
q bosTau4.chr1                                   ----------------------------------------------9999999999999999999999999----999999999999999999999-----------
i bosTau4.chr1          C 0 C 0
s monDom5.chr8          276528406 63 + 312544902 CATCCGATGGGAGCTCTCCCGG------------------------A-----GTAAACAAACACCCCACAA----CAACAAAAAAAAAATCTTGAA-----------
q monDom5.chr8                                   9999999999999999999999------------------------9-----9999999999999999999----999999999999999999999-----------
i monDom5.chr8          C 0 C 0
e myoLuc1.scaffold_7336     37698 5478 -    312611 I

a score=236874.000000
s hg19.chrY               7671373 84 +  59373566 AA--TCCAATACAGTTCCAAACTC-----AACAATAACTGAAAAGAAAGGCCACTTG----TTTCATCTTCCTTTTCCCCCAT-------CTTCTGCTTAGT
s monDom5.chr8          276528469 83 + 312544902 ----------AGCGTTCCAAACTTTATATAACAATAACTTAACAGAAAGGCTATTTAGGCTTTCTGTCTTTCT-TC-TCCCCA-------CCCCCCCTTAAT
q monDom5.chr8                                   ----------999999999999999999999999999999999999999999999999999999999999999-99-999999-------999999999999
i monDom5.chr8          C 0 C 0
s panTro2.chrY             524912 84 +  23952694 AA--TCCAATACAGTTCCAAACTC-----AACAATAACTGAAAAGAAAGGCCACTTG----TTTCATCTTCCTTTTCCCCCCT-------CTTCTGCTTAGT
q panTro2.chrY                                   00--00000000000000000000-----0000000000000000000000000000----0000000000000000000000-------000000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788589 83 + 189746636 AA--TCCAATACAGTTCCAAACTT-----CACAATAACTTAAAAGAAAGGCCAGTCA----TTTTATCTTCCCTTT-TTCCCT-------CTTCTGCTTAAT
q rheMac2.chr2                                   99--99999999999999999999-----9999999999999999999999999999----999999999999999-999999-------999999999999
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062784 71 - 202140232 AA--TCCAATACAGTTCCAAACTT-----AACAATAATTTAAAAGAAAGGCCACTTG----CTT-------------TCCCCT-------CTTCTGCTTTAT
q ponAbe2.chr3                                   99--99999999999999999999-----9999999999999999999999999999----999-------------999999-------999999999999
i ponAbe2.chr3          C 0 C 0
s cavPor3.scaffold_0      8267399 87 -  88675666 AA--TCTGATACAGTTCCAAACTT-----AACAATGATTTAAAAGAGAGGCTGGTTG----TTTTATCTTCC---T-TTCCCTACCCTTGCTTCTGCTTAAT
q cavPor3.scaffold_0                             99--99999999999999999999-----9999999999999999999999999999----99999999999---9-9999999999999999999999999
i cavPor3.scaffold_0    C 0 C 0
s mm9.chr17              50271821 72 +  95272651 CA--TCTGATACAGTTTCAGAGTT-----AGTGACAACTTGAAAGAAAGGCCAGTTG----TTCCATC------------TCT-------CCCCTGCTTGAG
i mm9.chr17             C 0 C 0
s rn4.chr9              107372614 80 - 113440463 CA--TGTGATACAGTTTCAGAGTT-----AGTGACGACTTGAAAGAAAGGCCAGTTG----TTCAGTCTTCC---G-TTTTCT-------CTCCTGTTTGAG
q rn4.chr9                                       99--99999999999999999999-----9999999999999999999999999999----99999999999---9-999999-------999999999999
i rn4.chr9              C 0 C 0
s oryCun2.chr14           2499313 83 + 163896628 AA--TCCAATACAGTTCCAAACTT-----AACAATGACTTAAAAGAAAGGCCACTTG----TCTCATCTTCCTCTT-TTCTCT-------CTTCTACTTGAT
q oryCun2.chr14                                  99--99999999999999999999-----9999999999999999999999999999----999999999999999-999999-------999999999999
i oryCun2.chr14         C 0 C 0
s bosTau4.chr1          157014971 70 + 161106243 AA--TCTGATGCAGTTTCAAACCT--------AAGGCCTTGAAAGAAAGGCCG-------------TCTTCCT-TT-TCCCCT-------CCCTGGCTTAAT
q bosTau4.chr1                                   99--99999999999999999999--------999999999999999999999-------------9999999-99-999999-------999999999999
i bosTau4.chr1          C 0 I 123
s canFam2.chr23          26016729 72 -  55389570 AAATTCTGATACAGTTCCACACTT-----TACAAGGACTT----GAAAGACCA-------------TCTTTCTCTT-TTTCCT-------CTTCTGCTTAAC
q canFam2.chr23                                  999999999999999999999999-----99999999999----999999999-------------9999999999-999999-------999999999999
i canFam2.chr23         I 5 C 0
s equCab2.chr16          22236884 74 -  87365405 AA--TCTGATACAGCTCCAAACTG-----AACTATAACTTAAAAGAAAGGCCA-------------TCTACCTTTT-TCCTCT-------CCTCTGCTTAAT
q equCab2.chr16                                  99--99999999999999999999-----999999999999999999999999-------------9999999999-999999-------999999999999
i equCab2.chr16         I 5 C 0
s myoLuc1.scaffold_7336     43176 73 -    312611 AA--TCTGATACAGTCCCAAACTT-----AACAATGACTTAAAAGAAAGGCTG-------------TCTTCCT-TT-TCCCCT-------CCTCTGCTTAAT
q myoLuc1.scaffold_7336                          23--64435425335144453344-----325463434526673557323544-------------5323154-56-547734-------516554343534
i myoLuc1.scaffold_7336 I 5478 C 0
s loxAfr3.scaffold_36      543063 81 -  24123610 AA--TCACACACA-CTTCAACCTT-----AACAATGACTT-AAAGAAAGGCCACTCA----TTCCATCTTCCTCTT-CACACC-------TGTGTGCTGGAT
q loxAfr3.scaffold_36                            99--999999999-9999999999-----99999999999-9999999999999999----999999999999999-999999-------999999999999
i loxAfr3.scaffold_36   C 0 C 0

a score=395440.000000
s hg19.chrY               7671457 114 +  59373566 AGAAGTATATGGTAATTTGCTTC-TTTTTAATAATTTGTAAAATCTGATGAGTGGTGA------------AATTTAGCCATGC-CCACATGTCAATAACAGATGTTAAAAATTTCAGAATTATAAGAT
s monDom5.chr8          276528552 122 + 312544902 ACAAGGGCATGGTAATTGGCTGCTTTTTAATAAAATTGTACAATCTT-TGGGCGGTAATTTAACCCAGTGGATTTG-----GCACCATGTGTCAGTTATAACTGCCTACAATCACGGCATTGTTAAAT
q monDom5.chr8                                    99999999999999999999999999999999999999999999999-9999999999999999999999999999-----99999999999999999999999999999999999999999999999
i monDom5.chr8          C 0 N 0
s panTro2.chrY             524996 114 +  23952694 AGAAGTATATGGTAATTTGCTTC-TTTTTAATAATTTGTAAAATCTGATGAGTGGTGA------------AATTTAGCCATGC-CCGCATGCCAATAACGGATGCTAAAAATTTCAGAATTATAAGAT
q panTro2.chrY                                    00000000000000000000000-0000000000000000000000000000000000------------0000000000000-00000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788672 109 + 189746636 ACAAGTACATGGTAATTTGCTTC-TTTCTAATAATTTGTACAATCTGATGAGTGGTGC------------AATTTA-----GC-CCCCATGTCAATTATGGATGCTAAAAATTTCAGAATTATAAGAT
q rheMac2.chr2                                    99999999999999999999999-9999999999999999999999999999999999------------999999-----99-99999999999999999999999999999999999999999999
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062855 109 - 202140232 ACAAATACATGGTAATTTGCTTC-TTTTTAATAATTTGTACAATCTGATGAGTGGTGC------------AATTTA-----GC-CCCCATGTCAATTATGGATGCTAAAAATTTCAGAATTATAAGAT
q ponAbe2.chr3                                    99999999999999999999999-9999999999999999999999999999999999------------999999-----99-99999999999999999999999999999999999999999999
i ponAbe2.chr3          C 0 C 0
s cavPor3.scaffold_0      8267486 111 -  88675666 ACAAGTACATGGTAATTTGCTTCTTTTTAATAAAACTGTACAATCTGATGAGTGGTAC------------AATTTA-----GCACCCCATGTTAATTATGGATGCTGAAATTTTCAGAATTATAACAT
q cavPor3.scaffold_0                              9999999999999999999999999999999999999999999999999999999999------------999999-----99999999999999999999999999999999999999999999999
i cavPor3.scaffold_0    C 0 C 0
s mm9.chr17              50271893 104 +  95272651 ACAAGGACGTGATAATTTGCTTC-TTTTAGGAAGATTGCTCTATTTGATGAGCTGTGC------------AATTTG-----GCACCCAGGCCAAATGATGGATGCTAGAATGCTCAGAATCA------
i mm9.chr17             C 0 C 0
s rn4.chr9              107372694 102 - 113440463 GCAGGTGTGTGATAATTTGCTTC-TCTAACTGAGATTGTTCTATCTGACGTGCTGTGC------------AGTTCA-----GCATCCGTGACAAATGATAGATGCTAAATT--TCAGAGTCA------
q rn4.chr9                                        99999999999999999999999-9999999999999999999999999999999999------------999999-----999999999999999999999999999999--999999999------
i rn4.chr9              C 0 C 0
s oryCun2.chr14           2499396 102 + 163896628 ACAAGTACATGGTAATTTGCTTT-CTGATGTGAAATTGTACAGTCTGATGAGTGGTGC------------AATTTA-----CCACCCTGTATCAATTACGGATGCTAAAAATCTCAGAAT--------
q oryCun2.chr14                                   99999999999999999999999-9999999999999999999999999999999999------------999999-----999999999999999999999999999999999999999--------
i oryCun2.chr14         C 0 C 0
s myoLuc1.scaffold_7336     43249 111 -    312611 ACAAGTATAGGGTAATTTTCTTCTTTTTAATAAAATTGTACAATCTGATGAGTGGTGC------------AATTTA-----GCACCCTATGTCAATTATGGATGCTGAAAATTTCAGAATCATGAGAT
q myoLuc1.scaffold_7336                           5562546745233512877565365665555789534644653835754678456454------------665864-----47578267858663656588537646899667754681497789855
i myoLuc1.scaffold_7336 C 0 I 77
s equCab2.chr16          22236958 111 -  87365405 ACAAGTACATGGCAATTTGCTTCTTCTTAATAAAATTGTACAATCTGATGAGTGGTTC------------AATTTA-----GCACCCCATGTCAATTATGGATACTAAAAATTTTAGAATCATGAGAT
q equCab2.chr16                                   9999999999999999999999999999999999999999999999999999999999------------999999-----99999999999999999999999999999999999999999999999
i equCab2.chr16         C 0 I 11
s canFam2.chr23          26016801 110 -  55389570 ACAA-CGCATGGCAATTTGCTTCCTTTTCTGAAAATTGTACAATCTGATGAGGGGTGC------------AATTTA-----GCACCCCATGTCAATTATGGATGCTAAGAGTTTCAGAATCAGGAGAT
q canFam2.chr23                                   9999-99999999999999999999999999999999999999999999999999999------------999999-----99999999999999999999999999999999999999999999999
i canFam2.chr23         C 0 I 16
s loxAfr3.scaffold_36      543144 111 -  24123610 ACAAGTACATGGTGATATGCTTCTTTTTCAAAAAATTGTACAATCTGATGAGTGGTGC------------AATCTA-----GCACCCCATGCCAATTATGGATGCTAAAGTCCTCAGAATCATGAAAT
q loxAfr3.scaffold_36                             9999999999999999999999999999999999999999999999999999999999------------999999-----99999999999999999999999999999999999999999999999
i loxAfr3.scaffold_36   C 0 C 0
e bosTau4.chr1          157015041 123 + 161106243 I

a score=-16211.000000
s hg19.chrY               7671571 23 +  59373566 CACCAAAATAATCACATCCAC---------------------------------------------CA--
s panTro2.chrY             525110 23 +  23952694 CACCAAAATAATCACATCCAC---------------------------------------------CA--
q panTro2.chrY                                   000000000000000000000---------------------------------------------00--
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788781 23 + 189746636 CACCAAAATTATCACATCCAC---------------------------------------------CA--
q rheMac2.chr2                                   999999999999999999999---------------------------------------------99--
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062964 23 - 202140232 CACCAAAATTATCACACCCAC---------------------------------------------CA--
q ponAbe2.chr3                                   999999999999999999999---------------------------------------------99--
i ponAbe2.chr3          C 0 C 0
s cavPor3.scaffold_0      8267597 21 -  88675666 TGCCAAAATTATCACATGTAC-------------------------------------------------
q cavPor3.scaffold_0                             999999999999999999999-------------------------------------------------
i cavPor3.scaffold_0    C 0 C 0
s mm9.chr17              50271997 19 +  95272651 --CCAAAAGTACTCCATACAC-------------------------------------------------
i mm9.chr17             C 0 N 0
s rn4.chr9              107372796 23 - 113440463 --CCAAAAGTATGCCACACAC---------------------------------------ACCA------
q rn4.chr9                                       --9999999999999999999---------------------------------------9999------
i rn4.chr9              C 0 N 0
s oryCun2.chr14           2499498 29 + 163896628 --CCTAAGGTcacacacatac-----------------------------------acacacacac----
q oryCun2.chr14                                  --9999999999999999999-----------------------------------9999999999----
i oryCun2.chr14         C 0 N 0
s bosTau4.chr1          157015164 21 + 161106243 cacacacacacacacacacac-------------------------------------------------
q bosTau4.chr1                                   999999999999999999999-------------------------------------------------
i bosTau4.chr1          I 123 C 0
s canFam2.chr23          26016927 21 -  55389570 CACACACATACACACACGCAC-------------------------------------------------
q canFam2.chr23                                  999999999999999999999-------------------------------------------------
i canFam2.chr23         I 16 C 0
s equCab2.chr16          22237080 16 -  87365405 -----ACACACGCGCGTGCAC-------------------------------------------------
q equCab2.chr16                                  -----9999999999999999-------------------------------------------------
i equCab2.chr16         I 11 C 0
s myoLuc1.scaffold_7336     43437 56 -    312611 cacacacacacacacacacacaGTGTATGTGTGTCGGGGAGAGAAAAAGAGGGGCG--------------
q myoLuc1.scaffold_7336                          88999989999999999999999799999899999999999899999999999989--------------
i myoLuc1.scaffold_7336 I 77 C 0
s loxAfr3.scaffold_36      543255 23 -  24123610 CACTAAAATTGTAAAAAAAAA-----------------------------------------------AA
q loxAfr3.scaffold_36                            999999999999999999999-----------------------------------------------99
i loxAfr3.scaffold_36   C 0 C 0

a score=42288.000000
s hg19.chrY               7671594 34 +  59373566 -AAAAAACCTGCTGGGGACAGCTC-ATCTTTTTCTT
s panTro2.chrY             525133 34 +  23952694 -AAAAGACCTGCTAGGGACAGCTC-ATCTTTTTCTT
q panTro2.chrY                                   -00000000000000000000000-00000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788804 35 + 189746636 -AAAAGACCTGCTGGGGACGGCTAGGTCTTTTTTTT
q rheMac2.chr2                                   -99999999999999999999999999999999999
i rheMac2.chr2          C 0 C 0
s ponAbe2.chr3           71062987 34 - 202140232 -AAAAGACCTGCTGGGGACAGCTA-ATCTTTTTCTT
q ponAbe2.chr3                                   -99999999999999999999999-99999999999
i ponAbe2.chr3          C 0 C 0
s cavPor3.scaffold_0      8267618 31 -  88675666 --ATAGACCTACTGGCAGCAGCCA-ACCTTTTTC--
q cavPor3.scaffold_0                             --9999999999999999999999-999999999--
i cavPor3.scaffold_0    C 0 C 0
s bosTau4.chr1          157015185 29 + 161106243 ------acCTGACGGGCCCAGTTA-GCCTTTTCTGT
q bosTau4.chr1                                   ------999999999999999999-99999999999
i bosTau4.chr1          C 0 C 0
s canFam2.chr23          26016948 27 -  55389570 -----GACCTGCT-GAGGCAGCTA-GTCTTTTCA--
q canFam2.chr23                                  -----99999999-9999999999-999999999--
i canFam2.chr23         C 0 C 0
s equCab2.chr16          22237096 29 -  87365405 -----GACCTGGT-GGGGCAGCTA-GTCTTTTTCTT
q equCab2.chr16                                  -----99999999-9999999999-99999999999
i equCab2.chr16         C 0 C 0
s myoLuc1.scaffold_7336     43493 34 -    312611 -AGCAGACATGTTAAGGGCAGCTA-GTCTTTTTTGC
q myoLuc1.scaffold_7336                          -98899999999999999999999-79999999699
i myoLuc1.scaffold_7336 C 0 C 0
s loxAfr3.scaffold_36      543278 35 -  24123610 AAAAAGACCCAGTCAGGGCATCTA-GTCATTTTTTT
q loxAfr3.scaffold_36                            999999999999999999999999-99999999999
i loxAfr3.scaffold_36   C 0 I 138

a score=181319.000000
s hg19.chrY               7671628 119 +  59373566 TTCAACCTACCTTATGCAGAAGGGTGAGCAGGGCATGCCCACATGTTGACAACCCTGGAGCCCCTTTTTCCCAGGGAGGA-----------CTTGAGCAGGAAAAGCAAGATGTAGG---ACAGAGAAAGACT
s myoLuc1.scaffold_7336     43527 130 -    312611 TTCCCTCCATTTTATGCAGAAGGCTGAGT-GGGCATGTCTGCAT-TTGGCAACTATGGAGACCTATTTTCCCAGGGAAAATGGG-TTATGGCTGGAGAGGGCAAAGCAAGATGCAAGAGAGAAGAAAAAGACT
q myoLuc1.scaffold_7336                           99999999999999899999999989998-99999999999999-999999999989999999999999999999999999999-999999979999999679998999999999999999999999999999
i myoLuc1.scaffold_7336 C 0 C 0
s equCab2.chr16          22237125 130 -  87365405 TTC---ACATCGTATGCAAAAGGCTGAACAGGGCATATCTGCATCTTGCCAACTATGGAGACTCATTCTCCCAGGGAAAATGAGTTTATGGCTGGAGAGGGCAAAGCAAGATGAAAGACAGAGGAGAAAGACC
q equCab2.chr16                                   999---9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i equCab2.chr16         C 0 C 0
s canFam2.chr23          26016975 127 -  55389570 -TC---GCCTCTTATGCAGAAGGCTGTGCAGGGCATGTCTACATCTTGCCAACTACCAAGCCCCATTTTTCCAGAGAAAATGGATTTACAGCTGAAGAGGGAAAAGCAAGGTATAAG--AGAGGAGAAAGACT
q canFam2.chr23                                   -99---999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999
i canFam2.chr23         C 0 C 0
s bosTau4.chr1          157015214 131 + 161106243 TTCACGGCATCTTGTGCAGAAGGCTGAGCTGAGCTTGTCCCCATCCTGCCAACTGTGAAGCCCCGTTTTCCCAGGGAAAACACACTTAGGGCTCCAGCGTGCAAAACCAAGTGTAAG--AGGGGAGGAAGACG
q bosTau4.chr1                                    999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999
i bosTau4.chr1          C 0 C 0
s cavPor3.scaffold_0      8267649  91 -  88675666 --------ATTCTATCCAGGAGACTTAGCAGGACATGT----------------AGGGAGCCCCCACCTCCCAGGGATGA-----------CTTGGGAGGGCAAAACAGTGCATA-------AGAGAAAGACT
q cavPor3.scaffold_0                              --------999999999999999999999999999999----------------99999999999999999999999999-----------999999999999999999999999-------99999999999
i cavPor3.scaffold_0    C 0 C 0
s ponAbe2.chr3           71063021 119 - 202140232 TTCACTATACCTTGTGCAGAAGGCTGAGCAGGGGATGTCCACATCTTGCCAACCCTGGAGCTCCATTTTCCCAGGGAGGA-----------CTTGAGCAGGAAAAGCAAGATGTAAG---ATAGAGAAAGACT
q ponAbe2.chr3                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99999999999999999999999999---9999999999879
i ponAbe2.chr3          C 0 C 0
s rheMac2.chr2          158788839 119 + 189746636 CTCACTAAACCTCGTGCAGAAGGCTGAGCAGGGCATGTCTGTATCTTGCCAACCCTGGAGCCCCATTTTCCCAGGGAGGA-----------CTTGAGCAGGAAAAGCAAGATGTAGG---ATAGAGAAAGACT
q rheMac2.chr2                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99999999999999999999999999---9999999999999
i rheMac2.chr2          C 0 C 0
s panTro2.chrY             525167 119 +  23952694 TTCAACCTACCTTATGCAGAAGGGTGAGCAGGGCATGCCCACATGTTGACAACCCTGGAGCCCCTTTTTCCCAGGGAGGA-----------CTTGAGCAGGAAAAGCAAGATGTAGG---ACAGAGAAAGACT
q panTro2.chrY                                    00000000000000000000000000000000000000000000000000000000000000000000000000000000-----------00000000000000000000000000---0000000000000
i panTro2.chrY          C 0 C 0
e loxAfr3.scaffold_36      543313 138 -  24123610 I

a score=82624.000000
s hg19.chrY               7671747 81 +  59373566 AATTCATAAAGGTAAGGGAGTCATGCCCTTA-AAAAAG-AAACACAAACTCTTCTAAAAGGTGAGGGAAACActcatgtgagg
s panTro2.chrY             525286 81 +  23952694 AATTCATAAAGGTAAGGGAGTCATGCCCTTA-AAAAAG-AAACACAAACTCTTCTAAAAGGTGAGGGAAACcctcatgtgagg
q panTro2.chrY                                   0000000000000000000000000000000-000000-00000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr2          158788958 63 + 189746636 AATTCATGAAAGTAAGGGAGTCATGCTCTTA-GAAGAG-AAACACAAACTCCTCTAAAAGGTGAG------------------
q rheMac2.chr2                                   9999999999999999999999999999999-999999-99999999999999999999999999------------------
i rheMac2.chr2          C 0 N 0
s ponAbe2.chr3           71063140 63 - 202140232 AATTCATAAAAGTAAGGGAGTCATGCCCTTA-AAAAAG-AAACACAAACTCCTCTAAAAGGTGAG------------------
q ponAbe2.chr3                                   9999999999999999999999999999999-999999-99995999839789599999999999------------------
i ponAbe2.chr3          C 0 N 0
s cavPor3.scaffold_0      8267740 54 -  88675666 AGT-----AAGATACAGAAATCATCTCCTTACAAAAAG-AAATAACTCCTGTTCTCAAGG-----------------------
q cavPor3.scaffold_0                             999-----999999999999999999999999999999-999999999999999999998-----------------------
i cavPor3.scaffold_0    C 0 N 0
s bosTau4.chr1          157015345 68 + 161106243 ACTGCATCAAAGTAATGGCGTCCGGCCT--C-ACGAAG-CAGCATAAGCGCCTCTGCATGGTGAGGAAGGCA-----------
q bosTau4.chr1                                   9999999999999999999999999999--9-999999-999999999999999999999999999999999-----------
i bosTau4.chr1          C 0 N 0
s canFam2.chr23          26017102 76 -  55389570 ACtttataaaagtaaaaaaaaaaa------a-aaaaaGTAAATACAAACTCCCCTCAGAGGAAAGGAAAACAAACTCGGGAGG
q canFam2.chr23                                  999999999999999999999999------9-999999999999999999999999999999999999999999999999999
i canFam2.chr23         C 0 N 0
s equCab2.chr16          22237255 71 -  87365405 AATTTATAACAGTAAAGGAATCACGCCCTTA-AAAAAAAAAACATGAACTCTTCAAAGAGGAGAGGAAAGCA-----------
q equCab2.chr16                                  9999999999999999999999999999999-9999999999999999999999999999999999999999-----------
i equCab2.chr16         C 0 N 0
s myoLuc1.scaffold_7336     43657 80 -    312611 GATTTATAAAAGGAAGCGACTCATGCCCCTA-AGAAAG-AAACATGAACTCTCCAC-TAGGCGAGGAAGGCAAACAAGGGAGG
q myoLuc1.scaffold_7336                          9999999999999999999999999999999-999999-99999999999999999-99999999999999999999999999
i myoLuc1.scaffold_7336 C 0 N 0
s loxAfr3.scaffold_36      543451 67 -  24123610 GATGTAAAAAAAAAAGGGAATCATGCCCTCA-AAAAAG-AAGCATGGACTCCTCTAAGAGGTGAGGAAA--------------
q loxAfr3.scaffold_36                            9999999999999999999999999999999-999999-999999999999999999999999999999--------------
i loxAfr3.scaffold_36   I 138 N 0

a score=409514.000000
s hg19.chrY    7671828 4451 + 59373566 tggtaccatgcagaagagtcacattaccttgaggctgggtccaggcatatgtcacaaccttcccttaggacaagacccaggcaagagagtttcaacaaataggtacatgttccacctttatgttgtaatgcttcatatgggcaaggctcaagcaggtagtcatatcacctaggtaacaggcccagatatatgtcacaatatcctccttgagacatgattctggggaaactctaccaccatctgtgtgccttgcctagcaatatgtcactatccaggtaagccagacccaagcaggagagcagaaatacgaacctgataggccaaggtatttgtcacaatccccttttttggacattaccctagaaaaagagtaccatcaacagtgtgccagtcccagccatgtgctactatcccctagtgtgagtacagcccattctaaagaggagatttgtacaacctaactggttgatacagtgatatgtcacaatgacttctgtgggcatggcttaggcaaaaatgtaacatgacctccgtgctggatctagtgatatatcactcttcttactgagagcaggatccaggcaggaaagtcacattacctagaggttggccaaggtagatataacagtaacatatgtgggctggaaccagtctggagagtcagatcacacaggtgtttggcagagatttatatcacaatCACACTGGCAAAAAATTCCCTGGATGAGATTTACAATACCACACATGTCCTTTTATCATGAGcaacagttggcttcatatatgtaagacagtgacagcgcttactgtcatctggtgtgaatatgagataatttcacctttctgctgggttctgctatgacactctctgtccaagccaagtgctacataaaatatctgaggctgttataatcttctttgagc---tttttttaccagaaagatatttaatcactcctttttctaaaacaagttataagagtcaaaattacacctatttgtgggatgcacatgtaagagtcattatcatgcctgtgaactgtgcctatatatgTAAGAATTTACTCTGTGTTGATGAAATAGACATGACAGTGAAGTAACCTAAATTCTGAGagagaaatgtgccaatattctccttgtaggtatgttcctggcagaaaagttgcataacttgggggttaaagacaggaatatggcacaatgcccattgtgggcagtgtccagacagaagaagagactcatatcacctaaatgacaaacccagaatatgtcacaatgtatcctgttgaaaggaccaggtaagagagtcacatcatttagatgcagtgcttaggaatgtgacaatccccattggaaggagggtcagggcaggagagGACAGTCAGGTAACTAGATCATGGGTCCAGAGACATGCAACAATCCTTCCTGAGGTTATTGTTAAGACAGGAGTGTCAAATCACTGTGGTGATCAGCTATGATATACGTCCAAATCTCATTTGTGGACTATACCTAAGCAGGATTATTAAATAACTCAGGAGATGGGCAAAGGTATATGTTACAATAATACAGGGTGAAAATTACAGGAatgggagtcaccgtcttgcatatgacatgtctccaggtttaagagtcataattagtcctcatatctggtctcagttatatggcacagtattacttgtgggcagagggcaagcaggaaggtgactttacctaggtgggtgctggtccagtaagatgtcacaatccttcttgtgggcaggacaatggaagaagagtcaaatcaccaggatgccgattttagtgatttatcaagattccccctgttaacagggattaggaaggtgagaagactcatgttacttttgcaattggcctagatatgtgtctcaatggctgctatgtgctaaaccaaggtatgaaagttgcctcaccttggccatgggtttagcaatatgtcacaatctcctctgtggtcagggcaagacatgagag-aaaaaatatttagattctgagacaagtgtttctgttggcagagcccaaaaaagagagtcacatcacctgcttgcggtgcccagttatgtgtcataatgcatgataagtgcagggccaaagcagtagaagggagtcacatcacttacacaatggacctggatataagccacatatatctagatatattgccttttataggcaagaatcaggcaaagaattcacatcacctgggagctgatcccagtgatacttaaaagtgccctttataggcctgcccagacaTCTTCACTTAGGTGTATGATCCATGTATATCACAATTTCATCACTAGTCATAACCTAAAAAGGAAAGTCAAGTTATTCAGGAGCTGTGCTACCTTTTTGTCCTAATCACACACTAGACAATATTCAGAAGTAAGATTCATAGTCCTGCAGAAGTCctggcttcttgcatgtgagtcaacacctcctgtgagttaggttaaagcagagaagtcacaatctcaacaataacaatgggtaacatccatgtataagatgcccaatctcacttgaagattgtgttccactagaggagtcacatcgtcacAGGTGTGTAGAATCATGCATCAGCAAATGACACATGAATAAGATCCATGTATGAGGGGAACATTTGCAACCTTTGACTGCTTTTATGtgtgagatttagtaacttaattttaggccctgttcttgtgagagaatgaaaattggatcagcttggtgtgcatccaagagtcacaaacgcacctggttgcttttccctgttatgacactctttgtaccactcaggctttacataatatgcctgagtgtcataatcttctgtgaactttatacaattaggagacccattactttacttattgccatgactggctttgagagtcaaaatagctctaatttctgagtccagttatgatggttatatttctgcatgtgagctgaaaccaagtatatgtcacaagttcaactgttggcagaaccaaggcagaagagtttcattgcctggattctgagctcaggatatattacaatctcctctgcaggcagggccaagtcagaagagtcacataacctggatacagacacaagtaatatggcaccatgtccactctaacaggattgaggaaagagagaagagtcgcaacacataggtgtttggctcagcaatatgtagtaaacctctcttttgacagaataaagaggagagtttccttacctaggttttgaactcagcggtatgacagaatttgtttagtgggtaggatctttgcagaagagccacatttcttagatgctacttgcaacaatgtcacaatattccttgagagaaaagtgcaggcaaagtagacaaattacctctgacaggctcagagatatgtgacaatatcccttgtttgcagagctcagggagaatggtcatattaTTATGATTCTAACCCAGTAATTTGTCAAAAATGCATGCTTTGAAAACAATGTAACCAAAAGTTTTAGCACATGGGTACTAAGCCCAGTGATATGACACAATATTCTcatttttgagggtgacatctttaactgctagcttggtatgcacatgagtcacaatgccacgtgtgtgtgctgggccattgtatgacaccctctaccacatccaagtgttttacacagtaggaaatgctctttactacccaggagtttatattatataaactagtgttctaaacttctgtgagctttgtagagacatgcaatccaggattttacctactcctctaaacctagtaaagagagccaaaatatcttttattggctgaatcccaatataagtttcaccaccatgcctgtgaattgaagcaagttataagtcatcttcctgtttgttggcCAAAAAAAGAGGggcagggagagtaacatcacttaggtgatgtggccagcaacatgtcacaatgctctctctaggcagaacctaggaaggagtgtcacattaactggttgctgagctcagcaatatgacacaactacacatgtaAAAATTTAGTGAAGGGATGAGAGCCAAAACACCTACAGAAtgggccaaaggtatgtcaaaatacccactgaggctctggcacaagcagaacagtagcatcatgaaggtgccagagacaccagtatgcaataattttccctttatttaggaaaatggcagaaaagtaatatcatttgagtgcaataggtcaaaatttctctttgtgggtatggttcagaaaaaaattgtatagttccaggacctaaacactggggtcagcaatatttcaccatcccaccttttcaaaggcccagacagaaaaagaagagagtcatatcatataggtcatgagctctaagatatgtcccaatgttcccagtatgaagggataaggcagacattgataacatatcacctaggtagctccctagaaatatgtcacagtgtaacattt
s panTro2.chrY  525367 4455 + 23952694 tggtaccatgcagaagagtcacattaccttgaggctgggtccagacatatgtcacaaccttcccttaggacaagacgcaggtaagagagtttcaacaaataggtacatgttctacctttatgttgtaatgcttcatatgggcaaggctcaagcaggtagtcatatcacctaggtaacaggcccagatatatgtcacaatgtcctccttgagacatgattctggggaaactctaccaccatctgtgtgccttgcctagcaatatgtcactatccaggtaagccagacccaagcaggacagcagaaataagcacctgataggccaaggtatttgtcacaatccccttttttggacattaccctagaaaaagagtaccatcaccagtgtgccaggcccagccatgtgctactatcccctagtgtgagtacagcccattctaaagaggagagttgtacaacctaactggttgatacagtgatatgtcacaatgacttctgtgggcatggcttaggcaaaaatgtaacatgacctccgtgctggatctagtgatatatcactcttcttactgagagcaggacccaggcaggaaagtcacattacctagaggttggccaaggtagatataacagtaacatatgtggtctggaaccagtctggagagtcagatcacacaggtGTTTGGCAGAGATTTATATCACAATCACACTGGCAAAAAATTCCCTGGATGAGATTTACAATACCACACATGTCCTTTTATCATGAGcaacagttggcttcatatatgtaagatagtgacagcgcttactgtcatctggtgtgaatatgagataatttcacctttctgctgggttctgctatgacactctctgtccaagccaagtgctacataaaatatctgaggctgttataagcttctttgagcttttttttttaccagaaagatatttaatcactgctttttctaaaacaagttataagagtcaaaattacacctatttgtgggatgcacatataagagtcattatcatgcctgtgaactgtgcctatatatgTAAGAATTTACTCTGTGTTGATGAAATAGACATGACAGTGAAGTAACCTAAATTCTGAGAGAGAAatgtgccaatattctccttgtaggtatgttcctggcagaaaagttgcataacttgggggttaaacccaggaatatggcacattgcccattgtgggcagtgtccggacagaagaagagactcatatcacctaaatgacaagcccagaatatgtcacaatgtatcctgttgaaaggacgaggtaagagagtcacatcatttagatgcagtgcttaggaatgtgacaatccccattggaaggagggtcagggcaggagaAGACAGTCAGGTAACTAGATGATGGGTCCAGAGACATGCAACAATCCTTCCTGAGGTTATTGTTAAGACAGGAGTGTCAAATCACTGTGGTGATCAGCTATGATATACATCCAAATCTCATTTGTGGGCTATACCTAAGCAGGATTATTAAATAACTCAGGAGATGGGCAAAGGTATATGTTACAATAATACGGGGTGAAAATTACAGGAATGGGAGTCACCGTCTTGCATATGACATGTCTCCAGGTTTAAGAGTCATAATTAGTCCTCATATctggtctcagttatatggcacagtattacttgtgggcagagggcaagcaggaaggtaacattacctaggtgggtgctggtccagtaagatgtcacaatccttcttgtgggcaggacactggaagaagagtcaaatcaccaggatgccgattttagtgatttatcaagattccccctgttaacagggattaggaaggtgagaagactcatgttacttttgcaattggcctagatatatgtctcaatggctgctatgtgctaaaccaaggtatgaaagtggcctcaccttggccatgggtttagcaatatgtcacaatctcctctgtggtcagggcaagacatgagagaaaaaaatatttagattctgagccaagtgtttctgttggcagagcccaaaaaagagagtcacatcacctgcttgcagtacccagttatgtgtcataatgcatgataagttcagggccaaggcagtagaagagagtcacatcacttacacaatggacctggatataagccacatatatctagatatattgccttttataggcaagaatcaggcaaagaattcacatcacctgggagctgatcccagtgatacttaaaagtgccctttataggcctgcccagacaTCTTCACTTAGGTGTATGATCCATGTATATCACAATTTCATCACTAGTCATAACCTAAAAAGGAAAGTCAAGTTATTCAGGATCTGTGCTACCTTTTTGTCCTAATCACACACTAGACAATATTCAGAAGTAAGATTCATAGTCCTGCAGAAGTCctggcttcttgcatgtgagtcaacacctcctgtgagttaggttaaagcagagaagtcacaatctcaacaataacaatgggtaacatccatgtataagatgcccaatctcacttgaagattgtgttccactagaggagtcacatcgtcacAGGTGTGTAGAATCATGCATCAGCAAATGACACATGAATAAGATCCATGTATGAGGGGAACATTTTCAACCTTTGACTGCTCTTATGtgtgagatttagtaacttaattttaggccctgttcttgtgagagaatgaaaattggatcagcttggtgtgcatccaagagtcacaaaagcacctggttgcttttccctgttatgacactctttgtaccactcaggctttacataatatgcctgagtgtcataatcttctgtgaactttatacaattaggagacccattactttacttattgccatgactggctttgagagtcaaaatagctctaatttctgagtccagttatgatggttttatttctgcatgtgagctgaaaccaagtatatgtcacaatttcaactgttggcagaaccaaggcagaagagtttcattgcctggattctgagctcaggatatattacaatctcctttgcaggcagggccaagtcagaagagtcacataacctggatacagacacaagtaatatggcaccatgtccactctaacaggattgaggaaagagagaagagtcacaacacataggtatttggctcagcaatatgtagtaaacctctcttttgacagaataaagaggagagtttcattacctgggttttgaactcagcggtatgacagaatttgtttagtgggtaggatctttgcagaagagccacatttcttagatGCTACTTGCAACGatgtcacaatattccttgagagaaaagtgcaggcaaagtagacaaattacctctgacaggctcagagatatgtgacaatatcccttgtttgcagagctcagggagaatggtcatattaTTATGATTCTAACCCAGTAATTTGTCAAAAATGCATGCTTTGAAAACAATGTAACCAAAAGTTTTAGCACATGGGTACTAAGCCCAGTGATATGACACAATCTTCTcatttttgagggtgacacctttaacttctagcttggtgtgcatatgagtcacaatgccacgtgtgtgtgctgggccattgtatgacaccctctaccacatccaagtgttttacacagtaggaaatgctctttactacccaggagtttatattatataaactagtgttctaaacttctgtgagctttgtagagatatgcaatctaggattttacctactcctctaaacctagtaaagagagccaaaatatcttttattggctgaatcccaatataagtttcaccaccatgcctgtgaattgaagcaagttatacgtcatcttcctgtttgttggcCAAAAAAAGAGGGGCGGggagagtaacatcgcttaggtgatgtggccagcaacatgtcacaatgctctctctaggcagaacctaggaaggagtgtcacattaactggttgctgagctcagcaatatgacacaaCTACACATGTAAAAATTTAGTGAAGGGATGAGAGCCAAAACACCTACAGAAtgggccaaaggtatgtcaaaatacccactgaggctctggcacaagcagaacagtagcatcatgacggtgccagagacaccagtatgcaataattttctctttatttaggaaaatggcagaagagtaatatcatttgagtgcaataggtcaaaatttctctttgtgggtatggttcagaaaaaaattgtatagtcccaggacctaaacactggggtcagcaatatttcaccatcccaccttttcaaaggcccagacagaaaaagaagagagtcatatcacacaggtcatgagctctaagatatgtcccaatgttcccagtatgaagggataaggcagacattgataacatatcacctaggtaactccctagaaatatgtcacagtgtaacattt
q panTro2.chrY                         000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 I 3112

a score=0.000000
s hg19.chrY    7676279 51 + 59373566 ggcaggagagtaagctcaccttggtgctggcttcagcaatatgtgacatac
e panTro2.chrY  529822 3112 + 23952694 I

a score=928790.000000
s hg19.chrY    7676330 10155 + 59373566 cactcagtggtatgtcacaattttttcagtgagcaggatccagacaggacaggagagtcacattacctagatgctatatctttcaatatgtcacagtgtaccctgttggcagggcactggcagaaaagacatatcatctagttaaaaggcctgaagatatgtgaaaatatcccctatttgcagggtccaggcagaagagtcacactgcacgattctgacccattgataggtaacgatgcttttatggaaaggaacttaaaccagaaagtttcaacaccagggtAGTAGGCCAAGGGAATTGACACAAGCTCCTcatctttaaaggtgacaccattaactcttagctatggtatatatgacagtcacaatctaacatgtgtcctggttataatatgaaactccctaccacatctgaaaattttgtatgagatgcataagtgttgcaaacctctctgaggcctacatgcatatatgtactcacgatcttacatattaccctaaacacagacatgacaaccgacatttctcctataggtttgctttagaaatgagacaatgattatgcctgtgatatggttctggaaatgggtcaccttcccatctgtggccagattcacttgtgaaatttacaattccaaGTTTATTCTTTATTTACCTGATagactcatgaccttaacaatgggctttgtaaatgtaggatggtaacaatatttactttcacctgcatatgtagtcaagagtcaatcttaaatttttcctgggccctgtaataaaattccctgtaccgcccacaatattttatgatatgagttaatattgtaaacttctgtgatctctgtacaaatatgaaatgaaggacattaccttttgatgtaaacaaagtggtgacaggtgaaatatctcctattcactgtatcccaatataagcttgatcagcatgctttgatccgaaactaggtacatgtcataatcccatttgtgagcaaaaaaccaaagagaatgttaacatcacttttgagttagtccaaacaatatatcacaatacctcctttaggcagggcctagcaaagagcatcacataaagcaagggctgcagccaacaatatgatacaaccacatgtggaagaaacccagggaaatgatgagagccaaaacacgtacagaatgggccaaagatatgtcaatataccttctgtggctctggtacaggcaggagagtcacatgattatggtgctggcccgagaaatatgccataattttctctttatgcatgaggtagaaagaagagtaacatcatccaggtgcagggccaggaaatacagcaaaagtcctctttgtgcacattgttcagttacaagacaagagtcacattacctaagtgttgggctcatcaatttgtcacaatcttctcactgaaaagtcccaggctgaaatagggagtcacatcacttgggtcataggctcagaaatatggcccaatgtcaccagtaggctggcctcaggcagaaaaagagggtcgtcttacttaggtgcttctttaggtgtatgtcacaattttatatttttacagaaacgaggatgaattgccacatcatctggttctgagttctgagatattcacaagtccccttagaaaacaactcaggcaagagagttacatcacctaggagcccgttccacccttatgtcacagtgcttcatgtgtacaggactaagaagaaagtcacatcacctagatgatagacccagagacacgtcacaaagccttcctgaaagcatggccctggcaaaatagtacaatcacctttgtacctggtctagcaatatgtcattattcaagtgtgcaggtaccaaggagaggagccatactacctatgttatatgccctgtgctatgtcaaaatgccttcttttcagcatggccctggaagaatgtatcatctcatatgtgactggcctaggaagatgtcactatcctgccatgtgtgcagggcccattttagagattagagttatgtcttcttctaagtcatggacccagtgatatatcactatgatgtctgtgagaatgggcaggcaggaatgtaatgtcacttgcattctagatccagtgatgtcacaattcttactgagggcagagcccagtcagaagagtcatatcttttacaggttggcccaagtagatgtcaaaaacccctatggATTAGATTTACAATACCACACATCTCTTGTTTTCATGTAGGAGagttgcctgcattcatctgtgatgatgaaagtccttactgtcagccaagtgtgcatatgagactcacaatttcctctgtttgctaaccactattatgacactctctattcaacccaacggttttataaaacatttgtcattgttataaactttggtgcctttttttttaccagaaggtaatcatggacatctctcatgtccctaaacctagtttatatgtggctgggtccacatatattagtcattatcatgtctgtgagctgtgcctaggtatgtgt-accatcctctctgtggttattaaacaggcaggacaaccacgttagctaaatcctaagccagaaatatttcaatattttctttgcaggtagggccctaacaaaagtcacaaacttgagtctaggctcaggtctgtggcataatcatccttgtggagattgtcctgacaggagaggagagtcatataacctaaataattggcccagagatatgtcacaatgcctcctgttaaaaaggccaggcaagagaggcatgccacctggatgtcatgctaagaaatgctacactcttcactgaaagcagggttcaggcagcagaagagagacacataacatggaggatgggtccaaatatatgttatgatccattttgaggacgttgataggacacaagagtcaaatcaccacagttcttgacccaggtatatgtcaaaatgtcatctgtgggctataactagaaaaaggttattaaatcactgtggagctgggctaaggtaaatatcccaataacacctgtgagaaggttaatagatgagagtcaaaatcctgagtatgtcctggctccaggtacaagagtcattattatgcctttgttgtggtctcaggtatatggtaaaatatcacctgtgggcagggagaagtaaggaaagtcacattaactgagtgggtttctggtccagagaaatgtcacaatcctcctcgtggacaggactctggagccaaattaactggatgctagtttctgttatatattggaatacctcctatggtcagggcttagacaggactggagacaatcttcacctaggcaatcggcctggatgtatgtcacaatggcccctgtgtgcaggacgaaggcaggagagtaagctcaccttggtgctggcttctgcaatatgtctgatttagcaatctctgtgctggtcagagccgaggcaagagagaagaaacatcacctaggtgctgaaccaagtgatatgttacaaatcttcctattggcagaatatccctaccccagaaaatagtcacatcacccaggtgcagtagccagttatgtctcacgatgcaccataagtgcagggccagggaggtagaaggaagtcacagcacttacatgattgacctagataaaagccatggtgccttttgtaggcaggtttcaggccaagattttacatcagctgggtgctggtcaaagtgatatgcaaaagttccctttgAAAATTGCCAAAGAAGTTGTTATATATTGTTTAGGTGCTGGTGCACACGTCACAATTTCAACTGTGCTCCGAGTCTAGAAAGCAGAGGCAAAAACTCGGATGCTGGTCAAAGTTATACTTGTCCATCAGACACCCAAAAATATTCAGAAataagtttcacaatcccacacaagtcctggattcgggtatgagagtcaacacctcctatggattgtgtcaaaatacatgagtcacattcttaacaatgcacaggatccatgtaaaaaccccaatcccacttgaagattgtgttccagcagaagagtGGAAGAACCATGGGTCTGCTGAATCATGGTTGAAATGTCACCAAAGTGTCCATGGATCAGACTCATGTATGAGAGTAACAAAATCAAGCTTATGTTGCTTATGTGtgtgagatttagtacctcattcataggctctgttcatatgtgagaatgacagtcatgtcagcttgttgtgcatccaacagtcacagtaacacctggttactggtgcctgttatgagattctttgtgccactcaggctttgtagagtatgacagagtcacatacttttctgtgaattcttacaagtgggagatctaggactttactcatgaccataggactggctatgagagtggaaatatttcccttggctgggcccatgtattagttattattgtgtatatgcgctgaatccatgtatatggcacaatttcacttttggacagagacaatacagaagaatcacatcatctcgttcttagccaaggatactttgtaatcccctttttaatcaggaccctgtcagaagagtcatatgccctggttacagtctcaaaaaatatgtcaTCCTTCCCACAATACACAGGGTTGAAAAATTATAGATagtcacattttctacttgctgggatcagcaatatgttataattccctgtcttggcacagtccagaacaaagggaacagtcacattgcttagcttttgcactcagtgttatgtcataattttttcagtgggcagtatcctggacggaaaggagattcacattacctaggtgctatatctagtgatatgtcacaatgttacctgtgggaagggcactggcaggagaaacacatcacctagctcataggcacagaaatatgtgattatattctttgttgtctgggtacaagcagaaaagtcaaattaTTATTATTCTGACCCAGCAATATGTAACAAGTCACCTATGGGAAAGAATGCAGGCCAAAAAGCCTCAACACCCAGGTAATAGCACCAGTGATATGACACAAACTCCTcatctttgaaggcgacacctttaacttttagctgagcatgtatagtagagtcacaatctcatgtgtgtcctgggccaatgtatgaaactctctacaatatccaaggggtttgtaaaatctgcatgagagttacaaatctttcagaggcctacaaactcatataaaattacaatcttatatattactctaaacccaggtttgatagtaaacatgtctcctataggcagggttaagggaaaagagccattattatgcctatgatctgggccagtcgtggtggctcacgcctgaaatcccagtactttgggaggctgaggcaggcagatcacgatgtcaggagatcgagaccatcctggttaacaccatgaaaccccatctctactaaaaatacatatagaaaaaattagacgggtatggtagtgggagcctgtaatcccagctacttgggaggctgaggcaggagaatggtgtgaacccaggaggcggaacttgcagtgagctgagatggtgccactgcactctagcccgggtgacacagcaagactccatttaaaaaaaaaaaaaaGTCACAATTCCAACTTTGTGCTGTATTCCATtgttagactcaggacctcaacagtggatattgtaaatgtaggatggtaacaacttttaatttcacctgaatgtgtagtcaagaatcacaatctgaacttttgttgggccctgatacctctaaaggccctccctaccaccagagagtttataccgtacaagttagtgatgtaaatttctgtgagattggtacaagtatgcaaaccaggaccttaactattgcccttagctcaatgataaaaagcaaaatatctcctgttggctgtaacccaatataagtttgatcatcatacatgtgaactgtgaactgaagcaaggtatatgtcttaatcccatttacgggcaaactttgggcaggagcataatatctacctaggtattgtgccaagcaatatgtccctatgtcttctctaggcagggtgcataaaattgggtcacattaactgggttctggacccagcaatatgacagcattccatatgtg--aaaaaaaaaaagcagccatgttaagggagccaaatcacatacatagtgagtccaggatatgtcacaatatcttggctggctcctgcacaggcaggaaagtctcatcataaatgtacatgacacagcaatatgcagtatgctacatgccataatttctcctttctgcagaacccaggaagaagagtaacatcatctggatgttgggccctgcaataggtcaaaatttctttgtgtgggcttggttgcagaaaaagagaagagtcacatgtcctgagtgctggtctcaacaatgtgtcaaaatcctcctattgtgaaggcttggcagaaaaagagagtcacaacacttaggtcatgggttcagagatatgttcaaatgtccccagaaggcaaagctcagaaacaggaggagagccatatcacctagatgtttccctaggaaagtcatagtgtaacatgtgggcagaaaccaggcaggagagccacagcacttgaatgctggatcctgagatatatcacaaggctctcttaggacaacacccaagcaaaagaattacatcaccttggtgcaggttctctgcttatgccacaatgctccatgtcaggagggcctaaggagggactcacttcatctaggtgataggcccagatatatgtcaaaatgtcctctgtgaagcatagtcttggcaaaggagcaccatcgcctgtgtgcctagcccagaattatgtcactctccaagttggctgggccaaagtagaaaagccacataacctaggtaatagacccagaggtatatcacagtaccctcttttgggcatggctctggccaaagaatacccttacccatgtgcctggccttgcaatatgttactatacttcctttgtgcagggtccattctacagaggagagttacagcaactgtgaggtgggcacagaaatatgtcacaataattttggtgggcattgggcagaccagcatgtaacatcacataggtgctagatccagtgatatgtcacaatcctaagagaaatgcccaggcatgagagtcacatcacctggaggttagcctacataaatatcacactcccatatatggactgaaaacagtctggagagtcaaattacacaggtGCTTCACAAATATTTATATCACAATCACACTGTCAGAAAATTCTAAATAAGAATACCACACATGTCCTGTTTTCATGCGTGATagttggctttatccatttgagatgatgacagtgctcactgtgagctgggtgtgcccatacaagattcacaatttcaccagttatgaaccctgctttgactctttctgtataacccaaatactttgtaaaatatgtgtgaatgttgtaatcttttgtgggctttgtatgacaaggtgacccaggacatcatgcatgtccctaaacctagtgacgagtcaaaatatcttttattggctgagtctatatattacagccatgatgatggctgtgagccatgcctagggatatgttacaatttcttctgtgtttatgaaggaggcagagcagccatgtcacctaaatgctggaccagaaatattccaaatatctctttgtaggcactgttctgtcaagaatgtcacataacatctaagataggtccagctaaggggcacaatgtccattgttggcagtgtttagtcaggagaggtgagtcatatcacataaatgatgggagcaaaaatatgttacaatgccttctgttgacagagtccaggcaagagagtcatatcatatggtaccagttcttataaatgatgaaattagcaaaggaagcagggtacaggcagaaaaggagagtcatgtaacctagatgatgggtccagaaatatgttgcattcccccttgaggacattgttaagatagcacagtcaaatcaccAAAGTTTCTGGCCCAAGTATTTGTCAAAATCTCATTTGTGGTCTATACCTAGACAGAC--ATTAAATTATCCAGGGGCTGAGCATAGGTATATGTCAAAATTTCACTGTGTAAAAGTTTAAAataagagtcaccatcctgcacgtgtcctggctccaggtacatgagttgttattatgcttttattatggtctcaggtatatggacacaatatcacctgtggccagaaagaaggcaagaaagtcacatcacatatgtgggtgcaggtctagagagatatcacaatccaccttgtgggcaggaccctggctaaacagtcacatcacctagatgctgatttcagtgtcatatcaaaactgattcggtgggtagaattttgcagaaatgagacacacatcacctaggcaattgtcctagatatatgtcaaaatgcaccttatgtatagtatcaaggctggagagtcacctcatattggtgctggtctcagcaatatgtcataatctccctgtggtcagggcccagaccaaagtgaagaaacatcacctaggtgttgagccaagtgatatgttataatgcttcctcttggcagaactcaaagaggggaatcactttaactagaaggagtacccacttatatgtcacaatggcactgcaagtgcagggccaaggcagtggaagggattcacatcacttacatgatggacccaggtgtaaaacataattctctttgtacacagatttcagggagataattcacatcacttaggaaatggcccctgttatatttaaaaagtgccattttaggcagagccagggaagTTGTTACACATTGCTTAGTTGCTTGTTACACATATGGCCCAATTTTATCTATGGTCTGGGCCTAGAAAAGAGGGTCAAATTATCCATGTGCTAAGCAAAGTTACCAGTCCCAATCACACTCTCAGAAAGTTTCAGAAATATCCTACAGAAGTCctggtttcatgtatgtaatttcactctctatgagttgggtcgagatagaacagtcacaatctaaaaaatgggcaagatccatgtatatgagccccaattccacttTAAGACTGTTCCAGTAGGGAAGTCACAGCACCACAGTTGTGCTGAATCGTAGTTCAAATGTTTCCAAACCACCTGTGAATCAGATCCATGTATGAGAGTAATTTTCACAGCCTTCAACCCTTTTTTATGTGTTTCatttagcacctcatttctagactctcttcatgtgtgagaatgataattgtatcatctaggtgtgcatacaagaatcacattcctacttggttgctggtctctgttatgacactctttgtatcattaaggcttcatatgatatatctgagtgttataattctttttgaattttatacaagtgaaaaatttaagacttcacccatgacagtgagactgaatatgatagtcagaatatctctagtggctaggtgtaggtatgagagttatttttgcacatgtgtgcttaactcagctatatgtcacaatttccactgtgagcagaaacaagggaggagagtctcattacttggaagctgagccagtaatacagtataatctcagtcatacgttggacctattcagaagagccgcattgcctgggtACTGTCTCAAATAGtatatcatcaagcacactatatacagggtagaagaaaaggggagagtcactccatctaagtgctgggatctgcaatatgtaattagcccctctcttggcagactctagaatataaaagagagtcatatcatacagatttcaaaatgactgctatgttacaatttcttgggtgagcaggaaacagacaggagaagagagtcatattgcgtagatgttaagtcaaacgatattttacaatgtcctgtgggagcagagcagaggcaggag-aaaaaaaatcatctaccttataggcccagagatatgtgataatatcccttgttggcagggcccaagcagaagggtcatattattaatattctatcccactgatatgtcacaatgcagccatgggaaggaatttaagccgagatgtctcaacaactgggtactagccctagtaatacgccaaatctccttgtattggagggtgacatat
s panTro2.chrY  532934 10144 + 23952694 cactcagtggtatgtcacaattttttcagtgagcaggatccagacaggacaggagagtcacattacctagatgctatatcttgcaatatgtcacagtgtaccctgttggcagggcactggcagaaaagacatatcatctagttaaaaggcctgaagatatgtgaaaatatcccctatttgcagggtccaggcagaagagtcaaactgcatgattctgacccattgataggtaacaatgcttttatggaaaggaacttaaaccagaaagtttcaacaccagggtAGTAGGCCAAGGGAATTGACACAAGCTCCTCACCTTtaaaggtgacatcgttaactcttagctatggtatatatgagagtcacaatctaacatgtgtcctggttataatatgaaactccctaccacatctgaaaattttgtatgagaagcataagtgttgcaaacctctctgaggcctacatgcatatatgtactcacgatcttacatattaccctaaacacagacatgacaactgacatttctcctataggcttgctttagaaatgagacaatgattatgcctgtgatatggttctggaaatgggtcaccctcccatctgtggccagattcacttgtgaaatttacaattccaaGTTTATTCTTTATTTCCCTGATagactcatgaccttaacaatgggctttgtaaatgtaggatggtaacaatatttactttcacctgaatatgtagtcaagagtcaatcttaaatttttcctgggccctgttataaaattccctgtacctcccaaaatattttatgatatgagttaatattgtaaacttctgtgatctctgtacaaatatgaaatgaaggacattaccttttgatgtaaacaaagtggtgacaggtacaatatctcctattcactgtatcccaatataagcttgatcagcatgctttgatccgaaactaggtacatgtcataatcccatttgtgagcaaaAAACCGAAGAGAATGTTAACATCACTTTTGAGTTAGGCCAAACAATATATCACAATACCTCCTTTAGGCAGGGGCTAGCAAAGAGCATCACATAAAGCAAGGGCTGCAGCCAACAATATGATACAACCACATATGGAAGAAACACAGGGAAATGATGAGAGCCAAAACACGTACAGAAtgggccaaagatatgtccatataccttctgtggctctggtaaaggcaggagagtcacatgattatggtgctggcccgagaaatatgccataattttctctttatgcatgaggtagaaagaagagtaacaccatccaggtgcagggccaggaaatacagcaaaagtcctctttgtgcacattgttcagttacaagacaagagtcacattacctaagtgttgggctcatcaatttgtcacaatcttctcactgaaaagtcccaggctgaaatagagagtcacatcacttgagtcataggctcagaaatatggcccaatgtcaccagtaggctggcctcaggcagaaaaagagggtcattttacttaggtgcttctttaggtgtatgtcacaatttaatatttttacagaaaccaggatgaattgccacatcatctggttctgagttctgagatattcacaagtccccttagaaaacaactcaggcaagagagttacatcacttaggagcccgttccacccttatgtcacagtgcttcatgtgtacaggactaagcagaaagtcacatcacctagatgatatacccagagacatgtcacgaagccttcctgaaagcatggccctggcaaaatagtacaatcacctttgtacctggtctagcaatatgtcactattcaagtgtgcaggtaccaaggagaggagccatactacctatgtcatatgccctgtgctatgtcaaaatgccttcttttcagcatggccctggaagaatgtatcatctcatatgtgactggcctaggaagatgtcactatcctgccatgtgtgcagggcccattttagagattagagttatgtcttcttctaagtcatggacccagtgatatatcactatgatgtctgtgagaatgggcaggcaggaatgtaatgtcacttgcattctagatccagtgatgtcacaattcttactgagggcagagcccagtcagaagagtcatatcttttacaggttggcccaagtagatgtcaaaaacccctatggATTAGATTTACAATACCACACATGTCTTTTTTTCATGTAGGAcagttgcctgcattcatctgtgatgatgaaagtccttactgtcagccaagtgtgcatataagacttacaatttcctctgtttgctaaccactattatgacactctctattcaacccaacggttttataaaacatttgtcattgttgtaaactttggtgcctttttttt-accagaaggtaatcatggacatctctcatgtccctaaacctagtttatatgtggctgggtccacatatattagtcattatcatgtctgtgagctgtgcctaggtatgtgtcaccatcctctctgtggttattaaacaggcaggacaaccacgttagctaaatcctaagccagaaatatttcaatattttctttgcagatagggccctaacaaaagtcacaaacttgagtctaggctcaggtctatggcataatcatccttgtggagattgtcctgacaggagaggagagtcatataacctaaataattggcccaaagatatgtcacaatgcctcctgttaaaaaggccaggcaagagaggcatgccatctggatgtcatactaaggaatgctacactcttcactgaaaggagggttcaggcagcagaagagagacacataacatggaggatgggtccaaagatatgttatgatccattttgaggacattgataggacacaagagtcaaatcaccacagttcttgacccaggtatatgtcaaactgtcatctgtgggcTATAACTAGAAAAAGGTTATTAAATCActgtggagctgggctaaggtaaatatcccaataacacctgtgagaaggttgatagatgagagtcaaaatcctgagtatgtcctggctccaggtacaagagtcattattatgcctttgttgtggtctcaggtatatggtaaaatatcacctgtgggcagggagaagtaaggaaagtcacattaactgagtgggtt-ctggtccagagaaatgtcacaatcctcctcgtggacaggactctggagccaaattaactgggtgctagtttctgttatatattggaatacctcctatggtcagggcttagacaggactggagacaatcttcacctaggcaatcggcctggatgtatgtcacaatggcccctgtgtgcaggacgaaggcaggagagtaagctcaccttggtgctggcttcagcaatatgtctgatttagcaatctctgtgctggtcagagcccaggcaagagagaagaaacatcacctaggtgctgaaccaagtgatatgttacaaagcttcctgttggcagaatatccctaccccagaaaatagtcacatcacccaggtgcagtagccagttatgtctcacgatgcaccataagtgcagggccagggaggtagaaggaagtcacagcacttacatgattgacctagataaaagccacagtgccttttgtaggcaggtttcaggccaagattttacatcagctgggtgctggtcaaagtgatatgcaaaagttccctttgaacattgccaaagaagTTGTTAGATATTGTTTAGGTGCTGGTGCACATGTCACAATTTCAACTGTGCTCCGGATCAAGAAAGCAGAGGCAAAAACTCAGATGCTGGTCAAAGTTATACTTGTCCATCAGACACCCAAAAATAttcagaaataagtttcacaatcccacacaagtcctggattcgggtatgagagtcaacacctcctatggattgtgtcaaaatacatgagtcacattcttaacaatgcacaggatccatgtaaaaaccccaatcccacttgaagattgtgttccagAGGAAGAGTGGAAGAACCATGGGTCTGCTGAATCATGGTTGAAATGTCACCAAAGTGTCCATGGATCACACTCATGTATGAGAGTAACAAAATCAAGCTTATGTTGCTTATGTGtgtgagatttagtacctcattcataggctttgttcatatgtaagaatgacagtcatgtcagcttgttgtgcatccaacagtcacaataacac--------tggtgcctgttatgacattctttgtgccactcaggctttgtagagtatgacagagttgcatacttttctgtgaattcttacaagtgggagatctaggactttactcatggccataggactggccatgagagtggaaatatttcccttggctgggcccatgtattagttattattgtgtatatgtgctgaatccatgtatatggcacaatttcacttttggacagagacaatacagaagaatcacatcatctcgttcttagccaaggttactttgtaatctcctttgtaatcaggaccccgtcagaagagtcatattctctggTTACAGCCTCAAAAAATATGTCATCCTTCCCACAATACACAGGGTTGAAAAATTATAGATagtcacattttctacttgctgggatcagcaatgtgttataattccctgtcttggcacagtccagaacaaagggaaaagtcacattgcttagcttttgcact--gtgttatgtcataattttttcagtgggcagtatcctggacggaaaggagattcacattacctaggtgctgtatctagtgatatgtcacaatgttacctgtgggaagggcactggcaggagaaacacatcacctagctcataggcacagaaatatgtgattatattctttgttgtctgggtacaagcagaaaagtcaaattaTTATTATTCTGACCCAGCAATATGTAACAAGTCACCTATGGGAAAGGATGCAGGCCAAAAAGCCTCAACACCCAGGTAATAGCTCCAGTGATATGACACAAACTCCTcatctttgaaggagacacctttaacttttagctgagcatgtatagtagagtcacagtctcatgtgtgtcctgggccaatgtatgaaattccctacaatatccaagggctttgtaaaatctgcgtgagagttacaaatctttcagaggcctacaaactcatataaaattacgatcttatatattactctaaacccaggtttgatagtaaacatgtctcctataggcagggttaagggaaaagagccattattatgcctatgatctgggccagtcgtggtggctcacgcctgaaatcccagtactttgggaggccgaggcaggcagatcacgatatcaggagatcgagaccatcctggttaacaccatgaaaccccatctctactaaaaatacatatagaaaaaattagccgggtgtggtagtgggagcctgtaatcccagctacttgggaggctgaggcaggagaatggtgtgaacccaggaggcggaacttgcagtgagctgagatggtgccactgcactctagcctgggtgacacagcaagactccatttaaaaaaaaaaaa--GTCACAATTCCAACTTTGTGCTGTATTCCATtgttagactcaggacctcaacagtggatattgtaaatgtaggatggtaacaacttttaatttcacctgaatgtgtagtcaagaatcacaatctgaacttttgttgggccctgatacctctaaaggccctccctaccaccaaagaatttacacagtacaagttagtgttgtaaacttctgtgagattggtacaagtatgcaaaccaggaccttaactattgcccttagctcaatgataaaaagcaaaatatctcctgttggctgtaacccaatataagtttgatcatcatacatgtgaactgtgaactgaagcaaggtatatgtcataatcccatttacgggcaaactttgggcaggagcataatatctacttaggtattgtgccaagcaatatgtccctatgtcttctctaggcagggtgcataaaattgggtcacattaactgggttctggacccagcaatacgacagcattccatatgtggaaaaaaaaaaaagcagccatgttaagggagccaaatcacatacatagtgagtccaggatatgtcacaatatcttggctggctcctgcacaggcaggaaagtctcatcataaatgtacatgacacagcaatatgcagtatgctatatgccataatttctcctttctgcagaacccaggaagaagagtaacatcatctggatgttggaccctgcaataggtcaaaatttctttgtgtgggcttggttgcagaaaaagagaagagtcacatgtcctgagtgctggtctcaacaatgtgtcaaaatcctcctattgtgaaggcttggcagaaaaagagagtcactacacttaggtcatgggttcagagatatgttcaaatgtccccagaaggcaaagctcagaaagaggaggagagccatatcacctagatgcttccctaggaaagtcatagtgtaacacattggcagaaaccaggcaggagagccacagcacttgaatgctggatcctgagatatatcacaaggctctcttaggacaacacccaagcaaaagaattacatcaccttggtgcaggttctctgcttatgccacaatgctccatgtcaggagggcctaaggagggactcacttcatctaggtgataggcccagatatatgtcaaaatgtcccctgtgaagcatagtcttggcaaaggagcaccatcgcctgtgtgcctagcctagaattatgtcactctccaagttggctgggccaaagtagaaaagccacataacctaggtaatagacccagaggtatatcacagtaccctcttttgggcatggctctggccaaagaataaccctacccatgtgcctggccttgcaatatgttactatacttcctttgtgcagggtccattccatagaggagagttacagcaactgtgaggtgggcacagaaatatgtcacaataattttggtgggcattgggcagaccggcatgtaacatcacataggtgctagatccagtgatatgtcacaatcctaagagaaatgcccaggcatgagagtcacatcacctggaggttagcctacataaatatcacactcccatatatggactgaaaacagtctggagagtcaaattacacaggtGCTTCACAAATATTTATATCACAATCACACTGTCAGAAAATTCTAAATAAGAATACCACACATGTCCTGTTTTCATGCGTGATagttggcttcatccatttgagatgatgacagtgctcactgtgagctgggtgtgc--atacaagattcacaatttcaccagttatgaaccctgctttgactctttctgtataacccaaagactttgtaaaatatgtgtgaatgttgtaatcttttgtgggctttgtatgacaaggtgacccaggacatcatgcatgtccctaaacctagtgacgagtcaaaatatcttttattggctgagtctatatattacagccatgatgatggctgtgagccatgcctagagatatgttacaatttcttctgtgtttatgaaggaggcagagcagccatgtcacctaaatgctggaccagaaatattccaaatatctctttgtaggcactgttctgtcaagaatgtcacataacgtctaagataggtccaactaaggg-cacaatgtccattgttggcagtgtttagtcaggagaggtgagtcatatcacataaatgatgggagcaaaaatatgtcacaatgccttctgttgacagagtccaggcaagagagtcatatcatatggtaccagttcttacaaatgatgaaattagcaaaggaagcagggtacaggcagaaaaggagagtcatgtaacctagatgatgggtccagaaatatgttgcattcccccttgaggacattgttaagatagcacagtcaaatcaccAAAGTTTCTGGCCCAAGTATTTGTCAAAATCTCATTTGTGGTCTATACCTAGACAGACTTATTAAATTATCCAGGGGCTGAGCATAGGTATATGTCAAAATTTCACTGTGTAAAAGTTTAAAataagagtcaccatcttgcacatgtcctggctccaggcacatgagttgttattatgcttttattatggtctcaggtatatggacacaatatcatctgtggccagaaagaaggcaagaaagtcacatcacatatgtgggtgcaggtctagagagatatcataatccaccttgtgggtaggaccctggctaaacagtcacatcacctagatgctgatttcagtgtcatatcaaaactgattctgtgggtagaatttggcagaaatgagacacacatcacctaggcaattgtcctagatatatgtcaaaatgcaccttatgtatagtatcaaggctggagagtcacctcatattggtgctggtctcagcaatatgtcacaatctccctgtggtcagggcccagaccaaagtgaagaaacatcacctaggtgttgagccaagtgatatgttataatgcttcctcttggcagaactcaaagaggggaatcactttaactagatggagtacccacttatatgttacaatggcactgcaagtgcagggccaaggcagtggaagggattcacatcacttacatgatggatccaggtgtaaaacataattctctttgtacacagatttcagggagataattcacatcacttaggAAATGGCCCCTATTATATTTAAAAAGTGCCATTTTAGGCAGAGCCAGGGAAGTTGTTACACATTGCTTAGTTGCTTGTTACACATATGGCCCAATTTTATCTGTGGTCTGGGCCTAGAAAAGAGGGTCAAATTATCCATGTGCTAGGCAAAGTTACCAGTCCCAATCACACTCTCAGAAAGTTTCAGAAATATCCTACAGAAGTCctggtttcatgtatgtaatttcactctctatgagttgggtcgagatagagcagtcacaatctaaaaaatgggcaagatccatgtatatgagccccaattccacttTAAGACTGTTCCAGTAGGGAAGTCACAGCACCACAGTTGTGCTGAATCATAGTTCAAATGTTTCCAAACCACCTGTGAATCAGATCCATGTATGAGAGTAATTTTTACAGCCTTCAACTCTTTTTTATGTGTTTCatttagcacctcatttctagactctcttcatgtgtgagaatgataattgtatcatctaggtgtgcatacaagaatcacattcttacttggttgctggtctctgttatgatactctttgtatcattaaggctttatatgatatatctgagtgttataattctttgtgaattttatacaagttaaaaatttaagacttcacccatgacagtgagactgaatatgatagtcagaatatctctagtggctaggtgtaggtatgagagttatttttgcacatgtgtgcttaactcagctatatgtcacaatttccactgtaagcagaaacaagggaggagagtctcattacttggaagctgagccagtaatacagtataatctcagtcatatgctggacctattcagaagagccgcattgcctgggtACCATCTCAAATAGtatatcatcaagcacactatatacagggtagaagaaaaggggagagtcactccatctaagtgctgggatctgcaatatgtaattagcccctctcttggcagactctagaatataaaagagagtcatatcacacagatttcaaaatgactactatgttacaatttcttgggtgagcaggacacagacaggagaagagagtcatattgcgtagatgttaagtcaaacgatattttacaatgtcctgtgggagcagagcagaggcaggagaaaaaaaaatcatctaccttacaggcccagagatatgtgataatatcccttgttggcagggcccaagcagaagggtcatattattaatattctatcccactgatacgtcacaatgcagccatgggaaggaatttaagccaagatgtctcaacaactgggtactagccctagtaatacgccaaatctccttgtATTGGAGGGTGACATAT
q panTro2.chrY                          000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--------000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000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00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY I 3112 C 0

a score=0.000000
s hg19.chrY    7686485 2999 + 59373566 tgtactgtgagctgcatgtgtatatgaccatcacaatctcacttgttttccggccatggtatgacaatccacaatatttaaagtctttaaacagcatgctagagagttgcaagccactctgaggcctacttgttcaaatggattcacaatgttacatattgccttaaactcagttataagagtcaacatctctcatgtaggctgaattcaggaatgagactcattattatgcctgtgacctggatccagaaatgagtcaccatcccacctatagccagatccacatatgaagttcacaattccaactttgtactgtatccacttgttaaactcaggaacttaacattgggctttggacatgtgtgatggtgacaatattttctttcacctcaatgtgtaatcgagaatcccaatctggtcttttcgctggtcgatctcttgaaactctccatatcactcaggagtatacacattatgagatagtgttgtaaatttctgtgagctttgtacaattttgctatgcaagacctaacctattgccctaagcataacaatgaaagacaatatatcttctattggctgactcccagtacaagttttaccatcatgcttgtgaactgaagtcaggtatatgtcatagtcccatttgtgggaaaatctaggaagaagggtaatgtcacttaggtgctgtgccaagcactatatcacattgccctcttcaggcagactataggaattggagtcacattacctgggtgctgaactcagtaattgacaccatcccacatgtggaaaaaacccagacaacttatgaggaccaaaaaacctacacaatgggctcagaatatgtcaaaataccttctgtggctctggcacattcctgagagtaacattatcagggtggtgggcccagcatgattctttctatatgcattaatttgcactatatgcaggacccaggcaaaagaataacattatctgcatgttgggccttgcaataggtgaaaatttctgtttgggggtatggtttgaaaaagaaaggagtatcaaataactcaataattcagcaataggtcacaatcccctcattttaaagaccaagtagaaaaatagagtcacttcacttagatcatgggctcatagatacatcccagtgtccccagtaggcagggaccatgcagaaaatgagagtaatataaactaggagcttccttaattacatgtaactatctaacatgtggacagaaaccaggcaggagagccatatcatctggtacagactcaagtaatatgttaccgtgcccaatgtagaccggTTTATAAGGAAAAAAGATATTTACCAAATGTGGGTgttgggctcaacaatatgcagtaacttcctttcttggaagattccaggacaaagaggacagtaatgacatctaggttttgcacttagttgtatgtcaacatttcatcagtggacagcaccaagcaggagaggagagtctaattaccctgatgctatatttattgatatgtcacagtgtaccctgtggacagggcactggcaggagagccatatcacctagcctatagacccagagatatgggaaaatatcacctgttggcagggcccagggagaagagtcattatcatgattctgacccagtgatatttaacaatgcccttatgaaaaggaatttataccaaaaagtctcaacaccAGCAAACTAGGCAAAGACATATGACATAAtattttcatctttaaggttgacaccagtaagtgttaaatagttgtgtatatgacagtcacaatcccacgtttactgaccattgcgtgacactctctacaacatccgagtactttatacaacatgtgtaagagttgtaaagctccgtgaagtgtatgcactgatgtggagtcacgatcttacatatttccctaaacccaggtattacaattaacatctctcctataggctggcttcagggatgagaccattattattcctgctagctgggtcaagaaatgagtcacctacccacctgtgggccagaatcacttacaaaattcacaatttcaaGTTGGTGTTGTATTCACTTGATagactcaggacttcaacaataggctttgtaaatgtaggatggtaacaacttttactttgacctgagtgtgtagtcaacagccacaactataacttttgctgggctctgttatgaaactttctgtaacactcaagaagttttcatgatatgagttagtgttgtaaacttctgtgaactttgtatcaaaatgcaatgaataaccttacctattgacctaaaccaagcagtgagaagaaaaatatctcctattgtatgaattttaaaatagggttgatcattatgcctttgaaatgaatcacagtatatgttctaatcccatttatgcacaaaaaaaatctaggcagaatttttacatcacttaggtgctttactaagcaatatgtcacacttttaagcagcaactaggagacaggatcacattaactaaaggctggagccagcaatatgatacaaCCACAGATGGAAGAAACCCAGCAAAGTTATGAGAGCCAAAACACTTACAAAATGAACCAAAGTAAAgtcaaagtattttctgtggctctgtcacaagcagaagagtcacattattaggttgctgggataagcaatatgccacaatttccaatttgtgcacaacctagggagaaaagtaacatgtcacaatcttccaattcgaaaagcccagacagaagagaagagtcacatcacaaacgtctttgactcagagatatggcccaatgtcaccagtagacaaggctctggaaggaaaagagagtcatatcacaaatgtacttctttaagtatatgtcacaatttcatatgtttgcagaaaccaggttgaagagccatatcacctagtcctgggtcctgaaatattcacatgacccctctttacaaaaaggatccaggcaagagagttacatcacccagg
e panTro2.chrY  543078    0 + 23952694 C

a score=496878.000000
s hg19.chrY    7689484 5441 + 59373566 tgcaggtttcactcttatgtcaccatgctccatgtgggcagggccaaatcataactcacatcacctaggtgatagacccagagatatgtcacaaagccttgcttaaagcatgaccctagcataagagaaccatcacttttgtgcctgacctagcattatttcactattcaagtgggcaggtcccaaacagaagagccatatcacgtatgagataggccctgtgatatgtaaaaatcctctcttttgggcatggaactggcaaaagagtatcatcatcATTGTGCCTGACCTAAGAACATGTGACTATCCTGCTTTTACTTCAGGGCTTATTCCAGGGAGGAGAGTTGAAATTTCTAACTAGTGGAAAAACTgatatgtcgcaatgatgtctgtgatcaggtttcaggcaagaatgtgttttcacatgggtgctagatccagtgatgtcacaatacttactgagagcagggcccaggcagaagtgtcacatcactccaagtttggtccaagtagatatcaaagtctcatatacagcagcatccagtctgaagagtgaaatcacacaggtgcttggcaaaggcaaaatttctattggcttgatccacatatgacagtcattatcatgcctgttagctgtgcataggtatatgtcaacttcacctctgtggTTCTTAAACAAGCAGGACAAACACATCACATAAATTCTAAGCCAGAAATATTCCAATATTTTCTTTACAGACGTGTAATagaaaagtcacaaaacttgggcactgggcccagctgtatgacataatgcttcttgtggagactgtccaggcaggagaagagagtcatatcacctaaatgatggtgccagacgtatgtcacattgcctcctgttgaaaggcctagacaataaaatcaggccatttggattcagtgcttacaaactctacactcttcattggaagcagtgttcatgcaggagaggagagtcacataacctagatgatgggtccaaagatatgttagaatcctatttgaggacactgttaagacacaagagtaaaatAAGTGAGGTTTTTGACCCAGGTATAATTTAAAATGTCATCTGTGGGCTATTACTAGGAAAAATTATCAAATCACTCAACAGGTGGGCAAAGGTAAATGTCACAATAACACCCATGGAAATAATCAGGGatgagagtcaccagcctgctcctcctggctccaggtacaagagtcatcataaggcctttgatttggtctcaggtatttggcaccacatcacctgttgtcaaggagaagaaagcaaagtcacttcacctgagtgggttcaggaccagtgaaatgtcacaatcttccttgtgggaaggactctagaagagtcgtcacatcaactggatgttggtttctgtgatatatccaaatcctccctgtggggagggtttaggcaagagacaagataaacttcacctcttcatttgtcctgaatatatgtcacaatgacccctgtgtgaaggatcaaagcaggagagtaacctcaccttgatgctgagtttagcaatatgtcacaatctgtgtgctggacaggtctcaggcaagagaaaagaaagattacatagttgctgaaccaagtggtaagttacaaagcttttcattgggagaacccccctcaaaaaaccaccaaacaacttgggtgcaataaccagttatgtgtcacaatgcaccagaactacagggccaaggcagtataagtaagtcacagcacttacatgattgacctagataaaagccaaaatgctagctgtaggcagtgttcaggctaagatttcacatcagctgggtgcttgtccaagtgacttgtaaatgtgtcttttggcacatggccATAGAAGGTGTTATACATTGCTTAGATACTTGATGTTCATGTGTCACAATTTCAACTGTGCTCTGGGCCTTGGTAGGAGACTGAAAACACTCAGATGGTAGGCAAGTCATAATTGTCAATCACAAACTCAAAAATATTCAGAAATAAGTTTCACAGTACCACAAAAGTCCTGGCTTTGTGTTTGAGAGCGAACACCTTCTATGAGTTGGATTGAAGTTCAGGAGTCACAATCTCAACAATAGCCAAGATTCAGTCAGAAGATCCCCAGTCCCACTTGAAGATTGTATTCCAGTAGGAGAATCAAAGCACTACAGGActtgtgaatcatggttcaaatatcaccaaaccacctgtgggtcagattcatatatgagaacaatttcaatcttcgactgcttatgtgtgagagatttagtacctcatttgtaggctctgtttatgtgtgagaatgacaatggtgtctgctggggcagcatccaagagtcacaatatcacctggttgttggtgtctattatgacacagtttgtaccactcaggcttggtataatatgcctgagcagcatacttttctgtgaattcttactggtgagggatctaggattttttccatggccgtaagactggctatgagagtcaaaatatcacccctggctgggtctaggtatgagagttattactatgcatatgagctgaatccagttatatatcacaatctcacctttggacaaagacaagacagaagagtcacatcatctgcatgcttagtgaggggtacattataatctcctctgtagtcaggacccagtcagatagtcttttcatctgtgtacaatctcaaataatatgtcatcatgcccactgtatacagcattgaaaaaaatgttgggtagtcacacttactaggtgctgtgctcagcaatatgttattattccctctttttgtagagtccaggacaaaggggagagtcaattcacctaggttttgcacacaattgtatctcacaatgtcttcagtggtgaggatccaggcaagagcaaagagtcacattacctagttgctacatatagtgatatatcacagtgtaacctgtgggcagggcactgggaggagagatacatcatccagctgataggcccagaaatatatgataatatcccctgttgcctgagtccaaacagaagagtcacaGTATTATGAATCCAACCTAACAATAATTTAAATTGCACCCATGGAAAAGAATTTAAGCTAAAAATTCTCAACTCCTAGGGATATTGGCCTTGTGAAATAAAATAATTTTATCATCTTTCAAgtgacacctttaactgttagcttggtgtgtatataaaagtcacaatctcatgtgtgttctgagtcattgtatgacacactacaacatccgaaggctttatgcaacatgcaggagagttgcaaaccactctgaggcctacatgcttatattgactcacaatcttaaatatttatttaaagccagataggacggtcaacatgtctcttataggctaagttcagatatgagacccactattacacctgtgatttgggtccagaaatgagttaccatctcacctatagcaagatccacatatgaaagtcacaattccatctgtgttctttatttacatgttagactcaggacttcaacactgggtttgctaaatgtgggagggtgacacattttgctatcacctggctaggtaatcaaggtcagaatcctcaccttttcctgggccctgttatcaaactgtgtaccacccaaggagtttttagaatatgagttaatgttgtaactttctgtgagctttattccaatatgcaactcataacagtacctattgccctaagtgtagcgatgagaggcaaaatatctactatATGTGGCATACCAATTTAAGTTTGATCAGCATGCTTCTGAATTCAAACAATGTAAATTTCACAATCGCATTTGTAAGAAAAAAGCTTGTCAGGAGGGCAGGACAACTTTGTTGTTCTgccaagcaatatgtcacaatgccattttttttt-gtttctctggcacagtccagagagttatatcatcagggttggggtcccagcaacatgccataaaagtatatcacaatggccactatgtgcaaaacaaaagtatgaaagtgacatcaccttaccaatggtttaacaatatgccacaatcttctctgtgatcagggtgaggcaacagtggagaaacatcacctaggttctgagcc-aagtgatatgttaacaaagctttctgttggcaggacccaaaacagagtcacattacctgggtacagtacccagttatgtgtcacaatgaactataagtgcagtctcaaggcagtaaaatggagtcatgtcact-acaaaatgaacctaaatataagccagaatgctttttatatgcaggggtaaggcaaataattcacatcacctgggtgctggtcacagtgatatgtaaaagtgctctttttaggcagtctcagacaactttgcttatgtgcatggcccacgtatgtcacaattgcatctgtcatcatggcctaaaatggaaagccaaattaTTCAGAAGCTGGAATAACTTTTATATTCTAATCAAACCAAATTGAATATTTAGAAATGTGCTTCCAGTTCCACAAATGTCCTGGCTTTTTGTACGTGAGTTGACACCTCCTGTGAGTTGGGTTGAAGCAGAGGAGTCACAATCTCAACAGTCAGCCAAGAGATTAAAGCCAAAACACCTACAGAATGAGccaaagatatgtcaaaaatactctctgttcctctggcacagacaggacagtatcatcatcagggtgatatgcctcccagtatgcaataattctcactttattgaggtctctggcagaagagtaacatcatctgtgtgcaataggtcaaaatttccctttctgggcatggttcatagaaaagagtagagtcaaaagaccaaaatgctgagctcaccaatatgccactatcccaccatattaaaggcccaggcagcataaaagagtcatatcacttaggtcatggctcagagacatgtaccaatatccccagtaggcaggactcaggcagaaaataagagtcgtatcacctaggtgcttctttaattatatgtcacaatataacacataggcagaaatcaggcagaggagccagagcacctgggtgctgggtcccgatatatgttgcaagttcccttaggatgaaccaagttgaaagagttcattgccttgatgcaagtataacattcgtttcacaatgtcctatgtggaagaggccaaagcattgagctacatcacttacttgataggaccagaaatatgtcacaatctcctccctgaaatataaccctggcaaaagagtgctacaatcttagtgccagcctagcaatatgtcattaccacccgctgttttcaggacccattccagagatgtcataattatttctgtgggtgtggcccaggcaagaatgtatcatcacttgggttttagatgcagggatatgtcacaatccttactgagagaacagccaagacaggagtatca
s panTro2.chrY  543078 5438 + 23952694 TGCAGGTTTCACTCTtatgtcaccatgctccatgtgggcagggccaaatcataactcacatcacctaggtgatagacccagagatatgtcacaaagccttgcttaaagcatgaccctagcataagagaaccatcacttttgtgcctgacctagcattatttcactattcaagtgggcaggtcccaaacaaaagagccatatcacgtatgagataggccctgtgatatgtaaaaatcctctcttttgggcatggaactggcaaaatagtatcatcatcATTGTGCCTGACCTAAGAATATGTGACTATCCTGCTTTTACTTCAGGGCTTATTCCAGGGAGGAGAGTTGAAATTTCTAACTAGTGGAAAAagtgatatgtcgtaatgatgtctgtgatcaggtttcaggcaagaatgtgttttcacatgggtgctagatccagtgatgtcgcaatacttactgagagcagggcccaggcagaagtgtcacatcactccaagtttggtccaagtagatatcaaagtctcatatacagcagcatccagtctgaagagcgaaatcacacaggtgcttggcaaaggcaaaatttctattggcttgatccacat--gacagtcattatcatgcctgttagctgtgcataggtatatgtcaacttcacctctgtggTTCTTAAACAAGCAAGACAAACACATCACATAAATTCTAAGCCAGAAATATTCCAATATTTTCTTTACAGACATGTAATagaaaagtcacaaaacttgggcactgggcccagctgtatggcataatgcttcttgtggagactgtccaggcaggagaagagagtcatatcacctaaatgatggtgccagacgtatgtcacattgccttctgttgaaaggcctagacaataaaatcaggccatttggattcagtgcttacaaactctacactcttcactggaagcagtgttcatgcaggagaggagagtcacataacctagatgatgggtccaaagatatgttagaatcctatttgag-acactgttaagacacaagagtaaaatAAGTGAGGTTTTTGACCCAGGTATAATTTAAAATGTCATCTGTGGGCTATTACTACGAAAAATTATCAAATCACTCAACAGGTGGGCAAAGGTAAATGTCACAATAACACCCATGGAAATAATCAGGGatgagagtcaccagcctgctcctcctggctccaggtacaagagtcatcataaggcctttgatttggtctcaggtatttggcaccacatcacctgttggcaagcagaagaaagcaaagtcacttcacctgagtgggttcaggaccagtgaaatgtcacaatcttccttgtgggaaggactctagaagaagagtcacatcaactggatgttggtttcagtgatatatccaaatcctccctgtggggagggtttaggcaagagacaagataaacttcacctcttcatttgtcctgaatatatgtcacaatgaccc--gtgtgaaggatcaaagcaggagagtaacctcaccttgatgctgagtt-accaatatgtcacaatctgtgtgctggacaggtctcaggcaagagaaaagaaagattacatagttgctgaaccaagtggtaagttacaaagcttttcattgggagaacccccctcaaaaaaacaccaaacaacttgggtgcaataaccagttatgtgtcacaatgcaccagaagtacagggccaaggcagtagaagtaaatcactgcacttacatgattgacctagataaaagccaaaatgctagttgtaggcagtgttcaggctaagatttcacatcagctgggtgcttgtccaagtgacatgtaaatgtgtcttttggcacatggccATAGAAGGTGTTATACATTGCTTAGATGCTTGGTGTTCATGTGTCACAATTTCAACTGTGCTCTGGGCCTTGGTAGGAGACTGAAAACACTCAGATGGTAGGCAAGTCATAATTGTCAATCACAAACTCAAAAATATTCAGAAATAAGTTTCACAGTACCACAAAAGTCCTGGCTTTGTGTTTGAGAGCGAACACCTTCTATGAGTTGGATTGAAGTTCAGTTGTCACAATCTCAACAATAGCCAAGATTCAGTTAGAAGATCCCCAGTCCCACTTGAAGATTGTATTCCAGTAGGAGAATCAAAGCACTACAGGActtgtgaatcatggttcaaatatcaccaaaccacctgtgggtcagattcatatatgagaacaatttcaatcttcgactgcttatgtgtgagagatttagtacctcatttgtaggctctgtttatgtgtgagaatgacaatggtgtctgctggggcagcatccaagagtcacaatatcacctggttgttggtgtctattatgacacagtttgtaccactcaggcttggtataatatgcctgagcagcatacttttctgtaaattcttactggtgagggatctaggattttttccatggctgtaagactggctatgagagtcaaaatatcaaccctggctgggtctaggtatgagagttattactatgcatatgagctgaatccagttatatatcacaatctcacctttggacaaagacaagacagaagagtcacatcatctgcatgcttagtgaggggtacattataatctcctctgttgtcaggacccagtcagatagtgttttcatctgtgtacaatctcaaataatatgtcatcatgcccactgtatacagcattgaaaaaaatgttgggtagtcacccctactaggtgctgcgctcagcaatatgttattattcccttttttggtagagtccaggacaaaggggagagtcaattcacctaggttttgcacacaattgtatgtcacaatgtcttcagtggtgaggatccaggcaagagcaaagagtcacattacctaTTTGCTACATATagtgatatatcacagtgtaacctgtgggcagggcactgggaggagagctacatcatccagctgataggcccagaaatatatgataatatcccctgttggctgagtccaagcagaagagtcacaGTATTATGAATCCAACCTAACAATAATTTAAATTGCACCCATGGAAAAGAATTTAAGCTAAAAATTCTCAACTCCTAGGGATATTGGCCTTGTGAAATAAAATAACTTTATCATCTTTCAAgtgacacctttaactgttagcttggtgtgtatataaaagtcacaatctcatgtgtgttctgagtcattgtatgacacactacaacatccgaaggctttatgcaacatgcaggagagttgcaaaccactctgaggcctacatgcttatattgactcacaatcttacatatttatttaaagccagataggacggtcaacatgtctcttataggctaagttcagatacgagacccactattacatctgtgatttgggtccagaaatgagttaccatctcacctatagcaagattcacatatgaaagtcacaattccatctgtgttctttatttacatgttagactcaggacttcaacactgggtttgctaaatgtgggagggtgacacattttgctatcacctggcttggtaatcaaggtcagaatccttaccttttcctgggccctgttataaaactgtgtaccacccgaggagtttttagaatatgagttaatgttgtaactttctgtgagctttattccaatatgcaactcataacagtacctattgccctaagtgtagtgatgagaggcaaaatatctactatATGTGGCATACCAATTTAAGTTTGATTAGCATGCTTCTGAATTCAAGCAATGTAAATTTCACAATCGCATTTGTAAGAAAAAAGCTTGTCAGGAGGGCAGGACAACTTTGTTgttgtgccaagcaatatgtcacaatgccattttttttttgtttctccggcacaggccagagagttatatcatcagggttggggtcccagcaacatgccataaaagtatatcacaatggccactatgtgcaaaacaaaagtatgaaagtaacatcaccttaccaatggtttaacaatatgccacaatcttctctgtgatcagggggaggcaacagtggagaaacatcacctaggttctgagcccaagtgatatgttaacaaagctttctgttggcaggacccaaaacagagtcacattacctgggtacagtacccagttatgtgtcacaatgaactataagtgcagtctcgaggcagaaaaatggagtcatgtcacttacaaaatgaacctaaatgtaagccagaatgctttttatatgcaggggtaaggcaaataattcacatcacctgggtgctggtcacagtgatatgtaaaagtgctctttttaggcagtctcagacaactttgcttatgtgcacggcccacatatgtcacaatttcctctgtcatcatggcctaaaatggaaagccaaattaTTCAGAAGCTGGAATAACTTTTATATTCTAATCAAACCAAATTGAATATTTAGAAATGTGCTTCCAGTTCCACAAATGTCCTGGCTTTTTGTATGTGAGTCGACACCTCCTGTGAGTTGGGTTGAAGCAGAGGAGTCACAATCTCAACAGTCAGCCAAGAGATTAAAGCTAAAACACCTACAGAAtgagccaaatatatgtcaaaaatactctctgttcctctggcacaggcaggacagtatcatcatcagggtgataggcctcccagtatgcaataattctcactttattgaggtctctggcagaagagtaacatcatctgtgtgcaataggtcaaaatttccctttctgggcatggttcatagaaaagagtagagtcaaaagaccaaaatgctgagctcaccaatatgccactatcccaccatattaaaggcccaggcagcataaaagagtcatatcacttaggtcatggctcagagacatgtaccaatatcaccagtaggcaggactcaggcagaaaataagagtcatatcacctaggtggttctttaattatatgtcacaatataacacatgggcagaaatcaggcagaagagccagagcacctgggtgctgggtcctgatatatgttgcaagttcccttaggatgaaccaagttgaaagagttaattgccttgatgcaagtataacattcgtttcacaatgtcctatgtggaagaggccaaagcattgagctacatcacttacttgataggaccagaaatatgtcacaatctcctccctgaaatattgccctggcaaaagagtgctataatcttagtgccagcctagcaatacgtcactaccacccactgttttcaggacccattccagagatgtcataattatttctgtgggtgtggcccaggcaagaatgtatcatcacttgggttttagatgcagggatatgtcacaatccttactgagagaacagccaagacaggagtatca
q panTro2.chrY                         0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0

a score=61536.000000
s hg19.chrY                7694925 147 +  59373566 catATGTTCAATGGGAAAATCCTCATAGAATACTCCTCAGTATGATTGAAAGAATGTTGTTCAATCAATCAT---TGATAGGTGCACAGTGAAGTAACTTCTGGTTTTAATTGGGTGCTCTCAAAGCTAGGA---TTGAAAACT--CTTGGTTCT
s ponAbe2.chr8           105358553 147 - 153482349 CATATGTTCTATGGGAAGATCCTCAGTGAAGACTCCTCAGTATGATAGACAAAATGTGGTGCAACCAGTCAT---TGATAGATGCACAGTGAAGTAACTTCTGGTTTTCATTTGGAGCTCTCACAGCTAGGA---TTGAAAACT--CTTGGTTGT
q ponAbe2.chr8                                     999999999999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999---999999999--999999999
i ponAbe2.chr8           N 0 C 0
s panTro2.chrY              548516 147 +  23952694 catATGTTCAATGGGAAAATCCTCATTGAATACTCCTCAGTATGATTGAAAGAATGTTGTTCAACCAATCAT---TGATAGGTGCACAGTGAAGTAACTTCTGGTTTTAATTGGGTGCTCTCAAAGCTAGGA---TTGAAAACT--CTTGGTTCT
q panTro2.chrY                                     000000000000000000000000000000000000000000000000000000000000000000000000---000000000000000000000000000000000000000000000000000000000---000000000--000000000
i panTro2.chrY           C 0 C 0
s rheMac2.chr3            61098263 136 + 196418989 -ATATGTTCAATGGGAAAATCTTCAGTGAAGACTCCTCAGTATGATAGACAAAATGTTGTG--------CAT---TGATAGATG--CAGTGAAGTAACTTCTGGTTTTCACTTGGAGCTCTCACAGCTAGGA---TTAAAAACC--CTTGGTTGT
q rheMac2.chr3                                     -999999999999999999999999999999999999999999999999999999999999--------999---999999999--9999999999999999999999999999999999999999999999---999999999--999999999
i rheMac2.chr3           N 0 C 0
s dasNov2.scaffold_67198      1062 134 -      8818 ------------------TTCACATGAGAAGAGGGCTAAGTATTATAGATACATCATAATGTGTTTAATCATCCCTTATTGATGAATGCTGAGGTCGCTTCTAGTTCCCAATT-CAACCCTCAGAGATGGGGAGTGGGAAAACTCACTTTATT--
q dasNov2.scaffold_67198                           ------------------99999977416633577677977765655399999999999999999999995999999999999999999999999999999999999999999-999999999999999999999999999999999999999--
i dasNov2.scaffold_67198 N 0 N 0

a score=258830.000000
s hg19.chrY      7695072 656 +  59373566 AAACTCACATGATGAGGAGTTATATTATGCTATCCTTTTCTGCACATTTGTTTATAGTCAGAGTTGTTTCAACTTGCCAATGAATAGAGTAGAAAATTGTTTCCCTGAGACCTACGCATCTCCCATTCATAGGTTTTTAGGTTGTGCATTTTTCATATTTCTTATAAGATCATGATCACAGAGATCATATTTGTCAAGATAAAGC-TCTGTTGCACAAGGATTATGTGAAGGCGTTTACTACCCATGGCTCAGGGTTCCTTTAGAAGCAGGATGAAGCTCAAAAACTATTACTGAAGCCAGAAAATGAAGAGAGAAGTTAAGGGCTACCCACAGGAAAAAGCAAAGTGCTTCCTTTCACTTTACAAGTGGTCACTGCTTATCCTGACATTAAACTTGCATCTGATCATGATGTGTTTCTTGTTCATCTCTCTTGGTATTCCACTAAATCTGCGTCCAATGAAAAGA-GACCTGGATGAGAGTAGTAAAGACAGTAACAGCATTTTTCTATATATTATGCCTTAGTGAGCTTTGAAGCACATTGAGCAGAGCCTG--AATTCTTCCTCACTTTTGGATAAgttgtgtcaaatttgacactgatgtaaatggtaccaggtttaatatgtcaaaagaagaaactcagaaccagtgaatgagac
s ponAbe2.chr8 105358700 650 - 153482349 AAACTCACATGATGAGGAGTTATGCTATGCTGCCCTCTTCTGCACATTTGTCTACCTTCCCAGTTGTTTGAACTTGCCAAGGAA-AAAGTGGGAAGTTGTTTCCCTCAGACCTACTCATCTCCTTTTCATAGGTCTTTATGTTGTGCATTGTCCAGATTGCTTAGAAGCTCATGATCACAGAGGTCATATTTGTCAAGTGAAAGCTTTTTTTGCACCAGGATTAAGTGAAGGTTTTTACCACCCAGGGTCCATGGTTTCCCCAGAGCCAGGATGGAGTTGAAAAACGATTACTGAAGCCAGAAAGTGATGACAGAATTTGAGGGCTGCCCACAGGAGAAAGCAAAATGCTTCCTTTTGCTTTCCAAGTGGTCACTGCTTATTCTGGCATTAATCTTGCTTCTGACCACGGTATGTTTCTTCTTCATCATTCTTGGTATTCTGCTGATTGTGCATCTAAGGAAAAGA-GC-----ATGAAAGTGGTAAAGAGAACAACTGCATCCTTCTATAGCTGATGCCCTGGTGAGCTTTGAAGCACATTGAGCAGAGCCTG-AAATCCTTCCTCACTATGGGGTAAGCTGTGTCAACTttgactcccatgtaaacggcaccagattcaaggtgtca-aagaagagactcagaaccagtgaatgaga-
q ponAbe2.chr8                           999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999499999999999999999999999999999999999999999999999998999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99-----99999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999-
i ponAbe2.chr8 C 0 I 165
s panTro2.chrY    548663 656 +  23952694 AAACTCACATGATGAGGAGTTATACTATGCTATCCTTTTCTGCACATTTGTTTATAGTCAGAGTTGTTTCAACTTGCCAATGAATAGAGTAGAAAATTGTTTCCCTGAGACCTACCCATCTCCCTTTCATAGGTTTTTATGTTGTGCATTTTTCATATTTCTTATAAGATCATGATCACAGAGATCATATTTGTCAAGATAAAGC-TCTGTTGCACAAGGATTATGTGAAGGCGTTTACTACCCATGGCTCAGGGTTCCTTTAGAAGCAGGATGAAGCTCAAAAACTATTACTGAAGCCAGAAAGTGAAGAGAGAAGTTAAGGGCTACCCACAGGAAAAAGCAAAGTGCTTCCTTTCACTTTACAAGTGGTCACTGCTTATCCTGATATTAAACTTGCATCTGATCATGATGTGTTTCTTGTTCATCTTTCTTGGTATTCCACTAAATGTGCGTCCAATGAAAAGA-GACCTGGATGAGAGTAGTAAAGACAGTAACAGCATTTTTCTATATATTATGCCTTAGTGAGCTTTGAAGCACATTGAGCAGAGCCTG--AATTCTTCCTCACTTTTGGATAAgttgtgtcaaatttgacactgatgtaaatggtaccaggtttaatatgtcagaagaagaaactcagaaccagtgaatgagac
q panTro2.chrY                           0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s rheMac2.chr3  61098399 626 + 196418989 AAACTCACATGATGAGGAGTTATAGTCTGCCAT---------CATAATTGT---------------TTTCAACTTGCCAAGGGAAAAAGTGGGAAATTGTTTCCCTCAGACCTACTCATCTCCCTTTCATAGGTTTTCAGGGTGTGCACTGTCCAGATTGCTTAGAAGCTCATGATCACAGAGGTCGTATTTGTCAAGAGAAAGC-TTTGTTGC---AGGATTAAGTGAAGGTGTTTACCACTCAGGACCCATGGGTCCTCCAGAGGCAGGATG-AGCTTAAAAATCATTCCTGAATCCAGAAAGTAATGACAGAAGTTGGGGGCTGCCCACAGGAGAAAGAAAAATGCTCCCTTTTCCTTTCCAAGTGGTCACTGCTTATTCTGGCATTACTCTTGCTTCTGACCACGATGTGTTTCTTAGTCATCTTTCTTGGTATTCCACTGACTGTGCATCTAAGGAAAAGATGAGATGGATGAGAGTGGTAAAGAGAACAACTGCATCCTTCTATAGCCGATGCCTTGGTGAGTTTTGAAGCACACTGAGCA---CTCGGAAATCCTTCCTCACTATGGGGTAAgttatgtcaaattcgactcccatggaaatggcaccaggttcaagatgtca-aagaagagactcagaaccagtgaatgaga-
q rheMac2.chr3                           999999999999999999999999999999999---------999999999---------------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999---999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999-
i rheMac2.chr3 C 0 I 268

a score=12777.000000
s hg19.chrY      7695728 52 +  59373566 agagtttcattcttgttgcccaggctggagttcaatggcccaatctcaactc
s panTro2.chrY    549319 52 +  23952694 agagtttcattcttgttgcccaggctggagttcaatggcccaatctcaactc
q panTro2.chrY                          0000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s ponAbe2.chr8 105359515 52 - 153482349 agagtttcactcttgttgcccaggctggagtgcaatggcacaattttggctc
q ponAbe2.chr8                          9999999999999999999999999999999999999999999909999999
i ponAbe2.chr8 I 165 C 0
e rheMac2.chr3  61099025 268 + 196418989 I

a score=34328.000000
s hg19.chrY               7695780 106 +  59373566 accacaaaccctgcccaccatgttcaattgattctcttgcctcagccttccaagtagctggaattaaaagcatgtgccaccacacccggctaattt--------tgtattatta-----------------------------
s ponAbe2.chr8          105359567 106 - 153482349 accacaaactccacctcttgggttcaagtgattctcctgcctcagcctcctgagtagctgggattacaggcatgtgccaccaggctcggctaattt--------tgtattttta-----------------------------
q ponAbe2.chr8                                    999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--------9999999999-----------------------------
i ponAbe2.chr8          C 0 I 53
s panTro2.chrY             549371 106 +  23952694 accacaaaccctgcccaccatgttcaattgattctcttgcctcagccttctaagtagctggaattaaaagcatgtgccaccacacccggctaattt--------tgtattatta-----------------------------
q panTro2.chrY                                    000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--------0000000000-----------------------------
i panTro2.chrY          C 0 C 0
s micMur1.scaffold_3418     13275 136 +    124966 acctcaaactc------ctgggctcaagcgatcctactgcctcagcctcccgagttgctgggactacaggcatgcgccaccatgccc-gctaattttttctatatatatttttagttggtaaattaatttatttatatcttta
q micMur1.scaffold_3418                           59996589999------9999899979999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999
i micMur1.scaffold_3418 N 0 C 0
e rheMac2.chr3           61099025 268 + 196418989 I

a score=6125.000000
s hg19.chrY               7695886 47 +  59373566 --agagaggcagcattaccatgttggtcaggctggt---gaaaccccagcct
s panTro2.chrY             549477 47 +  23952694 --agagaggcagcattaccatgttggtcaggctggt---gaaaccccagcct
q panTro2.chrY                                   --0000000000000000000000000000000000---0000000000000
i panTro2.chrY          C 0 C 0
s micMur1.scaffold_3418     13411 44 +    124966 gtagagacggggtctcac--------tcaggctggtttcgaactcctgacct
q micMur1.scaffold_3418                          999999999999999999--------99999999999999999999999999
i micMur1.scaffold_3418 C 0 C 0
e rheMac2.chr3           61099025 268 + 196418989 I
e ponAbe2.chr8          105359673 53 - 153482349 I

a score=28307.000000
s hg19.chrY               7695933 68 +  59373566 caggtgatccacccaccctggcctcccaaagttctgggattacaggcatgagccactgcacatggccA
s panTro2.chrY             549524 68 +  23952694 caggtgatccacccaccctggcctcccaaagttctgggattacaggcatgagccactgcacatggccA
q panTro2.chrY                                   00000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s ponAbe2.chr8          105359726 68 - 153482349 caggtgatccacccacctaggcctcccaaagtggtgggattacaggcatgagtcaccacacacagcca
q ponAbe2.chr8                                   99999999999999994999899999999999999999999999999999999999999999999999
i ponAbe2.chr8          I 53 C 0
s micMur1.scaffold_3418     13455 68 +    124966 tgagccatctgcccgccttggcctcccagagtgctagggttacaggcgtgagccaccgtgcccggccA
q micMur1.scaffold_3418                          99999999999999999999999999999999999999999999999999999999999999999999
i micMur1.scaffold_3418 C 0 C 0
e rheMac2.chr3           61099025 268 + 196418989 I

a score=36405.000000
s hg19.chrY               7696001 119 +  59373566 ----ggccac---------tgccagattttttaggttggaact-tgaacac---taagatgaattttttatatagtatcagt------------------cttcagctatgctaaagtcaagttaacactgtcagttgcatccaccacacaGGC--------------------------------------------------
s panTro2.chrY             549592 119 +  23952694 ----ggccac---------tgccagattttttaggttggaact-tgaacac---taagatgaattttttatatagtatcagt------------------cttcagctatgctaaagtcaagttaacactgtcagttgcatccaccacacaGGC--------------------------------------------------
q panTro2.chrY                                    ----000000---------000000000000000000000000-0000000---0000000000000000000000000000------------------000000000000000000000000000000000000000000000000000000--------------------------------------------------
i panTro2.chrY          C 0 C 0
s ponAbe2.chr8          105359794 116 - 153482349 ----ggccac---------tgctagattttttagcttggaactctgaacac---tcagaagcattttttatatagggtcagt------------------ct----ccatgcccaagtcaagttaacactgttacttgcatccatcatacaggt--------------------------------------------------
q ponAbe2.chr8                                    ----999999---------99999999999999999899999999999999---9999999999999999999999999999------------------99----999999999999999999999999999999999999999999999999--------------------------------------------------
i ponAbe2.chr8          C 0 C 0
s rheMac2.chr3           61099293 120 + 196418989 ----ggccac---------tactagattttttagcttaaaactctgaacat---tcagaagcattttttatacagggtcagt------------------ctccaggtatgcccgagtcaagttaacactgtcagttgcatccatcatacaGGC--------------------------------------------------
q rheMac2.chr3                                    ----999999---------99999999999999999999999999999999---9999999999999999999999999999------------------999999999999999999999999999999999999999999999999999999--------------------------------------------------
i rheMac2.chr3          I 268 C 0
s micMur1.scaffold_3418     13523 203 +    124966 GAACAGACACAATTTGAGATGACAGAGTCCCTTGGAAGGAGAATTCACCACCAGTCAGCTTTATTCTCAATGTA-TATCAATTCGCCTATCCCCTCAATGCTCTGTTAATTTTTAAATTGGGACAATGTGTCCTGCTGCAGATAACACACTGTTGAGCTCCAAAGAATGTTGAGCAGATGCTGAAATTCTCCCTCAGTGAGGGG
q micMur1.scaffold_3418                           99999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i micMur1.scaffold_3418 C 0 N 0

a score=896951.000000
s hg19.chrY      7696120 2250 +  59373566 CGGTTCAGGCAATGGAGATTCTTCTTTCTGAGACTCTAGATTCAAAAAAGTTTTTGCTGTTTCTTGAATAGTTGGTTTGACAGGAGTTTATCTAAAAGGTCTTATGTGTGTGCACATTGCTG-TATGGTTGTCTAAGTTAATGAGATGGCTTCTTAGTTGGCAGCGTCTCTTTCAGCTGCA----------AGTGTATACAGGCTGCTGAGGTGCCCCTTTACCAGATTTTTACTGGGGCATGACATTCTGGGGCCCCAGTTCAACTATTTTCCATGGTGGGACATGCTCAACGAGACCCTTAAATTGTGGTTCA-GGTGAACCGGCTGATGTTGCCCTTTAAAAAACAGAACTGCTTGGTTTATTTCTTATTTTACTTGTCATTCTAACATATCTTTTGGTATGGAGAACAGAAAAGAATGTGAATATGTGACAGAATTCTTCCTAGAGTTGGGGCTATTTATACATGATACTTAAGTGTCAAGGTAGGTTGACAGATCTATCTTCCTGGTGCAGCCTGTGTAGGATAGAGCACTGTGACCCCTATAGCTCAGCTCCTGCAACACTTCAGAGGAATTTC-AAAAACCATAGGATGTGGGGGTTAGAGAAAGAGCTGGTATAAATGGCAAGTTGCAAGTGAAAT----AATTGGAGGCAGGAAGATAACAGAACCTGTTTGGAACAGTATACATACTATTTGCATGCAGCTGAACAGCCAAGCCAGTTCTCTGATTTGGGCTGTGTACCAAGGAATTAACAGGCCCACTTCTGCTCTGGCCACGGTGCTGAACTCTTTGGTTCTAGAACCAAATGTAAGTTCTGG-----------CCTGTTCGGTTTCACAG------GCCAATAGAGTGAGGAGGCCCAGGTAGGCCAACAAATGTGGCTGTGGGTGGGCTTA--CCACACGTGACTGGTTGTGTCTGTGCCTACACTCACAAGGAAGAGGGATCTTCTTCCTCAAGGCAATCCTAGGGAATTTTAATACAAGCCCAGGCAGGTGTCAGGCTTATGGGAGCC-AGTGAAGAAAATAGTTCATGCCTCAGCCCAGTGCTTTTGCCTATCCTGGCTTGTGGCTTTGGGGGCTCAATATAATCATCAGAAAAATGAACAATGAAAGCCCCTCAGTGACTGGCTGTTCACCCCACTTTTACCAGGCCACCACACAGTACCCACCCTACAGCTCCAGGTATAGCCTGTGCTTCAAAATGCTGGGGGATTTCTGGGATGAGTTCAGGGCCCTGAGAGGGTTCTCCCCCACAGGGATCACTCATGCCAACACCTCTGTGTGCACTGGATAGCTCAGCATGTCTGCTATATGCCACCCTTATTACCTGCTCTTGTCAAGCCCATGTCTTCCTGGGTTGGCAAGGGGCACATGCTCACTGAAGTCCATGTGGCCTGTCCATCTTTCCTCCCATGCACAGCCTCAGGGAGCTGTCATCCAGATTTCCTCCTAGATTATGATCTCAGGGGGTAACAACAGCACATTCTTCTCCAACTTATTGACTAGTAAATCTATAGTTCACTTAATGTGCCAAGGTGGGTGTGGGCCTTGATACTCTTGATCTCTTTCCTCTAGTGGGACTTTATTGGGGGTTGCCATCCTGATTTCTTTGTGGAAATAGCCAGCAGGTGAGGCAGAACACAAGGGCCTGGGGCAGACAGGACAGAGCACCT------------------------------------AGGTAGGAGGTCTCAGTGTATTTCCAGGCCCGTTTTCTAAGTCAGTGCCCATATCCCTTTTCTGGGCCTCTAAGAATGGTTTACTCTATCTGCAACCTGCACCCACTGCTCTGTA------------------------------GGTGGTGAGCATCCATTTATCTTTTTGGATTTGATCTTGTCCTTCATTTCCATTGGATGTTCTCCTGGAAGAAATGCACAGGGAATCCTGAGCCTGTGCTGAAGGTTACCTAACAGCCAAAGTCAGTAAGAAGTTTTCAAAAATATAATTACTAGCATTTTCTGCACATTGTTATCTCATAGTTGATTTTGCCACAGAATGTGAAAAAGGAAATATTACAACTTTTATCCTTTCCCTTATTTTAATTAGATCATCATACAAAACTTTTATTTTTCTGAAATTTATTTTTTATGCCAATCATTGAATTTTTGTTTCCTCCTTTGTTCAAATTGTTACCTGTTTTAGAGGCAAAATCTTAAAAA--TATATGCTACAAAAATACTAACAGGTGATAGCAATTTATTTAGAATGTAATTAAGTTTCTTAAATAAGTAAATAATTTCAGTGAACTTAGTTTGCAGTATTTGTATAAATTATTT
s panTro2.chrY    549711 2242 +  23952694 CGGTTCAGGCAATGGATCTTCTTCTTCCTGAGACTCTAGATTCAAAAAAGTTTTTGCTGTTTCTTGAATAGTTGGTTTGACAGGAGTTTATCTAAAAGGTCTTATGTGTGTGCACATTGCTG-TATGGTTGTCTAAATTAATGAGATGGCTTCTTAGTTGGCAGCGTCTCTTTCAGCTGCA----------AGTGTATACAGGCTGCTGAGGTGCCCCTTTACCAGATTTTTACTGAGGCATGACATTCTGGGGCCCCAGTTCAACTATTTTCCATGGTGGGACATGCTCAACGAGACCCTTAAATTGTGGTTCA-GGTGAACCGGCTGAGGTTGCCCTTTTAAAAACAGAACTGCTTGGTTTATTTCTTATTTTACTTGTCATTCTAACATATCTTTTGGTATGGAGAACAGAAAAGAATGTGAATATGTGACAGAACTCTTCCTACAGTTGGGACTATTTATACATGATACTTAAGTGTCAAGGTAGGTTGACAGATCTATCTTCCTGGTGCAGCCTGTGTAGGATAGAGCACTGT--------TAGCTCAGCTCCTGCAACACTTCAGAGGAATTTC-AAAAACCATAGGATGTGGGGGTTAGAGAAAGAACTGGTATAAATGGCAAGTTGCAAGTGAAAT----AATTGGAGGCAAGAAGATAACGGAACCTGTTTGGAACAGTATACGTACTATTTGCATGCAGCTGAACAGCCAAGCCAGTTCTCTGATTTTGGCTGTGTACCAAGGAATTAACAGGCCCACTTCTGCTCTGGCCCCGGTGCTGAACTCTTTGGTTCTAGAACCAAATGTAAGTTCTGG-----------CCTGTTCGGTCTCACAG------GCCAATAGAGTGAGGAGGCCCAGGTAGGCCAACAAATGTGGCTGTGGGTGGGCTTA--CCACACGTAACTGGTTGTGTCTGTGCCTACACTCACAAGGAAGAGGGATCTTCTTCCTCAAGGCAATCCTAGGGAATTTTAATACAAGCCCAGGCAGGTGTCAGGCTTATGGGAGCC-AGTGAAGAAAATAGTTCATGCCTCAGCCCAGTGCTTTTGCCTATCCTGGCTTCTGGCTTTGGGGGCTCAATATGATCATCAGAAAAATGAACAATGAAAGCCCCTCAGTGACTGGCTGTTCACCCCACTTTTACCAGGCCACCACACAGTACCCACCCTACAGCTCCAGGTATAGCCTGTGCTTCAACATGCTGGGGGATTTCTGGGATGAGTTCAGGGCCCTGAGAGGGTTCTCCCCCACAGGGATCACTCATGCCAACACCTCTGTGTGCACTGGATAGCTCAGCATGTCTGCTATATGCCACCCTTATTACCTGCTCTTGTCAAGCCCATGTCTTCCTGGGTTGGCAAGGGGCACATGCTCACTGAAGTCCATGTGGCCTGTCCATCTTTCCTCCCATGCACAGCCTCAGGGAGCTGTCATCCAGATTTCCTCCTAGATTATGATCTCAGGGGGTAACAACAGCACATTCTTCTCCAACTTATTGACTAGTAAATCTATAGTTCCCTTAATGTGCCAAGGTGGGTGTGGGCCTTGATACTCTTGATCTCTTTCCTCTAGTAGGACTTTATTGGGGGTTGCCATCCTGATTTCTTTGTGGAAATAGCCAGCAGGTGAGGCAGAACACAAGGGCCTGGGACAGACAGGACAGAGCACCT------------------------------------AGGTAGGAGGTCTCAGTGTATTTCCAGGCCCCTTTTCTAAGTCAGTGCCCATATCCCTTTTCTGGGCTTCTAAGAATGGTTTACTCTATCTGCAACCTGCACCCACTGCTCTGTA------------------------------GGTGGTGAGCATCCATTTATCTTTTTGGATTTGATCTTGTCCTTCATTTCCATTGGATGTTCTCCTGGAAGAAATGCACAGGGAATCCTGAGCCTGTGCTGAAGGTTACCTAACAGCCAAAGTCAGTAAGAAGTTTTCAAAAATATAATTACTAGCATTTTCTGCACATTGCTATCTCATAGTTGATTTTGCCACAGAATGTGAAAAATGAAATATTACAATTTTTATCCTTTCCCTCATTTTAATTAGATCATCATACAAAACTTTTATTTTTCTGAAATTTATTTTTTATGCCAATCACTGAATTTTTGTTTCCTCCTTTGTTCAAATTGTTACCTGTTTTAGAGGCAAAATCTTAAAAA--TATATGCTACAAAAATACTAACAGGTGACAGCAATTTATTTAGAATGTAATTAAGTTTCTTAAATAAGTAAATAATTTCAGTGAACTTAGTTTGCAGTATTAGTATAAATTATTT
q panTro2.chrY                            00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000----------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--------0000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-----------00000000000000000------00000000000000000000000000000000000000000000000000000000--000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000------------------------------------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000------------------------------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s ponAbe2.chr8 105359910 2272 - 153482349 tggttCAGGCAGTGGACATTCTTCTTCCTGAAACTCTACAGTCAAAAAATCTTTTGCTTTTTCTTGAATTGTTGGGTTGACAGCAGTTTATCTATTAGGCCTGATGTGTGTGCACACTGCTGATATGGATGTCTAAATTTACAAGATGGCTTCTTAGTTGGTAGGGTCTGTTCCTGTTACA----------AGTGTGTACAGGCTGCTGAGATGCCCTTCT-CCAGATTTTC-TTGGCCCATGACACTCTGGGGCCCCAGTTCCACTATTTTCCAAGGCGGGGCATGCTAAACCAGACCTTGAAGTTGTGGTTCAGGGTGATCAGGCTGAGGCTGCCCTTTAAAAGGCAGAACTGCCAGGTTTGTATCTTATTTGCCTTGTCATTCTAACATGTCTTTTGGTATGGAGACCAGAAAAGAATCTGAGCATGTGACAGCCCTCCTGCTAGAGTTGTTACTATTTATACATGACTCTTAAGTGTCAAGGTAGGTTGAGAGATCTATCTTCCTGGCACAGCCTGAGTAGGCTAGAGTACTGTGACCCTTAATGCTTGGCTCATGCAGT-CTTCAGAAGAATTTC-AAAAACCATAGGATGTGGTGGGTAGAGAAAGAGCTGGTACAAATGACAAGTTGCAGGTGAAATGACAAGTTGCAGGCAGGGAGAGAATGTGACCTGCTTGGAACAGTACACACATTGCCTTGGTGCAGCTGAACAGTCAAGCCAGTTCTCTGATTTGGGACTTGTGCCGTGGAATTAACAGGACCACATCTGCTCTGGCCTAGGTGCTGAACTCTTTGGTTCTAGAACCAAATGTGAATCCTGGACTCTGGAATTCCCATTGGGTTTCACAGGCCAGTGCCAGTGAAGTGAGGAGGCCCAGGTGGGCCCACAAAAGTGGCTGTGGGTGGGCTTA--CCACACAAGCCTGGTTGCTTCTATGCCTACACTCACAAGGAGGAGGAATTTTCTTCCTCAAGGCAAGCCCAGGGAGTTTTCAGGGAAGGCCAGGAAAGTCTGACGCTTATGGGAGCC-AGTGAAGAAAAAAAGTGATGCCTCAGCCCAGTGCTTTTGGCCCTCCTGGCTTGTGGCTTTGGGGGCTCAATTTGCTCATCAGAAAATTGGGCAATGAAAGCCCCTCAGTGACTGGCTGCTCACCCCACTTTTACCAGGCCATTGCACAGTGCCCACCCTGCAGCTCCAGGTACAGCCTGTGCTTCAAAAGGCTGGGGGATCTCTGGGCTGAGTACAGTGCCCTGAGAGGGTTCTCCC------------CTCATGCCTACCCCTCTGTGCCCACCTGACAGCTCAGCATAT-GGCTGTATGCTACCCATATTCCCTGCTCTCATCAAGCCCATGTCTCCCCGGGTAGGCTAGGGGCACATTCTCATTGAAGCCCAGGTGGCCTCTCCATCCTTCCTCCAATGCACAGCCTCAGGCAGGTGCCACCCAGGTTTCCTCCCAGAATGTGATCTC-GGGGGTCACAG------------CTCTAACTTATGGACTAGATAATCAATAATTCACTTAATGTGCCAAGATGGGTGTGGGCCTTTACACTTTTGATCCCCTTCCTCTAGTGGGGCTGCATTGGGGGTTGCCATTCTGATTTCTTTGTGGAAAAAGCTAGCAGGTGAGGCAAGACTCAAGGGCCAGG----AACAGGACAGAACACCTAGGCTGGCCTCCCCCTGGGCCCTCTGAGGCCCCTGCAGGTAGGAGGACTCAGTGGAGTTCCAGGCCC-TTTTCTAGGATGGTGCCCATAGCCCCTTCCTGGACATCCAAGAAAGGCCTACTCTTTCTGCAACCTGCACCCACTGGCCTCTA------------------------------GGAGGTGAGCATTGATACATCTTTGTGGACATGGCCTTCTGTTTCATTTCCATTGGATATTCTCCTGGAAGAAATGCCTGGGGAATCCTGGGCCTGTGCTGGAGGTTCTCTAAGTGGCAAAGTCAGTAAGGGAGTCTCAAAAATGTAATTAATAGTGTTTTCTTCACATTATTATCTCAGGGTTACTTTTGCCTAATAATGTGTAAAAGCAAATATTATGATTTTTATCCTTTATGTTATTTTAATTAGGTCATTATACAAACCTTTTATTTTCCTGAAATTTA-TTTCCATGACAATCATTGAATTTTTGTTTCCTTCTCTGTTCATCTTGTTACCTGTTTTAGAGGCAAAATCTTAAAAA---AAGTGCTACAAAAATAATAACAGATGACAGCAATTTATTTAAAATGTAATTAGATTTCTTAAATAAGTAAAAAATTTCAGTAAACTTACTTTATATTACTTGTCT-GATTATTT
q ponAbe2.chr8                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------999999999999999999999999999999-9999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999------------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999------------------------------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999
i ponAbe2.chr8 C 0 C 0
s rheMac2.chr3  61099413 2237 + 196418989 TGGTTCAGGCAGTGGAGGTTCTTCTTCCTAAGA--CTATATTCAAAAAAGTATTTGCTTTTTCTTGAATCATTGGGTTGAC---AGTTTACT--AAAGGCCTGAAGTGTGTGCACATTGCTGGTACAGTTGTCTAAGTTAATGAGATGGCTTCATAGTTGGTAGGGCCTGTTCCCGTTACAGGTGTGACTGGGTGTGTACAGGCTGCTGAGGTGCCTCTTTTCCAGACTTTCATTGGACCATGATATTCTGAGGCCCCAGTTCCACCATTTTCCAAGGTGGGACGTGCTGAACCAGTCCCTGGAATTGTGGTTCAAGGTGACCAGGCTGCGGCTGCTCTTTAAAAGGCAGAACTGCCAGGTCTGTGTCTTATTTTCCTTGTCATTCTAACGTATCTTTTGATATGGAGACCAGCAAAG--TCTGAGTATGTGACAGCCCTCCTGCTAGAGTTGGTACTATTTATACATGACTCTTAAGAGTCAAAGTAGGTTGAGAGATCTCTCTTCCTGGCACAGCCTGAGTAGGCTAGAGTACTGGGACCCTTAAAGCTTAGCTCATGCAGT-CTTCAGGGGAATTTCAAAAAACCATAGGATGAGGGGG-TAGAGAAAAAGCTGGTATAAAT---AAGTTGCAGGTGAAAT----AATTGGAGGCAGGAAGAGAACGGGACCTGCTTGGAACAGTACACACACTGCCTGGGTACAGCTGAACAGTCAAGCCAGTTCTCTGATTTGGGCCTTGTGCAGTGGGATTAACAGGCCCACTTCTGCTCTGGCCTGGGTGCTGAACACTTTGGTTCTAGAACCAAATGTGGATTCTGGACTCGGGAATTCCAGTTGGGTTTCACAG------GCCAGTGAAGTGAGGAGGCCCAGGTGGGCCCACAAAAGTGGCTGTGGGTGAGCTTACGCCACACATGACTGGCTGCTTCTATGCCTACATTCACAAGACAG----ATCTTCTTCCTCAAAG--------------------GCATGCCCAGGGAGATCTGAGGCTCATAGGAGCCAAGTGAAGAAAAAAGGTGATGCCTCAGCCCAGTGCTTTTGCCCTTCCTGGCTTGTGGCTTTGGGGGCTCAAAGTGCTCATCAGAAAAATGGGCAATGAAA----------GACTGGCTGCTCACCCCACTTTTACCAGGCGACTGCACAATGCTCACTCTGCAGCTCCAGGTACAGCCTGTGTTTCAAAAAGCTGGGGGATCTCTGGGCTGAGTTCAG--------GAG-----TCCCCCTCAGGGACCCCTCCTGCCTACCCCTCTGTGCCCACCTGACAGCTCACCATGTCTGCTGTATGCCACCCTTATTGCCTGCTCTTGCCAAGCCCATGTCTCCCTGGGTTGGCTGGGGGCACATGCTCACTGAAGCCCAGGTGGCCTGACCATCCTTCCTCCAATGTACAGCCTTAGGCAGGTGCCACCCAGGTTTTCTCCTAGAATGTGATCTCAGGGGATCGCAGCAGCACATTCCACTCTAACTTACTGACTAGTTAATCAAAAAGTCACTTAATGTACCAAGGTGGGTGTGGGCCTTGACACTCTTGATATCCTTCCTCTAGTGGGGCTGCACTGGGGGTTGCCATCCTTATTTCTTGGTGGAAAAAGCTAGCAGGTGAGGCAGGACTCAAGCGCTAGG----GACAGGACAGAGAACCTAGGCTGGCCTCACCCAGGGCCCTCTGTGGCTCCTGCAGGCAGGAGGGCTCCATGGAGCTTCAGACCCCTTTTCTAGGATGGTGCCCATAGCCCCTTCCTGAATCTCCAAGAAGGGCCCACTCTTTCTGCAACCTGCACCTActggtctctaaatggaaggtgagcatctggtctctaaatggaaggtgagcatcCATTTATGTTTGTGGACATGGCCTTCTGCTCCATTTCCAT---------------GAGAAATATCTAGGGAATCCTGGGCCTGTGGTGGAGGTTCTCTAAGTGCCAAAGTCAGTAAG----TCTCAAGAATATAATTAATAGTATTTTCTGCACATTACTATCTCAGGGTTACTTTTGCCCAAAAATGTGTAAAAACAAATATTAAGATTTTTATCCTTTACATTATCTTAATTAGGTCATCATACAAACCTTTTATTTTCC----------------TCCCAATCATTGAATTTTTGTTTTATTC--TGTTTAAATTGTTACCTGCTTTAGAGGCAAAAACTTAAAAAAAAATACACTACACAAATACTAACAGGTAACAGCAATTTATTTA-AATGTAATTAGATTCCTT---TAAGTAAATAATTTAAGTAAAC--AGTTTATATTACTTGTATAAATTATTT
q rheMac2.chr3                            999999999999999999999999999999999--9999999999999999999999999999999999999999999999---99999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999-9999999999999999999999---9999999999999999----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999--------------------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--------999-----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------------99999999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------9999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999---9999999999999999999999--999999999999999999999999999
i rheMac2.chr3 C 0 C 0

a score=19252.000000
s hg19.chrY                7698370 80 +  59373566 ----TCTATCTTATCCTCAATCTTAAAAAAAAGTTATCTTGGTAAGCAAATC-AAAATTAACAGATTTTGT--AAACAGACAACTTA
s panTro2.chrY              551953 80 +  23952694 ----TCTACCTTATCCTCAATCTTAAAAAAAAGTTATCCTGGTAAGCAAATC-AAAATTAACAGATTTTGT--AAACAGACAACTTA
q panTro2.chrY                                    ----000000000000000000000000000000000000000000000000-000000000000000000--00000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105362182 80 - 153482349 ----TACATCTTATCCTACATCTT-AAAAAATTTTAGCTAGGTATGCAATTCAAAAATTGACAGATTTTTT--AAATAGGCAACTTA
q ponAbe2.chr8                                    ----99999999999999999999-9999999999999999999999999999999999999999999999--99999999999999
i ponAbe2.chr8           C 0 C 0
s rheMac2.chr3            61101650 81 + 196418989 ----TACATCTCACCCTCAATCTTAAAAAAAATTTAGCTAGGTATGCAATTC-AAAATTGACAGATTTTTTTAAAATAGGCAACTT-
q rheMac2.chr3                                    ----999999999999999999999999999999999999999999999999-999999999999999999999999999999999-
i rheMac2.chr3           C 0 C 0
s felCat3.scaffold_76377       405 38 -      1407 tctgtctctctctctctcaaaaataaacaaacattaaa-------------------------------------------------
q felCat3.scaffold_76377                          99999999999999999999999999999999999999-------------------------------------------------
i felCat3.scaffold_76377 N 0 N 0

a score=188172.000000
s hg19.chrY                 7698450 377 +  59373566 AAAACATTTT-TTGGACATGTTGGGTAATG-TAATTCTCAAATATTTTATCTTAGAAATCAACACACTTGACAATTGATATTCTTAGTGTCTATAAAAGTGACATTATGAATATGC--TTTTATACTTGACAAAAATT-------AAAAAAAGTATTCTAGTCTTCCTCAGTAAAACTT--AAAGATTATACAAATAAGATTAAATATACCAGAAAAACTGAATTAACCAGAAAAACTGAAACACATTCATTCA-------CTTTATCTTTCAGTATCTGATAATTAGCTGATGTTATGACATTAAGAATCTGCTTGAGTAAAGAAATAAGGCCAACCAGCTCTTGTGAAAGAATCATTAAAAATATACGGAACAAACATATCATGTATATTGTTTT
s speTri1.scaffold_130907     44473 364 -     46901 --aatattttattataCATGT----------TAATTCTCAAATATTTAAAATTAGAATTCAAGGAACTAGACAACTGCTATTCAGAACATCTATGAAATTG-TATTACTATCTTGTTTTTTTATGGTTGCTGAAAATAAGGGA--GAAAAATCTATTCTGGTTTTCAATAGTAAAGCTCAAAAAGGTTCTAGAAATGGGATTAAATTTAC--------TT---TTAGCCCTGAAAACTAAAA-ATAATAATTTACCAGGTTCTTTATCTTTCATCATCCCCTGGTAA---GATTTTAAGAGGTTCAGAATCTGTTCCAACATAGAAGTAAGGCCACCTGGTTTTGGTAGAAGAATCACTGAGACTATACAGGAGAGACTTGTCATCCACATTAT---
q speTri1.scaffold_130907                           --9999999999999999999----------9989999999999999999999999999999899999999999999999999999999999989999999-99999999999999999999999999999999999998999--99999999999999999999999999999999999999999999999999999999999999999--------99---9999999999999999999-99999999999999999999999999999999999999999999---99999999999999999999999999999899999999999899999369999779989994212111111113898989999999887626743791111244---
i speTri1.scaffold_130907 N 0 N 0
s panTro2.chrY               552033 377 +  23952694 AAAACATTTT-TTGGACATGTTGGGTAATG-TAATTCTCAAATATTTTATCTTAGAAATCAACACACTTGACAATTGATATCCTTAGTGTCTATAAAAGTGACATTATGAATATGC--TTTTATACTTGACAAAAATT-------AAAAAAAGTATTCTAGTCTTCCTCAGTAAAACTT--AAAGATTATACAAATAAGATTAAATATACCAGAAAAACTGAATTAACCAGAAAAACTGAAACACATTCATTCA-------CTTTATCTTTCAGTATCTGATAATTAGCTGATGTTATGACATTAAGAATCTGCTTGAGTAAAGAAATAAGGCCAACCAGCTCTTGTGAAAGAATCATTAAAAATATACGGAACAAACCTATCATGTATGTTGTTTT
q panTro2.chrY                                      0000000000-0000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000-------0000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000-------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s ponAbe2.chr8            105362262 384 - 153482349 AAAACATTTTATTGGATATGTTGGGTAACA-TAATACTCAAATAGTTTATATTAGAAATCAACATACTTGACAATCGATATTCATAGTATCTATGAAAGTGACATTATGAACATGC--TTTTATAGTTGCAAAAAATTTAGGTG-AAAAAATCTATTCTGGTCTTCAGTAGTAAAACTT--AAAGATTACAGGAATGAGATTAAATTTACCGG-----CTAAATTACCCACACAAACTGAAACAGATTCATTTACT-TGTTCTTTGTCTTTCAGTATCTGATAACAAAGAAACTTTACGATGTTCAGAATGGGCTTCGGTATAGAAATAAGGTCAAACAGCTCTTGTAAAATAATCATT-AAAATATACAGAACAAACCTATCATGTATATGATTTT
q ponAbe2.chr8                                      999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999999999999999-9999999999999999999999999999999999--99999999999999999999999999999999-----99999999999999099999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999
i ponAbe2.chr8            C 0 C 0
s rheMac2.chr3             61101731 369 + 196418989 --AACATTTTATTGGACAAGTTAGGTAATATTCATTCTCAAATATTTTATCTTAGAAATCAACACACTTGACAATTGATATTCATAGTATCTATGAAAGTGACATTCTGAACGTGC---TTTATACTTGCCAAAAATTTAGGAGAAAAAAATCTATTCTGGCCTTCAGCAGTAAAACTT--AAAGATTAAAGAAATAAGATTAAATTTACTGG-----TTAAATTACCCA-AAAAACTGAAACAGATTCATTTACT-TGTTCTTTATCTTTCAGTATCTGATAATGAACAGATTTTAAGATGTTCAGAATCTGCTTCAGTATAGAAATAAGGCCAAACAGCTCTTGTGAAAGAATCATT-AAAATATACAGAACAAACCTATCA-------------
q rheMac2.chr3                                      --999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999-----999999999999-9999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999-------------
i rheMac2.chr3            C 0 I 114

a score=943528.000000
s hg19.chrY      7698827 10293 +  59373566 TAAATATCACAAAatttgcatagaggtgtttatagtattctctgatggtagtttAATTAACCAGAAAAGCTGAAACAGATTCATTCACTTTATCTTTCAGTATCTGATAATGAGCAGATTTTTTGATATTAAtgaaatgcctaaccttgtttttactctaactcattactttgaattttgtcctgcttgtctctttaatcacctatccttgcttctcatgtaaataagactctctgtagctgggaaggccagacaaactccaactgaccccttaatttacaagacactaagggctcctttcccaacccccttttgtaaggagttggcctgggtaaacagatcctcagcatttcaaaggagtccaattaactgataaggtactaacaccaacaatgtatgaagttcccaggatttttctcaaagagataacaacataaaaccttgagttcatgtcttctatagactctatatctaattataatgaaagatttagaaccttgcacctggtacctttgctcttcttgtaaccatttgtcttttaagtggtttatctctctgtaaccattttgcttcttttgattcttgcatgtttttacttctgtagaattattgcatttgagtccccctccccttcctaaacctaggtataaaagttaatcaagccccttcctcggggccgagagaattttcagcattagccatctctttggccgccagcttaataaaggactcttaattcgtctcaaagtgtggcata-ttttttaactcgcttggatacaacataatggaggtcccagtgagaaattaactccactgggtgagagccggtctcactctgggctcccccggaaggacggctggcttggatggggggcgccacctgaggaaataatttttaaggtcccagaagagtaactgccttccggaggagagcggatcgaccaccgtgtcattgccctaaaattcaacatctgagtcctcagcttctgaccccggggtcaggtaagtcagatttgacttcgtttctggtaagaggggagtggccctgatgagggcgtccctcttttgactcagcctgttactctaggacactagtgggttgagccttggttttctggtaggtgcttttgtatcttggtttgggtaggaagtggtcctgacaaggaccctccactgacttagctcagggcccaggaggcgggagctaagccttggtttccggaagaccggactctcgatctctctctctctttctctcttgtctatcttacatccttctgttgttcaggtttcttggacaatctctgggaaagaaaaggaagaaaaaaagagaaaaaaattgttataaactctgtgtaaatggtgtgtgactgtgggaggacaaggggttgcatttgtcttccagtttgtagctctatggtgaaagctacagagttcaagtgggccctcacctgcggttccgtggcgacctcctaaggcttaaggcagcaccgggcatagctcgatctgagccaggggtttataccagcctgtcgatgctaagaggagcccaagtcccctctgggggatcagccaggcgggcatctgaatgacagcatcacgggaactccttcccttgtctgtctaataaagaaggtaaaaaagggaaaactgtcataattgtttacatgccctagggtcaattgtttgttttatgtttattgtttttttcagtgtctattgtcttgtttaatagttgtcaaggtgttatatgtcaggacatcgatattgtccatgaggtctgggtaaaaatttcttcaaggaccttagtgctgcttttttgtcacaagaggttaaatttctcatcaatcatttaggctggccaccacagtcttgtcttttctgtcataaacaagtaaggtgttgttatggaaaagagtgtggagaacattcacctgatcggaatttctggcaccattaaggttgcaggtatttagattgtcataccccacgtcctagtgattggtcctcttgtaaactgaactggtggtggattcaaaacagccaccttgcagaccttcttgctgatctcttttgttattttgtaacttttcctgtgcccttgaataagaccttgtgtagggaaacctacgaccgtcatgctttacttcgtttagactcctattctgttcccctgtggctacgctctcaccttaaggatgatctgagtggtccttttccccctcatccttgccccctaccccatgcatcttgttttccagtgtgacagcaagttcagcatctccaagacttggctctgctctcactccttgaacccttaagggaaaaagctgaatttgaactgtttgcttttgaatcgtggagacatcaaaaatatctaggatataggtctagaggaagaggaagagggagaatgcctagctcgaaccgtcccaggagaccttgggttgacccctaatccccctccctcaatctaaaagctacagaaatttggcaagtagtattagtttttgtggtttttctgttgttcttcctggtcatgttaattctgtttttccgacactccagccccccagggaaagaatttctctgcccgtgttggatctgatatccctgcttgagactttgctaaattgcctttaaataataaaaataataataaaatgggaaacacttcctcccagccctataaagtttggagccctctccagggtatgctgaaaaaattttctcttggtttctcagaggactatggagtccgccttagaaaaggcaagctccagacactctgtgaactagaatggccaaagtttggatttggatggccctctgaagggtcattaaatcctatcattgttcaaggcatgtggcgagttgttaccagaactcccagccaccctgatcagtttccatatatagatcaatggttaagtttggttaaaaatcctcctccatggctctgttcatgtgcctttcacaactccacctccaaaatcctcctgagccaggacgcatttttgcctcgaccctcagctgattcagctccccctgttttgcctccctatgaagaagaggagagtctccctcacccagttccaccaccttacaaccaacctgcccctctagcatcttcccatgtctcttccacgacatcccctgtgggctcaccaccctttgcctctcagctgtgactgcagcaggaggaagcagcccctctactgccactgagagaggcacaagtccctccaggggatgaacactcagccccctccctggtttatgccccttttcctacttctgacttgtataattagaaaaatcataatcctcccttctccgaaaagcctcaggctttgacctcactgaaggagtccatactgcagacccattgacccacctaggttgactgccaacagctccttttaactctctttatctctgaggagagggagcatatccaaagaaagaccagaaagcacttccttgcatcagccggcaggcctgaggaggaagctagagacctcctggaggaggtctttccctccacccagcctaattgggacacacattcctcaggtggaaggagagctttggacgattttcactggtatctccttgcaggtattaaaagagccacttggaagcccataaacttgtctaagacaactgaagctgtccaggggcctgatgagtcaccaggagtgtttttagaatgtctccaggaggcttattgaatttataccccttttgaccccatggctcccgagaatagctgtgctcttaatttggcatttgtggctcaggcagccccagatattaggagaaaactccaaaaactggaaggatttgctaggatgaacatcagtcagcttttagaaatagcccagaaagttattgaaaaccgagaatttgaaaaacaaaaacaagcaacacaggcaactgaaaaagccgctgataagccatgtaaaagacaagcaaaaatcttggaaaccgctatccaagagggcaaaaaggaaaggctcctattccagaagattgaccaaggaccctcgggttcccaccagaaaaataaaag--aggtgaacaggcccctctaggaaaagaccaatatgcctattgcaagcagactgggcattggaaaaaggagatccccctgctgccaaaagaaaagtcagaaaacaaaaagattctcaccctgcctgcaacagaggagcctgataattgatggggccagggctccctcactcttggcccccaggatcccatagtaactgctacagtggaggaccagcctgtacgtttcctagtagacactgaggcagaacactcagtactgcagactcccttgggcagtgtctcaaataaaaaaaataactgtacaaaggcaactggagctattcaagagtaccctgtcacacgctcccgagaagtaaacttgggacagaaaagagtgacacactcttttctggtggttccagagtgtccttttcctttatccttggacgagacctgctccataagttacaggcctcaatctccttttcagctcagcatgctcatctcacactaggaaatgaaacttccccaactgcccaactcttgctaactacctatctgtcagaagaataccttctggttttaccatcacaatcaccggaggaaaatactaatactcttttgttggacatacagacattttttccccaagtttgggccgagtcaaaccctcccagactggctaaacaccatctgccagaggttgtagaattcttggctactgccatactggtccaggtaaagcaataccccatgagtcagcaggctagagaggtgattaatccccacattcaatgactgttacaagctggcatacttacaccatgtcagtcggcctgtaacacaccatttttgccggtccagaaacctgggacaaatgattaccagccagtacaatacgtgagggaagttaataaatggactgttattgtccatccaaccatccctaatccttatactctactcagcctgctcccaccagaacatacagtatgtactgttcttgacctgaaagatgctttctttgcttttcctctggcccccaaaagccagcctatttttgcaattgaatggacagatccaagatcaggagacactacccagctgacttggactgagttacct--------------------caccctttttggggaggctcttcggcaagatcttatacccttccgagctagtcaccctaactgtactcttcttcagtatgtagatgatattttaatagctactgaaactatggacagttgtctacaacacacaagggacctgctctacctccttcaggagctcaggtatggagtctcagccaaaaaggcccaactttgtcttgccagagtgtcctacctggggtacgagataaaccaaggaaacagggcactcaccagtgcccggaaagaagccatcctgcgaatccccactcccaccaccaagagaagggtacgcgaattactgggagccatgggatactgtcatctctggatattgaggtttgcagagtttgcaaagcctttgtatactgctacaagaggtaatggcccactgatttggacagacactgaggaacagggttttcaaaatctgaaaaaggctttaactgcagcccctgctttagccctcccaaatatctcaaagccttttcatctgtttgtccatgagagccagggagttgctaaggggttgcttactcagactttaggaccttggagacgcccagtggcttatttatctaagaagctggatcctgtggcctcaggatggccaagttgcttgcaagacatagtggctacagcaagcctagtccaagaaactgataagttaactctaggccagaatttaacccttatggctcctcatgctgtagagattttactacaaagtgcttcaggtaaatgtatgtcaaatactcgcattttacaatatcagagtttactgttggatcagcctcacttgactttctctcccacaaggtgtttaaatcctgctacactactctcagatccagattctaatattcctgtccatgactgtcaggagctgttagaaactatcaaaactggcaggccagatcttcaagatgtgcccctgaaaaaggcggacgccaccgtgttcatggacagcagaagttccctcgagcaggggatacaaaaagccagtgcagctgttaccacagcgaacacctcagcgcagaaagctgaattaatcacccttactcaggctctccgatggggtaagaataaacgtattaacatttacactgacagcaggcatgctgttgctactgtgcatgtacctggagccatctaccaagaacgggggttactcacttcagccggaaaaattatcaagaacaaagaggaaattctagccctgcttgaagccatgtggttccctcagcaggtggctgtaatccattgtaaaggacatcacaaagaaaacacggccattgcctgcggtaaccaaaaagctgattcagcacctcaggaagtggcacggtcttcagtttggcccataaacctgctgccagcagtttcttttccacagccagatctgcctgacaaccctgcatactcagcagaagaagaaaaattggcttcacatcttagagcaaataaaaatcagaaaggttggtggattcttcctgactctagaatcttcataccccaagctcttggagaaactttagtcagtcatctacattataccacccatttaggtgggacaaaattagcccacctcctccagagctgttttaagatccctcatctacaaagcctaacaaatcaaccagttctctggtgcacagcctgtgcccaggtaaatgccaagcaaggtcctaaacccagcccaggtcaccatctccaaggaaactcaccaggagaaaagtgggaaattgactttactgaagtaaatccacacggggctgagtacaaataccttttagtattaatagacaccttctctggatggactgaggcattcgctaccaagaatgagactgctaacacagtagttaagttcttagtcaatgaaatcatcccccaatatgggctgcctgctgccatagggtctgataatggacctgctttcacctcatccatagctcagtgagtcagtaaggcattgaacattcagtggaagctccatggtgcctatcgaccccagagctctagacaggtagaaagcatgaaccgcaccctaaaaaacattcttacaaaattaattctagagaccggtgaaaattgggtaagtctcttcctttagccctatttagagtaaggtgcaccctttatcaggctgggttctcatcttttgaaattatgtatgggcaggcaccacgtatcctgcctgagctaaaagatgcccatttagcagaaatatcacaagctaatttattgcagtacatacagtctctccaacaggtacaagagatcttctgccacttgttcaagaagcccatcccagtccagttcctcaccaga-agggctctgccgttcgttccagcccagtgacctagtgtttgttaaaaagttccagagagaaggactaactcctgcttggaagggacctcacactgtcatcctcatgacgccaacagctctgaaggtggatggaattcctgcttggattcatcagtcccacatcaaaaaggacaacaaagcccaaacagaaacatgggtccccaagcctgggtcagagcccttaaaactgcacctgagtggggtgaaactgttagattaattctttttatttacttcttctgtttatccttgcctgtaatgtcttctgtgccttcctactccttcctcctcacctctttcacaacaggacgtgttttcaccaatgctacttggaagtctggtacctccaaggaagtcatctttgcaaatgacttatgtatactgttcccacaactggctcatacccacaaagagcataacaacctgccagtcatgggagcaggaagtgtcgaccttgcagcaggattttgacactctgggagccaagccggatgtggaagctgcaaagctgctgaaaaaggactccaaaatttgacttttacctctgtcctcgaaatcaccctgatgctagctgtcgagatacttaacagttcttctgcccagattggacatgtgtaactttagccacctactctgtgggatcaactagatctccaactctttcaataagtcgtgcttctcatcccaaatcatgttctaaaaataactgtaatcctcttaacataattgtccatgaacctaattcagctcaatgatattatggtatgtcatggggattaagactttacatcccaggattcgatgttggaactatgttcaccatccaaaagaaaattttggtttcctgaagcccacctaagccactcgggcctttcactgatctaggtgaccctacgttccaaaaatgccctgacaaagttgatttaattgttcctccaccattctcagttcctaagacccagctgcaaagacaataactccaacccagtcggatgtctatacttggtagagtacataatttccttaacctcacccagactaaactagcccaggattgttgactatgtttaaaagcaaaacccccttattctgtaggattaggagtagaggtgacacttaaaagtggtcctttatcctgtcacacatgacctcgtgctttcacattaggagatgtgtctggaaatgcttcttgtctaattagtactgggcatgacttatctatttctccttttcaggatgtttgtaattagtctctgcttactcccatgaggatctcagtctcttaccaagcacctaacaaaacctggctggcctgcacctcaggtctcactcgccgcattaatggaactgaaccaggacctctcttgtgtgttctggttcatgttcttccccaggtatacgtgtacagtggatcagaaggacaactcctcatcgcttccctggaattatatcccaggctacaccaagctgccccactactgtttcctctattagctgttctcagcatagctggatcagcagacattggcatggctgccctggttcagggagaaactggactaatgtccttgtctcaacaggtagatgctgatttaaataaccttcagtctgccatagatatactacattctcaggtagagtctctagctgaagtagtgcttcaaaaccgccgaggtctagatctgctgttcctctctcaaggaggattatgtgcagctctaggagaaagctcttgtttttacaccaatgaatctggactcataaaagataaactccaaaaagttcaagaaaatctagataggtgacaacaagaatgagaaaataacacaccctggtatcaaagcttgttcaactggaacccttggctaactactttaatcactgggtaagctggacccatcatcatcatattattgagtttgatttttgggccttgtatattaaactggttccttaattttgtaaagcaatgcatagactctgtcaaacttatgtttctaagaactcaatataacccccttgctgtaactgaagaatcaacgatttgattcccctaaaacacaagtggggaaatgaaatgcctaaccttgtttttactctaactcattactttgaattttgtcctgcttgtctctttaatcacctatccttgcttctcatgtaaataagactctctgtagctgagaaggtcggaccaactccaattgaccccttaatttataagacactaagggctccttacccaacccccttttgtaaggagttggcctgggtaaacagatcctcagcatttcaaaagagcccaagtaactgacaaggtactaacaccaacaatgtatgaagttcccaggatttttctcaaagagatgacaacataaaacctggagttcatgtctggcatagaccctatatctaattataatgaaagatttagaaccttgcacctactaccattgctcttcttgtaaccatttgtcttttaagttgtttatttctctgtaaccagtttgcttcttttgattcttgcatgtttttacttctgtagaattattgcatttgagtccccctcctcttcctaaacctaggtataaaagttaatcaagccccttcctcggggccgagagaattttgagcattagccatctctttggcgcccagcttaataaaggactcttaattcatctcaaagtgtggtgtattttttaacttgcttgggtacaaca
s panTro2.chrY    552410 10314 +  23952694 TAAATATCACAAAatttgcgtagaggtgtttctagtattctctgatggtagtttAATTAACCAGAAAAACTGAAACAGATTCATTCACTTTATCTTTCAGTATCTCATAATGAGCAGATTTTATGACATTAAtgaaatgcctaaccttgtttttactctaactcattactttgaattttgtcctgcttgtctctttaatcacctatccttgcttctcatgtaaataagactctctgtagctgggaaggccggacaaactccaactgaccccttaatttacaagacactaagggctcctttcccaacccccttttgtaaggagttggcctgggtaaacagatcctcagcatttcaaaggagtccaattaactgataaggtactaacaccaacaatgtatgaagttcccaggatttttctcaaagagataacaacataaaaccttgagttcatgtcctctatagactctatatctaattataatgaaagatttagaaccttgcacctggtaccattgcttttcttgtaaccatttgtcttttaagtggtttatctctctgtaaccattttgcttcttttgattcttgcatgtttttacttctgtagaattattgcatttgagtccccctccccttcctaaacctaggtataaaagttaatcaagccctttcctcggggccgagagaattttgagcattagccatctctttggccgccagcttaataaaggactcttaattcgtctcaaagtgtggcatatttttttaactcgcttggatacagcataatggaggtcccagtgagaaattaactccactgggtgagagccggtctcactctgggctccccaggaaggacggctggcttggatggggggcgccacctgaggaaataatttttgaggtcccagaagtgtaactgccttccggaggagagcggatcgaccaccgtgtcattgccctaaaattcaacatctgagtcctcagcttctgaccccggggtcaggtaagtcagatttgacttcgtttctggtgagaggggagtggccctgatgagggcgtccctcttttgactcagcctgttactctaggacactagtgggttgagccttggttttctggtaggtgcttttgtatcttggtttgggtaggaagtggtcctgacaaggaccctccactgacttagctcagggcccaggaggcgggagctaagccttggtttccagaagactggactctcgatctctctctctctttctctcttgtctatcttacatccttctgttgttcaggtttcttggacaatctctgggaaagaaaaggaagaaaaaaagagaaaaaaattgttataaactctgtgtaaatggtgtgtgactgtgggaggacaaggggttgcatttgtcttccagtttgtagctccatggtgaaagctacagagttcaagtgggccctcacctgcggttccgtggcgacctcctaaggcttaaggcagcatcgggcatagctcgatctgagccaggggtttataccagcctgtcgatgctaagaggagcccaagtaccctctgggggatcagccaggcgggcatctgaatgaccgcatcacgggaactccttcccttgtctgtctaataaagaaggtaaaaaagggaaaactgtcataattgttttcatgccctagggtcaattgtttgttttatgtttattgttttgttcagtgtctattgtcttgtttaatagttgtcaaggtgttatatgtcaggacatctatattgtccatgaggtctgggtaaaaatttcttcaaggaccttagtgctgctattttgtcacaagaggttacatttctcatcaatcatttaggctggccaccacagtcttgtcttttctggcataaacaagtaaggtgttgttacggaaaagagtgtggagaacattcacctgattggaatttctggcaccatttaggttgcaggtatttagattgtcataccccacgtcctagtgattggtcctcttctaaactgaactggtggtgggttcaaaacagccaccttgcagaccttcttgctgatctcttttgtcattttgtaacttttcctgtgcccttgaataagaccttgtgtagggaaacctacgtccgtcatgctttacttagtttagactcctattctgttcccctgtggctacgctctcatcttaaggatgatctgagtggtccttttccccctcgtccttgccccctaccccatgcatcttgttttctagtgtgacagcaagttcagcatctccaagagttggctctgctctcattccttgaacccttaagggaaaaagctgaatttgaactgtttgcttttgaatcgtggagacatcaaaaatatttaggatataggtctagaggaagaggaagagggagaatgcctagctcgaaccgtcccaggaaaccttgggttgacccctaatccgcctccctcaatctaaaagctacagaaatttggcaagtagtattagcttttgtggtttttctgttgttcttcctggtcatgttaattctgtttttccgacactccagccccccagggaaagagtttctctgcccgtgttggatctgatatccctgctccagactttgctaaattgcctttaaataataaaaataataataaaattggaaacatttcctcccagccctataaagtttggagccctctccagggtatgctgaaaaatttttctcttggtttctcagaggactatggagtccgccttagaaaaggcaagctccagacactctgtgaactagaatggccaaagtttggatttggatggccctctgaagggtcattaaatcctatcattgttcaaggcatgtggcgagttgttaccagaactcccagcgaccctgatcagtttccatatatagatcaatgcataagtttggttaaaaatcctcctccatggctctgttcatgtgccattcacaactccacctccaaaatcctcctgagccaggacgcattttcgcctcgaccctcagctggttcagctccccctgttttgcctccctgtgaagaagaggagagtctccctcacccagttccaccaccttataaccaacctgcccctctagcattgtcccatgtctcttccacgacatcccctgtgggctcaccaccctttgcctctcagctgtgactgcagcaggaggaagcagcccctctactgccactgagagaggcacaagtccctccaagggatgagcactcagccccctccctggtttatgcccctttttctacttctgacttgtataattagaaaaatcataatcctcccttctccgaaaagcctcaggctttgacctcactgaaggagtccgtactccagacccatcgacccacctaggttgactgccaacagctccttttaactctctttatctctgaggagagggagcatatccaaagaaagaccagaaagcacttccttgcatcagccggcaggcctgaggaggaagccagagacctcctggaggaggtctttccctccacccagcctaattgggacacacattcctcaggtggaaggagagctttggacgattttcactggtatctccttgcgggtattaaaagagacacttggaagcccataaacttgtctaagacaactgaagctgtccaggggcctgatgagtcaccaggagtgtttttagaatgtctccaggaggcttattgaatttataccccttttgaccccatggctcccgagaatagctgtgctcttaatttggcatttgtggctcaggcagccccagatattaggagaaaactccaaaaactggaaggatttgctgggatgaacatcagtcagcttttagaaatagcccagaaagttattgaaaaccaataatttgaaaaacaaaaacaagcaacacaggcaactgaaaaagccgccgataagccatataaaagacaagcaaaaatcttggaaacagctatccaagagggcaaaaaggaaaggctcctattccagaaaattggccaaggaccctcaggttcccaccagaaaaataaaaggtaggtgaacaggcccctctaggaaaagaccaatatgcctattgcaagcagactgggcattggaaaaaggagtgcctcctgctgccaaaagaaaagtcagaaaacaaaaagattctcaccctgcctgcaacagaggagcctgataattgatggggccagggctccctcactcttggcccccaggatcccatggtaactgctacagtgggggaccagcctgtacgtttcctagtagacactggggcagaacactcagtactgcagactcccttgggcagtgtctcaaataaaaaaaataactgtacaagggcaactggagctattcaagagtatcctgtcacacactcccgagaagtaaacttgggacagaaaagagtgacacactcttttctggtggttccagagtgtccttttcctttatccttggacgagacctgctccataagttacaggcctcaatctcgttttcagctcagcatgctcatctcacactaggaaatgcaacttccccaactgcccaactcttgctaactacccatctgtcagaagaataccttctggttttaccatcacaatcaccggaggaaaatagtaatactcttttgttggacatacagacactttttccccaagtttgggctgagtcaaaccctcccagactggctaaacaccatctgccagaggttgtagaactcttggctactgccatactggtccaggtaaagcaataccccatgagtcagcaggctagagaggtgattaatccccacattcaatgactgttacaagctggcatacttacaccatgtcagtcggcctggaacacaccatttttgccggtccagaaacctgggacaaatgattaccagccagtacaatacttgagggaagttaataaatggactgttactgtccatccaaccatccctaatccttatactctactcagcctgctcccaccagaacatacagtatgtactgttcttgacctgaaagatgctttctttgcttttcctctggcccccaaaagccagctgatttttgcttttggatggacagatccaagatcaggagacactacccagctgacttggactcagttacctcagggttttaaaaatctccccaccctttttggggaggctcttcggcaagatcttatacccttccgagctagtcaccctaactgtactcttcttcagtatgtagatgatattttaatagctactgaaactatggacagttgtctacaacacacaagggatctgctctacctccttcaggggctcgggtatcgagtctcagccaaaaaggcccaactttgtcttgccagagtgtcctacctggggtacgagataaaccaaggaaacagggcactcaccagtgcccggaaagaagccatcctgcaaatccccactcccaccaccaagagacgggtacgtgaattactgggagccatgggataatgtcatctctgtatattgaggtttgcagagtttgcaaagcctttgtatactgctacaagaggtaatggcccactgatttggacagacactgaggaacagggttttcaaaatctgaaaaaggctttaactgcagcccctgctttagccctcccaaatatctcaaagccttttcatttgtttgtccatgagagccagggagttgctaaggggttgcttattcagactttaggaccttggagacgcccagtggcttatttatctaagaagctggatcctgtggcctcaggatggccaagttgcttgcaagacatagtggctacagcaagcctagtcaaagaaactgataagttaactctaggccagaatttaacccttatggctcctcatgctgtagagattttactacaaagtgcttcaggtaaatgtatgtcaaatactcgcattttacaatatcagagtttactgttggatcagcctcacttgactttctctcccacaaggtgtttaaatcctgctacactactctcagatccagattctaatattcctgtccatgactgtcaggagctgttagaaactatcaaaactggcaggccagatcttcaagatgtacccctgaaaaaggcggacgccaccgtgttcacggacagcagaagttccctcgagcaggggatacaaaaagccagtgcagctgttaccacagcgaacacctcagcgcagaaagctgaattaatcacccttactcaggctctccgatggggtaagaataaacgtattaacatttacactgacagcaggcatgctgttgctactgtgcatgtacctggagccatctaccaagaacgcgggttactcacttcagccggaaaaattatcaagaacaaagaggaaattctagccctgcttgaagccatgtggttccctcagcaggtggctgtaatccattgtaaaggacatcaaaaagaaaacacggccattgcccgcagtaaccaaaaagctgattcagcacctcaggaagtggcacggtcttcagtttggcccataaacctgctgccagcagtttcttttccacagccagatctgcctgacaaccctgcatactcaacagaagaagaaaaattggctgcacaccttagagcaaataaaaatcagaaaggttggtggattcttcctgactctagaatcttcataccccaagctcttggagaaactttagtcagtcatctacattataccacccatttaggtggggcaaaattagcccacctcctccagagctgttttaagatccctcatctacaaagcctaacaaatcaagcagttctctggtgcacagcctgtgcccaggtaaatgccaagcaaggtcctaaacccagcccaggtcaccgtctccaaggaaactcaccaggagaaaagtgggaaattgactttactgaagtaaatctacacggggctgactacaaataccttttagtattaatagacaccttctccggatggactgaggcattcgctaccaagaatgagactgctaacacagtagttaagttcttactcaatgaaatcatcccccaatatgggctgcctgctgccatagggtctgataatagacctgctttcacctcatccatagcacagtcagtcagtaaggcattgaacattcagtggaagctccatggtgcctatcgaccccagagctctagacaggtagaaagcatgaaccgcaccctaaaaaacattcttacaaaattaattctagagaccggtgaaaattgggtaagtctcttcctttagccctatttagagtaaggtgcaccctttatcaggctgggttctgatcttttgaaattatgtatgggcaggcaccacctatcctgcctgagctaaaagatgcccatttagcagaaatatcacaagctaatttattgcagtacgtacagtctctccaacaggtacaagagatcttctgccacttgttcaagaagcccatcccagtccagttcctcaccagacggggctctgccattcgttccagcccagtgacctagtgtttgttaaaaagttccagagagaaggactaactcctgcttggaagggacctcacaccgtcgtcctcatgacgccaacagctctgaaggtggatggaattcctgcttggattcatcagtcccacatcaaaaaggaaaacaaagcccaaacagaaacatgggtccccaagcctgggtcagggcccttaaaactgcacctgagttgggtgaaactgttaaattaattctttttattta---cttctgtttatccttgcctgtaatgtcttctgtgccttcctactccttcctcctcacctctttcacaacaggacgtgttttcgccaatgctacttggaagtctggtacctccaaggaagtcatctttgcagatgacttatgtatactgttcccacaactggctcatacccacaaagagcataacaacctgccagtcatgggagcaggaagtgtcgaccttgcagcaggattttgacactctgggagccaagccggatgtggaagctgcaaaggtgctgaaaaaggactccaaaatttgacttttacctctgtcctcgaaatcaccctgatgctagctgtcgagatacttaccagttcttctgcccagattggacatgtgtaactttagccacctactctgtgggatcaactagatctccaactctttcaataagtcgtgcttctcatcccaaatcatgttctaaaaataattgtaatcctcttaacataattgtccatgaacctaatttagctcaatgatattatggtatgtcatggggattaagactttacatcccaggattcgatgttggaactatgttcaccatccaaaagaaaatttttgtttcctgaagcccacctaagccactcaggcctttcactgatctaggtgaccctatgttccaaaaatgccctgacaaagttgatttaattgttcctccaccattctcagttcctaagacccagctgcaaagacaacaactccaacccagtctgatgtctatacttggtagagtacataatttccttaacctcacccagactaaactagcccgggattgttggctatgtttaaaagcaaaacccccttcttctgtaggattaggagtagaggtcacacttaaaagtggtcctttatcctgtcacacatgacctcgtgctttcacattaggagatgtgtctggaaatgcttcttgtctaattagtactgggtatgacttatctatttctccttttcaggatgtttgtaatcagtctctgcttactcccatgaggatctcagtctcttaccaagcgcctaacaaaacctggctggcctgcacctcaggtctcactcgctgcattaatggaactgaaccaggacctctcttgtgtgttctggttcatgttcttccccaggtatatgtgtacagtggatcagaaggacaactcctcatcgcttccctggaattacatcccaggctacaccaagctgccccactactgtttcctctattagctggtctcagcatagctggatcagcagaccttggcatggctgccctggttcaaggagaaactggactaatgtccttgtctcaacaggtagatcctgatttaaataaccttcagtctgccatagatatactacattctcaggtagagtctctagctgaagtagtacttcaaaactgccgaggtctagatctgctgttcctctctcagggaggattatgtgcagctctaggagaaagctgttgtttttacaccaatgaatctggactcataaaagataaactccaaaaagttcaagacaatctagataggtgccaacaagaatgagaaaataacacaccctggtatcaaagcatgttcaactggaacccttggctaactactttaatcactgggtaagctggacccatcatcatcatgttattgagtttgatttttgggccttgtatattaaactggttccttaattttgtaaagcaacgcatagactctgtcaaacttatgtatctaagaactcaatataacccccttgctgtaactaaagaatcaatgatttaattcccctaaaacacaagtggggaaatgaaatgcctaaccttgtttttactctaactcattactttgaattttgtcctgcttgtctctttaatcacctatccttgcttctcatgtaaataagactctctgtagctgagaaggccggaccaactccaactgaccccttaatttataagacactaagggctccttacccaatccccttttgtaaggagttggcctgggtaaacagatcctcagcatttcaaaagagcccaagtaactgacaaggtactaacaccaacaatgtatgaagttcccaggatttttctcaaagagatgacaccataaaacctggagttcatgtctggcatagaccctatatctagttataatgaaagatttagaaccttgcacctggtaccattgctcttcttgtaaccatttgtcttttaagttgtttatttctctgtaaccagtttgcttcttttgattcttgcatgtttttacttctgtagaattattgcatttgagtccccctcctcttcctaaacctaggtataaaagttaatcaagccccttcctcagggccgagagaatttggagcattagccatctctttggcgcccagcttaataaaggactcttaattcatctcaaagtgtggtgtattttttaacttgcttgggtacaaca
q panTro2.chrY                             00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000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i panTro2.chrY C 0 C 0
e rheMac2.chr3  61102100   114 + 196418989 I
e ponAbe2.chr8 105362646     0 - 153482349 C

a score=18246.000000
s hg19.chrY                7709120 92 +  59373566 ATTAAGAATCTGCTTGAGTAAAGAAATAAGGCCAACCAGCTCTTGTGAAAGAATCATTAAAAATATACAGAA-AAACCTATCATGTATATTAT
s panTro2.chrY              562724 92 +  23952694 ATTAAGAATCTGCTTGAGTAAAGAAATAAGGCCAACCAGCTCTTGTGAAAGAATCATTTAAAATATACAGAA-AAACCTATCATGTATATTAT
q panTro2.chrY                                    000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000
i panTro2.chrY           C 0 C 0
s turTru1.scaffold_92999      3943 93 +     81125 ATTCAGAATCTGTTCCAGTATAGAAATAGGGACAAACAGCTTCTATAAAAGAATCATTAGAAGTATAGAGAAGAGATCTATCATTCACATTAT
q turTru1.scaffold_92999                          759974977989688849897949998979996699978999979659997965849964985877889688585668675958853659855
i turTru1.scaffold_92999 N 0 T 787
e rheMac2.chr3            61102100 114 + 196418989 I
e ponAbe2.chr8           105362646  0 - 153482349 C

a score=288247.000000
s hg19.chrY                7709212 3155 +  59373566 TTTTAAATATCACCAAattcacatagaggtctttatagtgttctctgatggtagtttgtatttctgtgggatcggttgtgatatcccctttatcattttttattgcatcaatttgattcttatctctcttcttgtttattagtcttgctaccagtctatcaattttgttgatcttttc-aaaaaacaagcccgtggattcattgattttttgaagggatttttgtgtctctgtctccttcagttctgctctgatcttagtcattacttgccttctgctagctttggaatgtgtttgctcttcattctctagttcttttaattatgatgctagggtgtcaattttagatctttcctgttttctcttgtgggcattgagtgctataaatttccctctacacactactttaaatgtgtcccagatattctggtgtattttttctttgttctcattggtttcatagaacatctttattttggccttcatttcattatgtacccagcagtcattcaggagcaggctgatcagtttccatatagttgagcagttttgagtgaatttcttaatcctgagttctagttttatttctctgtggtctgagaaagagtttgttataatttctgttcttttacattgctgaagagtgctttacttccaactatgtggtcaattttggaataggtgtggtgtggtgccgagaagaatgtatattctgttcatttggggtggagagttctgtagatgtctattaggtccgtttggggcagagctgagttcaattcctggatatcctttttaactttatgtctcgttgatctgtctaacgttgacagtggggtgttaaaatctcccattattattatgtgggagtctaagtctcttagtaggtctctagggacttgcttcatgaatctgggtggtcctgtattgggtgcatatatatttagaatagttagctcttcttgttgaattgattcctttaccattatgtaatgaccttctttgtctcttttgatctttgttggtttagagtctgttttatcagagactaggattgcaaccctgccatttttgttttccatttgtttggtagatattccttcatctctttattttgagcccatgtgtgtctctgcacatgagatgggtctcctgaatacagcacattgatgggtcttgactctttatccaatttgccagtctgtgtcttttagttggagcatttagcccatttacatttaaggataatattgttatgtgtgaatatgatcctttcattatgacattagctggttattttgttcattagttgatgcagtttcttcccagcatcaatggtctttacaatttggcatg-tttttgcagtggctggtaccagttgttcctttccatgattagtacttccttaaggagatcctgtaggtaggcctggtggtaacaaaatctctcagcatttgcttctctttaaaggattttatttctctttcacttgcgaagcttagtttggctggatatgaaattctggtttgatgcaagtaaactagaaaatctggaagaaatcgataaattcctggacacatacaccctctcaagactaaaacaggaagaagttgaatccctgaatagaccaccaacagggtctgaaattgaggcaataattaattgcctaacaacctaaaaaagtccaggaccagatggattcacagccaaattctatgcgacatacaaggaggagctagtaccattctttctgaaactattaccatcaatggaaaaggaaagaatcctccctaactcagtttatgaggccagcgtcatcctgataccaaagccaggcagagacacaacaaagaaagaattttagaccaatatccctgatgaaaattgatgcgaaaatcctcaattaagtacaggcaagctgaatccagcagcacatcaaaaagcttatccatgatgatcaagtgggcttcatccctgggatgcaaggctgcttcaacatatgcaaataaataaacataatacaacatataaacagaaccaaagacaaaaaccacaatgtctcaatagatgcagaaaagacctttgacaaaattcaacagcccttcatgctaaaatctctcaattaattagatattgatgggatgtatctcaaaataataagagctatttataacaaacacacagccaatatcatactgaatgagcaaaaactggaagcattccctttgaaaactggcacacgacagggatgccctatctccccactcctattcaacgtagtgttggaagttctggccagggcaataaggcaggagaaagaaataaagggtattcaattagaaaaagaagaagtcaaattttccctgtttgcagatgacatgattgaatatttagaaaaaccctttgtctcagcccaaaatctctttaagctgataagcaacttgagcaacatctcaggatacaaagtcaatatgcaaaaatcacaagcattcttatacatcaagaacagacaaacagagagccaaatcatgagtgaaatcccagtcacgattgcttcaaagagaagaaaatacctaggaatccaacttacaaaggatatggaggacctctttaaggagaactacaaaccactgcccaatgaaatagaagaggacacaaaaagtggtcgaacgttccatgctcatggataggaagaatcaatatcatgaaaatgtccatactgcccaaggtaatttatagattcaattccatccccatcaacctactaaggactttcttcacagaattggaaaaaactactttaaagttcatatggtaccaaaaaggagcccatattgccaagataatcctaagcaaaaggaacaaagctggaggcatcacgctacctgacatcaaactatactacaaggctacagtaaccaaaacagcttggtaccagtaccaaaacagagatatagaccaatggaacagaacagagccctcagaaataataccacacatctacaaccatctgatcttagacaaacctgacataaacaagaaatggggaaaagattccccatttaataaatgtgctgagaaaactggctagccatatgtagaaagctgaaactgtgtcccttccttacatcttgtaaaaaactagttcaagatgtat
s panTro2.chrY              562816 3157 +  23952694 TTTTAAATATCACCAAattcgcatagaggtctttatagtgttctctgatggtagtttgtatttctgtgggatcggtggtgatatcccctttatcattttttattgcatcaatttgattcttatctctcttcttgtttattagtcttgctaccagtctatcaattttgttgatcttttcaaaaaaacaagcccatggattcattgattttttgaagggatttttgtgtctctgtctccttcagttctgctctgatcttagtcattacttgccttctgctagctttggaatgtgtttgctcttcattctctagttcttttaattgtgatgctagggtgtcaattttagatctttcctgttttctcttgtgggcattgagtgctataaatttccctctacacactactttaaatgtgtcccagatattctggtatattttgtctttgttctcattggtttcatagaacatctttattttggccttcatttcattatgtacccagcagtcattcaggagcaggctgatcagtttccatatagttgagcagttttgagtgaatttcttaatcctgagttctagttttatttctctgtggtctgagaaagagtttgttataatttctattcttttacattgctgaagagtgctttacttccaactatgtggtcaattttggaataggtgtggtgtggtgctgagaagaatgtatattctgttcatttggggtggagagttctgtagatgtctattaggtccatttggggcagagctgagttcaattcctggatatcctttttaactttctgtctcgttgatctgtctaacgttgacagtggggtgttaaagtctcccattattattatgtgggagtctaagtctctttgtagttctctagggacttgcttcatgaatctgggtggtcctgtattgggtgcatatatatttagaatggttagctcttcttgttgaattgattcctttaccattatgtaatgaccttctttgtctcttttgatctttgttggtttagagtctgttttatcagagactaggattgcaaccctgccatttttgttttccatttgcttggtagatattccttcatctctttattttgagcccatgtgtgtctctgcacatgagatgggtctcctgaatacagcacattgatgggtcttgactctttatccaatttgccagtctgtgtcttttagttggagcatttagctgatttacatttaaggataatattgttatgtgtgaatttgatcctttcattatgacgttagctggtaattttgttcattagttgatgcagtttcttcccagcatcaatggtctttataatttggcatgttttttgcagtggctggtaccagttgttcctttccatgattagtacttccttaaggaggtcctgtaggtaggcctggtggtaacaaaatatctcagcatttgtttctctttaaaggattttatttctctttcacttgcgaagcttagtttggctggatatgaaattctggtttgatgcaagtaaactagaaaatctagaagaaatggataaattcctggacacatacaccctctcaagactaaaacaggaagaagttgaatccctgaatagaccaccaacagggtctgaaattgaggcaataattaattgcctatcaaccaaaagaagtccaggaccagatggattcacagccaaattctatgagacgtacaaggaggagctagtaccattctttctgaaactattaccatcaatggaaaaggagggaatcctccctaactcagtttatgaggccagcatcatcctgataccaaagccaggcagagacacaacaaagaaagaattttagaccaatatccctgatgaaaattgatgcgaaaatcctcaattaagtacaggcaagctgaatccagcagcacatcaaaaagcttatccacgatgatcaagtgggcttcatccctgggatgcaaggctacttcaacatatgcaaataaataaacataatacagcatataaacagaaccaaagacaaaaaccacaatgtctcaatagatgcagataagacctttgacaaaattcaacagcccttcatgctaaaatctctcaattaattagatattgatgggatatatctcaaaataataagagctatttataacaaacacacagccaatatcatactgaatgagcaaaaactggaagcattccctttgaaaactggcacacgacagggatgccctctctccccactcctattcaacgtagtgttggaagttctggccagggcaataaggcaggagaaagaaataaagggtattcaattagaaaaagaagaagtcaaattttccctgtttgcagatgacgtgattgaatatttagaaaaaccctttgtctcagcccaaaatctctttaagctgataagcaacttcagcaacatctcaggatacaaagtcaatatgcaaaaatcacaagcattcttatacatcaagaacagacaaacagagagccaaatcatgagtgaaatcccagtcacaattgcttcaaagagaagaaaatacctaggaatccaacttacaaaggaaatggaggacctctttaaggagaactacaaaccactgcccaatgaaataaaagaggacacaaaaagtggtcgaacgttccatgctcatggataggaagaatcaatatcatgaaaatgtccatactgcccaaggtaatttatagattcaattccatccccatcaacctactaaggactttcttcacagaattggaaaaaactactttaaagttcatatggaaccaaaaaagagcccatattgccaagataatcctaaggaaaaggaacaaagctggaggcatcatgctacctgacatcaaactatactacaaggctacagtaaccaaaacagcttggtaccagtaccaaaacagagatatagaccaatggaacagaacagagccatcagaaataataccacacatctacaaccatctgatcttagacaaacctgacataaacaagaaatggggaaaagattccccgttaaataaatgtgccgagaaaactggctagccatatgtagaaagctgaaactgtgtcccttccttacatcttataaaaaactagttcaagatgtat
q panTro2.chrY                                      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e rheMac2.chr3            61102100  114 + 196418989 I
e turTru1.scaffold_92999      4036  787 +     81125 T
e ponAbe2.chr8           105362646    0 - 153482349 C

a score=76876.000000
s hg19.chrY                7712367 457 +  59373566 taaggacttaaatgttagacctaaaaccatgaaaaccctggaggaaaacctaggcaataacattcac-gacataggcatgggaaaggacttcatgtctaaaacaccaaaagcaatggcaacaaaagccaaaattgacaaatgggatctcattaaactaaagtgcttctgcacagcaaaagaaactaccatcagagtgaacaggcagcata-aagaatggaagaaaaattttgcattctactcatctgacaaagg-gcaatatccagaatctacaaagaacacaaacaaatttataagaaaaaa--aaagaaccccataaaaaagtgggtgaaggatatgaacagacacttctcaaaagaagacatttatgcagccaacagacacatg--aaaaaatgctcatcatcattggccatcagagaaatgcaaatcaaaaccacaatgagataccatctcacaccagtt
s panTro2.chrY              565973 461 +  23952694 taaggacttaaatgttagacctaaaaccatgaaaaccctagaggaaaacctaggcaataacattcac-aacataggcatgggaaaggacttcatgtctaaaacaccaaaatcaatggcaacaaaagccaaaattgacaaatgggatctcattaaactaaagtgcttctgcacagcaaaagaaactaccatcagagtgaacaggcagcata-aagaatggaagaaaaattttgcattctactcatctgacaaagg-gcaatatccagaatctacaaagaacacaaacaaatttataagaaaaaaacaaagaaccccataaaaaagtgggtgaaggatatgaacagacacttctcaaaagaagacatttatgcagccaacagacacatgaaaaaaaatgctcatcatcactggccatcagataaatgcaaatcaaaaccacaatgagataccatctcacaccagtt
q panTro2.chrY                                     0000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s vicPac1.scaffold_20267      2698 461 +      8093 Taaagacttaaatataaggcaagacatgataaatctcctagaagaaaatataggcaa-aacactctctgacataaatcttagcaatgttctcctagggcaatctacccaggcaatagaaataagaacaaaaataaacaaatgggacctaattaaacttatacgcttttgcacagcaaaggaaaccataagcaaaacaaaacgacaacatatgagaatgggagaaaatatttgcaaatgatgtgactgacaaaggcttaatttccacaatatataaacagctcatacaacttaataacaaaaaaacaaacaacccaatccaaaaatgggcagagaacctaaacaaacaattctccagtgaagatatacaaatgactaataggcacatg--aaaaaatgctcaatatcactaattatcagagaaatgcaaatcaaaactacaatgaagtatcacttcacaccagtc
q vicPac1.scaffold_20267                           999999999989999998969999899987999999999959959439999999999-99999999999999999999999377999299889882997398979999999999999999999999999999999999999999999999999999999999999999998999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999
i vicPac1.scaffold_20267 N 0 C 0
e rheMac2.chr3            61102100 114 + 196418989 I
e turTru1.scaffold_92999      4036 787 +     81125 T
e ponAbe2.chr8           105362646   0 - 153482349 C

a score=53920.000000
s hg19.chrY                7712824 216 +  59373566 agaatggttatta----ttgaaaagtcagg---aaacaacatgtgctggagaggatgtggaaaaataggaacagttttacaccgttggtgagactagaaactggttcaaccattgtggaagacagtgtggtgattcctcaaggatctagaactaggaataccatttgacccagccatcccattactgggtatatacacaaa--------ggattataaatcatgctgctac
s panTro2.chrY              566434 216 +  23952694 agaatggttatta----ttgaaaagtgagg---aaacaacatgtgctggagaggatgtggaaaaataggaacagttttacactgttggtgagactggaaactggttcaaccattgtggaagacagtgtggtgattcctcaaggatctagaactaggaataccatttgacccagccatcccattactgggtatatacccaaa--------ggattataaatcatgctgctgc
q panTro2.chrY                                     0000000000000----0000000000000---000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--------0000000000000000000000
i panTro2.chrY           C 0 C 0
s vicPac1.scaffold_20267      3159 210 +      8093 agaatgaccatca----ttcaaaattccat---aaatgataaacgctggagagggtgtggagaaaagggaaccttcctacactgttggtgggaatgtagtttggtgcagccattatgggaaacagtatggagattcctcaaaagactgaaaatagatctaccatatcatccagcaatcccacttctgggtatatatccaga------gggaactcaaattcaa--------
q vicPac1.scaffold_20267                           9999999999999----9999999999999---999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------9999999999999999--------
i vicPac1.scaffold_20267 C 0 C 0
s turTru1.scaffold_92999      3249 219 +     81125 agaatggatataataattttaaaaaataatggaaaataaaaaatgttggagagaatgtagagaaattggaaccctcgtaatc---tcataggaatgtaaaatggtgcagccactat-gaaaacagtttggtggttcctcagaaaggtaaacataggattactgtatgacccagcaattccactcttaagtatatagccaaaggaattggaaacagaaactcaa--------
q turTru1.scaffold_92999                           9999999999999999999999999999999999999999999999999999999999999999999999999999999999---9999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--------
i turTru1.scaffold_92999 T 787 N 0
e rheMac2.chr3            61102100 114 + 196418989 I
e ponAbe2.chr8           105362646   0 - 153482349 C

a score=77160.000000
s hg19.chrY                7713040 369 +  59373566 aaagacatatgcacacttaacgtttattgtgacactattcacaatagcaaagacttggaaccaatcaaaatgtccatcaatgatagtctggattaagaaaatgtgtcacatatacaccatggaatactattcagcc-taaaaaatgatgagtgtgtgtcttttgtagggacgtggatgaagctggaaaccatcattctcagcaaac-tattgcaaggacaaaaaaccaaacaccagatattctcactcataggtgggaattgaaaaaat-------gagaacatctggac--------------------acaggaagggaaacatcacaactggggcctg---ttgtgggat-gaggggaagg---gggagggatagcat------------t----aggagatatacctaatg-taaatg
s panTro2.chrY              566650 369 +  23952694 aaagacatatgcacacttaacatttattgtgacactattcacaatagcaaagacttggaaccaatcaaaatgtccatcaatgatagtctggattaagaaaatgtgtcacatatacaccatggaatactattcagcc-taaaaaatgatgagtgtgtgtcctttgtagggacgtggatgaagctggaaaccatcattctcagcaaac-tattgcaaggacaaaaaaccaaacaccagatattctcactcataggtgggaattgaaaaaat-------gagaacatttggac--------------------acaggaagggaaacatcacaactggggcctg---ttgtgggat-gaggggaagg---gggagagatagcat------------t----aggagatatacctaatg-taaatg
q panTro2.chrY                                     0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000-------00000000000000--------------------0000000000000000000000000000000---000000000-0000000000---00000000000000------------0----00000000000000000-000000
i panTro2.chrY           C 0 C 0
s vicPac1.scaffold_20267      3369 402 +      8093 aaagatatatgtac-cccaatgttcatagcagcactatatacaatacccaagacatggaagcaacctaaatgtccactgagagatgactggataaagaagatgtggtatatttatacaatggaatacaactcagccataaaa--gaacacaataatgccatttgtagcaacatggatggatctggaggtcgtcattctaagtgaagttaagccagaaagagagcgaaaaataccatatgatatcactcatatgtggaatctaaaaaaagagaaaaaaggaaaaaaaggacactatgaactcaactacaagacagaaacagactca-cagacctagtaaacaatcttatggttaccagagaaagg---gggtgggaagggat-aaattagggagt----ttgatattta--------caaatg
q vicPac1.scaffold_20267                           99999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999---99999999999999-999999999999----9999999999--------999999
i vicPac1.scaffold_20267 C 0 I 830
s turTru1.scaffold_84820     27189 411 +     73389 aaagagtcatgtac-cacaatgttcattgcagcactatttacaatagccatgaaatggaagcaccctaagtgttcattgacagatgaatggataaagtagatgtggcccatatatatagtggaatattactcagccataaaaagaaacgaaattgagttatttgtagtgaggtggatggacctagagtctgtcatacagagtgaag-tacatcagaaagagaaaaagaaatagcatatactaacacatatatatggaatataaaaaaag-------gggaaaaaactgttctgaagaacctaggggcaggacaggaataaagacg-cagacatagagaatggacttgaggaca-cagggagggggaagggtaagctgggacgaagtgagagagtggcatggacatatacacactgccaaatg
q turTru1.scaffold_84820                           99999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999-------9999999999999999999999999999999999999999999999999-999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999
i turTru1.scaffold_84820 N 0 I 8
e rheMac2.chr3            61102100 114 + 196418989 I
e ponAbe2.chr8           105362646   0 - 153482349 C

a score=6675.000000
s hg19.chrY                7713409 121 +  59373566 atgagttattgggtgcagc--------------agaccaaaattgcac--------------------------------------------------------------------atgtatacatacgtaccaaacctgcacgttgt------gcacaagtaccctagaacttaaaatataacaata----aataaataataaaaataaaaa
s panTro2.chrY              567019 121 +  23952694 atgagttattgggtgcagc--------------agaccaaaattgcac--------------------------------------------------------------------atgtgtacatacgtaccaaacctgcacgttgt------gcacaagtaccctagaacttaaaatataacaata----aataaataaTAAAAATAAAAA
q panTro2.chrY                                     0000000000000000000--------------000000000000000--------------------------------------------------------------------00000000000000000000000000000000------0000000000000000000000000000000000----000000000000000000000
i panTro2.chrY           C 0 C 0
s turTru1.scaffold_84820     27608 209 +     73389 atagctagtgggaagcagccgcatagcacagggagatcagcttggtgctttgtgaccacctagaggggtgggatagggagggtgggagggagacgcaagagggaggagatatggggatatatgtatacatatagctgattcactttgttatacagcagaaactaacacaacattggaaagcaattatactccaataaatattaaaaaaa----
q turTru1.scaffold_84820                           99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----
i turTru1.scaffold_84820 I 8 N 0
e vicPac1.scaffold_20267      3771 830 +      8093 I
e rheMac2.chr3            61102100 114 + 196418989 I
e ponAbe2.chr8           105362646   0 - 153482349 C

a score=21897.000000
s hg19.chrY                7713530 104 +  59373566 taaaaatCACAAAATTCATACTTCAAACAAACACTAGTCTTACTGAGTTTTACTACTTGCAGAAGGTGGGTTGGCATAGAACATGATGGACCATAGCCACTTTT
s ponAbe2.chr8           105362646 104 - 153482349 TAAAAATCACCCAATTCATACTCCAAAAAAATACCAATCTTACTGGGTTTTACTACTGGCAGAAGCCAGGTTGCCTTAAGACTTGATGCAACATAACCACTCTT
q ponAbe2.chr8                                     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              567140 104 +  23952694 TAAAAATCACAAAATTCATACTTCAAACAAACACTAGTCTTACTGAGTTTTACTACTTGCAGAAGGTGTGTTGGCATAGAACATGATGGACCATAGCCACTTTT
q panTro2.chrY                                     00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e vicPac1.scaffold_20267      3771 830 +      8093 I
e rheMac2.chr3            61102100 114 + 196418989 I

a score=32244.000000
s hg19.chrY                7713634 73 +  59373566 TATATATCACCCAATTG-CCCATAATAAACCCAGAATTTAAGGCTGATCCTGTCAGTTCCTAAGAAGACAATCT
s panTro2.chrY              567244 73 +  23952694 TATATATCACCCAATTG-CCCATAATAAACCCAGAATTTAAGGCTGATCCTGTCAGTTCCTAAGAAGACAATCT
q panTro2.chrY                                    00000000000000000-00000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105362750 73 - 153482349 TATATATCACCCAATTG-CCCAAAATCCACCCAGAACTGAAGGCTGATCCTGCCAGCTCCTAAGAAGACAGCCT
q ponAbe2.chr8                                    99999999999999999-99999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s rheMac2.chr3            61102214 74 + 196418989 TATATATCATCCAATTGCCCCCAAATCAACCCAGAACTGAAGGTTGATCCTGCCAGGTCCTAAGAAGACCGTCT
q rheMac2.chr3                                    99999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3           I 114 C 0
e vicPac1.scaffold_20267      3771 830 +      8093 I

a score=86636.000000
s hg19.chrY                7713707 215 +  59373566 TGACACGCACACA-----ATTTTCCATTAAGATTGTTTCCCACTTCTACCTTCTA-GTAATGTCTGTCAGCCCTACACTTCTGAGAATCCAGGACAGCAGGGCACAAGTAAAATCTCCTTGAATTAT-AACAAATGTTTGG-TTTGTTCTTCCATATAACACAGC-TTTTCTATCCTCAGAAACAATAAGTTGAAAATGTGTTGTGTCAAGATATAGAATCAAG
s rheMac2.chr3            61102288 203 + 196418989 TGACACACACCCA-----ATTTTCACTTAGGATCGTTTCCCACTTCT-CCTTCCA-GTAATGTCTGCCAGAACTACACTTCTGAGAGCCCAGGACAGCAGGGCAGAAATAAAATCTCCTTGGGTTGT-AATAAACGTTTGGTTTTGTTCTTCC--ATTACACAGCTTTTTCTATCCTCGGAGACAGTAAGTTGAGGATGTGCTGTGTCAAGAT-----------
q rheMac2.chr3                                     9999999999999-----99999999999999999999999999999-9999999-99999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999--9999999999999999999999999999999999999999999999999999999999-----------
i rheMac2.chr3           C 0 I 750
s ponAbe2.chr8           105362823 203 - 153482349 TGACACACACACA-----ATTTTCATTGAGGCTTGTTTCCCACTTCTACCTTCCA-GTAATGTCTGCCAGAACTAC------------CCAGGACCCCAGGGCAGAAATAAAATCTCCTT-AGGTAT-AGCAAAAGTTCAGTTTTGTTCTTTCATATCACACACC-TTTTCTATCCTCAGGGACAATAAGTTGAGGATGTGCTGTGTCAACATTCAGAATCAAg
q ponAbe2.chr8                                     9999999999999-----9999999999999999999999999999999999999-99999999999999999999------------99999999999999999999999999999999-999999-9999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              567317 215 +  23952694 TGACACACACACA-----ATTTTCCATTAAGATTGTTTCCCACTTCTACCTTCTA-GTAATGTCTGTCAGCCCTACACTTCTGAGAATCCAGGACAGCAGGGCACAAGTAAAATCTCCTTGAATTAT-AACAAATGTTTGG-TTTGTTCTTCCATATAACACAGC-TTTTCTGTCCTCAGAAACAATAAGTTGAAAATGTGTTGTGTCAAGATATAAAATCAAG
q panTro2.chrY                                     0000000000000-----0000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000000000-0000000000000-00000000000000000000000-0000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s danRer6.chr4            44130518 205 +  71658100 TGATATACACACACCAGCATCTCCACTCCAGTCAATCTCCCAGTTACAGCGTCCACACACACTCTCTCTGCACAACACCTG-----------------AGGATCATAATCAAATCTGTCTGGATGATCAGGATACGGCTGA-TTCTCCCATACATGCTTCACCTC-TCTGTTCTCCTCAGACAGAATGAGTTGAGTGTTTGCTGTGTTTGGATCCAGAGTGAGG
i danRer6.chr4           N 0 N 0
e vicPac1.scaffold_20267      3771 830 +      8093 I

a score=49385.000000
s hg19.chrY                7713922 240 +  59373566 Tctgggaatggtggctcatgcctgtaatgccagcattttgtgaggtcaaggcaggaagatcacaaggtcaatatatccaaaacatgctgactcacatggtaaaaccccatctctactaaacatacaaaaatgtagtcaggcatgaaaaccccttcctgtagtcccagctacttgggaggctgacccaggggagtcacttgaacccaggaggtggaggtttcagtgagccaagatcatgcc
s ponAbe2.chr8           105363026 240 - 153482349 gctgggcgtgttggctcacacctgtaatcccagcaatttgggaggctgaggtgggaggatcacgaggtcaggagatccagaccatcctggctaacatggtgaaaccctgtctctactaaaaatacaaaaaattagctgggcatggtaacaggcccctgtagtcccaggtacttgggaggatgaggcaggagaattgcttgaacccaggaagaggaggttgcagtgagctgagatcacacc
q ponAbe2.chr8                                     999999999999999999999999999999997999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              567532 240 +  23952694 Tctgggaatggtggctcatgcctgtaatgccagcattttgtgaggtcaaggcaggaagatcacaaggtcaatatatccaaaccatgctgactcacatggtaaaacctcatctctactaaacatacaaaaatgtagtcaggaatgaaaaccccttcctgtagtcccagctacttgggaggctgacccaggggagtcacttgaacccaggaggtagagatttcagtgagccaagatcatgcc
q panTro2.chrY                                     000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e vicPac1.scaffold_20267      3771 830 +      8093 I
e rheMac2.chr3            61102491 750 + 196418989 I

a score=299.000000
s hg19.chrY                7714162 60 +  59373566 attgtgctc-------cagcctgggtg----------acatagtgagattctatatcaaaaaGTAAGTAAATAAATA
s panTro2.chrY              567772 59 +  23952694 actgtgctc-------cagcctggg-g----------acatagtgagattctatatcaaaaaGTAAGTAAATAAATA
q panTro2.chrY                                    000000000-------000000000-0----------0000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105363266 59 - 153482349 actgcactc-------cagcctgggca----------gcagagggagtctccatctcaaaaaa-aaaaaaaaaaaaa
q ponAbe2.chr8                                    999999999-------99999999999----------99999999999999999999999999-9999999999999
i ponAbe2.chr8           C 0 C 0
s danRer6.chr4            59684856 70 +  71658100 attttgctcactcgcgcaatctgcttgtcaacgtgtcgtaaaggcaaaatcaaaacaaaaatg---gcagaca----
i danRer6.chr4           N 0 C 0
s xenTro2.scaffold_239     1221110 34 +   1706063 -------------------------------------ATACAATCAGACTCT------AAGGGCACGTGAATTAAAA
i xenTro2.scaffold_239   N 0 I 9
e vicPac1.scaffold_20267      3771 830 +      8093 I
e rheMac2.chr3            61102491 750 + 196418989 I

a score=16628.000000
s hg19.chrY                7714222 78 +  59373566 AATCTAGAATCA---AGTCTACAT-------GAAAA-GGATTGATAATTCCGTCTAAGCC-----AGAATTTAGA--GAAGGAAGACAAAAACTGT----
s ponAbe2.chr8           105363325 78 - 153482349 GATCTAGAATCA---AATCTACTT-------GAAAT-GGCTTGATAATTCTGTCTAAGCC-----AGAATAGAGA--GGAGGAAGACTGAAACCAT----
q ponAbe2.chr8                                    999999999999---999999999-------99999-99999999999999999999999-----9999999999--9999999999999999999----
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              567831 78 +  23952694 AATCTAGAATCA---AGTCTACAT-------GAAAA-GGATTGATAATTCTGTCTAAGCC-----AGAATTTAGA--GAAGGAAGACAAAAACTAT----
q panTro2.chrY                                    000000000000---000000000-------00000-00000000000000000000000-----0000000000--0000000000000000000----
i panTro2.chrY           C 0 C 0
s vicPac1.scaffold_20267      4601 79 +      8093 GATCTAGAATCA---CATCTGCTT-------GAAAACTGCTTGATAATTTTGTTTAGGCC-----AGAATACTGT--GGAGGAAGATGGCAACCAT----
q vicPac1.scaffold_20267                          997999469796---799999999-------97792999999999999999999999999-----9999999999--9999999999999999999----
i vicPac1.scaffold_20267 I 830 C 0
s xenTro2.scaffold_239     1221153 70 +   1706063 AATCAAGGTCCA-----TCTCCAT-------TGACA-TAATC-ACAA-------TATGTC-----AAAATTCTGACTTTTTAAAAAAAAAAATTCT----
i xenTro2.scaffold_239   I 9 C 0
s danRer6.chr4            59684926 99 +  71658100 aacgtaaatgcattgattcttcagaggcgaagaaaa-agattagacaatatgacaaagcctacctaaattttggttttagtgaaggccaagacaagttaa
i danRer6.chr4           C 0 N 0
e rheMac2.chr3            61102491 750 + 196418989 I

a score=9998.000000
s hg19.chrY                7714300 59 +  59373566 ACTTTGTTAATCAAAATGAATAGAATT-CTGACC-------------ATGCATGTGGT----AAATAATATTAACAT
s ponAbe2.chr8           105363403 72 - 153482349 ATTTCATTAATCTAAATGAAAATAGTT-CAGGGCATTATAGGCTTTGATGCCTGTGGT----GCATACTATTCACAT
q ponAbe2.chr8                                    999999999999999999999999999-999999999999999999999999999999----999999999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              567909 59 +  23952694 ACTTTGTTAATCAAAATGAATAGAATT-CTGACC-------------ATGCATGTGGT----AAATAATATTAACAT
q panTro2.chrY                                    000000000000000000000000000-000000-------------00000000000----000000000000000
i panTro2.chrY           C 0 C 0
s vicPac1.scaffold_20267      4680 71 +      8093 ATTCCTTCAGTTGGAATGAAAAG-GTC-CAGGAGACTGTATGGTTTTACACTTGTGGT----GGATACTTTTAACAT
q vicPac1.scaffold_20267                          99999999999999999999999-999-999999999999999999999999999999----999999999999999
i vicPac1.scaffold_20267 C 0 C 0
s xenTro2.scaffold_239     1221223 56 +   1706063 AATGGGTTAATCACAATAGATATAATTACAGAAA-------------GTAATTGTG--------ATCATTTTGGCAA
i xenTro2.scaffold_239   C 0 C 0
s danRer6.chr4            46528343 60 +  71658100 ATTTCATTCATCAAGTTTAA---AATT-GGGGGC-------------ATCCATGTTTTTTTGACATACTTTaaacaa
i danRer6.chr4           N 0 C 0
e rheMac2.chr3            61102491 750 + 196418989 I

a score=13216.000000
s hg19.chrY                7714359 32 +  59373566 GTGTCAGCC--------ATTTCAAGTTTGACTGGATAGAC-
s panTro2.chrY              567968 32 +  23952694 GTGTCAGCC--------ATTTGAAGTTTGACTGGATAGAC-
q panTro2.chrY                                    000000000--------00000000000000000000000-
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105363475 32 - 153482349 GTGTCAGCA--------ATTCCAGGTTTGACTGAATAGAC-
q ponAbe2.chr8                                    999999999--------99999999999999999999999-
i ponAbe2.chr8           C 0 C 0
s rheMac2.chr3            61103241 32 + 196418989 GTGTCAGCA--------ATTCCAGGTTTGACTGCATAGAA-
q rheMac2.chr3                                    999999999--------99999999999999999999999-
i rheMac2.chr3           I 750 C 0
s vicPac1.scaffold_20267      4751 32 +      8093 CTGTCAGCA--------AGTCCAATTCTAATTCCGTATAT-
q vicPac1.scaffold_20267                          999999999--------99999999999999999999999-
i vicPac1.scaffold_20267 C 0 C 0
s xenTro2.scaffold_239     1221279 40 +   1706063 ATTGCAGCATTCACTGCATTTTAAAGCCAACTGAGGTGAC-
i xenTro2.scaffold_239   C 0 N 0
s danRer6.chr4            46528403 29 +  71658100 ----gagtt--------tctgcaggtttcaccaagttaaat
i danRer6.chr4           C 0 C 0

a score=64151.000000
s hg19.chrY                7714391 108 +  59373566 TTGTGCACTACCTCTCTCCATAGATGTTTAAA-----TGTAGAAACATAAT--CTGAAAATTTTAGGATGATTTCATTTAGTTTTGCTAAAATGTCC--ATCTCTTAATCTTGTTTC
s panTro2.chrY              568000 108 +  23952694 TTGTGCACTACCTCTCTCCATAGATGTTTAAA-----TGTAGAAACATAAT--CTGAAAATTTTAGGATGATTTCATTTAGTTTTGCTAAAATGTCC--ATCTCTTAATCTTGTTTC
q panTro2.chrY                                     00000000000000000000000000000000-----00000000000000--00000000000000000000000000000000000000000000--000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105363507 108 - 153482349 TTGCCTTCTACCTACCTCAGTAGATGTTTAAA-----TGTAGAAACATAAT--CTGAAAATTTTACAAGGTTTTCACTTAGTTTTGGTAAAAGGTCC--ATCTCTTCTTCTTGTTTC
q ponAbe2.chr8                                     99999999999999999999999999999999-----99999999999999--99999999999999999999999999999999999999999999--999999999999999999
i ponAbe2.chr8           C 0 C 0
s rheMac2.chr3            61103273 108 + 196418989 TTGCCCACTACCTCCCCCAGTAGATGTTTAAA-----TGTAGAAACATAAT--CTGAAAATTTTACAAGGTTTTCACTTCGTTTTGCTAAAATGTCC--ATCTCTTCATCTTGTTTC
q rheMac2.chr3                                     99999999999999999999999999999999-----99999999999999--99999999999999999999999999999999999999999999--999999999999999999
i rheMac2.chr3           C 0 C 0
s vicPac1.scaffold_20267      4783 105 +      8093 GTGCTCCTTACCTCCTTTAACAGATATTTTAA-----TGTGGAAACATGAT--CTGAAAATTTTGTTAGATTTTCATTTAGTTTTGCTAAAATATCC--ATTTCTTCATCTTGT---
q vicPac1.scaffold_20267                           99999999999999999999999999999999-----99999999999999--99999999999999999999999999999999999999999999--999999999999999---
i vicPac1.scaffold_20267 C 0 N 0
s danRer6.chr4            46528432  90 +  71658100 -------tta-----------agaattttaaagattttttaagaccattatgactg-aaattttaga-----ctcataAAG---GGCTAAAGGGTAAGGAATTTTTCAAATGGCTAA
i danRer6.chr4           C 0 C 0

a score=-2473.000000
s hg19.chrY                        7714499 18 +  59373566 AACTTTGAGAT----GTGGTCT
s rheMac2.chr3                    61103381 10 + 196418989 AATTGTAAGA------------
q rheMac2.chr3                                            9999999999------------
i rheMac2.chr3                   C 0 I 8
s ponAbe2.chr8                   105363615 18 - 153482349 AATTATGAGAG----TTAATTG
q ponAbe2.chr8                                            99999999999----9999999
i ponAbe2.chr8                   C 0 C 0
s panTro2.chrY                      568108 18 +  23952694 AACTTTGAGAT----GTGGTCT
q panTro2.chrY                                            00000000000----0000000
i panTro2.chrY                   C 0 C 0
s tupBel1.scaffold_94794.1-11926     10147 21 +     11926 -TGCATAAGATCCTCCTGCTCA
q tupBel1.scaffold_94794.1-11926                          -999999999999999999999
i tupBel1.scaffold_94794.1-11926 N 0 I 3
s danRer6.chr4                    46528522 18 +  71658100 GATGAAAAGAT----TTTATTT
i danRer6.chr4                   C 0 C 0

a score=25793.000000
s hg19.chrY                        7714517 47 +  59373566 -------TGCAGCATTGGTACAATTATGCTCTCTTCATATGCAAAATTAATGTC
s rheMac2.chr3                    61103399 47 + 196418989 -------TGCAACATGGGTACAATTATGCTCTCTTCATATGCAGAATTAATGTC
q rheMac2.chr3                                            -------99999999999999999999999999999999999999999999999
i rheMac2.chr3                   I 8 C 0
s ponAbe2.chr8                   105363633 47 - 153482349 -------TGCAGCATAGGTACAATTATGCTCTCTTCATATGCAGAATTAATGCC
q ponAbe2.chr8                                            -------99999999999999999999999999999999999999999999999
i ponAbe2.chr8                   C 0 C 0
s panTro2.chrY                      568126 47 +  23952694 -------TGCAGCATTGGTACAATTATGCTCTCTTCATATGCAAAATTAATGTC
q panTro2.chrY                                            -------00000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s tupBel1.scaffold_94794.1-11926     10171 41 +     11926 -------TGTAACGATAGTCCAATT------TGCTCAAATTCAGAATTGATTTC
q tupBel1.scaffold_94794.1-11926                          -------999999999999999999------99999999999999999755779
i tupBel1.scaffold_94794.1-11926 I 3 N 0
s danRer6.chr4                    46528540 47 +  71658100 TGCCCGATGaaaaaatatcataatt------taattataca-ataataaataat
i danRer6.chr4                   C 0 C 0

a score=75652.000000
s hg19.chrY      7714564 192 +  59373566 AT--TT-TTTACTATAGATATTTTAAATGTTTCACTTGAGACCACAGTCTAATTTT---------AAAAAGAATACTTATTTATAATTATGTAGCTTCCTTTACATAGTTAGTATTATCTTTGTTTACTTCATGTACATGTCAAAAAAACCTCATGACTTATTAAGAATTCTATTGTTTACTTGAATATATTGGGCCAATAAAA
s rheMac2.chr3  61103446 194 + 196418989 ATTGTT-TTTACTACAGATACTTTCCATTTTTCACCTGAGACCACAGGCTAATTTC---------AAAAAGAATATTTACTTCTAATTATGTAGCTTCTGTTACATAGCTAGTATTGTCTTTGTTTACTTCATGTATATGCCAAAAAGACCTGATAACTTATGAAACATTCAACTGTTTACTTCAACAAACTGGCTCAATAAAT
q rheMac2.chr3                           999999-9999999999999999999999999999999999999999999999999---------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3 C 0 C 0
s ponAbe2.chr8 105363680 193 - 153482349 AT--TTCTTTATTATAGATACTTTCAACTTTTCACCTGACACCACAAGCTAATTTT---------AAAAAGAATATTTATTTCTAATTATGTAGCTTCTATTACATAGCCAGTATTGTCTCTGTTTACTTCATGTTTATGCCAAAAAGACCTCATGACTTATTAAATGTTCAACTGTTTACTTGAATAAATTGGCCCAATAAAT
q ponAbe2.chr8                           99--9999999999999999999999999999999999999999999999999999---------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8 C 0 C 0
s panTro2.chrY    568173 192 +  23952694 AT--TT-TTTACTATAGATATTTTAAATGTTTCACTTGAGACCACAGTCTAATTTT---------AAAAAGAACACTTATTTATAATTATGTAGCTTCCTTTACATAGTTAGTATTATCTTTGTTTACTTCATGTACATGTCAAAAAAACCTCATGACTTATTAAGCATTCTATTGTTTACTTGAATATATTGGGCCAATAAAA
q panTro2.chrY                           00--00-0000000000000000000000000000000000000000000000000---------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s danRer6.chr4  46528587 190 +  71658100 ---att-tttaaaaattatattttagatattt--tttaGCAAAAGATTTAAAATTCTGTGTAGCAACAAGTAAGCTTTACTTGTATCCATACA-CTTTTTTTCCTAAGTAAACTTTCtttaaaattaataaataaataaatGAACAAATGCTTTAAACGTTTTAAAA--CCTATAATAAAC---AAAATATATGCACAACAA--
i danRer6.chr4 C 0 N 0

a score=76748.000000
s hg19.chrY      7714756 225 +  59373566 TTAATAAACTCAATTAT-GTCATTTTTATAGAGTAAAATAGACAACAACTAAACAAATATTGGCTTATTGGATTAAATAGAATTCTATAATTGA---AAAATGTAAAATGTACAAAATAAATAAC--------ATATACACACTATAAAATTACTCACATGTG-AAAATTATTTTCTGAAAAGCATTAAATTTTATCTAAGTCACTTTCATAATTTCTGAGGGGAGTGTAGAAAGAAT
s rheMac2.chr3  61103640 211 + 196418989 TTAATAAACACAATTAT-GTCAATTTTATAAAGTAAAATGAACAATAACTAAACAAA--------AATTGGATTAAATAGCATTCTCTAATTGAAACAAAATATAAAATATACTAAACATACA----------ATACATGCACTATGAAATTATTCACATGTGAAAAATTATTTTGTGAACACCATTAAATATTATCAAAGTCACTTTCATAATCTCTGAGGGGATTATA--------
q rheMac2.chr3                           99999999999999999-999999999999999999999999999999999999999--------9999999999999999999999999999999999999999999999999999999999----------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--------
i rheMac2.chr3 C 0 C 0
s ponAbe2.chr8 105363873 225 - 153482349 TTAATAAACTAAGTTAT-GTCGATTTTATAAAGTAAAATGAATAATAACTAAACAAA--------AATTGGATTAAATAGCATTCTTTAATGGAAACAAAATATAAAATATGCTAAATATAGAACATACA---ATATGCACACGGTTAAATTACTCACATGTG-ACACTTATTTTGTGCATACCATTAAATTTTATCAAAGTCACTTTCATAATCTCTGAGGGGATTATACAAAGAAt
q ponAbe2.chr8                           99999999999999999-999999999999999999999999999999999999999--------99999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8 C 0 I 245
s panTro2.chrY    568365 225 +  23952694 TTAATAAACTCAATTAT-GTCATTTTTATAGAGTAAAATAGACAACAACTAAACAAATATTGGCTTATTGGATTAAATAGAATTCTATAATTGA---AAAATGTAAAATGTACAAACTAAATAAC--------ATATACACACTATAAAATTACTCACATGTC-AAAATTATTTTCCAAAAAGCATTAAATTTTATCTAAGTCACTTCCATAATTTCTGAGGGGAGTGTAGAAAGAAT
q panTro2.chrY                           00000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000---0000000000000000000000000000--------000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s danRer6.chr4  53554105 196 +  71658100 tcaaaaaaccataatatgggctctTTAACAAAATAAA---TACACTATTTAAATAAA-------ATGCGCAATAAAATAGAAATCAACAAGTGA-----AATACAAGA------AACTGTAGAACTATTATGGTTATAAACTATATAAATACACACACATGTA-AGAGTCCATCTATTAGTCCCATGA--------CGGAGCTAACAGCATGGG---TGAAGGTTAAAT---------
i danRer6.chr4 N 0 C 0

a score=17800.000000
s hg19.chrY      7714981 250 +  59373566 GCCtgtttgtttgtttgtttgtttgtttgtttg--------tttgtttgttttttgagatgaagtttcacttcattgcccaggctggagtgcaa---tggcaccatcttggatcactttaatgtttg---tcccctgagttaaagtgattctc--------cattactcagccccctgagtagctgggattacaggagcccaaca-----tcatggccagataat-ttttgtaattttagtagagacaac--gtttcaccatgttggccaggctggtctc
s panTro2.chrY    568590 238 +  23952694 GCC------------TTtttgtttgtttatttg--------tttgtttgttttttgagatgaagtttcacttcattgcccaggctggagtgcaa---tggcaccatcttggatcactttaatgtttg---tcccctgagttaaagtgattctt--------ccttactcagccccctgagtagctgggattacaggagcccaaca-----tcatggccagataat-ttttgtaattttcgtagagacaac--gtttcatcatgttggccaggctggtctc
q panTro2.chrY                           000------------000000000000000000--------00000000000000000000000000000000000000000000000000000---000000000000000000000000000000---00000000000000000000000--------00000000000000000000000000000000000000000000-----000000000000000-000000000000000000000000--0000000000000000000000000000
i panTro2.chrY C 0 C 0
s danRer6.chr4  53554301 261 +  71658100 --------GCGTGTAAACCTTTTAGCACATGTGAAAAGAAATATTTTTGTTTGTTATAATTTATTTTAATTTGTTT--CTAGCTCAGAATTTTAATCTGACTCCAATTTATAATAATTTTAGATTTAGATTCATCTAATTCAAGCTGATTACCTAATAGGTCGTGATTAGGTC-------TAAGTTAGATTG-ATTAACCCAATAAATCCTTATATTTAATTAATGTTTCATCGTTTACTTAAAGTCGCTTAGAATCAGTATGCTGGCCAGTTTTATCT-
i danRer6.chr4 C 0 N 0
e rheMac2.chr3  61103851   0 + 196418989 C
e ponAbe2.chr8 105364098 245 - 153482349 I

a score=5624.000000
s hg19.chrY      7715231 80 +  59373566 aaactcctgatctctggagatctacctggcttggc----tgcccaaagtgctggaatttcaggcatgagccaccaagtccagcc
s panTro2.chrY    568828 80 +  23952694 aaactcttgatctctggagatctacctggcttggc----tgcccaaagtgctggaatttcaggcatgagccaccaagtccagcc
q panTro2.chrY                          00000000000000000000000000000000000----000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s danRer6.chr4  21698502 67 -  71658100 AATCTTTTCATAAAATGGAAGATATCTAGCCTGACAATATACTTCCATGGCCGGAA--------AAGATTTAGCA---------
i danRer6.chr4 N 0 C 0
e rheMac2.chr3  61103851  0 + 196418989 C
e ponAbe2.chr8 105364098 245 - 153482349 I

a score=15324.000000
s hg19.chrY      7715311 84 +  59373566 CAAAGAGTGT-TTTATGAAATTAGATGaa---aaaattatatattatatttaGGGTGAGCAACAGGCAAACATACAAAAAAAGAGAAA
s rheMac2.chr3  61103851 87 + 196418989 CAAAGAATGT-TTTATGAAATTAGACGAAAAGAAAATTACATATTATGTCTATGGTGAGCAATAGGCAAACAAACAAACAACAAAAAA
q rheMac2.chr3                          9999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3 C 0 I 4
s panTro2.chrY    568908 83 +  23952694 CAAAGAGTGT-TTTATGAAATTAGATGAA---AAAATTATATATTATGTTTAGGGTGAGCAACAGGCAAACATACAAAAAAA-AGAAA
q panTro2.chrY                          0000000000-000000000000000000---00000000000000000000000000000000000000000000000000-00000
i panTro2.chrY C 0 C 0
s danRer6.chr4  21698569 57 -  71658100 CCACGAGTGCACCTGTGGA-------------AAAAATAAATGT---------------CAGAGGGaaaatattaaataaaaaaa---
i danRer6.chr4 C 0 C 0
e ponAbe2.chr8 105364098 245 - 153482349 I

a score=72032.000000
s hg19.chrY      7715395 166 +  59373566 AATTTGCAGAAGATT----ATTCTAAGCCACTAGCAATAACACTTTACATCATGGAGTTTAATACAAAGCAGAGAAAATAGATTTGCTTTGAAAATCTTTGAAGTTTCTGGT----TTGTTGGTAAGATATGAACACTTGTAAAATTATCTGTTTTATTCTAATATTTTTCTTT
s rheMac2.chr3  61103942 166 + 196418989 AATTTGCACAAGATG----ATTCTAAGCCAGGAGCAATAACATTTTAGATAAATGAATTTAATACACAGCAGAGAAAATAGATTTGCTTTCAAAATCTTTGAAGTTTCTGGT----TTGCTGGTAACTGATCAAAGCTTGTAAAATTATCTATTTCACTCTAATATTTTTCTTT
q rheMac2.chr3                           999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3 I 4 C 0
s ponAbe2.chr8 105364343 163 - 153482349 AATTTGCACAAGATG----ATTCTAAGCCAGGAGCAATAACATTTTAGATAAATGAGTTTAATACAAAGCAGAGAAAATAGATTTGCTTTCAAAATCTTTGAACTTTCTGGT----TTGCTGGCAAGTTATCAACACTTGTAAAATTATCTATTTCATTCTAATATTT---TTT
q ponAbe2.chr8                           999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999999999999999999999999---999
i ponAbe2.chr8 I 245 C 0
s panTro2.chrY    568991 166 +  23952694 AATTTGCAGAAGATT----ATTCTAAGCCACTAGCAATAACATTTTACATCATGGAGTTTAATACAAAGCAGATAAAATAGATTTGCTTTGAAAATCTTTGAAGTTTCTGGT----TTGTTGGTAAGATATGAACACTTGTAAAATTATCTGTTTTATTCTAATATTTTTCTTT
q panTro2.chrY                           000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----0000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s danRer6.chr4  21698626 170 -  71658100 aattCACAATTCATTTTCATTTACAATTTAAAAACAATTACAAATAAAAAAAGACACATT--TATCAAGATGATTACACAAACTTAATCAGAAATTCACTACAGTTTATGGTAAAAATTCAGATAAGAAAAGAAACTGCATTTTCTTGTTGTTTTTATTCAGATATTTGTTT--
i danRer6.chr4 C 0 C 0

a score=25600.000000
s hg19.chrY              7715561 110 +  59373566 TCTTCTCAATGTAAG----CAA-----TGATAAACAAATATGATTA--T--------TTTCTATCA---------------------------------ATTTA--TTACATGCCTAAAGTTTATTTTACAGTAATATGCTTCTTATATTTAAATTCATGTAAA
s panTro2.chrY            569157 110 +  23952694 TCTTCTCAATGTAAC----CAA-----TGATAAACAAATATGATTA--T--------TTTCTATCA---------------------------------ATTTA--TTACACGCCTAAAGTTTATTTTACAGTAATATGCTTCTTATATTTAAATTCATGAAAA
q panTro2.chrY                                   000000000000000----000-----0000000000000000000--0--------000000000---------------------------------00000--0000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105364506 148 - 153482349 TCTTCTCAAAGTAGGTACATAA-----CCATAAACAAATATGATTA--T--------TCTTTATAATCATATTTAGATTACACACCTAAATATGATCATATTTAGGTTACACACCTAAAGTTTATTTTAGAGTGATATA-TCTGTATATTTAAATGCATGTAAA
q ponAbe2.chr8                                   9999999999999999999999-----9999999999999999999--9--------9999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s rheMac2.chr3          61104108 113 + 196418989 TCTTCTCAAAGTAGGTACACAA-----CCATAAACAAATACGATTACTT--------TCTCTATAA---------------------------------ATCTG--TTACA--CCTAAAGTTTATTTCATAGTGATATA-TTTGTATATTTAAATCCATGTAAA
q rheMac2.chr3                                   9999999999999999999999-----9999999999999999999999--------999999999---------------------------------99999--99999--99999999999999999999999999-999999999999999999999999
i rheMac2.chr3         C 0 C 0
s xenTro2.scaffold_337    592343  98 -   1286505 TATGCCCAATGCAAA------A-----TACAAAACAAATAAAACCG--C--------ATGTTAACA---------------------------------ATGT---TCACT---------TTTATTTTAAAAATACAAAACACCCATGCCAAAATGTAGATAGA
i xenTro2.scaffold_337 N 0 C 0
s danRer6.chr4          21698796 117 -  71658100 ATTTTTAAATGTAAAAAGTCAAATGTTTTAAATACAATTTTAATGA--TGGCGTCAGTATTTATTA---------------------------------ATTAA--TAATT-----GATTTTCATCATTAGGAAAAGTA-----AGCATTTAAATTTTTGTCAA
i danRer6.chr4         C 0 N 0

a score=37351.000000
s hg19.chrY              7715671 170 +  59373566 TCA----AAACTAAAGTTCTGTATGTGTTTATCAGAGCAGAGATGTCATATATTTAATAGAACAAAAGTAGGAT-AAAAGTTGTAAATAGTTGTTTAGTATTCAGAAACATATAGCTCCATTATACTAATTTATATCTTCATTACCACCATCATAATAAGCTGTAGTTACAAAGA
s panTro2.chrY            569267 170 +  23952694 TCA----AAACTAAAGTTCTGTATGTGTTTATCAGAGCAGAAATGTCATATATTTAATAGAACAAAAGTAGGTT-AAAATTTGTAAATAGTTGTTTAGTATTCAGAAACATATAGCTCCATTATACTAATTTATATCTTCATTACTACCATCATAATAAGCTGTAGTTACAAAAA
q panTro2.chrY                                   000----0000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105364654 166 - 153482349 TCA----AAACTAAAGGTCTGTATGTGTTTAGCAGACCAGAGAATTCATATGTTTAACAGAA-AAAAGTATGAT---ATTTTGTAAATAGTTGTTCAGAATTCAGAAACAAATAGCTCCATTATACTCATATA-ATCTTCATTACAACTGTCATAATAACCTGGAGTTACAAGAA
q ponAbe2.chr8                                   999----9999999999999999999999999999999999999999999999999999999-99999999999---99999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s rheMac2.chr3          61104221 164 + 196418989 ACA----AAATTAAAGGTCTGTATGTGTTTAGCAGACCAGAGAAGTC--ATGTTCAACAGAA-AAAAGTAGGATAAAATTTTGTTAATAGTTGTTCAGAATTCAGAAACATATAGCTCCACTATACTCATA---ATCTTTGTTACAACCATCATAATAACCTGTAGTTACAA-CA
q rheMac2.chr3                                   999----9999999999999999999999999999999999999999--9999999999999-99999999999999999999999999999999999999999999999999999999999999999999---99999999999999999999999999999999999999-99
i rheMac2.chr3         C 0 C 0
s xenTro2.scaffold_337    592441 129 -   1286505 GTGCTGCATACTAAA------TATATGT-----AGTACATATACGTAGTACATTTCCTATACAAGAAGT--------------TTAATAGGCAATCATTATT-----ACATCTA-------------AGTAGAGGTCTATACAAACCTTGTTGGGGGAAGATGTAGTTTAAG---
i xenTro2.scaffold_337 C 0 N 0
s danRer6.chr4          47311257 106 +  71658100 ----TAGAAACTATCTTTCTATATGT----------------CAGTTGTACA-----------ATCAGTTTGAT------TTCTCTACAG-TGTTTCGAGTTCA---------AGCTG----------------TTTTTTACTACCACCCTCT------GCTACTTTTACAGGTA
i danRer6.chr4         N 0 C 0

a score=108848.000000
s hg19.chrY             7715841 368 +  59373566 AAACAAAAATATAAGTTTTAAGAAATATACTTTCCAAATTATTT-----TAAGTTAAAAAACACTGACAACACAA---AAACATTACTAGAGATGTTATTCCCCTGTCCCCAAGTAGCATATTGTTACCATCTGTTACCTATAGCCTT-GGTTAATAT----GGGATAACTTAACATCGGTGGCAAGATACACATTCAATGTACA-ATAGCTTTAACATGA----TAACAACAATAT---TGGTTTATTAAAACAAATAGAGTCCACACATTGT---------CATTAAAAAGGCATTTTAGAATTCACTTTATTTTGATTACCTT-----AATTTGCA---AATGGTAAATCAATTT----------CCAACTAAAAATCAAATTGTT--TCTTT--TACTATGCAGAATGTT--------------GCCCTT
s panTro2.chrY           569437 368 +  23952694 AAACAAAAATATAAGTTTTAAGAAATATACTTTCCAAATTATTT-----TAAGTTAAAAAACACTGACAACACAA---AAACATTACTAGAGATGTTATTCCCCTGTCCCCAAGTAGCATATTGTTACCATCTGTTACCTACAGCCTT-GGTTAATAT----GGGATAACTTAACATCAGTGGCAAGATACACATTCAATGTACA-ATAGCTTTAACATGA----TAACAACAATAT---TGGTTTATTAAAACAAATAGAGTCCACACATTGT---------CATTAAAAAGGCATTTTAGAATTCACTTTATTTTGATTACCTT-----AATTTGCA---AATGGTAAAGCAATTT----------CCAACTAAAAATCAAATTGTT--TCTCT--TACTATGCAGAATGTT--------------GCCCTT
q panTro2.chrY                                  00000000000000000000000000000000000000000000-----00000000000000000000000000---0000000000000000000000000000000000000000000000000000000000000000000000-000000000----0000000000000000000000000000000000000000000-000000000000000----000000000000---0000000000000000000000000000000000---------0000000000000000000000000000000000000000000-----00000000---0000000000000000----------000000000000000000000--00000--0000000000000000--------------000000
i panTro2.chrY        C 0 C 0
s ponAbe2.chr8        105364820 367 - 153482349 AAACAAAAATGTAAGTTGTAGGAGCCATATTTTCCAAATTATTT-----TAAGATAAAGACCACTG-----ACAA---AGGAATCACTAGGGATGTTACTCCACTGTCACCCAATAGTATAGTGTTACCATCTCTTACCTACAACCTT-GGGTAAGAT----GGGATAAGTTAATATCAGTGGCAAGGTACACATTCAAAGTAAA-ATAGCCTTAATACAA----TAACAACAATTT---TGGTTTATTAAAACAAGTTAAGTCCACACATTGT---------CAATAAAAAGTCATTTTGAAATTCACTGTATTTTAATTGCCTT-----AATTTGCA---AATGGTAAAGCAATTT----------CCTTCTAAAATTCAAATCATT--TCTCT--TACTATGCAGAATATCCTGA----------TCACTT
q ponAbe2.chr8                                  99999999999999999999999999999999999999999999-----99999999999999999-----9999---9999999999999999999999999999999999999999999999999999999999999999999999-999999999----9999999999999999999999999999999999999999999-999999999999999----999999999999---9999999999999999999999999999999999---------9999999999999999999999999999999999999999999-----99999999---9999999999999999----------999999999999999999999--99999--99999999999999999999----------999999
i ponAbe2.chr8        C 0 C 0
s rheMac2.chr3         61104385 343 + 196418989 AAACAAAAATGTAAGTTATAGAAACCATATTCTCTAAATTATTT-----TAAGTTAAAGACCACTG-----ACAA---AGGGATCACTAGAGATGTTATTCCACTGTTACCCAACAGTATATTG----------TTACCTATAACCTTGGGTTAAGAT----GGGATAAATTATCATCAGTGGCAAGATACATATTCAGTGTAAA-ATAGCCTTAACACAG----GAACAACAATTT---TGGTTTATTAAAACAAATTAAGTTCACACGTTGT---------CATTAAAAAGGCATTTTGAAATTCACTGTATTTTAATAACCTT-----AATTTGCA---AATGGTAAAGCAATTT----------CCTTCTAAAATTCAAATTGTT--TCTCT--TACTAAGCAGA-------------------------
q rheMac2.chr3                                  99999999999999999999999999999999999999999999-----99999999999999999-----9999---9999999999999999999999999999999999999999999999----------999999999999999999999999----9999999999999999999999999999999999999999999-999999999999999----999999999999---9999999999999999999999999999999999---------9999999999999999999999999999999999999999999-----99999999---9999999999999999----------999999999999999999999--99999--99999999999-------------------------
i rheMac2.chr3        C 0 I 15
s xenTro2.scaffold_38    576641 304 -   3962478 AGAAAGAAATACTATTTTT---AATCGTACTT-----ATTATTTACAAATAAATTCAGAACCAATG-----AAAA---------TACTATGTATATTGGGAAGCTGCTTATAAAT-GCATTTTCTTTCATT---ATGCCAAAAAA----AATTGAGGT----GAAATAA---------AAAAACAAGAAGAATGTTTAGCATAAACACAG-------AAGA----TACAAAAAATAT---GGATTTATTAAAGCAAAT---------ACCCTGT---------AAGACAAGAGCTGTTGCTGA---CACAGTGTT---ATTCTTTG-----CATTTCCC---AGGAAT------------------------CTTAGAATTGGATGGTT--TGTTCCATGTTATGCAGGACCCT--------------G-TCTT
i xenTro2.scaffold_38 N 0 N 0
s danRer6.chr4         47311363 399 +  71658100 GAAATAAGACATAAGTTAGAATAGATTTAATTAGATAACTGGTT-----CATTGCAAATAAATGTG-----ACACATTAGGCTTTGATTAAAATTATAGTTTTCTGG-ATCAAGGAGCAATATGC---------AAACAAATATTTTT-TTTTACTACCAAAGGAATAAAGTATTGCATTATGTTATATACAGTATTATTGTACT-ATTATTACATCATGCATTTTAACAAAAACATACATTGTATATTACAACA--------TCACACTATGTGTtatatacagttgaagtctgatttattagcccgct---ttttaattttttttcaccaatttctgtttaatggagagaagatttgttcagcacattttttaaacatcaaagttttaataact--cattcctaagaactgttttattttatctttgccctg
i danRer6.chr4        C 0 C 0

a score=69438.000000
s hg19.chrY              7716209 315 +  59373566 ---------ACCACACTCTTATCATACTGTCATT--TATGATACCCAATTAAACCATCCACT--AAGTTGCCTCTGCACATATAAATTC-----------TTCAAGT------------------------ATATTAGATTT--------GGTTTTCCTCATCTTCC--ATGGAAAAGTATATAAATCTGTCCTTCT-------------------AATATAGAAGAATCTC----TCATAACTCTGGTGCAGCAACTATTG--ACCATGTTCTTTCACATACA---------------TTCCAGAAATAAAGATATAACATCAAA------------------GTAAGAGATAAA---TTACATCAATATTTGTTTTTGAAAATACtta--ttattttca--aaaaatattaaattattttaatataaata---ta--GATT
s rheMac2.chr3          61104743 295 + 196418989 ---------ACCACACTCCTATCATCCTGTCACT--TACGACACCGCTGTAAA----CTACT--AAGTGGCCTTTCCACTTAGGATTTC-----------TTCATGT------------------------ATCTTAGATTT-------CAGTTTACTTAATCTTCC--ATGGGAAAGTATATAAATCTGTCCATCT-------------------AATAGAGAAGAACCTC----TCATAACTCTGGTGCAGCAATCATTG--ACCATGT--TTTCACATAAA---------------TTCTAGAAATGAAGACATAGCATCAAA-----------------TGTAAGAATTAAA---TTACATCAATATTTGCTTTTG--------------------A--AAAAATACTGAATCCTTTTAATATAAAAA-AGTA--GGTT
q rheMac2.chr3                                   ---------9999999999999999999999999--99999999999999999----99999--9999999999999999999999999-----------9999999------------------------99999999999-------999999999999999999--9999999999999999999999999999-------------------9999999999999999----99999999999999999999999999--9999999--99999999999---------------999999999999999999999999999-----------------9999999999999---999999999999999999999--------------------9--99999999999999999999999999999-9999--9999
i rheMac2.chr3         I 15 C 0
s ponAbe2.chr8         105365187 300 - 153482349 ---------ACCACTCTCCTATCATCCTGTCACT--TATGATACTGTTGTAAACCAACCACT--AAGTGGCCTTTCCACTTAGAATATC-----------TCCATGT------------------------ATCGTAGATTT-------CAGTGTTCTTAATCATCT--ATGGGAAAGTATATAAATCTGTCCATCT-------------------AATATAGAAGAACCTC----CCACAGATCTGGTGCAGCAACCATTG--ACCATCTTCTTTCACATAAA---------------TTATAGAAATGAATACATAGCATCAAA-----------------TGTAAGTGTTAAA---TTATATCAATATTTGCTTTTG-----------------------aaatatattaaattcttttaatataaaaa-aGTA--GGTT
q ponAbe2.chr8                                   ---------9999999999999999999999999--99999999999999999999999999--9999999999999999999999999-----------9999999------------------------99999999999-------999999999999999999--9999999999999999999999999999-------------------9999999999999999----99999999999999999999999999--99999999999999999999---------------999999999999999999999999999-----------------9999999999999---999999999999999999999-----------------------99999999999999999999999999999-9999--9999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            569805 315 +  23952694 ---------ACCACACTCTTATCATACTGTCATT--TATGATACCCAATTAAACCATCCACT--AAGTTGCCTCTGCACATATAAATTC-----------TTCAAGT------------------------ATATTAGATTT--------GGTTTTCCTCATCTTCC--ATGGAAAAGTATATAAATCTGTCCTTCT-------------------AATATAGAAGAATCTC----TCATAACTCTGGTGCAGCAACTATTG--ACCATGTTCTTTCACATACA---------------TTCCAGAAATAAAGATATAACATTAAA------------------GTAAGAGATAAA---TTACATCAATATTTGTTTTTGAAAATACtta--ttattttca--aaaaatattaaattattttaatataaata---ta--GATT
q panTro2.chrY                                   ---------0000000000000000000000000--00000000000000000000000000--0000000000000000000000000-----------0000000------------------------00000000000--------00000000000000000--0000000000000000000000000000-------------------0000000000000000----00000000000000000000000000--00000000000000000000---------------000000000000000000000000000------------------000000000000---0000000000000000000000000000000--000000000--00000000000000000000000000000---00--0000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_173   1404008 380 -   2086552 ---------AGCAGAATGCAATTGCACTGCTATTAGCAAGAAAATGATAGAGGTCTACAGTA--AGGTTACCAGATCACATAAAAATTCAATAACACAAATTCATGTTGCAGGGCAGCACTGACTGGATTCAACTTTAATTA-------CAATTGGTGCAACCCTTCTAGTTGGATTTTTTTTAAATGTATCCCTAG-------------------ATTTTCAAGTGATTTTGTAACCCTAGTCTTGGGAGATTCACCTTTGTTACAATGG--GATCACATAAA---------------TTAGTCATATAGGATTAAGGGGTCAAACCCTAAGTTATGTCAGTTGTCACAAATCAGCCCTTGAGTCAGGATCTAATTTTAAAGAAGCTGAAGTGATTTGCAACAAACAAATTAGGTAACTGTAGTGTAAATA---TA------
i xenTro2.scaffold_173 N 0 N 0
s danRer6.chr4          47311762 359 +  71658100 atgacagtaaataatatttgactaga-tattctt--caagacacttttata------ccacttaaagtgacatttg-----aaggttta-----------actaggt------------------------aaattaggttaaataggcaggttagggtaattaggc--aagttattgtataacgatggtttgttttgtagactatgccaaaaaaaaaaaaaaaaaaagctt----aaagaggctcataatattgaccttga--aaaatgt-attcgaaataaaacaaataagactttctcccagaagaaaaaatat--tatcata-------------cctgtgGTAGCaaaaaa---ataaataaata--tattttta--aataaGTA--CTATTTCAA--GATAATACCTCAGACTCATTGTTTAGAAAAAGTACAAATT
i danRer6.chr4         C 0 N 0

a score=421775.000000
s hg19.chrY      7716524 1047 +  59373566 CCCTTTAGGGgaaagtgatctagattgctgactagaaagaggcagctagactgcggagttcccatagacaggaatgcaaggtgtgcataaatacataactttcagtggaaacttccagttatttccatcaggactaatcaaagaagcaacttaacataagaagaatggagtaaagcaagacaggacactgggactcttgaaaacaacatggaggcagggaaactgtcacacccagtaaggcagaatgtgaatgtgagatcctgggaacccatgattcttccacagatctttgcaaccctctggtgaggtgatcccctcataaacccacttcaccaaagccttctgtataggacacatagctacatggagtctcagcagagcagccgctcaggattgtgcagtgattcaaaagccttagata-gatatgtttctaggcttcccagaaaaagtagctgcaattccagaaaagaaggatgctacaaccctgtacatactcataggaaaaaggcagaatccagggggcttagcagtgatggtctgtaggaaacattttctcagtgcctcac------agatgtactggctttgaattccagccaatgattggtagaagcactgcacctccctgggatcaagcaatcagaaaaaggagttggccacaatctttgctgcttgataaacttagccattccagccttcagacttcgaggagcccaagcttactagaagcacaaaggatctcttagcacagtacaggtgctctaaaaagacatggccagactgcctgttaaagcaggtccccaatctccttcttcctcactgaaaagtacttcccaatgagtatctccagctaacatcactggccctgtttcgtagatggaattttgaaatcttttttggctatagttcctagagcaaagagtgagctgccattttttcctgtttgtgtgactaagctgttcctgcctcctggctttggaggatccaaataaactgtggatggaagtggtacctctgcaaagcagagctgttctacaaaaatgtggctagact
s rheMac2.chr3  61105038 1036 + 196418989 CCTTTTAGAGAAAAGtgatcgagactgctgactagaa----gcagctagactgtgtagttctcatagagaggaatgcaaggtatacacaaatacagcacctgcaactgaaacatccaggtacttgcattgggaataatcaaagaaacaact-----tatggagaatggagtaaagaaaggcaggacagtgggccacctgggaacaacgtggagccaagggaacctccccacccagtaaagcagtgagtgtatgtgtgaccctgggaacgcacaattctcccacagatcttcgcaaccttcaggtgaggagatactctcatggacccacttcaccaaggccttcagtttaacacacagagctacatggagtcttagcagagcagctactcaggcctgtgca--aattcaagagctttagata--ctggctttccaggctt-ccagaaaaagcagctgcaacttgagcaaagcaggagtttacacccctgtacatactcataggaaagaggcagaatccagggggctgagtagtgatggtctgtaggacccacttctacaatgcctcacacagtaagacctactggcttag-attccagccaaccattggtagcagcactgcacctccctgggatggagctaccagaaagaggagtgggtcaccatctttgctgcttgggcaacttagccattccagccttcaggcattgaagagcccaagctgactgggggcagaaaggatctcctagcacagtacaggtgctctaaaaagacaagaccagactgcctgttaaagcaggtccccagtttcattccttctcactggaaagtacttcccaatgagggtctccagctaccaccaccagcgctctttggtggatggagttttgaaacctctttgtgatatagttcctagaaggaagagtgagttgccatttttg-ctgtttgtgtg--ttagctcttccagccttctggctttggagaatccaaataaactgggggtggaagtggtacctctgaacagcagagttgtcctacaaaaatgcggttagact
q rheMac2.chr3                            9999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999--9999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3 C 0 I 2908
s ponAbe2.chr8 105365487 1044 - 153482349 CCTTTTAGAGAGAAGtgatcaagtttgctgattagaa----gcagctagactgggcagctctcctagagaggaatgcaaggtatgcataaatacagcacattcaactgaaacatccaggtactcgcattgggactaatcaaataaacaacttaagttatggagaatggagtaaagcaaggcaggacaatgggccacctgagaacaacactgagccaagggaacctccctacccagtaaagcagtgagtgcaggtgtgaccctgggaactcacgattctcccacagatctttgcaactctcaggtgaggagataccctcatgaacccacttcaccaaggccttcagttgaacacacagagctacatggagtcttagcagagcagccactaaggcctgtgcagagattcaagagccttagatcctccggctctccaggcttcccagaaaaattagttgcaactccagcaaaacaggagcttactcccttg----tacccataggaaacaggcaggatccaggggactgaacagtgatggtccgtaggacccacttccacagtgcctcacagggtaaggcctgctggcttagaattccagccaaccactggtagcagcactgcacctccctgggatggagctaccagaaagaggagtggcccaccatctttgctccttgggcaacttaggcattccagccttcaggctttgaagagctcaagctgactag-ggcagaaaggatctcctagcacagtacagatgttctaaaaagacatggccagactgtctgttaaagcctttccccagactcatttctcctcactagaaagtacttcccaaccagggtgaccagctaccaccactggtgctctttggttgatggaattttgaaacctctttgtgatatagttcctagagtgaagagtgagctgccatttttg-ctgtttatatgacttagctgtttcaggcttctggctttggagaatccaaaaaaactagcagtggaagtggtacctctacagagcagagctgtcctacagaaatgtggctagact
q ponAbe2.chr8                            9999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8 C 0 I 2881
s panTro2.chrY    570120 1031 +  23952694 CCCTTTAGGGGAAAGtgatctagattgctgactagaaagaggcagctagactgcggagtgcccatagacaggaacgcaaggtgtgcataaatacataactttcagtggaaacttccagttatttccatcaggactaatcaaagaagcaacttaacataaagagaatggagtaaagcaagacaggacactgggactcttgaaaacaacatggattcagggaaacagtcacacccagtaaggcagaatgtgaatgtgagatcctgggaacccatgattcttccacagatctttgcaaccctctggtgaggtgatcccctcataaacccacttcatcaaggccttctgtataggacacatagctacatgaagtctcagcagggcagccgctcaggattgtgcagtgattcaaaagccttagatacgatatgtttctaggcttcccagaaaaagtagctgcaactccagaaaagaaggatgctacaaccctgtacatactcataggaaaaaggcagaatccagggggcttagcagtgatggtctgtaggaaatattttctcagtgcctgac------agatgtactggctttgaattccagccaatgatcggtagaagcactgcacctccctgggatcaagcaatcagaaaaaggagttggccacaatctttgctgcttgataaacttagccattccagccttcagacttcgtggagcccaagcttactagaagcacaaaggatctctcagcacagtacaggtgctctaaaaagacatggccagactgcctgttaaagcaggtccccaatctccttcttcctcactgaaaagtacttcccaatgaatatctccagctaacatcac-----------------tggaattttgaaatcttttttggctatagttcctagagcaaagagtgagctgccattttttcctgtttgtgtgacttagctgttcctgcctcctggctttggaggatccaaataaactgtggatggaagtggtacctctgcaaagcagagctgttctacaaaaatgtggctagact
q panTro2.chrY                            000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000------000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-----------------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0

a score=190720.000000
s hg19.chrY      7717571 2207 +  59373566 ttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttccttccctccctccctccctccctccctcccttctttctctttctttctttctttctttccttccttccttccttccttccttccttccttccttccttccttccttccttctttctttctttctttctttctttctttctttctttctttctttctttcttccttccttccttccttctttctttcgagacagagtattccccctgttgcccaggctggagtgcactggggcaatctcagattaccacaacctctgcctgctgggttcaagaaattctcctacctcagccttccgactagctgggattacaggcatgtgccaccacgcctggataattgtgtatttttagtagagattcagtttcactatgttggtcacgctggtctctaactcccgactctggttgatctgcccacctcagcctcccaaagtgttgagattacaagcatgagctgctgcacccagcagactgctttcttaagtggatccccaatcactttcttttcactggggaatacctttcaagaggcatttccagctacatcctacaggtgcttttgggctgaaaacaggtttatacatccctgggatggaggtcccagagaaaagggcatgctgccattgttacttttttgcacattcactggtgataacttcagatgctggaaattctgaggtgactagatactgcagtggacacccagcctattgcagttgcagcagctcttcacagaagtggacagactgttacatgtgtttctgttcttatatattttcactgggtaggttcttcaggcctgggccactagccaatcattgccacagctattgagcaagtaacaacataagaactccatggacagagcttctgggggcaactgcatatatttattcactgtctctgcagtggaattgtccttgctgtcctgaaactaatgaaaaatccaaaaccctaagttccttattcacacctcaaacaagctgcagcataccaaaggaaaggaggtcagtccatcctccatgggtcccacagactccccagtgctcctcaccagacagtgagcccctaacttggccaaaagcacagattttccatccagggctgactgcactgagggattgatcacctacatctctcttagttgcagcccttcagaagactggcatacaggtggggcagcaagccagcttgttgatttctaagggtttggtgcaagagcatctatagcaaaatatggccagtgatggcgagttctctaggctgaactttctcctataagagattttagcctgaggggaaccattggaactaatttctacaggatgatgttgcaaatcagaagggggtggtccaactgaggactcttttgccacctggcctctcccagggtcgcagtctagctaaagcttcttacagggcagtctcaggtaccctagaagcccataccatagcatcagcctggtaatcaatgcttggcccctgaagagctccaggaaggcagacactatcattgcagcttacatgtatcttccccattctgcagcctacatgtatctttcccatactgcagcttcccctgacaccatggcaattccccatgttactttgctggcacatgtctgcaaaggtgggtttgactttgcttgccccaccagcaaatgggaatgcagtatgcttctactaccctcaggaacttctacagtagataaaactttggtaggcagaaagccagagagcctcatccctgcttttctgctaacactgtgtaacaaagagtgtattctcccactctctgaacaattattacttcatgggcggggggggcaaaaataaggcatcataaccttcactggcccgcatcctgcccaagccaacaccacctttagtgcaacagaccacacagtctccagcaggtacaggtgactcactctcagctgctttgtctttgccactgaggtgaatgcccaaagacagggagaaaccccatatccactaactctcttctaaagctgtgacaccttagtcacaaagagtggtggactccaaatatcaaggagccagaaaagacagttggagctcgatacaatttccccagagtatgcagcctctgaattgtgagctgagcatagcccctccaccaccaagaa
s panTro2.chrY    571151 2107 +  23952694 ttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcct-----------------------------------------------------tttccttcct-------------------------------------------ttctttctttctttctttctttctttctttctttctttctttctttctttctttctctctttcttccttctttctttcgagatagagtattccccctgttgcccaggctggagtgcactggggcaatctcagattaccacaacctctgtctgctgggttcaagaaattctcctacctcacccttctgactagctgggattacaggcatgtgccaccacgcctggataattgtgtatttttagtagagattcagtttcactatgttggtcacgctggtctctaactcccggctctggttgatctgcccacctcagcctcccaaagtgttgagattacaagcatgagctgctgcacccagcagactgctttcttaagtggatccccaatcactttcttttcactggggaatacctttcaagaggcatttccagctacatcctacaggtgcttttggactgaaaacaggtttatacctccctgggatggaggtcccagagaaaagggcatgctgccattgttacttttttgcacattcactggtgataacttcagatgctggaaattctgaggtgactagatactgcagtggacacccagcctattgcagttgcagcagctcttcacaaaagtggacagactgttacatgtgttcctgttcttatatattttcgctgggcaggttcttcaggactgggccactagccaatcattgccacagctattgagcaagtaacaacataagaactccatggacagaacttctgggggcaactgcatatatttattcactgtctctgcagtagaattgtccttgctgtcctgaaactaatgaaaaatccaaaaccctaagttccttattcacacctcaaacaagctgcagcataccaaaggaaaggaggtcagtccatcctccacgggtcccacagactccccagtgctcctcaccagacagtgagcccctaacgtggccaaaagcacagattttccatccagggctgactgcactgagggattgatcacctacatctctcttagttgcagcccttcagaagactggcaaaCAGGTggggcagcaagccagcttgttgatttctaagggtttggtacaagagcatctatagcaaaatatggccagtgatggccagttctctaggctgaactttctcctataagagattttagcctgaggggaactgttggaactaatttctacaggatgatgttgcaaatcagaagtgggtggtccaactgaggactcttttgccacctggcctctcccagggtcgcagtctagctaaagcttcttacagcgcagtctcaggtaccctagaagcccataccatagcatcagcctggtaatcaatgcttggcccctgaagagctccaggaaggcagacactatcattgcagcttacatgtatcttccccattctgcagcctacatgcatctttcccatactgcagcttcccctgacaccatggcaattccccatgttactttgctggcacatgtctgcaaagatgggtttgactttgcttgccccaccagcaaatgggaatgcagtatgcttctactaccctcaggaacttctacagtagataaaactttggtaggcagaaagccagagagcctcatccctgcttttctgctaacactgtgtaacaaagagtgtattctcccacactctgaacaattattacttcat----ggggggggcaaaaataaggcatcataaccttcactgccccgcatcctgcccaagccaacaccacctttagtgcaacagaccacacagtctccagcaggtactggtgactcagtctcagctgctttgtttctgccactgaggtgaatgcccaaagacagggagaaaccccatatccactaactctcttctaaagctgTGACACCTTAGTCACAAagagtggtggactccaaatatcaaggagccggaaaagacagttggagctcaatacaatttccccagagtatgcagcctctgaattgtgagctgagcatagcccctccaccaccaagaa
q panTro2.chrY                            000000000000000000000000000000000000000000000000000000000000-----------------------------------------------------0000000000-------------------------------------------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
e rheMac2.chr3  61106074 2908 + 196418989 I
e ponAbe2.chr8 105366531 2881 - 153482349 I

a score=0.000000
s hg19.chrY      7719778 167 +  59373566 aaaaatctcccaggaacaaagcttgttggttgcaaacaccttattccacatcaaatactccagaccattaaacggaataaaaaaattcaaaggtcaaccacctcaaagatatacatggaaacattagacaaaatcagtacaaaaattttgaaaacacaaaaagccgt
e rheMac2.chr3  61106074 2908 + 196418989 I
e panTro2.chrY    573258   0 +  23952694 C
e ponAbe2.chr8 105366531 2881 - 153482349 I

a score=612.000000
s hg19.chrY      7719945 48 +  59373566 agtgagttctttcatccaaatgatgaaattacatttccagtgaggcct
s danRer6.chr4   3019612 48 -  71658100 aggaaattattcaaaaggaaaaagggaatgaaatttataatgaagaca
i danRer6.chr4 N 0 C 0
e rheMac2.chr3  61106074 2908 + 196418989 I
e panTro2.chrY    573258  0 +  23952694 C
e ponAbe2.chr8 105366531 2881 - 153482349 I

a score=68021.000000
s hg19.chrY      7719993 830 +  59373566 -aaaaatctcccaggaaca----aagcttgttggttgcaaacaccttattccacatcaaatactccagaccattaaatgggataaaaaaattcaaaggtcagcagcctcaaagatatacatggaaacattagacaaaatcagtac----aaaaattttgaaaacacaaaaa----gtcatagtgacttctttcatccaaatgatgaaattacatttccagtgaggcctaagatgaca----gaagtagaattcagaataagg------aacttcattgagctacaaatttaactttcaacccattgcaatgaaggggaaaaaatgcaggaatggatagaa-----------aaaaacagccatttaggaggaaaatatgaccaa--tctgatagagctgaaaaaacacaatacaaaaactttataatttaatcacaagtataaacagtagaataggccaagcagaggaa----agaatctcagagcttcaacactggctttcttaaattagacaagaagag---------------taaaaacaataacaataataataataataaggaggaatgaaca-----aaacatctaag-atataagatttatgtaatgaatccaaatctgtggtcaaaaa---------gagtacctgaaggggatggagagaatgaaaaccacttgaaa------tacatatt----tctagata--tcatccatggaaa--------------------gccaagtcacctctaaat-gaaggacatcaaaca------aataataaatctttcagttga------aattctacttgtca----aagagatgaggggccaatattcaacattcttaa--gcaagaattttaaaccaaaatttatatccgataaaagtaaggttcaga-----------aataaaaaaatatatatgatcctattcagtt------------------------------aagc------------
s panTro2.chrY    573258 829 +  23952694 -aaaaatctcccaggaaca----aagcttgttggttgcaaacaccttattccacatcaaatattccagaccattaaatgggataaaaaaattcaaagctcagcaaactcaaagatatatatggaaacattagacaaaatcagtac----aaaaattttgaaaacacaaaaa----gccatagtgagttctttcatccaaatgatgaaattacatttccagtgaggcctaagatgaca----gaagtagaattcagaataagg------aacttcattgagctacaaatttaactttcaacccattgcaatgaaggggaaaaaatgcaggaatggatagaa-----------aaaaacagccatttaggaggaaaatatgaccaa--tctgatagagctgaaacaacacaatacaaaaactttataatttaatcacaaatataaacagtagaataggctaagcagaggaa----agaatctcagagcttcaatactggctttcttaaattagacaagaagag---------------tgaaaacaataacaataataataataataaggaggaatgaaca-----aaacatctaag-atataagatttatgtaatgaatccaaatctatggttaaaaa---------gagtacctgaaggggatggagagaatgaaaaccacttgaaa------tacatatt----tctagata--tcatccatggaaa--------------------gccaagtcacctctaaat-gaaggacatcaaaca------aataataaatctttcagttga------aattctacttgtca----aagagatt-ggggccaatattcaacattcttaa--acaagaattttaaaccaaaatttatatctgataaaagtaagcttcaga-----------aataaaaaaatatatatgatcctattcagtt------------------------------aagc------------
q panTro2.chrY                           -000000000000000000----00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----0000000000000000000000----00000000000000000000000000000000000000000000000000000000000000----000000000000000000000------000000000000000000000000000000000000000000000000000000000000000000000000-----------000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000000000000000000000000000000----000000000000000000000000000000000000000000000000---------------0000000000000000000000000000000000000000000-----00000000000-00000000000000000000000000000000000000000---------00000000000000000000000000000000000000000------00000000----00000000--0000000000000--------------------000000000000000000-000000000000000------000000000000000000000------00000000000000----00000000-000000000000000000000000--000000000000000000000000000000000000000000000000-----------0000000000000000000000000000000------------------------------0000------------
i panTro2.chrY C 0 C 0
s danRer6.chr4   3019660 949 -  71658100 aaagaatgtggtgggagaatgtgaagtat-ttagttaaaaa------gtttacgataaaatattgtagacaattacaaaattgtaaaaaatataaggaaaaggag-ctgaaagaaaaactagaaaacgaattgaaaaatgagaatggaaaaaaatatacaaaagataaaagaactgcaagaaaga-----ttgaaagaaatggaggaggagaaatttga---aggtgcaagattaagaagcaaagcaaaatttacagtagagggggaaaagtgcact-------aaatttttcttt-gatctagagaagagaagagggaag---tcagaaatgattagagaaataaggagcaaaaatgggaacatagtagaacaacatgaggagattttggaagaaataagatcatattatgagaaattgttttg-------cacaga-gggaataaaagaaaaag--aaaaaggggaattactaaatctaataaaatcaagagtaga------agaaggggaaaaaagagaatgtgacgaggagataagagaagaagaaataaaaagagcaattagt-ggattgaacaaaaagaaaagtccaggaatagatgggttgggtagtgaattttatattgtttttaaagatattttatctagtattttaaaggaa-gtatatgatgaa----atttgagaaATCATTAAAtgttacggtttaattaagttgtccggggaaaataaacgtaacacttataatattaaattatttctgagtagatggatggaaaatacaccaggacaccaaaatttacattcaattcatttattccttttatgaggagaagaaaaatgaagccaacaaaagagaggcttacatgtgtgcgctttgtac---aatgtatatataataataataagaagaagaagaagaagaagaaaaaaagaagaaatacaatcaaa---agttataggggaaaaaggaactagagtggcgccaaagcaaagaactaaac
i danRer6.chr4 C 0 C 0
e rheMac2.chr3  61106074 2908 + 196418989 I
e ponAbe2.chr8 105366531 2881 - 153482349 I

a score=7327.000000
s hg19.chrY                 7720823 75 +  59373566 ------aaatgctgaggaaatcttttaccacaagacctgccttttaagagcttctaaagaaaaca--ttaaataagaaagaga--
s panTro2.chrY               574087 75 +  23952694 ------aaatgctgaggaaatcttttaccacaagacctgccttttaagagcttctaaagaaaaca--ttaaataagaaagagg--
q panTro2.chrY                                     ------00000000000000000000000000000000000000000000000000000000000--0000000000000000--
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_289800       807 65 +      1831 ------aaatgccaagaaag-----tatcacaatgcatac------aaagaatccgaaaaagatgactcaattaagaaagaa---
q tarSyr1.scaffold_289800                          ------44532154242433-----646627769798999------699999999999999997999454425335547976---
i tarSyr1.scaffold_289800 N 0 C 0
s danRer6.chr4              3020609 78 -  71658100 aaaaccaaaagccacctaaa--ctagaacacaagatccccctct--aaacttactaataaaaat---caaaatgtgaaaaagaaa
i danRer6.chr4            C 0 N 0
e rheMac2.chr3             61106074 2908 + 196418989 I
e ponAbe2.chr8            105366531 2881 - 153482349 I

a score=492.000000
s hg19.chrY                 7720898 30 +  59373566 ctataaccagtcac--tacaaaaacacact--aa
s panTro2.chrY               574162 30 +  23952694 ctataaccagtcac--tacaaaaacacact--aa
q panTro2.chrY                                     00000000000000--00000000000000--00
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_289800       872 31 +      1831 -cagcaacaaaaat--tccaaaatcaaccttcaa
q tarSyr1.scaffold_289800                          -9656647239999--999999999999999999
i tarSyr1.scaffold_289800 C 0 N 0
s danRer6.chr3               224270 31 -  60907308 ccacacctgttcacaatcaagaaatcacct--a-
i danRer6.chr3            N 0 C 0
e rheMac2.chr3             61106074 2908 + 196418989 I
e ponAbe2.chr8            105366531 2881 - 153482349 I

a score=14539.000000
s hg19.chrY      7720928 137 +  59373566 aatacataaattg-ctgacactataaagca-accacataaatttgaaaatagcaaagatcatagtgacaaaatgaaatccatacacatgaatactaaacttgaatgaaaatgggctaaattccccaattaaaaaacaaa
s panTro2.chrY    574192 137 +  23952694 aatacataaattg-ctgacactataaagca-accacataaatttgaaaatagcaaagatcatagtgacaaaatgaaatccatacacatgaatactaaacttgaatgaaaatgggctaaattctccaattaaaaaacaaa
q panTro2.chrY                           0000000000000-0000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY C 0 C 0
s danRer6.chr3    224301 127 -  60907308 --aataggacctgtctgacaaagtgaagtagaccaaacgagcctcaaa--agctaga--catcatgccaaaatctaa---agacatttaaacac-aaatgagaaagaaaat--aCTAGTGTCACGAGTAAAAAAAAAAA
i danRer6.chr3 C 0 I 33
e rheMac2.chr3  61106074 2908 + 196418989 I
e ponAbe2.chr8 105366531 2881 - 153482349 I

a score=17788.000000
s hg19.chrY                7721065 149 +  59373566 gtggtgccaggcacggtggctcacacctgtaatcccagcactt--tgggaggccaagatgggc----agatcac--agggtcagga--gatcaagaccactctggctaacacggagaaaccccgtctctactaaaaatacaaaaaattagccatgaaaa
s panTro2.chrY              574329 149 +  23952694 gtggtgccaggcacggtggctcacacctgtaatcccagcactt--tgggaggccaaggtgggc----agatcac--agggtcagga--gatcaagaccaccctggctaacacggtgaaaccccatctctactaaaaatacaaaaaattagccatgaaaa
q panTro2.chrY                                     0000000000000000000000000000000000000000000--000000000000000000----0000000--0000000000--00000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s tarSyr1.scaffold_77585      5947 134 -      9862 CTCa-gccgggctcggtggttca-gcctgtaatccc-gtgctt--tgggaggctgaggtgagt----gtattgcctgagtccacgg--gttcgagacacgcctgggcaacttggtgagacctcatct---------atacaataaatca-----aaaaa
q tarSyr1.scaffold_77585                           9999-999999999999999999-999999999999-999999--999999999999999999----9999999999999999999--999999999999999999999999999999999999999---------9999999999999-----99999
i tarSyr1.scaffold_77585 N 0 C 0
s danRer6.chr3              224461 127 -  60907308 ---------------------cactcgcttactggcagtgcttgatgcaaatacagggtgagtgacaaaataat--aggcacacaaacgatcaataccatactgacaaacataaagagaaatgatgt--ggtataaatatgaaaaag-------ggaaa
i danRer6.chr3           I 33 C 0
e rheMac2.chr3            61106074 2908 + 196418989 I
e ponAbe2.chr8           105366531 2881 - 153482349 I

a score=14516.000000
s hg19.chrY                7721214 106 +  59373566 ttagccaggtgtggcagtgtgtgcctgtagtcccagctactcaggaggctgatggaggaggatggca----tgaacccagaaggaggagcttccagtga-------------gctgagattgc
s speTri1.scaffold_83644      6134  98 -      9325 TCagccagatgtggtgatgtatgcctttaatcccagagacttgggagacttaggctaaaggatcacaagtttgaggccagcatcagcatttttgaaaa-------------------------
q speTri1.scaffold_83644                           66849767858687689579775699979587999779698499989799579999999997987999897598946996778978989999579999-------------------------
i speTri1.scaffold_83644 N 0 C 0
s tarSyr1.scaffold_77585      6081 105 -      9862 ttagccagatgtggtagcgtgcatctgtggttccagcgacttgaaagcctggggcaaaaggatcgcc----agaccccagcaggttgaggctgcggtg--------------gccaggagtgt
q tarSyr1.scaffold_77585                           9999999999999999999999999999999999999999999999999999999999999999999----999999999999999998999999999--------------99999999999
i tarSyr1.scaffold_77585 C 0 C 0
s panTro2.chrY              574478 106 +  23952694 ttagccaggtgtggcagtgtgtgcctgtagtcccagctactcaggaggctgatggaggaggatggca----tgaacccaggaggaggagcttccagtga-------------gctgagattgc
q panTro2.chrY                                     0000000000000000000000000000000000000000000000000000000000000000000----0000000000000000000000000000-------------00000000000
i panTro2.chrY           C 0 C 0
s danRer6.chr3              224588  97 -  60907308 ---------------tgagagctcctgtgactgcaaata-----aaagcagatgacaagaggtaatc----tgtaacccagaacaggaggtgagagcaaaggcgtgaggtacggtgacagt--
i danRer6.chr3           C 0 C 0
e rheMac2.chr3            61106074 2908 + 196418989 I
e ponAbe2.chr8           105366531 2881 - 153482349 I

a score=4928.000000
s hg19.chrY                7721320 65 +  59373566 accactgc----actccagtctgggcaacagagcaagact---ctgtctcaa--------acaaaacaaaacaaaaaaat
s panTro2.chrY              574584 65 +  23952694 accactgc----actccagtctgggaaacagagcaagact---ctgtctcaa--------acaaaacaaaacaaaaaaat
q panTro2.chrY                                    00000000----0000000000000000000000000000---000000000--------00000000000000000000
i panTro2.chrY           C 0 C 0
s tarSyr1.scaffold_77585      6186 53 -      9862 gccactgt----actccagtctgggtgacagagtgagact---ccaactcaa--------------------aaaaaaat
q tarSyr1.scaffold_77585                          99999999----9999969999999999899999999999---995999969--------------------99999999
i tarSyr1.scaffold_77585 C 0 C 0
s speTri1.scaffold_83644      6232 44 -      9325 -----------------accctaaggaactcagcaagtct---ctgtctcaa----------------aattaaaAATAT
q speTri1.scaffold_83644                          -----------------59999989998999999979999---979999999----------------999999999999
i speTri1.scaffold_83644 C 0 C 0
s xenTro2.scaffold_529      518238 72 -    854086 attactgctttaactccaagctggagaggtgctgaacactgaaataatttaa--------aaaaaaataatacaaataat
i xenTro2.scaffold_529   N 0 C 0
s danRer6.chr3              224685 66 -  60907308 -----------accccctccctcaagaacgccccctggca---ttccctcaagactaacaatagacctgatgaaactgat
i danRer6.chr3           C 0 C 0
e rheMac2.chr3            61106074 2908 + 196418989 I
e ponAbe2.chr8           105366531 2881 - 153482349 I

a score=-40277.000000
s hg19.chrY                7721385 35 +  59373566 -aaaacagagtgacaagctg-------aacaaacagaca-------agat
s panTro2.chrY              574649 35 +  23952694 -aaaacagagtgacaagctg-------aacaaacagaca-------agat
q panTro2.chrY                                    -0000000000000000000-------000000000000-------0000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105369412 35 - 153482349 -aaaacagagtggcaagctg-------agtaaagaatga-------atat
q ponAbe2.chr8                                    -9999999999999999999-------999999999999-------9999
i ponAbe2.chr8           I 2881 C 0
s speTri1.scaffold_83644      6276 49 -      9325 -CAAAAAGAATGAGGATGTGTCTCAGTGGTAGAGGGCCACCAGACCAAAT
q speTri1.scaffold_83644                          -9999999998999999989999999799999999679799998999999
i speTri1.scaffold_83644 C 0 C 0
s xenTro2.scaffold_529      518310 28 -    854086 -aaaaaatgaagaccaattg---------caaatagtc------------
i xenTro2.scaffold_529   C 0 C 0
s danRer6.chr3              224751 20 -  60907308 c---------------aatg-------agagagctgttc-------aga-
i danRer6.chr3           C 0 C 0
s gasAcu1.chrXIII         16766643 33 +  20083130 --aaatatatatatatatta-------aaaaaaCAGTTT-------AAA-
q gasAcu1.chrXIII                                 --999999999999999999-------999999999999-------999-
i gasAcu1.chrXIII        N 0 C 0
s rheMac2.chr3            61108982 23 + 196418989 -------------caagctg-------aataaagaatca-------agat
q rheMac2.chr3                                    -------------9999999-------999999999999-------9999
i rheMac2.chr3           I 2908 C 0
s tarSyr1.scaffold_77585      6239  5 -      9862 ------------------------------aaaaa---------------
q tarSyr1.scaffold_77585                          ------------------------------99999---------------
i tarSyr1.scaffold_77585 C 0 C 0
s micMur1.scaffold_17116      7363 24 +     17168 ------------taaaaaaa-------aataaaaaataa-------aGAT
q micMur1.scaffold_17116                          ------------99999999-------999999999999-------9999
i micMur1.scaffold_17116 N 0 I 92

a score=-24160.000000
s hg19.chrY                7721420 41 +  59373566 ctaatggtatgctgtaatcaagacacccatctcaaa------------------------taacc---
s speTri1.scaffold_83644      6325 20 -      9325 -----------CTGCAGT-------GCAATCCCCAG------------------------TA------
q speTri1.scaffold_83644                          -----------9899999-------79979999999------------------------98------
i speTri1.scaffold_83644 C 0 C 0
s rheMac2.chr3            61109005 41 + 196418989 ctaacagtatgctttaatcaagacagccatctcaaa------------------------taagc---
q rheMac2.chr3                                    999999999999999999999999999999999999------------------------99999---
i rheMac2.chr3           C 0 C 0
s panTro2.chrY              574684 41 +  23952694 ctaatggtatgctgtaatcaagacacccatctcaaa------------------------taacc---
q panTro2.chrY                                    000000000000000000000000000000000000------------------------00000---
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105369447 41 - 153482349 ctaatggtatgctgtaattgagatacctatcacaaa------------------------taagc---
q ponAbe2.chr8                                    999999999999999999999999999999999999------------------------99999---
i ponAbe2.chr8           C 0 C 0
s xenTro2.scaffold_529      518338 20 -    854086 -----------------tcagaatattactcgtta-------------------------ta------
i xenTro2.scaffold_529   C 0 C 0
s gasAcu1.chrXIII         16766676 42 +  20083130 -----CGTGTGCAGGATACAGAATATGTTCAATGTTGACATTT---CAAA------------------
q gasAcu1.chrXIII                                 -----99999999999999999999999999999999999999---9999------------------
i gasAcu1.chrXIII        C 0 C 0
s danRer6.chr3              224771 68 -  60907308 atatccagagccagaatctaacacctctcctctgAAgagaagtacccagaagaccaacttcttccgac
i danRer6.chr3           C 0 C 0
e micMur1.scaffold_17116      7387 92 +     17168 I
e tarSyr1.scaffold_77585      6244  0 -      9862 C

a score=-19989.000000
s hg19.chrY                7721461 25 +  59373566 tcaaatgaaa-agagaa--aaa--aaaatc
s ponAbe2.chr8           105369488 26 - 153482349 tcaaa-ataa-agggaa--aaaggaaaatc
q ponAbe2.chr8                                    99999-9999-999999--99999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              574725 27 +  23952694 tcaaacgaaa-agagaa--aaagaaaaatc
q panTro2.chrY                                    0000000000-000000--00000000000
i panTro2.chrY           C 0 C 0
s rheMac2.chr3            61109046 26 + 196418989 tcaaa-ataa-ggggaa--aaagaaaagtc
q rheMac2.chr3                                    99999-9999-999999--99999999999
i rheMac2.chr3           C 0 C 0
s tarSyr1.scaffold_77585      6244 21 -      9862 ------gaaa-aaagaa--aagaaAAAGTC
q tarSyr1.scaffold_77585                          ------9999-999999--99999999999
i tarSyr1.scaffold_77585 C 0 N 0
s speTri1.scaffold_83644      6345 26 -      9325 -CAAAATTCA-GCAGAG--TGAGCAGTGTG
q speTri1.scaffold_83644                          -999999999-999999--89999999999
i speTri1.scaffold_83644 C 0 N 0
s xenTro2.scaffold_529      518358 24 -    854086 tcaaatgcac-gggtga--ac---aagctc
i xenTro2.scaffold_529   C 0 C 0
s gasAcu1.chrXIII         16766718 24 +  20083130 ----GATTTA-AAGTGATTACAGTAAATT-
q gasAcu1.chrXIII                                 ----999999-999999999999999999-
i gasAcu1.chrXIII        C 0 I 13
s oryLat2.chr2            16128580 23 +  31118443 ---TAACTCC-AAATAG--AAAGAATACT-
q oryLat2.chr2                                    ---9999999-999999--9999999999-
i oryLat2.chr2           N 0 I 7
s danRer6.chr3              224839 25 -  60907308 --aaaattcagaagtga--gcaacggatt-
i danRer6.chr3           C 0 N 0
e micMur1.scaffold_17116      7387 92 +     17168 I

a score=-56293.000000
s hg19.chrY                          7721486 65 +  59373566 ttctaagc---aaatagaaaacagaataaaagc-----------a----gaggttgcaat-----cc----ta-----------gtt----t----ctggcaaaacagac-t
s oryLat2.chr2                      16128610 59 +  31118443 -----------acatttaaaacaaaaaaacata-----------c----tcAAATGAACTAA---AC----TA-----------CTT----C----ATTTTTGGacaaat-t
q oryLat2.chr2                                              -----------9999999999999999999999-----------9----9999999999999---99----99-----------999----9----99999999999999-9
i oryLat2.chr2                     I 7 I 4
s gasAcu1.chrXIII                   16766755 73 +  20083130 TCACTAACACCACGTTACATGAAGGAAAAAACA-----------G----GCAAATTCAACAATGCCC----TG-----------TTT----T----ATTGCTGAAGATGT-A
q gasAcu1.chrXIII                                           999999999999999999999999999999999-----------9----999999999999999999----99-----------999----9----99999999999999-9
i gasAcu1.chrXIII                  I 13 N 0
s xenTro2.scaffold_529                518382 59 -    854086 -------t---ttaaAGAAAAAAGGATGAGAACCAGTTCAGGCAA----GAGCTCTAAAG-----TT----TA-----------GTT----T---ACTGG------------
i xenTro2.scaffold_529             C 0 I 31
s ponAbe2.chr8                     105369514 64 - 153482349 caccaagc---aaatagaaaacggaa-aaaagc-----------a----ggggttgcaat-----cc----ta-----------gtt----t----ctggcaaaacagac-t
q ponAbe2.chr8                                              99999999---999999999999999-999999-----------9----99999999999-----99----99-----------999----9----99999999999999-9
i ponAbe2.chr8                     C 0 C 0
s panTro2.chrY                        574752 65 +  23952694 ttctaagc---aaatagaaaacagaataaaagt-----------a----gaggttgcaat-----cc----ta-----------gtt----t----ctggcaaaacagac-t
q panTro2.chrY                                              00000000---0000000000000000000000-----------0----00000000000-----00----00-----------000----0----00000000000000-0
i panTro2.chrY                     C 0 C 0
s rheMac2.chr3                      61109072 63 + 196418989 taccaagc---aaatagaaaacagg--aaaagc-----------a----ggggttgcaat-----cc----ta-----------gtt----t----ctgacaaaacagac-t
q rheMac2.chr3                                              99999999---99999999999999--999999-----------9----99999999999-----99----99-----------999----9----99999999999999-9
i rheMac2.chr3                     C 0 C 0
s tarSyr1.scaffold_122003               1567 74 -      5638 ttatgTAC---ACATTGTACATAAAATAAGAGC-----------AATACAAACTTTTAGT-----TT----TA-----------ATTTACAT----TGAATGAAATAAACAA
q tarSyr1.scaffold_122003                                   99999999---9999999999999999999999-----------9999999999999999-----99----99-----------99999999----9999999999999999
i tarSyr1.scaffold_122003          N 0 C 0
s micMur1.scaffold_17116                7479 64 +     17168 TTTGTAAT---AAACTGATGTGGGACTAAAAGG-----------T----GGAGATGCAAG-----TT----TG-----------TCT----C----CTGTGTAAATTG-T-T
q micMur1.scaffold_17116                                    99999999---9999999999999999999999-----------6----99999999999-----99----99-----------999----9----999999999999-9-9
i micMur1.scaffold_17116           I 92 C 0
s tupBel1.scaffold_108750.1-142487     31111 70 +    142487 ccaaaatt---aactagaaaatag---aaaagc-----------a----aggattggatc-----ccagatca-----------gtt----tgatgctggagtatgagtt-c
q tupBel1.scaffold_108750.1-142487                          99999999---9999999999999---999999-----------9----99999999999-----99999999-----------999----9999999999999999999-9
i tupBel1.scaffold_108750.1-142487 N 0 C 0
s petMar1.Contig5115                   12395 44 +     23967 -------------------------ATCAATAC-----------A----TTAGTTGCTAT-----CC----TAAAACTTAACCGATT----T----TTGCT-----------
q petMar1.Contig5115                                        -------------------------99999999-----------9----99999999999-----99----9999999999999999----9----99999-----------
i petMar1.Contig5115               N 0 C 0

a score=-134473.000000
s hg19.chrY                          7721551  99 +  59373566 ttacataaa---tat------aggttttaaaaaaagacaa--a------------gaaggacatt---ac-------ataatag-taaaggtctatatatacacacacaccccca---------aaaaagcactcagattat
s speTri1.scaffold_114288               4702  77 -     52053 atatatcca---tct------atctctctatatac-acac--a------------cacatatat---------------------tatggatgtatacatacgcacatacacaca---------------cacTCAA-----
q speTri1.scaffold_114288                                    999999998---999------99999999999999-9999--9------------999999999---------------------999999899999999999999999999999---------------9999999-----
i speTri1.scaffold_114288          N 0 N 0
s tupBel1.scaffold_108750.1-142487     31181  49 +    142487 ttAATTCAA---GAT------AAGAGCCCAGAGAATG-----A------------GATGGGTACTG--AC-------ATAATAC----------------------------------------------------------
q tupBel1.scaffold_108750.1-142487                           999999999---999------9999999999999999-----9------------99999999999--99-------9999999----------------------------------------------------------
i tupBel1.scaffold_108750.1-142487 C 0 N 0
s micMur1.scaffold_17116                7543  85 +     17168 ATATATAAAATTTATTCCAGGAAGTTCATAAAGTAGATTAGCT------------GCAGTACACT---GCGTGGGTTGTAATGC-AAAGAGATCACACACA-----------------------------------------
q micMur1.scaffold_17116                                     9999999999999989999999999999999999999999999------------9999999999---9999999999999999-9999999999999999-----------------------------------------
i micMur1.scaffold_17116           C 0 N 0
s tarSyr1.scaffold_122003               1641  31 -      5638 ATATATCAC---TAA------AGCTTTATAAGTAAGATAA------------------------------------------------------------------------------------------------------
q tarSyr1.scaffold_122003                                    999999999---999------9999999999999999999------------------------------------------------------------------------------------------------------
i tarSyr1.scaffold_122003          C 0 N 0
s rheMac2.chr3                      61109135  67 + 196418989 tgaaattaa---cat------agatt---aaaaaa---aa--a------------aaagggcatt---ac-------ataatag-caaagggctatatatgcaccca-----------------------------------
q rheMac2.chr3                                               999999999---999------99999---999999---99--9------------9999999999---99-------9999999-9999999999999999999999-----------------------------------
i rheMac2.chr3                     C 0 I 15
s panTro2.chrY                        574817  99 +  23952694 ttacataaa---tat------aggttttaaaaaaagacaa--a------------gaaggacatt---ac-------ataatag-taaaggtctacatatacacacacaccccaa---------aaaaagcactcagattat
q panTro2.chrY                                               000000000---000------0000000000000000000--0------------0000000000---00-------0000000-000000000000000000000000000000---------000000000000000000
i panTro2.chrY                     C 0 C 0
s ponAbe2.chr8                     105369578  92 - 153482349 ttaaatcaa---tat------agattt--aaaaaagacaa--a------------gaagggcatt---ac-------ataatag-taaagtgctatatatgtgc-----ccaaca---------caaaagcacccagattat
q ponAbe2.chr8                                               999999999---999------999999--99999999999--9------------9999999999---99-------9999999-9999999999999999999-----999999---------999999999999999999
i ponAbe2.chr8                     C 0 C 0
s xenTro2.scaffold_529                518472  64 -    854086 CAAGGCAAA---TTA------TCCTACCCAAGTAAATGTA--A------------ATAAAACATT----C-------ATATTA-----AATACTGCACATG---------------------------------------GC
i xenTro2.scaffold_529             I 31 I 1315
s oryLat2.chr2                      16128673 118 +  31118443 -----ttta---ttt------acatttgaaagAAACAACA--ATCATTTCTCATTGCAGGACTTT---TCACTTACAGTGATACCTGCAGTTATTCATACTCCAGGGCAGGACTA-----TTTTTTGAAGCACTAGAACAAG
q oryLat2.chr2                                               -----9999---999------9999999999999999999--99999999999999999999999---99999999999999999999999999999999999999999999999-----9999999999999999999999
i oryLat2.chr2                     I 4 N 0
s petMar1.Contig5115                   12439 111 +     23967 TTGCAAAGC---ATG------AAGTTGTAAAAAACCAACA--A------------ATTGAGCATTTGCAA-------GTCATGG-TTAATATTGACATTTCCAGGTGATATCATAcagtcttaaaaaaaacattttatatat
q petMar1.Contig5115                                         999999999---999------9999999999999999999--9------------999999999999999-------9999999-999999999999999999999999999999999999999999999999999999999
i petMar1.Contig5115               C 0 T 6195

a score=-13219.000000
s hg19.chrY              7721650 36 +  59373566 aaagcaacttcttagagaccCTC---GTA----GATCATAAGT
s panTro2.chrY            574916 36 +  23952694 aaagcaacttcttagagaccCTC---GTA----GATCATAAGT
q panTro2.chrY                                  00000000000000000000000---000----0000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105369670 36 - 153482349 aaagcaagttcttagagaccttc---caa----gaTGTTAAGT
q ponAbe2.chr8                                  99999999999999999999999---999----9999999999
i ponAbe2.chr8         C 0 C 0
s rheMac2.chr3          61109217 27 + 196418989 aaag----ttcttagagaccctc---taa----gaT-----GA
q rheMac2.chr3                                  9999----999999999999999---999----999-----99
i rheMac2.chr3         I 15 C 0
s xenTro2.scaffold_676     84706 17 -    553874 AAGGGAACTCTTTAGAG--------------------------
i xenTro2.scaffold_676 n 1315 C 0
s petMar1.Contig5115        6355 27 +     23967 -------CTTCTTATGGACCTTC-----A----GGTTGCAATT
q petMar1.Contig5115                            -------9999999999999999-----9----9999999999
i petMar1.Contig5115   T 6195 C 0
s danRer6.chr3          59508724 17 +  60907308 ------------CAGGGTTCCTA---AAA----GAC-------
i danRer6.chr3         N 0 C 0
s tetNig2.chrUn_random  51483311 13 - 107808587 -----------------------GCAGAACCTTGAC-------
i tetNig2.chrUn_random N 0 C 0

a score=54738.000000
s hg19.chrY              7721686 54 +  59373566 -----TAAATGTTCTTCAACAGCCATTACCTTTATGTTACATTGGTTCAGTATAAAGTC
s rheMac2.chr3          61109244 54 + 196418989 -----TAAATGTTCTTCCATCGTTATTACATTTATACTGCATTTGTTCAGTATTAAATT
q rheMac2.chr3                                  -----999999999999999999999999999999999999999999999999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105369706 54 - 153482349 -----TAAATGTTCTTCAACAGTCATTACCTTTATACTGCATTTGTTCAGTATTAAGTC
q ponAbe2.chr8                                  -----999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            574952 54 +  23952694 -----TAAATGTTCTTCAACAGCCATTACCTTTATGTTACATTGGTTCAGTATAAAGTC
q panTro2.chrY                                  -----000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295      9334 54 -     44148 -----TGAATGCCTTTCCACATTCTTTGCatttataaggcttctctccactgTGCATTC
q macEug1.Scaffold5295                          -----999999999999999999999999999999999999999999999999999999
i macEug1.Scaffold5295 N 0 C 0
s xenTro2.scaffold_676     84723 54 -    553874 -----TGAATTTTTTCCCACATTCTTTACAGGTGAATGGTTTCACTCCAGTGTGAATTT
i xenTro2.scaffold_676 C 0 C 0
s danRer6.chr3          59508741 54 +  60907308 -----TAAACCTCTTGCTACACTGTAAACACTTGTACAGTTTCTCTCCAGTGTGAACCT
i danRer6.chr3         C 0 C 0
s tetNig2.chrUn_random  51483324 54 - 107808587 -----TGAaccctttcccacatgttttacacaaatatggtttctcacctgtgtgaactc
i tetNig2.chrUn_random C 0 C 0
s petMar1.Contig5115        6382 59 +     23967 TAATGAAAAATACTTTCCACAATCTTGGCATTCATACGGTTTTTCTCCAGTGTGTGTCC
q petMar1.Contig5115                            99999999999999999999999999999999999999999999999999999999999
i petMar1.Contig5115   C 0 C 0

a score=901.000000
s hg19.chrY              7721740 32 +  59373566 TCTGATGTTGAACACAAAATGAGGACTTGTTG
s rheMac2.chr3          61109298 32 + 196418989 TCTGATGTTGAACACGGTATGAGGACTTGtta
q rheMac2.chr3                                  99999999999999999999999999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105369760 32 - 153482349 TCTGATGTTGAACACAATATAAGGACTTGTTA
q ponAbe2.chr8                                  99999999999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575006 32 +  23952694 TCTGATGTTGAACACAAAATGAGGACTTGTTG
q panTro2.chrY                                  00000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295      9388 32 -     44148 TCTGATGTTTGGTAAGGTTGGAGCTATtgctg
q macEug1.Scaffold5295                          99999999999999999999999999999999
i macEug1.Scaffold5295 C 0 C 0
s xenTro2.scaffold_676     84777 31 -    553874 TTCCATG-TAAACGAAGGCTGCCCTTATGTGA
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  51483378 32 - 107808587 tcatgtgcaGAGCTAAAGCAGGGTGATGGCTG
i tetNig2.chrUn_random C 0 C 0
s gasAcu1.chrUn         59840832 32 +  62550211 TCATGTGTACCTTCAGATTATCACTTCGAGTG
q gasAcu1.chrUn                                 78999896767789897696787769799969
i gasAcu1.chrUn        N 0 C 0
s danRer6.chr3          59508795 32 +  60907308 TCTCATGCGATTTTAGAGAACCTAACAGACTA
i danRer6.chr3         C 0 C 0
s petMar1.Contig5115        6441 30 +     23967 TCTGATG--GGACTTGAGATGAGGTTTTTGTG
q petMar1.Contig5115                            9999999--99999999999999999999999
i petMar1.Contig5115   C 0 C 0

a score=48418.000000
s hg19.chrY              7721772 31 +  59373566 --AAGACTTTTCCACACTTTGAACACTTGTGGA
s rheMac2.chr3          61109330 31 + 196418989 --aaggcttttccacgtttttaacacttgtgga
q rheMac2.chr3                                  --9999999999999999999999999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105369792 31 - 153482349 --AAGGCTCTTCCACATTTTTAACACTTGTGGA
q ponAbe2.chr8                                  --9999999999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575038 31 +  23952694 --AAGACTTTTCCACATTTTGAACACTTGTGGA
q panTro2.chrY                                  --0000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295      9420 31 -     44148 --aaggccttcccacattccttacattcataag
q macEug1.Scaffold5295                          --9999999999999999999999999999999
i macEug1.Scaffold5295 C 0 C 0
s xenTro2.scaffold_676     84808 31 -    553874 --AAACATTTCCCACACTCTGTACAGGTGAATG
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  51483410 31 - 107808587 --AATGATTTCCCACATGCTTTACAGATGTACG
i tetNig2.chrUn_random C 0 C 0
s fr2.chrUn            369482153 31 + 400509343 --aaggttttcccacatctTTGATACAAATATT
i fr2.chrUn            N 0 C 0
s gasAcu1.chrUn         59840864 31 +  62550211 --AAACATTTACCACACTCTGTGCAGCTGAAAG
q gasAcu1.chrUn                                 --9998999989979999999899997999999
i gasAcu1.chrUn        C 0 C 0
s danRer6.chr3          59508827 31 +  60907308 --AATCTCTTGTCACAGTGTGAACACTTGAAAG
i danRer6.chr3         C 0 C 0
s petMar1.Contig5115        6471 33 +     23967 AAAAACCCCTGCCACATAGTGTGCATGTAAAAG
q petMar1.Contig5115                            999999999999999999999999999999999
i petMar1.Contig5115   C 0 C 0

a score=79437.000000
s hg19.chrY              7721803 28 +  59373566 GCTTCTCTCTAGTATGAATTATCTTATG
s rheMac2.chr3          61109361 28 + 196418989 gcttctctctagtatgaattctcttatg
q rheMac2.chr3                                  9999999999999999999999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105369823 28 - 153482349 GCTTCTCTCTAGTATGAATTCTCTTATC
q ponAbe2.chr8                                  9999999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575069 28 +  23952694 GCTTCTCTCTAGTATGAATTATCTTATG
q panTro2.chrY                                  0000000000000000000000000000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295      9451 28 -     44148 gcttctcttccgtgtgaattctctggtg
q macEug1.Scaffold5295                          9999999999999999999999999999
i macEug1.Scaffold5295 C 0 C 0
s xenTro2.scaffold_676     84839 28 -    553874 GTTTCTCCCCTGTGTGAATCCTTTCATG
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  51483441 28 - 107808587 GTTTCTCACCGGTGTGACTTCTCATGTG
i tetNig2.chrUn_random C 0 I 10402
s fr2.chrUn            369482184 21 + 400509343 GTCTCTCCC--GTGTGAACTCTC-----
i fr2.chrUn            C 0 C 0
s gasAcu1.chrUn         59840895 28 +  62550211 GTTTCTCCCCTGTGTGACATCTCATGTG
q gasAcu1.chrUn                                 8899999999999999999999996999
i gasAcu1.chrUn        C 0 C 0
s oryLat2.scaffold1367     20754 28 -     36351 GCTTCTCTCCGGTATGAGTTAACATGTG
q oryLat2.scaffold1367                          9999999999999999999999999999
i oryLat2.scaffold1367 N 0 C 0
s danRer6.chr3          59508858 24 +  60907308 GTTTCTCTCCAGTGTGAATTCTCT----
i danRer6.chr3         C 0 I 256
s petMar1.Contig5115        6504 28 +     23967 GTTTATCTCCAGTATGTGTTTTCTGATG
q petMar1.Contig5115                            9999999999999999999999999999
i petMar1.Contig5115   C 0 I 4

a score=344803.000000
s hg19.chrY              7721831 324 +  59373566 -----TCTAATGAAATG-TGAGAATG--------------------------------------------AGCTC-------------------------------AATGCTTTGCCACATTCTCCACAATTGTAGGGTTT-CTCTCCAGTGTGAATTATCTTA-TGATTGGTATGGTCTGATAAGCACT------TAAGGGTTTTGCCACATTCTTCATATTTGTAAGGTCTGTCTTCCATGTGAATTATTTTGTGGCTAGTAAGGGTTAAGGAGTAGGTAAAGGCTTTGCCACATTCTTCACAGATATAGGGTTTCTCTCCAGAATGAATTATTTTATGTTTA-TAAGGAGAGATAA------------------------------------------------------------------------------------CTACAT---------AATGGCTCTTCCATGTTCATTGTATTTGTAGAGTTTCTCTCTAGTATGA
s rheMac2.chr3          61109389 325 + 196418989 -----tctgatgaggtg-tgagaacc--------------------------------------------agctc-------------------------------gatgctttgccacattcttcacatttgtagggttt-ttctccagtgtgaattctctta-tgattagtcaggtctgagaagcact------tgaaggtcttgccacattcttcacatttataaggtctctcttccatatgaattctcttgtggttaaaaagggtggaggagcgggtaaaggctttgccacattcttcacagatgtagggtttctctccagtatgaattctcttatgtttactaagggccgagaa------------------------------------------------------------------------------------ccactt---------aaaagcttttccacattcattacatttgtagggtttctctccagtatga
q rheMac2.chr3                                   -----999999999999-99999999--------------------------------------------99999-------------------------------99999999999999999999999999999999999-9999999999999999999999-9999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------------------------999999---------9999999999999999999999999999999999999999999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105369851 321 - 153482349 -----TCTAATGAGATG-TGAGAATG--------------------------------------------AGATC-------------------------------AATGCTTAGCCACATTCTTCACATTTGTAGGGTTTCCTCTCCAGTGTGAA-----TTA-TGATTAGTAAGGTCTGAGAAGCACT------TAAAGGTTTTCCCATATTCTTCACATTTGTAAGGTCTCTCTTCCACATGAATTCTCTTCTGGTTAATAAGGGTTGAGGAGTGGGTAAAAGCTTTGCCATATTCTTCACAGATGTGGGGTTTCTCTCCAGTATGAATTCTCTTATGTTTACTAAGGGCTGAGAA------------------------------------------------------------------------------------CCATAT---------AAAATCTTTTCTACATTCATTACATTTGTAGGGTTTCTCTCCAGTATGA
q ponAbe2.chr8                                   -----999999999999-99999999--------------------------------------------99999-------------------------------99999999999999999999999999999999999999999999999999-----999-9999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------------------------999999---------9999999999999999999999999999999999999999999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575097 324 +  23952694 -----TCTAATGAGATG-TGAGAATG--------------------------------------------AGCTC-------------------------------AATGCTTTGCCACATTCTCCACAATTGTAGGGTTT-CTCTCCAGTGTGAATTATCTTA-TGATTGGTATGGTCTGATAAGCACT------TAAGGGCTTTGCCACATTCTTCATATTTGTAAGGTCTATCTTCCATGTGAATTATTTTGTGGCTAGTAAGGTTTAAGGAGTAGGTAAAGGCTTTGCCACATTCTTCACAGATATAGGGTTTCTCTCCAGAATGAATTATTTAATGTTTA-TAAGGAGAGATAA------------------------------------------------------------------------------------CTACAT---------AATGGCTCTTCCATGTTCATTGTATTTGTAGAGTTTCTCTCTAGTATGA
q panTro2.chrY                                   -----000000000000-00000000--------------------------------------------00000-------------------------------00000000000000000000000000000000000-0000000000000000000000-0000000000000000000000000------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000------------------------------------------------------------------------------------000000---------0000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295      9479 325 -     44148 -----tcgagtcaagga-tgacatct--------------------------------------------gCCTG-------------------------------AAGGCCTTGCCACATTCTTTACAAgtataaggctt-ctctccagtgtgaattctatGA-TGTTGAGTAAA---TAAAGAGCTTTTTC---TGAAGGCTTTGCCACATTCTAGACATTTATAAGGTtcctctccagtgtgaattctaaTATGTTCAGTAAGAGATGAGCTCCAgttgaaggccttcccacattctttacactgataaggtttctctccactatgaattCTTTCATGCTTAATAAGGGAAGACTG------------------------------------------------------------------------------------GTTggt---------gaaggccttcccacattccttacattGATAAGGTTTTtccccagtgtga
q macEug1.Scaffold5295                           -----999999999999-89999999--------------------------------------------99999-------------------------------99999999999999999999989999999999999-9999999999999999999999-99999999999---99999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------------------------999999---------9999999999999999999999999999999999999999999979699
i macEug1.Scaffold5295 C 0 C 0
s xenTro2.scaffold_676     84867 326 -    553874 -----TTATGAGAAGTGCTGCTCTTT--------------------------------------------TACTG-------------------------------AAACATTTCCCACATTCTGTACAGGTGAATGGTTT-CTCCCCAATGTGAATTTTTTGG-TGGCGATTAAG------GGTGCTCTTTTCAGTAAAACTTTTCCCACATTCTGTACAGGTACATGGTTTCACCCCGGTGTGAATTCTTTCATGTATGAGAAGGGTGCGCTTTTCAGTGAAGCTTTTCCCACATTCTGTACATGCAAATGGTTTCTCCCCAGTGTGCCTCATTTTATGTATGCAAAGGGAACTCTT------------------------------------------------------------------------------------TAGAGT---------GAAATTTTTCCCACATTCTTTACAGGTGAATGGTTTCACTCCAGTGTGA
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  73749439 320 + 107808587 ----------TCTAATT-TAAT-GTGAAGC-------------------------------------TATAActa-------------------------------aatgattttc--cacattttaaataaaaacggttt-ctcaccagtgtgagcTCCCATG-TGCTTTGTGAAATCAAAGCTATTAC------TGAATGATTTTTCACATGCTTTACAGCTATATGGTCTCTCACCAGTGTGATCTCCCAGGTGTCTGGGTAATTGACAGGTTTGACTAAA--TGATTTCCCACATTTTACAAATAT--GATCTCTCACCAGAATGAACTCTGACATGCTTAGTTAAATTAGTGCT------------------------------------------------------------------------------------GCAAct---------aaatgattttccacatgttttgcaactatatggtttctcaccagtgtga
i tetNig2.chrUn_random n 10402 C 0
s fr2.chrUn            369482205 321 + 400509343 --------------GTG-TGATAATGCACT-------------------------------------TTTGTTTG-------------------------------AAAGTTTCCCCACACATTTTACACCCGTATAATCT-CTCACCAATGTGAACTCTCGTGACGATTT---AATTCATCATTTcgtt------tgaaggttttcccacatgttttacacaaatagggtctctcatctgtgtgaactgccatgtgtttatttaatgcaGAAGGATGTCTGAAATTTTTGTCGCATGTTTTACAAACATGGGGTTTCTCACCTGTATGAACTCTCATGTAGATAGTTAATGTAGAACT------------------------------------------------------------------------------------TCGTCT---------GAAacttttcccacatgttttacacaaatagggtctctcatctgtgtga
i fr2.chrUn            C 0 C 0
s gasAcu1.chrUn         59840923 325 +  62550211 ------------TACCT-TCAGATTTTCAT-------------------------------------TTAGAGTG-------------------------------AAACATTTACCACACTCTGTGCAGCTGAAAGGTTT-CTCCCCTGTGTGACATCTCATG-TGAGTCTT-----CAGACGTCCGCTTGCAG-GGAAACGTTTACCACACTGTGAGCAGCTGAAAGGTTTCTCCCCTGTGTGACATCTCATGTGAGTCTTTAGACTTCCGCTTGCAGTGAAACATTTACCACACTGTGAGCAGCTGAAAGGTTTCTCCCCTGTGTGACATCTCATG------------TGAGTCTTTAG---------------------------------------------------------------------------------ACTTCCGCTTGCAGGGAAACGTTTACCACACTGTGAGCAGCTGAAAGGTTTCTCCCCTGTGTGA
q gasAcu1.chrUn                                  ------------99999-999999999999-------------------------------------99999999-------------------------------99999999999998999999999999999999999-9999999999999999999999-99999999-----99999779999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999958------------99969999999---------------------------------------------------------------------------------8789875779989999999969999999999999999989999999997999999899999999
i gasAcu1.chrUn        C 0 C 0
s oryLat2.scaffold1367     20782 325 -     36351 ------------AGATG-AGAGATTATACT-------------------------------------TTTTCCTG-------------------------------AAATCCTTGTTGCATTCCTTACAGGAATatggctt-ctctcctgtgtgagttaaCATG-TGATGAGTGAGGACAGATCTATACC------GGAAACATTTGTTGCATTCTTTACAGGAATATGGCTTCTCTCCAGTGTGGGTTAACATGTGAGATGTTAAATGAGACCTTTGAGTGAAACTTTTGCTGCATTCCTTACAGGAATAAGGCTTCTCTCCGGTGTGAGTTAGCATGTGATAAGAGAGATgagtttt------------------------------------------------------------------------------------atttct---------gaaatccTTGTTGCATTCCTTACAGGAataaggcttctctcctgtgtga
q oryLat2.scaffold1367                           ------------99999-999999999999-------------------------------------99999999-------------------------------99999999999999999999999999999999999-9999999999999999999999-9999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------------------------999999---------9999999999999999999999999999999999999999999999999
i oryLat2.scaffold1367 C 0 C 0
s danRer6.chr3          59509138 325 +  60907308 -----CTGAGTAAGGCG-TGATGATA--------------------------------------------GGCTG-------------------------------AAACTCTTCCCACACTGAGAACATGTGAACGGTTT-CTCTCCAGTGTGGATCATCATG-TGTTGATTAAGGGATAATAGTTGGG------AGAAACTCTTCCCACACTGAGTACATGTGTGTGGTTTCTCTCCAGTGTGGATCCTCATGTGTCTATTGCGGTGTGATGAGTGGCTAAAACTCTTCCCACACTGAGAACATGCATATGGTTTCTCTCCAGTGTGGATCATCTTGTGTTTACTAAAGTTTGATGA------------------------------------------------------------------------------------GTGTCT---------GAAACTCTTCCCACACTGAGGACATGTGAATGGTTTCTCTCCAGTGTGG
i danRer6.chr3         I 256 C 0
s petMar1.Contig5115        6536 489 +     23967 TTTAAGTTACTATAGTA-TGAAAAACTCTTCCCACACTCCTTACAGATAAATGGTCGTTCACTACTATGCATCTGTTGATGTTGTTTCAGAGAAGAAGGAAATGAAAATCTCTTTCCACAATCCGGGCAAAGAAATGTCTT-TTCTCCAGTGTGCAGCAACTGA-TGAGTCTTCAGAGAAGATGtttgtg------agaacctccttccacATTCCTGACAAATAAATGGCTGTTCACCATCGTGAGTCAATTTATGATTTTTTAGAGATGATCCCTGTGAAAATCCTTTTCCGCATTCCTTGCAGAGAAATGGCTTCTCTCCAGAATGTACAATTTCATGATTTTTTAAGGTAGACTTGAGTGAATATCCTTTTCCACAATGTTTGCAAATAAACGGTTTCTCTACACTATGTGTAAATTCATGCGTCTTCAACGTGGATTTCAATGC---------AAATCCTTTCCCACATATCTTGCATATAAAAGGCCTCTCTCCAGTATGT
q petMar1.Contig5115                             99999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999-9999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------9999999999999999999999999999999999999999999999999
i petMar1.Contig5115   I 4 C 0

a score=-5104.000000
s hg19.chrY                     7722155 34 +  59373566 ATTATCTTATGTTTAGTAAGG---------T-CTGAGAAC--------CA-----CT
s panTro2.chrY                   575421 34 +  23952694 ATTATCTTATGTTTAGTAAGG---------T-CTGAGAAC--------CA-----CT
q panTro2.chrY                                         000000000000000000000---------0-00000000--------00-----00
i panTro2.chrY                C 0 C 0
s gorGor1.Supercontig_0003259     52579 34 +     79431 GTTAACTTATGTTCAGTAAGC---------T-TTGAGGAC--------CA-----CT
q gorGor1.Supercontig_0003259                          111112223333313333121---------2-32212231--------11-----11
i gorGor1.Supercontig_0003259 N 0 C 0
s ponAbe2.chr8                105370172 34 - 153482349 ATTATCTTATGTTTCGTAAGG---------T-CTGAGAAC--------CA-----CC
q ponAbe2.chr8                                         999999999999999999999---------9-99999999--------99-----99
i ponAbe2.chr8                C 0 C 0
s rheMac2.chr3                 61109714 34 + 196418989 attatcttatgtttagcaagg---------t-ctgagaac--------ca-----cc
q rheMac2.chr3                                         999999999999999999999---------9-99999999--------99-----99
i rheMac2.chr3                C 0 C 0
s macEug1.Scaffold5295             9804 34 -     44148 attctctggtgtttAGTAAGG---------T-TTGATCTC--------TG-----AA
q macEug1.Scaffold5295                                 999999999999999999999---------7-99999999--------99-----99
i macEug1.Scaffold5295        C 0 C 0
s xenTro2.scaffold_676            85193 50 -    553874 -ATTTTTCATGTAAACGAAGGCTGCCCTTAT-CTGAAAACATTTCCCACA-----CT
i xenTro2.scaffold_676        C 0 I 234
s tetNig2.chrUn_random         73749759 34 + 107808587 actctcacaTGCTTAGTCAAA---------T-CAGAGCTA--------TG-----AC
i tetNig2.chrUn_random        C 0 C 0
s fr2.chrUn                   369482526 34 + 400509343 acTGCCATGTGTTTACTCAGT---------G-CAGAACTT--------TG-----Tg
i fr2.chrUn                   C 0 C 0
s gasAcu1.chrUn                59841248 26 +  62550211 CATCTCATGTGA-----------------------GTCTT--------TAGACTTCC
q gasAcu1.chrUn                                        999999859999-----------------------89996--------689999997
i gasAcu1.chrUn               C 0 C 0
s oryLat2.scaffold1367            21107 34 -     36351 gttaaCATGTGATGAGTGAGG---------A-CAGATCTA--------TA-----CC
q oryLat2.scaffold1367                                 999999999999999999999---------9-99999999--------99-----99
i oryLat2.scaffold1367        C 0 C 0
s danRer6.chr3                 59509463 34 +  60907308 ATCCTCATGTGTTGATTAAGG---------G-ATGATGAT--------AG-----GC
i danRer6.chr3                C 0 C 0
s petMar1.Contig5115               7025 31 +     23967 ATTCTTTTATGAGCCTTCAGG---------TGCTGACCTT-----------------
q petMar1.Contig5115                                   999999999999999999999---------9999999999-----------------
i petMar1.Contig5115          C 0 C 0

a score=99882.000000
s hg19.chrY                     7722189 46 +  59373566 T--------ATAGGCTTTATTACATTCTTCACCTTTGTAGAGTTTCTCTTCAGT
s panTro2.chrY                   575455 46 +  23952694 T--------ATAGGCTTTATTACATTCTTCACCTTTGTAGAGTTTCTCTTTAGT
q panTro2.chrY                                         0--------000000000000000000000000000000000000000000000
i panTro2.chrY                C 0 C 0
s gorGor1.Supercontig_0003259     52613 46 +     79431 T--------AAAAGCTTTGCCACATTCTTCACATTTGTAGGGTTTCTTTTCAGT
q gorGor1.Supercontig_0003259                          2--------121131232222221303333333330333313333131322222
i gorGor1.Supercontig_0003259 C 0 C 0
s ponAbe2.chr8                105370206 46 - 153482349 T--------ATAGGCTTTGTTACATTCTTCACATATGTAGGGTTTCTCTCCAGT
q ponAbe2.chr8                                         9--------999999999999999999999999999999999999999999999
i ponAbe2.chr8                C 0 C 0
s rheMac2.chr3                 61109748 38 + 196418989 t--------ataggctttgttacattcttcacatttgtagggtttc--------
q rheMac2.chr3                                         9--------9999999999999999999999999999999999999--------
i rheMac2.chr3                C 0 C 0
s macEug1.Scaffold5295             9838 46 -     44148 T--------GAAGGCTGTCCCACATTCCTCACATTCATAGGGCTTCTCTCCACT
q macEug1.Scaffold5295                                 9--------999999999999999999999999999999999999999999999
i macEug1.Scaffold5295        C 0 C 0
s xenTro2.scaffold_676            85477 46 -    553874 T--------AAAGCATTTCCCACATTCTGTACATGCGAATGGTTTCTCTCCAGT
i xenTro2.scaffold_676        I 234 C 0
s tetNig2.chrUn_random         73749793 46 + 107808587 T--------GAATGATTTTTCACAAGTTTTGCAactatatggtttctcaccagt
i tetNig2.chrUn_random        C 0 C 0
s fr2.chrUn                   369482560 46 + 400509343 c--------aaaggttttcccacatgttttgcacaaatatggtctctcacctgt
i fr2.chrUn                   C 0 C 0
s gasAcu1.chrUn                59841274 54 +  62550211 GCTTGCAGTGAAACATTTACCACACTGTGAGCAGCTGAAAGGTTTCTCCCCTGT
q gasAcu1.chrUn                                        679999999999899999999997999789888989997799999799898898
i gasAcu1.chrUn               C 0 C 0
s oryLat2.scaffold1367            21141 46 -     36351 G--------GAAGCATTTGTTGCATTCTTTACAGGAATATGGCTTCTCTCCAGT
q oryLat2.scaffold1367                                 9--------999999999999999999999999999999999999999999999
i oryLat2.scaffold1367        C 0 C 0
s danRer6.chr3                 59509497 46 +  60907308 T--------AAAACTCGCCCCACACTGAGAACATATGAATGGTTTCACTCCCGT
i danRer6.chr3                C 0 C 0
s petMar1.Contig5115               7056 49 +     23967 -----GAGAGAATTTATTTCCACAGTGTGTGCAAATATATGGTTTCACTCCAGT
q petMar1.Contig5115                                   -----9999999999999999999999999999999999999999999999999
i petMar1.Contig5115          C 0 I 5695

a score=-73417.000000
s hg19.chrY                     7722235 102 +  59373566 ATG-----------------------------------------AGTTGTCT---TATGTTCATGAAGT-------------------------------------------------------------------------------TCTGAGAACTA-----TC------------------------------------------------------------------------------------GATTGGCTTTGTTACATTCTTCACTCTTGTAGGGTTTCTCAGTAGTATGAATTCTATTATAATT
s panTro2.chrY                   575501 102 +  23952694 ATG-----------------------------------------AGTTATCT---TATGTTCATGAAGT-------------------------------------------------------------------------------TCTGAGAACTA-----TC------------------------------------------------------------------------------------GATTGGCTTTGTTACATTCTTCACTCTTGTAGGGTTTCTCAGTAGTATGAATTCTATTATAATT
q panTro2.chrY                                          000-----------------------------------------00000000---00000000000000-------------------------------------------------------------------------------00000000000-----00------------------------------------------------------------------------------------0000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                C 0 C 0
s gorGor1.Supercontig_0003259     52659  88 +     79431 ATG-----------------------------------------AATTTTCT---TATGTTTAGTAAGG-------------------------------------------------------------------------------TTTGAGGACCG-----GC------------------------------------------------------------------------------------TAAAAGCTTCACCACATTCTGTACATTTATAGAATTTCTCTGCAGTATGG--------------
q gorGor1.Supercontig_0003259                           222-----------------------------------------21111221---11111221111111-------------------------------------------------------------------------------11111111111-----11------------------------------------------------------------------------------------11222111111111112221111222222111121116777777777777--------------
i gorGor1.Supercontig_0003259 C 0 N 0
s ponAbe2.chr8                105370252  18 - 153482349 ATG-----------------------------------------AATTCTCT---TATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATT
q ponAbe2.chr8                                          999-----------------------------------------99999999---9999------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------999
i ponAbe2.chr8                C 0 C 0
s rheMac2.chr3                 61109786  26 + 196418989 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctccagtatgaattctcttatgatt
q rheMac2.chr3                                          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------99999999999999999999999999
i rheMac2.chr3                C 0 C 0
s macEug1.Scaffold5295             9884 102 -     44148 ATG-----------------------------------------AGTTCTTT---CATGTTTAATAAGG-------------------------------------------------------------------------------GAGGCCCGGTT-----Gg------------------------------------------------------------------------------------taaaggccttcccacattccttacattgataaggtttttctccagtgtgaattctatGATGTTG
q macEug1.Scaffold5295                                  999-----------------------------------------99999999---99999999999999-------------------------------------------------------------------------------99999999999-----99------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999999999999999999999
i macEug1.Scaffold5295        C 0 C 0
s xenTro2.scaffold_676            85523 185 -    553874 GTG-----------------------------------------AATTTTCT---GGTGCTTTTGAAGGCTGCAATTTGTAGTAAAACATTTCCCACATTCTGTACAGGTGAATGGTTTCACCCCAGTGTGAATTTTTCGTGGA----TTTGAAGGCTG-----CC----------------------------------------------------------------------------CTTTTCTGTAAAACATTTCCCACATTCTGTACAGGTGAATGGTTTCTTTCTAGTGTGAATTTTTTTGTGCTT
i xenTro2.scaffold_676        C 0 I 167
s tetNig2.chrUn_random         73749839 102 + 107808587 gtg-----------------------------------------aactctca---caTGCTTAGTTAAA-------------------------------------------------------------------------------TCAGAGCTATG-----GC------------------------------------------------------------------------------------TGAACGATTTTCTACATGTTTTACAACtgtatggtttctcaccagtgtgaattCTCATGTGACT
i tetNig2.chrUn_random        C 0 C 0
s fr2.chrUn                   369482606 102 + 400509343 gtg-----------------------------------------aattctca---tgtggacatttaat-------------------------------------------------------------------------------tcATTATTTCG-----TC------------------------------------------------------------------------------------GAAAGGTTTTCATACATGTTTTACACTCATGTGGTCTGTcatctgtgtgaactctcatgtgcTT
i fr2.chrUn                   C 0 C 0
s gasAcu1.chrUn                59841328 186 +  62550211 GTGACACCTCATATGTATCTTCAGGTGTTCGTTTTGAGCGAAACAGTTACCACACTGTGAGCAGCTGAA--------------------------------------------AGGTTTCTCCCCTGTGTGACATCTCATGTGATTCTTTAGACTTCCGCTTGCAG------------------------------------------------------------------------------------TGAAACGTTTACCACACTGTGAGCAGCTGAAAGGTTTCTCCCCTGTGTGACATCTCATGTGTTT
q gasAcu1.chrUn                                         789894449988567679997777776976776537773777797797689998997476677877777--------------------------------------------79979989899779976769899768789964967666774774666666777------------------------------------------------------------------------------------6777765667769796665576996864678879799795976678989798978987668879
i gasAcu1.chrUn               C 0 C 0
s oryLat2.scaffold1367            21187 102 -     36351 GTG-----------------------------------------GGTTAACA---TGTGAGATGTTAAA-------------------------------------------------------------------------------TGAGACCTTTG-----AG------------------------------------------------------------------------------------TGAAACTTTTGCTGCATTCCTTACAGGAATAAGGCTTCTCTCCGGTGTGAGTTAGCATGTGATA
q oryLat2.scaffold1367                                  999-----------------------------------------99999999---99999999999999-------------------------------------------------------------------------------99999999999-----99------------------------------------------------------------------------------------9999999999999999999999999999999999999999999999999999999999999999
i oryLat2.scaffold1367        C 0 C 0
s danRer6.chr3                 59509543 102 +  60907308 GTG-----------------------------------------AATCGTCA---TGTGTTTATTGAAG-------------------------------------------------------------------------------CTCGATACGTG-----TC------------------------------------------------------------------------------------TGAAACTCTTCCCACACTGAGTACAGGTGAATGGTTTCTCTCCAGTGTGGATCATCATGTGATA
i danRer6.chr3                C 0 C 0
s petMar1.Contig5115              12800 186 +     23967 ATG-----------------------------------------AGTCTTCT---GATGAGCTTTAAGA-------------------------------------------------------------------------------TTGTAATTTAG-----CGAAAAGCTTTTTCCACAAATATTACATGCATATGGCTTCTCTCCGGTGTGTATCCGCTGGTGGGTTTTCAAGTGAGGCTTTTGCGCAAAACCCCTTCCACAGTCTTTGCATATGAAAGGTTTTTCTCCAGTATGTGTCTTTTGATGAAC
q petMar1.Contig5115                                    999-----------------------------------------99999999---99999999999999-------------------------------------------------------------------------------99999999999-----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i petMar1.Contig5115          I 5695 C 0

a score=143692.000000
s hg19.chrY                7722337 89 +  59373566 AGTAAGGTTTCAGAAGCACTTAAAGGCTTTTCCACTTTCTTTGCATCTGTAGGTTCTGTCTCCAGTATAATTTCTCTTGTGTTTAATAA
s panTro2.chrY              575603 89 +  23952694 AATAAGGTTTCAGAAGCACTTAAAGGCTTTTCCACTTTCTTTGCATCTGTAGGTTCTGTCTCCAGTATAATTTCTCTTGTGTTTAATAA
q panTro2.chrY                                    00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           105370270 89 - 153482349 AGTAAAGTCTGAGAAAAACTTGAAGGCTTTACCACATTCTTCCCATTTGTTCAGTCTGTCTCCAGTATGATTTCTCTTGTGTTGAATAA
q ponAbe2.chr8                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s rheMac2.chr3            61109812 89 + 196418989 agtaaggtctgagaagcacttaaaggctttgccacattcttcacatttgtagggtctgtctccagtatgatttctcttgtgtttaacaa
q rheMac2.chr3                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3           C 0 C 0
s macEug1.Scaffold5295        9986 89 -     44148 AGTAAGGGATGAGCTCCAgttgaaggccttcccacattccttacaCTGATAAGGTTTTTCTTTAGTGTGAACtctctgatgttgagtaa
q macEug1.Scaffold5295                            99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i macEug1.Scaffold5295   C 0 C 0
s xenTro2.scaffold_676       85875 89 -    553874 TGTGAAGCTGCACATTGCAGTAAAACTTTTTCCACATTCTGTACAGGTGAATGGTTTCTCTCCAGTGTGAATTCTTTCGTGTATGTGAA
i xenTro2.scaffold_676   I 167 I 241
s turTru1.scaffold_89033      6424 65 +      6815 ------------------------GGCCTTTCCACATTCCTTACACTGATAGGGTTTCTCACCAGTATGAATCCTCTGATGTTGAGTAA
q turTru1.scaffold_89033                          ------------------------99999999999999999999999999999999999999999999999999999999999999999
i turTru1.scaffold_89033 N 0 C 0
s tetNig2.chrUn_random    73749941 89 + 107808587 AGTTAAATTAGAGTTATAACTGAATgactttccacatgttttacaactatatggtttctcaccagtgtgaactctcatgtgacTAGTTA
i tetNig2.chrUn_random   C 0 C 0
s fr2.chrUn              369482708 87 + 400509343 TTGTAGTGCAGAAGGATGTTTGAAAAGTTTTCCAC--GTTTTACAAACATAGGATTTCTCACCTGTATGAACTCTCATGTGGATAGTTA
i fr2.chrUn              C 0 C 0
s gasAcu1.chrUn           59841514 84 +  62550211 CTTCAGATTTCCTTTTTGAGCGAAACAGTTACCACACTCCGAGCAGCTGAAAGGTTTCTCCCCTGTGTG-----ACATCTCATGTGAGT
q gasAcu1.chrUn                                   899958889998779449997999999989999999885583798978788888899997886997667-----798979999856789
i gasAcu1.chrUn          C 0 C 0
s oryLat2.scaffold1367       21289 89 -     36351 AGAGAGATgagttttatttctgaaatccTTGTTGCATTCCTTACAGGAataaggcttctctcctgtgtgagtatACATGTGATGAGTGA
q oryLat2.scaffold1367                            99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i oryLat2.scaffold1367   C 0 C 0
s danRer6.chr3            59509645 89 +  60907308 ATTAAGGTGTGATGAGTCTCTGAAACTCTTCCCACACTGAGTACATGTGAATGGTTTCTCTCCAGTGTGGATCATCATGTGTTTGTTAA
i danRer6.chr3           C 0 C 0
s petMar1.Contig5115         12986 89 +     23967 AGTCATGGCACTGGAATATGAAAAACTCTTCCCACACTCTTTGCAAACATATGGTCTCTCTCCAGTATGAATTTTATGATGTTCCTTCA
q petMar1.Contig5115                              99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i petMar1.Contig5115     C 0 C 0

a score=-7139.000000
s hg19.chrY                7722426 20 +  59373566 GAGTTGAGGA--------GCAGG-----AAAAG
s rheMac2.chr3            61109901 20 + 196418989 gggttgagga--------gcagg-----taaag
q rheMac2.chr3                                    9999999999--------99999-----99999
i rheMac2.chr3           C 0 C 0
s ponAbe2.chr8           105370359 20 - 153482349 GGGTTGAGGA--------GCAGG-----TAAAG
q ponAbe2.chr8                                    9999999999--------99999-----99999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY              575692 20 +  23952694 GAGTTGAGGA--------GCAGG-----AAAAG
q panTro2.chrY                                    0000000000--------00000-----00000
i panTro2.chrY           C 0 C 0
s turTru1.scaffold_89033      6489 20 +      6815 GTTGTGAGCC--------ATGAC-----TAAAG
q turTru1.scaffold_89033                          9999999999--------99999-----99999
i turTru1.scaffold_89033 C 0 N 0
s macEug1.Scaffold5295       10075 20 -     44148 gaGATGAATT--------GCagc-----tgaag
q macEug1.Scaffold5295                            9999999999--------99999-----99999
i macEug1.Scaffold5295   C 0 C 0
s xenTro2.scaffold_676       86205 28 -    553874 GAATTTAAGATGGCTCTTGCGAG-----AAAAG
i xenTro2.scaffold_676   I 241 C 0
s tetNig2.chrUn_random    73750030 20 + 107808587 AATCAGAGCT--------ATAGC-----TGAAt
i tetNig2.chrUn_random   C 0 C 0
s fr2.chrUn              369482795 20 + 400509343 ATGTAGAACT--------TCGTC-----TGAAA
i fr2.chrUn              C 0 C 0
s gasAcu1.chrUn           59841598 25 +  62550211 CTTTAGATTT--------CCCCTTGCAGTGAAA
q gasAcu1.chrUn                                   9879798959--------599998999969999
i gasAcu1.chrUn          C 0 C 0
s oryLat2.scaffold1367       21378 20 -     36351 GCACAGAACT--------ATACC-----GGAAA
q oryLat2.scaffold1367                            9999999999--------99999-----99999
i oryLat2.scaffold1367   C 0 C 0
s danRer6.chr3            59509734 20 +  60907308 AGGTTGATGA--------GTCTC-----AGAAA
i danRer6.chr3           C 0 C 0
s petMar1.Contig5115         13075 20 +     23967 GGGTGGATGC--------CTGTA-----AAAAC
q petMar1.Contig5115                              9999999999--------99999-----99999
i petMar1.Contig5115     C 0 C 0

a score=106588.000000
s hg19.chrY              7722446 54 +  59373566 GTTTTATCACATCCTTTTCA-TTTGTAGGGTTTATCTCCTGTTTAAACTCT--TATG--
s rheMac2.chr3          61109921 56 + 196418989 gttttgccacatccttcaca-tttgtaaggtttctctccagtatgaactctcttatg--
q rheMac2.chr3                                  99999999999999999999-999999999999999999999999999999999999--
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105370379 57 - 153482349 GTTTTGAAACATTCTTCACATTTTGTAGGGTTTCTCTCCACTATGAACTCTCTTATG--
q ponAbe2.chr8                                  999999999999999999999999999999999999999999999999999999999--
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575712 56 +  23952694 GTTTTATCACATCCTTTTCA-TTTGTAGGGTTTATCTCCTGTTTAAACTCTCTTATG--
q panTro2.chrY                                  00000000000000000000-000000000000000000000000000000000000--
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295     10095 56 -     44148 gccttcccacattctttaca-CTTATAgagtttttctccagtgtgaagTCTCTGATG--
q macEug1.Scaffold5295                          99999999999999999999-999999999999999999999999999999999999--
i macEug1.Scaffold5295 C 0 C 0
s xenTro2.scaffold_676     86233 56 -    553874 CCTTTCCCACATTCTGTACA-AGTGTATGGTCTCTCCCCTGTGTGGATTCTTTCATG--
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  73750050 54 + 107808587 gatttcccacatgttttaca-aatACATGATTTATTACCTGTGTGAATTTT--AATG--
i tetNig2.chrUn_random C 0 I 35
s fr2.chrUn            369482815 54 + 400509343 CTTTTACCACATGTTtcaca-cacatatggtctctcattagtgtgaactct--catg--
i fr2.chrUn            C 0 I 6
s gasAcu1.chrUn         59841623 54 +  62550211 CAGTTACCACACTCTGTGCA-GCTGAAAGGTTTCTCCCCTGTGTGACATCT--CATG--
q gasAcu1.chrUn                                 99999999999999989999-954699988888888888888888888888--8888--
i gasAcu1.chrUn        C 0 I 6
s oryLat2.scaffold1367     21398 54 -     36351 CATTTGTTGCATTCCTTACA-GGAATAAGGCTTCTCTCCGGTGTGACTTAA--CATG--
q oryLat2.scaffold1367                          99999999999999999999-999999999999999999999999999999--9999--
i oryLat2.scaffold1367 C 0 I 6
s danRer6.chr3          59509754 54 +  60907308 CTTGTTTCACACTGAGTACA-TGTGAATGGTCTCTCTCCAGTGTGGATCCT--CATG--
i danRer6.chr3         C 0 I 6
s petMar1.Contig5115       13095 58 +     23967 CTTTTCCCACAATCTGTGCA-TATAAATGGCCTTTCTCCAGTGTGCGTGAACTGATGTG
q petMar1.Contig5115                            99999999999999999999-99999999999999999999999999999999999999
i petMar1.Contig5115   C 0 C 0

a score=14668.000000
s hg19.chrY              7722500  71 +  59373566 TTCAGAAAGTT-----TTGAAAAC-TTTTAAAGTCTTTGCCACATTCTTCACATTTACACCATCTGT-----GTATGAATTT-----------------------------------------------------------------------------------------------
s rheMac2.chr3          61109977  77 + 196418989 ttcagtaaggt-----ttgaaaactttttaaagggtttgccacattcttcacatttgtagcatctctctgcagtatgaactt-----------------------------------------------------------------------------------------------
q rheMac2.chr3                                   99999999999-----999999999999999999999999999999999999999999999999999999999999999999-----------------------------------------------------------------------------------------------
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105370436  76 - 153482349 ATCAGTAATGT-----TTGAGAAC-TTTTTAAGGCTTTGCCACATTCTTCACGTTTGTAGCATCTCTCTGCAGTATGAATTC-----------------------------------------------------------------------------------------------
q ponAbe2.chr8                                   99999999999-----99999999-999999999999999999999999999999999999999999999999999999999-----------------------------------------------------------------------------------------------
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575768  71 +  23952694 TTCAGAAAGTT-----TTGAAAAC-TTTTAAAGTCTTTGCCACATTCTTCACATTTGCACCATCTGT-----GTATGAATTT-----------------------------------------------------------------------------------------------
q panTro2.chrY                                   00000000000-----00000000-000000000000000000000000000000000000000000-----0000000000-----------------------------------------------------------------------------------------------
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold5295     10151  66 -     44148 TAGAATGAGGT-----TTGTATGCCTCGTGAAGACCTTACCACATTCTTCACAATCATAGA-----------GTTTGCCTTT-----------------------------------------------------------------------------------------------
q macEug1.Scaffold5295                           99999999999-----999999999999999999999999999999999999999999999-----------9999999999-----------------------------------------------------------------------------------------------
i macEug1.Scaffold5295 C 0 N 0
s xenTro2.scaffold_676     86289  77 -    553874 GAATTTAAGATGGATCTTGCGAGA-----AAAGCTTTTCCCACATTCTGTACAAGTGTATGGTCTCTCCCCTGTGTGGATTC-----------------------------------------------------------------------------------------------
i xenTro2.scaffold_676 C 0 C 0
s fr2.chrUn            369482875  73 + 400509343 ----TTTATTG-----CAGAAGTGTGTCTGAAACATTTACCACATGTTTCACAcgcatatggtctctcacctgtgtgaactc-----------------------------------------------------------------------------------------------
i fr2.chrUn            I 6 I 16
s gasAcu1.chrUn         59841683  73 +  62550211 ----TTCAGAT-----TTCCGCTTGCAGTGAAATATTTACCACACTCCGAGCAGCTGAAAGGTTTCTCCCCTGTGTGACATC-----------------------------------------------------------------------------------------------
q gasAcu1.chrUn                                  ----8888888-----888888888888888867888888888888888888888888888888888888888888888888-----------------------------------------------------------------------------------------------
i gasAcu1.chrUn        I 6 I 11
s oryLat2.scaffold1367     21458  73 -     36351 ----GTAACAT-----GAGACTTTTGAACAAACCTTTTGCCGCATTTTTTACAGGAATAAGGCCTTTTTCCTGTATGGGTAA-----------------------------------------------------------------------------------------------
q oryLat2.scaffold1367                           ----9999999-----999999999999999999999999999999999999999999999999999999999999999999-----------------------------------------------------------------------------------------------
i oryLat2.scaffold1367 I 6 I 11
s danRer6.chr3          59509814  73 +  60907308 ----TTAAGGT-----GTGATGAGTGTTTGAAACTCTTTCCACACTGAGTGCATGTGAATGGTCTCTCTCCTGTGTGGATCC-----------------------------------------------------------------------------------------------
i danRer6.chr3         I 6 I 11
s petMar1.Contig5115       13153 170 +     23967 --TTTTGAGGG-----AAGAAGGCTGAGAAAACCTCTGGCCACAATCTTGGCATGCATATGGCCTTTCTCCGGTGTGGGTCAACCGATGAACCTTCATGTAAGAAGCCTTTGAAAACCCTTTTCCGCAGTCATTGCAAACAAATGGCTTCTCTAAAGAATGTGTCAACGAATGTGTC
q petMar1.Contig5115                             --999999999-----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i petMar1.Contig5115   C 0 C 0
e tetNig2.chrUn_random  73750104  35 + 107808587 I

a score=-49521.000000
s hg19.chrY              7722571  42 +  59373566 TT-----TATAGTAAA---ATCT-----------------------------GAGAACAGCCTACAGTTTTTG-------------------------------------------------------CCACAT
s rheMac2.chr3          61110054  47 + 196418989 tcttatgtctagtaaa---atct-----------------------------gagaacaacctacagtctttg-------------------------------------------------------ccacat
q rheMac2.chr3                                   9999999999999999---9999-----------------------------999999999999999999999-------------------------------------------------------999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105370512  47 - 153482349 TCCTCTGTATAGTAAA---ATCT-----------------------------GAGAACAACCTACAGTTTTTG-------------------------------------------------------CCACAT
q ponAbe2.chr8                                   9999999999999999---9999-----------------------------999999999999999999999-------------------------------------------------------999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575839  42 +  23952694 TT-----TATAGTAAA---ATCT-----------------------------GAGAACAGCCGACAGTTTTTG-------------------------------------------------------CCACAT
q panTro2.chrY                                   00-----000000000---0000-----------------------------000000000000000000000-------------------------------------------------------000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_676     86366  47 -    553874 TTTCATGGATTTTAAG---ATCT----------------------CCCTTGCGAGAAAAGCC-------TTTT-------------------------------------------------------TCACAT
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  73750139  34 + 107808587 TT-----CAC-----AACCACTT-----------------------------------CCTCTCaaacctttc-------------------------------------------------------ccacat
i tetNig2.chrUn_random I 35 I 15
s fr2.chrUn            369482964  31 + 400509343 TT-----CAT-----A---ATTT-----------------------------------CGTCTAAAGGTTTTC-------------------------------------------------------TTACAT
i fr2.chrUn            I 16 N 0
s gasAcu1.chrUn         59841767 120 +  62550211 TT-----TAG---------ACTTCCACTTGCAGTGAAACATTTACCACACTGTGAGCAGCTGAAAGGTTTCTCCCCTGTGTGACACCTCATATGTAGCTTCAGGTGTTCGTTTTGAGCGAAACAGTTACCACAC
q gasAcu1.chrUn                                  88-----888---------8888888888888888888888888888888888888888888888888888888888888888888888888888888888855488475378888888888754788888888
i gasAcu1.chrUn        I 11 C 0
s oryLat2.scaffold1367     21542  36 -     36351 TT-----CAA---------ACTT-----------------------------TGAGCAGTTGTACAAGTTCTT-------------------------------------------------------CCACAC
q oryLat2.scaffold1367                           99-----999---------9999-----------------------------999999999999999999999-------------------------------------------------------999999
i oryLat2.scaffold1367 I 11 C 0
s danRer6.chr3          59509898  36 +  60907308 TT-----AAG---------GCTT-----------------------------GATGAGTATCGGAAACTCTTT-------------------------------------------------------CCACAC
i danRer6.chr3         I 11 I 7
s petMar1.Contig5115       13323  36 +     23967 -------------------------------------------TTCAATGTGGATTTAAGTGAAAAACGCTTT-------------------------------------------------------CCACAG
q petMar1.Contig5115                             -------------------------------------------999999999999999999999999999999-------------------------------------------------------999999
i petMar1.Contig5115   C 0 C 0

a score=-17183.000000
s hg19.chrY              7722613 22 +  59373566 TCTTCACA------------------TTTGCAGCATTTCT
s panTro2.chrY            575881 22 +  23952694 TCTTCACA------------------TTTGCAGCATTTCT
q panTro2.chrY                                  00000000------------------00000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105370559 22 - 153482349 TCTTTACA------------------TTTGTAGCATTTGT
q ponAbe2.chr8                                  99999999------------------99999999999999
i ponAbe2.chr8         C 0 C 0
s rheMac2.chr3          61110101 22 + 196418989 tcttcaca------------------cttgtagcatttct
q rheMac2.chr3                                  99999999------------------99999999999999
i rheMac2.chr3         C 0 C 0
s xenTro2.scaffold_676     86413 22 -    553874 ACTTTACA------------------TTTAAAAGCTTTCT
i xenTro2.scaffold_676 C 0 C 0
s tetNig2.chrUn_random  73750188  8 + 107808587 gcttggtt--------------------------------
i tetNig2.chrUn_random I 15 I 2
s fr2.chrUn            180279596  8 - 400509343 GTTTGGGA--------------------------------
i fr2.chrUn            N 0 I 2
s gasAcu1.chrUn         59841887 19 +  62550211 TCCGAACAGCTGAAAGGTT---------------------
q gasAcu1.chrUn                                 8888745888888888878---------------------
i gasAcu1.chrUn        C 0 I 251
s oryLat2.scaffold1367     21578  8 -     36351 TCTTGACA--------------------------------
q oryLat2.scaffold1367                          99999999--------------------------------
i oryLat2.scaffold1367 C 0 I 198
s danRer6.chr3          59509941 15 +  60907308 ACTTGATT-----------GGTTTCT--------------
i danRer6.chr3         I 7 C 0
s petMar1.Contig5115       13359 22 +     23967 TCTTGACA------------------TATAAAAGGCTTCT
q petMar1.Contig5115                            99999999------------------99999999999999
i petMar1.Contig5115   C 0 C 0

a score=-127810.000000
s hg19.chrY              7722635  91 +  59373566 GTCTGC-TA--AGGCTTTTTT-ATGTTCAGTGA-AGGTTGAGCAAAACTCAA----AAGC-TTTGCCATATTTATTAGGTTGGCA-------GGTTTTGCT-----GTG--------GGTA----
s panTro2.chrY            575903  92 +  23952694 GTCTGC-TA--AGGCTTTTTTTATGTTCAGTGA-AGATTGAGCAAAACTCAA----AAGC-TTTGCCATATTTATTAGATTGGCA-------GGTTTTGCT-----GTG--------GGTA----
q panTro2.chrY                                   000000-00--0000000000000000000000-000000000000000000----0000-000000000000000000000000-------000000000-----000--------0000----
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105370581  92 - 153482349 CTCTGC-TA--AAAATTTTCTTATGTTCAGCAA-AGGTTGAGCATAACTCAA----AAGC-TTTGCCACATTTATTACATTGGCA-------AGTTTTGCT-----ATG--------GGTA----
q ponAbe2.chr8                                   999999-99--9999999999999999999999-999999999999999999----9999-999999999999999999999999-------999999999-----999--------9999----
i ponAbe2.chr8         C 0 C 0
s rheMac2.chr3          61110123  92 + 196418989 ctcTGC-TA--AAAATTTCCTTATTTTCAGTGA-AGATTGAGCACAACTGGC----AATC-GCTGCCAAATTTATTACAATGACA-------GGTTTTGCT-----ATG--------GGTA----
q rheMac2.chr3                                   999999-99--9999999999999999999999-999999999999999999----9999-999999999999999999999999-------999999999-----999--------9999----
i rheMac2.chr3         C 0 C 0
s xenTro2.scaffold_676     86435  83 -    553874 CACCTG-TA--TGAATTGCTTGGTG-CCTGCAA-AGCTTTTCCATGTCAGAA----AAACTTTTACCACATTCACTACATGCATA-------GGGCTTG--------------------------
i xenTro2.scaffold_676 C 0 I 10433
s tetNig2.chrUn_random  73750198  63 + 107808587 cactgc-tc--tggattctccagtgtcctgtca-agtctg------acttga----actg-ttc-cactttttctc------------------------------------------ctg----
i tetNig2.chrUn_random I 2 n 2
s fr2.chrUn            180279606  61 - 400509343 TA-TGC-TCTTTGGATGAACTGTGGGCCAAACATCGTTCA------TCTTCA----GCTA-CT-----TGTTTTTG------------------------------------------GTG----
i fr2.chrUn            I 2 I 39
s gasAcu1.chrUn         59842157  51 +  62550211 TTCTCC-CC--TGTG--------TGACATCTCA-TGTGTG------TCTTCA----GATG-TC-----CACTTAGA------------------------------------------GTG----
q gasAcu1.chrUn                                  998777-78--8979--------8885789876-698633------587554----5865-94-----73689356------------------------------------------949----
i gasAcu1.chrUn        I 251 C 0
s oryLat2.scaffold1367     21784  70 -     36351 ctcttcatc--tgtagttgatgttgattcctca-tgttggtttccttcttcatcctgact-at-----cagttaca------------------------------------------tta----
q oryLat2.scaffold1367                           999999999--9999999999999999999999-99999999999999999999999999-99-----99999999------------------------------------------999----
i oryLat2.scaffold1367 I 198 C 0
s danRer6.chr3          59509956  47 +  60907308 --CTCC-GG--TG----------TGGATCCTCA-TGTGAA------GCTTAA----GACT-CT-----TTTTGGTT------------------------------------------CTG----
i danRer6.chr3         C 0 I 21
s petMar1.Contig5115       13381 110 +     23967 CTCCAG-TG--TGGGTCCTCAAATGAGCCTTCA-GGTGTTGG----CCTTGA----GAAA-ATCGC--TGTTCACAATGTTTGCACATGTATGGCTTCACTCCTGCATGTATTCTCTGGTGAACA
q petMar1.Contig5115                             999999-99--9999999999999999999999-99999999----999999----9999-99999--909999999999999999999999999999999999999999999999999999999
i petMar1.Contig5115   C 0 C 0

a score=-132272.000000
s hg19.chrY              7722726  89 +  59373566 GTTGAC---AAACATTGA----------------T----GAGGG-----------CCATTATAACTGCTTT------TCTGCACCTTGGAATTACCCACACTTTGG------TAGTCTTTCTTTAAGTTTA--------------AACT
s rheMac2.chr3          61110215  89 + 196418989 GTTGAA---AAACATTGA----------------T----GAAGG-----------CCATTATAACTGCTTT------TCTGCCCCTTGCAATTACCCACACTTTGG------TTGTCTTTCTTTAAATGTA--------------AATT
q rheMac2.chr3                                   999999---999999999----------------9----99999-----------9999999999999999------99999999999999999999999999999------9999999999999999999--------------9999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105370673  87 - 153482349 GTTGAC---AAACATTGA----------------T----GAAGG-----------CCATTATAACTGGTTT------TCTGCCCCTTGCAATTAGCAACACTTTGG------TAGTCTTTCTTTAAA--TA--------------AACT
q ponAbe2.chr8                                   999999---999999999----------------9----99999-----------9999999999999999------99999999999999999999999999999------999999999999999--99--------------9999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            575995  89 +  23952694 GTTGAC---AAACATTGA----------------T----GAGGG-----------CCATTATAACTGCTTT------TCTACACCTTGGAATTACCCACACTTTGG------TAGTCCTTCTTTAAGTTTA--------------AACT
q panTro2.chrY                                   000000---000000000----------------0----00000-----------0000000000000000------00000000000000000000000000000------0000000000000000000--------------0000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold839      67001  90 -     78316 ATGCAC---AGGCACTGA----------------TCTCACAAgt-----------ctctcctgac---ttc------cctgcCTCTTTAACTGGCTCTCACCTTCT------CTGTCATCCCCCCACATGG--------------AATA
q macEug1.Scaffold839                            999999---999999999----------------9999999999-----------9999999999---999------99999999999999999999999999999------9999999999999999999--------------9999
i macEug1.Scaffold839  N 0 C 0
s xenTro2.scaffold_529    519851 112 -    854086 -----T---GAGGATT-A----------------T----GAGAAGATTCACATTCCTGTGGTAACTGTTTTGGAACATTTAATCTTTTCTCTCGTCTATGCGTC--------TGAACATTTTTTAAATTTAAGTTTGAGGATTGTAATT
i xenTro2.scaffold_529 I 1315 C 0
s fr2.chrUn            180279706  92 - 400509343 GATGATATTAAACATGGCATCATTACTGTCAGGCT----CTTCT-----------TGCTTTTCACATAACT------TCGACATCCACAgatcctc----------------ctgctcttctttaaT--------------------TT
i fr2.chrUn            I 39 C 0
s gasAcu1.chrUn         59842208  76 +  62550211 ---------AAAC-------------------ATT----TACCA-----------CACTGTGAACAGCT---------------GAAAGGTTTCTCCCCTGTGTGATATTGCATGTGTTTCTTCAT-ATTT--------------GATT
q gasAcu1.chrUn                                  ---------8996-------------------759----97868-----------87866314355968---------------899766298867878894868616432548976433667853-7466--------------4414
i gasAcu1.chrUn        C 0 I 5
s oryLat2.scaffold1367     21854  97 -     36351 ---------aagctttgc-tgattgt--ttagatc----tgctt-----------cactgttctcatcttc------ctcataagtaggaatctccatcaatgtatca----gtctcctgcttcag-atca--------------agct
q oryLat2.scaffold1367                           ---------999999999-9999999--9999999----99999-----------9999999999999999------9999999999999999999999999999999----99999999999999-9999--------------9999
i oryLat2.scaffold1367 C 0 N 0
s danRer6.chr3          59510024  74 +  60907308 ---CAGGTCAAACGATTC---------------TT----GTCTC-----------TCCTTTTTAAAACACCAGAAG-TCTGTAAATTAGGGTTTTT----------------CTCAGCTTCAAC-------------------------
i danRer6.chr3         I 21 C 0
s petMar1.Contig5115       13491  66 +     23967 ---------------------------GCTAACGT----ACGCC-----------GACTTGAAAATGTTTT------TCCACACTGCTCACACATGTACATCTTCT------CTGCATTT-----------------------------
q petMar1.Contig5115                             ---------------------------99999999----99999-----------9999999999999999------99999999999999999999999999999------99999999-----------------------------
i petMar1.Contig5115   C 0 T 1132
e tetNig2.chrUn_random  73750261   2 + 107808587 I

a score=-46135.000000
s hg19.chrY              7722815 59 +  59373566 ATGAAGG-TCAT----------ATCTTCCATATTTTATCAGGAT-----CAGTTTTTG-----------AAATGAT--TCTTTTATGT
s rheMac2.chr3          61110304 59 + 196418989 ATTAAGG-TCAC----------AGCTTCCATATTTTCTCAGAAT-----CACTTTTTG-----------AAATGAA--TCTTTTATGT
q rheMac2.chr3                                  9999999-9999----------9999999999999999999999-----999999999-----------9999999--9999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105370760 59 - 153482349 ATTAAAG-TCAC----------AGCTTCCATATTTTATCAGAAT-----CACTTTTTG-----------AAATGAA--TCTTTTATGT
q ponAbe2.chr8                                  9999999-9999----------9999999999999999999999-----999999999-----------9999999--9999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            576084 59 +  23952694 ATGAAGG-TCAT----------ATCTTCCATATTTTATCAGGAT-----CAGTTTTTG-----------AAATGAT--TCTTTTATGT
q panTro2.chrY                                  0000000-0000----------0000000000000000000000-----000000000-----------0000000--0000000000
i panTro2.chrY         C 0 C 0
s macEug1.Scaffold839      67091 54 -     78316 GCAAAGA-TCAA----------CCCTTCTGAGTCTTTCTGTTAC-----CAGGTCCTG-----------GGATGAT--TCATT-----
q macEug1.Scaffold839                           9999999-9999----------9999999999999999999999-----999999999-----------9999999--99999-----
i macEug1.Scaffold839  C 0 N 0
s xenTro2.scaffold_529    519963 71 -    854086 CTAAAGGCTGAT----------CTCTTCTAGCATTTCGCAGCATGGAAACATATTTTGCTGAAAGGAAAAAGTGTG--CATTT-----
i xenTro2.scaffold_529 C 0 C 0
s tetNig2.chr5           3743095 61 +  13390619 GCGGGgg-ctcc--------tgccgctcctgctcctggcagGTC-----GTCTTCTCA-----------AGGTGACGGTCATC--TGA
i tetNig2.chr5         n 2 I 20
s fr2.chrUn            180279798 61 - 400509343 GTAGGGG-CTCC--------TGCCCCTCCTCATCCTGGCAAGAC-----ATCTTGTCA-----------AGGTGACGGTCATC--TGA
i fr2.chrUn            C 0 I 17
s gasAcu1.chrUn         59842289 47 +  62550211 GTGAAAT-ATTT-------------ACCACACTCCGAGCAGCTG-----A-------A-----------AGGTTTC--TCCCC--TGT
q gasAcu1.chrUn                                 5664983-6588-------------5777547633655758487-----7-------7-----------5463978--76668--795
i gasAcu1.chrUn        I 5 N 0
s oryLat2.chr17         11090363 47 +  31848461 ATGAAGG-CTTT-------------CTTACAAATCTCACAGGAA-----T-------A-----------AGGCCTC--tcacc--tgt
q oryLat2.chr17                                 9999999-9999-------------9999999999999999999-----9-------9-----------9999999--99999--999
i oryLat2.chr17        N 0 I 15
s danRer6.chr3          59510098 65 +  60907308 ATGACGT-TTCTCCTCTTCACTCTCCTTATTCTCCCCAAATGGG-----TCTGAAACA-----------AAGTTCC--TTTTT--T--
i danRer6.chr3         C 0 I 13
e petMar1.Contig5115       13557 1132 +     23967 T

a score=-27109.000000
s hg19.chrY              7722874 46 +  59373566 CATACTCCAGCAAT--------------------ATATCTACA-----GTAAGATAAAAAGACC------------------------------------CAGCTA----A-
s danRer6.chr3          59510176 71 +  60907308 AAAACAAATGTAGGATGAAAATTTGAAGTGTAAAGACTCTGTAAACACTGGCTACAAAAACATT------------------------------------AACTTT----A-
i danRer6.chr3         I 13 C 0
s oryLat2.chr17         11090425 37 +  31848461 aaTATTTAAGTaag--------------------aactttgaa------------aaaaacatt--------------------------------------tttg----a-
q oryLat2.chr17                                 99999999999999--------------------999999999------------999999999--------------------------------------9999----9-
i oryLat2.chr17        I 15 C 0
s fr2.chrUn            180279876 26 - 400509343 CAGAAAGCTGTAGA--------------------GGTTCTGCA-------------------------------------------------------------TG----A-
i fr2.chrUn            I 17 C 0
s tetNig2.chr5           3743176 26 +  13390619 CAGGAAGCTGCAGG--------------------GGCTCTGca-------------------------------------------------------------tg----a-
i tetNig2.chr5         I 20 C 0
s xenTro2.scaffold_529    520034 75 -    854086 --------AGTAGT--------------------AAAGCTTAT-----TTAAAAACTAAAGGGCAGATGCATATAGGGTGTGCCTCACAATTCATGATGACAACTA----AT
i xenTro2.scaffold_529 C 0 C 0
s panTro2.chrY            576143 46 +  23952694 CATACTCCAGCAAT--------------------ATATCTACA-----GTAAGATAAAAAGAGC------------------------------------CAGCTA----A-
q panTro2.chrY                                  00000000000000--------------------000000000-----0000000000000000------------------------------------000000----0-
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105370819 50 - 153482349 CGTGCTCTGGCAAT--------------------ATCTCTGCA-----GTAAAATGAAAAGAGC------------------------------------CAGCTGAATTA-
q ponAbe2.chr8                                  99999999999999--------------------999999999-----9999999999999999------------------------------------99999999999-
i ponAbe2.chr8         C 0 C 0
s rheMac2.chr3          61110363 46 + 196418989 CATGCTCCGGCAAT--------------------ATCTCTGCA-----GTAAAATGAAAAGAGC------------------------------------CAGCTG----G-
q rheMac2.chr3                                  99999999999999--------------------999999999-----9999999999999999------------------------------------999999----9-
i rheMac2.chr3         C 0 C 0
e petMar1.Contig5115       13557 1132 +     23967 T

a score=-32340.000000
s hg19.chrY              7722920 52 +  59373566 AAAAAAAAAGAACTAC--------AA-ATTTCTCCCT-----CATTAG-ACCCAG----------GTGAATACACTT
s rheMac2.chr3          61110409 48 + 196418989 AGAAAAAAAAAA------------AA-AATTCTCCCT-----CATTAG-ACTCAG----------GTGAATACACTT
q rheMac2.chr3                                  999999999999------------99-9999999999-----999999-999999----------999999999999
i rheMac2.chr3         C 0 C 0
s ponAbe2.chr8         105370869 53 - 153482349 AAAAAAAAAGAACAAC--------AAGATTTATTCCT-----CATTAG-ACTCAG----------GTGAATACACTT
q ponAbe2.chr8                                  9999999999999999--------9999999999999-----999999-999999----------999999999999
i ponAbe2.chr8         C 0 C 0
s panTro2.chrY            576189 52 +  23952694 AAAAAAAAAGAACTAC--------AA-ATTTCTCCCT-----CATTAG-ACCCAG----------GTGAATACACTT
q panTro2.chrY                                  0000000000000000--------00-0000000000-----000000-000000----------000000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_529    520109 52 -    854086 ATAAAAAAAGGGATCA--------AA-GTTAATCCTT-----TGGTCA-ACCCGG----------GCCATTTCACTC
i xenTro2.scaffold_529 C 0 C 0
s tetNig2.chr5           3743202 31 +  13390619 ga--------ggaaaa--------ca-ga-------------cCTTCAGACCTGG----------ATGAGC------
i tetNig2.chr5         C 0 I 9
s fr2.chrUn            180279902 48 - 400509343 GAGCatatggggaaaa--------aa-ga-------------tgttta-atTTGGTCATTGATCCATTAGC------
i fr2.chrUn            C 0 I 15
s oryLat2.chr17         11090462 44 +  31848461 caaactttacaagaat--------aa-gg-------------cttttc-gcctgt----------gtgagttctcat
q oryLat2.chr17                                 9999999999999999--------99-99-------------999999-999999----------999999999999
i oryLat2.chr17        C 0 N 0
s danRer6.chr3          59510247 44 +  60907308 ATGCACATAAATGTAA--------AA-TA-------------CATCAG-ATCGTG----------TTTAGTTTGGTC
i danRer6.chr3         C 0 I 27
s petMar1.Contig6813       17174 57 +     30809 ----ACAAGGGAATAACTTCTCAGAA-GATTTTGCTTGTGTACATTCC-ATGGAA----------AAGAAAAA----
q petMar1.Contig6813                            ----9999999999999999999999-999999999999999999999-999999----------99999999----
i petMar1.Contig6813   n 1132 C 0

a score=-71741.000000
s hg19.chrY              7722972 115 +  59373566 T----------------GCAAATATATAA-TTAACCAA-----AGCAC-----------ATTAATAAG---------GT-------------GACAAT-----------AAAATA------TTACAGGCTCTA-ATTCttttatataattt-----atataaatttatataaatttatataaatttataCTTA
s rheMac2.chr3          61110457  66 + 196418989 T----------------ACAAATATATAA-TTATACAA-----AGCAC-----------ATTAACAAA---------AT-------------GACAAT-----------AAAATA------CCACAGGCTCTATATTC-------------------------------------------------------
q rheMac2.chr3                                   9----------------999999999999-99999999-----99999-----------999999999---------99-------------999999-----------999999------99999999999999999-------------------------------------------------------
i rheMac2.chr3         C 0 I 35
s ponAbe2.chr8         105370922  74 - 153482349 T----------------ACAAATATATAA-TTATACAA-----AGCac-----------actaacaag---------gt-------------gacaat-----------aaaata------ccacaggctcta-attcctttataaa----------------------------------------------
q ponAbe2.chr8                                   9----------------999999999999-99999999-----99999-----------999999999---------99-------------999999-----------999999------999999999999-9999999999999----------------------------------------------
i ponAbe2.chr8         C 0 I 11
s panTro2.chrY            576241  86 +  23952694 T----------------GCAAATATATAA-TTAACCAA-----AGCAC-----------ATTAATAAG---------GT-------------GATGAT-----------AAAATA------TTACAGGCTCTA-ATTCTTTTATATAA----------------------------------ATTTATACTTA
q panTro2.chrY                                   0----------------000000000000-00000000-----00000-----------000000000---------00-------------000000-----------000000------000000000000-00000000000000----------------------------------00000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_529    520161 105 -    854086 TTACTTTTTGAACATTAGTAAATATAT-T-TTTTACAATTGGCAGCCC-----------AAAAATCAGGCACCTTTAGT-------------GAAAAG-----------AAAATA------ATA----------ATCCTTTTCTAGCAACT-----GTTTTAA------------------------------
i xenTro2.scaffold_529 C 0 n 0
s tetNig2.chr5           3743242  89 +  13390619 t----------------ggaaa-aaacca--aaactag-----aGGGC-----------A-----------------TT-------------AAAGTTGTCAGACTCTGACTGAACGTCTCCTTGTGCAGTTG-ACATCTGTCTAAA--------------------------------------TGTTCTaa
i tetNig2.chr5         I 9 I 25
s fr2.chrUn            180279965  66 - 400509343 t----------------gaaaataaacaa--taattaa-----aaggC-----------CAAC---AT---------TT-------------AAAATC-----------ACTGTA-------TTGTgatataa-atatgtattt-------------------------------------------------
i fr2.chrUn            I 15 I 26
s danRer6.chr3          59510318  94 +  60907308 T----------------GGAAATAAAAGA--CGACTAA-----GATGC-----------AGTCCCTGT---------TTGTACCCTGTTAAAAAAAAT-----------ACAGTA------CCAGTCAaaata-actgctgtcttaa--------------------------------------tgtatgta
i danRer6.chr3         I 27 I 30
s petMar1.Contig6813       17231 102 +     30809 T----------------GCAAATGGTTAAAATACTCAA-----AGTACTTGCATCTATTATTGTTTAG---------AA-------------GCAATA-----------AATACA------TCAGGTACAATA-TATTGTTTATGCAACTTCAAGCATATTCA------------------------------
q petMar1.Contig6813                             9----------------999999999999999999999-----9999999999999999999999999---------99-------------999999-----------999999------999999999999-99999999999999999999999999999------------------------------
i petMar1.Contig6813   C 0 C 0

a score=-15334.000000
s hg19.chrY              7723087 60 +  59373566 ACAGTAATATACTCA----CAAAATGCCTTTGTGA-GAACTCTAAGAATCAGGTATAAGTTTGCA
s panTro2.chrY            576327 61 +  23952694 ACAGTAATATATTGAT---CCAAATGCCTTTGTGA-GAACTCTAAGAATCAGATATAAGTTTGCA
q panTro2.chrY                                  0000000000000000---0000000000000000-00000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105371007 61 - 153482349 acagaaatatactgac---caaaatgcctttgtga-gaagtctaagaaccagctaagcatttgca
q ponAbe2.chr8                                  9999999999999999---9999999999999999-99999999999999999999999999999
i ponAbe2.chr8         I 11 C 0
s rheMac2.chr3          61110558 45 + 196418989 -------------------CAAAATGCCTTTGCGA-GAAGTCTAAGAACCAGTTAAGCATTTGCA
q rheMac2.chr3                                  -------------------9999999999999999-99999999999999999999999999999
i rheMac2.chr3         I 35 C 0
s tetNig2.chr5           3743356 62 +  13390619 --ATTAGGACAGTTGACCATTGTGTGGCTCTGCCA-GCCATTTTGCATCCCGGTTGGAAGATGCA
i tetNig2.chr5         I 25 I 14
s fr2.chrUn            180280057 63 - 400509343 TCATTCAGACCATTACACACTTTGGTTCTCTGTCAGGACACAAAGTAAACTGG--GAGAAATGTG
i fr2.chrUn            I 26 I 24
s danRer6.chr3          59510442 55 +  60907308 gcattattactattaacattaataat----------aataactaatattaagagtgatttatgaa
i danRer6.chr3         I 30 I 15
s petMar1.Contig6813       17333 52 +     30809 --AGTATTACACATA----CAGTACTGTTTATTGG-AATTACCAATGTCTAATTTTCCC------
q petMar1.Contig6813                            --9999999999999----9999999999999999-99999999999999999999999------
i petMar1.Contig6813   C 0 C 0
e xenTro2.scaffold_529    520266  0 -    854086 I

a score=-31347.000000
s hg19.chrY               7723147 58 +  59373566 GCACCGTAAGT--------------GAGCAAAATGCAAAAAACCACA-----TAGTAGT-TTTAAA-----AAAGTGTTTTGT
s rheMac2.chr3           61110603 58 + 196418989 GCATGCCAAGT--------------GAGC-AAATGCCAAGAACCACA-----TAGAAGCGTTAATA-----AAAGTATTTCAT
q rheMac2.chr3                                   99999999999--------------9999-99999999999999999-----99999999999999-----999999999999
i rheMac2.chr3          C 0 C 0
s ponAbe2.chr8          105371068 58 - 153482349 gcaccccaagt--------------gaggaaaataccaagaaccaca-----tagaagT-GTAACA-----ACGGTATTTCGT
q ponAbe2.chr8                                   99999999999--------------9999999999999999999999-----9999999-999999-----999999999999
i ponAbe2.chr8          C 0 C 0
s panTro2.chrY             576388 58 +  23952694 GCACCCTAAGT--------------GAGCAAAATGCAAAAAACCACA-----TAGTAGT-TTAAAA-----AAAGTGTTTCGT
q panTro2.chrY                                   00000000000--------------0000000000000000000000-----0000000-000000-----000000000000
i panTro2.chrY          C 0 C 0
s xenTro2.scaffold_1954     16139 61 +     25544 GAAACAAAAAT--------------TATT-TTATGCATGAAAATACA------ACTGAT-TTGGAATGTCCCATGTCTCCTGA
i xenTro2.scaffold_1954 n 0 C 0
s tetNig2.chr5            3743432 34 +  13390619 GCGTCTCAAGA-------------------------------ACGCCGCTATGGTCGCT-TTAAAA-----------------
i tetNig2.chr5          I 14 n 14
s fr2.chrUn             180280144 74 - 400509343 GCACAATAATATGTGTGTGGAATatgaataaaatggaaacagacagaaataacaTAGAC-TTAGAA--------TTACATTTG
i fr2.chrUn             I 24 I 2
s danRer6.chr3           59510512 36 +  60907308 gaagactTATA-----------------------------------------AACTACT-TTTGAA-----CAGTTATTTTAt
i danRer6.chr3          I 15 T 16686
s petMar1.Contig6813        17385 55 +     30809 ACATTGCAATC-------------TCAGCAAATTACGTGAAATGGTC-----AAACAGT-ACAACA---------TAATTCGT
q petMar1.Contig6813                             99999999999-------------99999999999999999999999-----9999999-999999---------99999999
i petMar1.Contig6813    C 0 C 0

a score=342.000000
s hg19.chrY               7723205 20 +  59373566 -ATGTACC---C-ACAACAACCATT
s rheMac2.chr3           61110661 20 + 196418989 -ATTTACC---C-AACACAGTCATT
q rheMac2.chr3                                   -9999999---9-999999999999
i rheMac2.chr3          C 0 C 0
s ponAbe2.chr8          105371126 20 - 153482349 -ATTTACC---C-ACCACAGCCATT
q ponAbe2.chr8                                   -9999999---9-999999999999
i ponAbe2.chr8          C 0 C 0
s panTro2.chrY             576446 20 +  23952694 -ATGTACC---C-ACAACAACCATT
q panTro2.chrY                                   -0000000---0-000000000000
i panTro2.chrY          C 0 C 0
s xenTro2.scaffold_1954     16200 20 +     25544 -ATGTGCC---A-ATAACAAATATA
i xenTro2.scaffold_1954 C 0 C 0
s fr2.chrUn             180280220 23 - 400509343 -ATCTATCAAAC-AAGATATCTAAA
i fr2.chrUn             I 2 C 0
s danRer6.chr3           59493862 22 +  60907308 -agttcaaaaac-aaggtagat-ta
i danRer6.chr3          T 16686 C 0
s petMar1.Contig6813        17440 22 +     30809 ATTTTACC---CTGCAGAAGCCACT
q petMar1.Contig6813                             99999999---99999999999999
i petMar1.Contig6813    C 0 n 0
e tetNig2.chr5            3743466 14 +  13390619 I

a score=16607.000000
s hg19.chrY               7723225 37 +  59373566 CTTCATCCTATGATGACTTTAAA----TATAGA-------CTCCCAGC
s rheMac2.chr3           61110681 37 + 196418989 CTTCATCCTATGATGACTCTAAC----TATAGA-------CTCCAAAC
q rheMac2.chr3                                   99999999999999999999999----999999-------99999999
i rheMac2.chr3          C 0 C 0
s ponAbe2.chr8          105371146 37 - 153482349 CTTCATCCTATGATGACTTTAAA----TATAGA-------CTCCCAAC
q ponAbe2.chr8                                   99999999999999999999999----999999-------99999999
i ponAbe2.chr8          C 0 C 0
s panTro2.chrY             576466 37 +  23952694 CTTCATCCTATGATGACTTTAAA----TATAGA-------CTCCCAGC
q panTro2.chrY                                   00000000000000000000000----000000-------00000000
i panTro2.chrY          C 0 C 0
s xenTro2.scaffold_1954     16220 48 +     25544 TATAGTTTTATGGAGATTTCTCACTTGTATAGGTCAAAAACTCCCAGC
i xenTro2.scaffold_1954 C 0 n 0
s fr2.chrUn             180280243 37 - 400509343 ACTCTGAACAAAATAAGAGCAAA----TATTGA-------TTGCTGCC
i fr2.chrUn             C 0 C 0
s danRer6.chr3           59493884 37 +  60907308 attcccattattataattcctaa----tattta-------ttattgtc
i danRer6.chr3          C 0 C 0
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I

a score=-5077.000000
s hg19.chrY                 7723262 67 +  59373566 TTCCATCTCCCCCATC-----CAG----CAATAAAGTATTGGCACCTCTGTCCATGCTTCTGGGTTTCTGAGACCT
s rheMac2.chr3             61110718 71 + 196418989 TCCTGTCTTCCCCCTC-----CAAAAATAAATAAAATAGTGGCACATGTGTCCATGCTTCTGGCTTATTGAGACCT
q rheMac2.chr3                                     9999999999999999-----9999999999999999999999999999999999999999999999999999999
i rheMac2.chr3            C 0 C 0
s panTro2.chrY               576503 67 +  23952694 TTCCATCTCCCCCATC-----CAA----CAATAAAGTATTGACACCTCTGTCCATGCTTCTGGGTTTCTGAGACCT
q panTro2.chrY                                     0000000000000000-----000----000000000000000000000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s ponAbe2.chr8            105371183 71 - 153482349 TCGTGTCTTCCCCCTC-----CAAAAATAAATAAAATAGTGGCACCTGTATCCATGCTTCTGGCTTTTTGAGACCT
q ponAbe2.chr8                                     9999999999999999-----9999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8            C 0 C 0
s speTri1.scaffold_140712    312805 26 +    431176 TTTCTTCCATTTCATT-----TAA----ATATAAA-----------------------------------------
q speTri1.scaffold_140712                          9997777988777788-----889----8889888-----------------------------------------
i speTri1.scaffold_140712 N 0 N 0
s fr2.chrUn               180280280 15 - 400509343 TG-TATCTCCCCCGCC------------------------------------------------------------
i fr2.chrUn               C 0 N 0
s danRer6.chr3             59493921 33 +  60907308 agccacttttaacattataaa--------------gagtttgaacat-----------------------------
i danRer6.chr3            C 0 I 38
e tetNig2.chr5              3743466 14 +  13390619 I
e petMar1.Contig6813          17462  0 +     30809 I
e xenTro2.scaffold_1954       16268  0 +     25544 I

a score=50818.000000
s hg19.chrY               7723329 139 +  59373566 TACCATAG---GCTAATTTCTATATTCCATGGTAGCGTTGAAAGGAAAGTTGGTA---ACTGACAGTTTTGGATATCTAAGATCAAAGATAAATGACTGTTACAAGTGAA--GAAAGACTT------TAGTATCAAAGACAGACAATGGGTAT
s ponAbe2.chr8          105371254 119 - 153482349 TACCAAAG---ACTAATTTCTATATTCCATGACAATATTGAAAGAAAAGGTGGTATACTTTGACAGTTTTG-----------------------GACTATTACAAGAGAA--GAAACACTT------CAGTAGCATAGACAGACAATGGGTAT
q ponAbe2.chr8                                    99999999---999999999999999999999999999999999999999999999999999999999999-----------------------9999999999999999--999999999------99999999999999999999999999
i ponAbe2.chr8          C 0 C 0
s panTro2.chrY             576570 139 +  23952694 TACCATAG---GCTAATTTCTATATTCCATGGTAGCGTTGAAAGGAAAGTTGGTA---ACTGACAGTTTTGGATATCTAAGATCAAAGATAAATGACTGTTACAAGTGAA--GAAAGACTT------TAGTATCAAAGACAGACAATGGGTAC
q panTro2.chrY                                    00000000---00000000000000000000000000000000000000000000---0000000000000000000000000000000000000000000000000000--000000000------00000000000000000000000000
i panTro2.chrY          C 0 C 0
s rheMac2.chr3           61110789 142 + 196418989 TACCAAAG---ACTAATTTCTATATTCCATGACAGTGTTGAAAGGAAAGGTGGTATATACTGACAGCTTCAGACAGATGAGACCAAAGGTAAATGACTGTTACAAGAGAT--GAAAGACTT------CAGTATCATAGACAGACAATGGGTAT
q rheMac2.chr3                                    99999999---999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999------99999999999999999999999999
i rheMac2.chr3          C 0 C 0
s danRer6.chr3           59493992 137 +  60907308 tacaataaaacgtcaacttttaaattaaattgtgcttttaaaagttaa-ttaaaa---att---aattttaaaaagttaaa---------aaaaaactgctgtacgtaaatgtaaagaattaacatatagtagctaattcaaaacctggaaat
i danRer6.chr3          I 38 N 0
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_1954     16268   0 +     25544 I

a score=16135.000000
s hg19.chrY               7723468 39 +  59373566 AGCAACTGACAACAGGATTTCAA---TAAGAAACATGGGGAA----
s ponAbe2.chr8          105371373 39 - 153482349 AGCAACTGACTATAGGATTTCAA---TAAGAAACATGGGGAA----
q ponAbe2.chr8                                   99999999999999999999999---9999999999999999----
i ponAbe2.chr8          C 0 C 0
s panTro2.chrY             576709 39 +  23952694 AGCAACTGACAACAGGATTTCAA---TAAGAAACATGGGGAA----
q panTro2.chrY                                   00000000000000000000000---0000000000000000----
i panTro2.chrY          C 0 C 0
s rheMac2.chr3           61110931 39 + 196418989 AGCAAGTGACTACAGGATCTCAG---TAAGAAACACAGGGAA----
q rheMac2.chr3                                   99999999999999999999999---9999999999999999----
i rheMac2.chr3          C 0 C 0
s danRer6.chr4           33157372 42 -  71658100 ----ggtagcaccagtgctcctaatttaaaaaatgtaggcgcatca
i danRer6.chr4          N 0 C 0
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_1954     16268  0 +     25544 I

a score=83535.000000
s hg19.chrY                        7723507 190 +  59373566 T-gctgggagtggttgcccacacctgtaatattggcactttgg----gaggctgaggcaggcagat------caccagaggtgaa-aagttcaagaccagcaaggtaaa-------------catggttaaaccttgtctctactaaa---------aatacaaaaa-ttagatgggcgtggtggcaggtttctgtaattcctgctactcaggaggctgaggcag------
s ponAbe2.chr8                   105371412 191 - 153482349 Tggctgggagtggtggcttatgcctgtaatcccaacagtttgg----gaggctgagataggtggat------cacctgaggtcag-aagttcaagatcagccaggtcaa-------------catggtgaaaccccgtctctacaaaa---------aatacaaaaa-ttagccaggtgtggtggcaggcacctgtgatcccagctgcgtgggaggctgaggcag------
q ponAbe2.chr8                                             9999999999999999999999999999999999999999999----9999999999999999999------9999999999999-99999999999999999999999-------------99999999999999999999999999---------9999999999-999999999999999999999999999999999999999999999999999999999------
i ponAbe2.chr8                   C 0 C 0
s panTro2.chrY                      576748 190 +  23952694 T-gctgggagtggttgcccacacctgtaatattggcactttgg----gaggctgaggcaggcagat------caccagaggtgaa-aagttcaagactagcaaggtaaa-------------catggttaaaccttgtctctactaaa---------aatacaaaaa-ttagatgggcgtggtggcaggtttctgtaattcctgctactcgggaggctgaggcag------
q panTro2.chrY                                             0-00000000000000000000000000000000000000000----0000000000000000000------0000000000000-00000000000000000000000-------------00000000000000000000000000---------0000000000-000000000000000000000000000000000000000000000000000000000------
i panTro2.chrY                   C 0 C 0
s rheMac2.chr3                    61110970 191 + 196418989 Tggccaggagtggtggctcacacctgtaatcccagcactttgg----gaggctgaggcaggaagac------cacctgaggtcag-aagttcaagaccaggcaggccaa-------------catggtgaaacctcgtctcaactaaa---------aatacaaaaa-taagtagggcatggtggcaggcgcccataattccagctacttgggaggctgaggcag------
q rheMac2.chr3                                             9999999999999999999999999999999999999999999----9999999999999999999------9999999999999-99999999999999999999999-------------99999999999999999999999999---------9999999999-999999999999999999999999999999999999999999999999999999999------
i rheMac2.chr3                   C 0 I 161
s otoGar1.scaffold_81905.1-95121     91072 187 -     95121 -Tgctgggtgcagtggttcacgtttgtaaacctagcactctgg----gagagtgag-tgagtggaa------tgcttcagcacag-gcatttgagagcagcctgagc---------------cagagtgtaaccctgtttataccaaa---------aatagaaaaagttagtggggcgt-gtggcagacacctgcagtcccagcaactcaggaggctgaggcaa------
q otoGar1.scaffold_81905.1-95121                           -999999999999999999999999999999999999999999----999999999-999999999------9999999999999-999999999999999999999---------------99999999999999999999999999---------99999999999999999999999-99999999999999999999999999999999999799997999------
i otoGar1.scaffold_81905.1-95121 N 0 C 0
s danRer6.chr4                    33157414 213 -  71658100 -accaaaattttgtcgcacccaccaattata--agcaccgttaccacaagttttatacaaacaaatttattgcatttgaaatcaatacgaatcaaactaacaagcaaaaaaatatatgcatgcatgaggaaaatatgtctcaacgaaatcccattatcacaaaaaaa-taccataaatgagggaccaaa-------------agatactcagaccactca-ccagcccttt
i danRer6.chr4                   C 0 C 0
e tetNig2.chr5                     3743466  14 +  13390619 I
e petMar1.Contig6813                 17462   0 +     30809 I
e xenTro2.scaffold_1954              16268   0 +     25544 I

a score=20388.000000
s hg19.chrY                        7723697 114 +  59373566 gcaaaccgctttaaccaagga-----gttggaggttgcagtgagcccagactgtgccattacactccagcctgtgtaacaggagtgaagctcccactcaaaaataaagaaagaaagaaa
s panTro2.chrY                      576938 114 +  23952694 gcaaaccgctttaaccaagga-----gttggaggttgcagtgagcccagactgtgccattactctccagcctgtgtaacaggagtgaagctcccactcaaaaaTAAagagagagagaga
q panTro2.chrY                                             000000000000000000000-----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s ponAbe2.chr8                   105371603 114 - 153482349 gagaattgcttgaacctggga-----gttggaggttgcagtgacccaagatcacatcattgcactccagcctgggcaacaaaagtgaaactccaactcaaaaaaaaaaaaaaaaaaaaa
q ponAbe2.chr8                                             999999999999999999999-----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8                   C 0 I 2984
s otoGar1.scaffold_81905.1-95121     91259 106 -     95121 gagtatctcttgagcccagca-----ggttgaggttgctgttaact---ataataccacagcactctttccatggtgaaa-----gacactcggtctcaaaaaTATAGAACTATATAAA
q otoGar1.scaffold_81905.1-95121                           999999999999999999999-----99999999999999999999---9999999999999999999999799999999-----9979999999999999999999999999999999
i otoGar1.scaffold_81905.1-95121 C 0 C 0
s danRer6.chr4                    33157627  94 -  71658100 acgcactgcttgacacaactgaatctgttaacgcttgctgtgctgttctacatttacatttacatttagtcatt-tagca-----gacgcttttatccaa-------------------
i danRer6.chr4                   C 0 C 0
e rheMac2.chr3                    61111161 161 + 196418989 I
e tetNig2.chr5                     3743466  14 +  13390619 I
e petMar1.Contig6813                 17462   0 +     30809 I
e xenTro2.scaffold_1954              16268   0 +     25544 I

a score=-3758.000000
s hg19.chrY                        7723811  86 +  59373566 GAGAGAGAGAGAGAGAGGaagaaa---------------------------agaaa-agaaaagaaaagaaaagaaaagaaa-------agaaaagaaaagaaaagaaaagaaatgaaacg-
s panTro2.chrY                      577052 114 +  23952694 gagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagaagagaagagaagagaagaga-------agagaagagaagaaaagaaaagaaaagaaaag-
q panTro2.chrY                                             0000000000000000000000000000000000000000000000000000000000000000000000000000000000-------00000000000000000000000000000000-
i panTro2.chrY                   C 0 C 0
s otoGar1.scaffold_81905.1-95121     91365  54 -     95121 -------ATGAAGTAAGAAAAAAA---------------------------TGATA-ATTACAAAAGGTGTAAAATATGGGA-------AGAAAAG--------------------------
q otoGar1.scaffold_81905.1-95121                           -------99999999999999999---------------------------99999-7999999999968999989989989-------8999999--------------------------
i otoGar1.scaffold_81905.1-95121 C 0 I 52
s danRer6.chr4                    33157721  70 -  71658100 ---------------------------------------------------agcga-cttacaaatgaggacaaggaagcaatttacacaactaagagcaacaatgaataagtactaaaggc
i danRer6.chr4                   C 0 C 0
e rheMac2.chr3                    61111161 161 + 196418989 I
e tetNig2.chr5                     3743466  14 +  13390619 I
e ponAbe2.chr8                   105371717 2984 - 153482349 I
e petMar1.Contig6813                 17462   0 +     30809 I
e xenTro2.scaffold_1954              16268   0 +     25544 I

a score=6841.000000
s hg19.chrY                        7723897 76 +  59373566 aaatgaaacgaaacg--------aaaagaaaagaagaaaaaaCATGGA--AAACttttttcttttt-----tttttttttttttttttttt
s panTro2.chrY                      577166 68 +  23952694 aaaagaaaagaaaag--------aaaagaaaagaagaaaaaaCATGGA--AA--------CCtttt-----tttttttttttttttttttt
q panTro2.chrY                                            000000000000000--------0000000000000000000000000--00--------000000-----00000000000000000000
i panTro2.chrY                   C 0 C 0
s otoGar1.scaffold_81905.1-95121     91471 88 -     95121 ATATGAAAGTAAACTTTTTCCTCAAAAGAAAAATAG---AGACCTGCATTAACTCTACTGGCTTTTCAGGGCTTATTAttttatttttatt
q otoGar1.scaffold_81905.1-95121                          999899997999779999999999999999999999---9979989899997999999998999999999999999999999999999999
i otoGar1.scaffold_81905.1-95121 I 52 C 0
s danRer6.chr4                    33157791 76 -  71658100 aagtttcaggtctgt--------aaagtctaagaagggaagtgttagt--agtttttttttttttt-----tttttttttttttttttttt
i danRer6.chr4                   C 0 N 0
e rheMac2.chr3                    61111161 161 + 196418989 I
e tetNig2.chr5                     3743466 14 +  13390619 I
e ponAbe2.chr8                   105371717 2984 - 153482349 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_1954              16268  0 +     25544 I

a score=25412.000000
s hg19.chrY                        7723973 148 +  59373566 gagatggagccttgctcttattgcccaggctggaa------ggcagcttggctcactgcaacttctgcctcccaggttcaagtgattctcctgcctcagtctccccagtagctgggattacaggagctcacccccacacttggctcatttttgt
s panTro2.chrY                      577234 148 +  23952694 gagatggagccttgctcttattgcccaggctggaa------ggcagcttggctcactgcaacttctgcctcccatgttcaagtgattctcctgcctcagtctccccagtagctgggattacaggagcccacccccacacttggctcatttttgt
q panTro2.chrY                                             00000000000000000000000000000000000------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                   C 0 C 0
s otoGar1.scaffold_81905.1-95121     91559 153 -     95121 gagacagagcctcaagc-tgtcactctgggtagagggctgtggcatcacagttcatagcaacctccaactcctgggctcaagggattctcctgcctctgcctcccaagtagctgggactacaggcacccgtcacaaggcccggctattttttgt
q otoGar1.scaffold_81905.1-95121                           99999999999999999-9999999999999999999999999999999999999999998799999999999999999999999999999965999989999999999999999999999999999999999999989999999999999999
i otoGar1.scaffold_81905.1-95121 C 0 N 0
e rheMac2.chr3                    61111161 161 + 196418989 I
e tetNig2.chr5                     3743466  14 +  13390619 I
e ponAbe2.chr8                   105371717 2984 - 153482349 I
e petMar1.Contig6813                 17462   0 +     30809 I
e xenTro2.scaffold_1954              16268   0 +     25544 I

a score=8371.000000
s hg19.chrY               7724121 93 +  59373566 atttttagtagagatggggttttgccatattggccatgctggtctcgaacccctgacctcagatgattcactcacctcagcctcccaaggGAA
s panTro2.chrY             577382 93 +  23952694 atttttagtagagatggggtttcaccatgttggccatgctggtctcgaactcctgacctcagatgattcactcacctcagcctcccaaggGAA
q panTro2.chrY                                   000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
e rheMac2.chr3           61111161 161 + 196418989 I
e tetNig2.chr5            3743466 14 +  13390619 I
e ponAbe2.chr8          105371717 2984 - 153482349 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_1954     16268  0 +     25544 I

a score=63636.000000
s hg19.chrY                7724214 166 +  59373566 AATTTTTTAAACTGAAAAACACACAAA------CTCAGACAAAGCATCCATAGAATAGGCTTCAGAGAC-CCAAGAATATCTAGCCTAAAAAATTTGTATTATATTCCCCCAGACAATAAAAAACTTAATAAA-----GATTTTG--ATGCCACTTT-TTATTATACAAATTGCAACCTAA
s panTro2.chrY              577475 166 +  23952694 AATTTTTTAAACTAAAAAACACACAAA------CTCAGACAAAGCATCCATAGAATAGGCTTCAGAGAC-CCAAGAATATCTAGCCTAAAAAATTTGTATTATATTCCCCCAGACAACAAAAAACTTAATAAA-----GATTTTG--ATGCCACTTT-TTATTATACAAATTGCAACCTAA
q panTro2.chrY                                     000000000000000000000000000------000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000-----0000000--0000000000-00000000000000000000000
i panTro2.chrY            C 0 C 0
s micMur1.scaffold_106697      797 168 -      1535 AGTTACTTTAAATGGAAAATAAACAAAAACTGTCACAGAAGAAACATCTTCAGAACAGATTT--GAGGCTCC-----TCCCCAGTACAGCGAATCGGTAGCAGAGTCCCCCAGGACA-AAGCCACTTGATGAA-----GTTTGTGAAAGCTAATTTTGTTAATTCTCAAATCTCAACCAAA
q micMur1.scaffold_106697                          99999999999999999999999999999999999999999999999999999999999999--99999999-----9999999999999999999999999999999999999999-999999999999999-----9999999999999999999999999999999999999999999
i micMur1.scaffold_106697 N 0 C 0
s tarSyr1.scaffold_470127      895 144 -      1157 ---------------------CACACA------CAGAGAAGACATATCCAAAGAACAGGTATGAGAGTCTCCTAGATTTTCTAACTT-ACTGATTGGTGTTATATTAATCTAGA-AA-AATTAACATTATAAA-----CATTATGACGTGTATATCT-TTGAATTTCAAATATCCAATTC-
q tarSyr1.scaffold_470127                          ---------------------999999------999999999999999999999999999999999999999999999999999999-99999999999999999999999999-99-999999999999999-----9999999999999999999-9999999999999999999999-
i tarSyr1.scaffold_470127 N 0 N 0
s rheMac2.chr3            61111322 165 + 196418989 ---TTTTTAAACTAAAAAACACACAAG------CCCAGAGAAAACATTCATAGAACGGGCTTGAGAGACTCCAAAAATCTCTAGCCTAAAAAACTGGTATCATATTCCCCCAGACAA-AAGTCACTTAATACA-----GATTTTGACATGTGGCTTT-TTATCGTACAAATTGCAACCTAA
q rheMac2.chr3                                     ---999999999999999999999999------999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999-----9999999999999999999-99999999999999999999999
i rheMac2.chr3            I 161 C 0
s ponAbe2.chr8            48201760 165 + 153482349 ---TTTTTTAACTAAAAAATACAGAAA------TCCAGAGAAAACATCCAGAGAACAAGCTTGAGAGACTCCAAGAATCTCTAGCCTAAATAATTGGTGTCATACTCCCAAAGACAA-AAGCCACTTAATAAA-----GATTTTGATATGTGGCTTT-TTATTATACAAATTGCAAACTAA
q ponAbe2.chr8                                     ---999999999999999999999999------999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999099999999-----9999999999999999999-99999999999999999999999
i ponAbe2.chr8            n 2984 C 0
s danRer6.chr4            56295828 124 +  71658100 AATTTTTTACTGGGTAAAGTGTCCAAA------CGCAGAGAAAACCTATATATAATAAGTCATGA-----CTAAGAGTAAGTGGCAAAAAAAGGT---------------TAAAATA-AAGACTTTTATTTGAGCGTGGCTTGTG--ACGCCA----------------------------
i danRer6.chr4            N 0 I 37
e tetNig2.chr5             3743466  14 +  13390619 I
e petMar1.Contig6813         17462   0 +     30809 I
e xenTro2.scaffold_1954      16268   0 +     25544 I

a score=28082.000000
s hg19.chrY                7724380  97 +  59373566 -------------------GATTACAACATATTCAAAAC-----ATCAAGATAATATGGttaatttaaatataaaaatatatatCCAGAAATCAAC---TAAAAA-AAGGTGATGTAAAAATTAC
s panTro2.chrY              577641  97 +  23952694 -------------------GATTACAACATATTCAAAAC-----ATCAAGATAATATGGTTCATTCAAATATAAAAATATATATCCAGAAATCAAC---TAAAAA-AAGATGATGTAAAAATTAC
q panTro2.chrY                                     -------------------00000000000000000000-----0000000000000000000000000000000000000000000000000000---000000-0000000000000000000
i panTro2.chrY            C 0 C 0
s ponAbe2.chr8            48201925  99 + 153482349 -------------------GATTACAACATATACAAAAC-----ATAAAGAAAATATGGCTCAATCAAAGATAAAAATGAATATCCAGACATCAATTA-TAAAAA-GAGGAGATTTAAAACTTAC
q ponAbe2.chr8                                     -------------------99999999999999999999-----999999999999999999999999999999999999999999999999999999-999999-0999999999999999999
i ponAbe2.chr8            C 0 C 0
s rheMac2.chr3            61111487  96 + 196418989 -------------------CATTACAACATATACAAAAT-----ATCAAGATAATATGGC----TCAAAGATAAAAATGAATATCCAGAAATCATTTATTTAAAA-AAGGAGATGTAAAAATTAC
q rheMac2.chr3                                     -------------------99999999999999999999-----9999999999999999----99999999999999999999999999999999999999999-9999999999999999999
i rheMac2.chr3            C 0 C 0
s micMur1.scaffold_106697      965  63 -      1535 -------------------GATTACAACATACACAAAAT-----GTCAGGGAAACA----------------------AAATAACAAGAAATCAAC---CATAAA-GTATTGG------------
q micMur1.scaffold_106697                          -------------------99999999999999999999-----999999999999----------------------999999999999999999---999999-9999999------------
i micMur1.scaffold_106697 C 0 C 0
s danRer6.chr4            56295989 105 +  71658100 GAAAGGTTTGTTTTAAAGCGTTTAC-ACTTATATAAACCAATTGATTAAAGTTTTAGTTTTTTTTC----------------ATTCAGTGCTAAAT---TATGAACCTGCTGTTGACAATATTAT
i danRer6.chr4            I 37 C 0
e tetNig2.chr5             3743466  14 +  13390619 I
e petMar1.Contig6813         17462   0 +     30809 I
e xenTro2.scaffold_1954      16268   0 +     25544 I

a score=2719.000000
s hg19.chrY                7724477 95 +  59373566 ------------------CAGAGACAATTTGAGTTAAAGT--CCAGATACatttttaaaaagaaaaaa------aaataaa----ttaCCCTTAAAAGTTAGCATTA-CCATCTCACTGATGCTCA
s rheMac2.chr3            61111583 90 + 196418989 ------------------ACGAAACAATTTGAATTAAAGT--CTAGATCTACTTTTTAAAAGAAAAAA----------AAA----TCACCCTAGAAAATCACAATTA--CATCTCAATGATGCTCA
q rheMac2.chr3                                    ------------------9999999999999999999999--99999999999999999999999999----------999----9999999999999999999999--99999999999999999
i rheMac2.chr3            C 0 C 0
s ponAbe2.chr8            48202024 92 + 153482349 ------------------CTGAGACATTTTGAATTAAAGT--Ctatatatatttttaaa---agaaaa------aaataaa----ttGCCCTGAAAAACTAAAGTTA-CCATTTCAGTGATGCTCA
q ponAbe2.chr8                                    ------------------9999999999999999999999--99999999999999999---999999------9999999----9999999999999999999999-999999999999999999
i ponAbe2.chr8            C 0 C 0
s panTro2.chrY              577738 94 +  23952694 ------------------CAGAGACAATTT-AGTTAAAGT--CCAGATACatttttaaaaagaaaaaa------aaataaa----ttaCCCTTAAAAGTTAGCATTa-ccatctcaatgatgctca
q panTro2.chrY                                    ------------------000000000000-000000000--00000000000000000000000000------0000000----0000000000000000000000-000000000000000000
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_74688      3750 80 +      9896 ------------------------catgtcgagcaaaa----------ctgtctttcaaaataaaaaatattcaaaatgaa----cagaaacagaaaaccttaatca-cta-------gccaccct
q tarSyr1.scaffold_74688                          ------------------------99999999999999----------999999999999999999999999999999999----9999999999999999999999-999-------99999999
i tarSyr1.scaffold_74688  N 0 C 0
s micMur1.scaffold_106697     1028 51 -      1535 -----------------------------------------------------------------ACA------TTATAAA----TTACCTGAAAAAATTAAAAATAACCATGTGAATGCTGCTTA
q micMur1.scaffold_106697                         -----------------------------------------------------------------999------9999999----99999999999999999999999999999999999999999
i micMur1.scaffold_106697 C 0 C 0
s danRer6.chr4            56296094 92 +  71658100 TTTAACCCTTTATTCTACGTATTACTATTTAACTCACAGTAATGAGGTCTATTGTTTAAATAAAGATA------AGATAAACCTTTTGTTCCCGAGAG----------------------------
i danRer6.chr4            C 0 I 43
e tetNig2.chr5             3743466 14 +  13390619 I
e petMar1.Contig6813         17462  0 +     30809 I
e xenTro2.scaffold_1954      16268  0 +     25544 I

a score=12332.000000
s hg19.chrY                7724572 53 +  59373566 ATGAATaa----aatggaaataaagaaattaagaa---------aatggaaataagtgaaataaca
s rheMac2.chr3            61111673 43 + 196418989 ATGAGTaa----aatggaaaaaaaaaaaacacca-------------------aaatgaaataaca
q rheMac2.chr3                                    99999999----9999999999999999999999-------------------9999999999999
i rheMac2.chr3            C 0 C 0
s ponAbe2.chr8            48202116 36 + 153482349 ATGagtaa----aatggaaataaaaca--------------------------aaatgaaataaca
q ponAbe2.chr8                                    99999999----999999999999999--------------------------9999999999999
i ponAbe2.chr8            C 0 C 0
s panTro2.chrY              577832 53 +  23952694 atgaataa----aatggaaataaagaaattaagaa---------aatggaaataaatgaaataaca
q panTro2.chrY                                    00000000----00000000000000000000000---------0000000000000000000000
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_74688      3830 59 +      9896 acgaaaaatgctaatggaagttcATTCATTGAAAAC-------TAAACATTTTAGAAAACATCACA
q tarSyr1.scaffold_74688                          999999999999999999999999999999999999-------99999999999999999999999
i tarSyr1.scaffold_74688  C 0 C 0
s micMur1.scaffold_106697     1079 43 -      1535 ATGTGTGA----AACTGGAACAATA-------------------CTGAGCACTAAATGAAATCAGG
q micMur1.scaffold_106697                         99999999----9999999999999-------------------9999999999999999999999
i micMur1.scaffold_106697 C 0 C 0
s danRer6.chr4            56296229 60 +  71658100 ATGAATAA----AAC--AAACAAAACAATTAAGAACATACCTGAAGAAAGTTTAAGTGAAGTAACA
i danRer6.chr4            I 43 N 0
e tetNig2.chr5             3743466 14 +  13390619 I
e petMar1.Contig6813         17462  0 +     30809 I
e xenTro2.scaffold_1954      16268  0 +     25544 I

a score=30222.000000
s hg19.chrY                7724625 223 +  59373566 taaattaaaccaa-------caaa----aaa-tataaagctcaaaaa-------ga--aataaaaatCGTAGAGTGGAAGTAC------AAAAAAGATTAATATTCCCTTCAACATTAG--AAAAAATATGAGAAA---ATC-----AGTaagc-----tcagcaaatttcaaataaaat--taatgtaagagagattt-----------acaagacacaa------------gttttgaaagtcacagaaa--------agagaatgagaaatgcaggaagaaaaaaaacagatgta
s rheMac2.chr3            61111716 238 + 196418989 aaaatgaaaccaa-------caaa----aagataaaaagcacagaaa-------gattaaaaaaaaTTGT---GTAGAACTAC-----AAAAAAAGACTAATATGCACTTCAACATTAG-TAAAAAATATAAGAAA---ATc-----aagaagc-----tcggcaaatttcaactaaaat--taacacaa-agagatttc--------taacaagacacaa-cataaac-aatgatttaaaagttgcagaca-----agaagagaatctggaattcaggaagaaaaaag--agatgtg
q rheMac2.chr3                                     9999999999999-------9999----9999999999999999999-------9999999999999999---9999999999-----9999999999999999999999999999999-9999999999999999---999-----9999999-----999999999999999999999--99999999-999999999--------9999999999999-9999999-9999999999999999999999-----99999999999999999999999999999999--9999999
i rheMac2.chr3            C 0 C 0
s ponAbe2.chr8            48202152 239 + 153482349 aaaatgaaaccaaac-----cata----aaa-taaaaagcacgaaaa-------ga--aataaaaATTGTGGAGTGTaagtac------aaaaaagaataatatgcacttcaacattag-taaaaaatataagaaa---atc-----aagaagc-----tcagcaaatttcaactaagat--taacacaa-agagatttc--------taataagacacaa-tgtaagc-aatgtattgaaagtcacagaga-----agtagagaatgtggaatgcaggaagaaaaaag--agatgcg
q ponAbe2.chr8                                     999999999999999-----9999----999-999999999999999-------99--9999999999999999999999999------999999999999999999999999999999-9999999999999999---999-----9999999-----999999999999999999999--99999999-999999999--------9999999999999-9999999-9999999999999999999999-----99999999999999999999999999999999--9999999
i ponAbe2.chr8            C 0 C 0
s panTro2.chrY              577885 224 +  23952694 taaattaaaccaa-------caaa----aaaatataaagctcaaaaa-------ga--aataaaaatcgtagagtggaagtac------aaaaaAGATTAATATTCCCTTCAACATTAG--AAAAAATATGAGAAA---ATC-----AGTaagc-----tcagcaaatttcaaataaaat--taatgtaagagagattt-----------acaagacacaa------------gttttgaaagtcacagaaa--------agagaatgagaaatgcaggaagaaaaaaaacagatgca
q panTro2.chrY                                     0000000000000-------0000----0000000000000000000-------00--0000000000000000000000000------000000000000000000000000000000--000000000000000---000-----0000000-----000000000000000000000--00000000000000000-----------00000000000------------0000000000000000000--------00000000000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_74688      3889 266 +      9896 AAATTAATTTTAACTTTTTGCAGATGGTAAA-TACAAGGAACAAAAAATGTCCTGT--AATTATCTTTCTGGAGAGTGAGCCC------CTCCTAGTACAAGAT----TTCAACACCAT-GTAAGTGTTCTAAAAACCCATC-----AGTATGCATGTTTCAGCTAGTGTTGTGAGAGGTTGTACTGTAGAAGAAACTTCCTGAGTTGTGGCAA-ACACAT------------GACTGCGaagatatgcatactaaccaaggtgaccgacagattcaacaaaatatttgccaaattca
q tarSyr1.scaffold_74688                           9999999999999999999999999999999-999999999999999999999999--9999999999999999999999999------999999999999999----99999999999-9999999999999999999999-----9999999999999999999999999999999999999999999999999999999999999999999-999999------------99999999999999999999999999999999999999999999999999999999999999999
i tarSyr1.scaffold_74688  C 0 C 0
s micMur1.scaffold_106697     1122 242 -      1535 AAAATGAGAATAA-------CAAT----AAAACATAGAA-GCAGAAG-------AA--AAGATACACTATTCAGCTGAGGCATACAATAACAaatgactgagaaaatctaaaaggaaagaataagtacatacacat---att-----gagaagc-----tctacatacttcagctaggaa--aaacacca-aaggaccc-----------acaaaggacaaatatatgcaaaagttttgaaagtcacacaca----acaaaggaatcttttaaggcagcaggagaaa----atacatg
q micMur1.scaffold_106697                          9999999999999-------9999----99999999999-9999999-------99--999999999999999999999999999999999999999999999999999999999999999999999999999999---999-----9999999-----999999999999999999999--99997886-79985577-----------767868545558888699765726154876768594868677----9741234455527735943354545324674----6533566
i micMur1.scaffold_106697 C 0 C 0
s danRer6.chr4            22794653 226 -  71658100 ----TCAGTTGAA-------CATG----TGA-TACTAAAATGCAAAA-------GA--TATGAAAAGCAGAGGGAGGAAATG-------AGAAAAGATCTAAGGGAAATAGGGATTCAG-GAAATAACATTAAAAG---GTTTACTAAATACAA-----AAGACAGGATTCAGACTAGAA--TACTTATA-AAGTATCT-----------GAGAGAAACAG------------GTGTTTATGATAGGATATA-----ATAATTTAAGTTATAAGGTAAAGGGAATAAAGTTAAATATA
i danRer6.chr4            N 0 N 0
e tetNig2.chr5             3743466  14 +  13390619 I
e petMar1.Contig6813         17462   0 +     30809 I
e xenTro2.scaffold_1954      16268   0 +     25544 I

a score=52833.000000
s hg19.chrY                7724848 158 +  59373566 ttatttatattcatg---cttctgcaagattaccagtaaatgtatga---acat-aaatctttcaag--caagaagggggtc----ggatgacatagttaaa----------------------accctgaaa-----gaaaaaggtgtaagcaaaaatactatattttgc---------aacagtatccttcaaaatgaaaa-----aaaa
s rheMac2.chr3            61111954 166 + 196418989 ttatttatatgcatg---cttctgccagattatgagtaaatttaaga---acac-aaatctttcagg--caagaagggagta----ggatgacatcgttaaa----------------------gcactggaaaaaaaaaaaaaagtccaagcaagaa-act-tatccagc---------aaaagtattcttcaaaatgaaaagaaaaaaaa
q rheMac2.chr3                                     999999999999999---99999999999999999999999999999---9999-999999999999--9999999999999----9999999999999999----------------------9999999999999999999999999999999999-999-99999999---------99999999999999999999999999999999
i rheMac2.chr3            C 0 C 0
s ponAbe2.chr8            48202391 157 + 153482349 ttatttgtgtgcaag---cttctgcaagattaccagcaaatttatga---acat-aattctctcagg--caagaagggagtg----gaaagacatagttaaa----------------------actctgaaa------aagaaagtctaagcaagaatactatatccagc---------aaaagtgtacttcaaaatgaaAA-----TAAA
q ponAbe2.chr8                                     999999999999999---99999999999999999999999999999---9999-999999999999--9999999999999----9999999999999999----------------------999999999------99999999999999999999999999999999---------99999999999999999999999-----9999
i ponAbe2.chr8            C 0 C 0
s panTro2.chrY              578109 159 +  23952694 ttatttatattcacg---cttctgcaagattaccagtaaatttatga---acat-aaatctttcaag--caagaaggcagta----ggatgacatagttaaa----------------------accctgaaa-----gaaaaaggtgtaagcaaaaatactatattttgc---------aacagtatccttcaaaatgaaaag----aaaa
q panTro2.chrY                                     000000000000000---00000000000000000000000000000---0000-000000000000--0000000000000----0000000000000000----------------------000000000-----000000000000000000000000000000000---------000000000000000000000000----0000
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_74688      4155 191 +      9896 ccatgt-----cat----ttttttcagaaatacaaaaaaccctaaaactcacatcaaacctctaaggtccatgaaaatgctacagtaattgaaacagtttagtgctatcataaggcagacagttacactgaaa---aatagacaggagtgaaataaatccttgcatttagattcaaatggaagagttattttcacaccgatat---------
q tarSyr1.scaffold_74688                           999999-----999----9999999999999999999989999999999999999999999999999999999999999999999999999999999999999999999999999999999999999799999---9697999999993999999977999999999999999999999999999999999999999999999---------
i tarSyr1.scaffold_74688  C 0 C 0
s micMur1.scaffold_106697     1364 148 -      1535 ttatctatataaatatgctttcttagagattactaatagatttatca---acag-aaaacatgcatg--ccagaaaacagtt----gg-tgatatagtcaag----------------------ttgctaaaa---aatgaaaaacttcaagtagaac----------------------caaactgcccttctaaatgaaga-----aaa-
q micMur1.scaffold_106697                          44868666732734765525134565866465634367532868654---4676-478326642265--3254598665523----31-1545689527449----------------------645687866---7455287714464134467321----------------------26874622743674354423635-----884-
i micMur1.scaffold_106697 C 0 N 0
e tetNig2.chr5             3743466  14 +  13390619 I
e petMar1.Contig6813         17462   0 +     30809 I
e xenTro2.scaffold_1954      16268   0 +     25544 I

a score=20685.000000
s hg19.chrY               7725006  98 +  59373566 GCTCTAAATATAATAT--------GATCTATA-----------TTAACAGctaactatgtcatgtcttc----gaaaagactcac-tcatatctaataaaaaaa------------gactaaaaatggcaggat
s tarSyr1.scaffold_74688     4346 119 +      9896 ----ttactgcaacat--------tactcacaaaatttaatacttgaaaacaagccaa---acatctttcatcaaagaagacaatttcaaatgcattgacaatggaatattattcagcctttaaatagcaggat
q tarSyr1.scaffold_74688                          ----999999999999--------9999999999999999997989999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999
i tarSyr1.scaffold_74688 C 0 I 19
s panTro2.chrY             578268  98 +  23952694 aCTCTAAATATAATAT--------GATCTATA-----------TTAACAActaactatgtcatgtcttc----aaaaagactcac-tcatatctaataaaaaaa------------gacgaaaaatggcaggat
q panTro2.chrY                                    0000000000000000--------00000000-----------00000000000000000000000000----000000000000-000000000000000000------------000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           48202548  79 + 153482349 AGTATAACTATATCAT--------GACCTATA-----------Tcaagatctaactgtgtcatgttttc-----aagagactcacttcagatctaataaaaaa-------------------------------
q ponAbe2.chr8                                    9999999999999999--------99999999-----------99999999999999999999999999-----99999999999999999999999999999-------------------------------
i ponAbe2.chr8           C 0 I 23
s rheMac2.chr3           61112120 106 + 196418989 aatctAACTGTATCATTATATCAAGATCTGTA-----------Tcaagatctaactat---atgtcttc-----aagagactcatttcagatctaataaaaaaaaa---------tgactgaaaatggcaggat
q rheMac2.chr3                                    99999999999999999999999999999999-----------999999999999999---99999999-----99999999999999999999999999999999---------9999999999999999999
i rheMac2.chr3           C 0 I 1
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_1954     16268   0 +     25544 I

a score=60642.000000
s hg19.chrY                       7725104 125 +  59373566 aaaaatacatt---------tcacgcaagtgttaaccaaatgagaggtgaagaggca-acaatt------------tattaaggtgaaaacttccataattcatata--------atttactttaagtcataat--ttacaagagac-aaagtaggac
s rheMac2.chr3                   61112227 125 + 196418989 aaaaatacaat---------ttattcaagtgttaaccaaatgagaggaaaagaggca-acaatt------------tattaagttgaaaactgtcatatttcatata--------atttactttaagtcaaaat--tcacaagagac-aaagtaggac
q rheMac2.chr3                                            99999999999---------9999999999999999999999999999999999999-999999------------9999999999999999999999999999999--------9999999999999999999--99999999999-9999999999
i rheMac2.chr3                   I 1 C 0
s ponAbe2.chr8                   48202650 124 + 153482349 agaaatatttt---------ccatacgaatgttaaccagatgagagaagaagaggca-ataata------------tatt-agttgaaaactgtcctatttcatgta--------atttactttaacttaaaat--tcacaaaagaa-aaagtaggac
q ponAbe2.chr8                                            99999999999---------9999999999999999999999999999999999999-999999------------9999-99999999999999999999999999--------9999999999999999999--99999999999-9999999999
i ponAbe2.chr8                   I 23 C 0
s panTro2.chrY                     578366 125 +  23952694 aaaaatacatt---------tcacgcaagtgttaaccaaatgagaggtgaagaggca-gcaatt------------tattaaggtgaaaacttccataattcatata--------atttactttaagtcataat--ttacaagagac-aaagtaggac
q panTro2.chrY                                            00000000000---------0000000000000000000000000000000000000-000000------------0000000000000000000000000000000--------0000000000000000000--00000000000-0000000000
i panTro2.chrY                   C 0 C 0
s tarSyr1.scaffold_74688             4484 131 +      9896 cagaataaatttggaggtgattattctaattgaaattagatagtagcaagagacacatacA----------------ACTAAATTGAAAGC------ATTTCACATACAAAGATGATATACACTCATTGATAA-----ACACATGATGAAAGTAGGAG
q tarSyr1.scaffold_74688                                  9999999999999999999999999999999999999999999999999999999999999----------------99999999999999------999999999999999999999999999999999999-----99999999999999999999
i tarSyr1.scaffold_74688         I 19 C 0
s otoGar1.scaffold_84011.1-44118     4797 139 -     44118 aaaaactcagc---------ctatgcaaatattaatcatactagagcaaagagggtc-acaattagagacaatatattctgagacaaaatctgccCTATTTCATAGA--------ATATAATTTAAGTTAGAACTGTTATAAAAGAC-AAAAAGGGGC
q otoGar1.scaffold_84011.1-44118                          99999999976---------9999999999999969999999999999999999899-6999999999999999999999999999999999999999999999999--------99999999999999999999999999999999-9999999999
i otoGar1.scaffold_84011.1-44118 N 0 N 0
e tetNig2.chr5                    3743466  14 +  13390619 I
e petMar1.Contig6813                17462   0 +     30809 I
e xenTro2.scaffold_1954             16268   0 +     25544 I

a score=59976.000000
s hg19.chrY               7725229 128 +  59373566 a--ttcaattataataagagggttcattcactaagaacttataaatatctgacaattttcccaaacacataaagcaaacattgacagaattgaaaccaaaatagacagca-------------------atataataatggaataatac
s rheMac2.chr3           61112352 128 + 196418989 a--ttcaattatagtaacagggttcattcactgagaacctataaatacaagacagttttcccaaacacataaagcaaacattgacggaactgaagcaaaaacagacagca-------------------atataataatggaaggatac
q rheMac2.chr3                                    9--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------------------99999999999999999999
i rheMac2.chr3           C 0 C 0
s ponAbe2.chr8           48202774 128 + 153482349 a--ttcaattatagtaagagggttcatttactgagaacctataaatatatgacatttttcccaaacaaataaagcaaacattgacagaactgaagcaaaaatagacagca-------------------atataacaatggaaggatac
q ponAbe2.chr8                                    9--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------------------99999999999999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY             578491 128 +  23952694 a--ttcaattataacaagagggttcattcactaagaacttataaatatctgacaattttcccaaacacataaagcaaacattgacagaattgaaaccaaaatagacagca-------------------atataataatggaataatac
q panTro2.chrY                                    0--00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-------------------00000000000000000000
i panTro2.chrY           C 0 C 0
s tarSyr1.scaffold_74688     4615 120 +      9896 AATTTCCAT------------GATTACTCACCTAGATAAAATAAA---ATGAC--------------CACTAACCAAGAATTAAATGAATTATAACAAAAATAAAATGTATACAACCATGTAAGTGCTTACATAATCTTGGCACAAGAC
q tarSyr1.scaffold_74688                          999999999------------999999999999999999999999---99999--------------9999999999999999999999999999999999999999999999999999999999999999999999999999999999
i tarSyr1.scaffold_74688 C 0 I 256
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_1954     16268   0 +     25544 I

a score=76637.000000
s hg19.chrY               7725357 187 +  59373566 atcaatatttcactctaagtaataaatgaagcatgacagaatatcaatgaaggaatggaaaatttgaatgcattatacaataattacacctaacaaatgtatacagacaacagaatacacattcttttcaatagcttataaaacattgttctagatggaccacatgtgacacgacataagaagcctt
s panTro2.chrY             578619 187 +  23952694 atcaatatttcactctaagtaataaataaagcatgacagaatatcaatgaaggaatgaaaaatttgaatgcattatacaatagttacacctaacaaatgtatacagacaacagaatacacattcttttcaatagcttataaaacattgttctagatggaccacatgtgacatgacataagaagcctt
q panTro2.chrY                                    0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr8           48202902 176 + 153482349 aacaatatcccactttcggtaataaataaagca-----------caatacaagaacaagaaacctgaatgcactgtaaaataattacacctaacaactgtatacagacaacagaatacacattattttcaatagctcataaaacgttttcctagatggaccacctgtgacaccacaaaagaggcctt
q ponAbe2.chr8                                    999999999999999999999999999999999-----------99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s rheMac2.chr3           61112480 186 + 196418989 atcaacatcccactttcagtaataaatagagcaagacagaatatcaatgagggaacaaaaaacttgaatgcactataaaataattacacctaacaaatgtatacagacagcagaatacaca-tcttttcaatatctcatgaaacatttttctagatggatgacctgtgacatcaaaaaagaagtctt
q rheMac2.chr3                                    9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999
i rheMac2.chr3           C 0 C 0
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_1954     16268   0 +     25544 I
e tarSyr1.scaffold_74688     4735 256 +      9896 I

a score=20028.000000
s hg19.chrY               7725544 59 +  59373566 aata--attttt-----taactaaaattttaca----attatttgtagcccaagaggaaagaaactagta
s rheMac2.chr3           61112666 65 + 196418989 aacatttttttt-----taattgaaattttacagactattatttatggtccaaatggaaggaaactagaa
q rheMac2.chr3                                   999999999999-----99999999999999999999999999999999999999999999999999999
i rheMac2.chr3           C 0 C 0
s ponAbe2.chr8           48203078 62 + 153482349 aaca--attttt-----taattgaaattttacggac-aatttttatagcccataaggaatggaaatagaa
q ponAbe2.chr8                                   9999--999999-----9999999999999999999-999999999999999999999999999999999
i ponAbe2.chr8           C 0 C 0
s panTro2.chrY             578806 59 +  23952694 aata--attttt-----taactaaaaatttaca----attatttatagcccaagaggaaagaaactagaa
q panTro2.chrY                                   0000--000000-----0000000000000000----000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s tarSyr1.scaffold_74688     4991 63 +      9896 AACA--ATCCTTTTATATAACTACAATTTT-CA----ACTTTTGGCATCTATGAAAAACAGACATTATGA
q tarSyr1.scaffold_74688                         9999--999999999999999999999999-99----999999999999999999999999999999999
i tarSyr1.scaffold_74688 I 256 I 80
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_1954     16268  0 +     25544 I

a score=15813.000000
s hg19.chrY               7725603 34 +  59373566 cacagtaacagcagaaaagctgaaaaattcaaaa
s rheMac2.chr3           61112731 34 + 196418989 atcaatagcagaagaaaagctgaaaaattcaaaa
q rheMac2.chr3                                   9999999999999999999999999999999999
i rheMac2.chr3           C 0 N 0
s ponAbe2.chr8           48203140 34 + 153482349 atcagtaacagaagaaaagctgaaaaattcaaaa
q ponAbe2.chr8                                   9999999999999999999999999999999999
i ponAbe2.chr8           C 0 n 0
s panTro2.chrY             578865 34 +  23952694 cacagtaacagcagaaaagctgaaaaattcaaaa
q panTro2.chrY                                   0000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_1954     16268  0 +     25544 I
e tarSyr1.scaffold_74688     5054 80 +      9896 I

a score=3949.000000
s hg19.chrY               7725637 46 +  59373566 cttataaagattaaacaacacagtttcctgTTTTGTTTAGTTTAGt
s panTro2.chrY             578899 46 +  23952694 cttataaagattaaacaacacaGTTTCCTAttttgttttgtttagt
q panTro2.chrY                                   0000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e tetNig2.chr5            3743466 14 +  13390619 I
e ponAbe2.chr8           48203174  0 + 153482349 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_1954     16268  0 +     25544 I
e tarSyr1.scaffold_74688     5054 80 +      9896 I

a score=44636.000000
s hg19.chrY               7725683 284 +  59373566 tttgttgagaaggagtatcactctttca-ctaggctgaagtgcagtggagcaatatcagctcactgcaagtttcacttcttaggttcaagtgattcttctgcctcagcctcctaagtagctgggattacaggcatgcaccatcttgcccagccaattttatgtattttagtagagacagtgttgcatcatgttggccaggattgtctcgatctcctgaact--agccctgtgccctccctggccttccaaagtgctg-ggttagaggcatgagcctctacacccagcT
s panTro2.chrY             578945 284 +  23952694 tttgttgagatggagtatcactctttca-ctaggctgaaatgcagtggagcaatatcagctcactgcaagtttcacttcctaggttcaagtgattcttctgcctcagcctcctaagtagctgggattacaggcatgcaccatcttgcccagccaattttatgtattttagtagagacagtgttgcatcatgttggccaggattgtctcaatctcctgaact--agccctgtgccctccctggccttccaaagtgctg-ggttagagacatgagactctacacccagct
q panTro2.chrY                                    0000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000-000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s tarSyr1.scaffold_74688     5134 285 +      9896 ttttttgagctggagtctcactctgtcacccagactggaatacagtggcacactcccagc-catcacaccctcgacctgctgggctccagcgatccttctgcctcagccttccaagtagccagaattacaggcacgtgctactatgcccagataatttt-tgatttattgtagagacgaggtcttgctaagttgccctggtgggtctcgaatccatgggctcaagcaatccactcactttggcctccaaaattgctgagattactgac-tgagtcaccaagcctggct
q tarSyr1.scaffold_74688                          999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998999999999-9999999999999999999
i tarSyr1.scaffold_74688 I 80 N 0
e tetNig2.chr5            3743466  14 +  13390619 I
e ponAbe2.chr8           48203174   0 + 153482349 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_1954     16268   0 +     25544 I

a score=50230.000000
s hg19.chrY              7725967 545 +  59373566 ACAGCGCCCTTTTTGTCATGTTGTTTTACAATGATTGGAAGACCTAATGTTGTGAATATGTCCATGCTGTTTAAAGTGACCAACACGTTATTATATAttgctctaaaccaggttgtattgtcaacatctataggcaggtttaagggagaagatccattattgtgcctgtgggctgggtccagaatgagtcaccatcgcccctgtggccaaatccacataaaaatgtcacaattttaactgtgtgctgtattcttttgtcaggctcaggacctcaagagtgggcactgcaaatgtggaatggtgacaactcttaatttcactatggtgtgtaaccaagagttccattctgaacctttttctggaccctgttatgaaactctttaccaccaaacagtttatacaatataagttagtgttgtaagctaatgtgagtttggtacaaatatgcaacccaggaccttacatattgccttaagacaaataatgagaggaaaaatatctcctattggctgtatcccaatgtaagtttcatcttcatgcctggg
s panTro2.chrY            579229 545 +  23952694 ACAGCGCCCTTTTTGTCATGTTGTTTTATAATgattggaagacctaatgttgtgaatatgtccatgctatttaaagtgaccaacacattATTATATAttgctctaaaccaggttgtattgtcaacatctataggcagggttaagggagaagatccattattgtgcctgtgggctgggtccagaatgagtcaccatcgcccctgtggccaaatccacataaaaatgtcacagttttaactgtgtgctgtattcttttgtcaggctcaggacctcaatagtgggcactgcaaatgtggaatggtgacaactcttaatttcactatggtgtgtaaccaaaagttccattctgaacctttttctggaccctgttatgaaactctttaccaccaaacagtttatacaatataagttagtgttgtaagctaatgtgagcttggtacaaatatgcaacccaggaccttacatattgccttaagacaaataatgagaggaaaaatatctcctgttggctgtatcccaatgtaagtttcatcttcatgcctggg
q panTro2.chrY                                   00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
e tetNig2.chr5           3743466  14 +  13390619 I
e ponAbe2.chr8          48203174   0 + 153482349 I
e petMar1.Contig6813       17462   0 +     30809 I
e xenTro2.scaffold_1954    16268   0 +     25544 I

a score=21661.000000
s hg19.chrY               7726512 210 +  59373566 aactgaagcaaggtatatgtcataattccatatgtgagcaaaaaa-caagacagtaggttaacattacatagatggtgtactaagcaatatgtcacaatgcctcctctaggtagggtataaa--aaaattgga-----------tcacagtaacttgatgctagactcagcATTGAACAACATCCCACATGTGGAAAATATCAAGCCAAGTTATAAGACACAAA
s panTro2.chrY             579774 211 +  23952694 aactgaagcaaggtatatgtcataattccatatgtgagcaaaaaaacaagacaggaggttaacattacatagacggtgtactaagcaatatgtcacaatgcctcctctaggtagggtataaa--aaaattgga-----------tcacagtaacttggtgctagattcagcATTGAACAACATCCCACATGTGGAAAATATCAAGCCAAATTATAAGACACAAA
q panTro2.chrY                                    00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--000000000-----------00000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s fr2.chrUn             287923700 203 + 400509343 AATTGGAATAAGTTAGA----AGAAATGCATTTGTGTGCAAGTGA-CA------GATGTAAATA----------AGAGTCCTGAAAAATGTATCTGTGCACCTCCTCTTTTCTTGGtataaatgcaaatgagggaCAAGTATTcccacagcatctccagaaGGTAATCCAGGTTCAACTTCATCCCACAACTGAAAGATATCCAACAGAATTAACATAAACAGA
i fr2.chrUn             N 0 N 0
e tetNig2.chr5            3743466  14 +  13390619 I
e ponAbe2.chr8           48203174   0 + 153482349 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_1954     16268   0 +     25544 I

a score=165065.000000
s hg19.chrY              7726722 1818 +  59373566 ACACTTACATAATGGGCCAAAGATATGTCGATGTATATTCGGTGGCTCTGTCATGggcagaagagtcacatcataagggtgctgggcccagcaatatgcaatatgccataatttctctttatgcacgatctaggaagaagagaaaaaaattacatggtattgggccacacaataggtcagaattccttctttctggttataattccagaaaaacaggagggtcaatgtcctgactgctgggctcagcaatatgtcaaaattctcctattttgaaggcccaggttgaaaaagacagtcacatcacttaggtcaagggctcagagatatttcaaagtgtccgaagtaggcagggctcaggcagatgaggagaatcatatcacctaggtgctgccctaggaatgtgttacagtgcaatatgagggcagcatccaggcagaagggccacatcactcaagtgctagttcctgaggtatttcacaaggatctcttaacaaaacacagaacaaagagagttacatcacctagctgaaggttctcttcttgtgccagactgccccatgtgggtaggacccaagaagggactcacatctcctaggggatatgcacagagatgtgtcacaatgtcttctgtgaagcatagcactggaaactaggcctgtgtacctggcctagaaat--gtcactctccaggttcacaggacccaagcaagagtcccacataacctaggtgacaggcccagagatatgtcacaatgcatttctttgggaatgactctggcaaaataattctctcatctgtgtgtttggccttgcaatatgtcactctacttcctttgtgcagggcccatttcagagagaagagttatatcacctgtggggtgaatagaaagatatatcacaataatttttgtgggcatggcagagggaaaaatataacatcacctgggtgctaaaagcagtgataagacacaatccttaccgagagatggacccaggcaagaaagtcacaAAACTTTGAGGTTGGCCTAGGTAGATATCACAATCACATATATGGACTGAAAGAAGTCTAGAGAGTCAAATTACACAAGTGCTTGGCAATAATTTATATCAAAATCACACTGCCAGAATATTCCAAAGGTGAGATTTACAATACCAAACATGTCCTGTTTTCATCTTTGAcagttgacttcatccatgtgaggtaatgacagttcttactgtgagatggatgtgcatacaagactaacaatatcacctgtgtgctgatcccagctttgactccttctgtataacccaaaaactttgtaaaatatgtatgagtgttataatcttttgtgacctttctataaaaggtgatccagggcatcaggcatgtccctaaaactagatatagaagtcaaaattgcatctttgcctgagtccacatatgacagtcattatcatccctcttagccatgcctaggtatagatttcaattccctctgcgtttatgaaacaggcagaacaggcacatcatctaagttctgggccagaagtattccatattctatttgtagtcagggttctgtcagaaatatcatacttgtgtgctaggtccagctctgtgtcctaatgtttcttttgggcactgtccaggcaggagaggagagtctatcatcaaaaagatgggccccaaaatatgtcacaatgcctactgttggcagggcccaggcaagagagtcgtatcatttagacacagtgtttagaaatgctacaattactaaaggaagcaagttacaggcaggagaggagagttgtgtaacctagatGATGGGTCCAGA
s panTro2.chrY            579985 1818 +  23952694 ACACTTACATAATGGGCCAAAGATATGTCGATGTATATTCAGTGGCTCTGTCATGggcagaagagtcacatcataagtttgctgggcccaccaatatgcaatatgccataatttatctttatgcacaatctaggaagaagagAAAAAA-TTACATGGTATTGGGCCACAcaataggtcagaattccttctttctggttataattccagaaaaataggagggtcaatgtcctgactgctgggctcagcaatatgtcaaaattctcctattttgaaggcccaggttgaaaaagacagtcacatcacttaggtcaggggctcagagatatttccaagtgtcccaagtaggcagggctcaggcagatgaggagaatcatatcacctaggtgctgccctaggagtgtgttacagtgcaatatgagggcagcatccaggcggaggggccacatcactcaagtgctagttcctgaggtatttcacaaggatctcttaacaaaacacacaacaaagagagttacatcacctagctgaaggttctcttcttgtgtcagactgccccatgtgggtaggacccaagaagggactcacatctcctagaggatacgcacaaagatgtgtcacaatgtcctctatgaagcatagcactggaaactaggcctgtgtacctggcctagaaatatgtcactctccaggttcacaggacccaagcaagagtcccacataacctaggtgacaggtccagagatatgtcacaatgcatttctttgggaatgactctggcaaaataattctctcatctgtgtgtttggccttgcaatatgtcactctacttcctttgtgcagggcccatttcagagagaagagttatatcacctgtggggtgaatagaaagatatatcacaataatttttgtggtcatggcagagggaaaaata-aacatcacctgggtgctaaaagcagtgataagacacaatccttaccgagagatggacccaggcaagagagtcacaAAACTTTGAGGTTGGCCTAGGTAGATATCACAATCACATATATGGGCTGAAAGAAGTCTAGAGAGTCAAATTACACAAGTGCTTGGCAATAATTTATATCAAAATCACACTGCCAGAATATTCCAAAGTTGAGATTTACTATACCAAACATGTGCTGTTTTCATCTTTGAcagttgacttcatccatgtgaggtaatgacagtgcttactgtgagatgcatgtgcatacaagactaacaatatcacctgtgtgctgatcccagctttgactccttctgtataacccaaaaactttgtaaaatatgtatgagtgttgtaatcttttgtgacctttctataaaaggtgatccagggcatcaggcatgtccctaaaactagatatagaagtcaaaattgcatctttgcctgagtccacatatgacagtcattatcatccctcttagccatgcctaggtatagatttcaattccctctgcatttatgaaacaggcagaacagccacatcatctaagttctgggccagaagtattccatattctatttgtagtcagggttctgtcagaaatatcatacttgtgtgctaggtccagctctgtgtcctaatgtttcttttgggcagtgtccaggcaggagaggagagtctatcatcaaaaagatgggccccaaaatatgtcacaatgcctactgttggcagggcccaggcaagagagtcatatcatttagacacagtgtttagaaatgctacaattactaaaggaagcaaggtacaggcaggagaggagagttgtgtaacctagatGATGGGTCCAGA
q panTro2.chrY                                    0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
e tetNig2.chr5           3743466   14 +  13390619 I
e ponAbe2.chr8          48203174    0 + 153482349 I
e petMar1.Contig6813       17462    0 +     30809 I
e xenTro2.scaffold_1954    16268    0 +     25544 I

a score=26552.000000
s hg19.chrY              7728540 258 +  59373566 AATATGTTACAAATCCCCTTGA-GGACATTGTTAAGA---TAGCACAGTCAAA-TCACCAAGTTACTTGGCTCAG---GTTCTTGTGAAAA--ATCTCATTTGTAGGCTACAC----------TTATGCAGAATTATTAAA----------TCACTTAAGAGCTGGGTAAATGTATAAGTCACAATTACACTTCTGTAAAGGTTTAAGAATAAAGGTCACCAACCTGTATACGTCCTGGCTCCACTCCTATAAGCTGTTATTAGGCTTTTGCTGTGGTCTCTGGTata
s panTro2.chrY            581803 258 +  23952694 AATATGTTACAAATCCCCTTGA-GGACATTGTTAAGA---TAGCACAGTCAAA-TCACCAAGTTACTTGGCTCAG---GTTCTTGTGAAAA--ATCTCATTTGTAGGCTACAC----------TTATGCAGAATTATTAAA----------TCACTTAAGAGCTGGGTAAATGTATAAGTCACAATTACACTTCTGTAAAGGTTTAAGAATAAAGGTCACCAACCTGTATAGGTCCTGGCTCCACTCCTATGAGCCGTTATTAGGCTTTTGCTGTGGTCTCTGGTata
q panTro2.chrY                                   0000000000000000000000-00000000000000---0000000000000-000000000000000000000---0000000000000--00000000000000000000----------000000000000000000----------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s gasAcu1.chrXI           841824 281 +  16706052 AGTATGTTACAAAACGTCTAAATGTGTATTCATAAAAGTCTGGTAAGTTCAAAGTCCTCAAGACATGTATGTTAGTGTGGAATTAAGAAAAGTATTTTGATTGCAGCTCAAACATTGAGATAGTCATTTTGAATT-TGAAATATAGGGCTTTTACTTTGGA--TAATTAACTGTATAAGGCAAAAGTATTTTTTTGTACAAGAGCAGTCATAATGGTCCTGAATATGCATACTTC----AATCATTGTTAAGAATGATTAAATAGCTTTTATTCCGGTTACTTGCATA
q gasAcu1.chrXI                                  999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999999999999999999999
i gasAcu1.chrXI         N 0 N 0
e tetNig2.chr5           3743466  14 +  13390619 I
e ponAbe2.chr8          48203174   0 + 153482349 I
e petMar1.Contig6813       17462   0 +     30809 I
e xenTro2.scaffold_1954    16268   0 +     25544 I

a score=60264.000000
s hg19.chrY              7728798 653 +  59373566 tggcacaatgtcacgtggccagagagaaggcaagaaattcacattacctatgtgggtatggctccagtgtgatgtcacaatttaccttttggacaggacacaggcagaaaagtcacatcacctgaatgctgatttcagtgacatatgaaaacaccatctgtgggcaagactttggcaagaaagagacttacttcacctgggcaattggcctagatatatgtcacaatgtctgttctgtgcagtaccaaagctgcagagtgacctcacatttgtgctgggaccagcaatatgtcacaaactccctgtggtcagcgtacaggttaaagtgggcaaacatcagctaggtgctcagccaagcgatatgttacaatgttttctgtttgcagagcccttgagaaagaatcacatcacctgggtacagtgttatgtgtcacaatgcactgtaagtgcagggccaaggcaatagaagagagtcacattacttatgtgatggatctagatataaaacataaattctctttgtaatcaggttttgggcagataatttacataacctgggtAACAATATGAGTAATATATAAAAATTCCCTTTGTAGGCAGAACCATGATAAATGCTATATATTGCATAGGTGTTTGTTATACTTATGGCATAA
s panTro2.chrY            582061 653 +  23952694 tggcacaatgtcacctggccagagagaaggcaagaaattcacattacttatgtgggtatggctccagtgtgatgtcacaatttacattttggacaggacacaggcagaaaagtcacatcacctgaatgctgatttcagtgacatatgaaaacaccatctgtggccaagactttggcaagaaagagacttacttcacctgggcaattggcctagatatatgtcacaatgtctgttctgtgctgtaccaaagctgcagagtgacctcacatttgtgctgggaccagcaatatgtcacaaactccctgtggtcagcgtacaggtaaaagtgggcaaacatcagctaggtgctcagccaagcgatatgttacaatgttttctgtttgcagagcccttgagaaagaatcacatcacctgggtacagtgttatgtgtcacaatgcactgtaagtgcagggccaaggcaatagaagagagtcacattacttatgtgatggatctagatataaaacataaattctctttgtaaccaggttttgggcagataatttacataacctgggtaacaatatgagtgatatataaaaattccctttgtaggcagaaccgtgataaatgctatatattgcataggtgtttgttatacttatggcataa
q panTro2.chrY                                   00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
e tetNig2.chr5           3743466  14 +  13390619 I
e ponAbe2.chr8          48203174   0 + 153482349 I
e petMar1.Contig6813       17462   0 +     30809 I
e xenTro2.scaffold_1954    16268   0 +     25544 I

a score=17577.000000
s hg19.chrY             7729451 149 +  59373566 TTTCATCTGCGGTCTGGGCCTAGAAAAAGAGTCATATCATTCATGTGCTGGTAAAAGTTGCCTGTCCCAGTCACACTTTCAGAAAAGTTCACAAATAAGTTTCACATTCCACATAAGTTCTGGTTTCCTGTATGTGGGTCAATACTTTT
s panTro2.chrY           582714 149 +  23952694 tttcatctgtggtctgggcctagaaaaagagtcatatcattcatgtgctggTAAAAGTTGCCTGTCCCAGTCACACTTTCAGAAAAGTTCACAAATAAGTTTCACATTCCACATAAGTTCTGGTTTCCTGTATGTGGGTCAATACTTTT
q panTro2.chrY                                  00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_916   103368 140 -    291918 TCTCCTCCTTGTTCTCTGTCCAAATAAAAACACAAAAATGTCCCATTTTTTCAAAATTTGGCTTTGGTTGTCA------CAGAAA---TCAGAAATAAGTTCCACTTACAAAATAATATCTTGTGCTTTATATATCTGTGTGTGTTTTT
i xenTro2.scaffold_916 n 0 T 47921
e tetNig2.chr5          3743466  14 +  13390619 I
e ponAbe2.chr8         48203174   0 + 153482349 I
e petMar1.Contig6813      17462   0 +     30809 I

a score=634450.000000
s hg19.chrY             7729600 7014 +  59373566 TATGAGTTTGGTGGAACTATGGGTCACAATCTCAACAATGGGCAAGATGCAGGCACAGGAGTTGCAATCCCATTTCAAGATTGTGTTCCAGTAGGGGACTCACAGCACCAGAGACAGGCTGAATCATGGTTCAAATATGACCAAAACACCTGTGAATTTAATCCATGTATAAGAGTAATTATTTCAATCTTTGACAGCTTTTATGtgtgaggtttagtgcctcattactaggccctgttaatatgtaagaatcacaattgtatcagttaggtgtgcatacaagtcacattcttacctgattgctgctctctgttatgacactgtttgtaccatacagggtttagatgacatacctgactgttataatcctttgtgaactttatacaagttaaaaacccaggactttttctttatcaataagaatggctataagagccaaaatatctctattggctgggtccagagacgaaatttaatgtagtgcatctgtgcttaaccaaggcatacgtcacaatttcacctgtgagcagagacaaggcaagggagtcacatcaactcggtgctgagtcagtgatacactataatctcattactaagctgggcctaataacaagagtcacattacctggTTACAGCCTCAAATAGTATTTCACCAAGCCCGCTATAGACAGTGAAGAAGAAAA---GAAGAGTCAgccaggtgtggtggctcatgcctgtaatcccagcactatgggaggccaaagtggggagatcatgagctcaggagttagagaacagcctgcccaacatagtgaaacctcatctctactaaaaacactatatagatagatgatagatagatagatagatagatagatagatagatagatagatacatacatacatacatacatacatacatacatacatacatagatacatagatacagcaatattgcagggcatgatggtggtgcctgtaatctcagctacatgggaggttgaggaaagcaaattgctttaacctgtggtgcagaggttgcagtatgctgagattgcaccactgcactccaggccaggcaagagtgagagactttgtcttaaaaaaataaataaataaaaaGAGAGAGAGAGAGAGAATCACTCCACCTAGATgctggggtcagcagtatgtaataaactttcctcttggcaaagtatagaatatgaaggaaagtaacatcacttaggttttgcaatcagaggtatgtcacaatttatttggtaagtgggacccaggcaggaggggagagtcactttaccaagtttttaagtcaaatcatatttcacagtttcctctgggggcaggacacaggcaggagagacaaataacctaacttattgtccaagagatatgtgacaatataccctgttggcaggttccacacagaagagtcacattattatgattctaacccagagatatgccacaatgcacccaagagaagaaatttaaaccaaaaattctcaacacctgggtactaggcctagttatatgccaAATCTTCTTGTCTTtgagggtgacaccattaactctgagctgaatgtgtatatgagagtcacaatctcatgtgtttcctgggttgttgtatgaaccttaatatgtactacatattaagtctttatacagcatgcatgagatttgaaaaccatttggagaacttcatactcctatggattcacgatcttacatactgccctaaaaccacaaataatagtcagtatctctgctgtaggctgggtccaggtatgaaaaccattattatgcctatgagctggatccagaaatgagccaccatctgacctgtggccagatccatatatgggcacaataccaacttgtactgaattcacttgttagaatcaggaccttaacagtgtgttttggacacatgggatggtgtcaacatctgcttttacctggatgtgtaatcaatagtcccaatctgagctttatgcaggtctttttcataaaaccctgccaagtctgccccacagaaacagcccaagtgatggatgaaagaatatcactgacacatgtatttttcctgagagtgtggttagctgactgTATGTTTAACACTGTCGATGAGAGTGCAGCAACAGCATCAGGAGAAGGAGTAGCTGAGACTGTAGCCACTATGAAGAGAGTGCAAGACCCACCAAAAGGATTCAGCAGCTGCTGAGAGAGTATAATTgcaacagcagcaaagtgtgtagagcagcagtagctgagagtgcagcggtgaacatccggtgacgctcaaatttatttagtagagatttaataacaaaggcttggagcaaacccagtttgtgtttaataaacattttccacttctcgattagagagcagtcctgcatgcaaatgatcaaaggttggtttctggagacatatgtaaaccaatgtatgtagataagcccctttgcattccctcattatcttccctttactctcaggctctgagtaagagagtttggatgccttcagagaaaattcttttccaaagttttgcaagaagtcctggtgttccaggaaaatttgcatatttcctatcattttttccatcacaccctgactgatgtcctacatctccctcttttctttctttttttttcatcaagttttgtttactgaagactacagatgtctgcagcaacaggattgtcagataccgtgcttataagtggtattctggctttgcatcctagaattactaaataacagaagacaaacatgaatataatcataaacattctattccaatcaaggagtggcatgtagtgttaattggcacctcagttcaatgtgtgctgttactaacgaatcccactgcgggtattttaacactttctatccaagcagttgcattgttagaagctgggaagggggtttctgtctaagtaacaggacagtagaaaggctgatttaaaagatgtgcctaatagagtgtaggagatatgggatgcaggcaaagtaagaaaataagaaaggttaataaaacataacaaggaacaaattttctggagtgaatcgtgtctgtgtccagagcaggattcactcagccttctgaattgtcttcttcagcctccctctggtaatgtctgggggcatgagttgtataaataagccacattctggggg-actgtggggtttgcatggttatttcctttatttctggtaccgggttgcattttagctatgctatgtttaggtttgatatattgtattggaattcaaagagggcctgaggaggtgtgaacataagcataccctcttacccatgttagcaaattatttggaccataccatacatgactaaccaaatctttctataaaactgtggggtttatgtcttgagaggttttagcaaagttcttttatatagctgaaatttgtcatttaaatttaagaaattaagggtaaagaaaacttgtactagtagtgttgcagggtctttactcatattccttcttctttgttttctgaggcaatatttaagagagcaatggacatattgtgtccttggggtttatatgggatgcctgtggaatgtaggacactccatatatgaaaaaattgtgtcaattgtgagatgacatatgccagaataattttgcaattaggcaatccttttttactgaggatcaaagcctgctttacgtgataactgtcacacagtagtgttactggtgggtctttgttctcagagctgccaagatggtggcaggcaacttccaagatggtggcaagtcttttgttctctgaccaagtgttcttggcctcatggtttcaaaggattgaaatttttttaccatgtggtggatgttatagctctattttctaatagagctattagatgtaggtcatggaagagaatggtggaacccagcaactagtgttcagctctattaggatgaatctgaagtcagtggcgagtctgtgatggtggtgaccagcactggtggatggcaaacaaaagctcagctcaagctggaacaaacatggaccagaagagtgtgcagttttaagatttaatagagtgaaaacagaggtcccatacaatgagaggggacacaaagtgggttgcctctgctgggacaaatgcctgggtatatatatcccaataattgtcccttccattgtgctgtcaggtgatatatgatttgattatttctttacctcctgctttcagcctaattggtactttagggagctctctttcctacctgatttgttgggtgtgagctgagttacaagccccgggattaaaggtgggtgtggtcacgttccccagccaggcttagaattcctagttggtctaggaaatccagctagccttttctctcagtaggactgctgagcatcccttgaggaagtactttctaattaaatctgtgagctgacctttcattattgctagctgctatggtaaatgcaaattattatgttctgttcttcaatgggaatagtataaaagcagccttttaagtcaataatgaccatagaccaatcttgaggaatagccatgggtgaaaagaatctcctgttgaaggggtgtgcaaattagcattgataggccataaatcatgcacaatctccatttgtgagacattttttgaatgaagaaaaagggcaaattccgagggctgtttgatgtctttatatagccagcttctgattgctcctcagcttattcatgggcttgttgtaacttctctccctttaaaagcttctgttctccccaaatcgcattttaagagagccatgtccagggaaggggaggaataacagtgcccattatcagaaagaagtctgtaaagtgaccttgattaaccctctcataaatgggctagtggttacattttttctaatgctttttcttatttctttatgtacatgattgccttgttgatttttgggcaggacaagatttccccttctaatgccacttgcctaagacagggtcccatatctgtagcatattccttgtcctttctctaatttattggaggagggagctcaggggaaaacctccattttctctgtggcacttttactctcaaatagtggaactgagggaggaggaggaggttgtaaggtaggtgatgattcttcctcccttctcttcttattctcttctgtgtagagtgagacaaaatcagtcctaactaaggctcataacattaaagatgttactggaaact--tactcttgtgcctgatgttatttaagatttctgcccactcattcccagaggtctatgtttagtgtgccttctgggaacaattggttatgaaaaaacaacaa----aaaaaacccagtttgcattaggttccttaattaagactttgaaactgaggctccactagctttaagcagctgtttcactatttttatatactgttgctgttgagctaataactgatgtcccatgatgaaaccctagcctgaacaattccctcaaatttggaaatcccaagcaggtatcaatgacttactcactgcacagtcttttcaccttcatttttgagggtttcatcatgatttgttgcagcattcctcacacaggacaccacctgctgcgtctgtctcatggactctggctgagcaatggatgaaagaagtttgctgacacaggtattttgcctgagagcTCCACAAAAGGACTGCATGCTCAGCATCACTGGCAAGCATgcagcagcagcagcagcaacaacaacaacaacgactgcagcagcagcaggagcCAAGAGTGCAGCCACCACAAAGAGAATGCAGTAGCCACTGATACAGTGTAGCAGCTGCCAAGAGTGCATCATAACAACAGCAAGAGTGCAgcccccagaagccagtgacacttgcatttaggtagtacagaattaatgacaaaggcttgacacaaacaaaatttttgggtagtaagatttttgactccctgactagacagcattctttgttcattcatgtgaatgaaaaaaagattggtttctggaaacataaatacaccaaattatctagataactttctttatatttccttgttatctaatatttgctttcaggttctgggtaagagaatttgtctgctttcagcccaaattattttctgaagagtttggaatatctcccagccttccaagaaggtttgcgtttttcctataatttttccaccaccctgatacatctcctacaAAactctcagtaccacccaaggagttgacactttgtgagtaagtgttgtaaatttcagtgagtttggtataaatatgaattactggaccttacctattgacctaagcctagaaatgaaaggcaaaatatctcttatttgctgaatcccagtataagtttaaccatcatgacttaaaactgaagtaaggtatttgttatagtctcatttgtgggcaaaAAAATTGACCAaagaataacatcacctaggtgatgtgccaagcaacatgtcacaatgccctctctagttaggatatagaaattagagtcacattaacttgatactagatgcactaatatgacacaatcccatatgtgggG-GAAAAAAAAACAGCCAAAAGATGAGAGCTAAAACACCTACATAGtgggccaaggatatgtcaaaatgcctcatgtgcctctcgtacagtaatgaaagtaacattatcagagaatgggcctagaatatgccataattttctgtatatacaggactcaggtgaaagagtaacattatatgggtgctgggccctgtgatagaccaaaatttctgattgtcagcatggtttaggacaaaaaggagtgtcaaataacctgaatgctgggctccgcaatatgccacaatctctccattgtaaagaccaggcagaagaagagtcactacacttaggtcatgggctcagcgatttatctcagtgtccccagtagacaggcccaggcaggaaaacagagtcatatcacctgggtGCTTCTTTAGTAAAaatgcacctgtgggaaagtatttgagtta
s panTro2.chrY           582863 7006 +  23952694 TATGAGTTTGGTGGAACTATGGGTCACAATCTCAACAATGGGCAAGATGCAGGCACAGGAGTTGCAATCCAATTTCAAGATTGTGTTCCAGTAGGGGACTCACAGCACCAGAGACAGGCTGAATCATGGTTCAAATATGACCAAAACACCTGTGAATTTAATCCATGTATAAGAGTAATTATTTCAATCTTTGACAGCTTTTATGtgtgaggtttagtgcctcattactaggccctgttcatatgtgagaatcacaattgtatcagttaggtgtgcatacaagtcacattcttaactgattgctggtctctgttatgacactgtttgtaccatacacggtttagatgacatacctgactgttataatcctttgtgaactttatacaagttaaaaacccaggactttttctttatcaataagaatggctataagagtcaaaatatctctattggctgggtccagagatgaaatttaatgtagtgcatctgtgcttaaccaaggcatacgtcacaatt-cacccgtgagcagagacaaggcaagggagtcacatcaactcggtgctgagtcagtgatacactataatctcattactaagctgggcctaataacaagagtcacttcacctggTTACAGCCTCAAATAGTATTTCACCAAGCCTGCTATAGACAGTGAAGAAGAAAAAAAGAAGAGTCagccaggtgtggtggctcatgcctgtaatcccagcactatgggaggccaaagtggggagatcatgaggagaggagttagagaacagcctgcccaacatagtaaaacctcatctctactaaaaacactatatagatagat-------agatagatagatagatagatagatagatagatagatagatacatagatagatagatacatagatagatagatacatagatacatagatagagcaatattgcagggcatgatgctggtgcctgtaatctcagctacatgggaggctgaggaaagcaaattgctttaatctgtgttgcagaggttgcagtacgctgagattgcaccactgcactccaggccaggcaagagtgagagactttgtcttataaaagtaaataaataaaaaGAGAGAGAGAGA----ATCACTCCACCTAGATgctggggtcagcagtatgtaataaactttcctcttggcaaagtatagaatatgaaggaaagtaacatcacttaggttttgcaatcagaggtatgtcacaatttatttggtaagcgggacccaggcaggaggggagagtcactttaccaagtttttaagtcaaatcatatttcacagtttcctctggcggcaggacacaggcaggagagacagataacctaacttattgtccaagagatatgtgacaatatatcctgttggcaggttccacacagaagagtcacattattatgattctaactcagagatatgccacaatgcacccaagagaagaaatttaaaccaaaaattatcaacacctaggtACTAGGCCTAGTTACATGCCAAATCTTCTTGTCTTtgagggtgacaccattaactctgagctgaatgtgtatatgagagtcacaatctcatgtgtttcctgggttgttgtatgaaccttaatatgtactacatattaaggctttatacagcatgcatgagatttgcaaaccatttggagaactacatactcctacggattcacaatcttacatactgccctaaaaccacaaatcatagtcagtatctctgctgtaggctgggtccaggtatgaaaaccattattatgcctatgagctggatccagaaatgagccaccatctcacctgtggccaggtccatatatgggcacaataccaacttgtactgaattcacttgttagaatcaggaccttaacagtgtgttttggacacatgggatggtgtcaacatctgcttttacctggatgtgtaatcaatagtcccaatgtgagctttatgctggtctttttcataaaaccctGCCAAGTCTGCCCCACAGAAACAGCCCAAGTGATGGATTAAAGAATATCACTGACACATGTATTTTTCCTGAGAGTGTGGTTAGCTGACTGTATGTTTAACACTGTCGATGAGAGTGCAGCAACAGCATCAGGAGAAGGAGTAGCTGAGACTGTAGCCACTATGAAGAGAGTGCAGGAGCCACCAAAAGGATTCAGCAGCTGCTGAGAGAGTATAATcgcaacagcagcaaagtgtgtagagcagcagtagctgagagtgcagcggcgaacatccagtgatgctcaaatttatttagtagagatttaataacaaaagcttggagcaaacccagtttgtgtttaataaacattttccacttctcgattagagagcagtcctgcatgcaagtgatcaaaggttggtttctggagacatatgtaaaccaatgtatgtagataagcccctttgcattccctcattatcttccctttactctcaggctctgagtaagagagtttggatgccttcagacaaaattcttttccaaagttttgcaagatgtcctggtgttccaggaaaatttgcatatttcctatcattttttccatcacaccctgactgatgtcctacatctccctcttttctttctttttttttcatcaagttttgtttactgaagactacagatgtctgcagcaacaggattgtcagatacagtggttataagtggtattctggctttgcatcctagaattactaaataacagaagacaaacatgaatatgatcataaacattctattccaatcaaggagtggcatgtagtgttaattggcacctcagttcaatgtgtgctgttactaacgaatcccactgggggtattttaacactttctatccaagcagttgcattgttagaagctgggaagggggcttctttctaagtaacaggacagtagaaaggctgatttaaaagatgtgcctaatagagtgtaggagatatgggatgcaggcaaagtaagaaaataagaaaggttaataaaacataacaaggaacaaattttctggagtgaatcgtgtctgtgtccagagcaggattcactcagccttctgaattgtcttcttcagcccccctctggtaatgtctaggggcatgagttgtataaataagccacattttggggggactgtggggtttgcatggtcatttcctttatttctggtacagggttgcattttagctatgctatgtttaggtttgatgtattgtattggaattcaaagagggcctgaggaggtgtgaacataagcataccctcttacc-acgttagcaaattatttggaccataccatacatgactaaccaaatctttctataaaactgtgggttttatgtcttgagaggttttagcaaagttcttttatatagctgaaatttgtcatctaaatttaagaaattaagggtaaataaaacttgtactagtagtgttgcagggtctttactcatattccttcttctttgttttctgaggctatatttaagagagcaatggacatattctgtccttggggtttatatgggatgcctgtggaatgtaggacactccatatatgaaaaaattgtgtcgattgtgagatgacatatgccagaataattttgcaattaggcaatccttttttactgaggatcaaagcctgctttacatgataactgtcacacagtagtgttactggtgggtctttgttctcagagctcccaagatggtggcaggcaacttccaagatggtggcaagccttttgttctctgaccaagtgttcttggcctcatggtttcaaaggattgaaatttttttaccatgtggtggatgttatagctctattttctaatagagctattagatgtaggtcatggaagagaatggtggaacccagcaactagtgttcagctctattaggatgaatctgaagtcagtggcgagtctgtgatggtggtgaccagcactggtggatggcaaacaaaagctcagctcaagctggaacaaacatggaccagaagagtgtgcagttttaagatttaatagagtgaaaacagaggtcccatacaatgagagaggacacaaagcgggttgcctctgccgggacaaatgcctgggtatatat--cccaataattgtccctcccattgtgctgtcaggtgatatatgatttgattatttctttacctcctgctttcagcctaattggtactttagggagctctctttcctacctgatttgttgggtgtgagctgagttacaagccccgggattaaaggtgggtgtggtcacgttccccagccgggcttagaattcctagttggtctaggaaatccagctagccttttctctcagtaggactgctgagcatcccttgaggaagtactttctaattaaatctgtgagctgacctttcattattgctagctgctatggtaaatgcaaattattatgttctgttcttcaatgggaatagtataaaagcagccttttaagtcaataatgaccatagaccaatcttgaggaattgccacgggtggaaaga-tctcctgttgaaggggtgtgcaaattagcattgataggccataaatcatgcacaatctccatttgtgagacattttttgaatgaagaaaaagggcaaattccgagggctgtttgatggctttatatagccagcttctgattgctcctcagcttattcatgggcttgttgtaacttctctccctttaaaagcttctgttctccccaaatagcattttaagagagccatgtccggggaaggggaggaataacagtgcccattatcagaaagaggtctgtaaaatgaccttgattaaccctctcataaatgggctagtggttacattttttctaatgctttttcttatttctttatgtacatgattgccttgttgatttttgggcaggacaagatttccccttctaatgccacttgcctaagacagggtcccatatctgtagcatattccttgtcctttctctaatttattggaggagggagctcaggggaaaacctccattttctctgtggtacttttactctcaaatagtggaactgagggaggaggaggaggttgtaaggtaggtgatgattcttcctcccttctcttcttattctcttctgtgtagagtgagacaaaatcagtcctaactaaggctcataacattaaagatgttactggaaactgttactcttgtgcctgatgttatttaagatttctgccaactcattcccagaggtctatgtttagtgtgccttctgggaacaatcggttatgaaacaacaacaacaaaaaaaaaaacagtttgcattaggttccttaattaagactttgaaactgaggctccaatagctttaagcagctgtttcactatttttatatactgttgctgttgagctaataactgatgtcccatgatgaaaccctagcctgaacaattccctcaaatttggaaatcccaagcaggtatcaatgacttactcacggcacagtatcttcaccttcatttttgagggtttcatcatgatttgttgcagcattcctcacacagggcaccatctgctgagtctgtctcatggactctggctgagcaatggatgaaagaagtttgctgacacaggtattttacctgagagcTCCACAAAGGGACTGCATGCTCAGCATCACTGGCAAGCATgcagcagcagcagca---acaacaacaacaacgactgcagcagcagcaggagcCAAGAGTGCAGCCACCACAAAGAGAATGCAGTAGCCACTGATACAGTGTAGCAGCTGCCAAGAGTGCAGCATAACAACAGCAAGAGTGCAgcccccagaagccagtaacacttgcatttaggtagtacagaattaatgacaaaggcttgacacaaacaaaatttttgggtagtaagatttttgactccctgactagacagcattctttgttcattcatgtgaatgaaaaaaagattggtttctggaaacataaatacaccaaattatctagataactttctttatatttccttgttatctaatatttgctttcaggttctgggtaagagaatttgtctgttttcagcccaaattattttctgaagagtttggaatatctcccagccttccaagaacgtttgcgtttttcctataatttttccaccaccctgatagatctcctacaAAactctcagtaccacccaaggagttgatactttgtgagtaagtgttgtaaagttcagtgagtttggtataaatatgaattactggaccttacctattgacctaagcctagaaatgaaaggcaaaatatctcttatttgctgaatcccagtataagtttaaccatcatgacttaaaactgaagtaagatatttgttatagtctcatttgtgggcaaaAAAATTGACCAaagaataacatcacttaggtgatgtgccaagcaacatgtcacaatgccctctctagttaggatatagaaattagagtcacattaacttgatactagatgcactaatatgacacaatcccatatgtggggtaaaaaaaaaacagccaaaagatgagagctaaaatacctacatagtgggccaaggatatgtcaaaatgcctcatgtggctctggtacagtaatgaaagtaacattatcagagaatgggcctagaatatgccataattttctgtatatacaggactcaggtgaaagagtaacattgtatgggtgctgggccctgtgatagaccaaaatttctgattgtcagcatggtttaggagaaaaaggagtgccaaataacctgaatgctgggctccgcaatatgccacaatctctccattgtaaagaccaggcagaaaaagagtcactacacttaggtcatgggctcagcgatttatctcagtgtccccagtaggcaggcccatgcaggaaaacagagtcatatcacctgggtGCTTCTTTAGTAAAaatgcacctgtgggaaagtatttgagtta
q panTro2.chrY                                   000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000---00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466   14 +  13390619 I
e ponAbe2.chr8         48203174    0 + 153482349 I
e petMar1.Contig6813      17462    0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=566676.000000
s hg19.chrY              7736614 2602 +  59373566 aaaagtctcaatacctgggtactaggcccagtgatatgacacaGTCTCTTCATTTTGTAGATtgacacctttaacttatagctgagcatgtacattagagttaaaatctcacttgtgtgctgggtaaatgtatggtactctgtacaacatctgagtggtttataaaacatgcatgagacttccaaacatttctgaggccttcatgctggtatggacccacaatcttacatgttgccctaaacccaggttttatagtaaaaatatctcccaatatcaaggttaaggaagaatacccattattttgtatgtgggctgggcaccaaaatgagtcagcatccaccttgttgcccaatccgggcataaaagtcacaatttcaactctgtgctgtattcccttgctggatttaggacctcaacagtgctcattgtaaatgggggatggtggacaattttaacttgact------tttaactgagagtcccaatctgaacattttgctgggcactgttaagaaactctctaccaccaaagagtttacaca--ctaagttagtgttgtaagcttctatgatcttggtacaaatatgcaatgcaggactttatctattgccctaaacttaactatgcaaggcaaaatacctcctattcattgcatcccaatagaagtttgatcgttatgcctgtgaactgaagcaaggtatatgtcataatcccatttgtgggcaaaaaagtaggcaggaaggtaacatcacttaggtgctgtgccaagcaatatgtcacaatgccttctctaggcaaggtataagaaattgagtcacattaactagatgttggacccagcaatatgaaaccaatcccacatgtggAAAAAAAACCAGCCAATTTATGTGAGCCAAAACACCTACATAAtgagcacaagatatatcagaataccttcagtggctccagcacagccaggagggtcatat--taaggtagctgtgtgcagcaataggcaatatgccataattttgtatttatgcagaacccaggcagaagagtaa---catctggattatgcaccttgcaataggtcaaaatacctttttagtggacatgattt---gaaaacaggagagccacatattctaagagctgagctcagtaaggtgtcaaaatccttctaccatgaatacacagagagaaaaagggagtcaaaacat----gtcaaggactcagagatatgtcccaatatcaccagtaggcagagttcagccacatgaggagagtcatatcacatacgtgcttccctaggaatatgtcacaatttaacatgtttacagaaaccaggcagaaaagccatatctcttgggaacttggttctgagatatttcataagactttcttatgacatcacccaggccagagggttacataacctatgtgcaggttctttgcttatatcacaatgctccttgtgagtagggcacaaggagggagccagtttaccaaggtgataggtctacagatatgtcaaaatgttctctatgaagcataggccaggcaaacgactaccataacctgtgtgcatggcatagaaatatgtcactttctaggttgacagggcccaaactgtagagccacataatctaggtagtaggcccagag-tatgtcacagagcctgccattgtgcatggctctggcaaaagagtatcctcatctgtgtgcctggccttgcaatatgtcactatcattccttagtgtgggccccattccagagagaagagttacatcacctatgaagtggaaacagaaatatgtcacaataattgtggtggaaatggagcaggcaagaatgtaacatcacctgggtgctagatccagtgacatatcacaattcctactgagagaagtgcccatccaggagagtcacaccaccCCACGGTTGGCCTAGGTAGCTATCACAAGC-CATATATGGCCTGAAACAAGTCTGGACAGTCAAGTTACAGAGGTGCTTGGCAAAGATTTATATCACAATTACACTGTCAGAAAATTCAAAAGATAAGATTTACAATACCATGCATGTCCTGTTTTCAAATGTGACTATTAATtttatccatgtgagatcatgaccattcttactgtcaactgggtatgcatacaagactcacaattttaactgtttactgagccctgctttgactctatctgtataacccaaaggc--tgtaaaatatgtgtgagtcttgtaatattttgtaaccttggaacaagaaggtgatccacgacatcacgcatgttcctaaacctagttataagagtcaaaatatcccttattgtttgagtccatatatgaaagtcattatcatgcctatgagctgtgcctaggtatatgttacaattccatctgtgattatgaagcaggcagaactgccacattacctaaatgctgggccataaatattccaatattctctttgtaagcaaggtctcttcagaaa-gtcacataacttgtgttctaggtccagctatgtggcaaaatgtcccctgtgggcagtgtctaggcagaagaggggagtcatataacctaaaatctgggtccaaaaatgtgtcaaaatgcttcttgttgacagggcccaggca
s panTro2.chrY            589869 2599 +  23952694 aaaagtctcaatacctgggtactaggcccagtgatatgacacaGTCTCTTCATTTTGTAGATtgacacctttaacttatagctgagcatgtacattagagttaaaatctcacttgtgtgctgggtaaatgtatggtactctgtacaacatctgagtggtttataaaacatgcatgagacttccaaacatctctgaggccttcatgctggtatggacccacaatcttacatgttgccctaaacccaggttt-atagtaaaaatatctcccaatatcaaggttaaggaagaatacccattattttgtatgtgggctgggcaccaaaatgagtcagcatccaccttgttgcccaatccgggcataaaagtcacaattccaactttgggctgtattcccttgctggatttaggacctcaacagtgctcattgtaaatgggggatggtggacaattttaacttgact------ttaaactgagagtcccaatctgaacattttgctgggcactgttaagaaactctctaccaccaaagagtttacaca--ctaagttagtgttgtaagcttctatgatcttggtacaaatatgcaatgcaggactttatctattgccctaaacttaactatgcaaggcaaaatacctcctattcattgcatcccaatagaagtttgatcgttatgcctgtgaactgaagcaaggtatatgtcataatcccatttgtgggcaaaaaagtaggcaggaaggtaccatcacttaggtgctgtgccaagcaatatgtcacaataccttctctaggcaaggtataagaaattgagtcacattaactaggtgttggacccagcaatatgaaaccaatcccacatgtggaaaaaaa-ccagccaATTTATGTGAGCCAAAACACCTACATAAtgagcacaagatatatcagaataccttcagtggctccagcacagccaggagggtcatat--taaggtagctgtgtgcagcaataggcaatatgccataatttagtctttatgcagaacccaggcagaagagtaa---catctggattatgcaccttgcaat-ggtcaaaatacctttttagtggacatgattt---gaaaacaggagagtcacatATTCTAAGAGCTCAGCTCAGTAAGGTGTCAAAATCCTTCTACCACGAATACACAGAGAGAAAAAGGGAGTCAAAACAT----GTCAAggactcagagatatgtcccaatatcaccagtaggcagagtgtagccacatgaggagagtcatatcacatacgtgcttccctaggaatatgtcacaatttaacatgtttacagaaaccaggcagaaaagccatatctcttgggagcttggttctgagatatttcataagactctcttatgacatcacccaggccagagggttacataacctatgtgcaggttctttgcttatatcacaatgctccttgtgagtagggcacaaggagggagccagtttaccaaggtgataggtccacagatatgtcaaaatgttctctatgaagcatagcccaggcaaaagactaccataacctgtgtgcatggcatagaaatatgtcactttctaggttgacagggcccaaactgtagagccacataatctaggtagtaggcccagag-tatgtcacagagcctgccattgtgcatggctctggcaaaagagtaccctcatctgtgtgcctggccttgcaatatgtcactatcattccttagtgtgggccccattccagagagaagagttacatcacctatgaagtggacacagaaatatgtcacaataattgtggtggaaatggagcaggcaagaatgtaacatcacctgggtgctagatccagtgacatatcacaattcctactgagagaagtgcccatccaggagagtcacaccacctCACGGTTGGCCTAGGTAGCTATCACAAGC-CATATATGGCCTGAAACAAATCTGGACAGTCAAGTTACAGAGGTGCTTTGCAAAGATTTATATCACAATTACACTGTCAGAAAATTCAAAAGATAAGATTTACAATACCATGCATGTCCTGTTTTCAAATGTGACCATTAATtttatccatgtgagatcatgaccattcttactgtcaactgggtatgcatacaagactcacaattttaactgtttactgatccctgctttgactctgtctgtataacccaaaggc--tgtaaaagatgtgtgagtcttgtaatattttgtaacctttgaacaagaatgtgatccacgacatcacgcatgttcctaaacctagttataagagtcaaaatatcctttattgtttgagtccatatatgagagtcgttatcatgcctatgagctgtgcctagatatatgttacaattccatctgtgattatgaagcaggcagaactgccacattacctaaatgctgggccataaatattccaatattctctttgtaggcaaggtctcttcagaaa-gtcacataacttgtgtgctaggtccagctatgtggcaaaatgtcccctgtgggcagtgtctaggcagaagaggggagtcacataacctaaaatcttggtccaaaaatgtgtcaaaatgcttcttgttgacagggcccaggca
q panTro2.chrY                                    0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000------000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000---000000000000000000000000-0000000000000000000000000000000---0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr8         105374701 2619 - 153482349 aaaattctcaacatctgggtACTATACCCAGTGATATGACACAATCTCATTTTCCTtgagggtgacacctctaacttttagctgagtgtgtatattagagtcacaatctcacgtctgtgctgggccaatgtacgacattctcttcaacatccaagaactttataaaacctgcatgagagttgcaaacctctctgaggcctacgtgctggtatggactcacaatcttacatattgccctaaacccaggtttgatagtcaagatctctcctacaggcagggttaagg-agaagacccattattcc---tgtgggctgggtccagaaatgagtcaccatcccacctgtgtccagatccacatataaaagtcacaattgtaactttgtgctgtattcccttgttagactcaggacctcagcagtgggca-tataaatgtgggatggtgacaacttctaatttcacttgggtgtgtaactgagcgtcccaatctgaactttttgctgggccctgttatgaatctctctaccacaaaagagtttataaaatataaattagtgttgtaagcttctgtgagtttggtatgaatatgcaacccagcaccttaaatattgccctaagcttaacaaagagaggcaaaatacttcctattggctgaatcccaatataagcttgatcatcatgcctgtgaactgaagcaaggtatgtatcataattccatttgtgggcaaaaaactaggcaggagggtaacatcacttagatgctgtaccaggcaatgtgtcacaatgccttcgctgggctgggtatagaaaattgggtcacattatctgggtgctggacccagcaatatgacacc-atcccatatgtggaaaaaac-ccagccaacttatgagagccaaaacacctacataatgggcccaagatatgtcaaaataccttcgccggctccagcacaggcagaagagtcacatcataagggtgctgggcccagaaatatgcaatatgccataatttcctctttatgcagaacccaggcagaagagtaacatcatctgggtgctgggctgtgcaacaggtcaaaattccttttttgtgggcatggttcaggaaaaagaagagagtcacatatcctgagtgctgggctcagcaatgtgtcaaaatcctcctatggtgaaggcccaggcagaaaaagagagtcacatcacttaggttatgagctcagagatatgtcccaatgtccccagtaggcagggctcaggcagacaaggagagtcatatcgcctaggtgcttccctagaaatatgtcacaatgtagcatgtgggcagaaaccaggcagaatagccacatcacctgggtgctgggtcttgagatatgtcacaaggctctcttaggacagcactcaggcaagagagttacatcacctagatgcatgttgtgtgattattccacagtgctccatgtgggtagggtccatgaaggacatcacttcacttcagtgatagactcagagatatgtcacaatgtcctctatgaagcatagccctggcaaaagagtaccatcacctgtgtgcctggcctagaagtatgtcactccccaggttggcagggcccaagcaggagagccacatcacctaggtgataggcccagagatatgtcacaatgccttccattgggcatggctctagcaaaagagtacattcacctgtgtacctggccttgcaatatgtcactatccttcctttgttcagggcccattccagagaggagagttacatcacgtatgaggtggacacagaaatatgtcacaataattttggtgggcatgtcccaggaaagaatgtaacatcacctggatgccagatccagtgatatgtcacaatgcttactgagagaagggcccaggcaggagagtcacatcatctcaaggttggcctatgtagacatcacaatcttatatatgggttggaacaagtctggagagtcaaattacacaggtGCTTGGAAAAGATTTATATCACAATCACACTGTCAGAAAATTCCAAAGATGAGATTTACAATACCACACATGTCCTGTTTTCATGTGTGAcagttcgcttcatccatgtgagatgatgacagtccttactgtcagctgggtgtgcatggaagactcacagtttcatctgtgtgccgagccctgctttgactctgtctgtacaattcaaagaccttgtaaaatacatgtcaatgttgtaatcttttgtgacctttgtacaagaaggtgatccaggacatcatgcatgtccctgaatttagttataagagtcaaaatatcctctattggctgagtccacatataagagccattatcat-tctgtgagccatgcctaggtatatgttacaatttcatctgtagttattaagtagacagaacagccacatcacctaaatgctgggccagaaatatttcaatattccttttgtaggcagggtcctgtcagaaatgtcacataacttgtgtgctaggtccagctatgtggcacaatgtcccttgtcggcagtgtccaggcagaagagaagagtcatatcacctaaatgatgggtgcaaacatttgtcacaatgcctcctgttgccagggcccaggca
q ponAbe2.chr8                                    999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999949999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999990999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999996999998969999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999895497764847774366149999896999197667774746777995999954795793698862156647442223297874533424642374764765765269778877665723644457253996869597696285766768599667797765776724314666764341345355567846884766244546664456566767227665536497621548899732599778349879533655698489849978949082588998986852999979999999868786996635699699986780804999967968499888466997879979899889996999998978986999878999989997980988999999799999997798593982998899997996488999999999799699996899989997989599999999789999999999999599999999999999999999959997999929999499999999999999997999699999969999999999999999999999999999999999999999999988999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr8         I 2984 N 0
e tetNig2.chr5           3743466   14 +  13390619 I
e petMar1.Contig6813       17462    0 +     30809 I
e xenTro2.scaffold_916    103508 47921 -    291918 T

a score=2048783.000000
s hg19.chrY            7739216 22396 + 59373566 agagtgtcataacatttagatgcagtgtttataaatgctaccatttccaaagaaagcagggtgcaggcaagagagGAGAGCCATGTAACCTAAACGATTGGTCCAGAAGTATGTTAAAATCCCACCTAGGCACCTTTTTATAATAACACAGTTAAATCACCAATATgcttgtcccaggtatttgtcaaaatctcatttgtgggctacacctaggcagtattattaaatcattcaagaactgggcaaaggtgtatggcacaattacacttgtggaaaggtttcagaataagagtcacCATTCTGCACTTATTCTGGCTCCAGGCATATGAGTTGTTTCTAGGCTTGTCTTATGGTCTCAGATATACAGCATAATATCACTTGTGACCAGAGAGAAGGCAAGAAAGTTACATCATCTATGTGGCAAATCAAAACGCTTTCTCTGGGCAGAAATTTGACACAAAAGGAGACTAACTTCACCTAGGGAATTggcctagatataagtgacaatgacttttatgtgcagtaccaagcctggagcgtgacctcacattggtgctgggcacagcaataaatcaaaatcttcctgttgtcacaatacaggcaaaagggaagaaacatcttgtaaaagctgagtcaagtgatatattatataatgcttcctgttggcagaacgtaaaagaagaatcatatcacctgggtgctttgcccagttatatttcacaatgcactgtaagtgcatggaaccaaggcaatagtcacaATTCCAACTTTGTGCTGTATCCCCTtgttagactcaggacctcaacagtgggcatggtaaatgtcagatgatgacaacctttaatttcgcatgtgtgtgtaactaagtgtcccaatctaaacttgttgctgggccctgctttctctaaaggccctttctaccaccaaagggcttatacaatgtaaattaatgtagaaagattctgtgaacttgttacaaatatgcaacccaggatcttatcaaatgccctaagcctaacaatgagaggcaaaatatcttttattggttgaatcccaatacaagtttgattatcatgcctgtgaactgaagacaggtatatgtcataatcccatttgtgggtagaaatattaggaaggagcgtaacatcatttagatgttttgccaagcaatacatca----caatgccttctctaggcagtgtataggACATTGGGTTACATTAACTTGATTCTTAACACACTAATATAACATCATTCCACGTGTGGAAAATATTCAAGCCAAGTTATGAGAGCCAAAACACCTACATAAtgggcccaagatatgtcaaaatatgtttcctggctccagcataaacagggcagtcacatccaaaatatgctgcacccagcaatatgcaatatgccataatttcctctttatgcagaatccaggtggaagagtaacataatctgggtgtttggccctgtaatgcatcaaaattacttttttgtggtcatcattagggagaaagatgagactcacataccctgaatgctgggttcaacaatgtgtcaaaatccttctattgtgaaggcccagacagaaaaagagagtcacttctcttaggttatgtactcagagttatatatcagcgtccccagtaggaaagaatcaggtcaacaaggagagtcatgtcacctaggtgcttcctagaaatatgtcacagtgtaatatgagggcagaatccaggcagaagacccacatcacttgggtgctgggtcctgagatatgtcacaagccactcttaggaaaagcccagacaagagaattacattacctcagtgcaggttctctgcttaagcctcaataatacatgtgggtagagtccaaggagggagtcccttcacctaggtgataggcccagatatatgtcaaaatgttttctatgaagcacagtactggcaaattagtaccatcacctCTGCCCCGGCCCAGAATTATGCCACTCTTCAGGTTGGCGAGGCTGAAGCAGGAAAGTGAAAAACCTACGTGAtaggcccagagatatgttttaatgtcctcctttgggtatggctctggtgaaagaatactatcatctgtttgcctgaccttgtaatatgtcattatcctttatctgtgtagggcccattccagagaggagagtaacaacacctATGAGGGGAACAcagaaataagtctcaataatttttgaagacacggaacagcaagaatgtaacatcaattggatgttagatccagggttatgtcacaatacttactgttagaaaagcccaggtaggaaagtcacatcacctcaaggttggcaaaggtagatatcacaatcccatatatgagctggaataaatctggagagttaaattacACAGGCTCTTGGCAAAGATTTATATCACAATCACATTGTCAGAAAATTCCAAAGATGAGATTTACAGTACCACATGTATCCTGTTTGTATGTGTGAcagttggttttatgcatgtgaaatgatgactgtacttactgtcagctgggtttacatacaagactcaaaattttaaatgtgtgctgagccttgctttgactctgtctgtataaaccaaagactttgtaaaatatgtatgaatgttatattatttcatgactttgtacatgaaggtgatgaaggacatcacatatgtccctaaacttagttgtaagagtcaaaatatcctctattggttaaccccacgtatgagagtcattatcatgcttgtgagccatgcctatatatatgttaccTTATATGTTATATTAATATGTTATATTTtgctggtccctgtcatgaaactgtctgtaccaccaaaagaggttataaattatgagttagtgctgtaaagtcctgtgagctttgtagcaatatgcaaatcaggacattaactattgtgctaagtctaatgatgaaaggcaaaaatgtcccctgctggctgaatcccaggttaagtttgaccatcattactgtgaacagaagtcaagtataggtaatagtcccatatgtggggaaaaaactaggcaggagggtactatcacttgggtggtgtaccaagcagtgtgtcacaatgccctcttgaggcagagtataggaattagagtcacattaactgggtgatggactcagcaatatgacaccatcccacatgtggAAAAAAACTGCTAAGTTATCAGAGCCAAAATACTATGTAATGGGCCTAAGATATAACAAAATACCATCTGTGGCTCCTGCACAGGCATGAGCATCACATTTTCAGGTTgctgagcccagtaatatgccctaattttctctatatgcaggatgcagataaaagagtaacactgcatgctgagccctccaataaatgaaaacttgtgtttgtgggcatggtttgagaaaaaaaaaaaggtgaatcaaataaactgagtgctaggctcagcaatatgtcacaatcctcccattgtaaagaccaggtaggagaaaagagtaacttcactaatatcatgggctcatagatatatcccagtgtcccctataggaaggttccaggcagaaaaggaaagtcatattgcctaggtgcttccctagatacatgtcacaatctcatgagtgggtagaaacagacagaaaagctacatcacctgggtgcatcctgatgtaatgtgtcaccacacccaatgtaaacagattttaagattaaaaaaaaaaa-cagaatcacaacacctgggtgttgggctcagcagtatgtaatagttctctttctgggcagcgtcaaggaaaaagagtagagtcatgtcacctaggatttgcactcagtggcatgtcacaatttcttcagcaggcagaatccaggcaggagaggagagtcacattacctagatgctacatctatcgatatgtcatagtgttccctgtgggtagtacactggcaggagagacacTGGGGTCTTCAGCCAACAATGCAATAAAAACCACACGAGGAAGAAACCCAACAAATTGATGACAGCCAAAAAACCTACAGAAtgggccaaagatatttcaaaataccttttgtggctctggcacaagccaaagagtcacatcattagggagcagggtgaagcaatatgccataattccctctttattaatgaccaaggcagaaaagaaacagcatctgggttctgggcgctgaaatatacagcaaaagtcctgtttgtgggcattgttcagcaacaagacaggtgtcagtttacctaagtgctgcagctggactcctcagtgtattacagtcctgccattgttaaggctaagatagaagaagagagtcttatcacttaggtcatgggctcagacataaggccaagctagcagtaagcagggctcaggcagaaaaaacaagttatatcacctaggtgcttatttaggtatatgccacaattttatatgtgggtagaaaccaggctgaagagctacatcacctggcccaggtacctgagatattcacaagtccctcttaaaaaaattacccaggcaagagagttatgtcaccAAAGTGCAGGATTCATCCTtatatcgcaatgcttcatgtaggcaaggccaagccgtaagtcacgtcaccaaggagatagtcccagagataagtcacaaagccttccttaaagcatgaccctgtcagaagagtaccatcatctcaatgcctggcctagaattatgccactattcaagtaggaaattcccaaacagaacagccatataacttacatgatatgccctgtgatatgtcaaaatgtcatatcttggaaatggctcttgcaaaagaatatcatcacctgtgtgtatggcctaggaatatgtcactattttgcactgtgtgcagggcccattccagagaagagttttgtctcataactgagggacacagtggtatgtcacaatcatgtctgtgggaatggtgcagccaagaatgtaacatcacctgtgtgctggatccagtgatgtcacaatacttactgagagcagggcccaagaagaacaatcacatcacttcaaggttgaccaagttaaatatcaaaattccatttgtaggctcgcacctgtctgaagagtgaaatcacacaggtGTTTGACAAAGATATATATCACAGTCACAATGGAAGATAATTCTAGGGCTTAGATGTATAATACCATATAAGTCCTATATTCATGTAGGAGAATTGCcttcatccatctgtgatggagaaagcctttagtgtcagctgggtgtgcataagagacttacaatttcctctgtgtgctagaccctgttatgacactctctatacaatgcaagggtgttataaaatatgtgtgagtgttttaatcttctttgacatttttaccagaaggagatcctggacatcactcatgtccctcaaccttgttataaaagtggccttattggctgggtcaacatatgggagtcattatcatgcctcttaactgtgcctaggaatatgtcacatccccactgtgattataaaacaggcaggacaaacacatcacctaagtcctaagccacaaatatttcaatattctctttgttggcacggccataagagaaatatcacAAAATTTGTGGgctatgcacagctttaaggtgtaatgtcccttgtggaaagtgtccaggcaggagaggagagacataccacataaaggatggaccacagatatatgacaatgcctcctgttgaaaaggcttaggcaagaggatcatgtaatttgtatgtagtgcttagaaatggtacattattcactggaagcagggtttacgcaggagagaagagtcacataaccaagattattgattcagagatatgttaaaatcccatctgaggacagtgttaaaacatgagaatcaaatcactgaggtTTTTTGTCCAGGTTTATGTCAAAATGACATGTGGAGGCTGAAACTAGGAAGGGTTATTAAATCACTCAGGATATGGGGATGGTAAAACTCACAATAACCCCTGTGGAAAGATTCAGAGatgagtgtcaccatcctgcgtatcctggctccaggtacaagagtcattattaggctttttatctggtctcagctatatggcactatataacccatgggttggaagaagaaaggaaagcctcatcatctgagtgggtactggtacagtgaaatgttacaattctccttgtgagcaggatattggtagaagattcacatcacctggatgcaggtttcagtaatatatctaaatcctgcctgtgagtaggactcaggcagtgaaggagacaaactctacctaggctgttggtcaggatatgttgcagagtggcccctatgtgcaggaccaaggcaggagaacgatctcacctgggtgcttggttctgcaatatgtcgcaatctctgtgctggtcagggcccagaaaaaatagaagacacatcaccaaggtgctaagccaagtgatatgttacaaagctttctgttgggagaatcctctccaaaaagagtcacatcacctgtgttgaataaccagttatgagtcacagtgcaccctaagtgcagggccaaggcagtagaaaaaagtcacataatttatgtaatggacctagataaaagccatagtgctttttggaatcagtgttaaggccaagattttacatcagctgggtGCTGGTTTAAGTGGTCTGTAAAAGTGCCCTTTGTCACATTGCCAAAGAAAGTGTTATTTTTTGCTTAGGTGCTTGGTGCACCTATGTCACAATTTCAACTGTGTTCTGGGCCTAGAAATGATAGTCAAAGTACTCAGATGCTGGGTAAGCTCATACTTTTCAATTGTATCCTTGAAAACGTTCAGAAATAAGTTTCACAGTCCCACACAAGTCCTGGTTTTTGGTATGAGAGTTAACACGTCCTATGAGTTGGCTTGAAGGGTAACAGAAGTCACAGTCTCAACAATGAGCAAGATCCATGTATCGTAGCCCAAATCCTGCTTGAAGATTGTGTTCCAGTAGAAGAGTCAAATGACCAAACCTCTGATGAATCACGGTTGAAATgtcacaaaaccacctgtggatcagatttatgtatgagagtcacaacttcaatatttgactgcttatgtgtgtaagatttagtacctcactggtaggctctgttcatgtgtaagaaatacaattgtgtcagctaggtgtacatccaaaagtcacaatactacctggttgcaggtgcctctaatgatactctttgtatccctcaggctttatatgatatgcctggtagcatacttttctgtcagttcctacaggtgggaaatctaggacttGGCAAGCAATATGTAACAATGCATTCTCTAGAAATGAGGGTTACCTTAACTGGGTACTGGCCCAGCAATATGACAAAATCCCAAATATAGAAAAAGTAAACCCACCCAAATAATGAGAGCACAATCACTTACAGAGTGTGCACAAGGTATATAAAAATGCTTTCTGTTTCTCTGACACATGCAAGACAGTTACATCATCAGGATTGGGGTGtgggcagcaataggacataattatctctttatgcctgacctaggcagaaaaggaatatcatctgagtgctgggccctgcaatgcatcaaaattcattttcttgggcattgcttgggacaaaaaacagtgtcatattacctaagcattgggcttagcaatatgtcacataaccccatttcaaaggctggcagaagaagagtcacatcacttatgagtcagactcacatatatggcttaatgtcccaagtaggtagggctcaggcagaaaataagagtcatatcacctaagtccttctctccttatatgaaaaaatctaacatgtgaggtgaagccaggcagaagagtcacatcaacttgatggtggaacctacgatatgtctcaaggctcccttaggacagtacccaggcaagagtgttacagcaaataagtgcatgttctgcccttatgtaacaatgccacatgtggatagggcctaagcagggagtcacatcacctaggtgataagcccagagatatgtcacaatgtcatccttgaggcatggcctcaaggaagtgctgaaagactatcactacctgtttgcttagcctagcaatatgtcacaatctaggtaagcaggacccaagcaggagagcaatatcacctatgtgataggcccacagatttttcacattgccctttttatgacatggccctagccaaagagtactgtcatctgtgtgcctggcccagccatatgtcactattccccactgtgtgcaaggtccattctaatgaggagagttacatcacctaggtggttgacacagcgatatgtcacaatgatttctgtgggcatggttcaggcGATTCTTACTGAGAGTAGGGCCCATGCAGGAGGGTCAAATCACCTAAAGATTGTCCCACATTGATTTCGAAATAACGTAACTGGGCTGGAAACAGTCAGAGAGTCAAATCAGACAAATGCTCAGAAAATATTTACATCACAATCACACTGGCAGAAAATTCCCAGGATAAGATTAACAATACCACACATGTTCTGTTTTCATTAGTGAcaattggctttatatatgtgaggtggtgacagtccttactgtcagttgggtgttcatatgagactcacaattttacctttctgacaggttctgttatgacactttctatacaagacaaagccttttccatatcacttatactgttataatcttccatgacctttttaccataaagagatttaatcacttgtgtttctaaaacaagttaagagagtcaaaattactcctatttggtggagggagtctacatatgacagtcattatcatgcctgtgagcttttcttaggtatatgtcccaacttactctgtggTAATGAAACAGGCATGAGATCCATATAATCTAAATGCTGTGGCAGAAATCTTCcaatattcttttttggcaaatttctagaagaaaaatcacataactttggggctacgcccgactgtatgggacaacaccccttgtgggcagtgtttgacagaagaggagagaaatattaaataaatggtaggttcagagataagttatagtggtaacttgttgaaaggaccaggcaagaaaatcatatcaTTTAAATGCAGTCCTTAGAAATACTACAATCTCCAGTGGAAGTAGAATCCAGGCGGGACATGACAGTGAGGCACCTAGATTGAgggtccagagacatgttacaaagcttcctaaagatactgttaagccaggagagtcaaatcaccaaagtgctcagctgagatatatgtccaaatctcaattgtgtgctgcacctaggcagGATTACTAAATCACTCAGGGGCTGGGCAAAAGTATATGTCACTATAACACTAGTGGAAAATTCCAGGAATAGGAGTCACCATCATGCCTATGACCTGGCTCTAGGTTTAAGAGTCATGATTAGTCCTCTTATctggtctcagttatatgggacaatatcccttgtgagcgcagaggaagcaaaatatcacatcacctgggtggatgttggtccagtgagatgtcacaatcatcgtgggcagaattctggaagaagggtcacatcacctggatgctggtttaactgatttatcaaaattccccttttgggctgggcttagaaaggagaggggactcacttcacctaggcaattggtgtacatatgtgtcacaatggccactgtgtgcaggactaatgtttggaagagatcacaacttggtgctggatttagccatatgtcacaatctcccttgtggtcagcgcaaggcaagagaggaaaaacatcacctaggtgctgtgctgagccaagttatgtgttacaaagctttctgatggcaaaacccaaaatgcagtcacatcacttgggagcagtaccccgttatttgtaacaatgcaccattaatgcagggccaagggattagaattggataacatcacttacatgatgaacccagacataagccacagtgctttttataggtagggattaggcaaataattcacatcacctgggagatggtcctagttgacatgtaaaagggccctttttatataggcccaagAACCTATGCTTAGGTGTATGGTCCAAGTATATCACAATTTCATCTGTGGTCATGGCCTAAAAAAACCAGTCAGATTATTCAGGAGCTGGGATAACTGTTATGTCCTAATCACACACTAGACGATATTCAGAAATAAGTTTCACAGTCCCACACAACTCctggctttgtgtatgtgagttaacacctcctgtgagttgggtcaaagcagaggagtcccagtctcaaaaattggcaagatccatgtataagatgcccaatcccacttgaagactgtgttccagtgggggagtcacagcctcacaggtgtgcagaatcatgcaaaaccaaatcactcatgaatcaggtccgtgtataagaggaacaatttcaACCTTAAATTGCTCATTTGtgtgagatttagtaccttatttgtagataatattcttgtgagaaaatgacaatcatgccagctaggtgtgtatccaagagtcacaatcacacctggttagcgttccctgttacgacagtttttgtaccactcaggctttatatgatatgcctgagtgtcataatcctttgtgaactttatacaattaggtgactcatttctttacttatggccatgaagctgactatgagaggcaaattatcgctcctttctgggtaatggtaagataattaaatttgtgcctgtaagctgaacccagatgcatgtcaaaatttcccctgagggcagaaacaaagcagcatagtcatgttacctggattctgagcacagaatacattataatctccttcacatgcaggccaagtcagaagagtcatgtcaAATTGTAACAACCTCAaggaatatggcaccatgtaaactgtagacatggttgaagaaaaaaaagtcacaccatgtaggtgcttagctcagcaatatgtaataatttcctcttttggctgattccagaataaagaggagagttacattacctaggttttgcactcagtagtatgtcacaattccttttgtgagcagaacctaggcaagagatgagagtcacatttcctagatgctatgaccagcaatgtcacaatgtgccttggggcaaaagcaaaggaaaaatatgcaaatcatctaactgataggctcagagaaatgtgataatatcccttgctatcagggcccaggcagaaaagtcacatttttatgattcttactcaatgatatgccaaaatacACACATGGGAAACAATGTAAGCAAAAGTTTTAACACATGGGTACTTGGCCCAGTGATATGACACAATATCCTA---tttttttgtttgtttgtttgagacagagtcttgctctgtcacccaggctggagtgcagtggcatgatctcagctcactgcaagctccgcatcccaggctcatgccattctcctgcctcagcctcccgagtagctgggactacaggcacccgccaccatgcctggctaattttttgtatttttagtagagacggggtttcaccatgttagccttgatctcctcacattgtgatctgccctccttggcctcccaaagtgctgggattacaggcctgagccaccacactcagccCAATATCCTAAGTTTtgagagtgacacttttaactgttagcttggggtctataacaaagtcacacggtcacatgtgtactgggacaccaaatgacattgtctacaacatcccagggcttcatatggcatgaattatatttgcaaacttctctgaggcccatatgcttgtatgaactcacaatcttatatattgccttaaattcaggtacaatagtcaacatctctcatttgggctacgttcaggaaggagaaccatttttatgcctgtgaggtgggtccaaaaataagtcacgatcgcacctgaggccagatgcacatgtgagagtcacaattccatttttgtactgttttctcatgttaaacttagtaactcagcagtatactttgtaattgtgggatggtgacaattttactttcacctgggtgtgcaactgagagtcaaaattttaactttttgctgggccttgttatgaaactctctgtaccacccataaagtttatacaaaaatgaattgtttttgtaaacttccatgagctttgtacaaatatgcaacccagaattttttctattgccataagcctagtgatgagaggcaaaatatcttctattggctgaatcccaatataggtttgatcatcatgcctgtgaactgagcaaggtatgttccataatcccatcagtgggAAAAAAGTTAGAaaaagagtaacatcacttaggtgatgtggcaatcaacatgtcagaatgttccctctaggcagaatctaggaaggagggtcacattaactgggtgctggaaccagcaatatgtcaATTCCACATGTTGAAAAACATAAAAAAGTGATGAGAGCCAAAACACTTAAGAATAAGTCAAAGATATTTCAAAATACTCTCTGTGGCTCTGGCAtaggcaggacagaactgcagtgaaagaattatattaccttggtgcaggtttaacttttatgtcacagtgatctatacaggtgaggcccaagtattcagtcacatcacctaggtgataagcccagagatatgtcacaaggacctccttgaaatatagccctggcaaaatgtatcattacctgtgttcctgatctaccaatatgtcaccccatcctctgtgctcagggcaccttccagagaaaggagttacatcacctaagaggtgaacacagtaatatgtcacaatgatatctgtgggtgtggtccaggcaagaatataacatcatctggatgttagatccagtgatatgtcattatccttactgagaaaagggaccaggcaggagaatcacatcacctagacattggatcAGGATGAGGTAGAGATTATAATCCCATATATGTGCTAGAACCTGTCTGGAGAGTCAAATCACACAGATGCTTGGCAA-GATATGAATGACATTCACACTTGGAGGATATTGCAGAGATGAGATTTACAATAACATACATGTCCTGTTTTCATGTTTCAcagtaggcttcatatttatgagatgcagacaatacttcctgtcagctggatatgtatatgagactcccaatttcatcttttggctgggttttgttatggcattatctgcacaagccaaaagttgtaaaatatctcaggctgctataatcttctgtgaactttttaccagaaagatatctgagacatcacttgcattgctaaaccaagttacatgagtcaaacttactcctatttcaggggtccacatatgagtcattatcatgcctgtgagctgtgcctagttatttgtcaaatgttactctgtagtaatgaaacaggcatgacagtcacataacgtaaatgctgagacagaaatgttccaatattctctttgtaggcaggttcttcacagaaaaatcacataacttcgggggtctatgcccaactctacggcacagtgtctcttgtgggtaatgtcaggcagaagaagagagtcatattacctaaatgataggcccatagatatgttacaatgccacctgttgaaagggctaggcagGTATCATTTATAATTATAGTCATTTTgtatcttattgtagctttgatttgcatttttctaataataatgttgagcatctttgcacacgcttggccatttctatgtcttctttggagaaatgtcacttggtgtctcttgcctattactaaattttctgttatttttgctttaagtttctcatatattctttatatttttccattgccatatgtatattttgcaagtatattctcccacactgtaagttgttccttcactctgttaatttatttttgctatgtaattattattattattttttttagaatctggtaattttatttgtccgcttttgtttttcttgcctgttcttttgaggtcttatttaaattttttttcctgtcctatttggtaaagaatttctctatgttttattcaaataattttatacatttgagtttacatttcaatcttctacttatttttatttaaattattttaatatggtaacaggtaggaacctagttgtattcctctgtatttaaataatcaattttcccagtaccattcattgaaaagattgtcttttcttaaatgtatgttctgaaccactcaaaaattacttggctctaggtttatgaattttattactgggatcactggatactttggtctatgtgtctgttttctatgccattatcatgctgttttgcttgttatagctttgcagtatgttttgaattcaggtggtttgatattgtcagctttgttcttttttcacaggattactttagctatttcaagagtttgtttgtttgtttgttttggttccacataaattttgtgcctctttatctcatttctatacaaaaatattcatgatatttttagagagtttgcatagaatctgtagatttcttgtgtagcatagctatcttacctatattttttataactcatgagaaaaatatctattttttttacttttttaccaatgttttataatttattgtgtggagactttttctctttttaattaagtctacttctacacacctttattttttATTCtagataaacaaaaagtatttggaaaattttacatgcctttgtaattaaaacaagttaacaaattaggtatagatgttatgtacttcaacacagctaaggcaaaatatgacaaatcaatagcAGTTATtgttactggtgggtcttctttattctcagagctcccaagatggtagtaggctgctcccaacatgaggcagacagctcccaagatgacagcaagctttttcttctctgacctggggtcttggcctcagggattccaaggaatgg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tttctgtatctctttgtctactctctgtctctctctctttctgtgtctctctctcattcctctctgtttctatctctcttctctctctcttttctcctctctctctcctttctctctttgcagatggattttggaaacacagtagaagtacagttgcttgttgctccaatttgccactataggaatatgtgccaccctttaattactcaatttgggaaagaaagtgaaagtctgaagcattagtatctaggaggcagggatcagaggaaatagattcagaggtaatgagaattttgttgatacattttcaagaaatcatggtcaggacccaggaggtattggtcaggagaggtaggggtgcatgcatgggtgactgctgagtagagacttctggatgtgaaatgatcttgaccaaccaatgccaggagtttgggacgacagttttctgcctctagttgatcctcagcttccccaggataattgtgaaagtggaagctggttccaggcagaccaatgctcccaatgcagaagg-ttgggggttattagaaagccttttccccaaaagcctcacacctgagtctttagtctggcagctatgctaattgtttttaaccagccgagaggtgcccagtattttcttccaattctaagaaaggataggacaaaacagcaagtgaaagtggtctgatattactcgcctctttggaaaagccccatatgggtcaccaaatgttaccagtgggtctttgttcatagagttcccaggatgatggggggccactgccaagatggggcgggctgctcccaagatgacagcaagccttttgttctctgacctgggtttgttgaccttacagattccaaggaatggaactttgggccatgtggtgagttttatagctctattagaagccatgggtcatggaagagaaccatcagacccagtgactagtgttcagctagattaggatgaacccaggcacttagccatgcagaaacaatgatgagcctgtcgcccaatcaggagtggcaatgggatcctcactggatcaggagtgctgtgaacaccctgctagatctagggagatgggattcagcagtgggtatgcaatgatagcattcagtagtggtggatggtgagcaaaagctcagctccagccagaaaacagaccagaagaccgtgtacttacaagatttaatagagtgaaaacagagctcccttacagtgggagaggacccaaaggggattgacacccccactctaatgctttagtttgtatcccaataattgtccatccccttgtgctctaaggtgatatatgatttcactatttctttacctcctgcttttgcctaattggcattttattgagccctctttactaattgattggtaaggtgtgagctgagttacatgccccatgtttaaaggtaggtgaagtcaccttccctagctaggattgggaatttcttaatcagcctaggaaatccagctagtcctgtctcATATTATCacagcaaactggaaaggaaagtgctttttactgaagatctgaaacaagacaattatgtcaacttttacaatttgtattcaacagagtactggaaggcccagaaagatcatttatgcaagataaagaaataaagcacatccaaataaaaaattagaacatcaaaatttctctgtttgcagatcacatgattgtctctatagcaaacctaaaatactgcactaaaaatcttgagaattaataaaaaattcgatgaagtggcagaataccaaattaacatacaaaaattagtagAAGCAGGGTTTTTTTGAGATAGAGTCTTGCAGCAGAAGCATTTTGGTATGCCACCAATAAGTCGTCTGAAAAAAAAATTAAAGAAAAAATATTTAGAAGAGCTATAATATATGTTTTACTTAATTTTAATTTTATGTTTGTGGAAAGGGTCACCTTTGtttgtttatttgtttatttatttatttttgagacagagtctttctctgtcacccaggctggagtgcagtggcatgattccgcttcactggaagccccactgcccaggttcacgccactctcctgcctcatcctcctgagtagctgggactacaggtgtccaccatcactcctgcctaatgtttttgtatttttagtagagacagggtttcaccagttagccaggatggtctcgatctccttacttcatgatccacccacctcagcctctgaaagtgctgggattacacgcgtgagccaccgcacccaaccAGTTCAACTTTATTTGTTGTAATTCGGACATACAGCACTCTCGCTCCAACCAATTTGGTAAAAAGACTGTTTCTTTCTCATTTTGAGTGATAGAGACAGGAGCTAGTCAAGGGGCTTTTTCTCATTTTAAGTAATGGAGACATGGGATAGTCAAGGGAAATTTTT
s panTro2.chrY          592468 22402 + 23952694 agagtgtcataacatttagatGCAGTGTTTATAAATGCTACCACTTCCAAAGAAAGCTGGGTGCAGGCAAGAGAGGAGAGCCATGTAACCTAAACGATTGGTCCAGAAGTATGTTAAAATCCCACCTAGGCACCTTTTTATAATAACACAGTTAAATCACCAATATgcttgtcccaggtatttgtcaaaatctcatttgtgggctacacctaggcagtattattaaatcattcaagaactgggcaaaggtgtatggcacaattacacttgtggaaaggtttcagaataagagtcacCATTCTGCACTTACTCTGGCTCCAGGCATATGAGTTGTTTCTAGGCTTGTCTTATGGTCTCAGATATACAGCATAATATCACTTGTGACCAGAGAGAAGGCAAGAAAGTTACATCATCTATGTGGCAAATCAAAACGCTTTCTCTGGGCAGAAATTTGACACAAAAGGAGACTAACTTCACCCAGGGAATTggcctagatataagtgacaatgacttttatgtgcagtaccaagcctggagcgtgacctcacattggtgctgggcacagcaataaatcaaaatcttcctgttgtcacaatacaggcaaaagggaagaaacatcttgtaagagctgagtcaagtgatatattatataatgcttcctgttggcagaacgtaaaaggagaatcatatcacctgggtgctttgcccagttatatttcacaatatgctgtaagtgcatggaaccaaggcaatagtcacaATTCCAACTTTGTGCTGTATCCCCTtgttagactcaggacctcaacagtgggcatggtaaatgtcagacgatgacaacctttaattttgcatgtacatgtaactgagtgtcccaatctaaacttgttgctgggccctgctttctctaaaggccctttctaccaccaaagggcttatacaatataagttaatgtagaaagattctgtgaacatgttacaaatacgcaacccaggatcttatcaaatgccctaagcctaacaatgagaggcaaaatttcttttattggttgaatcccaatacaagtttgattatcatgcctgtgaactgaagacaggtatatgtcataatcccatt-gtaggtagaaatattaggaaggagcgtaacatcatttagatgttttgccaagcaatatatcaatcacaatgccttctccaggcagtgtataggACATTGGGTTACATTAACTTGATTCTTAACACACTAATATAACATCATTCCACGTGGGGAAAATATTCAAGCCAAGTTATGAGAGCCAAAACACCTACATAAtgggcccaagatatgtcaaaatatgtttcctggctccagcataaacagggcagtcacatcaaaaatatgctgcactcagcaatatgcaatatgccataatttcctctttatgcagaatccaggtggaagagtaacataatctgggtgtttggccctgtaatacatcaaaattacttttttgtggtcattattagggagaaagatgagactcacataccctgaatgctgggttcaacaatgtgtcaaaatccttctattgtgaaggcccagacagtaaaagagagtcacttctcttaggttatgtactcagagttacatatcagcgtccccagtaggcaagaatcaggtcaacaaggagagtcatatcacctaggtgcttcctagaaatatgtcacagtgtaatatgagggcagaatccaggcagaagacccacatcacttgggggctgggtcctgagatatgtcacaagccactcttaggaaaagcccagacaagagaattacattacctcagtgcaggttctctgcttaaaccacaataatacatgtgggtagagtccaaggagggagtcccttcacctaggtgataggcccagatatatgtcaaaatgttttctatgaagcatagtactggcaaatgagtaccatcacctTTGCCCCGGCCCAGAATTTTGCCACTCTTCAGGTTGGCGAGGCTGAAGCAGGAAAGTGAAAAACCTACGTGAtaggcccagagatatgttataatgtcctcctttgggtatggctctggtgaaagaatactatcatctgtttgcctgaccttgtaatatgtcactatcctttatctgtgtagggcccattccagagaggagagtaacaacacctATGAGGGGAACAcagaaataagtctcaataatttttgaaggcatggaacagcaagaatgtaacatcaattggatgttagatccagggttatgtcacaatacttactgttagaaaagcccaggtaggaaagtcacataacctcaaggttggcaaaggtagatatcacaatcccatatatgagctggaataaatctggagagttaaattacACAGGCTCTTGGCAAAGATTTATATCACAATCACATTATCAGAAAATTCCAAAGATGAGATTTACAGTACCACACGTATCCTGTTTGTATGTGTGAcagttggttttatgcatgtgaaatgatgactgtacttactgtgagctgggtttacaaacaagactcagaattttaaatgtgtgctgagccttgctttgactctgtctgtataaaccaaagactttgtaaaatatgtatgaatgttatattatttcatgactttgtacatgaaggtgatgaaggacatcacatatgtccctaaacttagttgtaagagtcaaaatatcctctattggttaaccccacgtatgagagtcattatcatgcttgtgagccatgcctatatatatgttaccTTATATGTTATATTAATATGTTATATTTtgctggtacctgtcatgaaactgtctgtaccaccaaaggaggttataaattatgagttagtgctgtaaagtcctgtgagctttgtagcaatatgcaaatcaggacattaactattgtgctaagtctaatgatgaa-ggcaaaaatgtcccctgctggctgaatcccaggttaagtttgaccatcattactgtgaacggaagtcaagtataggtaatagtcccatatgtgggcaaaaaactaggcaggagggtactatcacttgggtggtgtaccaagcagtgtgtcacaatgccctcttgaggcagagtataggaattagagtcacattaactgggtgatggactcagcaatatgacaccatcccacatgtggAAAAAAACTGCTAAGTTATCAGAGCCAAAATACTATGTAATGGGCCTAAGATATAACAAAATACCATCTGTGGCTCCTGCACAGGCATGAGCATCACATTTTCAGGTTgctgagcccagtaatatgccctaattttctctatgtgcaggatgcagataaaagagtaacactgcatgctgagccctccaatacatgaaaacttgtgtttgtgggcatggtttgagaaaaaaaaaa-ggtgaatcaaataaactgagtgctaggctcagcaatatgtcacaatcctcccattgtaaagaccaggtaggagaaaagagtaacttcactaatatcatgggctcatagatatatcccagtgtcccctataggaaggttccaggcagaaaaggaaagtcatattgcctaggtgcttccctagatacatgtcacaatctcatgagtgggtagaaacagacagaaaagctacaacacctgggtgcatcctgatgtaatgtgtcaccatacccaatgtaaacagattttaagattaaaaaaaaaaagcagaatcacaacacctgggtgctgggctcagcagtatgtaatagttctctttctgggcagcgtcaaggaaaaagagtagagtcatgtcacctaggatttgcactcagtggcatgtcacaatttcttcagcaggcagaatccaggcaggagaggagagtcacattacctagatgctacatctatcgatatgtcatagtgttccctgtaggtagtacactggcaggagagacacTGGGGTCTTCAGCCAACAATGCAATAAAAACCACACGAGGAAGAAACCCAACAAATTGATGACAGCCAAAAAACCTACAGAAtgggccaaagatatttcaaaataccttttgtggctctggcacaagccaaagagtcacatcattagggagcagggtgaagcaatatgccataattccctctttattaatgaccaaggcagaaaagaaacagcatctggattctgggcgctgaaatatacagcaaaagtcctgtttgtgggcattgttcagcaacaagacaggtgtcagtttacctaagtgctgcagctggactcctcagtatattacagtcctgccattgtaaaggctaagatagaagaagagagtcttatcacttaggtcatgggctcagacataaggccaagctagcagtaagcagggctcaggcagaaaaaacgagttatatcacctaggtgcttatttaggtatatgccacaattttatatgtgggtagaaaccaggctgaagagctacatcacctggcccaggtacctgagatattcacaagtccctcttaaaaaaattacccaggcaagagagttatgccaccAAAGAGCAGGATTCATCCTtatatcgcaatgcttcatgtaggcaaggccaagccgtaagtcacgtcaccaaggagatagtcccagagataagtcacaaagccttccttaaagcatgaccctgtcagaagagtaccatcaactcagtgcctggcgtagaattatgccactattcaagtaggaaattccaaaacagaacagccatataacttacatgatatgccctgtgatatgtcaaaatgtcatatcttggaaatggctcttgcaaaagaatatcatcacctgtgtgtatggcctaggaatatgtcactattttgccctgtgtgcagggcccattccagaaaatagttatgtctcataactgagggacacagtggtatgtcacaatcatgtctgtgggaatggtgcagccaagaatgtaacatcacctgtgtgctggatccagtgatgtcacaatacttactgagagcagggcccaagaagaacaatcacatcacttcaaggttgaccaagttaaatatcaaaattccatttgtaggctcgcacctgtctgaagagtgaaatcacacaggtGTTTGGCAAA------TATCACAGTCACAATGGAAGATAATTCTAGGGCTTAGATGTATAATACCATGTAAGTCCTATATTCATGTAGGAGAATTGCcttcatccatctgtgatggagaaagcctttagtgtcagctgggtgtgcataagagacttacaattttctctgtgtgctagaccctgttatgacactctctatacaatgcaagagtgttataaaatatgtgtgagtgttttaatcttctttgacatttttaccagaaggagatcctggacatcactcatgtccctcaaccttgttataaaagtggccttattggctgggtcaacatatgggagtcattatcatgcctcttaactgtgcctaggaatatgccacatccccgctgtgattataaaacaggcgggacaaacacatcacctaaatcctaagccacaaatatttcaatattctctttgttggcagggccgtaagagaaatatcacaaaacttgtgggctatgcatagctttaaggtgtaatgtcccttgtggaaagtgtccaggcaggagaggagagacataccacataaaggatggcccacagatatatgacaatgcctcctgttgaaaaggcttaggcaagaggatcatgtaatttgtatgtaaggcttagaaatggtacattattcactggaagcagggtttacgcaggagagaagagtcacataaccaagattattgattcagagatatgttaaaatcccatctgaggacagtgttaagacatgagaatcaaatcactgaggttttttgtccaggtttatgtcaaaatgacatgtgggggctgaaactaggaagGGTTATTAAATCACTCAGGATATGGGGACAGGTAAACTCACAATAACCCCTGTGGAAAGATTCAGAGatgagtgtcaccatcctgcgtatcctggctccaggtacaagagtcattattaggctttttatctggtctcagctatatggcactatataacccatgggttggaagaagaaaggaaagcctcatcacctgagtgggtactggtacagtgaaatgttacaattctccttgtgagcaggatattggtagaagattcacatcacctggatgcaggtttcagtaatatatctaaatcctgcctgtgagtaggactcaggcagtgaaggagacaaactctacctaggctgttggtcaggatatgttgcagagtggcccctatgtgcaggaccaaggcaggagaacgatctcacctgggtgcttggttctgcaatatgtcgcaatctctgtgctggtcagggcccagaaaaaatagaagacacatcaccaaggtgctaagacaagtgatatgttacaaagctttctgttgggagaatcctctccaagaagagtcacatcacctgtgttgaataaccagttatgagtcacagtgcaccctaagtgcaaggccaaggcagtagaaaaaagtcatatAATTTATGTAATGGACCTAGATAAAAGCCATAGTGCTTTTTGGAATCAGTGTTAAGGTCAAGATTTTACATCAGCTGGGTGTTGGTTTAAGTGGTCTGTAAAAGTGCCCTTTGTCACATTGCCAAAGAAAGTGTTATTTTTTGCTTAGGTGCTTGGTGCACCTATGTCACAATTTCAACTGTGTTCTGGGCCTAGAAATGATAGTCAAAGTACTCAGATGCTGGGTAAGGTCATACTTTTCAATTGTATCCTTGAAAACGTTCAGAAATAAGTTTCACAGTCCCACACAAGTCCTGGTTTTTGGTATGAGAGTTAACACGTCCTATGAGTTGGCTTGAAGGGTAACAGAAGTCACAGTCTCAACAATGAGCAAGATCCATGTATCGTAGCCCAAATCCTACTTGAAGATTGTGTTCCAGTAGAAGAGTCAAATCACCAAACGTCTGATGAATCACGGTTGAAATgtcacaaaaccacctgtggatcagatttatgtatgagaatcacaacttcaatatttgactgcttatgtgtgtaagatttagtacctcactggtaggctctgttcatgtgtaagaaatacaattgtgtcagctaggtgtacatccaaaagtcagaatactacctggttgcaggtgcctctaatgatactctttgtatccctcaggctttatatggtatgcctggtagcatacttttctgtcagttcctacaggtgggaaatctaggacttGTCAAGCAATATGTAACAATGCATTCTCTAGAAATGAGGGTTACCTTAACTGGGTACTGGCCCAGCAATATGACAAAATCCCAAATATAGAAAAAGTAAACCCACCCAAATAATGAGAGCACAATCACTCACAGAGTGTGCACAGGGTATATAAAAATGCT----GTTTCTCTGACACATGCAAGACAGTTACATCATCAGGATTGTGGTGtgggcagcaataggccataattatctctttatgcctgacctaggcagaaaaggaatatcatctgagtgctgggccctgcaatgcatcaaaattcattttcttgggcattgcttgggacaaaaaacagtgtcatattacctaagcattgggcttagcaatatgtcacataactccatttcaaaggctggcagaacaagagtcacatcacttatgagtcagactcacatatatggcttaatgtcccaagtaggtagggctcaggcagaaaataagagtcatatcacctaagtccttctctccttatatgaaaaaatctaacatgtgaggtgaagccaggcagaggagtcacatcaacttgatggtggaacctaagatatgtctcaaggctcccttaggacagtacccaggcaagagtgttacagcaaataagtgcatgttctgcccttatgtaacaatgccacatgtggatagggcctaagcagggagtcacatcacctaggtgataagcccagagatatgtcacaatgtcgtccttgaggcatggcctcaaggaagggctgaaagactatcactacctgtttgcttagcctagcaatatgtcacaatctaggtaagcaggacccaagcaggagagcaatatcacctatgtgataggcccacagatttttcacatttccctctttatgacatggccctagccaaagagtactgtcatctgtgtgcctggcccagccatatgtcactattccccactgtgtgcaaggtccattct---gaggagagttacatcacctaggtggttgacacagaaatatgtcacaatgatttctgtgggcatggttcaggcaATTCTTACTGAGAGTAGGGCCCATGCAGGAGGGTCGAATCACCTAAAGATTGTCCCACATTGATTTCAAAATAACGTAACTGGGTTGGAAAGAGTCAGAGAGTCAAATCAGACAAATGCTCAGAAAATATTTACATCACAATCACACTGGCAGAAAATTCCCAGGATAAGATGAACAATACCACACATGTTCTGTTTTCATTAGTGAcaattggctttatatatgtgagatggtgacagtccttactgtcagttgggtgttcatatgagactcacaattt-acctttctgacaggttctgttatgacactttctatacaagacaaagccttttccatatcacttatactgttataatcttccatgacctttttaccataaagagatttaatcacttgtgtttctaaaacaagttaagagagtcaaaattactcctatttggtggagggagtctacatatgacagtcattatcatgcctgtgaactTTTCTTAGGTATATGTCCCAATTTACTCTG--GTAATGAAACAGGCATGAGATCCATATAATCTAAATGCTGTGGCAGAAATCTTCcaatattcttttttggcaaatttctagaagaaaaatcacataactttggggctacgcccgaatgtatgagacaacaccccttgtgggcagtgtttgacagaagagGAGAGAAATATTAAATAAATGGTAGGTTCAGAGATAAGTTATAGTGGTAACTTGTTGAAAGGACCAGGCAAGAAAATCATATCATTTAAATGCAGTCCTTAGAAATACTACAATCTCCAGTGGAAGTAGAATCCAGGCGGGACATGCTAGTGAGGcacctagattgagggtccagagacatgttacaaagcttcctgaagatactgttaagccaggagagtcaaatcaccaaagtgcttagctgagatatatgtccaaatctcaattgtgtgctgcacctcggcagGATTACTAAATCACTCAGGGGATGGGCAAAAGTATATGTCACTATAACACTAGTGGAAAATTCCAGGAATAGGAGTCACCATCATGCCTATGACCTGGCTCTAGGTTTAAGAGTCATGATTAGTCCTCTTATctgatctcagttatatgggacaatatcccttgtgagcgcagaggaagcaaaatatcacatcacctaggtggatgttggtccagtgagatgtcacaatcatcgtgggcagaattctggaagaagggtcacatcacctggatgctggtttaactgacttagcaaaattccccttttgggctgggcttagaaaggagaggggactcacttcacctaggcaattggtgtacatatgtgtcacaatggccactgtgtgcaggacaaatgtttggaagagatcacaacttggtgctggatttagccatatgtcacaatctcccttgtggtcagcgcagggcaagagaggaaaaacatcacctaggtgctgtgctgagccaagttatgtgttacaaagctttctgatggcaaaacccaaaatgcagtcacatcacttggcagcagtaccctgttatgtgtaacaatgcaccattaatgcagggccaagggattagaattggataacatcacttacatgatgaacccagacataagccacagtgctttttataggcagggattaggcaaataattcacatcacctgggagatggtcctagttgacatgtaaaagggccttttttatataggcccaagAACCTATGCTTAGGTGTATGGTCCAAGTAGATCACAATTTCATCTGTGGTCATGGCCTAAAAAAACCAGTCAGATTATTCAGGAGCTGGGATAACTGTTATGTCCTAATCACACACTAGACGATATTCAGAAATAAGTTTCACAGTCCCACACAACTCctggctttgtgtatgtgagttaacacctcctgtgagttgggtcaaagcagaggagtcccagtctcaaaaactggcaagatccatgtataagatgcccaatcccacttgaagattgtgttccagtaggggagtcacagcctcacaggtgtgcagaatcatgcacaaccaaatcactcatgaatcaggtccgtgtataagagaaataatttcaACCTTAAATTGCTCATTTGtgtgagatttagtaccttatttgtagataatattcttgtgagaaaatgacaatcatgccagccaggtgtgtatccaagagtcacaatcacacctggttagcgttccctgttatgacagtttttgtaccactcaggctttatatgatatgcctgagtgtcataatcctttgtgaactttatacaattaggtgactcatttctttacttatgaccatgaagctgactatgagagtcaaattatcgctcccttctgggtaatggaaagataattaaatttgtgcctgtaagctgaacccagatgcatgtcaaagtttcccctgagggcagaaacaaagcagcatagtcacgttacctggaatctgagcacagaatacattataatctccttcacatgcaagccaagtcagaagagtcatgtcaAATTGTAACAACCTCAaggaatatggcaccatgtcaactgtagacatggttgaagaaaaaaaagtcacaccatgtaggtgcttagctcagcaatatgtaataatttcctcttttggctgattccagaataaagaggagagttacgttacctaggttttgcactcagtagtatgtcacaattccttttgtgagcagaacctaggcaagagatgagagtcacatttcctagatgctatgaccagcaatgtcacaatgtgccttggggcaaaagcaaaggaaaaatatgcaaatcatctaactgataggctcagagaaatgtgataatatcccttgctatcagggcccaggcagaaaagtcacatTTTTATGACTCTTACTCAATGATATGCCAAAATACACACATGGGAAACAATGTAAGCACAAGTTTTAACACATGGGTACTTGGCCCAGTGATATGACACAATATCCTAATTtttgtttgtttgtttgtttgagacagagtcttgctctgtcacccaggctggagtgcagtggcatgatctcagctcactgcaagctccgcatcccgggctcatgccattctcctgcctcagcctcccgagtagctgggactacaggcacccaccaccatgcctggctaagtttttgtatttttagtagagacagagtttcaccatgttagccttgatctcctcacattgtgatctgccctccttggcctcccaaagtgctgggattacaggcctgagccaccacactcagccCAATATCCTAAGTTTtgagagtgacacttttaactgttagcttggggtctataacaaagtcacacggtcacatgtgtactgggacaccaaatgacactgtctacaacatccaagggcttcatatggcatgaattatatttgcaaacttctctgaggcccatatgcttgtatgaactcagaatcttatatattgccttaaattcaggtacaatagtcaaaatctctcatctgggctacattcaggaaggagaaccatttttatgcctgtgaggtgggtccaaaaataagtcacgatcgcacctgaggccagatgcacatgtgagagtcacagttccatttttgtactgttttctcgtgttaaacttagtaactcaacagtatactttgtaattgtgggatggtgacaattttactttcacctgggtgtgcaactgagagtcaaaattttaactttttgctgggccttgttatgaaactctctgtaccacccataaagtttatacaaaaatgaattatttttgtaaacttccatgagctttgtacaaatatgcaacccagaattttttctattgccataagcctagtgatgagaggcaaaatatcttctattggctgaatcccaatataggtttgatcatcatgcctgtgaactgagcagggtatgttccataatcccattagtgggcaaaaagttagaaaaagagtaacatcacttaggtgatgtggcaatcaacacgtcacagtgttccctctaggcagaatctaggaaggagggtcacattaactgggtgctggaaccagcaatatgtcaATTCCACATGGTGAAAAACATAAAAAAGTGATGAGAGCCAAAACACTTACGAATAAGCCAAAGATATTTCAAAATACTCTCTGTGGCTCTGGCAtaggcaggacagaactgcagtgaaagagttatattaccttggtgcaggtttaacttttatgtcacaatgatctatacaggtgaggcccaagtattcagtcacatcacctaggtgataagcccagagatatgtcacaaggacctccttgaaatatagccctggcagaaagtatcattacctgtgttcctgatctaccaatatgtcaccccatcctctgtgctcagggcaccttccagagaaaggagttacatcacctaagtggtgaacacagtaatatgtcacaatgatatctgtgggtgtggtccaggcaagaatgtaacatcatctggattttagatccagtgatatgtcattatccttactgagaaaagggaccaggcaggagaatcacatcacctagatattggatcAGGATGAGGTAGAGATTATAATCCCATATATGTGCTAGAACCTGTCTGGAGAGTCAAATCACACAGATGCTTGGCAAAGATATGAACGACATTCACACTTGGAGGATATTGCAGAGATGAGATTTACAATAACATACATGTCCTGTTTTCATGTTTCAcagtaggcttcatatttatgagatgcagacaatacttcctgtcagctgggtatgtatatgagactcccaatttcatcttttggctgggttttgttatggcattatctgcacaagccaaaggttgtaaaatatctcaggctgctataatcttctatgaactttttaccagaaagatatctgagacatcacttgcattgctaaaccaagttacatgagtcaaacttactcctatttcaggggtccacatatgagtcattatcatgcctgtgagctgtgcctagctatttgtcaaatgttactctgtagtaatgaaacaggcatgacagtcacataacctaaatgctgagaccgaaatgttccaatattctctttgtaggcaggttcctcacagaaaaatcgcataactttgggg-tctatgcccaactctatggcacagtgtctcttgtgggtaatgtcaggcagaagaagagagtcatatcacctaaatgataggcccacagatatgttacaatgccacctgttgaaagggctaggcagGTATCATTTATAATTATAGTCATTTTgtgtcttattgtagctttgatttgcatttttctaataataatgttgagcatctttgcacacgtttggccatttccatgtcttctttggagaaatgttacttggtgtctcttgcctattactaaattttctgttatttttgctttaagtttcttatatattctttatatttttccattgccatatgtatattttgcaagtatattctcccacactgtaagttgtcccttcactctgttaatttatttttgctatgtaattattattatt---ttttttagaatctggtaattttatttgtctgcttttgtttttcttgcctgttcttttgaggtcttatttaaattttttttcctgtcctatttggtaaagaatttctctatgttttattcaaatagttttatacatttgagtttacatttcaatcttctacttatttttatttaaattattttaatatggtaacaggtaggaacctagttgtattcctctgtatttaaataatcaattttcccaataccattcattgaaaagattgtcttttcttaaatgtgtattctgaaccactcaaaaattacttggctctaggtttatgaattttattactgggatcactggatactttggtctatgtgtctgttttctatgccattatcatgctgttttgcttgttatagctttgcagtatgttttgaattcaggtggtttgatgttgtcagctttgttcttttttcacaggattactttagctatttcaagagtttgtttgtttgtttgttttggttccacataaattttgtgcctctttatttcatttctatacaaaaatattcatggtatttttagagagtttgcatagaatctgtagatttcttgtgtagcatagctatcctacctatattttttataactcatgagaaaaatatctattttttttacttttttaccaatgttttataatttattgtgtagagactttttctctttttaattaagtctacttctacacacctttattttttATTCtagataaacaaaaagtatttggaaaattttacatgcctttgtaattaaaacaagttaacaaattaggtatagatgatatgtacttcaacacagctaaagcaaaatatgacaaatcaatagcAGTTATtgttactggtgggtcttctttattctcagagctccaaagatggtagtaggctgctcccaacatgaggcagacagctccgaagatgacagcaagctttttcttctctgacctggggtcttggcctcagggattccaaggaatgg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q panTro2.chrY                                  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i panTro2.chrY         C 0 C 0
e tetNig2.chr5         3743466    14 + 13390619 I
e petMar1.Contig6813     17462     0 +    30809 I
e xenTro2.scaffold_916  103508 47921 -   291918 T

a score=95761.000000
s hg19.chrY             7761612 460 +  59373566 ATTTTGAGTGATGAAGACAGGAGATAGCCAAGGGACCTATTCTCTTTTTGAGtgatggagacaagagatagtcacaggtcctggccaaaactccatcttcaagcttaaaacagcctgaagcctgaaaaactggatagcttgtttc-----acactcacccttttctaatctcttctcactgagtaatatctacctctacattgggaaaaggaagtggagacatttaaattcacaccttttggcagggcaggagcctggactttttcgttggcatgtggtgaactagcgttcatcaacctgtgaaa-aggggcctattaaaaggagtcccactcactttgctgacaggtttctttctctttgtttgtttgtatttttttctttttgcccaataaattttattcttcccccttcagtgtgtcctttagcctattaactcctgatcatgtgacaagatcctggttttag
s panTro2.chrY           614870 460 +  23952694 ATTTTGAGTGATGAAGACAGGAGATAGCCAAGGGACCTATTCTCTTTTTGAGtgatggagacaagaaatagtcacaggtactggccaaaactccgtcttcaagcttaaaacagcctgaagcctaaaaaactgggtagcttgtttc-----acactcacccttttctaatctcttctcactgagtaatatctacctctacattgggaaaaggaagtggagacatttaaattcacaccttttggcagggcaggagcctggactctttcgttggcatgtggtgaactagcattcatcaacctgtgaaa-aggggcctgttaaaaggagtcccactcactttgctgacaggtttctttctctttgtttgtttgtatttttttctttttgcccagtgaactttattcttcccccttcagtgtgtcttttagcctattcactcctgatcatgtgacaagatcctggttttag
q panTro2.chrY                                  0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-----00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23117121 449 + 157549271 attTTGAGTGATAGAGACAGTAGATAGCCAAGGGACCTTTTCTCATTTTGAGtgacagagacaggagacagtcaaaggtcctgggcgaaactctgccttcaagcctaaaacagcctgaaggctgaaaaactggactgctggtttcggatgaagcctgccctttcctgaatgtttctctctgaataatgcccacctgtgcactggggaaacaagttggagccatagaaattcacatcttttggcaggggaggagcctggactcttcagttgctatgtggtgacctggtgttcatcaatatgtgaggtgggggcccgttaacaggagtccctctcactttgctgacagttttttttc-----------------cttttcctttttgcccaataaactttactcctcacccttcagtatgtctgttagcctattagttcctgttcatgtgataagatcctagttttag
q ponAbe2.chr7                                  4487255436454545384565655212265586112187736545784665363745472746445373356684636454785555851845484656655515688585561358478535688998456548763856995887579955366697898934696477988969458848975889979879689687999689498889299959979699979996939799849698976989999996899896999998998999989899999999999998999999999999999999999999999999999999999999999999999999999999999-----------------9999999999999979998999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         N 0 I 11
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=4681.000000
s hg19.chrY             7762072 53 +  59373566 ctTTCCaaaaaacaaataataataaaaaaaaacaaaataaagaaaagaaagaa
s panTro2.chrY           615330 53 +  23952694 ctTTCCaaaaaacaaataataattaaaaaaaacaaaataaagaaaagaaagaa
q panTro2.chrY                                 00000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e ponAbe2.chr7         23117570 11 + 157549271 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=67869.000000
s hg19.chrY             7762125 356 +  59373566 aaaaaCTTCTAAAACATTTCAGTGTCTAGATGTggggcttgaggaggggtaataggtataccaa--aaaaaaaaaaattatattttgtttataagacttttcatccttggatttctcctgaggctagaggaaac--tgcaccacctcaccccacaagccccaggCACATCC--CATGGAGAGATGTATGGTGGC-CCTCACCCTTATCTCCTCTGGGATGGAAAAtgccaagcattcatggtgtctaccccttcactggccaagggattcagtctcctctaaaagcaatt--gtttttctctctgttgataaaaaccatttgcagaagaatgaatattttcttcccTCCCCTACACTTTAGACTT
s panTro2.chrY           615383 352 +  23952694 aaaaaCTTGTAAAACATTTCAGTGTCTAGATGTggggcttgaggaggggtaataggtataccaagaaaaaaaaaaaaatctatttcgtttataagacttttcatccttggatttctcctgaggctagaggaaac--tgcaccacctcaccccacaagccccaggcacatcc--catg--------tatggtggc-ccttatccttatctcctctgggatggaaaatgccaagcattcatgttgtctaccccttcactggccaagggattcagtctcctctaaaaacaattatgtttttctctctgttgataaaaaccatttgcaaaagaatgaatattttcttcccTCCCCTACACTTTAGCCTT
q panTro2.chrY                                  00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000000--0000--------000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23117581 358 + 157549271 aaaaagttc--aacaaTTTCGGTGTctcgatgtggggcttgaggaagggtaagatgtaaacc----aaagtatctttttttcctttgcttgtaagccttttcatccttggacttctcccaagggtagaggaaactgtgcaccaccccaccccaacagccccaggcacatgcgggatggacaggtgaatggcggctcctcacccccatctcctctgggctggaaaatgccaggcattcatggtgtcttcccctttaccggccaagggatccagccccatccaataacaattaagtttttccctctgttga-aggaatcatttgcataagaatgaaaatgtttttccctgccctacacttaagcctt
q ponAbe2.chr7                                  999999999--999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999979999999999999999999999999999999999999
i ponAbe2.chr7         I 11 I 15
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=4227.000000
s hg19.chrY             7762481 56 +  59373566 TCATTTTTGTTTTTGTGTCTTTTATTGTTTGTATTGTCTTATGGttgttgtttttc
s panTro2.chrY           615735 53 +  23952694 TCATTTTAGTTTTTGTGTCTTTTATTGTTTGTATTGTCTTAt---tgttgtttttc
q panTro2.chrY                                 000000000000000000000000000000000000000000---00000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e ponAbe2.chr7         23117939 15 + 157549271 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=271950.000000
s hg19.chrY             7762537 1246 +  59373566 ttcacactgtctgcagtttccttttaaataaaagggttttttaat-ttttcttcatagaaaatgttttgctgggataagaccccaacgatcactgcttatattctttgtactgttttaatcgtgaaagggtatttttgaggttgatcttgagctgtggccaatctggcatgctttctatgtgattctctatgattgttagaaaattgtgcagcaggcctccatcttgttttatgcttt-agaaacatgacctgtcaccaggttgtaatgttttattttggcctcttcagttttatgatggtggcccaggtttaattctggcttagggaatgtgtctcttctggtttcacatcagcatgtga-ttttgctatttgcagattctcttccccttcacaaactaccttaaccttttctt----ctctgagcacctggtaaggtatctctgataaagtttgaaagccagaaatactggctacttggtacttcttgcatcaggtaataa-gcatgtaaaaggattttcttaaagagtactcaactcaattaaaagtacatatccaaataataggtatggttaaaagacat----atttttctcttctgggtttttgtttggctggggaaagg-atttttctcagctaactgaattatttttctttatttgggcttgccactctcctgcataaatgagagtccagtaattctatcaggaaaatcgcaaataaaaaacatattggctactgggttttcgtttgccagtctgtgtagttatatatgtgctatgtgagtgacatctataaagaagagctc---taataaattcacttaaagaatgataagaccttggatcaaacattttctgaagggaagataaaagctatatacctttaagttcacatgattttca-tcttagagacataaaaacagccttaaagatgataaaaaaaacaacaa---cacaaatgtcatcaatgtatgagtaggtgcactaaattatgcaggtcagatactaggcttgctaaatattttaaggttataaactgattttttggttttagagaacagttcaactttgctttacaattggtaaggcctgagaacaaatggaattaaccacacccttaa----gctgaaaggagacaaaaccttggctgcacttagtacataataacaacaatttacctggcattacattaaagttaaaattactagaatttgccattacaacatgtaatcaaaaccaatggaaatatatttacaaatgactt
s panTro2.chrY           615788 1255 +  23952694 ttcacactgtctgcagtttccttttaaacaaaagggtcttttaat-ttttcttcatagaaaatgttttgctgggataagaccccaacgatcactgcttatattctttgtagtgttttaatcgtgaaagggtatttttgaggttgatcttgagctgtggccaatctggtatgctttctatgtgattctctatgattgttagaaaattttgcagcaggcctccatcttgttttatgcttt-agaaacatgacctgtcaccaggttgtaatgttttattttggcctcttcagttttatgatggtggcccaggtttaattctggcttagggaatgtgtctcttctggtttcacatcagcatgtgacttttgctatttgcagattctcttccccttcacaaactaccttaacctttttttt---ctctgagcacctggtaaggtatctctgataaagtttgaaagccagaaatactggctactttgtacttcttgcatcaggtaatat-gcatgtaaaaggattttcttaaacagtactcaactcaattaaaagtacatatccaaataataggtatggttaaaagacatttatatttttctcttctgggttcttgtttggctggggaaagg-aattttctcagctaactgaattatttttctttatttgggcttgccactctcctgcataaatgagagtccagtaattctatcaggaaaatcgcaaataaaaaacatattggctactgggttttcgtttgccagtctatgtagttatatatgtgctatgtgagtgacatctataaagaagagctc---taataaattcacttaaagaatgataagaccttggatcaaacattttctgacgggaagataaaagctatatacctttaagttcacatgattttca-tcttagagacataaaaacagccttaaagatgataaaaaaaaaaaaaaaaacacaaatgtcatcaatgtatgagtaggtgcactaaattatgcaggtcagatactaggcttgctaaatattttaaggttataaactgattttttggttttagagaacagttcaactttgctttacaattgataaggcctgagaacaaatggaattaaccacacccttaa----gctgaaaggagacaaaaccttggctgcacttagtacataataacaacaatttacctggcattacattaaagttaaaattactagaatttgccattacaacatgtaatcaaaaccaatggaaatatatttacaaatgactt
q panTro2.chrY                                   000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000---000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000---0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23117954 1245 + 157549271 ttcaccctgtcagcagtttacttttaagcaacaggcttttttcttcttctcttcttagaaaatgttttgctggtctaggacctcaacgatcactgcttatattttttgtagagttttaatagtgaaagggtatttgtgaagtcgatcttgagctgtggccaatctggtatgctttgtatgtcattctctatggttgtcaggaaattttgctgtaggcctctaccttgttttatgttttcaggagcatgacctgtaaccaggtggcaatgttctgttttggtctctgccattttacaatggtagcccaggtttaatcctggcttagggaataagtcccttctggtttcctatcagcatgtaacttttgccatttgcggattctcttccccttcacaaactgccttaatttttttcttttcCACTGAGcacctggtaagttgcctttgataaagtttgaaagccagaaatactggctgcttggcactgctagagtcaggtaataaggaatttaaaaggattttcttaaagagtgctcaacttaattaaaattgcatatccaaattataggtatatttaaaaaacctttatgtttttctcttctgggatcttgttttgctggggaaaggtttttttctcagccaattgaattctt----tttattttgtcttgccactgtaatgcatgcctgagaggccagtaattcaatcaggaaattggcaaataaaaaaccta-tggctactgggttttcttctgcctgtctgtgtagttatgtatgtgttgtgtgtgtgatgtctataaaaaagagctctaataataaatttacttaaagaatgataagcacttggatcaaatattttttgaagggaagaaaaaagctgtgtaccttttagttcacatgactgttactctttgagaaataaaaacagccttaaagattattggcaaaa---------cacaaatgccatcaatatacgagtaggtgaagtaaattatgcaggtcagatactaagtttgctatatgttttaaggttataaactacttttttggttttttagaacagttcaactttgcttcacaattg-taagacctgaagacaaatggaattaaccacacccctaattatgctgaaagcagccaaacccttggctgcacctagcatataatgaaaacaatttacctggttttacattaaagtagaaattgctagaagttaccattgtaacatgtaattgaaaccactggaagtagattta----------
q ponAbe2.chr7                                   9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------
i ponAbe2.chr7         I 15 I 42
e tetNig2.chr5          3743466   14 +  13390619 I
e petMar1.Contig6813      17462    0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=142204.000000
s hg19.chrY             7763783 634 +  59373566 agattataagaagtcatggtaatataaattcttggctaggcttgaacaattgttttgaaatagataaaatgaagttaacagttcaaacaaattgtagaagtattgtaaaactaaatgatgacaaagaaattcttcatgtgaacattaattaaattc-taaaggtattatatggagattttgtaaattaaacattgaaataaaa--acagcacagtagtcttaatgcaataatctgctctttagcataatttttgaagaatt----attaaaagtttctgctttttacatttctaagtcatcgttttggttaaataagttatttatgataatctggaattttatttcataacattaagtgttttaaaccactaacatgtaacatgcttctcaaaatcaatgttt-gttataaaattgtcattctgaatttctggcttttagatgatacagagggcccatggagtatccacaagagaggcaaacaggattatatgacatgattagttacattaaattgacaaaatggtgttcaatattctttagatgatgttttggtgagtaatgctagtacatgttttaaaactgtttgggatttctaaaattctaatatctgaagtatatgctatcaaccacaattaaagtt
s panTro2.chrY           617043 634 +  23952694 agattataagaagtcatggtaatataaattcttgactaggcttgaacaattgttttgaaatagataagatgaagttaacagttcaaacaaattgtagaagtattgtaaaactgaatgatgacaaagaaattcttcatgtgaacattaattaaattc-taaaggtattatatggagattttataaattaaacattgaaataaaa--acagcacagtagtcttaatgcaataatctgctctttagcataatttttgaagaatt----attaaaagtttctgctttttacatttctaagtcatcattttggttaaataagttatttatgataatctggaattttatttcataacattaagtgttttaaaccactaacatgtaacatgcttctcaaaaccaatgttt-gttataaaattgtcattctgaatttctggcttttagatgatacagagggcccatggagtatccacaagagaggcaaacaggattatatgacatgattagttacattaaattgccaaaatggtgttcaatattctttagatgatgttttggtgagtaatgctagtacatgtttcaaaactgtatgggatttctaaaattctaatatctgaagtatatgctatcaaccacaattaaagtt
q panTro2.chrY                                  000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23119241 640 + 157549271 agattgtaagaaggcatggaaatataaattattgcctagagtaaaacaattgttttgaattacacaagataaagctaaaagttcaaacaagttgtagaaggattgtaaaaataaatcttgccaaaaaaattct--gtgtgaacattaattaaattcaaaaaggtattatatgagttttttataaattgagcattgacataaaagcacaacaaggtactcttaaggcactaatctgctctttggcaacatttgtaaagaatttaaaattaaaggtttttgctttttacatttctaagtcatcattttggttaaataagcaatttatggtcatctgaaattttatttcataacatcaagcgttttaaacccctaacatgtaacatccttctcaaaatcaaactctagttacaaaattgtctttcctaattcctggcttttggatgctaaagagggctcctggagtatccacaagagaggtaaataggattatatgacaggtttagttacatagaatcgccaaaatggtgttcaatattctttagatgatactgtggtgaataatactaatacatgttccaaaattgtatgggatttctaaaattctaatgtctgaagtatatgctatcaaccgcaattaaggtt
q ponAbe2.chr7                                  9999999999999999999999999999999999999999990999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         I 42 I 524
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=64638.000000
s hg19.chrY             7764417 717 +  59373566 gttatgttaagttgttggaaccacagaaataaacaatttttttttgtcaaagaaatagccaaaatattttatcaatcatgtttcttactgtaattaccctagacatttgttatacacagatagttcttttcctgttttgatttttttcaaaaaaaggatgaatcagctatagaactttgcacagatgctctcaaatacaggtttctgataactttgtagatttacataaaagttaaattaaagttaaagtcaaattaattaaatttgaagttaaagtaaaattaaagttaaaattaaagattgtgatattagaaaacagaaaaaatgtacaggactcatggagagctaaaatgttcatgattatgaaacaaaacaagagttaactgaacagactggaagaatagagaaccaaaataatctttctcacttttgcttgtaccattaatgatcattgtattgtttatcatagtcaaggaaacatattttgagtttcttatagcctttaatgtttgactaagttgtactcttgtgaccaaaatttagagcatgtttttctctctctgcctggcttctgcacaatttgaaaaatagttgtgactatttttaactttagacaatgtatctatttgcatcagtgccataataataacttttcttttacaacaggacacaactaaaaaaactgattgttttaccaaagccgtgactaaaatggtc
s panTro2.chrY           617677 712 +  23952694 gttatgttaagttgttggaaccacagaaataa-----ttttttttgtcaaagaaatagccaaaatattttgtcaatcatgtttcttactgtaattacccttgacatttgttatacacagatagttcttttcctgttttgatttttttcaaaaaagggatgaatcagctatagaactttgcacagatgctctcaaatacaggtttctgataactttgtagatttacataaaagttaaattaaagttaaagttaaattaattaaatttgaagttaaagtaaaattaaagttaaagttaaagattgtgatattagaaaacagaaaaaatgtacaggactcatggagagctaaagtgttcatgattatgaaacaaaacaagagttaactgaatagactggaagaatagagaaccaaaataatctttctcacttttgcttgtaccattaatgatcattgtattgtttatcatagtcaaggaaacatattttgagtttcttatagcctttaatgtttgactaagttgtactcttgtgaccacaatttagagcatgtttttctctctctgcctggcttctgcacaatttgaaaaatagttgtgactatttttaactttagacaatgtatctatttgcatcagtgccataataataacttttcttttgcaacaggacacaactaaaaaaactgattgttttaccaaagccatgactaaaatggtc
q panTro2.chrY                                  00000000000000000000000000000000-----00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e ponAbe2.chr7         23119881 524 + 157549271 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=328875.000000
s hg19.chrY             7765134 1549 +  59373566 tgctttcctttaaggagtcaagttctacttgcagagccaatgaaagtcccttggaagaactgggcttataccttgtcttcacagtccttgcacaggg-----ttcctgatctgtgg-taagtaaagaatgaaactttctgacaggcccagtagctccaagtttctcttgggatcatagcagga---gattacccaagtcataattaattgatgatacaagccaattgcttggcatgaattttgaaagtcctatcggaaatttcttctggaacagagttccatcaaatctaacataaaagacctacggatacaaaattattcttgctgcactttatgcaaataattaggccctatataagactaaagtttatttcacaaacaaatcagtcctattgtgatttgtcttt-ttaaattagaggactggacagagaaagattatgtatcaaaactcactatgcatttgtcattaaattttaaaaccatgag-tttgaatttttgcccacattttagatcaaccatgcttgttcctgtgaaataacttgcaatcttcaactgcagctcagaagaaacaaaaagggatgagtaatgtaaaagtctggtttaatattctggttctgggcagttatcctgcaaatttttcag-gtagtgaaaataaataggatgcccacccacatcttagcaagt-ttaactattgtcactagttatctgggtttgtcacaagacatttttattttctcttcc-tgtggaaagaggactaaattccacaactttatcttagcattcagctattaataaggagtccgtgcaatcccctgagaaacatttttgtcccaacctcaattcctagcctcaagttgaagtcctaagaaagtatactggagctgagaaacccagaagtagatgattatgggggttaaaattcacagtggaggagagcatgactaattccagtggattaagccaagcctcacatttcatggataaaggtcatgatactatctgttacgtaaatgagatctagtgaactccagaactactgacagcaggggagatatgacatatgtaggtaacagcagatatttccacccccaacaggggtccatgttaacatgagtgaaagctgctttgacatccatgggttgcaccctatcacaatcactgggatttgaggatacaaggatgcaagggggaaagacaacattccttcttc-------tatctctcaacatacactggatatttggtagaaagataaaggaatcaggaataccttct-ctctctttctagatgtgtag----tcattcattttcagtctatattccttttaaatgcatcctaaaattttgggcctcctttgaaaaagtgcttactttttacctttttttctcctctgtcctctgtttatagacaggtattcatgtctttatactacgggacagtcacctcagatgcatcctagaagtttggaatagttaatttcccaaagcttagactggttggcttagcttaggattggactcaggacagaggaacacagaagccagacatgcttgcaaaagggtaaaaa
s panTro2.chrY           618389 1556 +  23952694 tgctttcctttaaggagtcaagttctacttgcagagccaatgaaagtcccttggaagaactgggcttataccttgtcttcacagtccttgcacaggg-----ttcctgatctgtgg-taagtaaagaatgaaactttctgacaggcccagtagctccaagtttctcttgggatcatagcagga---gattacccaagtcataattaattgatgatacaagccaattgcttggcatgaattttgaaagtcctatctgaaatttcttctggaacagagttccatcaaatctaacataaaagacctacggatacaaaattattcttgctgcactttatgcaaataattaggccttatataagactaaagtttatttcacaaacaaatcagtcctattgtgatttgtcttt-ttaaattagaggactggacagagaaagattatatatcaaaacttactatgcatttgtcattaaattttaaaaccatgag-tttgaatttttgcccacattttagatcaaccgtgcttgttcctgtgaaataacttgcaatcttcaactgcagctcagaagaaacaaaaagggatgagtaatgtaaaagtctggtttaatattctggttctgggcagttatcctgcaaatttttcag-gtagtgaaaataaataggatgcccacccacatcttagcaagt-ttaactattgtcactagttatctgggtttgtcacaagacatttttattttctcttcc-tgtggaaagaggactcaattccacaactttatcttagcattcagctattaataaggagtccgtgcaatcccttgagaaacatttttgtcccaacctcaattcctagcctccagttgaagtcctaagaaagtatactggagctgagaaacccagaagtagatgattatgggggttaaaattcacagtggaggagggcatgactaattccagtggattaagccaagcctcacatttcatggataaaggtcatgatactatctgttacgtaaatgagatctagtgaactccagaactactgacagcaggggagatatgacatatgtaggtaacagcagatatttccacccccaacaggggtccatgttaacatgagtgaaagctgctttgacatccatgggttgcaccctatcacaatcactgggatttgaggatacaaggatgcaagggggaaagacaacattccttcttccttcttctatctctcaacatacactggatatttggtagaaagataaaggaatcaagaataccttct-ctctctttctagatgtgtag----tcattcattttcagtctatattccttttaaatgcatcctaaaattttgggcctcctatgaaaaagtgcttactttttacctttttttctcctctgtcctctgtttatagacaggtattcatgtctttatactacgagacagtcacttcagatgcatcctagaagtttggaatagttaatttcccaaagcttagactggttggcttagcttaggattggactcaggacagaagaacacagaagccagacatgcttgcaaaagggtaaaaa
q panTro2.chrY                                   0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-----00000000000000-000000000000000000000000000000000000000000000000000000000000000000---00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000----00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23120405 1535 + 157549271 tgcttccctttatggagtcaagctcaacttgcagagccaataaaagccccttggaaaaactggcctcatacctcatctacatagtccttgtgcagggttccattcctgatccgtggttaagtaaagaatgacactttctgataggcccaggagccccaagtttatcttgggaccacaagaggagaggatcacccaactcataagtatttgatagtacaaacccatggctgggcttgacttcagaaagtcctatctaaaatttcttgtggaacagaattccatcgaagccaatgtaaaagacctatgtaaaaataattattcttgctgcactttatgcaaacaatcaggccaagtataagactaaagtttatttcacaaataactcagtcctatcatgattcgtttttaacagaaaagaggactggat----aaagattatgtttcaaaacttattatacaatagtcattaaattctaaactcattagttttgagtttttgcctacattttagaccaaccctgcttattcctgtgaaccacctggcgatcttcaactgcagctcagaagaaacaaaaagggatgggtaatgtaaaaatctggattaatattctacttctgggcaattattctgcaaatcctgcagagggatggaaataaatagggtgctcatcccaatctcagcaagcattaactgtagccactagttatctgggtgtgtcaaaagacattc---ttttctctcccttgtggaaagatgactcaataccacagcttcatttcagcattcagctcatgataaggagtctatgcaatcccctgagacacatttttgtcccaacctcaattccaagcttcaaaatgaagccttaggaaagaatactggatctgagaaatccacaggcagatgataatggaggttaaaaggcactgtgcaggggagcatgactaattccagccgattaagccaagcctcccatttcatagataaatatcatgctaggatctgtggaataaatgaggtctagtgaactccagaacaactgacagcaggggagatagga----------taagagcaagtatttccaccccc-ctaggcctccctgttaaccagggtggaagctgcttggacactgatggatggcaccctgtcacaatcactggg-cacagggatacaaagatggaaggggaaaagagaacattctttcttc-------tatctgtcaacatac-ccgggtatttgctaggacgaaaaaggaaccagggacacttgctcctctctttctagataagtaaccattcattcatcttcagtctacaccctttttgaatgcatcctgaacccttgggactcctttgaaaacatgttttcctttta--------tcccctctgtcttctctttacagataggtaatcatgtcttcatactatgggatggtcccctcagatgcatccttcaagcttggaagaattaattttccaaaccttagactgggtg-----gcttaggattggactcaagacaaaagaactcagaagcctgacatgctggcaaaagggtaaaag
q ponAbe2.chr7                                   9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------99999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999-------999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--------9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         I 524 I 65
e tetNig2.chr5          3743466   14 +  13390619 I
e petMar1.Contig6813      17462    0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=4669.000000
s hg19.chrY             7766683 65 +  59373566 aaaaaaaaagtttcttttgaagttgtgccttcattgcccttcttcctgtgcaaactggaaaaaat
s panTro2.chrY           619945 62 +  23952694 aaaaat---ttttcttttgaagttgtgctttcgttgcccttcttcctgtgcaaactggaaaaaat
q panTro2.chrY                                 000000---00000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e ponAbe2.chr7         23121940 65 + 157549271 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=101643.000000
s hg19.chrY             7766748 477 +  59373566 atcttggaatttttgcgctgtactttacaccttctccttgtttcattttaatgcatgttttttaataacccagtttgattcttctcacatttaggctaccaaacttctgacactcatgccaccagaggctcagacaa-gtcccctttcactagagacatttaggtagggattttaggaaaaactgactgctggttttccaaaacagtgccccctgttagcaggaagctcttaaaagtggtgtttgtcctgatccttctccttattctaatggcagttagatatacctctttatatggggaaCTTACagagttagaaaacagccaaatggtcctgggtgaaaccccaccttcaagcctaaaacaccataatgactgaaaaatcagactgcttctcctggaggaagccacccttttttcaaccaattcattctgaataatgtccacctccacaatgggggaagtgattggagccatggag
s panTro2.chrY           620007 477 +  23952694 atcttggaatttttgcgctgtactttacaccttctccttgtttcattttaatacatgatttttaataatccagtttgattcttctcacatttaggctaccaaacttctgacactcatgccaccagaggctcagacaa-ggcccctttcactagagacatttagatagggcttttaggaaaaactgactgctggttttccaaaacagtgccccctgttagcaggaagctcttaaaagtggtgtttgtcctgatacttctccttattctaatggcagttagatatacctctttatatggggaaCTTACagagttagaaaacagccaaatggtcctgggtgaaaccccaccttcaagcctaaaacaccataatgactgaaaaatcagactgcttctcctggaggaagccacccttttttcaactgattcattctgaataatgtccacctccacaatgggggaagtgattggagccatggag
q panTro2.chrY                                  00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23122005 470 + 157549271 accttggaatttttgagctttccttgccacctgccccttgtttcgttttaatacatgttttttaataacccagtttgattcttcccaccttcaggctaccaaacttcaaagagtcacacaaccagagccttggacaatggcccctttcacagggaatgcttagataggcctcttagggagatctgactgccatttttccaaaacagtgccccctgtcagcaggaagcagttaaaagtggttttcgttctcatctttattttgattctaacagcagttagacatacttctttagagagggaaataacagagttagaaaacagccaag-ggtcctgggtgaaaccccatcttcaagcctaaaaca-------gcctaaaaaatcagactgctggtcccagatgaagcctgcctttttctaactgattctctctgaataatgtccacctgcacactgggggaaggcagtggagccatggaa
q ponAbe2.chr7                                  99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999-------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         I 65 I 129
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=12855.000000
s hg19.chrY             7767225 151 +  59373566 ccacggagtgttcactcttgttcaaggagaagactggcctctgcagttcttgtgttacagtttagtgttaatctacctggaaggtggggcctcctcctaggactcccactcactttgttgacagtttatgttttcttctttttatcttttt
s panTro2.chrY           620484 145 +  23952694 ccacggagtgttcactcttgttcaaggagaagactggcctctgcagttcttgtgttacagtttagtgt------atctggaaggtggggcctcctcctaggactcccactcactttgttgacagtttatgttttcttcttttaatcttttt
q panTro2.chrY                                  00000000000000000000000000000000000000000000000000000000000000000000------00000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e ponAbe2.chr7         23122475 129 + 157549271 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=202280.000000
s hg19.chrY             7767376 973 +  59373566 acccaatcaactctactcctcatccttcagagtatccctgagcctcatcttccacagtcatgtgagaagaacccaattttgctgaagtgaggagaaagttctgcaaAATGAGGATTGTGAATCCTCATTTATGGTAagctgagtataagcatgtggatttctttctggcttctcttactggtttcaacaattatttttctgtctttatgccatcaccacacaattttgactaatgtaactttgcaatatgtttggaaatACAAAAC-AATTATTCCTCTGAGATTTTTTTT-------AGGTTGTTTTCTTTCTTGTGGTTTTTTTGAGTGT---------TTATAGGGCAATA-TTTGTtggctcactcctgtaaatccagaactttgggaagccaaggtaggtagattgcttgagtccaggagtttgagaccagcctgggaaatatagtgaaaccctgtctcttaaaaaaaaaaaaatacaaaaactttctgagcttactggcgttcacctgcagtttcag-cacttctgaagctgtggtgggagaatcaattgagctttagacttcaaggatacagtgagcaatgattatgacactaca-----gcctgagtgacacagGTAAATATTGATTCAAACATTTTATCATAATTTAGTATTTCTGC-AAAAATTATCATTG------TTTAAAGAGTTCTCACTGATGTGTAGATCACTTTGTATATCATTAATATCTAAA-AATCTTGCATGTTCTAACTCTTGAAAAATAGTATGGTAAAGAATATATCTATTTTTCAAATACATGCAAACATGCTAGtttt-------gttttaacttccagttatattttactgtagtcagaaataatactttttgtgaataccatctgtttaaatatgctaaaaatagtatgctaccttagaagtttgcctattttagaaaaggtgtcatatgcaattagtagtgttatgtattatgctattgttgggtaaagtgttttgtagatTA
s ponAbe2.chr7         23122604 989 + 157549271 acccaatcaactctactcctcatccttcagagtgtctctgagcctaatctttcctagtcatgtgataagaacccaattttgctgaag------gaaagttctgcaacaTAAAGATttggaaccctcatttaagataagcttagtatatgcatgtgggtctctttctggcttc---tatctgtttcaac----atttttctgtctttatgccaacaccacagtattttgatcactgtaaatttgcaatatatttttaaacaaaaaaagaattatgcctctgagtttattatttatttccaggttgtttggctacttgtggtttttttgagtgtttatagaaattatagggcagtattttggtggctcactgttgtgatctcagaactttgggaagccaaggcaggtggattgcttgagcccaggagtttgagaccagcttgggcaatatggtgaaactctgtctct-----acaaaaaa-tacaaaaacttgctgagcctggtggcatgcacctgcaggcccagttacttgtaaggctgaggtgagaaaatcaattgagcttgagaggtcaaggctacactgagccgtgattatgacactgcactgcagcctgggtgacacagctaaatattgactcaaacattttagaatattttaatacttctgcaaaaaagtaccattggtttttttgaaagagatctcattgatttgtagatCATTTCAAATACCATTAACGTCTAAAGAAACTTGCATGTTCTAACTCTTGAAAAATAGTATGCTAAAGAATTTGTCGAGttttcatatatatgcaggcaagctagttttcttttggcttttaacttccagttatatttcattgtagtcagaaataatactttttatgattaccatttgtt----tatgctaaaacttgcattctagcttagaagtttgcctatcttagaatatgtgccatatgcaattagaaatattatttattatgctattgttgggtgaaatgttttgtagatTA
q ponAbe2.chr7                                  999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999999999---9999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----99999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         I 129 I 438
s panTro2.chrY           620629 974 +  23952694 acccaatcaactctactcctcatccttcagagtatccctgagcctcatcttccatagtcatgtgagaagaacccaattttgctgaagtgaggagaaagttctgcaaAATGAGGATTGTGAatcctcatttatggtaagctgagtataagcatgtggatttctttctggcttctcttattggtttcaacaattatttttctgtctttatgccagcaccacacaattttgattaatgtaactttgcaatatgtttggaaatacaaaac-aattattcctctgagattttttt--------aggttgttttcttacttgtggtttttt-gAGTGT---------TTATAGGGCAATA-TTTGTtggctcactcctgtaaacccagaactttgggaagccaaggtaggtagattgcttgagtccaggagtttgagaccagcctgggaaatacagtgaaaccctgtctcttaaaaaaaaaaaa-tacaaaaactttctgagcttactggcgtgaacctgcagtttcag-cacttctgaagctgtggtgggagaatcaattgaactttagacttcaaggatacagtgagcaatgattatgacactatactctagcctgagtgacaaagGTAAATATTGATTCAAACATTTTATCATAATTTAGTATTTCTGC-AAAAATTATGATT-------TTTAAAGAGTTCTCACTGATCTGTAGATCACTTTGTATATCATTAACATCTAAA-AATCTTGCATGTTCTAACTCTTGAAAAATAGTATGGTAAAGAATATATCTATTTTTCAAATACATGCAAACACGCTAGtttt-------gttttaacttccagttatattttactgtagtcagaaataatactttttgtgaataccatctgtttaaatatgctaaaaatagtatgctaccttagaagtttgcctattttagaaaaggtgtcatatgcaattagtagtgttatgtattatgctattgttgggtaaagtgttttgtagatAA
q panTro2.chrY                                  00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000--------000000000000000000000000000-000000---------0000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000-------000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000-------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=41050.000000
s hg19.chrY             7768349 470 +  59373566 ACTTAACATCTCATTTCTCTGTTCAACatttttatttctttgtgcatttgtcatctttattttgtttctctttatttttatttattttcattttttctgttaatttaattta----------tattattTCTCGTTATATTCTCTTCATCTCCAATATACTCCAAGTTGTATCTTGTTTGTAGCAGtttaattttatattgttacttttatttatttctcttcatattccttcatattaatttttcttatttaatttttattttttctttattctgaaaatttttactgcaaattatttcatttctgtttatttcttttttgtatttattgtttatcttaatcttaatttttatctCACTGATTTAATTGCATTTCTCAttatttttctctattttatttcagtttattttatttGTCCTTACATTTTTCACttattttacatttatttttatattttatttctcttgatttttcttatg
s panTro2.chrY           621603 479 +  23952694 ACTTAACATCTTATTTCTCTGTTCAACatttctatttctttgtgcatttgtcatctttattttgtttctctttatttttatttattttcatttttTCTGttaatttaatttaatttagtttaTATTATTTCTCGTT-TATTCTCTTCATCTCCAGTATACTCCAAGTTGTATCTTGTTTGTAGCAGtttaattttatattgctacttttatttatttctcttcatattccttcatattaatttttattatttaatttttattttttctttattctgaaaatttttactgcaaattatttcatttctgtttatttcttttttgtatttattgtttatcttaatcttaatttttatttCACTGATTTAATTGCATTTCTCGttatttttctctattttatttcagtttattttatttGTCCTTACATTTTTCACTTACtttaaatttatttttatattttatttCTCTTGATTTTTCTTATG
q panTro2.chrY                                  0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e ponAbe2.chr7         23123593 438 + 157549271 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=99428.000000
s hg19.chrY             7768819 446 +  59373566 tatttttctatattttgctttgtAAAACAGAAGAGATGAGATATTTTAGATTGGCCCAGCCATAGCAGTCAAGACTCGTGTTTGCTGGGGCTCTCTGACAGCTACTGTACCCTAGGAGTCTTCAATGAAAAGTATGATCAGGGCATCCTAGCAAGACTGCTAAGATCCCTGGACAGATCTTCCATTGCTACAGGCCCATCTAGCATTCAGTGTCATGGGTCATTTCTGCTGCTTTCAGAAGGCCCCTGCAAGCCTCAGTGTTGCTAGGCCAAAGCCCTGACTGCCTCTTTGTTTGTGTCCCAATGGATCCCCCACACATAATCCAGGATCCTGACTGTTCTTTCTTTTTTCCCAGAACAGGGTCACACCCACTCCACTCCACATCAGAGCATATCTAGACCATAAGTGTGTCTTTGTGTTTTTA-AAAAGAGTATCttttttttttg
s ponAbe2.chr7         23124031 430 + 157549271 TATTTTTCTGTATTTTGCTTTGTAAAACAGAAGGGATGAGCTATTTTAGATTGGCCTAGCCATAGTGGTCAAGACTC--GTTTGCTGAGGCTCTCTGGCAGCCACTCTACCCCAGGAGTCTCCAACCTAGGGTATAGTCAGGGCCTCCTAGGAAGATTGCTAAGATCCCTCGGCAGATCTTTCATTGTTACAGGCCCATCTAGCATTCAGCGTCATGGGCCATTTCTGCTGCTTTCTGAAGCCCCCTGGAAGCCCTAGTGTTGCCAGGCCAAGACCCTGACTGCCTC----TTTGCGTCCCAATGGATCCCCCACACATAATCCAGGGCACTGA---------CTTCTTTCCCAGGAGAGGGCCACACCCACTCCACTGCAC--CAGGGCATGTCTGGACCATATGTGTGTCTTTCCTTTGTTATAAAAGAAtttttttgttttttg
q ponAbe2.chr7                                  99999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----9999299999999999999999999999999999999999999---------999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         I 438 I 74
s panTro2.chrY           622082 446 +  23952694 TATTTTTCTATATTTTGCTTTGTAAAACAGAAGAGATGAGATATTTTAGATTGGCTCAGCCATAGCAGTCAAGACTCATGTTTGCTGTGGCTCTCTGACAGCTACTGTACCCTAGGAGTCTTCAATGAAAAGTATGATCAGGGCATCCTAGCAAGACTGCTAAGATCCCTGGACGGATCTTCCATTGCTACAGGCCCATCTAGCATTCAGTGTCATGGGTCATTTCCGCTGCTTTCAGAAGGCCCCTGCAAGCCTCAGTGTTGCTAGGCCAAAGCCCTGACTGCCTCTTTGTTTGTGTCTCAATGGATCCCCCACACATAATCCAGGATCCTGACTGTTCTTTCTTTTTTCCCAGAACGGGGTCACACCCACTCCACTCCACATCAGGGCATATCTAGACCATAAGTGTGTCTTTGTGTTTTTA-AAAAGAGTATCttttttttttg
q panTro2.chrY                                  0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=6249.000000
s hg19.chrY             7769265 66 +  59373566 gacagataattgctttatgattcaggctggagtgcaatgacacgatgtctgttcaatgcaatctct
s panTro2.chrY           622528 66 +  23952694 gacagataattgctttatgattcaggctggagtgcaatgacacgatgtctgttcaatgcaatctct
q panTro2.chrY                                 000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e ponAbe2.chr7         23124461 74 + 157549271 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=319969.000000
s hg19.chrY             7769331 1480 +  59373566 gcctcatggatttaagtgattctcctgcctcagcctcccaagcacctgggattacaagtgcctgtca-------------------------------tttttt-aaatatctagtagagatggtgcttcacca--tttgccaggcttgttttgaactcttgacttcaagtgatccatccttctcggcttccaaaagtgctgggattacaggtgtgagccaccactcccagTTG------------ATTTTTTTT-AATATATGTTCACTTGACATATAACTGATTTATTGTGAAAATATCAGCTTTATTGGTAGATACACATGCAAATTTCTGCAAAAATGCTAATGATGTTAGGAGATG-ACATTTCTACATTTCATCTGATGATTTCATGGTGTTGCTATTTTACTTTTTCCGGTCTTTATCTCTATATTTTCAATGGGAAAATCCTCAATGAAGAATCCTCAGTATGATAGACAAAATGTTGTTTAA-TTGATCATTGATAGACGCAATGAGTTAACTTCTGGTTTTTACTTGGAGTTCTTACAGCTAGGATTAAAAACTCTTGGTTGTATACTCACACGATGAGGAGTTATACTATGCTGTCCTCTTCTATACATTTGTCTGCTGTCACAACTTTTCGAACTTGCCAACGGAAATTGAGGAAAATTGTTTCCCTCAGACTTACTCATTTCCCTTTAGTAAATTTTAAAGTGGTGCATTATTTAGATTTCTTATAAGCTCATAATCACAGAGGCCATATTTGTCAATAGAAAGATTTCTTGCATCAGGATTAAGTAAAGGTGTTTAACAATCATGGCTTATGGTTCCTCCAGAGGCAAAATGGAGCTTAAAAACCATTACTGAAACAAAAAAGTAATAAAAGAAGTTGAGGGCTGCCCAGAGGATAAAGAAAAAAATGCTCCCTTTTACTTCCCAAGTGGTCACTGCTTATTTTGGCATTAATCTTGCTTCTGACCATGATGTGTTTCTTACTGATCTTTCTTGGTATTCCACTGATTGTGCATCT-ATAAAAAGAGGCCTGGATGAAAGTAGTAAAAAGAACAACTGCATCCTTCTATAGCTGATACCTTGTTGAGCTGTGAAGCACATTGAGCAGAGTCTGAAATCCTTCCTCACTATGGGGTAAgttgtgtcaaactcaacaccaattgaaatggcacaaggatcaagatgccaaagaagagactcagaaccagtacatgagatatggacttttagtggaaacttctatagagggcagaaagtacagtgtcaatgggcttaactgaataactgtgcccacttgcaaaaagtctgcagtttgtatagcctttttatctggcacttttttcctgaagaaactttcacctgtcagccttcatttaacaaaaatggaatagcctcaattccatgtgtggcctgtgttccatgtcacaagatgagacagaacagatgctcagacattccttatagataaatagtaatctccaggttgactacaactagactttttagcactggaacta
s ponAbe2.chr7         23124535 1487 + 157549271 gcctcccgggttcaagtgattttcctgcctcagcctcccaagtagctgggattacaggtgtctgccaccacacccagctaactttttttttttttttttttttttgtatttttagtagagacaggatttcaccatgttggccaggctggtttcgaactcctgacctcaggtgatccacccgcctcagccttcacaagtgctaggattacacgtgtgagccactgtgcccagTTGAGAAAAAAAAAAATTTTTTTA------------ACTTGACATGTAACTGACTTATTATGAAAATGTCAGCCTTATGGGTAGATACACATGCAAATATGTGCAAAAATGCTAATCATGTGAGAAAATGAATATTTCTACATTGTATTTAATGATTTCATAGGGTTGCTATTTTACCCTTTCCTGTCTT------TCTATGTTCAATGGGAAAATCCTCAGTGAAGACTCCTCAGTATGACAGACAAAATGTTGTGCAATCTAATCCCTGATAGATGCAGTGAAGTAACTTCTGGTTTTCATTCGGAGCTCTCACAGCTAGGATTAAAAACTCTTAGTTGCAAACTCACATGATGAGGAGTTATAGTATGCTGTCCTCGTCTGCACA-TTGTCTGCCGTCATAATTTTTTCAACTTGCCAAGGGAAAAAGTGGGAAATTGTTTCCCTCAGACCTACTCATCTCCCTTTCATAGGTTTTCAGGTTGTGTATTGTCCAGATTGCTTAGAAGCTCATGATCACAGAGGTCATATTTGTCAAGAGAAAGCTTTATTG---CAGGATTAAGTGAAGGTGTTTACCACTCAGGGCCTACGGTTCCTCCAGAGGCAGGAT-GAACTTAAAAATCATTCCTGAATCCAGAAAGTAATGACAGAAGTTGGGGGCTGCCCACAGGAGAAAG--AAAAATGCTCCCTTTTGCTTTCCAAGTGGTCACTACTTATTCTGGCATTAATCATGCTTCTGACCACGATGTGTTTCTTAGTCATCTTTCTTGGTATTCCACTGATTGTGCATCTAAGGAAAAGAGGCCTGGATGAGAGTGGTAAAGAGAACAACTGCATCGTTCCATAGCTGATGCCTTGGTAAGCTTTGAAGCACACTGAGCAGAGTCTGAAGTCCTTCCTCACTATGGGGTAAgttgtgtcaaattcgactcccatggaaatggcaccaggttcaagatgtcaaagaagagactcagaaccagtgaatgagatacggagttttactggggacttacatagag---agaaggtccagtgtcagtgggcttagcaggataactatgcccacttgcaaaaagcatgcagtttgtatagcatttttatttagtactttttt-ctgaacaacctttcacctgtcagacttcatttaacaaaaaaggaatggcctcaatccc--gtgtggcctgtgttccatgccacaggatgggacggaccagg-gctcagatgtttctcataaataaaaaataatcacgagactggctcctactagactttttag-----------
q ponAbe2.chr7                                   999999099999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------9999999999689999999876999999999999779999999999989999699999499999989979999999999999995783999999699999999999999799999999999999999999999996999999999999999999------999689999999999999899999879999899999999999999999999999999896799999999999979999899999999997999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999974273588999999999999999999999999999999999999999999999999997999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999-----------
i ponAbe2.chr7         I 74 I 8
s panTro2.chrY           622594 1482 +  23952694 gcctcatggattcaagtgattctcctgcctcagcctcccaagcacctgggattacaagtgcctgtca-------------------------------tttttttaaatatttagtagagatggtgcttcacca--tttgccaggcttgttttgaactcttgacttcaagtgatccatccttctcggcttccaaaagtgctgggattacaggtgtgagccaccactcccagTTG------------ATTTTTTTTTAATATATGTTCACTTGACATATAACTGGTTTATTGTGAAAATATCAGCTTTATTGGTAGATACACATGCAAATTTCTGCAAAAATGCTAATGATGTTAGGAGATG-ACATTTCTACATTTCATCTGATGATTTCATGGTGTTGCTATTTTACTTTTTCTGGTCTTTATCTCTATATTTTCAATGGGAAAATCCTCAATGAAGAATCCTCAGTATGATAGACAAAATGTTGTTTAA-CTGATCATTGATAGACGCAATGAGTTAACTTCTGGTTTTTACTTGGAGTTCTTACAGCTAGGATTAAAAACTCTTGGTTGTATACTCACACGATGAGGAGTTATACTATGCTGTCCTCTTCTATACATTTGTCTGCTGTCACAACTTTTCGAACTTGCCAACGGAAATTGAGGAAAATTGTTTCCCTCAGACTTACTCATTTCCCTTTAGTAAATTTTAAAGTGGTGCATTATTTAGATTTCTTATAAGCTCACAATCACAGAGGCCGTATTTGTCAATAGAAAGATTTCTTGCATCAGGATTAAGTAAAGGTGTTTAACAATCATGGCTTATGGTTCCTCCAGAGGCAAAATGGAGCTTAAAAACCATTACTGAAACAAAAAAGTAATAAAAGAAGTTGAGGGCTGCCCAGAGGATAAAGAAAAAAATGCTCCCTTTTACTTCCCAAGTGGTCACTGCTTATTTTGGCATTAATCTTGCTTCTGACCGTGATGTGTTTCTTACTGATCTTTCTTGGTATTCCACTGATTGTGCATCT-ATAAAAAGAGGCCTGGATGAAAGTAGTAAAAAGAACAACTGCATCCTTCTATAGCTGATAGCTTGTTGAGCTGTGAAGCACATTGAGCAGAGTCTGAAATTCTTCCTCACTATGGGATAAgttgtgtcaaactcaacaccaattgaaatggcacaaggatcaagatgccaaagaagagactcagaaccagtacatgagatatggacttttagtggaaacttctatagagggcagaaagtacagtgtcaatgggcttaactgaataaccgtgcccacttgcaaaaagtctgcagtttgtatagcctttttatctggcacttttttcctgaagaaactttcacctgtcagccttcatttaataaaaatggaatagcctcaattccatgtgtggcctgtgttccatgtcataagatgagacagaacagatgctcagacattccttatagataaatagtaatctccaggttgactacaactagactttttagcattggaacta
q panTro2.chrY                                   0000000000000000000000000000000000000000000000000000000000000000000-------------------------------000000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000------------0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466   14 +  13390619 I
e petMar1.Contig6813      17462    0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=339225.000000
s hg19.chrY             7770811 1588 +  59373566 tgaacaatcaaaagcatttatttatgcagggtcagtatccaggtattcccaagtcaacactgtcagttttgtccatcatacaGGCTGGGTCAGGCTGTGGAGTTTCTTCTTCCTGAGATTCTAGATTCAAAATAGTTTTTGCTTTTACTTGAATTTTTGAGTTGACAGGAGTTTATCTAAAAGGCCTGATGTATGTGAACTTTGCAGGTACAGTTGTATAAGTTAATGCGATGACTTTTTAGTTGGTAGAGTTTCTGTCTGTTACAGGTGTGACTGTGTGTTTACAGGTTGCTGAGGTGAC-CTTCTCCAGATTTTCATTAGACCGTGACATTCTGGAGCCCCAGTTCCACTATTTTCCAAGGTGGGACATGCTGAACCAGACCCTGAAATTGTGGTTCAGTGTGACCAGGCTGAGACTGACCTTTAAAAGAAAGAACTGCAAAGTTGGTGTCTTATTTTCCTTGTCATTCCAGTGTATCTTTTGGTAAAGAGACCAGAAAAGACTACTTTGGTATGGAGACCAGAAAAGAGAGAGTATGTGACAGCCCTCCTCATAGAG-TGGTACTATTTATTCATGACTCCAAAGCGTCAAGAAAAGTTGAGAGAACTGTCTTCCTGGCACAGCCTGAGTAGGCTAGAGCACTGTGACCCTTAATACTTAGTTCATGTATTCTTCACAGAAA--TTAAAAAAAATAGTATATGGGGG-TAGAGAAATGGTTGGTACAAATAACAAGTTGCAGGTGAAATAATTGGAGACAGGAAGAGAATGGAATCTGCTTACACCAGTACACATACTGCCTAGGTGCTGCTGAACAGTCAAGTCAGTTCTCTGATTTGAGCCTTGTGTCTTGGAATTAACAGGCCCACTTCTGCTCTGGCCTGAGTGCTAAACTTTTTTGTTCTAGAATCAAATGTGAATTCTGGACTCTGGAATTCCAGTTGCGTTTCACAGGCCAGTGGATTAAGGAGGCCCAAATCAGCCCACAAAAGGGGTTGTGGATGGCTCTACCACAAATGACTGGTTGCTTTTGTGCCTACACTCATGAAGAAGAGGCATCATCTTCCTC-AAGGCAAGCCCAGAGAGATCTGAAGCGTACAGGTGCCAGTGAAGGAAAAAGGTAATGCCTCAGGCCATTGCTTTTGCCCCTCCTGTGTTGTGTCTTTGGAGGCTCTATTTGCTCATCC-AAAAATGGGCAATGAAAGCCCCTCGGTGACTGGCTGCTCACCCCACATTTACCAGGCCACTGCAGAGTGCCCACCCTGCAGCTCTAGGTACATCCTCTGCTTCAAAAAGCTGGGGAAACTCTGGGCTGAGTTAATAGCCCTGAGAGGGTTCTCCCACTCTGGGAGCACTCCTGCCCGCCCCTTTATATCCACGTGACAGCTGAGCATGTCTGCTATATGCCAACCTTATTGTCTGCTTTTGCCAAGCCCAGGGCTTCACTGATTGGCTAGGGGAACGTGCTCACAGAAGCCCAGGTGAACTATCTATACTTTCTCCAATGCACAACCTCATGCAGGTGCCACCCAGGTTTTCTTTTAAATTGTAATCTTAGGGGGTTAGAAGGCACTAAATTATTCACTAATA
s panTro2.chrY           624076 1589 +  23952694 tgaacaatcaaaagcatttatttatgcagggtcagtatccaggtattcccaagtcaaccctgtcagttttgtccatcatacaGGCTGGTTCAGGCTGTGGAGTTTCTTCTTCCTGAGATTCTAGATTCAAAATAGTTTTTGCTTTTACTTGAATTTTTGAGTTGACAGGAGTTTATCTAAAAGGCCTGATGTGTGTGAACTTTGCAGGTACAGTTGTATAAGTTAATACAATGACTTCTTAGTTGGTAGAGTTTCTGTCTGTTACAGGTGTGACTGTGTGTTTACAGGTTGCTGAGGTGAC-CTTCTCCAGATTTTCATTGGACCGTGACATTCTGGAGCCCCAATTCCACTATTTTCCAAGGTGGGACATGCTGAACCAGACCCTGAAATTGTGGTTCAGTGTGACCAGGCTGAGACTGCCCTTTAAAAGAAAGAACTGCAAAGTTGGTGTCTTATTTTCCTTGTCATTCCAGTGTATCTTTTGATAAGGAGACCAGAAAGGACTATTTTGGTATGGAGACCAGAAAAGAGTGAGTATGTGACAGCCCTCCTCATAGAG-TGGTACTATTTATTCATGACTCCTAAGTGTCAAGAAAAGTTGAGAGAACTGTCTTCCTGGCACAGCTTGAGTAGGCTACAGCACTGTGACCCTTAATACTTAGTTCATGTATTCTTCACAGAAA--TAAAAAAAAATCGTATATGGGGGGTAGAGAAATGGTTGGTACAAATAACAAGTTGCAGATGAAATAATTGGAGACAGGAAGAGAATGGAATCTGCTTACACCAGTACACATACTGCCTAGGTGCTGCTGAACAGTCAAGTCAGTTCTCTGATTTGAGCCTTGTGTCTTGGAATTAACAGGCCCACTTCTGCTCTGGCCTGAGTGCTAAACTTTTTTGTTCTAGAATCAAATGTGAATTCTGGACTCTGGAATTCCAGTTGCGTTTCACAGGCCAGTGGATTAAGGAGGCCCAAATCAGCCCACAAAAGGGGCTGTGGATGGCTCTACCACAAGTGACTGGTTGCTTTTGTGCCTACACTCATGAAGAAGAGGCATCTCCTTCCTC-AAGGCAAGCCCAGAGAGATCTGAAGGGTACAGGTGCCAGTGAAGGAAAAAGGTAATGCCTCAGGCCATTGCTTTTGCCCCTCCTGTGTTGTGTCTTTGGAGGCTCTATTTGCTCATCC-AAAAATGGGCAATGAAAGCCCCTCGGTGACTGGCTGCTCACCCCACATTTACCAGGCCACTGCAGAGTGCCCACCCTGCAGCTCTAGGTACATCCTGTGCTTCAAAAAGCTGGGGAAACTCTGGGCTGAGTTAACAGCCCTGAGAGGGTTCTCCCACTCTGGGAGCACTCCTGCCCGCCCCTTTATATCCACATGACAGCTGAGCATGTCTGCTATATGCCAACCTTATTGTCTGCTTTTGCCAAGCCCAGGGCTTCACTGATTGGCTAGGGGAACGTGCTCACAGAAGCCCAGGTGAACTATCTATACTTTCTCCAATGCACAACCTCATGCAGGTGCCACCCAGGTTTTCTTTTAAAGTGTAATCTTAGGGGGTTAGAAGGCACTAAATTATTCACTAATA
q panTro2.chrY                                   0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23126030 1524 + 157549271 tgaacattcagaagcatttttttatacatggtcagtctccaggtatgcccaagtaaatactgtcagttgcatccatcatacaGGCTGGTTCAGGCAGTAGAGGTTCTTCTTCCCGAGACTCTAGATTCAAAAAAGTTTTTGCTTTTTCTTGAATCATTGGGTTGAC---AGTTTA-CTAAAAGGCCTGATGTGTGTGCACATTGCTGGTACAGTTGTCTAAGTCAATGAGATGGCTTCACTGTTGGTAGGGCCTGTTCCTGTTACAGGTGTGACTGGGTGTATACAGGCTGCTGAGGTGCCTCTTCTCTAGACTTTCACTGGACCATAACATTCTGGGGCCCCAGTTCCACTATTTTCCAAGGTGGGACATGCTGAACCAGACCCTGGAATTGTGGTTCAAGGTGACCAGGCTGAGGCTGCTCTTTAAAAGGCAGAACTGCCAGGTC--TGTCTTATTTTCCTTGTCACTCTAATGTATCT---------------------------TTTGGTATGGAGACCAGAATA----GAGTCTGTGACAGCCCTCCTGCTAGGGTTGGTACTATTTATACATGACTCTTAAGTGTCAAGGTAGGTTGAGAGACCTTTCTTCCTGGCACAGCCTGAGTAGGCTAGAGCACTATGACCCTTAATGCTTGATTCATGCAGTCTTCAGAGGAATTTTAAAAACCATAGGATGTGGGGGGCAGAGAAAGAGCTGGTACAAATGACAAGTTGCAGGTGAAATAATTGGAGGCAGGAAGAGAATGGGACCTGCTTGGGACAGTACACACACTGCCTGGGTGCAGCTGAACAGTCAAGCCAGTTTTCTGATTTGGGCCTTGAGCAGTGGGATTAACAGGCCCACTTCTGCTCTGGCCTGGGTCCTAAACACTTTGGTTCTAGAATCAAATGTGAATTCTGGACTCAGGAATTCCAGTTGGGTTTCACAGGCCAGTGGAGTGAGGAGGCCCAGGTGGACCCACAAAAGTGGCTGTGGGTAGGCTTACCACACATGACTGGTTGCTTTTATGCCTACAGTCAC----AAGAGAGTTCTTCTTCCCCAAAGGCAAGCCCAGGGAGATCTGAGGCTCATGGGAGCAAGTGAAGAAAAAAGGTGATGCCTCAGCCCAGTGCTTTTGCCCCTCCTGGCTTGTGGCTTTGGGGGCTCACACTGCTCATCAGAAAAATGGGCAATGAAAGCCTCTCAGTGACTGGCTGCTTATCC--CTTTTACCAGACCACTGCACAGTGCTCACTCTGCAGCTCCAGGTACAGCCTGTGCTTCAAAAAGCTGGGGGATCTCTGGGCTGAGTTCAGGGCCCT--GAGGTTTCTCCCCCTCACGGACTCCTCCTGTCTACCCCTCTGTGCCCACCTGACAGCTCACCATGTCTGCTGTATGCTACCCTTATTGCATGCTCTTTCCAAGCCCATGTCTCCCTGGGTTAGCTTGGGGCACATGCTCACTGAAGCCCAGGTGGCCTGACCATCTTTCCTCCAATGTACAGCCTCAGACAGGTGCCACCCAGGTTTTCTCCTAGAATGTGATCTCAGGGGATC--------------------------
q ponAbe2.chr7                                   9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999899999999999999999999999999999999999997999---999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999---------------------------999999999999999999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999783436479999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--999999999999999994999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998999999999999999999999999999999999999999999999999999999999999999997999999999999999999999999999999--------------------------
i ponAbe2.chr7         I 8 I 10
e tetNig2.chr5          3743466   14 +  13390619 I
e petMar1.Contig6813      17462    0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=19271.000000
s hg19.chrY             7772399 87 +  59373566 AGTCTTCTCTAACTTCTTGACTAATAAATCAATAAGTC----AATGGGAAAAGATGGGTGTGGGCCTTGATATTCTTAATCTCCTTCCTCT
s ponAbe2.chr7         23127564 91 + 157549271 ATTCCACTCTAACTTATTGACTAGTTAATCAATAAGTCACTTAATGTGCCAAGATGGGTGTGGGCCTTGACACCCTTGATCTCCTTCCTCT
q ponAbe2.chr7                                 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7         I 10 C 0
s panTro2.chrY           625665 91 +  23952694 AATCTTCTCTAACTTCTTGACTAATCAATCAATAAGTCACTTAATGGGAAAAGATGGGTGTGGGCCTTGATATTCTTAATCTCCTTCCTCT
q panTro2.chrY                                 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=48569.000000
s hg19.chrY               7772486 226 +  59373566 AGTGGGA---CTGAATTGG-GGTTGTCATCCTGATTTCTTTTTCAAA-AAAGCTAGCAAGTGAGGCGGGACTCAAGG----------TCCAGGAACAGTACCAAACTC---------------CTAGGCTGGAGTCGCGCAGGG-----CCTTCTGAGGTCCCTGCAGATAGGAGGCCTTAGTGGAGGTCCAGCTCCCTTTTCTAGGATGATAAC--------------TATGGACCCTTCCTGAAACACCAAGGAGGGCCTACTCTTTCTGCAA
s panTro2.chrY             625756 226 +  23952694 AGTGGGA---CTGAATTGG-GGTTGTCATCCTGATTTCTTTTTCAAA-AAAGCTAGCAAGTGAGGCAGGACTCAAGG----------TCCAGGAACAGTACCGAACTC---------------CTAGGCTGGAGTCGCGCAGGG-----CCTTCTGAGGTCCCTGCAGATAGGAGGCCTTAGTGGAGGTCCAGCTCCCTTTTCTAGGATGATAAC--------------TATGGACCCTTCCTGAAACACCAAGGAGGGCCTACTCTTTCTGCAA
q panTro2.chrY                                    0000000---000000000-000000000000000000000000000-00000000000000000000000000000----------000000000000000000000---------------000000000000000000000-----000000000000000000000000000000000000000000000000000000000000000000--------------0000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr7           23127655 227 + 157549271 AGTGGGG---CTGCACTGGCGGTTGCCATCCTGATTTCTTGGTGGAA-AAAGCTAGCAGGTGAGGCAGGACTCAAGG----------GCCAGGGACAGGACAGAGCAC---------------CTTGGCTGGCCTCACCCAGGG-----CCCTCTGAGGCTCCTGCAGGCAGGAGGGCTCCATGGAGCCCCAGACCCCTTTTCTAGGATGGTGCC--------------CACAGCCCCTTCCTGGACCTTCAAGAAGGGCCTACTCTTTCTGCAA
q ponAbe2.chr7                                    9999999---9999999999999999999999999999999999999-99999999999999999999999999999----------999999999999999999999---------------999999999999999999999-----999999999999999999999999999999999999999999999999999999999999999999--------------9999999999999999999999999999999999999999999999
i ponAbe2.chr7           C 0 I 43
s myoLuc1.scaffold_25368     4979 244 -      8779 AGTGGGGTATCTGAAGCTG-GCTTATAACCCGAATTTTTTTTTTAAATATAGTCTACGAGTGGCCCGGTGCACAAAAATTTGTGCACTCGGGGGGCATCGCTCAGCCCAGCCTGCCCCCTCTAACAGTCTGGGAGCCCTCACAGGATGTCCTACTGATGTCCCTGTGAGGAGCGGGCCTAAGCCGAAGTCTGGCCTCCCTCTGT-GGAAGGCAACTGGCCAATCAGGTATATAGATACTTTCTGAA-----------------------------
q myoLuc1.scaffold_25368                          9999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999-----------------------------
i myoLuc1.scaffold_25368 N 0 N 0
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_916     103508 47921 -    291918 T

a score=5833.000000
s hg19.chrY             7772712 85 +  59373566 ATTGCAATCTCTGGTTTCTGAGGGGTGAGACtgtgtgtatgtgtgtatgtgtgtgtatgtgtgtgtatgtgtgtgtgtgagtgtg
s panTro2.chrY           625982 75 +  23952694 ATTGCAATCTCTGGTTTCTGAGGGGTGAGATtgtgtgtatgtgtgtatgtgtgtgtgtgtgtgtgagtgt----------gtgtg
q panTro2.chrY                                 0000000000000000000000000000000000000000000000000000000000000000000000----------00000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e ponAbe2.chr7         23127882 43 + 157549271 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=6939.000000
s hg19.chrY             7772797 45 +  59373566 tgtgGACATGGCCTTCTGCTTCATTTCCAGGGGTTGTTTCCCTAG
s panTro2.chrY           626057 44 +  23952694 tgtgGACATGGCCTTCTGCTTCATTTCCAGGGG-TGTTTCCCTAG
q panTro2.chrY                                 000000000000000000000000000000000-00000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23127925 28 + 157549271 TGTGGACATGGCCTTCTGCTTCATTTCC-----------------
q ponAbe2.chr7                                 9999999999999999999999899999-----------------
i ponAbe2.chr7         I 43 I 2
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=20794.000000
s hg19.chrY             7772842 96 +  59373566 AAGAAATTCCTAGGGAATCTTGAGACTGTGCTGGAGGTTGTCATACTGCCAAAGTCAGTAAGAGTGTCTCAAGGCTATAATTAATA-TGTTTTCTGC
s panTro2.chrY           626101 96 +  23952694 AAGAAATTCCTAGGGAATCTTGAGACTGTGCTGGAGGTTGTCATACTGCCAAAGTCAGTAAGAGTGTCTCAAGGCTATAATTAATA-TGTTTTCTGC
q panTro2.chrY                                 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23127955 95 + 157549271 AAGAAATGCCTAGGGAATCCTGGGCCTGTGCTGGAGGTTCTCTAAGTGCCAAAGTCAGTAAGA--ATCTCAAGAATATAATTAATAGTATTTTCTGC
q ponAbe2.chr7                                 998999999999899997999999999999999996999999999899897999999789989--89999899989989999999999999999999
i ponAbe2.chr7         I 2 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=-3121.000000
s hg19.chrY             7772938 133 +  59373566 ACATTATTTTGTCAAGATTACTTTTGCCAAATAATGTGTAAAAAA------AAGTT---GTTTATCCTTTAC-------ATTATTT--TAATTAGGTCATCAAACAAACCTTTTA--------------TTTTC--TTCAAATTTATTTTCAAGACACTTA--TTTAAT---
s ponAbe2.chr7         23128050 108 + 157549271 ACATTACTATCTCAGGGTTACTTTTGCCCAA-AATGTGTAAAACAAATATTAAGAT---TTTTATCCTTTAC-------ATTATCT--TAATTAGGTCATCATACAAACCTTTTA--------------TTTTC--T-----------------------------------
q ponAbe2.chr7                                  7999999999999759999999999999999-999989899999699999899892---9999889989999-------6989998--988986556766958996998699989--------------99997--7-----------------------------------
i ponAbe2.chr7         C 0 I 241
s panTro2.chrY           626197 133 +  23952694 ACATTATTTTGTCAAGATTACTTTTGCCAAATAATGTGTAAAAGA------AAGTT---GTTTATCCTTTAC-------ATTATTT--TAATTAGGGCATCAAACAAACCTTTTA--------------TTTTC--TTCAAATTTATTTTCATGACACTTA--TTTAAT---
q panTro2.chrY                                  000000000000000000000000000000000000000000000------00000---0000000000000-------0000000--000000000000000000000000000--------------00000--0000000000000000000000000--000000---
i panTro2.chrY         C 0 C 0
s danRer6.chr4         28116159 142 +  71658100 ACATTAATTCATCACTAATAATAAAGCG--ATAATATAAGGGTCA------CACAT-TAATGCATCTTCAAT-------AATAAAC--CAATAATATAATAATGCACACGCATTA---------ATTCATCCCTAATTATAATCCATTAACAAAG---TTAACATTAATAAT
i danRer6.chr4         N 0 C 0
s gasAcu1.chrUn        46852675 127 +  62550211 ----------------------------AAACAGTCTGCAACCAA------AATGTGTTCTTTGTCTCCAACCTGTTGGACTAAACATTAAAACTAAAATGATCTCTCTACATTAAATGTGTATATGGATGCGT--TTAATATTTGTTCTTAAAG--------ATAAATAA-
q gasAcu1.chrUn                                 ----------------------------99999999999999979------99999999999999999929999989999999999999999999899999989999999989999999997998999987979--9999999999899899999--------98999999-
i gasAcu1.chrUn        N 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=12300.000000
s hg19.chrY             7773071 145 +  59373566 ----TTTTGTTTTCTTCTTTGTTCAAATTGTTACCTGATTTAGAGCCAAATATT-T--AAAGAATGTGATACACAAATACTAAAAAGTGACAACAATTTATTTGA--------GATGtaattaaatttcttaaattagtaaataatttcaataaacttag
s panTro2.chrY           626330 145 +  23952694 ----TTTTGTTTTCTTCTTTGTTCAAATTGTTACCTGATTTAGAGCCAAATATT-T--AAAGAATGTGATACACAAATACTAAAAAGTGACAACAATTTATTTGA--------GAAGtaattaaatttcttaaattagtaaataatttcaataaacttag
q panTro2.chrY                                  ----00000000000000000000000000000000000000000000000000-0--00000000000000000000000000000000000000000000000--------00000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23128399 147 + 157549271 ----TTTTGTTTTCTTCTTTGTTCAAATTGTTACGTGCTTTAGAAGCAAAAACT-TAAAAAAAAAACGCTACACAAATACTAACAGGTAACAGCaatttatttaa--------aatgtaattagatttcttaaataagtaaataatttaagtaaacttag
q ponAbe2.chr7                                  ----58854578716546735545795345752101454845666365999657-45999999995765636596835435439554554754977794679799--------99576987769669969599988767895899795996959969989
i ponAbe2.chr7         I 241 C 0
s danRer6.chr4         28116301 146 +  71658100 CTTCTTTAATTTTCTATTTCGCAGACATAGAT---TAAATTACTAACAGAC----T--AAAATATAAGTAACTTCAAT-TTAAAGAAATAGTTTGATATATTGAATATGTATGAAGACAGTTG---TGCCTTGTCTACTAAAGAAAGAAAATTGATTGA-
i danRer6.chr4         C 0 C 0
s gasAcu1.chrUn        46852802  98 +  62550211 ----TTTAACAT--TATTCTGCA-------------TCATCATCAATAAACACTTT--AAACTGCAAATAAAAT--AC-CTGAAGGAACCGAACCATTTATTCAC--------AAAACAGTT-------------TACTA----------------TGA-
q gasAcu1.chrUn                                 ----99999999--999998998-------------99999799899999999999--9999999999999999--99-99999999999999999999999989--------999999999-------------99999----------------999-
i gasAcu1.chrUn        C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916   103508 47921 -    291918 T

a score=1851.000000
s hg19.chrY              7773216 232 +  59373566 tttatgttacttatataaattatttttCATCTTATC--------CTTAATCTTAAA--AAAATTTAGCTAGGTACACAATTCAAAATTGA-GGGATGATTT-AAATAGGCAACTTAA---AAATATTTTATTAGACATGTTGAGTAGT-TTAATTCTCAAATATTTTTTCTTAGA--------AACCAATATACTTGACAATTGAT---ATTGATAGTATCTACATAA----GTG----------------------GCATTATAAACATGCTTTTAT--AGTTTCC
s ponAbe2.chr7          23128546 237 + 157549271 tttatattacttgtataaattattttacatattatC--------CTCAATCTTAAAACAAAATTTAGCTAGGTATGCAATTCAAAATTGATAAGATTTTTTAAAATAGGCAACTTAA---AAACATTTTATTGGACAAGTTGGGTAATATTAATTCTCAAATATTTTATCTTAGA--------AATCAACACACTTGACAATTGAT---ATTCATAGTATCTATGAAA----GTG----------------------ACATTCTGAATGTGCTTGTAT--ACTTGCC
q ponAbe2.chr7                                   899697799793889989779789996969799389--------6999486999996799997979999999999899889999999898999988999998999999899989999---9989689999968999999999999999999989999999999999999999999--------99999999999999999999999---9999999999999999999----999----------------------999999999999999999999--9999999
i ponAbe2.chr7          C 0 C 0
s panTro2.chrY            626475 232 +  23952694 tttatgttacttatataaattatttttCATCTTATC--------CTTAATCTTAAA--AAAATTTAGCTAGGTACACAGTTCAAAATTGA-GGGATGATTT-AAATAGGCAACATAA---AAATATTTTATTAGACATGTTGAGTAGT-TTAATTCTCAAATATTTTTTCTTAGA--------AACCAATATACTTGACAATTGAT---ATTGATAGTATCTACATAA----GTG----------------------GCATTATAAACATGCTTTTAT--AGTTTCC
q panTro2.chrY                                   000000000000000000000000000000000000--------000000000000--00000000000000000000000000000000-0000000000-000000000000000---0000000000000000000000000000-00000000000000000000000000--------00000000000000000000000---0000000000000000000----000----------------------000000000000000000000--0000000
i panTro2.chrY          C 0 C 0
s xenTro2.scaffold_1417    22782 246 +     72846 TTTAGTTTACCCAGGAAAACTATATATCATTTTTTTCAGGACAACCTAAGCTTCAA--AATAT-------GGT---------GGAATTGT-TGTGTAATTCCAATTCTGTAAC---A---AGATATAGGCTTCTAAATGTCTAAAAAA-TTAAAACAAAAATATTTTCCCTTATA--------TAAACACATACACCAGAAACAAA---AATTATTTTATGCACAAAA----ATACAACTGATTTGGAAAGTCCCATGTCTCCTGAACATGCCAATACCAAATATAT
i xenTro2.scaffold_1417 n 47921 C 0
s danRer6.chr4          28116447 170 +  71658100 TTTATGTT--TAATACAAGCAAGGCGTTGTATTGCT--------TTATGCTGGAAA--AAAGT--------------------TAATCGC-CCCTCCATTG-GAT-------TTTGGTTGAGAAACCTTATAA--CATGC---------TTG-------------GCTCTTGAAA--------AGCTCACATATATAATAAGGAAA----------AAATCCACTGAATTTTGTG----------------------ACATCTGGGAGGTGTTTT------------
i danRer6.chr4          C 0 N 0
s gasAcu1.chrUn         46852900 204 +  62550211 -----------AACACAATGAAGAACTTGTTTCATG--------TTAAAGATAAAT--AAGGT--------------------AAGATGA-GGCTTTATGT-GATGACGTAACTTAAAACAAAAGCCTTTTAATGCAAGC---------TTAAC-----ATTGTTGTTCTTTAGAAAAAAAGTAGCT-ATACATTTCAAAATAAAATGATCCCAGTAAATCTACTCTAGATGTTT----------------------ACACCACAAATACTATTTTG---AGTTTCT
q gasAcu1.chrUn                                  -----------9999999999999999999999999--------999999999999--99999--------------------9999999-9999999999-99999999999999999999999999999999999999---------99999-----9999999999999999999999999999-99999999999999999999999999999999999999999999999----------------------99999999999999999999---9999999
i gasAcu1.chrUn         C 0 I 7
e tetNig2.chr5           3743466  14 +  13390619 I
e petMar1.Contig6813       17462   0 +     30809 I

a score=-27573.000000
s hg19.chrY              7773448 319 +  59373566 AAAATTTTAGAAGAAAAAAATCTATTCTTGTCTT--------CATCAGTAAA--ACTTTAAGATTACAGCAATGAGATTATGTTGACCGGCTAAATTACCCACAAAAAACTGAAACAGATTAATTTACTTACTCTGTATCTTTCAGTATCTGAT--AATGAACAGA-------------------------TTTTA-----------AGAGGCTCAGAA-TCTGC----TTCAGTATAGAAATAAAGCCAAACAACTCTTC-TGAAAGaattatta------aaaatttacagaaaaaattgatta---tttataata-tttaaaaaattGCCCAATTCATAGTTCAAAA-AATACCATTCTTACTGTGTTTTACTACTGGCAG-----------
s ponAbe2.chr7          23128783 297 + 157549271 AAAAATTTAAGAGAAAAAAATCTATTCTGGCCGT--------CAGTAGTAAA--ACTTAAAGATTAAAGAAGTAAGATTAAACTTACTGGCTAAATTAC-----------------------ATTTACTTGTTCTTTATCTTTCAGCATCTGAT--AATGAACAGA-------------------------TTTTA-----------AGACGTTCAGAA-TCTGC----TTCAGTATAGAAACAAGGCCAAACAGCTCTTG-TGAAAGAATCATT-------AAAATATACAGAACAAACCTATCA---TTTATATTACTTTAAAAAATCACCCAATTCATAGTCCAAAAGAATACCAATCTTACTGGATTTTACTACTGGCAG-----------
q ponAbe2.chr7                                   9999999999999999999999999999999999--------9999999999--999999999999999999999999999999999999999999999-----------------------99999999997667999999999999999999--9999999999-------------------------99999-----------999999999999-99999----99999999999999999999999999999999-9999999999999-------999999999999999999999999---999999999999999999999999999999999999999999999999999999999999999999999999999-----------
i ponAbe2.chr7          C 0 C 0
s panTro2.chrY            626707 319 +  23952694 AAAATTTTAGAAGAAAAAAATCTATTCTTGTCTT--------CATCAGTAAA--ACTTTAAGATTACAGCAATGAGATTATGTTGACCGGCTAAATTACCCACAAAAAACTGAAACAGATTAATTTACTTACTCTTTATCTTTCAGTATCTGAT--AATGAACAGA-------------------------TTTTA-----------AGAGGCTCAGAA-TCTGC----TTCAGTATAGAAATAAAGCCAAACAACTCTTC-TGAAAGAATTATTA------AAAATATACAGAAAAAACTGatta---tttataata-tttaaaaaattGCCCAATTCATAGTTCTAAA-AATACCATTCTTACTGTGTTTTACTACTGGCAG-----------
q panTro2.chrY                                   0000000000000000000000000000000000--------0000000000--0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--0000000000-------------------------00000-----------000000000000-00000----00000000000000000000000000000000-00000000000000------000000000000000000000000---000000000-0000000000000000000000000000000-000000000000000000000000000000000-----------
i panTro2.chrY          C 0 C 0
s xenTro2.scaffold_1417    23028 322 +     72846 ATAGTTTTATGGAGA--------TTTCTTACTGA--------CATAGGTCAA-------AAACTCCCGGCAGTA-----------CCCTACCAAATTCC---CAAAGCACTGCTTCAGA--AAGCTGCATACTTTAGATTTCAAGGCCACAAATTCCACTAACAGAAGgtttatcccagaaaattatacattttta-----------gaaagaacagat-tctgtggaatccagaatagatagaactgcctgctactcc--------aaactatcaagtcgcaatgctttcctaaagtttttattggtttttatcaaaatttgtgaaatttcttaa-aaattgcttcaaa-gcttccagtc-tatagtatcttatctcctacag-----------
i xenTro2.scaffold_1417 C 0 n 0
s gasAcu1.chrUn         46853111 282 +  62550211 -TAATTCTTTGAAAA-------TATCTACAGAAT-------AGAATAACAAAAAACTATAATAAACTGATGA-ATCAATGAATTTGATCTCACCACC-TTCACTG---AACATTACAGAGAAATAT--------CAGTTTTTCAGACAGATTGTGATATCAGCAG--------------------------TTTCA-----------GCATCACCAGAC-TCTCC----AATATTG-AAATATGGGA---AGAGTTTCTCAGTGAAAGTGTCTCTA------TAAGTGTAGA------------TG---TGAGTCGTG-TCT---------------TCAGGGTCGTAAA-AGGACACGTC-CCCCCTGTCGTAGTCCAGCTGGACTCTGATCCT
q gasAcu1.chrUn                                  -99999999999999-------999999999999-------9999999999999999999999999999999-999999999999999999999999-9999999---999999999999999999--------9999999998999999999999999999999--------------------------99998-----------999999999999-99999----9999999-9999999989---99999999999999999999899999------9999997999------------77---889899969-999---------------9989999999999-9998989999-999999999999999999999998999999999
i gasAcu1.chrUn         I 7 C 0
s danRer6.chr5          71450273 285 +  74451498 -AAGGTATTT------------TATTCTCAACGTTGTTGCGAGGTCAGTAAAAGACTTTTATTTTATATCTA-AAGAGCATCTTTGCTATCAAGACTATTTACTGTTTAAAAAAATAAATAAATta--------tatatatatatatatatatatatatatatat--------------------------atacatatatatatatatatatatatatatatat----attattgtgaatttaaag---agcatctcttc-tgaaacaaacttta------tatatatata------------ta---tatat-ata-tat---------------atatatatatata-tatatatat--------------atatatatatatatatatac-
i danRer6.chr5          N 0 C 0
e tetNig2.chr5           3743466  14 +  13390619 I
e petMar1.Contig6813       17462   0 +     30809 I

a score=-12706.000000
s hg19.chrY             7773767 176 +  59373566 AAGGTGTGTTTT---------CTTAATGACCTGACACAACATAACCACTCTTTGTATAT--------------------TATTTA-ATTG-CCCAAAATCTA-CCCAGAACTGAAGGCTAAT-----TCTGCCAGTTCCTAAA----AAGACAGTTTTCAGACACAAAA--CC-ATTTTCATTTAGGCTTGTTGCCTACATTGACCTTCCAGTAATGTCT
s ponAbe2.chr7         23129080 174 + 157549271 AAGGTGGGTTTT---------CTTAG-GACCTGATGCAGCATAACCACTC-TTATATGT--------------------CATCCA-ATTGCCCCCAAATCAA-CCCAGAACTGAAGGCTGAT-----CCTGCCAGGTTCTAAG----AAGACAATCTT--GACACACAC--CTAATTTTCATTTAGACTTGTTTCCTACCTCTACCTTCCAGTAATGTCT
q ponAbe2.chr7                                  999999999999---------99999-99999999999997999999999-99999999--------------------999999-9999999999999999-9999999999999999999-----9999999999999999----99999999999--999999999--9999999999999999999999999999999999999999999999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           627026 176 +  23952694 AAGGCATGTTTT---------CTTAATGACCTGACACAACATAACCACTCTTTATATAT--------------------TATTTA-ATTG-CCCAAAATCTA-CCCAGAACTGAAGGCTAAT-----TCTGCCAGTTCCTAAA----AAGACAGTTTTCAGACACAAAA--CC-ATTTTCATTTAGGCTTGTTGCCTACATTGACCTTCCAGTAATGTCT
q panTro2.chrY                                  000000000000---------00000000000000000000000000000000000000--------------------000000-0000-00000000000-0000000000000000000-----0000000000000000----0000000000000000000000--00-0000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_328   536941 174 +   1326055 AAGA---GTCTTGGAGGGGGACTCAAGAGCCT-------TGTAAGCATTC-CCATTTCT--------------------CAGCCAGATTG-CCCAGTAGCCATTCTTGGGGTTAAGCTTGATCTTCCCTTTCCGGTTGCT--G----GATTCGCTTGCCATTCCCACAT--CC------CACGCGGTTTTGTCTCCCACATCGACTTCCCAGTAGTGGCG
i xenTro2.scaffold_328 n 0 C 0
s gasAcu1.chrUn        46853393 160 +  62550211 ----------------------------------------CTGGAGACTC-TTCTTCACTCGGAGAGGCCGACCAACTCCATTAG-TGTA-TATCTCATTGT-GAAGAGCTAAACACCAGAA-----TCCATCACCTGTTGAAGCACCTGTCTCTCCCTTTCTGTCAACTGAC-TCTTTAACCAAACC----------TACAAACCATAGAGGATGGTCT
q gasAcu1.chrUn                                 ----------------------------------------9999999999-9999999999999999999999999999999999-9999-99999999999-9999999999999999999-----9999999999999999999999999999999999999999999999-99999999999999----------9999999999999999999999
i gasAcu1.chrUn        C 0 I 26
s danRer6.chr5         71450558 148 +  74451498 --------------------------------------------ataCAC-TTATGTATGTATGTGG------------TATTTA-AGTA-CTCAACGTTGT-TGCGAGGTTAGTTCCTAGT-----GCTTTTA--TTTTGAA--ACTAAACATTCCTCAGCCGGAAAC--AC-GCTTTGGCTAAGCCGCTTGACTCATGTAAACTTGTCAAAATAGTCT
i danRer6.chr5         C 0 N 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I

a score=24920.000000
s hg19.chrY             7773943 70 +  59373566 GCCAGAACTACACTTCTAAGAGCCCAGGAGAGTAGGGCAGAAATAAAGACTCCTTGGGTTATAACAAATA
s ponAbe2.chr7         23129254 70 + 157549271 GTCAGAACTACACTTCTGAGAGCCCAGGAAAGCAGGGCAGAAATAAAATCTCCTTGGGTTATAACATACG
q ponAbe2.chr7                                 9999999999999999999999999999999999999999999999999999999999799999999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           627202 70 +  23952694 GCCAGAACTACACTTCTAAGAGCCCAGGAGAGTAGGGCAGAAATAAAGACTCCTTGGGTTATAACAATTA
q panTro2.chrY                                 0000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_328   537115 70 +   1326055 CCCAGAATCGAATCCCTCTGATCCCAGGACAAGAATACACTGACTAAAGCGCTTGGGGTTATCAGGGACA
i xenTro2.scaffold_328 C 0 I 5
s gasAcu1.chrUn        46853579 70 +  62550211 CCCTGAGCTGAAGCCCTCAGAGCCCAGAACATCTGCATACTTAGTGAATCTCTCTGGATTATCAGGAAGC
q gasAcu1.chrUn                                9999999999999999999999999999999999999999999999999999999999990909999999
i gasAcu1.chrUn        I 26 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I

a score=41018.000000
s hg19.chrY               7774013 103 +  59373566 TTTGGTTTTGTTCTTCCATATCACACAGTATTTCTATCC-TCAGAGACAATAAGTTGAGGATGTGCTGTGTCAAGATCTACAATCAAggcaaggtgtagtggct
s ponAbe2.chr7           23129324 101 + 157549271 TTTGGTTTTGTTCTTCC--ATCACACAGCTTTTCTATCC-TCGGAGACAGTAAGTTGAGGATGTGCTGTGTCAAGATCTAAAATCAAggacaggcgcggtggct
q ponAbe2.chr7                                    99999999999999999--99999999999999999999-9999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7           C 0 C 0
s panTro2.chrY             627272 103 +  23952694 TTTGGTTTTGTTCTTCCATATCACACAGTATTTCTATCC-TCAGAGACAATAAGTTGAGGATGTGCTGTGTCAAGATCTACAATCGAggcaaggagtagtggct
q panTro2.chrY                                    000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s micMur1.scaffold_15453     8912 103 +     14698 TTTTGTTTTGTTCTTCCATACCGCACAGCTTTTCTATCC-TCAGAGACAATGAGTTGAGGATGTGCTGTGTCGACATCTAGAATCACATCTACTTGAAATGGCT
q micMur1.scaffold_15453                          999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999
i micMur1.scaffold_15453 N 0 C 0
s xenTro2.scaffold_328     537190  74 +   1326055 CTTACTATCG-----CCATACTTGAC-GCTGGTCAGTCCATCTGACAGGATCAGGTTTGGGTGAGCTGTGCTTGGGTCCA------------------------
i xenTro2.scaffold_328   I 5 n 5
s gasAcu1.chrUn          46853649 101 +  62550211 TGCTGCTTTATGATTCCATATCTCACACTGGTCAGATCA-TCAGACAGAGAGAGAAAGTAGTTTGCAGTGTTTGGGTCCAGAATGACAG--GACTGAAGTGGAC
q gasAcu1.chrUn                                   999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999--9999999999999
i gasAcu1.chrUn          C 0 C 0
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I

a score=6980.000000
s hg19.chrY               7774116 37 +  59373566 catgtctgtaatcttagc----acttt-------agggtgccaaggtg
s ponAbe2.chr7           23129425 37 + 157549271 cacatgtgtattcccagc----acttt-------ggaaggctgaggtg
q ponAbe2.chr7                                   999999999999999999----99999-------99999999999999
i ponAbe2.chr7           C 0 C 0
s panTro2.chrY             627375 37 +  23952694 catgtctgtaatcttagc----acttt-------agggtgccaaggtg
q panTro2.chrY                                   000000000000000000----00000-------00000000000000
i panTro2.chrY           C 0 C 0
s gasAcu1.chrUn          46853750 48 +  62550211 CTGGTCCTTCATCTTCTCCCAGACTCTGAAGGACAGGTTGCCCAGGTG
q gasAcu1.chrUn                                  999999999999999999999999999999999999999999999999
i gasAcu1.chrUn          C 0 N 0
e micMur1.scaffold_15453     9015  0 +     14698 C
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_328     537264  5 +   1326055 I

a score=15001.000000
s hg19.chrY               7774153 66 +  59373566 ggcagatcacaaggttaggagatcaagaccatcttgcctaaaacggtgaaacctcatctctactaa
s ponAbe2.chr7           23129462 66 + 157549271 ggtggatcatgaggtcaggagatcaagaccatcctggctaacatggtgaaaccccatccctactaa
q ponAbe2.chr7                                   999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7           C 0 I 209
s panTro2.chrY             627412 66 +  23952694 ggcagatcacaaggttaggagatcaagaccatcttgcctaaaacggtgaaaccttatctctactat
q panTro2.chrY                                   000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e micMur1.scaffold_15453     9015  0 +     14698 C
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_328     537264  5 +   1326055 I

a score=17743.000000
s hg19.chrY               7774219 192 +  59373566 ctggccatcagagaaatgcaaatcaaaaccacaatgagataccatctcacaccagttagaatggcaatcattaaaaagtcaggaaacaacaggtgctggagaggatgtggagaaataagaacacttttacactgttagtgggactgtaaactagttcacccattgtggaagtcagtgtggcgattcctcagg
s panTro2.chrY             627478 192 +  23952694 ctggccatcagagaaatgcaaatcaaaacaacaatgagataccatctcacaccggttagaatggcaatcattaaaaagtcaggaaacaacaggtgctggagaggatgtggagaaataagaacacttttacactgttagtgggactgtaaactagttcacccattgtggaagtcagtgtggtgattcctcagg
q panTro2.chrY                                    000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e micMur1.scaffold_15453     9015   0 +     14698 C
e tetNig2.chr5            3743466  14 +  13390619 I
e ponAbe2.chr7           23129528 209 + 157549271 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_328     537264   5 +   1326055 I

a score=3467.000000
s hg19.chrY                        7774411 30 +  59373566 gatctagaactagaaatcccatttgaccca
s panTro2.chrY                      627670 30 +  23952694 gatctagaactagaaatctcatttgaccca
q panTro2.chrY                                            000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s otoGar1.scaffold_92867.1-125821    40501 18 +    125821 gacctaca------------atttgaccct
q otoGar1.scaffold_92867.1-125821                         99999999------------9999999999
i otoGar1.scaffold_92867.1-125821 N 0 I 59
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=5363.000000
s hg19.chrY                        7774441 58 +  59373566 gccatcccattactgggtgtatacacaaaggactataaatcatgctgctataaggaca
s panTro2.chrY                      627700 58 +  23952694 gccatcccattactgggtatatacacaaaggactataaatcatgctgctataaggaca
q panTro2.chrY                                            0000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e otoGar1.scaffold_92867.1-125821    40519 59 +    125821 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=3840.000000
s hg19.chrY                        7774499 43 +  59373566 catgcacacgtatgtttattgtggcactattcacaatagcaag
s panTro2.chrY                      627758 43 +  23952694 catgcacacgtatgtttattgtggcactattcacaatagcaag
q panTro2.chrY                                            0000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s otoGar1.scaffold_92867.1-125821    40578 22 +    125821 tttacacacaaatgtttatagc---------------------
q otoGar1.scaffold_92867.1-125821                         9999999999999999999999---------------------
i otoGar1.scaffold_92867.1-125821 I 59 I 37
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=3781.000000
s hg19.chrY                        7774542 40 +  59373566 gacttgggaccaacccaaatatccaacaatgataggctgg
s tarSyr1.scaffold_170768              376 35 -      5317 ggcatggaacaaaccaggctgaccatcg-----aagctgg
q tarSyr1.scaffold_170768                                 9999999999999999999999999999-----9999999
i tarSyr1.scaffold_170768         N 0 C 0
s panTro2.chrY                      627801 40 +  23952694 gacttgggaccaacccaaatatccaacaatgataggctgg
q panTro2.chrY                                            0000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s otoGar1.scaffold_92867.1-125821    40637 24 +    125821 ----------------aagtgctcatcaacccatgaatgg
q otoGar1.scaffold_92867.1-125821                         ----------------999999999999999999999999
i otoGar1.scaffold_92867.1-125821 I 37 I 29
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=8217.000000
s hg19.chrY                        7774582 37 +  59373566 attaagaaaatgtggcacatatacaccatggaatact
s tarSyr1.scaffold_170768              411 37 -      5317 actggaaaaatgtggtacatatacacaatggaatatt
q tarSyr1.scaffold_170768                                 9999999999999999999999999999999999999
i tarSyr1.scaffold_170768         C 0 C 0
s panTro2.chrY                      627841 37 +  23952694 attaagaaaatgtggcacatatacaccatagaatact
q panTro2.chrY                                            0000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e otoGar1.scaffold_92867.1-125821    40661 29 +    125821 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=3646.000000
s hg19.chrY                        7774619 20 +  59373566 ---atgcagccataaaaaatgat
s panTro2.chrY                      627878 20 +  23952694 ---atgcagccataaaaaatgat
q panTro2.chrY                                            ---00000000000000000000
i panTro2.chrY                    C 0 C 0
s tarSyr1.scaffold_170768              448 19 -      5317 ----tgcagccataaagaaggac
q tarSyr1.scaffold_170768                                 ----9999999999999999999
i tarSyr1.scaffold_170768         C 0 C 0
s otoGar1.scaffold_92867.1-125821    40690 22 +    125821 attccgctgtcagaaagatgga-
q otoGar1.scaffold_92867.1-125821                         9999999999999999999999-
i otoGar1.scaffold_92867.1-125821 I 29 I 39
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=5719.000000
s hg19.chrY                        7774639 39 +  59373566 gagttcatgtcctttgtagggacatggatgaaactggaa
s tarSyr1.scaffold_170768              467 39 -      5317 aaacatatggactttgcagaaacttggattaatttagag
q tarSyr1.scaffold_170768                                 999999999999999999599999999967978989499
i tarSyr1.scaffold_170768         C 0 C 0
s panTro2.chrY                      627898 39 +  23952694 gagttcatgtcctttgtagggacatggatgaaattgaaa
q panTro2.chrY                                            000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
e micMur1.scaffold_15453              9015  0 +     14698 C
e tetNig2.chr5                     3743466 14 +  13390619 I
e otoGar1.scaffold_92867.1-125821    40712 39 +    125821 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462  0 +     30809 I
e xenTro2.scaffold_328              537264  5 +   1326055 I

a score=12921.000000
s hg19.chrY                        7774678 112 +  59373566 atcata-attctcagtaaactatcacaaggacagaaaaccaaacaacacatgttctcactcataggtgggaattgaacaatg---agaacacgtggatacaggaaggggaacatca
s panTro2.chrY                      627937 112 +  23952694 atcata-attctcagtaaactatcacaaggacagaaaaccaaacaacacatgttctcactcataggtgggaattgaacaatg---agaacacgtggacacaggaaggggaacatca
q panTro2.chrY                                             000000-000000000000000000000000000000000000000000000000000000000000000000000000000---0000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s tarSyr1.scaffold_170768              506 108 -      5317 tcactc-atactcagtgatctatcacagaagcaaagaacagagtaccatatgttctcactcataagcgaaccttgaatgattatcataatactataataaagggattgg-------
q tarSyr1.scaffold_170768                                  999999-999999599979999997999998999999989997996869999989996999599879698487998999878989899989999989999999562896-------
i tarSyr1.scaffold_170768         C 0 C 0
s otoGar1.scaffold_92867.1-125821    40751  84 +    125821 --aatatactctaggtaaagtatcacaagattgaaaa----aagattgcctatactcactactaatttgaaactaggAGATT---AACAATCA-----------------------
q otoGar1.scaffold_92867.1-125821                          --99999999999999999999999999999999999----99999999999999999999999999999999999999999---99999999-----------------------
i otoGar1.scaffold_92867.1-125821 I 39 N 0
e micMur1.scaffold_15453              9015   0 +     14698 C
e tetNig2.chr5                     3743466  14 +  13390619 I
e ponAbe2.chr7                    23129528 209 + 157549271 I
e petMar1.Contig6813                 17462   0 +     30809 I
e xenTro2.scaffold_328              537264   5 +   1326055 I

a score=15816.000000
s hg19.chrY                7774790 165 +  59373566 cactctggggactgttgtggggtggggggaggggggagggatagcattaggaggtatacctaatgctaaatgatgagttaatgggtgcatcacaccagcatggcacatgtatacatatgtaactaacctgcacattgtgcacatgtaccctaaagtataata-ata-----
s panTro2.chrY              628049 165 +  23952694 cactctggggactgttgtggggtggggggaggggggagggatagcattaggaggtatacctaatgctaaatgatgagttaatgggtgcatcacaccagcatggcacatgtatacatatgtaactaacttgcacattgtgcacatgtaccctaaagtataata-ata-----
q panTro2.chrY                                     000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-000-----
i panTro2.chrY            C 0 C 0
s tarSyr1.scaffold_170768      614 145 -      5317 cagtagagggatactgccagagaagggggagtg----ggaTTGGCAGTTGAGGGAA-----ACTGCTAGTGGAGG----GAGGGGCACACCTCATCA-------ACAAGAGTACCTGCATAATCAACCT-----TTGTATACCTA-ACCCTGAATTATATCACACATCTTT
q tarSyr1.scaffold_170768                          686795969776678989629199699959579----9752695786666959599-----55694666494939----999999888879999999-------9999999999999999999999999-----99999999999-9999999999999999999999999
i tarSyr1.scaffold_170768 C 0 N 0
e micMur1.scaffold_15453      9015   0 +     14698 C
e tetNig2.chr5             3743466  14 +  13390619 I
e ponAbe2.chr7            23129528 209 + 157549271 I
e petMar1.Contig6813         17462   0 +     30809 I
e xenTro2.scaffold_328      537264   5 +   1326055 I

a score=17431.000000
s hg19.chrY               7774955 207 +  59373566 acaataaaaaaaaatacaaagaattagctgggcttggtggagggtgcccgtattctcaactacttagtatgctgaggcaggagaatcaaacctcggagacagaggttgcagattgtaccattgcactacagcctgggtgacagatggagactccatctcaaaggaaaaaaaaaaCAACAACCTAGAGTTAAATGTAAAAAAATGGAG
s panTro2.chrY             628214 205 +  23952694 acaat-taaaaaaatacaaagaattagctgggctttgtggagggtgcctgtattctcaactactcagtatgctgaggcaggagaatcaaacctgggagacagaggttgcagattgtaccattgcactacagcctgggtgacagatggagactccatctcaaaggaaaaaaaaaa-aaaaaCCTAGAGTTAAATGTAAAAAAATGGAG
q panTro2.chrY                                    00000-000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000
i panTro2.chrY           C 0 C 0
e micMur1.scaffold_15453     9015   0 +     14698 C
e tetNig2.chr5            3743466  14 +  13390619 I
e ponAbe2.chr7           23129528 209 + 157549271 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_328     537264   5 +   1326055 I

a score=35713.000000
s hg19.chrY               7775162  95 +  59373566 TGATAATTCTGTCTAAGCCAGAATATAGAGGGGGAAGACTAATACC-------ATGTTTTGTTAATCTAAATGAAAAGACTACAGGACATTTTAGGTTTCAA------------
s ponAbe2.chr7           23129737 102 + 157549271 TGATAGTTCTGTCTAAGCCAGAATATAGAGGAGGAAGACTAAAACCATATTTTATATTTTGTTAATGTATATGAAAAGAGTTCAGGGCATTTTAGGTTTCGA------------
q ponAbe2.chr7                                    999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999------------
i ponAbe2.chr7           I 209 C 0
s panTro2.chrY             628419  95 +  23952694 TGATAATTCTGTCTAAGCCAGATTATAGAGGGGGAAGACTAATACC-------ATGTTTTGTTAATCTAAATGAAAAGACTACGGGACATTTTAGGTTTCAA------------
q panTro2.chrY                                    0000000000000000000000000000000000000000000000-------0000000000000000000000000000000000000000000000000------------
i panTro2.chrY           C 0 C 0
s micMur1.scaffold_15453     9015 107 +     14698 TGATAGTTCTGTCCAGGCCAGAATGCTGGGGAGGAAGTCTGAAACC-------ATAGTTTGTTAAACTAAATGAAAAGGTTTCAGGGTATTTCAGGTTTTGATACTCTTAAGAG
q micMur1.scaffold_15453                          9999999999999999999999999999999999999999999999-------9999999999999999999999999999999999999999999999999999999999999
i micMur1.scaffold_15453 C 0 C 0
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_328     537264   5 +   1326055 I

a score=10714.000000
s hg19.chrY               7775257 40 +  59373566 TATCTGTTC---TGAATACCCTTAACA--TGTGTCAGCCATTCCA
s panTro2.chrY             628514 40 +  23952694 TATCTGTTC---TGAATACCCTTAACA--TGTGTCAGCCATTCCA
q panTro2.chrY                                   000000000---000000000000000--0000000000000000
i panTro2.chrY           C 0 C 0
s ponAbe2.chr7           23129839 40 + 157549271 TACCTGTGG---TGCATACTCTTAACA--TCTGTCAGCAATTCCA
q ponAbe2.chr7                                   999999999---999999999999999--9999999999999999
i ponAbe2.chr7           C 0 I 154
s tarSyr1.scaffold_19995     4901 42 -     27809 aatgttctc---gccacacaaataataactatgtgaggtATTTAT
q tarSyr1.scaffold_19995                         999999999---999999999999999999999999999999999
i tarSyr1.scaffold_19995 N 0 C 0
s micMur1.scaffold_15453     9122 43 +     14698 TATCCACTCAGATGGATACTCTTAACA--CAGGCCAGTAATTCCG
q micMur1.scaffold_15453                         999999999999999999999999999--9999999999999999
i micMur1.scaffold_15453 C 0 C 0
e tetNig2.chr5            3743466 14 +  13390619 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_328     537264  5 +   1326055 I

a score=1071.000000
s hg19.chrY               7775297 50 +  59373566 ---TAGG-----CTTACCATCTGCCC-----------------TCCTTAGTAAATGTTCAAATGTAGAAACATAA
s panTro2.chrY             628554 50 +  23952694 ---TAGG-----CTTACCATCTGCCC-----------------TCCTTAGTAAATGTTCAAATGTAGAAACATAA
q panTro2.chrY                                   ---0000-----00000000000000-----------------00000000000000000000000000000000
i panTro2.chrY           C 0 C 0
s tarSyr1.scaffold_19995     4943 47 -     27809 ---TAGGTAAACCTAAGCATTTGCACCAAGTCAACATTTTTTTTTTTTAA-------------------------
q tarSyr1.scaffold_19995                         ---99999999999999999999999999999999999999999999999-------------------------
i tarSyr1.scaffold_19995 C 0 N 0
s micMur1.scaffold_15453     9165 58 +     14698 TGTCTGA-----CTGCACACATGCCC----------TTTGTCTCCTTCAGAAGATGCTTTACTGTGGAAACAT--
q micMur1.scaffold_15453                         9999999-----99999999999999----------9999999999999999999999999999999999999--
i micMur1.scaffold_15453 C 0 N 0
e tetNig2.chr5            3743466 14 +  13390619 I
e ponAbe2.chr7           23129879 154 + 157549271 I
e petMar1.Contig6813        17462  0 +     30809 I
e xenTro2.scaffold_328     537264  5 +   1326055 I

a score=2570.000000
s hg19.chrY                7775347 46 +  59373566 ATGTTCAAATGTAGAAACATAAACC-AAAAAAAATACAA--GTTTTTTA
s myoLuc1.scaffold_135055      672 44 -     10110 TCCTTTGAGATTGGAAAGATGGTCT----GAAAATGCAGTTGTGTTTG-
q myoLuc1.scaffold_135055                         9999999999999999999999999----9999999999999999999-
i myoLuc1.scaffold_135055 N 0 C 0
s panTro2.chrY              628604 47 +  23952694 ATGTTCAAATGTAGAAACATAAACCAAAAAAAAATACAA--GTTTTTAA
q panTro2.chrY                                    000000000000000000000000000000000000000--00000000
i panTro2.chrY            C 0 C 0
e tetNig2.chr5             3743466 14 +  13390619 I
e ponAbe2.chr7            23129879 154 + 157549271 I
e petMar1.Contig6813         17462  0 +     30809 I
e xenTro2.scaffold_328      537264  5 +   1326055 I

a score=23781.000000
s hg19.chrY                7775393 146 +  59373566 TTCAATTATGCACTCTTCCTGTGAACAATTAATGTCA--TTTCTTTACTACAGCTATTGTTAA----------------------TTTTTCACCTGAGACAACAGGCTAATTTC----------AGAAA-GAATATTTATTTCTAATTATGTAGCTTCTATTACATAGCTA-----ATTTTGTTTT-----------
s panTro2.chrY              628651 146 +  23952694 TTCAATTATGCACTCTTCCTGTGAACAATTAATGTCA--TTTCTTTACTACAGCTATTGTTAA----------------------TTTTTCACCTGAGACAACAGGCTAATTTC----------AGAAA-GAATATTTATTTCCAATTATGTAGCTTCTATTACATAGCTA-----ATTTTGTTTT-----------
q panTro2.chrY                                     0000000000000000000000000000000000000--000000000000000000000000----------------------00000000000000000000000000000----------00000-00000000000000000000000000000000000000000-----0000000000-----------
i panTro2.chrY            C 0 C 0
s danRer6.chr3             5021981 157 +  60907308 TTTAATTCTGCAGGGTTC---TGGATCACTCATGTTC--TCGCTGTCCTTCAG------TAAA----------------------CTCTTCACTTGAGTCTGATGGGAATATTCCTGCATTTATAACAG-AAACATTTGCAT-TAAATATTCAGTATATAATTAACAATCA-----TAACCGTTTCTGAAACATCAT
i danRer6.chr3            N 0 C 0
s myoLuc1.scaffold_135055      716 157 -     10110 --CAATGAG------TTTCTGT------TGAATGTC---CTTCTCTTCTTCAGCTAGCCTTGAGAGGACTTCCTCTTGCTCGCGCTTTATAACTTGAGACAGATGCTCAAACTC----------AGAAGCTAATTTCTGTTCCTGTTTTTGCACCTTCTCTCTCAGTTCTATGAGCTTTTTGTT-------------
q myoLuc1.scaffold_135055                          --9999999------9999999------99999978---979999889999999999996999999999999999999999999999997999999999898969998999998----------979999999699999977978999969969999999999899999899999999999999-------------
i myoLuc1.scaffold_135055 C 0 N 0
s ponAbe2.chr7            23130033 143 + 157549271 --CAATTATGCTCTCTTCATATGCAGAATTAATGTCATTTTTTTTTACTATAGATATTTTCCA----------------------TTTTTCACCTGAGACCACAGGCTAATTTC-------------AA-AAATATTTACTTCTAATTATGTAGCTTCTATTACATAGCTA-----GTATTGTCTT-----------
q ponAbe2.chr7                                     --9999999999999999999999999999999999999999999999999999999999999----------------------99999999999999999999999999999-------------99-99999999999999999999999999999999999999999-----9999999999-----------
i ponAbe2.chr7            I 154 C 0
e tetNig2.chr5             3743466  14 +  13390619 I
e petMar1.Contig6813         17462   0 +     30809 I
e xenTro2.scaffold_328      537264   5 +   1326055 I

a score=14837.000000
s hg19.chrY                7775539 53 +  59373566 TTTTTACTTCATGTATATGCCAAAAAGACTGTATGACTTATAAAA--CATTCAAC
s turTru1.scaffold_115454   140521 38 +    243983 TTTTTAT---------------AAACAACCCCATGACTTATGAAT--TCTCCAGG
q turTru1.scaffold_115454                         9999999---------------99999999999999999999999--99999999
i turTru1.scaffold_115454 N 0 C 0
s ponAbe2.chr7            23130176 53 + 157549271 TGTTTACCTCATGTATATGCCAAAAAGACCTCATGACTTATGAAA--CGTTCAAC
q ponAbe2.chr7                                    999999999999999999999999999999999999999999999--99999999
i ponAbe2.chr7            C 0 C 0
s panTro2.chrY              628797 53 +  23952694 TTTTTACTTCATGTATATGCCAAAAAGACCGTATGACTTATAAAA--CATTCAAC
q panTro2.chrY                                    000000000000000000000000000000000000000000000--00000000
i panTro2.chrY            C 0 C 0
s danRer6.chr3             5022138 53 +  60907308 TAATTGTATTAAAAACATAC--AAAATACAACAACACTGATAAAAAGTATTTAAG
i danRer6.chr3            C 0 C 0
e tetNig2.chr5             3743466 14 +  13390619 I
e petMar1.Contig6813         17462  0 +     30809 I
e xenTro2.scaffold_328      537264  5 +   1326055 I

a score=2089.000000
s hg19.chrY                7775592 56 +  59373566 -TATTCACTTGAATGAATTG--------GTCCTTTACATTTA--ATAAACTCa-tttatataaatttt
s panTro2.chrY              628850 56 +  23952694 -TATTCACTTGAATGAATTG--------GTCCTTTACATTTA--ATAAACTCa-tttatataaatttt
q panTro2.chrY                                    -0000000000000000000--------00000000000000--000000000-00000000000000
i panTro2.chrY            C 0 C 0
s ponAbe2.chr7            23130229 52 + 157549271 -TGTTTACT----TAAATTG--------GCCCAATAAATTTA--ATAGACTCG-ATTATGTCAATTTT
q ponAbe2.chr7                                    -99999999----9999999--------99999999999999--999999999-99999999999999
i ponAbe2.chr7            C 0 C 0
s turTru1.scaffold_115454   140559 52 +    243983 -TTTTCACC----TGATCTG--------TCACAGTTAAGTGA--ATAACTGTG-ATGATGTCATTTAC
q turTru1.scaffold_115454                         -99999999----9999999--------99999999999999--999999999-99999999999999
i turTru1.scaffold_115454 C 0 N 0
s xenTro2.scaffold_7       1061327 59 -   5836443 -TAATTTCTTTTAGGAATTA-------TATACTATGaatataatataactttt-tcaataaaaatgtt
i xenTro2.scaffold_7      n 5 C 0
s danRer6.chr3             5022191 66 +  60907308 TAtttcagtcttatcaatgataaatattgtcaaattcctcca--gaaaacacattttctaaacatttt
i danRer6.chr3            C 0 I 4
e tetNig2.chr5             3743466 14 +  13390619 I
e petMar1.Contig6813         17462  0 +     30809 I

a score=29967.000000
s hg19.chrY           7775648 234 +  59373566 ataaaataaaa-----tgaattataaCTAACCAAAAAATGGATT-AATAGGATT-TTTAATTGAAACAACTTA-TAAAATGTACTAAATAAATAACATACAGTA-ATACACTGTGAAA-------TTACTC-----------ATATATGAAAATTATTTT---GTGA-------------ACACCATTAAATTTTAT-----CAAAGCTAT------------------------TTTCATAATCTGCGAGGAAATTATACAAATAATGTTTTATAAAATTAAACAAA-----------CACCAAATTGTGTATT-AT
s ponAbe2.chr7       23130281 231 + 157549271 ATAAAGTAAAA-----TGAACAGTAACTAAACAAAAATTGGATTAAATAGCATTCTCTAATTGAAACAAAATA-TAAAATATAC----TAAATAACATACAATACATGCACTATGAAA-------TTACTC-------------ATGTGAAAATTATTTT---GTGA-------------ACACCATTAAATTTTAT-----CAAAGTCAC------------------------TTTCATAATCTCTGAGGGGATTATACAAAGAATGTTTTATGAAATTAGATGAA-----------AAGAAAATTATGTATT-AT
q ponAbe2.chr7                                99999999999-----999999999999999999999999999999999999999999999999999999999-9999999999----999999999999999999999999999999-------999999-------------9999999999999999---9999-------------99999999999999999-----999999999------------------------99999999999999999999999999999999999999999999999999999-----------9999999999999999-99
i ponAbe2.chr7       C 0 C 0
s panTro2.chrY         628906 234 +  23952694 ataaaataaaa-----tgaattataaCTAACCAAAAAATGGATT-AATAGGATT-TTTAATTGAAACAACTTA-TAAAATGTACTAAATAAATAACATACAGTA-ATACACTGTGAAA-------TTACTC-----------ATATATGAAAATTATTTT---GTGA-------------ACACCATTAAATTTTAT-----CAAAGCTAT------------------------TTTCATAATCTGCAAGGAAATTATACAAATAATGTTTTATAAAATTAAACAAA-----------CACCAAATTGTGTATT-AT
q panTro2.chrY                                00000000000-----0000000000000000000000000000-000000000-000000000000000000-000000000000000000000000000000-0000000000000-------000000-----------000000000000000000---0000-------------00000000000000000-----000000000------------------------00000000000000000000000000000000000000000000000000000-----------0000000000000000-00
i panTro2.chrY       C 0 C 0
s xenTro2.scaffold_7  1061386 237 -   5836443 ataaaataaaaaCGTCTGAGT--TTGCTATTTAAA---TCAATT-AATGTTTCTGTCAATTTTCAGCCTCCT-----GATGCGATCCTGGAATTTTAATCAGTG-AGACAGAATATAT-------TTCCCC-----------AATTAGAGATGCTACTTT---GTGGAAAATGGATACCTATACTGCTTTATGTAAC-----TAAACAGAT------------------------TTTTACAATATCT-------TTATA--------ATTTT----AATTAGACAGATTGTCACACTTCTACAAATTGTGTTTTGGT
i xenTro2.scaffold_7 C 0 C 0
s danRer6.chr3        5022261 266 +  60907308 --aaaatattt---cctgaat----------taaaacactctct-aatatcatt-ttaaa--aatacatcctattaaaatatgttttatcaccaaaatattctc-acacaagctacaaataggtgtttctcccctgttcaataaatgtgtgtgtaagtcttgagtgg-------------ccgattctacatgtcatgtgtgcagcgtgatcatgtctCTGATTGTTTACATTTATCTCTCAATATTTTAATGAATTA-------AGTGTTTTATATTATTATACTGA-----------TCCCAAATTCTGTTTT-AC
i danRer6.chr3       I 4 I 25
e tetNig2.chr5        3743466  14 +  13390619 I
e petMar1.Contig6813    17462   0 +     30809 I

a score=5629.000000
s hg19.chrY           7775882 33 +  59373566 ATTTATGGGTAACAACATGCAAACTG-------ATATAAA
s xenTro2.scaffold_7  1061623 30 -   5836443 GTTT---GTTTAAAACACAGAAACTA-------AAAAAAA
i xenTro2.scaffold_7 C 0 C 0
s panTro2.chrY         629140 33 +  23952694 ATTTGTGGTTAACAACATGCAAACTG-------ATATAAA
q panTro2.chrY                               00000000000000000000000000-------0000000
i panTro2.chrY       C 0 C 0
s ponAbe2.chr7       23130512 40 + 157549271 GTCTATGGTGAGCAACAGGCAAACAGACAAACAACAAAAA
q ponAbe2.chr7                               9999999999999999999999999999999999999999
i ponAbe2.chr7       C 0 C 0
e tetNig2.chr5        3743466 14 +  13390619 I
e danRer6.chr3        5022527 25 +  60907308 I
e petMar1.Contig6813    17462  0 +     30809 I

a score=17477.000000
s hg19.chrY           7775915 105 +  59373566 AAAAGAATTTGCACAAG-ATGTTT---CTAAGC---------CAGCAGCAATGACATTTTAGATAAATAAATTTAATACAAAGCAGAGAAAATAAATT------TGCTTTCAAAATCTTTGAAG---
s ponAbe2.chr7       23130552 102 + 157549271 AAGAGAATTTGCAC----ATGATT---CTAAGC---------CAGGAGCAATAACACTTTAGATAAATGAATTTAATACACAGCAGAGAAAACAGATT------TGCTTTCAAAATCTTTGAAG---
q ponAbe2.chr7                                99999999999999----999999---999999---------99999999999999999999999999999999999999999999999999999999------99999999999999999999---
i ponAbe2.chr7       C 0 I 42
s panTro2.chrY         629173 105 +  23952694 AAAAGAATTTGCACAAG-ATGTTT---CTAAGC---------CAGCAGCAATGACATTTTAGATAAATAAATTTAATACAAAGCAGAGAAAATAAATT------TGCTTTCAAAATCTTTGAAG---
q panTro2.chrY                                00000000000000000-000000---000000---------00000000000000000000000000000000000000000000000000000000------00000000000000000000---
i panTro2.chrY       C 0 C 0
s xenTro2.scaffold_7  1061653 112 -   5836443 AAAAGAAATGGAATGGA-ATATTTAGACTAAGCTGATGCACACAGCTACAATTATACTTTATA--------------GCCAAGCAGTAATAACATTCTGCCTGGTGCACTTACTGTTTTTCAAATGA
i xenTro2.scaffold_7 C 0 C 0
s danRer6.chr3        5022552  88 +  60907308 TCAAGAGTTTACACAAGCATATGT---TCAGTT---------AAACAGTCA--ATATTCAATATAATCAGCATTAAACTACCTCTTAGTGAATGAATT------AGAT-------------------
i danRer6.chr3       I 25 N 0
e tetNig2.chr5        3743466  14 +  13390619 I
e petMar1.Contig6813    17462   0 +     30809 I

a score=2893.000000
s hg19.chrY           7776020 36 +  59373566 ATTTTGGTTTGCTGATAATTT---AGTGCTCGTAAAATT-
s panTro2.chrY         629278 39 +  23952694 ATTTTGGTTTGCTGATAATTTATCAGTGCTTGTAAAATT-
q panTro2.chrY                               000000000000000000000000000000000000000-
i panTro2.chrY       C 0 C 0
s xenTro2.scaffold_7  1061765 40 -   5836443 GCTCTGGTTGGCTTGTTTTCTGCCAAAGCATGAAGAAATT
i xenTro2.scaffold_7 C 0 C 0
e tetNig2.chr5        3743466 14 +  13390619 I
e ponAbe2.chr7       23130654 42 + 157549271 I
e petMar1.Contig6813    17462  0 +     30809 I

a score=3107.000000
s hg19.chrY           7776056 27 +  59373566 GTTTCATTAT-------AATATTTTTCTTG-----TAAA---
s panTro2.chrY         629317 27 +  23952694 GTTTCATTAT-------AATATTTTTCTTG-----TAAA---
q panTro2.chrY                               0000000000-------0000000000000-----0000---
i panTro2.chrY       C 0 C 0
s ponAbe2.chr7       23130696 32 + 157549271 GTTTCATTCT-------AATATTTTTCTTTTCTTCTCAA---
q ponAbe2.chr7                               9999999999-------9999999999999999999999---
i ponAbe2.chr7       I 42 C 0
s xenTro2.scaffold_7  1061805 32 -   5836443 CTTTAATTAGCATCATAAATATTTA----------TAAAAGA
i xenTro2.scaffold_7 C 0 n 0
e tetNig2.chr5        3743466 14 +  13390619 I
e petMar1.Contig6813    17462  0 +     30809 I

a score=14104.000000
s hg19.chrY             7776083 64 +  59373566 ATTAGGTACACGATCAT---AAA-AAATATGATTA--TTCTTTATAAATCTGTTACACCTAAAGTTCATT
s xenTro2.scaffold_677   478492 57 +    553670 ATCAGGTATCGGCACATTTCGAA-AGATATGA-----GGCTTTCTGAACCAGTT-------GAGTTTTTG
i xenTro2.scaffold_677 n 0 C 0
s ponAbe2.chr7         23130728 67 + 157549271 AGTAGGTATACAACCAT---AAACAAATATGATTACTTTTTCTATAAATCTGTTACACCTGAAGTTTATT
q ponAbe2.chr7                                 99999999999999999---99999999999999999999999999999999999999999999999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           629344 64 +  23952694 ATTAGGTACACGATCAT---AAA-AAATATGATTA--TTCTTTATAAATCTGTTACACCTAAAGTTCATT
q panTro2.chrY                                 00000000000000000---000-00000000000--000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I

a score=13069.000000
s hg19.chrY             7776147 72 +  59373566 TTACAGTGATAGATTTGTATATTTAAATC-CATGTAAACCAAAACTGAAGATGTGTATATGTTTAGCAGACCA
s panTro2.chrY           629408 72 +  23952694 TTACAGTGATAGATTTGTATATTTAAATC-CATGTAAACCAAAACTGAAGATGTGTATATGTTTAGCAGACCA
q panTro2.chrY                                 00000000000000000000000000000-0000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s ponAbe2.chr7         23130795 72 + 157549271 TTACAGTGATATATCTATACATTTAAATC-CATGTAAACCAAAACTAAAGGTCTGTATGTGTTTAGCAGACCA
q ponAbe2.chr7                                 99999999999999999999099999999-9999999999999999999999999999999999999999999
i ponAbe2.chr7         C 0 C 0
s xenTro2.scaffold_677   478549 66 +    553670 TCCAGATAATATTTTTCTA-GTATAAATC-CCTATATTATGAAAAAGCAATTTT-----TCCTTGGGGGGCGG
i xenTro2.scaffold_677 C 0 I 6
s danRer6.chr15          684517 63 +  47237297 TGTCAATAGTCAACTCTTATGTGCAAAGCTCACAAAATGTCAAGCACAATATTTAAATTTGCT----------
i danRer6.chr15        N 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I

a score=520.000000
s hg19.chrY              7776219 35 +  59373566 GAG----AAGTTGTAT--TT-CCAAAAAAAAGTGGGATAAAA
s ponAbe2.chr7          23130867 36 + 157549271 GAG----AAGTCATGT--TCAACAGAAAAAAGTCGGATAAAA
q ponAbe2.chr7                                  999----999999999--999999999999999999999999
i ponAbe2.chr7          C 0 C 0
s panTro2.chrY            629480 35 +  23952694 GAG----AAGTTGTAT--TT-CCAAAAAAAATTGGGATAAAA
q panTro2.chrY                                  000----000000000--00-000000000000000000000
i panTro2.chrY          C 0 C 0
s speTri1.scaffold_6131   123254 37 -    197004 GGG----AGGTTGTTTGACT-CTCTAGAATTGAAGGATAAAA
q speTri1.scaffold_6131                         999----9999999999999-999999999999999999999
i speTri1.scaffold_6131 N 0 N 0
s xenTro2.scaffold_677    478621 39 +    553670 GAGCTCTGAATCTTGT--TC-CAGAAGTGGAAATACACAAAA
i xenTro2.scaffold_677  I 6 I 2
s danRer6.chr15           684580 26 +  47237297 ---------ATTAATT--CT-----GTAGTAGCGGAATGAAT
i danRer6.chr15         C 0 C 0
e tetNig2.chr5           3743466 14 +  13390619 I
e petMar1.Contig6813       17462  0 +     30809 I

a score=3548.000000
s hg19.chrY             7776254 31 +  59373566 -TTTTGTAAATAGTTGTTCAGAATCCCAAAAC
s ponAbe2.chr7         23130903 31 + 157549271 -TTTTATAAATAGTTGTTCAGAATTCAGAAAC
q ponAbe2.chr7                                 -9999999999999999999999999999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           629515 31 +  23952694 -TTTTGTAAATAGTTGTTCAGAATCCCAAAAC
q panTro2.chrY                                 -0000000000000000000000000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_677   478662 26 +    553670 -TCTGGCAGAT-----TTAGAAATCTCAGTGT
i xenTro2.scaffold_677 I 2 n 2
s danRer6.chr15          684606 25 +  47237297 TCATAGCAGAT-----GTCAGTTTTTTTAC--
i danRer6.chr15        C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I

a score=51936.000000
s hg19.chrY             7776285 408 +  59373566 ATATATTTCC-ATTATATTCA---TAATCTTCATTGCAACCATCATAATAATCTGTAGTTACAAGAAAAACAAAAATGTAAGTGGTA----GAAACCATATTCTCCACATTATT---------------------TTCAGTTAAAGACCAC-AACAAA---GTAATC-------------ACTAGAGATGT----------TATTCCACTG-TCACCCAATAGTACATT----------GTTACCAT----CTGTTACCTACAA--------CCTTGTG-TAAAATGGGATAAGTTAACATCAGT-GGCA-----AGATACACATTC---AATGTTAAATAGCC-----------TTAATACAATAATAACAATTTTGATTTAT-----------TACAAC-------------AAATTAAGT-TCACAC-TTGTCATTAAAAAG----GACTTTTT---AAATTAACTGTATTTTAAT--------------TACCTTAATTTGCAAATG----GTAAAGCAATTTC-------CTTCTAAAATTCGTA--TTGT--TTCT---CTTACTGT
s ponAbe2.chr7         23130934 401 + 157549271 ATATAGCTCCAATTATACTCA---TAATCTTCGTTACAACCATCATAATAACCTGTAGTTACAAG-AAAACAAAAATGTAAGTTGTA----GAAACCATATTCTCTAAATTATT---------------------TTAAGTTAAAGACCACTGACAAA---GGGATC-------------ACTAGAGATGT----------TAGTCCACTG-TCACCAAATAGCATAT------------------------TGTTACCTACAA--------CCTTGGGTTAAGATGGGATAAATTAACATCAGT-GGCA-----AGATACACATTC---AATGTAAAATAGCC-----------TTAACACAATAACAACAATTTTGGTTTAT-----------TAAAAC-------------AAATTAAGT-TCACACATTGTCATTAAAAAG----GCATTTTG---AAATTCACTGTATTTTAAT--------------TACCTTAGTTTGCAAATG----GTAAGGCAATTTC-------CTTCTAAAATTCAAA--TTGT--TTCT---CTTACTAA
q ponAbe2.chr7                                  999999999999999999999---99999999999999999999999999999999999999999-999999999999999999999----99999999999999999999999---------------------99999999999999999999999---999999-------------99999999999----------9999999999-9999999999999999------------------------999999999999--------999999999999999999999999999999999-9999-----999999999999---99999999999999-----------99999999999999999989999999999-----------999979-------------999999999-999999999999999999999----99999999---9999999999999999999--------------999999999999999999----9999999999999-------999999999999999--9999--9999---99999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           629546 408 +  23952694 ATATATTTCC-ATTATATTCA---TAATCTTCATTGCAACCATCATAATAATCTGTAGTTACAAGGAAAACAAAAATGTAAGTGGTA----GAAACCATATTCTCCACATTATT---------------------TTCAGTTAAAGACCAC-AACAAA---GTAATC-------------ACTAGAGATGT----------TATTCCACTG-TCACCCAATAGTACATT----------GTTACCAT----CTGTTACCTACAA--------CCTTGGG-TAAAATGGGATAAGTTAACATCAGT-GGCA-----AGATACACATTC---AATGTTAAATAGCC-----------TTAATACAATAATAACAATTTTGATTTAT-----------TAAAAC-------------AAATTAAGT-TCACAC-TTGTCATTAAAAAG----GACTTTTT---AAATTAACTGTATTTTAAT--------------TACCTTAATTTGCAAATG----GTAAAGCAATTTC-------CTTCTAAAATTCATA--TTGT--TTCT---CTTACTGT
q panTro2.chrY                                  0000000000-0000000000---000000000000000000000000000000000000000000000000000000000000000----00000000000000000000000---------------------0000000000000000-000000---000000-------------00000000000----------0000000000-00000000000000000----------00000000----0000000000000--------0000000-0000000000000000000000000-0000-----000000000000---00000000000000-----------00000000000000000000000000000-----------000000-------------000000000-000000-00000000000000----00000000---0000000000000000000--------------000000000000000000----0000000000000-------000000000000000--0000--0000---00000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_916    55587 516 -    291918 atatgtctcc-tTTAAATTTAATCTTGTTTTCATTTGAACAATATCATTGATAAATGGAGACTACAAGACCAGATATGTATGATGTGCTATGAAATAAAATTATCTCAGTAATCAAAGCAAGTGATGATGCCCTATCCATTTGCAACCCTA-ATCTAA---AGAATCTTATATATCTACAGCTGGGGGTTG----------GACTCAACTGAGCACTGATCAGAGTATTGGGGAAAGGGGTTCAGATGGTACTGCTCTCTAAAAGA-----GCTTTGAG-TTAGCTTTGTGACATTGTGCTCACTAGGCA-----AGGCACATTCTCCTGAATCCAAAATGGGTAaatatgtcagctactgcaaaatcaatacatttactgcatttaatgtggggtaaaacttaa-------aaaaagtgagt-tcaccc--------caaaaagccatatatttttgggaagtacacattctctcaatgggtaaata-----tgtctttctactcaaaagtaccatagcacaaagtt-------tccctaaagttagggatttgtaattac---atttctgt
i xenTro2.scaffold_916 T 47921 C 0
s danRer6.chr15          684631 419 +  47237297 ATTTTTTTTC-AGTTTCTTT----TAACCTGTATTTCAAGTCTTATGATCTTC-----------------CAGATTTCTAT----------GAAACAA-ACTCTCCTACTAAAT---------------------TGTGTTGAAACTCCAC-ACCTAAACTGAAGTG-------------ATGAGAAATATGCAGATAGCACATTTCAATG-CTATTCATTTATTTGC-----------ATTCACAT------ATTTACTACAATACCATTTCCTTTCT-TCTATTCTAAccttttaaggctcaa-ggtgtttttacatgcattttt---tatttctcttcgct----------------------------atttgggcttat-----------tggaacctaattagaataaaacctaagtatcatct-tt-----tgatatg--atgtactttt---agagaaaaatgatgttcatatatgtggactcgtggtcctaatttac---------ataaaacactttttaatgcatatataaaatagaca--tttt--ttttttacttgctgt
i danRer6.chr15        C 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I

a score=-624.000000
s hg19.chrY                7776693 40 +  59373566 GTATAATATTAACGTGA-----TCACTTAACAGACTCCTGTCATC------
s panTro2.chrY              629954 37 +  23952694 GT---ATATTAACGTGA-----TCACTTAACAGACTCCTGTCATC------
q panTro2.chrY                                    00---000000000000-----00000000000000000000000------
i panTro2.chrY            C 0 C 0
s ponAbe2.chr7            23131335 40 + 157549271 GCAGATTATTATCCTGA-----TCACTTACCACACTCTTATCATC------
q ponAbe2.chr7                                    99999999999999999-----99999999999999999999999------
i ponAbe2.chr7            C 0 C 0
s myoLuc1.scaffold_155489   197597 33 +    205280 -----ATCTTACATTAA-------AGGAAAAAAATCCCCTTCATA------
q myoLuc1.scaffold_155489                         -----999999999999-------999999999999999999999------
i myoLuc1.scaffold_155489 N 0 N 0
s xenTro2.scaffold_916       56103 40 -    291918 -----aaatcacctcaaagcttCCACTTTGCAGCATCCTATCTTC------
i xenTro2.scaffold_916    C 0 C 0
s danRer6.chr15             685050 38 +  47237297 ------gactatcagaa-------agttaaaaacaacattttatcccattt
i danRer6.chr15           C 0 C 0
e tetNig2.chr5             3743466 14 +  13390619 I
e petMar1.Contig6813         17462  0 +     30809 I

a score=5934.000000
s hg19.chrY             7776733 32 +  59373566 CTGACACTTATAA-----TACTGCTGCAAACCAACCA
s ponAbe2.chr7         23131375 32 + 157549271 CTATCACTTATGA-----TACTGCTGTAAACTAACTG
q ponAbe2.chr7                                 9999999989999-----7999999999999999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           629991 32 +  23952694 CTGACACTTATAA-----TACTGCTGCAAACCAACCA
q panTro2.chrY                                 0000000000000-----0000000000000000000
i panTro2.chrY         C 0 C 0
s xenTro2.scaffold_916    56143 32 -    291918 CATAAAGTTATAA-----TACACCTAAGGAACAACAA
i xenTro2.scaffold_916 C 0 n 0
s danRer6.chr15          685088 29 +  47237297 tggacagttacagctgattacaactacgc--------
i danRer6.chr15        C 0 C 0
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I

a score=13687.000000
s hg19.chrY             7776765 62 +  59373566 CTAAGTGACATTTCTACTTAGATTTTCTTCATGTATCTT----AGATTTCACTTTCCTTAATCTTC
s ponAbe2.chr7         23131407 62 + 157549271 CTAAGTGGCCTTTCCACTTAGAATTTCTTCATGTATCTT----AGGTTTCAGTTTACTTAATCTTC
q ponAbe2.chr7                                 999999985999998699999999999999999999999----99999999999999999999999
i ponAbe2.chr7         C 0 C 0
s panTro2.chrY           630023 62 +  23952694 CTAAGTGACATTTCTACTTAGATTTTCTTCATGTATCTT----AGATTTCACTTGCCTTAATCTTC
q panTro2.chrY                                 000000000000000000000000000000000000000----00000000000000000000000
i panTro2.chrY         C 0 C 0
s danRer6.chr15          685117 48 +  47237297 -------atattgctatctaaaatttatttaagcagggtagcaagatctaatttt-----------
i danRer6.chr15        C 0 I 13
e tetNig2.chr5          3743466 14 +  13390619 I
e petMar1.Contig6813      17462  0 +     30809 I
e xenTro2.scaffold_916    56175  0 -    291918 I

a score=32522.000000
s hg19.chrY             7776827 155 +  59373566 CATAGAAAAGAATGTAAATTTATCTATATAATATAGAA--AACCTCTCATAACTCTGGTACAGCAATCATTGAACATGTTCTTTCATGTAAATTCTA--------TAAATGAAGAGAT--CATCAAATGTATGAGTTAAATTACATCAATAATTGCTTT----AAAAATTA
s ponAbe2.chr7         23131469 150 + 157549271 CATGGAAAAGTATATAAATCTGTCCATCTAATATAGAA-GAACCTCTCATAACTCTGGTGCAGCAACCATTGACCATGTTCTTTCACATAAATTCTA--------GAAATGAAGACATAGCATCAAATGTAAGAGTTAAATTACATCAAAATTTGCTTT------------
q ponAbe2.chr7                                  99999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999--------999999999999999999999999999999999999999999999999999999------------
i ponAbe2.chr7         C 0 I 3538
s panTro2.chrY           630085 155 +  23952694 CATAGAAAAGAATGTAAATTTATCTATATAATATAGAA--AACCTCTCATAACTCTGGTACAGCAATCATTGAACATGTTCTTTCATGTAAATTCTA--------TAAATTAAGAGAT--CATCAAATGTATGAGTTAAATTACATCAATAATTGCTTT----AAAAATTA
q panTro2.chrY                                  00000000000000000000000000000000000000--000000000000000000000000000000000000000000000000000000000--------0000000000000--000000000000000000000000000000000000000----00000000
i panTro2.chrY         C 0 C 0
s danRer6.chr15          685178 163 +  47237297 cataaatatgcacaggcattttttt---taactcaaaatgaaactttattaa--cagaaacacctaaca-taaacacacacattcatgcaggttgtagagaagagtaaaggaaggaaa--agcagaatttgagagtgaaataatataaaacctcaagttctgtaagactta
i danRer6.chr15        I 13 N 0
e tetNig2.chr5          3743466  14 +  13390619 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916    56175   0 -    291918 I

a score=303772.000000
s hg19.chrY             7776982 3300 +  59373566 CATTATAttttttatttttgtttgagacataatctcactctgtcaccaggctggagtgcagaggtgcgatctcagctaactgcaaccttcacctcctgggttcaagggatctttctgcgtcagcctcatatgtagctgagactacaggcacccaccactatggccagctaattttattgcatttttagtacagatggagtttcaccacattggacaagatggtctggatttcttgacctcctgatctgtcctgggcattccaaactgctgggattacaggagtgagccac-ggcCAGACCTAATTTCTTTTAAAATAGTTAATTAGGTTTCTTTTAGAGAAaagtaatcaagattgccaactagaaacttctagaccctgttgttctcacagagagaaatgcgaaatgttcagaaatacagcacattcaactgaaacatccaggtacttacgttgggatcaatcaaagaaacaatttatctaatggaaaatggaacaaaacaaggcaagaaaatgggccacccaggaaaaacatgaagccaagggaaattccccacccagtaaatcagtaattgcttatgtggccctaacaacctgtgattctctcacagatctttgcagccctcaggtaacgagataccctcatgaacccacttcatcatagccttccatttaacacacagagttacataaagtctcagaagatcagccactcaggctagtgcagagattcaagagtcttagataatctgtctttcaagccttcccagaaaaattagctgcaactccagcaaagcaggaggttaaatgcttttccatacccacaggaaagaggcagaatccatggtgctgagcagtgatggtctgtagaactcacttccacaattcctcacagggtaagacctactggcttagaattccagccaaccattgaaacagaatttcaccttcttgtgatagagctacaccagaaagaaaattgggccgccatctttgttgcttgtgcaagttagccatttcagccttcaggctgagaagagcccaagccaactgggaacagaaagaatctcctaccatggtacaggtgctctaaaaagacatggtcagactgcctgttaaagcaggtctgcaatctcattcctcctcactggaaagtgctttccaaccagcgtgtccagctaccgccacttgtgctattttgtagatggaattttgaaacatatttgggatgtagttcctggagggaagagtgagctgccacatttgctgtttgtgtgacttagctgttccagccatctggcttttgagaatccaaataaactgagtgtaaaagtggtacctctgtccagcaaagctgtcctacaaaaatgtggctaaactgctttttaagtgggtccccaatcacattatcctcactgcctaaacctttcaacagaggtttttagctacctcctatatgtgcttttgtcctggaaacaggtctatacctccctgggatagagtgcccagagaaaagggcatgctgccattgttgctgctttgcagcatttactgttgataacttcaggtactggaaaatctgaggtgactagaaactgtagtggacactcagcatcctgcagcagcccttcagaaagtagtcagactgttacataagcagctgttctcatgtattctcactgggaagattctccaggactgggccactaatgaatcattgccagagctattgaaccagtagaaaattagcaattccctggacaggggctccagcaccaactgaatatatttctgccactgcttctgcagtagatctgtccttgcttccctcaggttaatgaaaaatccaaaaatctaagtgctttattcacaatttaaacaagctgcagtttacccaaggagaggaggccagtccatcctccatgggttccacacactactcacagctgctcaccagaagtgaacctctaacttggccaaaagcacagatcctccatcctgggctgactgcactgagggattgctgacctacatccctcggagattcagcccccagaagagaagcaaagaagtggggcagcaagccagcttatgtggtgtccagtgggtttggcacaagagcatctgtattaaagtgtggccagtggtggccatttctctaggctaaactttctctcataaaaggctttagccctagagaacctgttggacctaacttctgcaggatgtttttacaaatgagaagaaactgctccaagtgagaacttttaagtctgctcagctctcccaggatcccagtctggctgcagctgcttacagtgtagtctcagctcccctagaagagtagtttaccataccatagcatctgcattggtgggccatgcctcagccctatgtgctccagcaaggcagcccctatgactgcaccagcccacatttatactccccatatgcagcttctccagagaccatagcaactcctgatattactttggtggcacatgtctgcaaaggtgggtttcgctttccttgccccaccagcaaatgagaatgcagtatgcccctgccatccacagcagctgccattatagatgaagtttggtgggcagaaagccacaactctgcctttgtgctaacactgtgaagagaaatgtgtattctcccacactctgaaccatcactgtgttattggtggggcacaaagaaggcatcacaacatttgttggccagcatgctgccccaagctaacatcaccattagtgcaacagcacacacagtctccagaaggtaacttccagttccccttccagcttctttgctcctgccagtaaggtaaatgcccaaagacaggcagaaaacccatatccactagcactttgctgcagctgTGGCAGGTTAGTCATAcagagtaatggactccaaatatcaaggagccacagaagacagttggaaaaaaatacaactgcccaagagcatgcagcctctgagttgtgagctgagcattgccaaacacaccaccaaaaaacaaacaaacaaaaatattccaggaacaaaggctgttggcttaatccaccttataccacagtcaaatattacagacaattgaataggatcaaaaaaagaatactccattcaaagatcagcaacctcaaagttatgcccacaaagattaggcaaaaatcactgcaaaaatgttgaaaacaaaaaaagccacagtgacttcttttatgcaaatgaccaaaattacataatttggtcaagatgacagaaggccaaagatgacagaaggagaattcagaatt
s panTro2.chrY           630240 3299 +  23952694 CATTATAttttttatttttgtttgagacataatctcactctgtcaccaggctggagtgcagaggtgcgatctcagctaactgcaaccttcacctcctgggttcaagggatctttctgcatcagcctcatatgtagctgggaatacaggcacccaccactatggccagctaattttattgtatatttagtacagatggagtttcaccatgttggacaagatggtctggatttcttgacctcctgatctgtcctgggcattccaaactgctgggattacaggtgtgagccacgggccagaccTAATTTCTTTTAAAATAGTTAATTAGGTTTCTTTTAGAGAAAAGTAATcaagactgccaactagaaacttctagactctgttgttctcacagagagaaatgtgaaatgttcagaaatacagcacattcaaccgaaacatccaggtacttatgttgggatcaatcaaagaaacaatgtatctaatggaaaatggaacaaaacaaggcaagaaaatgggccacccaggaaaaacatgaagccaagggaaattccccacccagtaaatcagtaattgcttatgtggccctaacaacctgtgattctctcacagatctttgcagccctcaggtaacgagataccctcatgaacccacttcatcatagccttccatttaacacacagagttacataaagtctcagaagatcagccactcaggctagtgcagagattcaagagtcttagataatctgtcttccaaggcttcccagaaaaattagctgcaactccagcaaagcaggaggttaaatgcttttccatacccacaggaaagaggcagaatccatggtgctgagcagtgatggtctgtagaactcacttccacaattcctcacagcgtaagacctactggcttagaattccagccaaccattgaaacagaatttcaccttcttgtgatagagct--accagaaagaaaattgggccgccatctttgttgcctgtgcaagttagccatttcagccttcaggctgagaagagcccaagccaactgggaacagaaagaatctcctaccatggtacaggtgctctaaaaagacatggtcagactgcctgttaaagcaggtctgcaatctcattcctcctcactggaaactgctttccaaccagcgtgtccagctaccaccgcttgtgctattttgtagatggaattttgaaacatatttgggatatagttcctggagggaagagtgagctgccacatttgctgtttgtgtgacttagctgttccagccatctggcttttgagaatccagataaactgagtgtaaaagtggtacctctgtccagcaaagctgtcctacaaaaatgtggctaaactgctttttaagtgggtccccaatcacattattctcactgcctaaacctttcaacagaggtttttagctacctcctatatgtgcttttgtcctggaaacaggtctatacctccctgggatagagtgcccagaaaaaagggcatgctgccattgttgctgctttgcagcatttactgttgataacttcaggtactggaaaatctgaggtgactagaaactgtagtgcaccctcagcatcctgcagcagcccttcagaaagtagtcagactgttacataagcagctgttctcatatattctcactgggaagattctccaggactgggccactagccaatcattgccagagctattgaaccagtagaaaattagcaattccctggacaggggctccagcaccaactgaatatatttctgccactacttctgcagtagatctgtccttgcttccctcaggttaatgaaaaacccaaaaatctaagtgctttattcacaatttaaacaagctgcagtttacccaaggagaggaggacagtccatcctccatgggttccacacactactcacagctgctcaccagaagtgaacctctaacttggccaaaagcatagatcctccatcctgggctgactgcactgcgggattgctgacctacatccctctgagattcagcccccagaagagaagcaaagaagtggggctgcaagccagcttatgtggtgtccagtgggtttggcacaagagcatctgtattaaagtgtggccagtgatggcaatttctctaggctaaactttctctcataaaaggctttagtcctagagaacctgttggacctaacttctgcaggatgtttttacaaatgagaggaaactgctccaagtgagcacttttaagtctgctcagctctcccaggatcccagtctgtctgcagctgcttacagtgtagtctcagctcccctagaagagtagtttaccataccatagcatctgcattggtgggccatgcctcagccctctgtgctccagcaaggcagcccctatgactgcaccagcccacatttatactccccatatgcagcttctccagagaccatagcaactcctgatattactttggtggcacatgtctgcaaaggtgggtttggctttccttgccccaccagcaaatgagaatgcagtatgcccctgccacccacagcagctgccattatagatgaagtttggtgggcagaaagccacaactctgcctttgtgctaacactgtgaagagaaatgtgtattctcccacactctgaaccatcactgtgttattggtggggcacaaagaaggcatcacaacatttgttgggcagcatgctgccccaagctaacatcaccattagtgcaacagcacacacagtctccagaaggtaacttccagttccccttccagcttctttgctcctgccagtaaggtaaatgcccaaagacaggcagaaaacccatatccactagcactttgctgcagctgtggcaggttagtcatacagagtgatggactccaaatatcaaggagccacagaagacagttggaaaaaaatacaactgcccaagagcatgcagcctatgagttgtgagctgagcattgccaaacacaccaacaaaaaacaaacaaacaaaaatattccaggaacaaaggctgttggcttaatccaccttataccacagtcaaatattaaagacaattgaataggatcaaaaaaagaatactccattcaaaggtcagcaacctcaaagttatgcccacaaagattaggcaaaaatcactgcaaaaatgttgaaaacaaaaaaagccacagtgacttcttttatgcaaatgaccaaaattacataatttggtcaagatgacagaaggccaaagatgacagaaggagaattcagaatt
q panTro2.chrY                                   000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000--00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY         C 0 C 0
e tetNig2.chr5          3743466   14 +  13390619 I
e ponAbe2.chr7         23131619 3538 + 157549271 I
e petMar1.Contig6813      17462    0 +     30809 I
e xenTro2.scaffold_916    56175    0 -    291918 I

a score=12433.000000
s hg19.chrY             7780282 141 +  59373566 tggatagaaataaactttattgagctacaaatgtaagttgtaacacaatgcaatg----------aagggaaaaaattgcaggaactgctagaaaaagcagccaatcaggaggaagatgtggtcaactggatagagctaaaacacaaaata------
s panTro2.chrY           633539 141 +  23952694 tggatagaaataaactttattgagctacaaatgtaacttgtaacacaatgcaatg----------aagggaaaaaattgtaggaactgctagaaaaagcagccaatcaggaggaagatgtggtcaactggatagagctaaaacacaaaata------
q panTro2.chrY                                  0000000000000000000000000000000000000000000000000000000----------00000000000000000000000000000000000000000000000000000000000000000000000000000000000000------
i panTro2.chrY         C 0 C 0
s danRer6.chr4         20932622 150 -  71658100 tgaaaggcaatgttctaaatttaccactcaatctaggttcctactcacatctatggttatgactaaaaggacaagatctcggtaacaaccggACA-------CATTTTGCAAAATGTTATGACCTGCTTGTTTGAGTTGCACCATAAAAGTGAGATG
i danRer6.chr4         N 0 C 0
e tetNig2.chr5          3743466  14 +  13390619 I
e ponAbe2.chr7         23131619 3538 + 157549271 I
e petMar1.Contig6813      17462   0 +     30809 I
e xenTro2.scaffold_916    56175   0 -    291918 I

a score=1715.000000
s hg19.chrY              7780423 121 +  59373566 caaaaactttataatgtaatcacaagtattaac---ag----aaaaatgggccatgtagtg------aaaagaatc--tcaaagcttcaag------------actggctttctgagataa-------------aacagagaaaaatagtgagagaaaata
s panTro2.chrY            633680 120 +  23952694 c-aaaactttataatgtaatcacaagtattaac---ag----aaaaatgggccacgtagtg------aaaagaatc--tcaaagcttcaag------------actggctttctgagataa-------------aacagagaaaaatagtgaaagaaaata
q panTro2.chrY                                   0-0000000000000000000000000000000---00----0000000000000000000------000000000--0000000000000------------000000000000000000-------------000000000000000000000000000
i panTro2.chrY         C 0 C 0
s fr2.chrUn            102966235 150 - 400509343 --caaacatttaataaaaatgacaaaaaatagc---agtttaaaagcttgatggcaaggta------aaaataatttggaaaaGCTTTGAATTCCAAATAGATACTGGCGCCCTGATAGTGTGGATCTGCCCATAAGAATGAGAACTGTTTGGggaaaata
i fr2.chrUn            N 0 C 0
s danRer6.chr4          20932772 120 -  71658100 ---AGACA---------------ACAAAATAGCCTGAATGCAAATGATTTATTATAAAATGTAACTCAGAACAATCAATCAAAGCAACCAA---CAAATTTCTA-----GGCATAATAATG-------------AAGATAAAGAAC--TTATGATATAATC
i danRer6.chr4         C 0 N 0
e tetNig2.chr5           3743466  14 +  13390619 I
e ponAbe2.chr7          23131619 3538 + 157549271 I
e petMar1.Contig6813       17462   0 +     30809 I
e xenTro2.scaffold_916     56175   0 -    291918 I

a score=7936.000000
s hg19.chrY              7780544 102 +  59373566 aagatgaatgaacaaagtctctaagaaatgcaagattatgtaatgaaaccaaatctatgattaaaaagagtgcctgaaagtgagggggagaatg-aaaacaac
s panTro2.chrY            633800 102 +  23952694 aagaggaatgaacaaagtcgctaagaaatgcaagattatgtaatgaaaccaaatctatggttaaaaagagtgcctgaaagtgagggggagaatg-aaaacaac
q panTro2.chrY                                   0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000
i panTro2.chrY         C 0 C 0
s fr2.chrUn            102966385  89 - 400509343 --------taatttaattCAC------ATCaaacttcagtcactgtgaacAATtccttaattaaaaaaaaagataataataaaatcAGTGAATGTTCAACATC
i fr2.chrUn            C 0 I 8
e tetNig2.chr5           3743466  14 +  13390619 I
e ponAbe2.chr7          23131619 3538 + 157549271 I
e petMar1.Contig6813       17462   0 +     30809 I
e xenTro2.scaffold_916     56175   0 -    291918 I

a score=16311.000000
s hg19.chrY               7780646 113 +  59373566 tggaaatacatatttccagatattatccaacaacaaatctttcagctgaaatcctacaaatcaaaagagacttggggccaatattcaacattcttaaaaaaaaaaagaattcc--
s panTro2.chrY             633902 112 +  23952694 ttgaaatacatatttccagatattatccaacaacaaatctttcagctgaaatcctacaagtcaaaagagacttggggccaatattcaacattctt-aaaaaaaaaagaattcc--
q panTro2.chrY                                    00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000--
i panTro2.chrY          C 0 C 0
s oryLat2.chr2           23856668 102 -  31118443 tggtaacacacaaACTTAGATGGTATACAGTACTCATTGTCGCAGaataaa--ctacaaccacaatgataaacaaaacaact-ttaaac----------caaaataaaatactgc
q oryLat2.chr2                                    999999999999999999999999999999999999999999999999999--99999999999999999999999999999-999999----------9999999999999999
i oryLat2.chr2          N 0 C 0
s fr2.chrUn             102966482  72 - 400509343 CAAGATCCCATAGGCCT-GCTGCTGTATTTTGCTGGT---------------------------GTGATGCACAGACCGTTTATtgaac----------taaaataaaac-----
i fr2.chrUn             I 8 C 0
s ponAbe2.chr7           23135157  81 + 157549271 ----------------------------aacaacgaatctttcagctgaaatcctacaagtcaaaagagattaggggccaatattcaacattctt----aaaaaaagaattcc--
q ponAbe2.chr7                                    ----------------------------9999999999999999999999999999999999999999999999999999999999999999999----99999999999999--
i ponAbe2.chr7          I 3538 C 0
s papHam1.scaffold23501     15995  81 -     34585 ----------------------------aacaacaaacctttcatctgaaatcctacaagtcaaaagagattaggggccaatattcaacattctt----aaaagaagagttcc--
q papHam1.scaffold23501                           ----------------------------6357558637586354555586257554575577996377778679863878777977977797797----99999999999999--
i papHam1.scaffold23501 N 0 I 2196
e tetNig2.chr5            3743466  14 +  13390619 I
e petMar1.Contig6813        17462   0 +     30809 I
e xenTro2.scaffold_916      56175   0 -    291918 I

a score=-31997.000000
s hg19.chrY               7780759 342 +  59373566 aaacc-----agaattttatatctta-ccaaagtaagcttca-aa--------ataaataataaatataatcgtatttggataaac-aacagctgaggaaatctattaccacaaga-cctgtcctac-----aagagcttccgaaa---aaagcattaa----ataag---------agact----attagc--------agt--cactacaaaaaaaa----------atacactaaagtacataaatagctagcactttaaagcaactac----ataaatgtgcaaaataaccagttaag---at-catagtgacagaatcaaat----ccacactcataaatagtaatgcta-----aatgtaaatggg-----ctaaatgccccaattgaaaaac--------agttgaatgcagg--tttaatatttaatg
s panTro2.chrY             634014 348 +  23952694 aaacc-----agaattttatatctta-ccaaagtaagcttca-aa--------ataaataataaatataatcctatttggataaac-aacagctgaggaaatctattaccacaaga-cctgtcctac-----aagagcttccgaaa---aaagcattaa----ataag---------agact----attagc--------agt--cactacaaaaaaaaaaaaat----atacactaaagtacataaatagctagcactttaaagcaactac----atgaatgtgcaaaataaccagttaag---at-catagtgacagaatcaaat----ccacactcataaatagtaatgcta-----aatgtaaatggg-----ctaaatgccccaattgaaaaac--------agttgaatgcagg--tttaatatttaatg
q panTro2.chrY                                    00000-----0000000000000000-000000000000000-00--------000000000000000000000000000000000-00000000000000000000000000000-0000000000-----00000000000000---0000000000----00000---------00000----000000--------000--00000000000000000000----0000000000000000000000000000000000000000000----00000000000000000000000000---00-0000000000000000000----000000000000000000000000-----000000000000-----0000000000000000000000--------0000000000000--00000000000000
i panTro2.chrY          C 0 C 0
s ponAbe2.chr7           23135238 356 + 157549271 aacac-----agaatttcatatctgacccaaggtaagcttcagaa--------gtaaaaaatatatatgatcctattcagataagc-aaatgctgagaaaatctgttaccacagga-tctgtcttaa-----aggagcttctgaag---aaagcattaa----ataag-----aaaaagact----attacc--------agc--cactacaaaa--------------gcacactaaagtatacaaactgcggacactataaagcaaccacagaaacaaatgtgcaaaatagccagctaag---at-cctaataacagaatccaat----ccacacatatgaatactaacctta-----aatgtaaatggg-----ctaaatacccaaattaaaacacagatggcaagctgaaaaaaga--atcaagatctaatg
q ponAbe2.chr7                                    99999-----99999999999999999999999999999999999--------999999999999999999999999999999999-99999999999999999999999909999-9999999999-----90999999999999---9999999999----99999-----999999999----999999--------999--9999999999--------------9999999999999999999999909999999999999999999999999999999999999999999999999---99-9999999999999999999----999999999999999999999999-----999999999999-----9999999999999999999999999999999999999999999--90999999999999
i ponAbe2.chr7          C 0 C 0
s xenTro2.scaffold_1263     81128 342 +    112973 AAAC--------AACTAAATATCTTA-------CAATCTACACAT--------TTAGACAAACTACATGGTATGATACAGAAATAC-TCAAG----GAATATCCACTCCTAGTCGA-AGCATCCCA--------GTACTTCCAAAACCTACAGCACCAA----GAAATTGATCAGCAAAACT----ACGAACCCCCCAGGAGC--CAACAAATAAACAGAATGTTGGCCATACACCA----ACACGA--------------GAAGTAACTCT----CACGAGGCCCAGGTAAACTAGCTATG---------AGTAGAAAGTTCCAATTTTGTTATACTGTAAAGGTTAAATGTTA-----AACTTAAATGTT-----CTCATTACCAATATTCTATTAC---TACCAAGATGTATGCAAG---TCAATATCTCATC
i xenTro2.scaffold_1263 n 0 I 2
s oryLat2.chr2           23856770 301 -  31118443 aaaatataaaaatattaatcaaccta-taaaattatacaaca-aa--------ttaaaaaacga---------aaaacatcaatacaaGTAA----TGACACTTTTGACCGATAAAAGCTGTTCATC--------AGATATAGATT---TAACTATtagatttaaaag-----caaaacatt-tgtatttac--------aGG--TACATCAAAGAga-----------attatttatgtaaaaaaa-----tggaTATTT-TTGCCGAAAT----A-AAAGTTTCATATTAAGGGTGAAACTCATTGTCTAGTATCAA----TCCT----CTAtttttttGAATATTGATA--------ATTGTAGCTGAT--------------------AAAATCC-----------TAAAACATAG----------------
q oryLat2.chr2                                    99999999999999999999999999-999999999999999-99--------99999999999---------9999999999999999999----9999999999999999999999999999999--------99999999999---9999999999999999999-----999999999-999999999--------999--9999999999999-----------999999999999999999-----999999999-9999999999----9-99999999999999999999999999999999999999999----9999----999999999999999999999--------999999999999--------------------9999999-----------9999999999----------------
i oryLat2.chr2          C 0 C 0
s fr2.chrUn             102966554 353 - 400509343 ----------aaaattaaataatcCA--ATAATTCTTCAGCA-GGTAGTCGCCTTAAGATGTAGCTGTTAT--AAGTTGTATAtac-agcag----ttttatttttttccgcCATA---TGTCCATCTGCAGTTGAGATTCCGAGT---TGAATA--AG----AAAAG-----CGATTCGTTCCGCTTTGAC--------AGGCTTGCGTTAAATACG-----------GTTGTCTTTAGCAAATTA--GGTTGGAACTGTATTGCCAGCAG----A-ATAGatccaaaataaataatggac---ATGTTTATAGGCAG------CT----CAGTTCTTTGTAATGGTGACAAAATAGTTATTagaaatgatgtgaaataaata---aaataaaaatcc--ttgTGTAGTTGGGTCACAGACTTTAATTTTTAA--
i fr2.chrUn             C 0 C 0
e tetNig2.chr5            3743466  14 +  13390619 I
e papHam1.scaffold23501     16076 2196 -     34585 I
e petMar1.Contig6813        17462   0 +     30809 I

a score=-21060.000000
s hg19.chrY                         7781101  99 +  59373566 gtatgttgtaatctagacacc-----catct--a-----aaataagttcaaaa--tacagggaaaaagaacattctaccaagcaaatag-----------aaagca-ga---------aaaaaagcaggggt-ta
s ponAbe2.chr7                     23135594 100 + 157549271 gtatgctttaatcgagacacc-----catct--c-----aaataagctcaaaa--taaagggaaaaagaaaagcctaccaagcaaatag-----------aaaacagga---------aaagaagcaggggt-tg
q ponAbe2.chr7                                              999999999999999999999-----99999--9-----99999999999999--9999999999999999999999999999999999-----------999999999---------99990999999999-99
i ponAbe2.chr7                    C 0 C 0
s panTro2.chrY                       634362  99 +  23952694 gtatgttgtaatccagacacc-----catct--a-----aaataagttcaaaa--tacagggaaaaagaacattctaccaagcaaatag-----------aaagca-ga---------aaaaaagcaggggt-ta
q panTro2.chrY                                              000000000000000000000-----00000--0-----00000000000000--0000000000000000000000000000000000-----------000000-00---------00000000000000-00
i panTro2.chrY                    C 0 C 0
s otoGar1.scaffold_84493.1-113195     61481  79 -    113195 gtgtgccatatttttGACACA-----CCTTT-----------TGGGGACAAGA--CACAAGTATAAGACAGACTTTACCTAACAAGT-G-----------AAATCA-G-------------------------TG
q otoGar1.scaffold_84493.1-113195                           999899999999999999999-----99999-----------99999989999--99999999999998999999999999999999-9-----------999999-9-------------------------99
i otoGar1.scaffold_84493.1-113195 N 0 C 0
s xenTro2.scaffold_1263               81472 127 +    112973 AAATGTTGTAATAGATATATT-----TGATA--ATATGCaaataaaaacaatatttaaaaaaaaaaaaagtatatttttatGAAAATGGTTTATTTAGATGAAACA-GGGTTTTACACATGAACTTGGGGGTATA
i xenTro2.scaffold_1263           I 2 C 0
s oryLat2.chr2                     23857071  73 -  31118443 --------tatctttgacatttttatcatGT--C-----AGAT-----CAatc--aaaaaag---atgttttctgtgCATA------------------TCAGACA-TC---------AGTGGACT---------
q oryLat2.chr2                                              --------99999999999999999999999--9-----9999-----99999--9999999---9999999999999999------------------9999999-99---------99999999---------
i oryLat2.chr2                    C 0 I 25
s fr2.chrUn                       102966907  98 - 400509343 ------TCTGTTCTAGGCATTGTTAGCCTTTAAC-----AGATAGATGCAGTA--GAGGAAGACAATGAACACTGGGAAAAGAAAGCAG-----AGAGTTCATGCA-GG---------AAAGGTTT---------
i fr2.chrUn                       C 0 I 12
e tetNig2.chr5                      3743466  14 +  13390619 I
e papHam1.scaffold23501               16076 2196 -     34585 I
e petMar1.Contig6813                  17462   0 +     30809 I

a score=-54545.000000
s hg19.chrY                         7781200 59 +  59373566 caattatagt-ttcttgtacaacaggctt------------ttagttaacat------ggatta---------aaaaaa-gacaaaaa
s fr2.chrUn                       102967017 46 - 400509343 -AAATGGTGT----CTTTAACGTTGGTTACTACAG-------------CCAC------TGTTTA---------CAGGGC---------
i fr2.chrUn                       I 12 I 9
s gasAcu1.chrXX                     2345596 66 +  19732071 CAACTATTAG-ATGTTTTACGATGCGCCACTGTGC------TTTCTCGTCGT------CATTAAGCGCACCGGCAAAAA---------
q gasAcu1.chrXX                                            9999999999-999999999999999999999999------99999999999------999999999999999999999---------
i gasAcu1.chrXX                   N 0 I 3
s oryLat2.chr2                     23857169 63 -  31118443 GAGTTCTTGT-ATGCTTTCAGATAAGCTATACGACAAAAATTTTAGCtgcat------tcttta---------caaaaa---------
q oryLat2.chr2                                             9999999999-99999999999999999999999999999999999999999------999999---------999999---------
i oryLat2.chr2                    I 25 I 7
s xenTro2.scaffold_1263               81599 66 +    112973 CAGGCATAGTCCTCTTCCAGGAGACAAGT------------CTCCCCAACGC-TCCTGATATTA---------ATAGAGCGACTAGAG
i xenTro2.scaffold_1263           C 0 n 0
s otoGar1.scaffold_84493.1-113195     61560 54 -    113195 TAACT-TGGT-TTCTTGTACACTCAA---------------TGAATCACCAA------CAATTA---------AAAAAA-ATCAAAA-
q otoGar1.scaffold_84493.1-113195                          99989-9965-999999799999999---------------99999999999------999999---------999999-9997999-
i otoGar1.scaffold_84493.1-113195 C 0 I 2201
s panTro2.chrY                       634461 59 +  23952694 caattatagt-ttcttgtacaacaggctt------------ttagttaacat------agatta---------aaaaaa-gacaaaaa
q panTro2.chrY                                             0000000000-000000000000000000------------00000000000------000000---------000000-00000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23135694 53 + 157549271 ctatcctagt-ttctgacaaaacagactt------------gaaattaacat------agatta---------aaa-------aaaaa
q ponAbe2.chr7                                             9099999999-999999999999999999------------99999999999------999999---------999-------99999
i ponAbe2.chr7                    C 0 C 0
s petMar1.Contig5115                  12425 45 +     23967 --------------------AACCGATTT------------TTGCTTTGCAAAGCATGAAGTTG---------TAAAAA-ACCAACA-
q petMar1.Contig5115                                       --------------------999999999------------99999999999999999999999---------999999-9999999-
i petMar1.Contig5115              T 1132 C 0
e tetNig2.chr5                      3743466 14 +  13390619 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=-49036.000000
s hg19.chrY                         7781259  90 +  59373566 agaatattccataagagtaaa-gtg--------ctat--atatacatccaatgcaaa--------agc-atccagattataaagcaagttctcagatac-------cctccaagaTG
s panTro2.chrY                       634520  90 +  23952694 agaatattccataagagtaaa-gtg--------ctat--atatacatccaatgcaaa--------agc-atccggattataaagcaagttctcagatac-------cctccaagaTG
q panTro2.chrY                                              000000000000000000000-000--------0000--000000000000000000--------000-000000000000000000000000000000-------00000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23135747  90 + 157549271 agggcattacataaaagcaaa-ggg--------ctat--atatgcacccaacatata--------agc-aaccagattataaagtaagtccttaaagac-------cctctaagaTG
q ponAbe2.chr7                                              999999999999999999999-999--------9999--999999999999999999--------999-999999999999999999999999999999-------99999999999
i ponAbe2.chr7                    C 0 C 0
s xenTro2.scaffold_676                96951  90 -    553874 AAGATCTCCTTTGCGAGAAAA-GCC--------TTTTTCACATACTTTACATTTAAA--------AGCTTTCTCGCCTGTA---TGAATTGCTTGGTGC-------CTGCAAAGCTT
i xenTro2.scaffold_676            I 10433 C 0
s oryLat2.chr2                     23857239  93 -  31118443 tttctcctgtgtgaattctcatgtgtttttCGATTCG--AGACACATC----CCTTA--------Act-tgttaaacatt--tttgacaagTATAAGGC-------TTCTCGACTGT
q oryLat2.chr2                                              9999999999999999999999999999999999999--999999999----99999--------999-99999999999--99999999999999999-------99999999999
i oryLat2.chr2                    I 7 I 30
s gasAcu1.chrXX                     2345665  84 +  19732071 TAATACCTACAGGAACTTTAA-GTG-----AAATTTA--AGACAATTTAAAACCTTA--------ATT-AGCCGGATTTT---------AATTTAAGAC-------ATTTTAAGGAC
q gasAcu1.chrXX                                             999999999999999999999-999-----9999999--999999999999999999--------999-99999999999---------9999999999-------99999999999
i gasAcu1.chrXX                   I 3 I 17
s fr2.chrUn                       102967072 104 - 400509343 GATCTACCAATTGATCTATTT-GTG--CCGACAATTG--TAACACATAAAGAGCTGAGTAATAACATC-TACAAAAATGTACATGAAGACATTTAGGAC-------TCTTTATGTAA
i fr2.chrUn                       I 9 I 626
s petMar1.Contig5115                  12470  97 +     23967 AATTGAGCATTTGCAAGTCAT-GGT------TAATAT--TGACATTTCCAG-GTGAT--------ATC-ATAcagtcttaaaaaaaacattttatatatacaagCACTTCTATACA-
q petMar1.Contig5115                                        999999999999999999999-999------999999--999999999999-99999--------999-99999999999999999999999999999999999999999999999-
i petMar1.Contig5115              C 0 C 0
e tetNig2.chr5                      3743466  14 +  13390619 I
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=-97618.000000
s hg19.chrY                         7781349  96 +  59373566 T--CAA---ATTAAATGGTCTTAAACAGTCATTACCTTTATA----TTGCATTTGTTCAGTGTT--------------------------------------------------------------AAATCTCTGTTGCTGAACA------------------CA---ATGTGCGGACTTG----TTAAAGG----------------------
s panTro2.chrY                       634610  96 +  23952694 T--CAA---ATTAAATGGTCTTAAACAGTCATTACCTTTATA----TTGCATTTGTTCAGTGTT--------------------------------------------------------------AAATCTCTGTTGCTGAACA------------------CA---ATGTGAGGACTTG----TTAAAGG----------------------
q panTro2.chrY                                              0--000---000000000000000000000000000000000----000000000000000000--------------------------------------------------------------0000000000000000000------------------00---0000000000000----0000000----------------------
i panTro2.chrY                    C 0 C 0
s xenTro2.scaffold_676                97041  68 -    553874 TTCCAAGTCAGAAAATGTTTTACTACATTCACTACATACATAGGGCTTGCATTTGTGAGTTGTT--------------------------------------------------------------TCAT------------------------------------------------------------------------------------
i xenTro2.scaffold_676            C 0 I 10138
s fr2.chrUn                       102967802  96 - 400509343 -----TCAGTCTGAActcttttccacatgttttacagatATG----CGGCTTCTCACCggtgtg--------------------------------------------------------------aattctcatgtggctGGAC------------------AAATTTGCAC---TTTGT----CTGAAAT----------------------
i fr2.chrUn                       I 626 I 1
s gasAcu1.chrXX                     2345766  97 +  19732071 -----ATGATCAGAATAGTTCCTCAAAGGATTTGCATCTATG----ACGTTTTACCCTTGTGT----------------------------------------------------------------ATTCT----TCTCATGTG------------------GGCATATAAGCTGTTAGAACTTCTAAAAT----------------------
q gasAcu1.chrXX                                             -----9999999999999999999999999999999999999----99999999999999999----------------------------------------------------------------99999----999999999------------------99999999999999999999999909999----------------------
i gasAcu1.chrXX                   I 17 I 1
s oryLat2.chr2                     23857362  96 -  31118443 -----TTTGcctaaaacttttattacattctttacaagaata----aggcttttctcctgtatg--------------------------------------------------------------agttctgaGGTGTCTTTTG------------------AG---ATCAGACGTTTGA----CAAAaac----------------------
q oryLat2.chr2                                              -----9999999999999999999999999999999999999----999999999999999999--------------------------------------------------------------9999999999999999999------------------99---9999999999999----9999999----------------------
i oryLat2.chr2                    I 30 I 1
s ponAbe2.chr7                     23135837  91 + 157549271 ----------ATAAATGTTCTTCCACTGTCATTACATTTATA----CTGCATTTGTTCAGTATT--------------------------------------------------------------AAATTTCAGATGTTGAACA------------------CA---GTATGAGGACTTG----GTAAAGG----------------------
q ponAbe2.chr7                                              ----------99999999999999999999999999999999----099999999999999999--------------------------------------------------------------9999999999999999999------------------99---9999999999999----9999999----------------------
i ponAbe2.chr7                    C 0 I 421
s echTel1.scaffold_192474              3291  92 -      4319 ---------ATTAAAGGCTTTTCCAAATTCCTTACGTTCATA----ATGCCTCTCTCCACTGTG--------------------------------------------------------------AATTCTCATATGTTGAATG------------------AG---GCTTGTGGAGTGA----GTAAATG----------------------
q echTel1.scaffold_192474                                   ---------999999999999999999999999999999999----996999999999999989--------------------------------------------------------------9979999999797789969------------------99---9998969999889----9999989----------------------
i echTel1.scaffold_192474         N 0 I 1
s danRer6.chr3                     59514870  78 +  60907308 -----------------------AACACTGATCACATGTGTA----CGGCTTCTCTCCAGTGTG--------------------------------------------------------------AATCCTCTCATGTCTTTTC------------------AG---GGTTCCTAAATGA----CTAAACC----------------------
i danRer6.chr3                    N 0 I 1
s tetNig2.chrUn_random             51493871  70 - 107808587 -------------------------------ttacacaaata----ggGTTTCTcccctgtgtg--------------------------------------------------------------aactctcatgtgctcagtt------------------aA---CGCACAGGTTTGG----ATGAATG----------------------
i tetNig2.chrUn_random            I 10402 I 184
s petMar1.Contig5115                  12567 191 +     23967 ------------TCatgcttatatatatttaaaataaaaatg----cttcaCTTGCCTTGTCTGGTGTTCTTCGTTTTCTCATCTTCCCACATCGGACAAGCTACTTGGATTTCCTGTGAATATGAAATTTCTTTACGTCCAACGTTACCTTCATCATACTGAAA---GTTCTCTTTTTGG----ATGGACATAACCTGCACAGCATCAACATT
q petMar1.Contig5115                                        ------------999999999998999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---9999999999999----99999999999999999999999999999
i petMar1.Contig5115              C 0 C 0
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=30473.000000
s hg19.chrY                         7781445 53 +  59373566 -----TCCACTTTTTTTTTTTAACACTTATGGACCTTCTCTCTACTATGAATTATCTT
s panTro2.chrY                       634706 51 +  23952694 -----TCCAC--TTTTTTTTTAACACTTATGGACCTTCTCTCTACTATGAATTATCTT
q panTro2.chrY                                             -----00000--0000000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s echTel1.scaffold_192474              3384 51 -      4319 -----TCTCT--TGCATTCTTTACACTCATAAGGCCTCTCTCCACTGTGAATTCTCAT
q echTel1.scaffold_192474                                  -----99999--6997999999999999999996899999999999979999999999
i echTel1.scaffold_192474         I 1 C 0
s xenTro2.scaffold_676               107247 51 -    553874 -----TTTCC--CACATTCTTTACAGGTGAATGGTTTCACCCCAGTGTGAATTCTCAA
i xenTro2.scaffold_676            I 10138 C 0
s fr2.chrUn                       102967899 51 - 400509343 -----TTTTC--CACATGTGTTGCAAATGTAAggcttctcacctgtgtggacCCTCAC
i fr2.chrUn                       I 1 C 0
s gasAcu1.chrXX                     2345864 51 +  19732071 -----TCTTT--TGCACATTTTACAGGAATATGGCTTCTCATTGGAGTGAGTCGGTGT
q gasAcu1.chrXX                                            -----99999--9999999999999999999999999999999999999999999999
i gasAcu1.chrXX                   I 1 C 0
s oryLat2.chr2                     23857459 51 -  31118443 -----tttat--cacattctttacaagaaaaaagcttttctcctgtgtgagttctcat
q oryLat2.chr2                                             -----99999--9999999999999999999999999999999999999999999999
i oryLat2.chr2                    I 1 C 0
s danRer6.chr3                     59514949 51 +  60907308 -----CTTGC--TACACTGTGAACACTTGTACAGTTTCTCTCCAGTGTGAACCTTCTC
i danRer6.chr3                    I 1 I 252
s tetNig2.chrUn_random             51494125 36 - 107808587 ----------------------ACACATATagggtttctcacctgtgtgaactctcat
i tetNig2.chrUn_random            I 184 C 0
s petMar1.Contig5115                  12758 54 +     23967 TTCACtttgt--aatttgttttgttCACATAAATCTCCT--TTAAGATGAGTCTTCTG
q petMar1.Contig5115                                       9999999999--999999999999999999999999999--99999999999999999
i petMar1.Contig5115              C 0 C 0
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I
e ponAbe2.chr7                     23135928 421 + 157549271 I

a score=-17283.000000
s hg19.chrY                         7781498 33 +  59373566 ATGTCCAATGAG-------CTGTGAAAACAAGCTCAATGT
s panTro2.chrY                       634757 33 +  23952694 ATGTCTAATGAG-------CTGTGAAAACAAGCTCAATGA
q panTro2.chrY                                             000000000000-------000000000000000000000
i panTro2.chrY                    C 0 C 0
s echTel1.scaffold_192474              3435 33 -      4319 ATGCCGATTGAG-------TTTTGAGGAATGATTAAAGGC
q echTel1.scaffold_192474                                  999969997999-------999998999989999999999
i echTel1.scaffold_192474         C 0 C 0
s xenTro2.scaffold_676               107298 33 -    553874 ATGTGTACGAAGGCTGCCCTTATCTGAAAAACC-------
i xenTro2.scaffold_676            C 0 C 0
s tetNig2.chrUn_random             51494161 33 - 107808587 gtgcttGGTTAG-------TTCGGAGGTTTGCACGAATGA
i tetNig2.chrUn_random            C 0 C 0
s fr2.chrUn                       102967950 33 - 400509343 ATGTCTTGACAA-------TGCATTgctttgtttgaaggc
i fr2.chrUn                       C 0 C 0
s gasAcu1.chrXX                     2345915 33 +  19732071 ATGAGACTTCAA-------ATGTGATGACTGAGTGAATGT
q gasAcu1.chrXX                                            999999999999-------999999999999999999999
i gasAcu1.chrXX                   C 0 C 0
s oryLat2.chr2                     23857510 33 -  31118443 gtgtcttttaag-------ATCAGATCTTCgaacaaaact
q oryLat2.chr2                                             999999999999-------999999999999999999999
i oryLat2.chr2                    C 0 C 0
s danRer6.chr3                     59515252 33 +  60907308 ATGCATCTTCAG-------CTGTGAAGCACTTAAAAATGT
i danRer6.chr3                    I 252 C 0
s petMar1.Contig5115                  12812 32 +     23967 ATGAGCTTTAAG-------AT-TGTAATTTAGCGAAAAGC
q petMar1.Contig5115                                       999999999999-------99-999999999999999999
i petMar1.Contig5115              C 0 C 0
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I
e ponAbe2.chr7                     23135928 421 + 157549271 I

a score=255686.000000
s hg19.chrY                         7781531 444 +  59373566 -TTTGTCACATTTTTCACATTTGTAGGGTTTCCCTACAGTTTGAATTTTCTTATG--ATTAGTAAGGTCTGAGAAGTACTTAAAGGCTTTACCACATTCTTCACATTTGTAGGGTTTACCTCCAGTATGATTTCTCTTGTGTTTAAATAAGGGTTGAGGAGCATGTAAATG-TTTGCCACGTTCTTTATATTTGTAGGGTTTTGTTCCAGTATGGACTCTTTTATGTTCAGTAAGGCTTGAAAACTTTTTA-----AAAGCTTTGTCACATTCTTTACATTTGTAGGA-TTATTTGCAATATGAATTATCTTTTT----TATAGTAAAATCT---------GAGAACAACCTACAGTCTTTGCCACA-----------TT-------CTTCACATTTG----TAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTTCTCTCCACT-AAATTTTTTTTATGCT---------CACTG---AAGTTTGAGCACA-ACTC--------TAAAGCTTTGCCACATTTATTACA----CTGACAAG----------------
s ponAbe2.chr7                     23136349 446 + 157549271 -TTTGTTACATTCTTCACATTTGTAGGGTTTCTCTCCAGTATGAATTCTCTTATG--ATTAGTAAGGTCTGAGAAGCACTTAAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTGTCTCCAGTATGATTCCTCTTGTGTTT-AACAAGGGTTGAGGAGCAGGTAAAAGTTTTGCCACATCCTTCACATTTGTAAGGTTTCTCTCCAGTATGAACTCTCTTATGTTCAGTAAGGTTTGAAAACTTTTTA-----AAGGCTTTGCCACATTCTTCACATTTGTAGCATCTCTCTGCAGTATGAATTTTCTTATG----TCTAGTAAAATCT---------GAGAACAACCTACAGTCTTTGCCACA-----------TT-------CTTCACATTTG----TAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTTCTCTCTGCTAAAAATGTCTTTACGTT---------CAGTG---AAGATTGAGCACA-ACTG--------AAAAGCTCTGCCACATTTATTACA----CTGACAGG----------------
q ponAbe2.chr7                                              -999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999099999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----99999999999999999999999999999999999999999999999999999999999----9999999999999---------99999999999999999999999999-----------99-------99999999999----999------------------------------------------------------------------------------------------------------------------------------------------------------------------------9999999999999999999999999999999---------99999---9999999999999-9999--------999999999999999999999999----99999999----------------
i ponAbe2.chr7                    I 421 C 0
s panTro2.chrY                       634790 445 +  23952694 -TTTGTCACATTTTTCACATTTGTAGGGTTTCCCTCCAGTTTGAATTTTCTTATG--ATTAGTAAGGTCTGAGAAGTACTTAAAGGCTTTACCACATTCTTCACATTTGTAGGGTTTACCTGCAGTATGATTTCTCTTGTGTTTAAATAAGGGTTGAGGAGCATGTAAATG-TTTGCCACGTTCTTTATATTTGTAGGGTTTTGCTCCAGTATGGACTCTTTTATGTTCAGTAAGGCTTGAAAACTTTTTA-----AAAGCTTTGTCACATTCTTTACATTTGTAGGATTTATCTGCAATATGAATTATCTTTTT----TATAGTAAAATCT---------GAGAACAACTTACAGTCTTTGCCACA-----------TT-------CTTCACATTTG----TAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTTCTCTCCACT-AAATTTTTTTTATGCT---------CACTG---AAGTTTGAGCACA-ACTC--------TAAAGCTTTGCCACATTTATTACA----CTGACAAG----------------
q panTro2.chrY                                              -000000000000000000000000000000000000000000000000000000--000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000-----00000000000000000000000000000000000000000000000000000000000----0000000000000---------00000000000000000000000000-----------00-------00000000000----000------------------------------------------------------------------------------------------------------------------------------------------------------------------------00000000000000-0000000000000000---------00000---0000000000000-0000--------000000000000000000000000----00000000----------------
i panTro2.chrY                    C 0 C 0
s echTel1.scaffold_192474              3468 446 -      4319 -TTTTCCACATTCTTTACATTCATAAGGCCTCTCTCCACTGTGAATTCTCATATG--TTGATTGAAGTTTGAGGAATGAGTAAAGGCTTTTCCACAATCCTTACATTCATAAGGCTTCTCTCCACTGTGAATTCTCATATGTTG-AATGAGGCTTGTGGATTGAGTAAATGTTTTCTTGCATTCTTTACACTCATAAGGCCTCTCTCCACTATGAATTCTCATATGTTGATTGAAGTTTGGGGAACGATTA-----AAGGCTTTTCCACAATCCTTACATTTATAAGGCCTCTCTCCACTGTGAATTCTCATATG----TACTTTGAGGTGT---------GTGGATGTATTAAAAGATCTCTCACA-----------TT-------CCTTACATTCA----TAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCCTCTCTCCACTGTGAATTCTCATATGTT---------GATTG---AAGTTTGAGGAAC-GTTT--------AAAGGCTTTTCCACATTCCTTACA----TTCATAAG----------------
q echTel1.scaffold_192474                                   -999999999999999999999999999999999999999979999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998699999-----99999999999999999999999999999899999999999999999999999999999----9999799876667---------99999669989999999899998999-----------99-------99969979977----698------------------------------------------------------------------------------------------------------------------------------------------------------------------------7657898899979675676899878499997---------99776---6679889979766-8578--------998977999596666998779776----98748878----------------
i echTel1.scaffold_192474         C 0 N 0
s xenTro2.scaffold_676               107331 446 -    553874 -TTTCCCACATTCTGTACAGGTGAATGGTTTCTCTCCAGTGTGAGTTCTCTCATG--TATACGAAGGCCGCCCTTATCTGTAAAACATTTCTCACATTCTGTACATGCGTATGGTTTCTCTCCGGTGTGGATTTTTTGGTGGCG-ATTAAGGGTGCTCTTTTCAGAAAAACTTTTCCCACATTCTGTACAGATACATGGTTTCTCCCCGGTGTGGATTCTTTCATGTACGAGAAGGCT-----GCGCTTTACAGCGAAACTTTTCCCACATTCTGCACAGGTGAATGGTTTCTCTCCAGTGTGAGTCCGTTGATG----TTTTTGAAGAATG---------TTTTTTTTATTAAAACATTTGCCACA-----------TT-------CCGTACAGGTG----TAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTCTCTCCCCTGTGTGAATTCTTTCATG--------------------GATTTTAAGATG-GCTCTTGCGAATAAAACATTTGCCACATTCTGCACA----AGTGTATG----------------
i xenTro2.scaffold_676            C 0 I 2
s tetNig2.chrUn_random             51494194 446 - 107808587 -TTTCCCACATGTTTCACAACTATAGGGTTTCTCACCGGTGTGACTTCTCATGTG--GACAACTAGTTCAGAATTTTGTTTAAAAGCTTTCCCACATGTTTCACAGATGTATGGTTTCTCGCCTGTGTGATTTCTCATGTGGAC-TTTTAATGCAGAACTTGTTTTGAACCCTTTctcacatgttttacacaaatagggtttctcacctgtgtgaactctcatgtgtTGAGTTAATGCAGAAGTCTGATTG-----AATGATTTCCCACATGTTTCACAACTGTATGGTTTCTCACCCGTGTGACTTCTCATGTG----GACGGTTAGGGTA---------TAACTATGTTTGAaccctttcccaca-----------tg-------ttttacacaaa--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------taggTCTTCTGACCCGTGTGCTGCATCATGTGGTCCTC---CAGTCTGCtttttttACC--------AAAGGCTTCGCCACAGGTTTTACA----AACATGAG----------------
i tetNig2.chrUn_random            C 0 C 0
s fr2.chrUn                       102967983 471 - 400509343 -ttttccacatgtgGTGCAAATATAGGGCTTTTCACCTGTATGGATTCTCATGTG--GTGTGACAAGTCAGTGCTTTGTGTAAAAGCTTTCCCACAGGTGTTGCAAACATACGGTTTGTCACCTGTATGGATTCTCATGTGTCG-CGATAATTCATAGCTGCGTTTGAAAGCTTTCCTACATGTGGTGCAAACATATTGCTTCTCACCAGTGTGGATTCTTGTGTGTCGCGATAActcctcattttctttg-----aaagCTTTTCCGCATGTTGCACAACTAAATGGTTTC---CCCGTGTGGACTTTCAGGTGCCTCTGCAGTTTTGACA---------GGA----ACTTAAAGTCTTTTCCACAATCAAAACACTTGAAAGAATTTGTACCTGAAAGACAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTTTGTAAGTCCGCAGGGTTGTGCGCACTGACAGATGACCCTG---AGGGTTGGTTTTC----------------GTTTACATTAGAGTTCTTATAGAGCAGCCTCAA----------------
i fr2.chrUn                       C 0 C 0
s gasAcu1.chrXX                     2345948 446 +  19732071 -TTTCCCACATGTGTTGCAGGAATATGGCTTCTCCCCAGTGTGGACCCTTGTATGAAGCTTCAAAGAT--GGTGCGTGAGTGAATGTTTTCCCACATGTGTTGCAGGAATATGGCTTCTCCCCAGTGTGGATCCTTGTATGAAG-CTTTAAATGTGATTTGTCTCTGAATGTTTTCCCACATGTGTTGCAGGAATATGGCTTCTCCCCAGTGTGGACCCTTGTATGAAGCTTCAAAGATGCTGCGTGATTG-----AATGTTTTCCCACATGTGATGCAGGAATATGGCCTTTCACCAGAATGAATTTCCGTGTG----AAGTTTTATGCTA---------CTACTAAATTTGAATGTTTTTCCACA-----------TG-------TTTTGCAAGAA----AAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCTTCTCATCACTATGAACTCTTTTATGAT---------TCTTA---CATGCTGATTCAT-GAAT--------GAATCTTTTCCCACAGGTGTTGCA----TACATATG----------------
q gasAcu1.chrXX                                             -9999999999999999999999999999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----99999999999999999999999999999999999999999999999999999999999----9999999999999---------99999999999999999999999999-----------99-------99999999999----999------------------------------------------------------------------------------------------------------------------------------------------------------------------------9999999999999999999999999999999---------99999---9999999999999-9999--------999999999999999999999999----99999999----------------
i gasAcu1.chrXX                   C 0 C 0
s oryLat2.chr2                     23857543 438 -  31118443 -tttattacat---tcacAAGAAAAGGGCTTCTCgcctgtgtgagttttcatgtg--tcCTCTAAGATGAGATCTATCCTtgaaacttttatcacattctttacaagaatagGGCTTCTcgcctgtgtgagttctcatgtgttt-tttgagatcaCATAGGCGACAataacttttatcacattcttcacaagaaaaaggcctttctttTGCATGATTTCTCATGTGTTCTTTTAAATAAGACAACTTTCTA-----AAATCTTTATTGCATTCTTTACAGATAAAAAGTCTTTCAACAGGCTCA--------GTA----ATGTCTTTGTCTACATGAGGACCAACTACTCTTGAGT-TTTCACCAGA-----------CT-------TTAAagaggaa----att------------------------------------------------------------------------------------------------------------------------------------------------------------------------attttttcct---ttggggATTGTTTGCGTT---------TCTTAACCAAAGCTGCCTTCT-T--T--------GATTTTTTAccaacatcagagtca----cac---tg----------------
q oryLat2.chr2                                              -9999999999---99999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----999999999999999999999999999999999999999999999999--------999----9999999999999999999999999999999999999-9999999999-----------99-------99999999999----999------------------------------------------------------------------------------------------------------------------------------------------------------------------------9999999999---999999999999999999---------999999999999999999999-9--9--------999999999999999999999999----999---99----------------
i oryLat2.chr2                    C 0 C 0
s danRer6.chr3                     59515285 446 +  60907308 -TTTGCTGCAGTGTTCACATTTGTGTGGTTTCTCTCCGGTGTGGATCTTCATGTG--CTGAGTAAGGCGTGATGATAGGCTGAAACTCTTCCCACACTGAGAACATGTGAACGGTTTCTCTCCGGTGTGGATCCTCATGTGTTG-ATTAAGGGATGATGGTTCAGAGAAACTCGTCCCACACTGAGTACATGTGTGTGGTTTCTCTCCAGTGTGGGTCCTCATGTGTCTATTGCGGTGTGATGAGTGGCTA-----AAACTCTTCCCACACTGAGAACATGCGTATGGTTTCTCTCCAGTGTGGATCATCTTGTG----TTTAGTAAAGTTT---------GATACGTATCTGAAACTCTTCCCACA-----------CT-------GAGGACATGTG----AAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTTCTCTCCGGTGTGGACCCTCATGTGCT---------GATTA---AGGGATGATGATA-GCCT--------GAAACTCTTCCCACACTGAGAACA----TATGAAAG----------------
i danRer6.chr3                    C 0 C 0
s petMar1.Contig5115                  12844 631 +     23967 TTTTTCCACAAATATTACATGCATATGGCTTCTCTCCGGTGTGTATCCGCTGGTG--GGTTTTCAAGTGAGGCTTTTGCGCAAAACCCCTTCCACAGTCTTTGCATATGAAAGGTTTTTCTCCAGTATGTGTCTTTTGATGAAC-AGTCATGGCACTGGAATATGAAAAACTCTTCCCACACTCTTTGCAAACATATGGTCTCTCTCCAGTATGAATTTTATGATGTTCCTTCAGGGTGGATGCCTGTAAA-----AACCTTTTCCCACAATCTGTGCATATAAATGGCCTTTCTCCAGTGTGCGTGAACTGATG----TGTTTTGAGGGAA---------GAAGGCTGAGAAAACCTCTGGCCACA-----------AT-------CTTGGCATGCA----TATGGCCTTTCTCCGGTGTGGGTCAACCGATGAACCTTCATGTAAGAAGCCTTTGAAAACCCTTTTCCGCAGTCATTGCAAACAAATGGCTTCTCTAAAGAATGTGTCAACGAATGTGTCTTCAATGTGGATTTAAGTGAAAAACGCTTTCCACAGTCTTGACATATAAAAGGCTTCTCTCCAGTGTGGGTCCTCAAATGAG---------CCTTC---AGGTGTTGGCCTT-GAGA--------AAATCGCTGTTCACAATGTTTGCA----CATGTATGGCTTCACTCCTGCATG
q petMar1.Contig5115                                        9999999999999999999999999999999999999999999999999999999--999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----99999999999999999999999999999999999999999999999999999999999----9999999999999---------99999999999999999999999999-----------99-------99999999999----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---------99999---9999999999999-9999--------999999990999999999999999----999999999999999999999999
i petMar1.Contig5115              C 0 C 0
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=-20375.000000
s hg19.chrY                         7781975 20 +  59373566 --TTTTGCTCTGGGTAG-----TTGAT
s panTro2.chrY                       635235 20 +  23952694 --TTTTGCTATGGATAG-----TTGAT
q panTro2.chrY                                             --000000000000000-----00000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23136795 20 + 157549271 --TTTTGCTATGGGTAG-----TTGAC
q ponAbe2.chr7                                             --999999999999999-----99999
i ponAbe2.chr7                    C 0 C 0
s xenTro2.scaffold_676               107779 25 -    553874 --CTCTCCCCTGTGTGGATTCTTTCAT
i xenTro2.scaffold_676            I 2 C 0
s tetNig2.chrUn_random             51494640  6 - 107808587 ----------------G-----ACTGT
i tetNig2.chrUn_random            C 0 T 957
s fr2.chrUn                       102968454  3 - 400509343 ----------------G-----TC---
i fr2.chrUn                       C 0 I 11
s gasAcu1.chrXX                     2346394  6 +  19732071 ----------------G-----TTGAT
q gasAcu1.chrXX                                            ----------------9-----99999
i gasAcu1.chrXX                   C 0 C 0
s oryLat2.chr2                     23857981  6 -  31118443 ----------------a-----cctgc
q oryLat2.chr2                                             ----------------9-----99999
i oryLat2.chr2                    C 0 C 0
s danRer6.chr3                     59515731  6 +  60907308 ----------------G-----TTTCG
i danRer6.chr3                    C 0 I 13
s petMar1.Contig5115                  13475 22 +     23967 TATTCTCTGGTGAACAG-----CTAAC
q petMar1.Contig5115                                       99999999999999999-----99999
i petMar1.Contig5115              C 0 C 0
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=-70606.000000
s hg19.chrY                         7781995 71 +  59373566 AAACATTGATGAAATCCATTA-------AACT----GCTCTTCTGCC---CTTTGCAA--------TTACCCACACTTT-----------------GGTAGTCTTTCTTT
s panTro2.chrY                       635255 71 +  23952694 AAACATTGATGAAATCCATTA-------AACT----GCTTTTCTGCC---CTTTGCAA--------TTACCCACACTTT-----------------GGTAGTCTTTCTTT
q panTro2.chrY                                             000000000000000000000-------0000----00000000000---00000000--------0000000000000-----------------00000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23136815 72 + 157549271 AAACATTGATGAAGGCCATTGT------AACT----GCTTTTCTGCC---CCTTGCAA--------TTACCCACACTTT-----------------GGTAGTCTTTCTTT
q ponAbe2.chr7                                             9999999999999999999999------9999----99999999999---99999999--------9999999999999-----------------99999999999999
i ponAbe2.chr7                    C 0 C 0
s xenTro2.scaffold_676               107804 68 -    553874 GAATTTTAA-GATGGCCCTTGCG---AGAAAA----GCCTTTTTCACATACTTTACAT--------TTA--AAAACTTT-----------------A-------TCATCT
i xenTro2.scaffold_676            C 0 C 0
s fr2.chrUn                       102968468 60 - 400509343 ---------CAGAGACCACTGAACCTATAATA----TACCTTATTAT---GTCTTCACTCTGGTCATTTTCATCAT----------------------------------
i fr2.chrUn                       I 11 C 0
s gasAcu1.chrXX                     2346400 68 +  19732071 CAACAC--TGTGAGCTCTTTTCACGTGAGACAACAAGCCATTTTTAT---GTTTGAAGTA------TTTCCCACATTTT-------------------------------
q gasAcu1.chrXX                                            999999--999999999999999999909999999999999999999---9999999999------9999999999999-------------------------------
i gasAcu1.chrXX                   C 0 N 0
s oryLat2.chr2                     23857987 74 -  31118443 tgacat-gtgagagctgtccgcactttggaca-------tgtcttct---gtctcttctc------ttcctcttatctctgttctgtgggt-------------------
q oryLat2.chr2                                             999999-9999999999999999999999999-------99999999---9999999999------9999999999999999999999999-------------------
i oryLat2.chr2                    C 0 N 0
s danRer6.chr3                     59515750 50 +  60907308 ----------------CATCATGTGTTTAATA--ACGCTCAATTCGT---GTTTGAAACT------TTTCCCACACT---------------------------------
i danRer6.chr3                    I 13 I 459
s petMar1.Contig5115                  13497 78 +     23967 -------------GTACGCCG-ACTTGAAAAT----GTTTTTCCACA---CTGCTCAC--------ACATGTACATCTTCTCTGCATTTGTAGCCGATTGATTTTTC---
q petMar1.Contig5115                                       -------------99999999-9999999999----99999999999---99999999--------99999999999999999999999999999999999999999---
i petMar1.Contig5115              C 0 C 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=-28628.000000
s hg19.chrY                         7782066 51 +  59373566 AAATGAA--AATCAGTAAAGTCACAGCTTTCATATTTTATCAGAATCAC-----TTTT
s panTro2.chrY                       635326 51 +  23952694 AAATGAA--AATCAGTAAAGTCACAGCTTTCATATTTTATCAGAATCAC-----TTTT
q panTro2.chrY                                             0000000--0000000000000000000000000000000000000000-----0000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23136887 51 + 157549271 AAATGTA--AATTATTAAGGTCACAGCTTCCATATTTTCTCAGAATCAC-----TTTT
q ponAbe2.chr7                                             9999999--9999999999999999999999999999999999999999-----9999
i ponAbe2.chr7                    C 0 C 0
s xenTro2.scaffold_676               107872 50 -    553874 ATATGAATTGCTTGGTGCCTGCAAAGCTTTTCCA---TGTCAGAATAAT-----TTTT
i xenTro2.scaffold_676            C 0 I 135
s fr2.chrUn                       102968528 54 - 400509343 AAATAGG--AGTCAAGATAACTGCATCAGTCTCC-TGTTTCAGCACAAT-CTGCTCTC
i fr2.chrUn                       C 0 C 0
s gasAcu1.chrUn                     4399272 29 -  62550211 ----GAG--TGTTATAATAAT--------------AATACCTTCA---------TTTT
q gasAcu1.chrUn                                            ----999--999999999999--------------9999999999---------9999
i gasAcu1.chrUn                   N 0 C 0
s oryLat2.chr4                     15867903 46 -  34636364 GACTCAG--TGTCAGACTGATCTGATCTGTGACA-GCTGTCCACA---------TTTC
q oryLat2.chr4                                             9999999--9999999999999999999999999-9999999999---------9999
i oryLat2.chr4                    N 0 C 0
s danRer6.chr3                     59516259 54 +  60907308 CACCAGA--AGTCTGTAAATTAGGGTTTTTCTC--AGCTTCAACATGACGTTCCTCCT
i danRer6.chr3                    I 459 C 0
s petMar1.Contig5115                  13575 46 +     23967 AAAATAG--ATTCACTTAAAGGATCATTTCCGTAATCCATATGATTCA----------
q petMar1.Contig5115                                       9999999--999999999999999999999999999999999999999----------
i petMar1.Contig5115              C 0 N 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I

a score=-15219.000000
s hg19.chrY                         7782117 29 +  59373566 TGGAATGAATCTT----------------------------------TTCTTTTGTGGTCTGT
s panTro2.chrY                       635377 29 +  23952694 TGGAATGAATCTT----------------------------------TTCTTTTGTGGTCTGT
q panTro2.chrY                                             0000000000000----------------------------------0000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23136938 29 + 157549271 TGAAATGAATCTT----------------------------------TTATGTCATGATCCGG
q ponAbe2.chr7                                             9999999999999----------------------------------9999999999999999
i ponAbe2.chr7                    C 0 C 0
s fr2.chrUn                       102968582 44 - 400509343 CCTCAGGATTAATGCAGaggtcctcctc-------------------ttcctctttgatttgt
i fr2.chrUn                       C 0 T 1519
s gasAcu1.chrUn                     4399301 13 -  62550211 ATATAGCGTTTTT--------------------------------------------------
q gasAcu1.chrUn                                            9999999999999--------------------------------------------------
i gasAcu1.chrUn                   C 0 I 1
s oryLat2.chr4                     15867949 39 -  34636364 TGACAGTACTTTTGC-----TCCTCCCA-------------------TCTCTTTTCAGTGGGT
q oryLat2.chr4                                             999999999999999-----99999999-------------------9999999999999999
i oryLat2.chr4                    C 0 I 4
s danRer6.chr3                     59516313 58 +  60907308 CTTCACTCTCCTTAT-----TCTCTCCAAATGGGTCTGAAACAAAGTTCCTTTTTTAGTAAGT
i danRer6.chr3                    C 0 C 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e papHam1.scaffold23501               16076 2196 -     34585 I
e xenTro2.scaffold_676               107922 135 -    553874 I

a score=-714.000000
s hg19.chrY                         7782146 72 +  59373566 CAATATCTCTGCAGTTAAATGAAAAGAGCCAACT------GAAGACAAAAGAAAAAAATTTCTCCCTCATTAGACTCA
s panTro2.chrY                       635406 72 +  23952694 CAATATCTCTGCAGTTAAATGAAAAGAGCCAACT------GAAGACAAAAGAAAAAAATTTCTCCCTCATCAGACTCA
q panTro2.chrY                                             0000000000000000000000000000000000------00000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23136967 70 + 157549271 CAGTATCTCTGCAGTAAAATGAAAAGAGCCAGCT------GGAGAAAAAAAATAAAA--TTCTCCCTCATTAGACTCA
q ponAbe2.chr7                                             9909999999999999999999999999999999------99999999999999999--9999999999999999999
i ponAbe2.chr7                    C 0 C 0
s gasAcu1.chrUn                     4399315 60 -  62550211 CTAAATACCCAAAGACGCTTTACAAAGGGCAAAG------ACAGACAAAAACAAAAG---ACACAAACA---------
q gasAcu1.chrUn                                            9999999999999999999999999999999999------99999999999999999---999999999---------
i gasAcu1.chrUn                   I 1 C 0
s oryLat2.chr4                     15867992 73 -  34636364 CTCTCCATCTGTAGTTGCAT--CAAAGCTCCAAGTGAGCAGCTGCTGAGAGTGAAAA---TCGGCCTCATTGTGCTCA
q oryLat2.chr4                                             99999999999999999999--99999999999999999999999999999999999---999999999999999999
i oryLat2.chr4                    I 4 T 1340
s danRer6.chr3                     59516371 33 +  60907308 -----------------CAATAAAAAATAAAAAG------------TAGGATGAAAA---TTTGA-------------
i danRer6.chr3                    C 0 C 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e fr2.chrUn                       102968626 1519 - 400509343 T
e papHam1.scaffold23501               16076 2196 -     34585 I
e xenTro2.scaffold_676               107922 135 -    553874 I

a score=6739.000000
s hg19.chrY                         7782218 51 +  59373566 GGTGAGTACATTTTACAAACATGTAATTATACAAACCacattaac---aaagtg
s panTro2.chrY                       635478 48 +  23952694 GGTGAGTACATTTTACA---ATGTAATTATACAAATCacattaac---aaagtg
q panTro2.chrY                                             00000000000000000---0000000000000000000000000---000000
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23137037 51 + 157549271 GGTGAATATACTTCACAAATATATAATTATACAAAGCACATTAAC---AAAACG
q ponAbe2.chr7                                             999999999999999999999999999999999999999999999---999999
i ponAbe2.chr7                    C 0 C 0
s gasAcu1.chrUn                     4399375 47 -  62550211 -GAACAGAACATTTAAGAAAA-GTAGT--TGCAGGCGAGATTGAA---GAGGTG
q gasAcu1.chrUn                                            -99997999989999999999-99999--9989998999969979---697869
i gasAcu1.chrUn                   C 0 I 819
s danRer6.chr3                     59516404 50 +  60907308 AGTGTAAAGACTCTGTAAACA-CTGGC--TACAAA-AACATTAACTTTGATGCA
i danRer6.chr3                    C 0 I 4
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e fr2.chrUn                       102968626 1519 - 400509343 T
e papHam1.scaffold23501               16076 2196 -     34585 I
e oryLat2.chr4                     15868065 1340 -  34636364 T
e xenTro2.scaffold_676               107922 135 -    553874 I

a score=63985.000000
s hg19.chrY                         7782269 352 +  59373566 acaatagaataccatagtccctaattccttta---cagacatat---aaatttaacagtaatatacttaccaaaatgcctttgtgagaagtctaagaatcagttaagcatttgcagcaccccaagtgagTAAAATGCCAAGAAACATATAG---AAGTGTAACAAAACTATTTCATATTTACACACCACGGACATTTTTTATCCTATGAAAAATGTAG----AGACT-GATAACTCCTATCTT-ACCCTCCAAAAATAAATAAACT--GGTGGCACTTAT----GTCCATGCTTCTGGCTTTCTGAGACCTTATCAAAGACT-------AATTTGTATATT-CACAACAGTGTTTAAAG--GAAAGGTGGTAAACTTTGACAG--
s panTro2.chrY                       635526 351 +  23952694 acaatagaataccatagtccctaattccttta---cagacatat---aaatttaacagtaatatacttaccaaaatgcctttgtgagaagtctaagaatcagttaagcatttgcagcaccccaagtgagcaaaatgccaagaaCCGTATAG---AAGTGTAACAAAACTATTTCATATTTACACACCACGGACATTTTTTATCC--TGAGAAATGTAG----AGACT-GATAACTCCTATCTG-ACCCTCCAAAAATAAATAAAAT--AGTGGTACTTAT----GTCCATGCTTCTGGCTTTCTGAGACCTTATCAAAGACT-------AATTTGTATATTCCACAACAGTGTTTAAAG--GAAAGGTGGTAAACTTTGACAG--
q panTro2.chrY                                              00000000000000000000000000000000---000000000---00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000---00000000000000000000000000000000000000000000000000--000000000000----00000-000000000000000-0000000000000000000000--000000000000----00000000000000000000000000000000000000-------000000000000000000000000000000--0000000000000000000000--
i panTro2.chrY                    C 0 C 0
s ponAbe2.chr7                     23137088 357 + 157549271 ACAATAAAATACCACAGGCTCTATATTC-TTA---CAGACGTAT---AAACCTAACAGAAATATACTGACCAAAATGCCTTTGCGAGAAGTCTAAGAACCAGTTAAGCATTTGCAGCACACCAAGTGAGCAAAATGCCAAGAACCACATAG---AAGTGTAATAAAAGTATTTCATATTTACCCACCACAGCCATTCTTCATCCTATGATGACTCTAACTATAGACT-CCAAACTCCTGTCTTCCCCCTCCGAAAATAAATAAAAC--AGTGGCACACGT----GTCCATGCTTCTGGCTTACTGAGACCTTACCAAAGACT-------AATTTCTATATTCCATGACAGTGTTGAAAG--GAAAGGTGGTATACACTGACAG--
q ponAbe2.chr7                                              9999999999999999999999999999-999---999998999---99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999--999999999999----99999999999999999999999999999999999999-------999999999999999999999999999999--9999999999999999999999--
i ponAbe2.chr7                    C 0 C 0
s danRer6.chr3                     59516458 341 +  60907308 AATGTAAAATACATCAGATCGTGTTTAGTTTGGTCTTGTCATATTCAATGTTTAACAA-------------AACATGGAAATAAAAGACGACTAAGATGCAGT-----------------CCCTGTTTGTACCCTGTTAAAAGAAATACAGTACCAGtctaa-ataactgctttgtaactgcattgtatgta-gtttcaaatgaaatgattactccag----tcattacattattactattac-caatgttaataataactaatattaagagtgatttatgaaggatcatgcgact------ctgaagactTATAAACTACTTTTGAACAGTTATTTTAtt-gaccttattcttcaatgctgaagtgcgctcgtttttgcgattg
i danRer6.chr3                    I 4 C 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e otoGar1.scaffold_84493.1-113195     61614 2201 -    113195 I
e gasAcu1.chrUn                     4399422 819 -  62550211 I
e fr2.chrUn                       102968626 1519 - 400509343 T
e papHam1.scaffold23501               16076 2196 -     34585 I
e oryLat2.chr4                     15868065 1340 -  34636364 T
e xenTro2.scaffold_676               107922 135 -    553874 I

a score=2225.000000
s hg19.chrY                         7782621 28 +  59373566 ---------TTTTG-GGCAGTTGTGACTAAAGACAAAA
s ponAbe2.chr7                     23137445 28 + 157549271 ---------TTTCG-GACAGCTGAGACCAAAGGTAAAT
q ponAbe2.chr7                                             ---------99999-99999999999999999999999
i ponAbe2.chr7                    C 0 C 0
s panTro2.chrY                       635877 28 +  23952694 ---------TTTTG-CGCAGTTGTGACTAAAGACAAAA
q panTro2.chrY                                             ---------00000-00000000000000000000000
i panTro2.chrY                    C 0 C 0
s otoGar1.scaffold_84493.1-113195     63815 28 -    113195 ----------ACTGGGGGTGCTGAAACAAAAGGTAAAA
q otoGar1.scaffold_84493.1-113195                          ----------9999999999989999999999999999
i otoGar1.scaffold_84493.1-113195 I 2201 C 0
s papHam1.scaffold23501               18272 23 -     34585 ---------------GACAACTGAGACCAAAAGTAAAT
q papHam1.scaffold23501                                    ---------------99999999999999999999999
i papHam1.scaffold23501           I 2196 I 374
s danRer6.chr3                     59516799 37 +  60907308 ttttagaactttcgattcagctgcgtatgggagaaat-
i danRer6.chr3                    C 0 C 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e gasAcu1.chrUn                     4399422 819 -  62550211 I
e fr2.chrUn                       102968626 1519 - 400509343 T
e oryLat2.chr4                     15868065 1340 -  34636364 T
e xenTro2.scaffold_676               107922 135 -    553874 I

a score=12965.000000
s hg19.chrY                         7782649 106 +  59373566 GACCATCAAAAG---AAAAAATCTTCAGTGTCATAGACAGACAATGGGCATC-CAGCTGACTGCAGGATCTCAATGAGAAATATGGGGAATTActgggagcgttgattca
s otoGar1.scaffold_84493.1-113195     63843  89 -    113195 TATTGTTACTGCACCAGAGAAACTCCAATACAACAGACAAATTCAGGTCTAG-CAAGCGATTACAAGCTCTTAGGAGGAAATGTGGGGAA--------------------
q otoGar1.scaffold_84493.1-113195                           9999999999999999999999999999999999999999999999999993-9999899998987543122269899999873688999--------------------
i otoGar1.scaffold_84493.1-113195 C 0 N 0
s ponAbe2.chr7                     23137473 110 + 157549271 GACTGTTACAAGAGAAGAAAGACTTCAGTATCATAGACAGACAATGGGTATAGCAAGTGACTAAGGGATCTCAATAAGAAACATAGGGAATggccagaagtggtggctca
q ponAbe2.chr7                                              99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7                    C 0 C 0
s panTro2.chrY                       635905 106 +  23952694 GACCATCAAAAG---AAAAAATCTTCAGTGTCATAGACAGACAATGGGCATC-CAGCTGACTGCAGGATCTCAATGAGAAATATGGGGAATTActgggagcgttgattca
q panTro2.chrY                                              000000000000---0000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000
i panTro2.chrY                    C 0 C 0
s danRer6.chr3                     59516836  43 +  60907308 gactaggaataa------------------taaacggcagaaaacggtcaaa-ctgctagct------------------------------------------------
i danRer6.chr3                    C 0 N 0
e tetNig2.chrUn_random             51494646 957 - 107808587 T
e gasAcu1.chrUn                     4399422 819 -  62550211 I
e fr2.chrUn                       102968626 1519 - 400509343 T
e papHam1.scaffold23501               18295 374 -     34585 I
e oryLat2.chr4                     15868065 1340 -  34636364 T
e xenTro2.scaffold_676               107922 135 -    553874 I

a score=26602.000000
s hg19.chrY               7782755 118 +  59373566 cacctg--taattccagcac----------ttt-ggaggctgaggagggtggatcaa---ctgaggtcaaaagttcaagaccagctaggtcaacatggtgaaaccctgt--ctctactgaaaatacaaaagttagc
s panTro2.chrY             636011 118 +  23952694 cacctg--taattccagcac----------ttt-ggaggctgaggagggtggatcaa---ctgaggtcaaaagttcaagaccagctaggtcaacatggtgaaaccctgt--ctctactgaaaatacaaaagttagc
q panTro2.chrY                                    000000--000000000000----------000-00000000000000000000000---0000000000000000000000000000000000000000000000000--0000000000000000000000000
i panTro2.chrY          C 0 C 0
s ponAbe2.chr7           23137583 119 + 157549271 cacctg--taatcccagcac----------tttgggaggctgaggcaggtggaccac---ctgaggtcagatgttcaagaccagacaggccaacatggtgaaaccttgt--ctcaactaaaaatacaaaaattagc
q ponAbe2.chr7                                    999999--999999999999----------999999999999999999999999999---9999999999999999999999999999999999999999999999999--9999999999999999999999999
i ponAbe2.chr7          C 0 I 57
s danRer6.chr5           71576218 118 +  74451498 TACCTGTTTAACTCTGAAACAGACCCAAAATAT-GAAGAATAAAGGCGAGAAGTCAAGAGATGCAGTCGGATCTTT--------CCAGTCTGACCTGGTGTGACCTAGTTGTTCATCTTAAAacaca---------
i danRer6.chr5          N 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrUn           4399422 819 -  62550211 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18295 374 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=3282.000000
s hg19.chrY               7782873 43 +  59373566 cacagcagaaaccagtaatccaagctcttaagtaggcagaggc
s panTro2.chrY             636129 43 +  23952694 cacagcagaaaccagtaatccaagctcttaagtaggcagaggc
q panTro2.chrY                                   0000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s danRer6.chr5           71576336 31 +  74451498 caca------------cacacacacacacaaacacacacatac
i danRer6.chr5          C 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrUn           4399422 819 -  62550211 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18295 374 -     34585 I
e ponAbe2.chr7           23137702 57 + 157549271 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=14293.000000
s hg19.chrY               7782916 74 +  59373566 agga-gaattgc----------ttgaatctgggatgtggaggttgcagtc----------agccaagtttatgccattgcactccagcctgggca
s ponAbe2.chr7           23137759 74 + 157549271 agga-gaattgc----------ttgaagtcaggaggtggaggttgcaatg----------agccaagcttgtaacattgcactccagtctgggca
q ponAbe2.chr7                                   9999-9999999----------9999999999999999999999999999----------99999999999999999999999999999999999
i ponAbe2.chr7          I 57 C 0
s panTro2.chrY             636172 74 +  23952694 agga-gaattgc----------ttgaatctgggatgtggaggttgcagtc----------agccaagtttatgccattgcactccagcctgggca
q panTro2.chrY                                   0000-0000000----------0000000000000000000000000000----------00000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s danRer6.chr5           71576367 86 +  74451498 aGAATGAATTGTTGCTTCAAAGTTAAATGGCAAATAAGGGGGGTACAAACTCAGAGGGAGAGAGAATTTCAGACAAT----CTTCagctt-----
i danRer6.chr5          C 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrUn           4399422 819 -  62550211 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18295 374 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=-13.000000
s hg19.chrY                     7782990 43 +  59373566 acaacagtgaaactccaactcaaaaataaaaaataaaaataaa
s panTro2.chrY                   636246 43 +  23952694 acaacagtgaaactccaactcaaaaataaaaaataaaaataaa
q panTro2.chrY                                         0000000000000000000000000000000000000000000
i panTro2.chrY                C 0 C 0
s ponAbe2.chr7                 23137833 26 + 157549271 acaagagtaac------actcaaaaaaaaaaa-----------
q ponAbe2.chr7                                         99999999999------999999999999999-----------
i ponAbe2.chr7                C 0 C 0
s micMur1.scaffold_27112           9224 34 +      9508 AAAACACTTTTACTCATGCTCTAAAATTTGAAGG---------
q micMur1.scaffold_27112                               9999999999999998999999999999999999---------
i micMur1.scaffold_27112      N 0 C 0
s papHam1.scaffold23501           18669 22 -     34585 ---------------------aaaaaaaaaaaaaaaaaaaaaa
q papHam1.scaffold23501                                ---------------------7779999999999999999999
i papHam1.scaffold23501       I 374 C 0
s gorGor1.Supercontig_0010025      3451 28 -      8833 ---------------caaatcaaaaaaaaaaaaaaaaaaagga
q gorGor1.Supercontig_0010025                          ---------------9999999999999999999999999999
i gorGor1.Supercontig_0010025 N 0 C 0
s danRer6.chr5                 71576453 40 +  74451498 ---aaagggacagttcagcccaaaattcaacatttactcaagt
i danRer6.chr5                C 0 C 0
e tetNig2.chrUn_random         51494646 957 - 107808587 T
e gasAcu1.chrUn                 4399422 819 -  62550211 I
e fr2.chrUn                   102968626 1519 - 400509343 T
e oryLat2.chr4                 15868065 1340 -  34636364 T
e xenTro2.scaffold_676           107922 135 -    553874 I

a score=-9331.000000
s hg19.chrY                     7783033 15 +  59373566 gg----------aaagaaGAAAACA--
s panTro2.chrY                   636289 15 +  23952694 gg----------aaagaaGAAAACA--
q panTro2.chrY                                         00----------0000000000000--
i panTro2.chrY                C 0 C 0
s micMur1.scaffold_27112           9258  2 +      9508 -----------------------CT--
q micMur1.scaffold_27112                               -----------------------99--
i micMur1.scaffold_27112      C 0 N 0
s papHam1.scaffold23501           18691 20 -     34585 aaaaaaaaaaaaaaGGAGGA-------
q papHam1.scaffold23501                                99999999999999999999-------
i papHam1.scaffold23501       C 0 I 1367
s gorGor1.Supercontig_0010025      3479  2 -      8833 ga-------------------------
q gorGor1.Supercontig_0010025                          99-------------------------
i gorGor1.Supercontig_0010025 C 0 N 0
s gasAcu1.chrV                  9098811 15 +  12251397 ------------GGAAAATCAAACATA
q gasAcu1.chrV                                         ------------999999999999999
i gasAcu1.chrV                n 819 C 0
e tetNig2.chrUn_random         51494646 957 - 107808587 T
e danRer6.chr5                 71576493  0 +  74451498 C
e fr2.chrUn                   102968626 1519 - 400509343 T
e ponAbe2.chr7                 23137859  0 + 157549271 C
e oryLat2.chr4                 15868065 1340 -  34636364 T
e xenTro2.scaffold_676           107922 135 -    553874 I

a score=4808.000000
s hg19.chrY               7783048  96 +  59373566 AGAAAAAAAC-------ATGAGGAAATCTTTTTAACAAACAAAC-----AACAAAAAACAGAG-------AAAGCATCCAAAGAA------CAGGCTTGAGAGACTCCAAGAACCTCTAGC
s ponAbe2.chr7           23137859  84 + 157549271 -------------------GGCGAATACTTTTTAACTAAAAAAC-----ACACAAGCTCAGAG-------AAAacatccatagaa------caggcttgagagactccaagaatctctagc
q ponAbe2.chr7                                    -------------------9999999999999999999999999-----99999999999999-------999999999999999------999999999999999999999999999999
i ponAbe2.chr7          C 0 C 0
s panTro2.chrY             636304 101 +  23952694 AGAAAAAAAA-------ATGAGGAAATCTTTTTaacaaacaaacaaacaaacaaaaaacaGAG-------AAAGCATCCAAAGAA------CAGGCTTGAGAGACTCCAAGAACCTCTAGC
q panTro2.chrY                                    0000000000-------0000000000000000000000000000000000000000000000-------000000000000000------000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s gasAcu1.chrV            9098826 110 +  12251397 TGAAACAAACAAAAACTAAATCAGCTTCTTTTTCCCAAACACAC-----AACAAAAAGGAAAAT------AAAAAACCCAAAGAGACGCATCACATCTGTGCATCACCAGGGATCACTGAC
q gasAcu1.chrV                                    99999999999999999999999999999999999999999999-----999999999999999------999999999999999999999999999999999999999999999999999
i gasAcu1.chrV          C 0 n 0
s danRer6.chr5           71576493 102 +  74451498 ggttataagc-----ctttatgagttactttattc----tgtta-----aacaaaaaagaagatattttgaagaaagct--ggaaacctgtaaccactgacttacattaaaccttact---
i danRer6.chr5          C 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=46949.000000
s hg19.chrY               7783144 261 +  59373566 ----CTAATAAA--------TTGGTATCATATTCCCCCAGAC-AAAGCCAC------------TTAATGGAGATTTTGAAATGTTGTTTTTTATTATAC---------GAATTGCAACCTAAGATAACAACATAT-------ACAAAACATCAAGAT----AATATGGCTCAAAGATAAACATGAATATCCAGAAATCAACTATAAGAAAATAGAGATGTAAAAATTACCAGAGGCAATTTGGATTAAATTCTAGGtttatttttaaaaag-aaataaataaattatgctaaaatttaaaatCGCCA
s ponAbe2.chr7           23137943 257 + 157549271 ----cTAAAAAA--------TTGGTATCATATTCCCTCAGACAAAAGTCAC------------TTAATACAGATTTTGACATGTAGCTTTTTATTACAC---------AAATTGCaac-----attacaacatat-------acaaaacatcaagat----aatatggctc-aagataaaaaagaatatccagaaatcaattattaaaaaaaggagatgtaaaaattacatgagacaatttgaattaaagtcttgatctattttttaaaagaaaaaaaataaattaccctagaaaatcaaaattaca
q ponAbe2.chr7                                    ----99999999--------9999999999999999999999999999999------------999999999999999999999999999999999999---------9999999999-----999999999999-------999999999990999----9999999999-999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i ponAbe2.chr7          C 0 C 0
s panTro2.chrY             636405 261 +  23952694 ----CTAATAAA--------TTGGTACCATATTCCCCCAGAC-AAAGCCAC------------TTAATGGAGATTTTGAAATGTTGTTTTTTATtatac---------aaattgcaacctaagataacaacatat-------acaaaacatcaagat----aatatggctcaaagataaaaatgaatatccagaaatcaactataagaaaaaagagatgtaaaaattaccagaggcaatttggattaaattctaggtttatttttaaaaag-aaataaataaattatgctaaaatttaaaatcgcca
q panTro2.chrY                                    ----00000000--------0000000000000000000000-00000000------------000000000000000000000000000000000000---------000000000000000000000000000-------000000000000000----00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-00000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s danRer6.chr5           71576595 276 +  74451498 ttctttaaaatacactgttttgggtttaacAT-----CAAAG-AAAGCCATGCCGGTTGCAagttaatgatgac----aattttaatttttgagtgaactacccctgtaaTTTATTACTGAACATCAGAAAATACTGCTGTAAGAGATCATTGAAATTCTGCATGTGATTGATTTATCAGCAAGGTTTTCCCAAACACAGAAATAACGCAA--------TAAAATGTAGCTGAATCTGCGTACAGTGAAT------TTTACCATCACACAA-AACGACATGAACTGTT------TATGAAACTGGCA
i danRer6.chr5          C 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936   0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=2928.000000
s hg19.chrY               7783405 31 +  59373566 TCTCAATGATG-TTAATCAG----Taaaatggaaat
s panTro2.chrY             636666 31 +  23952694 tctcaatgatg-ttaatcag----taaaatggaaat
q panTro2.chrY                                   00000000000-00000000----000000000000
i panTro2.chrY          C 0 C 0
s ponAbe2.chr7           23138200 32 + 157549271 tctcaatgatgctcaatgag----taaaatggaaat
q ponAbe2.chr7                                   99999999999999999999----999999999999
i ponAbe2.chr7          C 0 I 2
s ornAna1.Ultra523          62346 30 +    140355 ----aatcacatttattgagcatttatcttgggc--
q ornAna1.Ultra523                               ----999999999999999999999999999999--
i ornAna1.Ultra523      N 0 I 177
s danRer6.chr5           71576871 30 +  74451498 TCTGGAAAATA-TTATTAGG----CA-AGTATAAGT
i danRer6.chr5          C 0 I 9
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936  0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=31912.000000
s hg19.chrY               7783436 168 +  59373566 aaag-------aaaaaaataaaaaaaga-aaa--gaaaccaacaaaaagattaaaatccca-aaataaataaaaatTGTGGAGTAGAAGT---ACAAAAACAGGCTAA--TATGAACTTCAAC-ATTAGTA--AAAAAAT---------TTAAGAAAATcaagaagctcagctaattttaactaaggttaacagaa
s ponAbe2.chr7           23138234 169 + 157549271 aaaa-------aacaaaatgaaataaca-aaaatgaaaccaacaaaaagataaaaagcacagaaagaaataaaaattgtgtagcagaact---acaaaaaaagactAA--TATGCACTTCAAC-ATTAGTA---AAAaat---------ataagaaaatcaagaagctcaccaaatttcaactaaga-taacacaa
q ponAbe2.chr7                                    9999-------99999999999999999-9999999999999999999999999999999999999999999999999999999999999---999999999999999--9999999999999-9999999---999999---------99999999999999999999999999999999999999-99999999
i ponAbe2.chr7          I 2 C 0
s panTro2.chrY             636697 167 +  23952694 aaag--------aaaaaataaaaaaaga-aaa--gaaaccaacaaaaagataaaaatccca-aaataaataaaaattgtggagtagaagt---acaaaaacaggctaa--tatgaacttcaAC-ATTAGTA--GAAAAGT---------TTAAGAAAATcaagaagctcagctaattttaactaaggttaacagaa
q panTro2.chrY                                    0000--------0000000000000000-000--000000000000000000000000000-0000000000000000000000000000---000000000000000--0000000000000-0000000--0000000---------00000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s danRer6.chr5           71576910 187 +  74451498 AAAGCATTGCTAGTACACCTAAACATCACAAA--GCTAATTACAAAATGCCTAACACACta-taataatttataattataatatattaGTGTAGCGAAATTAGctcaatttgtgaatattaacgattaataataacaagttattattaattatgaatataaaga-----attaacttgcagctaatt-taacaaaa
i danRer6.chr5          I 9 N 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936   0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e ornAna1.Ultra523          62376 177 +    140355 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=6805.000000
s hg19.chrY               7783604 37 +  59373566 agatatttctaat-ggacaaaatataagcaaagttgtg
s ponAbe2.chr7           23138403 38 + 157549271 agagatttctaacaagacataacataagcaatgtttta
q ponAbe2.chr7                                   99999999999999999999999999999999999999
i ponAbe2.chr7          C 0 C 0
s panTro2.chrY             636864 37 +  23952694 agatatttctaat-ggacaaaatataagcaatgttgtg
q panTro2.chrY                                   0000000000000-000000000000000000000000
i panTro2.chrY          C 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936  0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e ornAna1.Ultra523          62376 177 +    140355 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=45853.000000
s hg19.chrY               7783641 244 +  59373566 aaagtcacagacaagaagataatctggaattcaggaagaaaaaatagatgtg-------tatgtatgcttctgcaag--attacta-caaatttatgaacgtcaatcttttgggcatgaagggtataagacgatgtagttaaaacactgaaaaaaaaaaaagcctaagcaggaatactatagcctccaaaaGTAGCCATCC-AATGAAAAAACAA-----------ATCTGACTATACCATAATCTGTATCAAGAACTAACTATTT
s panTro2.chrY             636901 245 +  23952694 aaagtcacagacaagaagataatctggaattcaggaagaaaaaatagatgtg-------tatgtatgcttctgccag--attacta-caaatttatgaacgtcaatcttttgggcatgaagggtataagatgatgtagttaaaacactgaaaaaaaaaaaagcctaagcaggaatactatagcctccaaaagtagccatccaaaTGAAAAAACAA-----------ATCTGACTACACCGTAATCTGTATCAAGAACTAACTATTT
q panTro2.chrY                                    0000000000000000000000000000000000000000000000000000-------000000000000000000--0000000-00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000-----------0000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s ponAbe2.chr7           23138441 242 + 157549271 aaagtcgcagacaagaagagaatctggaattcaggaagaagaaagagatgtgttatttatgtgcatgcttctgcaag--attacgagtaaatttaagaacataaatctttcaggcaagaagggagtaagatgacatagttaaagcaccggaaaaaaaaaaagtctaagcaagaatactatatccagcaaaagtatccttcaaaatgaaaaaaaaa-----------ATCTAACTATATCATGATATATATCAAGA-----------
q ponAbe2.chr7                                    99999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------99999999999999999999999999999-----------
i ponAbe2.chr7          C 0 N 0
s ornAna1.Ultra523          62553 219 +    140355 aaggtcacagac-tgaagtgcataggggacgcagaagggagagTGGtctgtt---gctatat-tgtactctcccaagcccttagta-cagtgctttgcac------ccactaagcactcaataaataca----------------actgaatgaaaagagagtttaatcagg-------------------gcaggcctcttggagaagatgtgaccttagtattcattcattcattcaatagtatttattgagcgcttactatgt
q ornAna1.Ultra523                                999999999999-999999999999999999999999999999999999999---9999999-99999999999999999999999-9999999999999------99999999999999999999999----------------999999999999999999999999999-------------------999999999999999999999999999999999999999999999999999999999999999999999999999
i ornAna1.Ultra523      I 177 N 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936   0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=6237831.000000
s hg19.chrY               7783885 68494 +  59373566 AGAACAGGTAACTATTTATTAAGTTGAAAGCTATTATATTTTCTATAATTattttaagtcaaaattcacaatagacaaagtaagacattcaaatatagtaagaggtttaattcactgaatacctataaagacagttcttccaaacacataaaccaacattgacagaattgaatgaaaaataggcagcaatataataatggatgtatacatcaatatcttactttcagtaataaataaagcaagacagaatatcaataagggaacaaaaaactggaatgcactatacaataattacacctaacaaatgtatgcagacaacagaatagacattcttttcaatagctcataaaacattttcctagatggatgatctgtgacaccagagatgaagccttaataatttttagtagaaattttacagaaaattatttatagcccaggttgaatgaaactagaattcaataacaaaagaagagcagaaaaaccccaaaaatataaaaaataagcaacaGtttgtttattt--------tttatttatttatttatttattatttatttatcttttgatggagtatcactctgaagctaggctagagtccagtggcacaatctcagctccactgcaatcttcaccttttgtgttcaagtgattctcctgattcagcctccagagtagctgtgactacaggaatgcaacaacaagcccagaac-tttttttttattttagtagagatggggtttcattatgttgtccaggaccacctgtatctcctgatctttctatgcatgctactcagcctccaaaagtgctgggtttacaggcatgagccactgcacacagccAACAGCACACTTTTAAGCATGCTGTTTTTCTAgggttggaagataaaatattgtgaagatgtccatgctactcaaagtgacacaaacccacaacacaccctttttcaatttttaattttacttttccaaaatagaaaaaacccacaaaattacataagattccaagaaaccatgaaaagtccaacaatcttaaaaaaaaagaaaaagaaaaatattggaagcattacatataacaatttccaaacactaagcaaacctacagtaacaaaggactttgctaccagtataaaggtagaacaccaaagtaatgaaataaaatgcagcacagatataaactcTTGAATagacaggagagacatcataccacctaggtttttcattcagccatatgtcacaattccttcaataagcaagacccaggcaggagatcagagttacattacgtagatgctagtttcagtgatatttcaaaatgtcctctgggtgaaggacacaggctgcagagacatatcacctacctgaaaggcccagaaatatgtaatagtaccccctattgacagggcccaggcaaaagagtcatgttattatgattctgacccatcaatatgtaacaatgaacccatgggaaggaatatgagccaaaaagtctcaacacctgggtACTAGGATGAGTCATATGATCCGATCTCCAcatctttgagtgtgacagctttaacttttacctgagaaagtatattacagtcacagtcttatatgtgttgcaggacaatatataacactgtctacaggagatgagggttttataaacctgtatgagagttgcaaagttctctgaggtctacatgctcctatggactcacaatcttacatattgctccaaactcaggtctaatagtcaacatctttcctataggcagggttaagaaaaaaatccattattatgccaatgagctggatccacaaatgagttaccatcccaattcttgtcggattaacatataaaagtcaaacctccaactttgtgctgtattcctttgttagactcaggacctcaacattgggcattataaatattggatggtgacaattttaatttcacctaggtatgtaaacatgagtctcaatctgaactttttgctgggccctgttaggaaacactctaccaccaaggagtttgaaaaatataagtcagtgttgtaagcttctgtaacattggtagaaatatgtaacagaggaccttacctattgctctaaacctaatgatgtgagataagatatctcctattggctgaatcccaacataaatttgatcatctatgcctgtcaactaaagcaaggtgtatgtattaatcccatatgtgggcaaataactaggcaggagggaaatatctcttatatgctgtgccagccaatatgtcaaaataccttttctaggcagggtataggatataaggtcacattaactgggtgctggacccagtaatatgaccctattccacatgtggaaaatacccagccaagttatgagagccaaaacatcgacataatgggctgaagctatgtcaaaataccttcagtggctccaacacaggccgaaaagtcatatcataaggatgctggtcttagcaatatgcaatatgccataatttcttctttatggaaaacacaggcaggagagtaacatcatcaggatgttggtccgtgcaattggtcaaaattccttttttgtgggcatgttcagaaacaagaggagagttacatattctgagtgctgggatcagctatgtgccaaaatcttcttattgtgaaggcccagtcaaaaaatagagtcatatcttcatactatgggctcagaaatatgtccaaatgtttccattaggtaggtctcattgagatgaggaaagtcatatcctaggtgcttcccttcatatatgaacaaagtaacatgtttgcagaaatcatgaagaagaaccacatcacttgggtgctgggtcctgagatatgtcacaaggccttctTAGAATATCATCAAGCACAGAGGGTAACATAAACTATGTGCAGATTCTCTGTTtattccacaatgttccatgagtgtaggtcccagagagggagtcatttcagtcaggtgacagcccaagagacatgttacaatgtcctctgtgaagcatagacctggctaaagagtaccctcacctgtatgcctggcctagaaatatgtcactcttaaggttggcagggcccaagcaggagaaccacataacctaggtgatgggcccagatatatgtcataatgtcctgctttcaggttggctctggcaaaagagtatcctcacatgcttgattggccttgctatatgccgctatccttcctttgtgcagggcccactccagagatgagagttacatcacctatgaggtggacacagaaacatgacacagtaattttgatggacatggcactggcaagaatgtaacatcaccaagctgctagatccagtgatatgtcgcaaccctcactgagag-agcacccaggtaggagagtcacatcccctcgaggttgaactaggtagatatcacaatTTCATATATAAACTCGGACCTTTCTGCAAAGTAAAACTACACAGGTGCTTGGCAAATATGTGTATCAAAATAACACTGTCAGAAAATGTCAAAGGGGAGATTTACAATACCGCTCATGTTCTGTTTTATATGTGAcagttggcttcatccatgtgaaatgatgactgttctgtcagctgggttttcatacaagactcacaattttgcctgtgtgctgagtgctacgttagctctgcttatataacccaaatactttttaaagtatgtgtgagtgttgtaatcttttgtgacctttgtacaagaaagtgatccatgacatcacacatgtcactacacctagttataagagcctaaatattctctatttgctgagtccacatataaaagtcattatcattcctgtgagccctgcctaggtatatgttgcaattccatcttggttataaagcaggcagaacagcctcatcacctaaattctgggcctaaaatatttcaatattctctttgtaggcagggtcttgtcagaaatgtcacataagttttgtgctagggccaggtctgtggcacaatgacccttgtgggcagtgtctgggcagaaaaggagagtaatatcacctaaatgatgggctgacatatatgtcaaaatgctgcctgttgacagagcccaggaaagagagtcatataatttggatgcagtgtttagaaatgttacaattatcaaaggaagcagggtacaggcaggagaggaatcatgtaacctagatGGTGTGTTCAGAAATATGTTACAATGTCCCCTGAAGACATTGTTAAGATAACACAATAAAATCACCAAGTTACTTGGTCAGGTATTTgtcaaaatctcatttgtgggctatacctagggagaattattaaatctatccagagctgggcaaagatatgtgtcacaatttcacttgtggaaagatttaagaattagagtcaccatcctgcacatgtcctggctctaggcatatgagTTGTTCTTAGGCTTTTGTTTtggtctcagttgtatggcataatatcacctgtggccagagataaggcaagaaactcatataatctacatgggtgagggtccagtgagatgttacaatccacctggtgggcaaagcccttgcagaagagtcacatcacttggatgctggtttcagcgatacgtaaaaaccattctctgaggtaaggactttggcatgagaggagacccacttcatctaggcaattggcctagatatatgtcacaatgaccattaactgcaggaataaggctaaagaatgacctcaccttggtgctgtgcccagcagtatgtcacatgctccctgaggtcagggcacaatgaaaagtaaagaaacatcaccttggtactgagagaagttataggttacaatgcttcctattggcaaccccccaaccaaaaaaaaaatcacatctcctgggtgcactaccctgttatgtgtcacaatgctctgtaactgcagggccaagacagtagaagggagtcacataatttatgtgatggacctaaatataacacacaattctctttgtaggcagttttcaggtgggtaaatcacatcacctgggtgatggtcccagtgatatataaaactgcactttgtaggcagaacAAAGTATGATGTTATGTATTGATTTGGGGCTTTTTCCACATATGGCACAATTTCATCTGTGGTTTGGGCCTAGAAAAGTTCATCAAACTACCCATGTCCTGGGCAGAGTTACCTGACCCACTCACACTTTCAGAAAGGTTCAGAAATAATTTTCAGTCCACACAAATCctagcttcaggtatgagaatcaacaccttctgtgagttgggtcaaagtacaggactcacaatcaacaatgggaaggtcagtgtgtaagaactccaatcccacttgaagattgtgttcCAATAAGAGAGACACAACACCACAGTTCTGCTTAATCATGGTTCAAACATCAT----CAAACACCTGCGGATCAGATTTATATATGAGAGTAACAATTTCAAGCTTTGATGGCCTATGTGAgtgagatttagtatcacattggtaggatctgtttatgtgtgaaaaaaaacaattgtgtcagctgggtgtgcatccaagacaccctggcttctggtgcctgttatgagacactttggaccactcaggctttatatgatatgcctcagtgggatacttttctgtgtattcttacaggttggtgatataggacttttctcatggctgtaagactagatatgagagttgaaataccttcccaggctggcagtagttttgagagttattattatgcacataagctgaatccaggtatatgtcacaagctcacctttggacagagacaagacagaagagtcctaccatctgggctctgatccagggatacattttaatctacttcataggcaggatccagtccaaagagtcatgtcacctgggtacagtcttaagtaatatgtcattatgcccactgtaaatacagggttgaaaaagtagtggataatcacattctcttgggattggcctcagtaatatgttataatttcctctattggcagagtccaggacaaagaggagggtcacatcacctagattttacactcagtcatatgtcacaatttattcagtgggcaggatcctgcaggagaggagattcacattacctagattcttcatctagcgatatgtcacagtgtcctctttgggcagggcactggcaggag---agatacacaacctagctgataggcctaaagatatgtgataatatcccctgctgtcagggttcaagcaaaagggtttcattattgtaattcaaacccagggatattttacaatacaaccattgaaaagaatttaagccaaaaattctcaacacctggAGGTACTAGTCCTAGTGACATGGAACAAtctctttatgtattagggtgacaactttgaatctttacttggtgagtatataagagtcacaatctcatatgtgttctggctgatcccatgacacactctacaacatacaaaggctttaagcaacatgcatgagagttgcaatccattctgaggactacatgctcctattgactcacaaagatatgtattgctttaaacttggttatgataatcaacatcccttttacaggttatgttcagacaggagacccattattatgcctgtgatttgggtccagaagtaagtcaccatctcacctgtagcaagagccatatgtgaaattcacaaatctatctttgtactttatttgcttgttaaactcagtgcttcaacagtgggctttgtgaatgtgggatgttgacaacttttgctctcaccttcatgtgtaatcaagagtcacaatcttaacttttgctgggccctgttataaaactctgtgtaccaagcaaggagt--------------ttagtgttgtaacattctgtgaactttctacaaacttgcacctcataaacttacctgttgttttaagtgtagcaatgaaaggcaaaacatatagtattggTGAAATTCCAATTTCAGTTCGATCATGATGCTTCTGAATTGAAGCAATGTAAATTTCATAACACCATTTGTAGAAAACAAAAAACTTTTCAGAAAGGTAGAAAACTGACGTgctgtgtcaagaaacatgtcacaatgtcccctccatgcagggtctagtaattgggttatgataactgggtgctggactcagtggaatgacacaaCTCTAAACATAGAAAATGTAGGAAAAACAAACACATACAAATGATGAGAACAAAATTATTTACAGAATAGGCGCATGGTATGTAAAAATACTTTCTGCTACTCTGGAAcaggcagaagatttacatcatcagggtgggagtcccagcaatatgccataactctctctttatgttggacctagttagaggagaaacatcatctgtatgctgggcccagcaataaaccaaagttccttttcatagtcatggttcaggaaaaaagaagtcatattacctaagtattaggcttagcaatatgtcacatcaccccattctaaagcctcttgcagaagaaaaggttcacataacttaagacacaggctcagatacaaggcatgatgtcccaagtaggtagtgctcatgcagaagagaagagtcatatcacctaggtgcttcctaggtatatgacacaatctaacatgcgaggggaaaccaggcagaagagtcacttcatcttgatgctgggttctaagttatgtcacatggcttccttaagacagcacacaggcaagagagttacaaaaaataagtatgaaaaatgtcacaatgctccataaggacaggacacaagcagggagccacatcacctaggtgactgacccatatatatatgtcacaatgtccacattgagtcatggccctggtgaaagagtaccatcacctgtgtgcatagcctagcaatatgtcactatcttagtaagcagaacccaagcagattagcaacatcacctaggtgataggccaagagatttgtcacaatgccctctttaggacatagtcctagcatataagtactgtcacctctgtgcctggcccagtcatatatcactatcactcactgtgtgcagtacccaTTCTAATGGGGAGAGTTTTGTTGCCTAAGTGGTTggcacagtggtatgtcccaatgatttctgtatgcatggctcaggcaaaaatgtaacatgacttggatactggatctagtgatatgtagtgactcttactgagagcagggcccaggcaggagcatcatatcacctaaagttttgctcacgtagatatcacaatagcatatgtgggctggaacaagtctgggagtaaaatcacACAAGTGTTTGGCAAAGATTTATGTCACAGTCACACTGGCAGAAAATTCTCAGGATGAGATGTACAATACCACACATGTCCTGTTTTTATGATTGACAGTTTGCATCGTATATGTGAGACAGTGACAGTGGTTACTGTCAGGTGGGTGTACATATAAGACTCACAGTTTCACCTTTCTCTTGGGTTCTGTTCTGAAACTCTTTGTATGAGCCAAGTTCTTTACAAAATATGAGGCTGTTGTAACCTTCCTTGTCTTCTTTTTTACCAGAAAGTGATTCAATCCATTGTGTTTCTGAAGCAAGTTATAAGGCTCAAAATTACTCCTATTTATGGGTACCACATATAACGGTCATTATCATGCCTGTAAGTTCTGCCTAGGTATATGTAACAATTTACTCTgtgatgtgttacaatattctccttgtaggcaaagtcctggcagaaaagttgtatcacctgggggttacacccatatatatggcacaatgccccttttggcacagtctccagacagaagaagagactcatatcacctatatgctaggcccagtgatatgtcaaaatgtctcatgttaaagggatcaggcaagagagtcatatcatttggatggcatgcttagaaacactataatccccagtggaaggagggtccagacaggagagGAGAGTGAGATAACTAGATGGATGATGAGTCcagtg------------ccttcctgaggatactgttgagacaggagagtcaaatcgtcaaggtgctcagctgaggaatatatccaaatatcatttgtgggcaacatttaggcagGATTATTAAGCCACTCAAGAGATGGGAAATGAAATATGTCACAATAACACTGGTGGAAAGCTCCAGGAATGGAAGTCTCCATCTTGGATATGACCTGGCTTCAGTTTTAAGCATCTTGATTGGTCCTCTCATTTGGTGTcaactatatggcactatgtaatctataggcagagagaaagcagaaatgtcacatcacctgtgagggtgctcgtcctgtgagatgtcactttttttcttgtggccaggaccctggaataaaaggtacatcacctggatgttgattttagtgatatatcaaaatttcttctgtgggcagggcttaaggtgaggagaatcactttacctagacaattggcctagatatatgtcacagtggctgctatgtacagaaccgaggtatgaaagtgacctcaccttggtgctgggtttatcaatatgtcacaatctcccctgtggtcagagcaaggcaagaaggtagaaacatcacctaggtgctgagccaagtgatatgttacaaagctttctgtttgtagaacacaaaatttagtgtcatattacctgggtgtaatatccagttatgtgtcacaattca-cataattgcaggcaaaggcagtagaagtaagccacatcacttatgtgatagacctagatataagccacagtgctttatataggcaggaatcaggcaaagaattcacattacctgggtgcctgtcccagtgatatgtaaaagtgccatttgtaggcaggAACATGTACCTTTTCTTAGGTGTTTGGTCCATGTATATAACAATTTCATCTCAGGTTATGGCCTAAGAAGGACAGTCAAATTACTCAGGAGCTGGGCTAACTTTTATGCCCTAATCACACACCAGGAAATATTCAAAAGTAAGTTTCACAGTCCCACACAAGTCCTGGCTTTGTGTACATAAGTAAACACCTCCTGTGAGGTGGGTCAAAACAGAGGAGACACAATCCCAACAATGGGCATAATCCATGTAAAAGATGGCAAAACCAGTTGATGACTGTCAAGTGGAGATGAGTGTCAAGTGGAGATGAGTGTCAAGTGGGAGAGTCACAGCCTCATATGTGCACTGAATTATGCATCCCCAAATCACCTGTAGGTCAGATCAACATATGAGAGGAAAAATTTCATACTTTGACTGCTCTTTTGgtgagatttagtaccttatttggaggccatgttcttgtgaggcaatgacaattgtgtctgatgagtgtgaatccaataatcccaatagcattgggttgctgttcactgttataacactatgtatacctctcacactttatatgatatgctggagtgtcataatactgtgtgaactttataccattaggagactcattactttacttatggctataagactgggtaggagcatcaaaatatctctcctttttggagccaggtatgatagttatatttgtgcatggtaggtgaacacaggtgtatgtcaaacttttacctgtgggcagaaacatggcaggagagtctcatcacctggaaggtgagctcaggatacattataatctcctttgcaggcagggccaagtcagaagagtcacatcacctgattacagcctcaagtaatgtgacaccatgtcaaatgtgaacagggttaaagaaatggaggagagtcacacaacctagatgctgggctcagcaacatggaataatccccattttggcagaatctagaataaagaggagaattgcattacctaggttttgcattcagcatcatgtcacaattcttttagccggcaggacctaggccgcagagaagagtcacaattcctagatgttacacccagtgatgtcacaatgttctttggggaaaaagcacaagcaaaatagacaaatcacctagcagataggctcagatatatataatgtccctaccttgcaggactaaggcaaaagagtcacattattatgactgtgacctaacgatatgtcacaatgcacacatggcaaacaattaagtcagtttttacacctgggtactaggcccagtgatatgacagaatctcctcatcttttagatgacacctttaactgtcagctttgcgtgtatataagtcacattgtcacatgtgtgctgaaccattacatgacaccctttagaacatctgaaagttttttacaacatgcatgagatttgctaactactctgaggtctacatggtcatatcaactctgaatcttgtatattgccttaaacccagacatgatagtcaacatctctcatttatgcttagttcaggaatgagacttatttttatgcctgtgagatgggtctaaaaatgagtcactattgagcctgtggcaaaatccccaaatgagaatcacaattccatctttgtactgttttcacttgttagagtcagcatctcaaaaatgggctttgtaaatgagggatggtgacaacttttatttgcacctgcctgtgtaattgagagtcacaatcttaaacattttgctgggccttgtgaggagagtctgtgtaccacccaaggagtttatacaatattgattattgttgtatacttctgtgagctttgtacaaatatgcaacccaggattttacctattgccttaagccttgtgatgagagataaaatatcttctattggctgaatcaaatgtaagttttaccatcatacctgtgaactgaagcaagctatatttcataatcccatttctcggcaaaaaagagtcacatcatgtaggtgatgtggcatgtgatgtggcatgcagcatgtcacagtgacttctctaggcagaatatagaaaggagggtcacattaacgaggtgttggatccaacaatatgATGAAATTTTACTTGTAAAACAACGTATCCAAGGGAAGAAAGCCACAACACTTACAGAATGGACTGAAAATGTGTCAAAATACTCTTTATGGCTCTGGCACTGAGAGGACAGTAGCATCATTAGGGTGCTGGACCCACCATTATGCAGTAACTCCCTCATTATTCAGGACTCTTGTAGAAGAGTAACATCATCTGACTgcaataggtcaaaatttccacttgtgcaaatggtttagaaaaaagaaaatagtcacataccctaaatcctggtctcaaaaatatgtcacactctcagcattttaaaggctgaggcaggggaggaaagtcatatcacttagttcatcagctcagagatatgttccaatgtcccagtaggcagaactcaggcagaagaggcttctttaggtatagtctcaatccaacacgtgagcagaaaccaggcagaagagccacatcatctgggagctgggtcctaagatatgtcacaagtccccattaggacagaaccaaggcaaaagagttacatcaccttggtgtatgtttctcttttatgtcacaatgctctatgtgcatgaggccaaagcattcaatcccattgactagttgataggcccaagagataggttacaaagtcctctgtgaagcatagtcctggcaaaagagtatcatcacctgtgtgtcttgcctagaaatatgttactctccaggttgtcatcacccaagcaggagagccacctaacctaagtgataggcatagagatgtgtcacaatgtcctagtttgggcatgactctggcaaacaatacccacagctgtacgcctggctttacaatatgtcactatccttcctttgtgcaggatccgttccagagatgagacttacatcacctatgaggtgcacacaaatatatgtcacaataattgtgattggcatggcataagcaagaatgcaacatcaatagtatgctagatccagtgatatgtacaatacttactgagagaagggcccaggcaggagagtcacatctccttaaggttagcctaggtagatatcacagtcccatatatgcactggaacaagtctggagagtcaaattacactggTGTTT-GCAAAGATTTATATCAGAACCACACTATCAGAAAATTCCAAAGATGAGTTTACAGTACAACACATGTCCTGTTTTCATGTGTGAcaattgacttcatccatgagagatgatggcagtccttactgtcagttgggtgtgcatacaagactcacaatttcacttgagttgaaccctggtttgactttttcattataaaccaaagactttgtaaaatatgtgtgagtgttgtaatcttctgtgacatttgtacaagaaagtgattcaggacatcccacatgtctgtaatctgagttacaagagtcaaaatatcatctattggctgagtccatatattaataagagtcattattattcctgtgagccattcctagttatttgttacaatttcctctgtggttatgaatcaggccaaacaatcacatcacctaaatgctgggccagaaatatcccattattattttttcaggcagggtgctgtctgaaatatcacataacttgtgtgctaaatccagctctgttgcacagtgttcattttgggatgtgtctaggaaggagaggagagtcatataacctaaaatctgggttcaaacatacatcaaaatggctcctgttgaggaggtccaaaacagagagtcatgtcCTTTGAATGTGGTGATTAGAAATGCTACAATTACTAAAGGAAGCAGGGTACAGGTCAAAGAGGAGAGTTATATGCCTTTGATAAtgggtccagaaatatgtgactattctgcctgaggacagttttagacagcacagtcaaatcaccaaggtgcttgatgcagatatttgtcaaaatctcattcatgggctatatctaggcagaaTTATTAAGTCACTCAGGAACTGAACTAAAATATATGTCACAATTACACTTGTGGAAAGGTTTAGGAATAAGActcaactgttggctttctaaatgtaggatggcggcaacttttaatttcacctgggcatgtaatcaagagtcccaatttgaactttttgctggcccctgctatgaaaatttctacaacaaaagagtttataaaatataagttagttgtgtaagcttctgtgagcttgctacaaatatgcaacctaggacctttcctattccccaagcctaagaatgaaaagcaaaagattttctattggctgaatcccaatatgagtttcatcatcatggctgtgaactgaagcagagtatatgttataatcaaatatgtgggcagaacactatgcagaagggcaatagcacttagatgttgtgttaggcaatatgtcacaataccttctctatgcagggtgtacaaaattgaatcacattaactgggtgccggacccagA----------AATTTCATATGTGGAAAAAACCCAGCCAAGTTATGAGAGTCAAAATGCCTACATAAtgggcccaatatatgtcaaaatacattcagtattagcagcacacgcagaaacatcacatcttaatgttgctgggcccagctatatgcaatatgccgtaattatctctttatgcagatcccatgcagaagagtaacatgatctgtgtgctgagcaacgttatatgtcagatttcttttttgtgggcatggttcaggagaaagtggagagtcacatatcctgagtgctgggctcagcaaagtgacaaaatcctcctattgtgaaggcccaggaagaaaaagagagtcgcattacttaggt-------tcagagatacatctcaatgcccccagtaggcagagctcaggtagatgaggacagtaatatcacctatgtttttcccacagaatatgtcacagtttaacatgtagacagaaaccaggtagaagcactatatcacttgtgtgctgtgtcctgtgatatgtcataagtctctcttaacacaacacctaggcaagagagatacatcatactaggtGCCGGTCACTTGGTtataacacaatccttcatctggttaggacccaaggagagagttactacatttaggtgataggcccagagatatgtcacagtgtactgtatgaagcataatgctgg-aaagagtaccatcacctgtgtgcctggcctagaaatatgtcactttcaaggttggaaggaccctagcagaagagccacataacatagatgatagccccggagatatgccacattgccctccactggtcatccacaggataaggaggaaatttgcctgtgtgtcagtccttgcaatatgtcactattcttctgttgtgcagtgtccattgcagagaggagactcacatcacctatgaggtaaacacagaaatatgttacaataattttggtggtcatggcccaagtaaggatgtaacattacctgggtgctatatccagtgatatgtcacaatcattactgagagataggacaagtaagacaggaaagtcatatcacGTAGAGGTTGGCCTAGGTAGATATCATAACCCCATATATAAGAAGGGACAGGTCCAGAGAACCAAATTACACAGGTGCTTAGCAAAAATTTACGTCATCATAACACTGTCAGAAAATTCCAAAGATGAGATTTACAATACCACACATGTCCTGTTTTCATATGTGACAGATCCctctgtctatgtgagataagttgtccttactttcagctgggtgtacatacaagactcacaatttcacctatgtgctgagtcctgctttgattttgtctgtataaaccaaagagtttgtaaaatatgtatgagtgttgtaataatttttgacctttgtacaagaaagagacaaaggacaccatgcatgtccctaaactgagttctaagattcaaaatattctctattgactgagtccacatatgacagtcattatcatggctgtgaaccatgcataggtatatgttacaattccctctgcggTTAAGAAGGAGGCCTAACAGCCACATCACATAAATGCTGGGTCAGAATACTCAAATatgctttttgtagtcagggctgtctcagaaatatcacataacgtgcatgctatgtcaagctctgtgacaccataccccttgtgggcagtgtccaggcaggagaagagagtaatatcacctaaaggatgggcccaaaattatgtcaaaatgcttcctattgacaaggcccaggcaagagggtcatatcatttggatGCAGTATTTATAAATACTACAATCACCAACAgaagcagggtacagtcaggagaggagagtcatgtaacctagatgaagcatccagaaatatgttacaatatcccctgaggACATTTTAAGATACATCAGTCAAATCACAAAGGTGCTCAGCCAATCTATCTGTCAAAATCTCATTTGCTATACCTAGGCAGAATTATTAAATCACTCAGGAGTTAGGCAAATGTATATGTCACAATTAGACTTGTGGAAAGACTTAAGACTAAGAGTCACCATCCTGCACAAGTCCTAGGCTCCAGTCTTGTGAGTTGTTATTAGGCTTTTGTTTAGGTCTCTGGTATGTGGCCAGAAAAAACACAAGAAAGTCCCATCGCCTACGTGGGTCCAggtccagtgagatgtcacaaattcaacaagggggcaggaacctgttgtaatagttacattgcatggatttcagtgacatatcaaaattccctatctgggcaggactttggcaagaagggagactcacttcaccaaggcaattggcctagatatatgtcacaatgtctattctgtgcagtaacaaagctgtagagaggcatcacacaggtgttgtgctcaggaaatatgtcacaatctccttgtggcctgggccaaggcaaaagcaaagaaacatcacttaggttctgagccaagtgatatgtcacaatgcttcctgttggcagaacccaaaaagaagaatcacatcccctgaatgcagtacccggttatttgtcacaattccctgcaactgcagggcaaaggaagaagtgagtaacatcacttacatgatggatctacgtatgtcacaaaattctttttgtaggaaggtttcaggcagataactcacatcacctgggtgatggtcccagtgacatatgtaaaatttccctttgaaggcagagccACGATGGATGTTATCTATTGCTTAGCTGCTTGTTCCACATATGGCACAATTACTTCTGTGATCTGGGCCTAGAAAAGGAGTCAAATTATTCATTTACTGGGCAAAGTCACCTGTCCCAA--TCACACTCTCATATATGTTCGGAAATAAGTTTCATATCCCACATAAGTCctggttttgtgtatgtgagttaattctttctataagttgggtcaaaatagaggattcaaaatctcaacagtgggcaagatccatgtataagagctgtaatcccacttgaacattgtggtccaggaggggagttacAGCACCACAGACATGCTGAATCCTGGTTCAAATGTTAATGAACCACCTGCGGATCAGGTCCATATGTGTGAGTAATTATTTCAAACATCAACAGCTTTTTATGtgtgagatttagtatttcattcctaggccctgttaatgtgtgacaatgaaaatcatgtcagctaggtgggcattcaagagtcacattctcacctggttggtggcctctgttatgacactgtttgcaccattaaggctttatatgatctacctgagtattataatccttcatgacttttatacaagtgaaaaacacagggctaaacccatcgctatgagagtcaaaatatctctactggctggctccagttatgagagttatttttgtgcatgtgctcttaacctagttatatgtcacaatttcacctgtaagaacagacaaggcaaaagagtcaactcacctcgatgctgaaccagtgatacagcataacctcatttgcatactgggtctagtcagaggagtcacttcacctaggtATAGCCTCAAATAGTTTGTCAGCAAGCCTACTATACACAGGGAAGAAATAAATGAGGACAGTCACTCCACCTAGGTgctggactttgcaatatataacaaacctctctcagaagagtttagaatgtggaggagagccatataatgtcagtttttcaatcagtggtatatcacaatttattttctgagcaagacccaggcaggagaggagagttgcattacctagatgttaagtgaaatgatatctcaaaatgtcttctgggggatggacactgacagaaaagaaaaatcagaaaagaaaaatcatcttgcttatagaccccaagatgtgtgataatatcccctcttggcaggatcaagacagaacagtcacagtatgattctaacatagtgatatgtcacaatgcacccaaagaaatgaatttaggccaaatagtctcaacacctaagtACTAGACCTATTCATACACCAATTCCCCTTGTCTTtgagggtgaccctataaactctgagctagtgtacatatgggagtaacaatcttgcatgtttcctgggccattgtatgaaactctacaatattcaaaagcattatacatcatgcatgagagtttcaaaccactctaaggcctacatgttcatatgtactcatgatcttgcatattgccctaaacccaggtataacagtcatcatctcttctctaggctgggttagaagtgagacccatttttatgcctgtgagctggatctagaaataagtcacaattccacctgtggatagatccatatacgaaggtcatacttccaactttgtactacattcatttgtaaaactcaggttcttaacagtgacctttggacataaagaatgatgacaacacttgcttttacctgggtatgtaatcaagagtctcaaactgaaattttttttggtccctgtcaccaaaatctctataccatcaaaggagttcatacattatgagttagaattgtaaagctctgtgagcttggcacaattatgcaaactagtactttgtctattgccctaggcctagtgatgaaaggtaaaatatctcatattggctgaatcacaatataatcccaatataagtttgaccatcatgactgtgaactgaagccaTAGTCGCATTTGTGTGGAAAAAAA-AAAAACAAAAACTGggccagagggtaacaacacttaggtgctatgccaagcaacatgtcacaatatcccctctaggtaaggtataggacttagaatcacagtaactgggttctggactcagcaatatgacacaatccattatgttggAAAAAAAAAAAAAACAGCAAAAAGTTGAGAGCCAAAACACCTATATAATtggcccctgctctgtgaaaataccttctgtggctccagcacagtcatgagttttacattatcagggtgctgggcccagcagtatgtcataatattctctacatacataacgcatgtaaaaagagtaacattatctgggtgctgggccctgcaagaggtcaaaatttctgtttgtgggcatgatttgagaaaaaaaaaaggtaaatcagataacctgattattaggctgagcagtctttcacaatccctccactgtaaagaccaggcagaaaaaaagagtcactttccttagttcatggactcagatatatgtcccagtatcccaagtggagagggcccaggcagaaagggagtgtcatatcacttaaatgcttcactagttatatgtgaaaatcttaactgtgggcagaaaccagtcagaagacccacatcatctgggtacaaccagaagtaatatctcatgatctccactatagataggA--TTTTTTTAAAAAAAATAATGACACcatcacgtgggtgctgtgctcaccaatatgtaataattccctctcttgacagactcaagtacaaaaaggtgatttatgtcacataggttttgcactcaagggtatatcacagttttttcagtgaggaggatccaggcaagagaaatg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gcatggcagtagaagggagtcacatcacttacatgatgaatgtagatataagccataatgccttttataggcaggtataaggcaaataattcacattacatgagtGCTGGTCCCAGTAATATGTAAAATTTCCCTTTATATGCACACCCAGGCACCTACGCTTAGGTGTACGATGGTCAAATTATTCAAGCACTCAGCTAACTTTTATGTCCTAATTACATGCTAGGAAATATTTAGAAATAAGTTTCCCAGTACCACACAAGTCctggatttgtgtatgtgaatcaacacttcctgtgagttgggtcaaagcagaggagtcacagtcttatcaatggtcaagattcatgcataagatgcccaattttacttgaagattgtgttccaatagaggagtcacaaccccacaggtgtgctgaatcATGCATCACCAAACTAACCATATAGGAGAGGAGCAATTTTAACCTTTGACTGCTCTGTTtatgaggtttaacaccttatttctaggccctgttcttgtgagagaatgaatactggatcagctggctgcacattcaagagtcacaatcgtacctctttcctgttccctgttataacactgtttttaccattcagactttatatactatgtcagagtgtcataatcctctgtgaaatttaggccattgggagacatagtactttacttgtggctataagactggctataagaatcaaaatatctctctgattctacgtatgacccttatatttgtgcatgtgggctgaacccagttatatgtcataacttaacctgtgagcagaagcaaggggggagagtctcatcacctggattctgaactcaggatacattgtaatctcctttgcaggcagggccaagtcagaagtgtcacatcacctgggtactgcagcaagtaatatggcatcatgtccactgtagacaggtttgaagaaaaagaggagagtcacaccacctaggtgatgggctcagcaatatatagtaattacctcatttggctgactccagtataaggaggagagttgcattacctaggttttgtactcagctgtatgtcgcaattcattcagtggtcagggtctaggcaggagacaagcatcacatttccAGATACTACTTCAAgagatgtcataattttccttgggggtagagcacaggcaaaataaagaaatcacctagttgataggctcagagatctgtgataatatacattttggggcaaagcccaggcagaggagtcatattgttatgattctaaaccaatgatatatcacaatgcAAACATGGGAAAAAATTTATGCAAGTTTTAACACCTGGGTAATAGGACCAGAGATAAGACACAATCTCCTcatctttgagagtgacacctttaactgttagcttggtgtgtatatgagtcacaatgtcaca---tgtgtgctggctcatcctatgacactctctagaatgtctgagggctttatatggcttgcatgagagttgcaaactactctgaggcccacatgcgtatattaaatcacaatctcatatattgcattacacacaggtacgatagcaaacatctctcatttaggctgatatcaggaatcagacttattttatacctgtgggcttggtcaaaagtgagtcacaatcatacctgtggccagatccatatatgagagccacaattttatctTTACATTATCTTCAGTtgttaaactcagtacaccaacagtgggcttggtaaatgtgaaatagtgatatcttttactttcacctggttgtttaattgagagtcacaatcttaac--tctgctgggacttgttttgaaactctgtatcacccaaatagtttatacaagataaactagtgctgtaaacttcaatgagctttgtacaaatttccaacccagaattttacctattgccccaagactagcaacaagaggcaaaatatcttctcttgcctgaatcctaatataagtgaccatcatacctttaagctgaagcaaggtatatgtcataatcccatttgtgggccaaaaaaatagggaaaagagtaacatcacatagctgatatggcaattaacatgtcacaatgtcctctctaggcagaacctaggaagaaggcttacattaactgggtgctggaacaggtaatatTACAGAATTCTGCATATGAAAAAACTTAGCAAAGGGGTAAGAGCCAAAACACCTACGGAATAAACAAAAGATATGTCAGAATACTTCCTGTGGCTCTGTCATGTAATATTACAGAATTCCACATATGAAAAATCTTAGCAAAGGGGTAAGAGCCAAAACACCTACAGAATAAACCAAAGATATATCAAAATACTTCCTGTGGCTCTGTCACAGGCATGACAGTAGCATCATCAGGGTGATTGGCCCACCATCTGCAATAATTTTCTCTTTATTC---ACTTTGGCAAAAAAGTAACATCATCTGAGTCcaataggtcataatttctttctggtcatggttcagaaaaaagaatagagtcacacgatgttaatgttgggctcagcaatatgtcacaatcctgccattttaaaggccctggcagaagagagtcatattacttaggtcatgggctcagagatgtatcccaatgtccctagtaggcagggctcaggtggtcaaggagattcatatcacatgcatgtttcccacggaatatgtcacagtgtaacaagtgggcagaaaatagacaggagagccacatcacttgggtactgcatcctgagatatttcacaagtctctcttaggacatcaaccagacagtggagttacatcacctacatgcagtttctcggcttatgccacattgctccatgtgggtggtatcaaaggaggaagtcactttaccaaggtgatagggccaaagatatgtcacaatgtcctctatgaagcatagccctggcaaaagagtaccatcacctctgtgcctggccttgaaatatgtcatgctccaagttggcagtgcccaagcaggagagccacataaccagagatatttcaaaatcctctcttttgggcatggctttggcaaaagggtagcctcacctgttttcttggccttgaatcatgtcactaccttttctttgttcaaggcccattccagagagaagagttacattgcttATGAGGTGGACACAGAAATATTTCACAATAATTTTGTTGGGTGTGCTGCAGGCAAGAATGTAATATAACATGGGTGCTAGATCCAGTGATATATCACCATTCTTACTGTTAAGAGGGTCCAGACAGGAGAGTAATATCACTTTGAGGTAGGACTAGGTAGATATCACAACCCCATATATGGACTGGAAGCATTCTGGAGAGTCGAATTACACAGGTTGTTGAAAAAAATCTATAAAACATTCGCACTGTCAGAAAATTCCAAAGATGAGATTTAGAATACTACACATGACCTGTTTTCACGTGTGACAATGGCATCAtccatgtgagatgatgacaatccttactatcagctgggtgtgcaaagaagactcacaatttcacctatgtgctgagccctgctttgactcagtctgtataagccaaagacttagtaaaatatgtgtgagtgttataaacatttctgatgtttgcacaagaagctgatgcaggatgtcatgcctgtctctaaacatacttatgagagtatgtttagatacttttgagagtatgtttagataataggggatacttatgggagtatcccctattagctgagtccacatataagagtcattatcattgctgtgacctgtgcctaagtatatgttacaattccctctgtggttatgaagcaggaagaatgaccacatcacataaatgctgggccagaaatattccaatattgtctttgtactaagtatcctgtcagaaatgtcacataccttgtgtgttaggtctagctctgtggcacaatgtcccttgtaggcagtgtccagggagaagaggagagtcatatcacataaatgatgggctccataatatgtcacaatgcctcctgttgtcaaagccaacaggcaaggtattaatattatttggatgcagtgtttagaaaagctacaattaccaaagaaagcagggtacagacagaagaggagagtcatgtaacctaaattctagatccagaaatatgttacaatACCCCCAAGGACATTTTTAAGATAGCACAGTGAAATCATCAAGGTActtggctcaagtatttgttaaaatctcatctgtgggctatacctaggcagaattattaaatcactcaggagctgggcaaagttgtaagtcacaattagacttgtgggaaggtgtaagaataagagtcaccacactgaatattaggtttggttatgttctcaggtatatggcacaatatcacctgtagccagagagaaggcaagaaagtcacatcaactatgtatgtgtgggtccagtaaaatgtcacaatacactttgtggtaggaccctggcagaagagccatatcatctggatgctgctttcagtgatatatcaaaatccactatgagggcaggactttggaaagaaaggagactcacttagcctaggcaactgacccaagtatacgtcacaatggcccttatatgcagtaccaagtctggagagtgaccttaactacatgctgtgtgcagcagtacatcactatttccctgtggtcaggacccaggaaaaattgaagaagcatcacctaggtgctgagccaaatgatatgttccaattcttcctgtttgcagagctcaaaaacaagaatctcatcacctgggtgcagtacccagttatgtgtcatatagcagtgtaagtgcagggccaaggcagtagaagggactcacataacttatgtgatatgcctagatttaagacacaattctccttgtaggcagttttcaggcagataacttacatcacttgggtgattgtcccagtgacatataaaagtgccctttgCAATGGGAGCTCTGGAAGCTGTTATATACGGCACGTAAGGAATATATATGGTACAATTTAATCTGTGGCCTAGGAGTAGAAAAGAGTCAGATTATTCATATGCTAGGCAAAGTTGCCTCTCCTTTTTATGTTCTCAGAAAGATTTGGAAATAAGTTTCACATCCCACAAAAGTATTTCTtctgtgtatgtgattcaattttttctgtgacttgggttgaagtagaggagtcgcaatctcaacaatgagcaagatgcatgtacaagagccccaatcacacttgaagatggttttccagtaagggagtcacAGCACTACAGGCATGTTGAATCATGGTTCATATGTTACTAAGTCACCTGTGAATGAGATCCACATATGAGAGTAATTATTTCAATCTTTCACTGCTTTTTATGtgtgagatttagtacctcattcctaggccctgttcatgtgtaagaatgtcaattgtgtcagctaagtgtgcatgcaagggtcacattgtcaccgcgttgctggtttctgttattacactctttgcatcattaaggttttatatgatatacctgagtgttataatccttcatgaaatttatactagtgaaaaatacaggactttacccattgccataagactggctgtgagag-------tctctactggattgggccaggtatgagaattattattgtgcatgtgtgcttaaaccacatatatgtcacaactggacctgtgagcagaaaaaaagtcaggagagtcacattaccttggtgctgagccagttatatagtataatcttatttgtaggctgggaccaatcagaagagtcacatcacttcacctgggtgctgagccagtgaaagagtgtatactcattttttggcttggcctagtcagaagagtcacatcacctgggtacagcctaaaatagtatgtcaccaagcccattgtggacaggaaagaagaaaatgaggaatgtcccacaacctaggtactgagctctgcaatatgtaataatctcttctcttgaaagagtctagaatatgaaggagatctacatcacctaggtattgcaatcagcagtatgtcacaacttctatggtgagcagggctcaggcaggagaggatagtcagattttctaattattaagtaaactgatatttcacaatgtcttctgggggcagggcacaaataggagagaaaaatcacctagcttatgggcccagagatatgtgataatattccctgttttcagggtcaaggtagaagagtcacattattataattctaacccagggatatgtcacaatgaatccatgggaaggaatttaaggcaaaaatctcaacatctgagtactaggcctcataatatgccagaactccttgtctttcagggtgacatgatttgctgtgagctgggtgtgaatatgagaaacacaatctcatgtgtttccaggatcatttgatgacactctacagctttgaaaggctttgtacagccttcatgagaattgcaaaccactgtgaggcctacatggttgtacagattcatgatcttacacattacccaaaagaaagatataatagttaacatatcctctgtaggctgggttcagaaataatatccatgattttcttgagagctggatccagaaataagtcaccatcccatttgtggccagatcaacatatgaagatcacaattccaactttgtactCTATTCACTTTTagactcagaaacttaatagtgggctttgtacatgtgggatggtgacaaca-ttgctttcacctgggtatctaatggagagtccaaatctaaatttttgctcatctc-ttttataaaactctctgtacaacacaataaatgtagtcatcatgagttaatttctgtaaagtttttgaatttgatagaaatataaaacccaggacctcatctattgccctaagcctagtaatgaaatgtaaaatatatcctattggccgaatcacaggataggtttgtccatcatgcctgtgaactgaagtaaggtatatgatatatttacatttgtgggcaaaaaaaaactaggcaggaaggtaacatcacttacatgctgtgacaagcatcatgtcataatgtcctctgtaagaatggtatatgaattagagtcacattaactgggtgttggatcctgcaatatgacaaaatcccatatgtggAAACAAACCAACCTAGAAGTGAGAACAAAAATGCCAACAGAAtgggcccaggatatgtcaaaatatgttctgtggctttgggacaggcatgaaagtcacattattagggtgctgggcccagcaatatgccacaactccccatatatgtaggacccaggcaaaagagtaacattatctgtgtgctggcccctgcaatagtcaaaatTTTTGTTTTTCTATTAACATGAGTgttgtgttcagcaatatgtcacaatcctctcattgtaaagaccaggcaggagaagagattcatttcacttaggtcatggtctcagagatatatcccactgttctctccatgcagggatcaggtagaaagaagagtcatatcacctatgtgtttctctagttaaatgtcacaatctgacatgcaggcagaaaccagggagaagagccacatcacctgggtacagcctcaagtaatatgtcaccatgcccaatgtagacatgttcaaaaaaagaaaatcacaccacaagaattctgggctcaataatatgtaataattccctctttatacagagtccatgacaaagattagagccatatcacctagaatttgtgctcagtggtatgtcacaatttcttcaatgaacaggatccacgcaggagaggagagtcatattacctagataccatatctagcaatatgtcacagagtcccctgtgagcagggcactggcaggagagaaatgtcacctagccaataggcccagagatatgtgaaaataactgttgtttgcagggccaagacagaagagtcacattatcatcgttctgatccagtgataggtaacactgccctcatggaaaggaatttaaaccaaaaagtctcaataccAGTATACTTGGCCAAGGGATATGACATAATCTCATCTTTAAATgtggcagcattttagctgttatctagttatatatatgacagtcacaaactcctgagtgtccttgccattgtatgatactctctacaacatctgaaaactttatacaacacgcatgagtgttgcaaaacttgctgagtcctacacacttatatggactcataatcttccatattgccataaaccgaggtatgtcaggcaacatgtcttctatcggctggcatcagagttgagaccattattagggctgtgagctgggtacagaaatgggattcaccatctcacctgtagtcagattcacttatgagagtcacaatttgaactttgggttgtattgacttgtttgattcaggacctcaacaataagctttgtaaatgtaggatgtgagctaatgttgtaaaattctgtgatctttgaacaaatgtgtaatggaggaccttaactattgaccaaaacctaggggtgagaggcaaaatatctcctattggcttaatcacacagcgaacttgatcatcatgtctttgaactgaagcaaggcatatgtcataatctcatttttggggaaagactaggcagaaggttaacatcatttaggtgctgtgccaagcaacttatcccaatgtcttctccaggcagggcctaagaaacggagtaacattaactgggggctggaaccctcaatatgacacaaaaccatgtggaagaaacccagCAAACTGATCAGTGGCAAAATACATATAGAATGAGccaaagatgtgtcaaaatactatctgtggccctggcacagagagaagagtctcatccttagggtgctgggccaagcaatatgccacaattccctctttatgcatgacctaggcagaagagtaacattatctgggtgtagggtcccgaaatacagcaaaattcctgttcatgggcactctttagcaacaagacaagagtcacacaacctgagtactgggcttctcaatatctcacagatctccgattgtaaaagcccagacagaagtgagtcaaattacttagactgtgggttcaaagagaggacccaatgtctttagtaggcagggctaaggcaaaaaaagtgaatcatatcacctaggtgttttctttaagtatacgtcacaatttaatgtgtgggaagaaaccaggctgaagtgccacatcacgtggtcctggttcccaagatattcacaaatcccccttagaaaaggacccaggcaagagagttacatcacctaggagcaggttcctccctgatgttacaatgctccatgtgggcagcccatgaaggaattcacatcatctaggtgataggcctagagatatgtcacataaccttcctgaaagcatggccctggcaaaagagtaccataacctttgtgcctcgtctagcaatatgtcactatacaagtgggcaggtttcaaacaaaaaagccatatcatctatataataggccctgtaatatgtcataatattgtcttttatgcatggtcgtggaaaaaaaatcatcattacctgtgtgccttgcctatgaatatgtcactctcctgccctgtgtgtagggcccattccagagaggaaagttacatcacctcagtggtggacacataatatgtcacaaggttgtctaggggcagggagcaggcaagaatgtaatgtcacctaagcactgaatccaatgatgtcacaatccttaatgagatcagggcccaggcagaagtgtcacaaaacttcagtgttggcccaggtaaatatcaaaatcctttatgtaggctggaactagtctgaagagtgaaatcacAAAAGTGCATGGAAAAGCTTTATATCACAGTCACGATAAAATAAAATTCTAGGGATTATTTTAAAATACCACATGTGTCTTGTTTTCATGTAGaacagtagcctttatcttctgtgatggtaaaaatctttacagttagctaagtgttcataagagactcacaatttactctttatgagaggccttgttatgacactctccataacttaatgcctttataacttaatggtgttataaaatgtgtaagtgttgtaatcttctgtgactttgttaatagtaggagatgcttgacatcactcatgtctctaaacctagttgtaagagtcaaaatttttcctattgactgtgtccacatatgagagtcattgtcatgcctgttagctgtgtccaggtatatgtcaccatgccctcagtggttattaaacagggaggacacagcattacctaaatcctaagccagaaatattccaatgtactctttgtaggcaagactctaacagagaagtcacagaatttaggtgctatgcccagctatatggcataatatcccttgtggagagtgtccaggcaggagaagagagtcatatcacctacatgatggatccagagatatatcacaatgcctcctgttgtaatgaccccagaaaagagtcatatcatttggatgtaatgcttagaaatgctacacttttcactttaagcagggttcagtcaggagaggaaagtcacataagctagatgatatgtccagagatatgttatcatcccttcggagggcattgttaagacaaaagtcaaatcaccaaagttttggcccagttatatgtaaaaatgtcttatctaggcTATAAATAGGCAGGATTGTTAAATCATTCAGTAGCTGGGCAAAAGTAAATGTCATAATAACACTTGTGGAAAGGTTCAGGGTTGAGAGTCACAATACTGTACATGTTGTGGTTCCTGGTACAAGAGTCATTATTATGCCTTTTATCTCGCTCACATatatggcagagtatcacctgtggggagggagaggaaacaaaaggagagttacaccacttaagtgggtgcatgtccagtgaaatgtcacaattctccttgtaggttggattcttggagaagattcagtcaactggatgctggtttcagtgacatatctaaatcctccctgttggcaaggcttaggcaggagagGAGAGAAACTGCATATAGACACCTTGCCTTTATAAGtgtcaaaatggcccttgtgtgtaggatcaagtcaggagagtgaccttaccttggtgctgggttcagcaatatgtcaaagtctctctgtttgtcagagccaaggca--agagaggaaacatcacctagggcctgagccatttaatatgttacaaagctttttattggcagaactcccctcagaaaagtttcacatcacctgagtgcagtacccagttgtatgtcacaatacaccataagtgtagggccaaggcagtacaagaaactcacatcatttacatgatggacctagataaaagccacaatgctctttatagctagggtttaggccaagagttcacatcagctcactgctggtaccagtgatacataaaatgccccTAGTTGCATTGCCAAAAAGTTGTTATACATTGCTTAAGTGCTGGTGCACATATGTCAGAATTTCTAGGTTTTCAGCCTAGAAAGATTACTCAAAATACTCAGATGCTGGACAAAGTCAAACTTCACAATCACACATTTGAAAATGTTCAGAAATAAATTTTACAGTCCCACACAACTgctggctttgggtatgacagtcaacacctcctatgagttgggtcaaagtaaaggagtcataatctcaacaatggGCAAGATGCATGTGTAAAAGCCCCAACCACATTGAAGGTTGTGTTCCAGTAGGTTAGTC-ATGCACCACAGGTCTGGAGAATCATGGTTTAAATGTCACCAAACCATCTGTGGATAAGACTCATGTACGACAGTAACAATGTCAAGCTTTGTCTCCTTATGTGtgtgagattttgtaactcatttgtaggctctgttcatgtgtgaaaattacagctgtgtcagctgaatgtgcataatacctagttggtggtgcctgttatgacactctttgtaccatgcagatgttatatgatacacctgcataggatactcttgtctgaattttattgggggagatctaggacttcacccatggccataaactggctatgagagtcaaaatatctcccttggctgggtccatgcatgagagttattattgtgcatatcagttgaatccaggtatatgttagaatttcatctttggactgagacagtatagaaatgtcacatcatctggtgtcctgagtcagaaatatattaatcttatttttaggcagcatccaatcagaagagtcatgtcacctgggtacagtctcaaataatatatcatcttgaccactgtataca-ggttgaaaaaatagaggatagtcacagtccctaggtgctgggctcagcaatatattataattccttctcatggcagattccatcacaaagagaagagtcataccacctaggttttgcattcagtggtatgtcacaatttcttaggtaggtgagatccaggcaggagaggagagtcacattacctagatgctgtatccagcataagctcagtgtcccctgtgagagcgcactgtgagaggagagacatataacctagctgataggccaagagatatgtgacaatatccccttctggctggatccatgcagaagagtcacctttttatgattctaacccagcaatatttcacaatgcacccacgggaaagaatttaagccaagaatctcaacactggggtgctagactttgtgatataacacaatCACTTCATCTTTTAGTtgacacctttaactgttagcttggtatgtatataagagtcacaatctcttgtgtgttctaggtcatcctatgagactctctacaacatctgaaggatttatccaaaataccttagagttgcaagccactctgaagcctacatacttgtttgactcaaaacatacatattgatataaaccttgttatgataatcgacagatctcttataggctggtttcagacagaaaacgcattatggtgcctataatctgggtccagaaatgagtcaccatctcatctgtagcaagatccacatatgaaagtcacagttccatctttgtattttatttacttcttagagtcagaatttcaacagcgggctttgtgaatatgggatgctaaaaactttttctctcacctgcatttgtaatcaagggtcacgattttaatcttttgctgggccctgttataaaacactgtgtaccacccaagtttatagaatatgagttagtgttgtaaacttctgtgagctttgtacaaatatgaaactcataaacataactagtgccctaagcatagtgatgagaggcaaaaatctactatttgtggaatgccaattatgtttgatcattatgtcactgagttgAAGCAATGTAAATATCATGATCTCATTTTTAGAAAAAAACTTGTTGgaagggtagcacaacttatttgctgtggcaagcaatatgtcaccaaaccctctctaggcagggtctagaaaggaggattacattacctgggtgctggagtgctagacccagcaatatgacacaatcccAAATGGGGAAAAACAAGCCCAAACAAATGAAGAGACCAAAAACGCCCACATATtgggcccaagatatataaaaatactttcagttgctctggtacaagcaggagaattacaccatgagtgtgaggggccaagcaatatgccataattgtctctttctgcaagacccaggcagaaatgggacatcatctgggtgctgtaccctgcaatacatcaaaatttattttcattggcatggttttgggaaaaaaaaaagaagagtcactttatctaggtattggacatagcaaaacatcacaccacatcattgtaagggatcaggttgaataaaagatacacatgacatatgacacaggcttagatatatgacccaatgtcccaagtaggcagggctcagtcagaagagaagagtaatatcacctaggtgcttccctgggtatataacacaatctaatatgtgaggtgaattcaagcagaagagtcacatcacttttatactgggtcctgagatatatcacaatgctcccttaggacaggacacatttaggagagttacaacaaatagttacaggtttcaggtttcacatttatgttgcaatgctccatgtgggcaggactcaagcagtgaattatatcacgtagacccaggccaagagatttgtcacaatgccctctttagaagttcctatcaaaggagttccaacacctctgtggctagcactcatacatcactacaccacactctgtgcagagcccaatctaatgaggagagtcatatcacctgagtggctgacagagtgatatgtcacaataatttctgtgggcatggcttaggaaaaaaagtaacatgatctaggtgctggatgtaatgatttgtcatgattcttactgggagaaaggcccaggcaggagagtcataccacctgaggttggcccaggtgggtaccacaataacacatgtgggctgaaaccagtgtagggattcaaatcacacaggtGCTTCACAAAAATTTAAATTACAAACACACTGGCAGAACATTCCCAGGGTAAGATTTACAATAACACACATTACTTGTTTTGATAAGTGACAGTCATCTTCATATatttgtgaaaatgacattccttactgtcatctgactctgcatatgagactcacaatttcacctttctgctgggttctgtcataaaactctctgtataagcagaggacattataaaatatcagactctattataatcttctttgaacttttttattaccagaaagagactgaatcactcttgtttcaaaagcaagttaagaaagtcaaaatttcttctatttgtgaggtctacatatgacagttattatcatgcctgtgagatgCTtgtaagttgagcattgaaatataagctcaacaaggtactcttaaggcattaatctgttccttaccaaaattcataaagaattataaaatgttattgctttttacatttctaagtcatcattttagttaaatatgtaatttatgataacctggaattgtatttctttacacaaggggtgttttaaacccctaacatgtaacatccttctcaaaatcaagctttagctacaaaattatctttcttaatttctggcttttggatgctacagagggcccatggagtatccacgagagagttaaactggattatatgacaggattaattacatagaatttccaaaatggtgttcaatattctttagatgatgttttgatgactaatactaacacatgttccaaaattatgtggtatttctaatatctgaagtatatgctattatcaacaattaaggttgttacagtattttaaaccatagaaataatagaaatttttgtcatgtttctgactgtaactaccctggacattttcttataaacagatgattgttgtcttgttttaattttttataaaagcattttctaatcagctgtagatctttgacaggtgctctcacttgcaggtttctgataactttggagtctgtgacactggcatacaggaaaaacttacaggactcttaaagagctaaaatatccatgaatatcaaacaaaagaagtgttaactgaatggactggactaatagaaaactgaagtaatctttttgccttttacatgaaacattactgattcttgtattgtttaccagagtcaaggaaacagccattaatatttgagtaaggtgtactcctgtgtacacaatttgaaacatgtttgtctttctctgcagggtttttccagaatttcaaaaatagttgtgagtgttcttaacttatggcaatataggtgtttgcatcagagcaataatagtccaatttcttttccaacagaagagaactggagaaactgtttttttaccaaggccttgactgaaaaagaagcttccctgtaaggagtcaagttcaacttgcagagccaagaacacttcggtggcaaaattggcttcacacctcatctaaacagtcctttagcagggttccttatgtgtggtaagtaaagaatgacattactgagaggcccaacagctccaactttatgttgggaccata--aggagagaatcacccaactgaaaagtatttgatggtacaaacccatggctggggttgactttagaaagtcctgtctgaaatttcttgtggaacagaggtccatcaaagccaatataaaagacttatacagaaatatttattcttgctgcactttatgaaaataataaggtcaagtataagagtaaagtttgtcttacaaacaactcagtcctatcttgatttgttttttttaacagaaaagaggattggataaagataatatttcgcaatttattatagatttgtcattatattttaaacgcattggttttgaatttttgcctacattttagaacaatcctgcttatttctgtgactcaactagtgatcttcaactgcagcccccccgccccccacacacacacaaaaggagttggtaatgtaaacatctggattaacattctagttctggacaattttcctgcaaattctgcagagtgatgggaataaataaagtgcccacccaaattttataactacaacggtagccactagtttcctcaatgtgt--cagtcattcttttctcttccttatggaagaagaactcaattccacaactttatcttagcattcagctcgtgataaagagtccatacaatgccctgagacaaatttttctcccaacctcaattccaagcttctggttgacactgtagaaaaaaatagaaaatttgagaaatccagaggcaggtgataacagaggtaaacagcatggtgcaggtgagcataattaatttccactgattaagccaagcctctgatttcatggataaagattatgctactatccatactataaatgaggtctagtgaactccagaactaccaacagcaggggagatagggaacatgtggttaagagcagatatttccaccccccaggcctccctgttaacactattcaaagctgccttgacacccatgggtggcagcctgttacaatcactgggacttgggtatacaaggattgaagtgggaaaaataatattccttctcttatagctcaacatactctgggaatttgctaggaagagaaaagaaccagggacacctgctcctctctctctttctagataaatagtcattcatctttagtctatacccattttgaatgcatcctgaacccttagaatgcctttgaaaaaatgcttacttttcattttttctcctctgtttgctgtttacagagaggtaatcacgtctccatactttgggttgttccacttcaatgcatcctccaagtttggaagagttaatttccaaaacattaaactggatggcttaggattggacccaggagaaaagaacccagaagactgatatgctgtccaaagggtaaaTTtttgtttgtttgtttgtttgtttgtttTCcctgttgggcttttggcatccctctccctatgcaaactggtgaaagaccttgaattttttgaactgtccattcaacttttcccttgtttcatttaaatacgtgtttcttaattacccagtttgattctcttcaccttcaggctatcaaacttcaaagagtcacactatcagagcAAGAATTCAtcttacaggttctctcagaggctggcttcagttttttcttcttttaaccctttgatgagaatgcagtgtcttggctggtgctggtgtattggaaattgtagatattgtgcctgtgctaagatacctcttataatctttgttaaagagcaggttagcacttttagaaaaacatgtgcttttaatatccagtttacagactgtatgtcacctttATTGCCTGCTTTTGCCAAACCCATGTCTCCCTGGGTTGGCTAGGGGCACACGTTCACTGGAACCCTCAGGTAGCCTGTTGATCCTTCCTCCAATGCAAAGTGTCAGTAAGGTATCACCCAAGTTTCCTCCTAAAATGTGATTTCAGGAGGTCACAGAAGCACATTCTGCTCTAACTTATTGACTAATTAATCAATAATTCACTTAATGTTTCAAAATGGCTGTGAACCTTGACACTCTTGATCTCCTTCCTCTAGTAGGGCTGTATTGGTGGGAGCCATCCTGATTTATTTGTGGAAAAACTAGCAGGTAAGGCAGGGTAGGAATAGGTCAAACCACCTAGGCCGGCATCCCTCAGGGCCCTTTGAGTCCTCTGCAGGCAAGCGGGCTCAGTGGAGTTCCAGGAACTTTATCTACTTTGGTGCCCAGAGACCCTAGCTGGACCCCCAAGACAGGACTACTCCTTCAGCAACCTGCACCTACTGGTATCTAGGAGGCGAGCATCCATTTATCTTTGTGAATGTGGCCTTCTGCTTCATTTCCATTGGTTGTTCTCTTGGAAGAAGTGCCTAGGGAATACTGGGCCTGTGTTGGAGGTTTTCTAAGTGCAAAAGTCAATAAGAAAGTCTTAAAATATAATTATAGTATTTTCTGCATATTTCTATCTCAGAGTT
s panTro2.chrY             637146 68618 +  23952694 AGAACAGGTAATTATTTATTAAGTTGAAAACTGTTATATTTTCTATAATTATTTTAAGTCAAAATTCACAATAGACAAAGTAAGACATTCAAATATAGTAAGAGGTTTAATTCACTGAACACCTATAAAGACAGTTCTTccaaacacataaaccaacatcgacagaattgaatgaaaaataggcagcaatataataatggatgtatacatcaatatcttactttcagtaataaataaagcaagacagaatatcaataagggaacaagaaactggaatgcactacacaataattacacctaacaaatgtatgcagacaacagaatagacactcttttcaatagctcataaaacattttcctagatggatgatctgtgacaccacagatgaagccttaataatttttagtagaaattttacagaaaattatttatagcccaggttgaatgaaactagaattcaataacaaaagaagagcagaaaaaccccaaaaatataaaaaataagcaaGAGtttgtttgtttattttttatttatttatttatttatttattatttatttatCTTTTgatggagtatcactctgaagctaggctagagtccagtggcacaatctcagctccactgcaatcttcacctttggtgttcaagtgattctcctgattcagcctccagagtagctgtgactacaggcgtgcaacaacaagcccagaacttttttttttattttagtagacatggggtttcattatgttgtccaggaccacctgtatctcctgatctttctatgcatgctactcagcctccagaagtgctgggtttacaggcatgagccactgcacccagccAACAGCACACTTTTAAGCATGCTGTTTTTCTAgggttggaagataaaatattgtgaagatgtccacgctgctcaaagtgacacaaacccgcaacacaacatttttcaatttttaattttacttttccaaaatagaaaaaacccatgaaattacataagattccaagaaaccatgaaaagtccaacaatcttaaaaaaaaagaaa---aaaaatattggaagcattacatataacaatttccaaacactaagcaaacctacagtaacaaaggactttgctaccagtataaaggtagaacaccaaagtaatgaaataaaatgcagcacagatataaactcTTGAATagacaggagagacatcataccacctaggtttttcattcagccatatgtcataattccttcaataagcaagacccaggcaggagatcagagttacattacgtagatgctagtttcagtgatatttcaaaatgtcctctgggtgaaggacacaggctgcagagacacatcacctacctgaaaggcccagaaatatgtaatagtactccctattgacagggcccaggcaaaagagtcatgttattatgattctgacccatcaatatgtaacaatgaacccatgggaaggaatatgagccaaaaagtctcaacacctgggtACCAGGATGAGTCATATGACCCGATCTCCAcatctttgagtgtgacagctttaacttttacctgagaaagtatattagagtcacagtcttatatgtgttgcaggacaatatataacactgtctacaggagctgagggttttataaacctgtatgagagttgcaaagttctctgaagtctacatgctcctatggactcacaatcttacatatcgctccaaactcagatctaatagtcaacatctttcctataggcagggttaagaaaaaaatccattattatgccaatgagctggatccacaaatgagataccatcccaattcttgtcagattaacatataaaagtcaaacctccaactttgtgctgtattcctttgttagactcgggacctcaacattgggcattataaatattggatggtgacaattttaaattcacctaggtatgtaaacatgagtctcaatctgaactttttgctgggccctgttaggaaacactctaccaccaaggagtttgaaaaatataagtcagtgttgtaagcttctgtaacattggtagaaatatgtaacagaggaccttacctattgctctaaacctaatgatgtgagataagatatctcctattggctgaatcccaacataaatttgatcatctatgcctgtcaactaaagcaaggtgtatgtcctaatcccatatgtgggcaaataactatgcaggagggaaatatctcttatatgctgtgccagccaatatgtcaaaataccttttctaggcagggtataggatataaggtcacattaactgggtgctggacccagtaatatgaccctattccacatgtggaaaatacccagccaagttatgagagccaaaacatctacataatgggctgaagctatgtcaaaataccttcagtggctccaacacaggccgaaaagtcatatcataaggatgctggtcttagcaatatgcaatatgccataatttcttctttatggaaaacaaaggcaggagagtaacatcatcaggatgttggtccgtgcaattggtcaaaattccttttttgtgggcatgttcagaaacaagaggagagttacatattctgagtgctgggatcagctatgtgccaaaatcttcttactgtgaaggcccagtcaaaaagtagagtcatattttcaaactatgggctcagaaatatgtccaaatgtttccattaggtaggtctcattgagatgaggaaagtcatatcctaggtgcttcccttcatatatgaacaaagtaacatgtttgcagaaatcatgaagaagaaccacatcacttgggtgctgggtcctgagatatgtcacaaggccttcttagaatatcatcaagcacagagggtaacataaactatgtgcagattctctgtttattccacaatgttccgtgagtgtaggtcccagagagggagtcatttcagtcagctgacagcccaagagacatgttacaatgtcctctgtgaagcatagacctggctaaagagtaccctcacctgtatgcctggcttagaaatatgtcactcttaaggttggcagggcccaagcaggagaaccacatagcctaggtgatgggcccggatatatgtcataatgtccttctttcaggttggctctggcaaaagagtatcctcacatgcttgattggccttgctatatgccgctatccttcctttgtgcagggcccactgcagagatgaaagttacatcacctatgaggtgggcacagaaatatgacacagtaattttgatggacatggcactggcaagaatgtaacatcaccaagctgctagatccagtgatatgtcacaaccctcactgagagaagcacccaggtaggagagtcacatcccctcgaggttgaactaggtagatatcacaatTTCATATATAAACTCGGACCTTTCTGCAAAGTAAAACTACATAGGTGCCTGGCAAATATGTGTATCAAAATAACACTGTCAGAAAATGTCAAAGGGGAGATTTACAATACCGCTCATGTTCTGTTTTATATGTGAcagttggcttcatccatgtgaaacgatgacagttctgtcagctgggttttcatacaagactcacagttttgcctgtgtgctgagtgctacgttagttctgcttatataacccaaatactttataaagtatgtgtgagtgttgtaatcttttgtgacctttgtacaagaaagtgatccatgacatcacacatgtcactacacctagttataagagcctaaatattctctatttgctgagtccacatataaaagtcattatcattcctgtgagccctgcctaggtatatgttacaattccatcttggttataaagcaggcagaacagcctcatcacctaaattctgggcctaaaatatttcaatattctctttgtaggcagggtcctgtcagaaatgtcacataagttttgtgctagggccaggtctgtggcataatgacccttgtgggcagtgtctgggcagaagaggagagtaatatcacctaaatgatgggctgatatatatgtcaaaatgctgcctgttgacagagcccaggaaagaaagtcatataatttggatgcagtgtttagaaatgttacaattaccaaaggaagcagggtacaggcaggagaggagtcatgtaacctagatGGTGTGTTCAGAAATATGTTACAATGTCCCCTGAAGACATTGTTAAGATAACACAATAAAATCACCAAGTTActtggtcaggtatttgtcaaaatctcatttgtgggctatacctacggagaattattaaatctatccggagctgggcaaagatatgtgtcacaatttcacttgtggaaagatttaagaattagagtcaccatcctgcacatgtcttggctctaggcatatgagttcttcttaggcttttgttttggtctcagttatatggcataatatcacctgtggtcagagataaggcaagaaactcatatcatctacatgggtgagggtccagtgagatgttacaatccacctggtgggcaaagcccttccagaagagtcacatcacttggatgctggtttcagcgatacataaaaaccattctctgaggtaaggactttggcatgagaggagacccacttcatctaggcaattggcctagatatatgtcacaatgaccattaactgcaggaataaggctaaagagtgacctcaccttggtgctgtgcccagcagtatgtcacatgctccctgaggtcagggcacaatgaaaagtaaagaaacatcaccttggtactgagagaagttataggttacaatgcttcctattggcaacccccccacc-aaaaagaaatcacatctcctgggtgcacaaccctgttatgtgtcacaatactctgtaactggagggccaagacagtagaagggagtcacgtaatttatgtgatggacctaaatataacacacaattctctttgtaggcagttttcaggtgggtaaatcacatcatctgggtgatggtcccagtgatatataaaactgcactttgtaggcagaacAAAGTATGATGTTATGTATTGATTTGGGGCTTTTTCCACATATGGCACAATTTCATCTGTGGTTTGGGCCTAGAAAAGTTCATCAAACTACCCATGTCCTGGGCAGAGTTACCTGACCCAATCACACTTTCAGAAAGTTTCAGAAATAATTTTCAGTCCACACAAATCctagcttcaggtatgagaattaacacgttctgtgagttgggtcggagtacaggactcacaatcaacaatgggaaggtcaatgtgtaagaaccccaatcccacttgaagattgtgttcCAATAAGAGAGACACGACACCACAGTTCTGCTTAATCGTGGTTCAAACATCATCAAACAAACACCTGCGGATCAGATTTATATATGAGAGTAACAATTTAAAGCTTTGATGGCCTATGTGAgtgagatttagtatcacattggtaggatctgtttatgtgtg-aaaaaaacagttgtgtcagctgggtgtacatccaagacaccctggcttctggtgcctcttatgacacactttggaccactcaggctttatatgatatgcctcagtgggatacttttctgtgtattcttacaggtgggtggtataggacttttctcatggctgtaagactcgatatgagagttgaaataccttcccaggctgggagtagttttgagagttattattatgcacataagctgaatccaggtatatgtcacaatctcacctttggacagagacaagacagaagagtcctatcatctgggctctgatccagggatacattttaatctacttcataggcaggatccagtccaaagagtcatgtcacctgggtacagtcttaagtaatatgtcattatgcccactgtaaatacagggttgaaaaagtagtggataatcacattctcttgggattggcctcagtaatatgttataattttctctattggcagagtccaggacaaagaggagggtcacatcacctagattttacactcagtcatatgtcacaatttcttcagtgggcaggatcctgcaggagaggagattcacattacctagatgcttcatctagcgatatgtcacagtgtcctctttgggcagggcactggcaggagagtagctacacaacctagctgataggcctaaagacatgtgataatatcccctgctgtcaggattcaagcaaaagggtttcattattgtaattcaaacccagggatattttacaatacaaccattgaaaagaatttaagccaaaaattctcaacacctggaggtactagtcctagtgacatggaacaatctctttatgtattagggtgacaactttgaatctttacttggtgagtatataagagtcacaatctc--atgtgttctggctgatcccatg--acactctacaacctacaaaggctttaagcaacatgcatgagagttgcaatccattctgaggactacatgctcctattgactcacaaaggtatgtattgctttaaacttggttatgataatcaacatcccttttacaggttatgttcagacaggagacccattattatgcctgtgatttgggtccagaagtaagtcaccatctcacctgtagcaagagccatatgtgaaattcacaaatctatctttgtactttatttacttgttaaactcagtgcttcaacagtgggctttgtgaatgtgggatgttgacaacttttgctctcaccttcatgtgtaatcaagagtcacgatcttaacttttgctgggccctgttataaaactctgtgtaccaagcaaggagtttataggttatatgttattgttgtaacattctgtgaactttctacaaacttgcacctcataaacttacctgttgttttaagtgtagcagtgaaaggcaaaacatatagtattggTGAAATTCCAATTTCAGTTCGATCATGATGCTTCTGAATTGAAGCAATGTAAATTTCATAACACCATTTGTAGAAAACAAAAAACTTTTCAGAAAGGTAGAAAACTGACATgctgtgtcaagaaacatgtcacaatgtcccctccatgcagggtctagtaattgtgttatgataactgggtgctggactcagtggaatgacacaaCTCTAAACATAGAAAATGTAGGAAAAACAAACACATACAAATGATGAGAACAAAATTATTTACAGAAtaggcgcatggtatgtaaaaatactttctgctactctggaacaggcagaagatttacataatcagggtgggagtcccagcaatatgccataactctctctttatgttggacctagttagaggagaaacatcatctgtatgctgggcccagcaataaaccaaagttccttttcatagtcatggttcaggaaaaaagaagtcatattacctaagtattaggcttagcaatatgtcacatcaccccattctaaagcctcttgcagaagaaaaggttcacttaacttaagacacaggctcagatacaaggcatgatgtcccaggtaggtagtgctcatgcagaagagaagagtcatatcacctaggtgcttcctaggtatatgacacaatttaacatgtgaggggaaaccaggcagaagagtcacttcatcttgatgctgggtcctaagttatgtcacatggcttccttaagacagcacacaggcaacagagttaaaaaaaataagtatgaaaaatgtcacaatgctccataaggacaggacacaagcagggagtcacatcacctaggtgactgacccatatatatatgtcacaatgtccaccttgagtcatggccctggtgaaagagtaccatcacctgtgtgcatagcctagcaatatgtcactatctgagtaagcaggacccaagcagattagcaacatcacctaggtgataggccaagagatttgtcacaatgccctctttaggacatagtcctagcatatgagtactgtcacctctgtgcctggcccagtcatatatcactatcactcactgtgtgcagtacccaCTCTAATGGGGAGAGTTTTGTTGCCTAAGTGGTTggcacagtggtatgtcccaatgatttctgtatgcatcgctcaggcaaaaatgtaacatgacttgggtactggatctagtgatatgtagtgactcttactgagagcagggcccaggcaggagcatcatatcacctaaagttttgctcacgtagatatcacaatagcatatgtgggctggaacaagtctgggagtaaaatcacTCAAGGGTTTGGCAAAGATTTATGTCACAGTCACACTGGCAGAAAATTCTCAGGACGAGATGTACAATACCACACATGTCCTGTTTTTATGATTGACAGTTTGCATCGTATATGTGAGACAGTGGCAGTGATTACTGTCAGGTGGGTGTACATATAAGACTCACAGTTTCACCTTTCTCTTGGGTTCTGTTCTGAAACTCTTTGTATGAGCCAAGTTCTTTACAAAATATGAGGCTGTTATAACCTTCCTTGTCTTCTTCTTTACCAGAAAGTGATTCAATCCATTGTGTTTCTGAAGCAAGTTATACAGCTCAAAATTACTCCTATTTATGGGTACCACATATAACGGTCATTATCATGCCTGTAAGTTCTGCCTAGGTATATGTAACAATTTActctgtgatgtgttacaatattctccttgtaggcatagtcctggcagaaaagttgcatcacctgggggttacacccatatatatggcacaatgccccttttggcacagtgtccagacagaagaagagactcatatcacctatatgctaggcccagtgatatgtcacaatgtctcatgttaaagggatcaggcgagagagtcatatcatttggatggcatgcttagaaacgctataatccccagtggaaggagggtccagacaggagaggagagtaagataactagatggattatgagtccagtgccatgttacaatccttcctgaggatactgttgagacaggagagtcaaatcgtcaaggtgctcagctgaggaatatatccaaatatcatttgtgggcaacatttaggcagGATTATTAAGCCACTCAAGAGATGGGAAATGAAATATGTCACAATAACACTGGTGGAAAGCTCCAGGAATGGAAGTCTCCATCTTGGATATGACCTGGCTTCAGGTTTAAGCATCTTGATTAGTCCTCTCATTTGGTGTcaactatatggcactatgtaatctataggcagagagaaagcagaaatgtcacatcacctgtgagggtgctcatcctgtgagatgtcactttttttcttgtggccaggaccctggaataaaaggtacatcacctggatgttgattttagtgatatatcaaaatttcttctgtgggcagggcttaaggtgaggagaatcactttacctagacaattggcctagatatatgtcacagtggctgctatgtgcagaactgaggtatgaaagtgacctcaccttggcactgggtttatcaatatgtcacaatctcccctgtggtcagggcaaggcaagaaggtagaaacatcacctaggtgctgagccaagtgatatgttacaaagctttctgtttgtagaacacaaaattgagtgtcatattacctgggtgtaatacccagttatgtgtcacaattcaccataattgcaggcaaaggcagtagaagtaagccacatcacttatgtgatagacctagatataagccaca-tgctttatgtaggcaggaatcaggcaaagaattcacattacctgggtgcctgtcccagtgatatgtaaaagtgccatttgtaggcaggAACATGTACCTTTTCTTAGGTGTTTGGTCCACGTATATAACAATTTCATTTCAGGTTATGGCCTAAGAAGGACAGTCAATTTACTCAGGAGCTGGGCTAACTTTTATGCCCTAATCACACACCAGGAAATATTCAAAAATAAGTTTCACAATCCCACACAAGTCCTGGCTTTGTGTACATAAGTAAACACCTCCTGTGAGGTGGGTCAAAACAGAGgagacacaatcccaacaatgggcataatccatgtaaaagatggcaatcccacttgatgac-----------------tgtcaagtggagatgagtgtgaagtgggagagtcacagcctcatatgtgcactgaattatgcatccccaaatcacctgtaggtcagatcaacatatgagaggaaaaatttcaTACTTTGACTGCTCTTTTGgtgagatttagtaccttatttggaggccatgttcttgtgaggcaatgaaaattgtgtctgatgagtgtgaatccaataatcccaatagcattgggttgctgttccctgttataacactatgtatgcctctcacactttatatgatatgctggagtgtcataatactgtgtgaactttataccactaggagactcattactttacttatggctataagactgggtaggagcatcaaaatatgtctcgtttttggagccaggtatgatagttatatttgtgcatggtaggtgaacacaggtgtatgtcaaacttttacctgtgggcagaaacatggcaggagagtctcatcacctggaaggtgagctcaggatacattataatctcctttgcaggcagggccaagtcagaagagtcacatcacctgattacagcctcaagtaatgtgacaccatgtcaaatgtgaacaaggttaaagaaatagaggagagtcacaccacctagatgctgggctcagcaatatggaataatccccattttggcagaatctagaataaagaggagaactgcattacctagattttgcattcagcatcatgtcacaattcttttagcgggcaggacctaggccacagagaagagtcacatttcctagatgttacacccagtgatgtcacaatgttctttggggaaaaagcacaagcaaaatagacaaatcacctagcagacaggctcagatatatataatgtccctaccttgcaggactaaggcaaaagagtcacattattatgactgtgacctaacgatatgtcacaatgcacacatggcaaacaattaagtcagtttttacacctggatactaggcccagtgatatgacagaatctcctcatcttttagatgacacctttaactgtcagctttgtgtgtatataagtcacattgtcacgtgtgtgctgaaccattacatgataccctctagaacatctgaaagttttatacaacatgcatgagatttgctaactactctgaggtctacacggtcatatcaactctgaatcttgtatattgccttaaacccagatatgatagtcaacatctctcatttacgcttagttcaggaatgagacttatttttatgcctgtgagatgggtctaaaaatgagtcactattgagcctgtggcaaaatccccaaatgagaatcacaattccatctttgtactgttttcacttgttagagtcagcatctcaaaaatgggctttgtaaatgagagatggtgacaacttttatttgcacctgcctgtgtaattgggagtcacaatcttaaacattttgctgggccttgtgaggagagtctgtgtaccacccaaggagtttatacaatattgattattgttgtatacttatgtgagctttgtacaagtatgcaacccaggattttacctattgccttaagccttgtgatgagaggtaaaatatcttctattggctgaatcaaatataagttttaccatcatacctgtgaactgaagcaagctatatttcataatcccatttctcggcaaaaaagagtcacatcacgtaggtgatgtggcacgtgatgtggcatgcagcatgtcacagtgacttctctaggcagaatatagaaaggagggtcacattaacgaggtgttggatccaacaatatgATGAAATTTTAATTGTACAACAACGTATCCAAGGGAAGAAAGCCACAACACTTACAGAATGGACTGAAAATGTGTCAAAATACTCTTTATGGCTCTGGCACTGAGAGGACAGTAGCATCATTAGGGTGCTGGACCCACCATTAAGCAGTAACTCCCTCATTATTCAGGACTCTTGTAGAAGAGTAACATCATCTGACTgcaataggtcaaaatttccacttgtgcaaatggtttagaaaaaagaaagtagtcacataccctaaatcctggtctcaaaaatatgtcacactctcagcattttaaaggctgaggcaggggaggaaagtcatatcacttagttcatcagctcagagatatgttccaatgtcccagtaggcagaactcaggcagaagaggcttctttaggtatagtcctaatccaacacgtgagcagaaaccaggcagaagagccacatcatctgggagctgggtcctaagatatgtcacaagtccccattaggacagaaccaaggcaaaagagttacatcaccttggtgtaggtttctcttttatgtcacaatgctctatgtgcatgaggccaaagcattcaatcccatcgactagttgataggcccaagagataggttacaaagtcctctgtgaagcatagtcctggcagaaaagtatcatcacctgtgtgtcttgcctagaaatatgttactctccaggttgtcagcacccaagcaggagagccacctaacctaagtgataggcatagagatgtgtcacaatgtcctagtttgggtatgactctggcaaacaatacccacagctgtatgcctggcttcacaatatgtcactatccttcgtttgtgcaggatccattccagagatgagacttacatcacctatgaggtgcacacaaatatatgtcacaataattgtgattggcatggcacaagcaagaatgcaacatcaatagtatgctagatccagtgatatgtgcaatacttactgagagaagggcccaggcaggagagtcacatctctttaaggttagcctaggtagatatcacagtcccatatatgcactggaacaagtctggagagtcaaattacactggTGTTTGGCAAAGATTTATATCACAACCACACTATCAGAAAATTCCAAAGATGAGTTTACAGTACAACACATGTCCTGTTTTCATGTGTGAcaattgacttcatccatgagagatgacggcagtccttactgtcagttgggtgtgcatacaagactcacaatttcacttgagttgaaccctggtttgactttttcattgtaaaccaaagactttgtaaaatatgtgtgagtgttgtaatcttctgtgacatttgttcaagaaagtgattcaggacatcccacaagtctgtaatctgagttataagagtcaaaatatcatctattggctgagtccatatattaataagagtcattattattcctgtgagccattcctaggtatttgttacaatttcctctgtggttatgaatcaggccaaacaatcacatcacctaaatgctgggccagaaatattccattattattttttcaggcagggtgctgtctgaaatatcacataacttgtgtgccaaatccagttctgttgcacagtgttcattttgggatgtgtctaggaaggagaggagagtcatataacctaaaatctgggttcaaacatacatcaaaatggctcctgttgaggaggtccaaaaaagagagtcatgtcctttgaatgtagtgattagaaatgctacaattactaaaggaagcagggtacaggtcaaagaggagagttatatGCCTTTGATAAtgggtccagaaatatgtgactattctgcctgaggagagttttagacagcacagtcaaatcaccaaggtgcttgatgcagatatttgtcaaaatctcattcatgggctatatctaggcagaattattaagtcactcaggaactgaactaaaatatatgtcacaattacacttgtggaaaggtttaggaataagactcaactgttggctttctaaatgtaggatggcagcaacttttaatttcacctgggtgtgtaatcaagagtcccaatttgaactttttgctggcccctgctatgaaaatttctactacaaaagagtttataaagtataagttagttgtgtaagcttctgtgagcttgctacaaatatgcaacctaggacctttcctattccccaagcctaagaatgaaaagcaaaatattttctattggctgaatcccaatatgagtttcatcatcatggctgtgaactgaagcagagtatatgttataatcaaatatgtgggcagaacactatgcagaagggcaatagcacttagatgttgtgttaggcaatatgtcacaataccttctctatgcagggtgtacaaaattgaatcatattaactgggtgctggacccagaaatatgacacaatttcatatgtggaaaaaacccagccaagttatgagagtcaaaatgcctacataatgggcccaatatatgtcaaaatacattcagtatcagcagcacacgcagaaacatcacatcttaatgttgctgggcccagctatatacaatatgccgtaattatctctttatgcagatcccatgcagaagagtaacatgatctgtgtgctgggcaacgttgtatgtcagatttcttttttgtgggcatggttcaggagaaagtggagagtcacatatcctgagtgttgggctcagcaaagtgacaaaatcctcctattgtgaaggcccaggaagaaaaagagagtcacattacttaggtcatgggctcagagatacatctcaatgcccccagtaggcagagctcaggtagatgaggacagtaatatcagctatgtttttcccacagaatatgtcacagtttaacatgtagacagaaaccaggtagaagcactatatcacttgggtgctgggtcctgtgatatgtcataagtctctcttaacacaacacctaggcaagagagatacttcatactaggtGCAGGTCACTTGCTtataacacaatccttcatctggttaggacccaaggagagagtcactacatttaggtgataggcccagagatatgtcacagtgtactgtatgaagcataaccctggaaaagagtaccatcacctgtgtgcctggcctagaaatatgtcactttcaaggttggaaggaccctagcagaagagccacataacatagatgatagccctggagatatgtcacattgccctccgctggtcatccacaggataaggaggaaatttgcctgtgtgtcagtccttgcaatatgtcactattcttctgttgtgcagtgcccattgcagagaggagactcacatcagctatgaggtaagcacagaaatatgttacaataattttggtggtcatggcccaagtaaggatgtaacgttacctgggtgctatatccagtgatatgtcacaatcattactgagagatagggcaagtaagacaggaaagtcatatcacgtagaggttggcctaggtagatatcataaccccatatataagaagggacaagtccggagaaccaaattacacaggtGCTTAGCAAAAATTTACGTCATCATAACACTGTCAGAAAATTCCAAAGATGAGATTTACAATACCACACATGTCCTGTTTTCATGTGTGACAGATCCcttcatctatgtgcgataagttgtccttactttcagctgggtgtacatacaagactcacaatttcacctatgtgctgagtcctgctttgattttgtctgtataacccaaagactttgtaaaatatgtatgagttttgtaataatttttgacctttgtacaagaaagagacaaaggacaccatgtatgtccctaaactgagttctaagattcaaaatattctctattgactgaatccacatatgacagtcattatcatggctgtgaaccatgcataggtatacgttacaattccctctgcggTTAAGAAGGAGGCCTAACAGCCACATCACATAAATgctgggtcagaatactcaaatatgctttttgtagtcagggctgtcttagaaatatcacataatgtacatgctacgtcaagctctgtgacaccataccccttgtgggcagtgtccaggcaggagaagagagtaatatcacctaaaggatgggcccaaaattatgtcaaaatgcttcctattgacaaggcccaggcaacagggtcatatcatttggatgcagtgtttataaatactaaaatcaccaacagaagcagggtacagtcaggagaggagagtcatgtaacctagatgaagcatccagaaatatgttacaatatcccctgaggACATTTTAAGATACATCAGTCAAATCACAAAGGTGCTCAGCCCATCTATCTGTCAAAATTTCATTTGCTATACCTAGGCAGAATTATTAAATCACTCAGGAGTTAGGCAAATGTATATGTCACAATTAGACTTGTGGAAAGACTTAAGACTGAAAGTCACCATCCTGCACAAGTCCTAGGCTCCAGTCTTGTGAGTTGTTATTAGGCTTTTGTTTAGGTCTCTGGTAtgtggccagaaaaaacacaagaaagtcccatcgcctacgtgggtccgggtccagtgagatgtcacaaattcaactaggggacaggaacctgttgtaatagttacatcgcatggatttcagtgacatatcaaaattccctatctgggcaggactttggcaagaagggagactcacttcaccaaggcaattggcctagatatatgtcacaatgtctattctgtgcagtaacaaagctgtagagaggcctcacaccggtgttgtgctcaggaaatacgtcacaatctccttgtggcctgggccaaggcaaaagcaaagaaacatcacttaggttctgagccaagtgatatgtcacaatgcttcctgttggcagaacccaaaaagaagaatcacatcccctgaatgcagtacccggttatttgtcacaattccctgcaactgcagggcaaaggaagaagtgagtaacatcacttacatgatgcatctacgtatgtcacaaaattctttttgtaggaaggtttcaggcagataactcacatcacctgggtgatggtcccagtgacatatgtaaaatttccctttgaaggcagagccACGATGGATGTTATCTATTGCTTAGCTGCTTGTTCCACATATGGCACAATTACTTCTGTGATCTGGGCCTAGAAAAGGAGTCAAATTATTCATTTGCTGGACAAAGTGACCTGTCCCAATGTGACACTCTCATATATGTTCGGAAATAAGTTTCACATCCCACACAAGTCctggttttgtgtatgtgagtcaattctttctgtaagttggatcaaaatggaggagtcaaaatctcaacagtgggcaagatccatgtataagagctgtaatcccacttgaacactgtggtccaggaggggagttacagcaccacaggcatgctgaatcctggtTCAAATGTTAATGAACCACCTGTGGATCAGGTCCATGTGTGTGAGTAATTATTTCAAACATCAACAGCTTTTTATGtgtgagatttactatctcattactaggccctgttaatgggtgacaatgaaaatcatgtcagctaggtgggcattcaagagtcacattctcacctggttggttgcctctgttatgacactgtttgcaccattaaggctttatatgatctacctgagtattataatccttcatgacttttatacaagtgaaaaacacagggctaaacccattgctatgagagtcaaaatatctctactggctggctccagttatgagagttatttttgttcatgtgctcttaacctagttatatgtcacaatttcacctgtaagaacagacaaggcaaaagagtcaactcacctcgatgctgaatcagtgatacagcataacctcatttgcatactgggtctagtcagaggagtcacttcacctaggtATAGCCTCAAATAGTTTGTCAGCAAGCCTACTATACACAGGGAAGAAATAAATGAGGACAGTCACGCCACCTAGGTgctggactctgcaatatataacaaacctctctcagaagagtttagaatatgaaggagagccatataatgtcagtttttcaatcagtggtatatcacaatttatttgctgagcaagacccaggcaggagaggagagtcgcattacctagatgttaagtgaaatgatatctcaaaatgtcttctgggggaaggacactgacagaaaagaaaaatcagaaaagaaaaattatctggcttatagaccccaagatgtatgataatatcccctcttggcaggatcaagacagaacagtcacagtatgattctaacatagtgatatgtcacaatgcacccaaagaaatgaatttaggccaaatagtctcaacacctaagtACTAGACCTATTCATACACCAATTCCCCTTGTCTTtgagggtgaccctataaactctgagctagtgtacatatgagagtaacaatcctgaatgtttcctgggccattgtatgacactctacaatattcaaaagcattatacatcatgtatgagagtttcaaaccactctaaggcctacatgttcatatgtactcatgatctcgcatattgccctaaacccaggtataacagtcatcatctcttctctaggctgggttagaagtgagacccatttttatgcctgtgatctggatctagaaataagtcacaattccacctgtggatagatccatatacgaaggtcatacttccaactttgtactacattcatttgtaaaactcaggttcttaacagtgacctttggacataaagaatgatgacaacacttgcttttacctgggtatgtaatcaagagtctcaaactgaaatttttgttggtccctgtcaccaaaatctctataccatcaaaggagttcatacatcatgagttagaattgtaaagctctgtgagcttggcacaattatgcaaactagtactttgtctattgccctaggcctagtgataaaaggtaaaatatctcatattggctgaatcacaatataatcccaatataagtttgaccatcatgactgtgaactgaagccaTAGTCGCATTTGTGTGGAAAAAAACAAAAACAAAAACTGggccagagggtaacaacacttaagtgctatgccaagcaacatgtcacaatgtcccctctaggtaaggtatagaacttagaatcacagtaactgggttctggactcagcaatatgacacaatccattatgtggg--GGAAAAAAAAACCAGCAAAAAGTTGAGAGCCAAAACACCTATATAATtggcccctgctctgtgaaaataccttctgtggctccagcacagtcatgagttttacattttcagggtgctgggcccagcagtatgtcataatattctctacatacataacccatgtaaaaagagtaacattatctgggtgctgggtcctgcaagaggtcaaaatttctgtttgtgggcatgatttgagaaaaaaaaaagataaatcagataacctgattactaggctgagcagtctttcacaatccctctactgtaaagaccaggcagaaaaaaagggtcactttccttagttcatggactcagatatatgtcccagtatcccaagtggagagggcccaggcagaaagggagtgtcatatcacttaaatgcttcactagttatatgtgaaaatcttaactttgggcagaaaccaggcagaagacccacatcatctgggtacaaccagaagtaatatctcatgatctccactatagataggattttttttttaaaaaaataatGACACcaccacgtgggtgctgtgctcaccaatatgtaataattccctctcttgacagactcaagtacaaacaggtgatttatgtcacataggttttgcactcaagggtatatcagagttttttcagtgaggaggatccaggcaagagaaatg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gcatggcagtagaagggagtcacatcacttacatgatgaacgtagatataagccataatgccttttataggcaggtataaggcaaataattcacatcacatgggtgctggtcccagtaatatgtaaaattgccctttatatgcacacccaggcaCCTACGCTTAGGTGTACGATGGTCAAATTATTCAGGCACTCAGCTAACTTTTATGTCCTAATTACATGCTAGGAAATATTTAGAAATAAGTTTCCCAGTACCACACAAGTCctggatttgtgtatgtgagtcaacacttcctgtgagttgggtcaaagcagaggagtcacagtctcatcaatgggcaagattcatgcataagatgcccaattttacttgaagattgtgttccaatagacgagtcacaaccccacaggtgtgctgaatcATGCATCACCAAACTAACCATATAGGAGAGGAGCAATTTTAACCTTTGACTGCTCTGTTtatgaggtttaacaccttatttctaggccctgttcttgtgagagaatgaatactggatcagctggctgcacattcaagagtcacaatcgtacttctttcctgttccctgttataacactgtttttaccactcagactttatatactatgtcagagtgtcataatcctctgtgaaatttaggccattgggagacctagtactttacttgtggctataagactggctataagaatcaaaatatctctctgattctacatatgacacttatatttgtgcatgtgagctgaacccagttatatgtcataacttaacctgtgagcagaagcaaggggggagagtctcatcacctggattctgaactcaggatacattgtaatctcctttgcaggcagggccaagtcagaagtgtcacatcacctgggtactacagcaagtaatatggcatcatgtccactgtagacaggtttgaagaaaaagaggagagtcacaccacctaggtgatgggctcagcaatatataataattacctcatttggctgactccagtataaggaggagagttgcattacctaggttgtgtactcagctgtatgtcgcaattcattcagtggtcagggtctaggcaggagacaagcatcacatttccAGATACTACTTCAAgagatgtcataattttccttggggatagagcacaggcaaaataaagaaatcagctagttgataggctcagagatctgtgataatatacattttggggcaaagcccaggcagaggagtcatattattatgattctaaaccaatgatatatcacaatgcAAACATGGGAAAAAATTTATGCAAGTTTTAACACCTGGGTAATAGGACCAGAGATAAGACACAATCTCCTTATCCTtgagagtgacacctttaactgttagcttggtgtgtatatgagtcacaatgtcacatattgtgtgctggctcatcctatgacaccctctagaatgtctgagggctttatatggcttgcatgagagttgcaaactactctgaggcccacatgcgtatattaaatcacaatctcatatattgcattacacacaggtatgatagcaaacatctctcatttaggctgatatcaggaatcagacttattttatacctgtgagcttggtcaaaagtgagtcacaatcatacctgtggccagatccatatatgagagccacaattttatctTTACATTATCTTCAGTtgttaaactcagtacaccaacagtgggcttggtaaatgtgaaatagtgatatcttttactttcacctgggtgtttaattgagagtcacaatcttaactttttgctgggccttgttttgaaactctgtatcccccaaatagtttatacaagataaactagtgctgtaaacttccatgagctttgtacaaatttccaacccagaattttacctattgcctcaagactagcaacaagaggcaaaatatcttctcttgcctgaatcctaatataagtgaccatcatacctttaagctgaaccaaggtatatgtcataatcccatttgtgggccaaaaaaatagggaaaagagtaacatcacatagctgatatggcaattaacatgtcacaatgtcctctctaggcagaacctaggaaaaaggcttacattaactgggtgctggaaccggtaatattacagaattctgcatatgaaaaaacttagccaaggggtaagagccaaaacacctATGGAATAAACAAAAGATATGTCAGAATACTTCCTGTGGCTCTGTCATGTAATATTACAGAATTCCACATATGAAAAATCTTAGCAAAGGGGTAAGAGCCAAAACAACTACAGAATAAAACAAAGATATATCAAAATACTTCCTGTGGCTCTGTCACAGGCATGACAGTAGCATCATCAGGGTGATCggcccaccatctgcaataattttctctttattcaggactctggcaaaaaagtaacatcatctgagtccaataggtcataatttctttctggtcatggttcagaaaaaagaatagagtcacatgatgttaatgttgggctcagcaatatgtcacaatcctgccattttaaaggccctggcagaagagagtcatattacttaggtcatgggctcagagatgtatcccaatgtccctagtaggcagggctcaggcggtcaaggagattcatatcatatgcatgtttcccacggaatatgtcacaatgtaacaagtgggcagaaaatagacaggagagccacatcaattgggtactgcgtcctgagatatttcacaagtctctcttaggacatcaaccagacagtggagttacatcacctacatgcagtttctcggcttatgccacattgctccatgtgggtagtatcaaaggaggaagtcacttcaccaaggtgatagggccaaagatatgtcacaatatcctctatgaagcatagccctggcaaaagagtaccatcacctctgtgcctggccttgaaatatgtcatgctgcaagttggcagtgcccaagcaggagagccacataaccagagatatttcaaaatcctgtcttttgggcatggctttggcaaaagagtagcctcacctgttttcttggccttgaatcatgtcactaccttttctttgttcaaggcccattccagagagaagagttacattgcttATGAGGTGGACACATAAATATTTCACAATAATTTTGGTGGGTGTGCTGCAGGCAAGAATGTAATATAACATGGGTGCTAGATCCAGTGATATATCACCATTCTTACTGTTAATAGGGTCCAGACAGGAGAGTAATATCACCTTGAGGTAGGACTAGGTAGATATCACAACCCCATATATGGACTGGAAACATTCTGGAGAGTCGAATTACACAGGTTGTTGAAAAAAATCTATAAAACATTCGCACTGTCAGAAAATTCCAAAGATGAGATTTAGAATACTACACATGACCTGTTTTCACATGTGACAATGGCATCAtccatgtgagatgatgacaatccttactatcagctgggtgtgcaaagaagactcacaatttcacctgtgtgctgagccctgctttgactcagtctgtataagccaaagacttagtaaaatatgtgtgagtgttataaacatttctgatgtttgcacaagaagctgatgcaggatgtcatgcgtgtctctaaacatacttatgagagtatgtttagatacttttgagagtatgtttagataataggggatacttatgagagtatccactattagctgagtccacatatgagagtcattatcattgctgtggcctgtgcctaagtatatgttacaattccctctgtggttatgaagcaggaagaatggccacatcacataaatgctgggccagaaatattccaatattgtctttatactaagtttcctgtcagaaatgtcacataccttgtgtgttaggtttagctctgtggcacaatgtcccttgtaggcagtgtccagggagaagaggagagtcatatcacataaatgatgggctccataatatgtcacaatgactcctgttggcaaagccaacaggcaaggtattaatatcatttggatgcagtgtttagaaaagctacaattaccaaaggaagcagggtacagacagaagaggagagtcatgtaacctaaatactagatccagaaatatgttacaatccccccaaggacatttttaagatagcacagtcaaatcatcagggtacttggctcaagtatttgttaaaatctcatctgtgggctatacctaggcagaattattaaatcactcaggagctgggcaaagttgtaagtcacaattagacttgtgggaaggtgtaagaataagagtcaccacactgaatattaggtttggttatgttctcaggtatatggcacaatatcacctgtagccagagagaaggcaagaaagtcacatcaactatgtatgtgtgggtctagtaaaatgtcacaatacactttgtggtaggacactggcagaagagccatatcacctgcatgctgctttcagtgatatatcaaaatccactatgagggcaggactttggaaagaaaggagactcacttagcttagtcaactcgcccaagtatatgtcacaatggcccttatatgcagtaccgagtctggggagtgaccttaacttcatgctgtgtgcagcaatacatcactatttccctgtggtcaggacccaggaaaaattgaagaagcatcacctaggtgctgagccaaatgatatgttccaattcttcctgtttgcagagctcaaaaacaagaatctcgtcacctgggtgcagtacccagttatgtgtcatatagcagtgtaagtgcagggccaaggcagtagaagggactcacataacttatgtgatatgcctagatttaagacacaattctccttgtaggcagttttcaggcagataacttacatcacttgggcgattgtcccagtgacatataaaagtgccctttgCAATGGGAGCTCTGGAAGCTGTTATATATGGCACGTAAGCAATATATATGGTACAATTTAATCTGTGGCCTAGGAGTAGAAAACAGTTAGATTATTCATATGCTAGGCAAAGTTGCCTCTCCTTTTTATGTTCTCAGAAAGATTTGGAAATGAGTTTCACATCCCACAAAAGTATTTCTtctgtgtatgtgattcaattttttctgtgacttgggttgaagtagaggagtcgcaatctcaacaatgagcaagatgcatgtacaagagccccaatcacacttgaagatggttttccagtaagggagtcacAGCACTACAGGCATGTTGAATCATGGTTCATATGTTACTAAGTCACCTGTGAATGAGATCCACATATGAGAGTAATTATTTCAATCTTTCACTGATTTTTATGtgtgagatttagtacctcattcctaggccctgttcatgtgtaagaatgtcaattgtgtcagctaagtgtgcatacaagggtcacattgccaccgcgttgctggtttctgttattacactctttgcatcattaaggttttatatgatatacatgagtgttataatccttcataaaatttatactagtgaaaaacacaggactttacccattgccataagactggctgtgagagtcggttatctctactggattgggccaggtatgagaattattattgtgcatgtgtgcttaaaccacatatatgtcacaactggacctgtgagcagaaaaaaagtcaggagagtcacattaccttggtgctgagccagttatatagtataatcttatttgtaggctgggaccaatgagaagagtcacatcacttcacccgggtgctgagccagtgagagagtgtatactcattttttggcttggcctagtcagaagagtcacatcacctgggtacagcctaaaatagtatgtcaccaagcccactatggacaggacagaagaaaatgaggaatgtcccaccacctaggtactgagctctgcaatacgtaataatcccttctcttgaaagagtctagaatatgaaggagatctacatcacctaggtgttgcaatcagcactatgtcacaacttctatggtgagcagggctcaggcaggagaggatagtcagattttctaattattaaataaactgatatttcacaatgtcttctgggggcagggcacaaataggagagaaaaatcacctagcttataggcccagagatatgtgataatattccctgttttcagggtcaaggtagaagagtcacattattataattctaacccagggatatgtcacagtgaatccatgggaaggaatttaaggcaaaaatatcaacacctgagtactaggcctcataatatgccagaactccttgtctttcagggtgacatgattcactgtgagctgggtgtgaatatgagaaacacaatctggtgtgtttcctggatcatttgatgacactctacagctttgaaaggctttgtacagccttcatgagaactgcaaaccactgtgaggcctacatggttgtacagattcatgatcttacacattaccccaaaaaaagatataatagttaacatatcctctgtaggctgggttcagaaataatacccatgattttcttgagagctggatccagaaataagtcaccatcccatttgtggccagatcaacatatgaagatcacaattccaactttgtactCTATTCACTTTTagactcagggacttaatagtgggctttgtacatgtgggatggtgacaacatttgctttcacctgggtatctaatggagagtccgaatctaaattcttgctcatctctttttataaaactctctgtacaacacaataaatgtagtcatcatgagttaatttttgtaaagtttttgaatttgatataaatatgaaacccaggacctcatctattgccctaagcctagtaatgaaatataaaatatatcctattggctgaatcacaggataggtttgtccatcatgcctgtgaactgaagtaaggtatatgatatatttacatttgtgggc--aaaaaaactaggcaggaaggtaagatcacttacgtgctgtgacaagcatcatgtcataatgtcctctgtaagaatggtatatgaattagagtcacattaactgggtgttggatcctgcaatatgacaaaatcccatatgtggAAACAAATCAACCTAGAAGTGAGAACCAAAATGCCAACAGAAtgggcccaggatatgtcaaaatacattctgtggctttgggacaggcatgaaagtcacattattagggtgctgggcccagcaatatgccacaattccccatatatgtaggacccaggcaaaagagtaacattatctgtgtgctggcccctgcaatagtcaaaatTTTTGTTTTTCTATTAACATGAGTgttgtgctcagcaatatgtcacaatcctctcattgtaaagaccagacaggagaagagattcatttcacttaggtcatggtctcagagatatatcccactgtcctctctatgcagggatcaggtagaaagaagagtcatatcacctatgtgtttctctagttaaatgtcacaatctgacatgcaggcagaaaccagggagaagagccacatcacctgggtacagcctcaagtaatatgtcaccatgcccaatgtagacatgttcaaaaaaagaaaatcacaccacaagcattctgggctcaataatatgtaataattccctctttatacagagtctatgacaaagattagagccatatcacctagaatttgtgctcagtgttatgtcacaatttcttcaatgaacaggatccacgcaggagaggagagtcatattacctagatgccatatctagcaatatgtcacagagtcccctgtgagcagggcactggcaggagagaaatgtcacctggccaataggcccagagatatgtgaaaataactgttgttttcagggccaagacagaagagccacattatcATGGTTCTGATCCAGTGATAGGTAACACTGCCCTCATGCAAAGGAATTTAAAGCAAAAAGTCTCAATACCAGTATACTTGGCCAAGGGATATGACATAATCTCATCTTTAAATgtggcagcattttagctgttatctagttatatatatgacagtcacaaactcctgagtgtccttgccattgtaggatactctctacaacatctgaaaactttatacaacacgcatgagtgttgcaaaacttgctgaggcctacacacttatatggactcataatcttccatattgccataaaccgaggtatgtcaggcaacatttcttctataggctggcatcagggttgagaccattattagggctgtgagctgggtgcagaaatgggattcaccatctcacctgtagtcagattcacttatgagagtcacaatttgaactttgggttgtattgacttgtttgattcaggacctcaacaataagctttgtaaatgtaggatgtgagctaatgttgtaaaattctgtgatctttgaacaaatgtgtaatggaggaccttaactattgacctaaacctaggggtgagaggcaaaatatctcctattggcttaatcacacagcgaacttgatcatcatgtctttgaactgaagcaaggcatatgacataatctcatttttggggaaaaactaggcagaaggttagtatcatttaggtgctgtgccaagcaacttatcccaatgtcttctccaggcacggcctaagaaacggagtaacattaactgggGGCTGGAACCCTCAATATGACACAAAACCATGTGGAAGAAACCCAGCAAACTGATTAGTGGCAAAACACATATAGAATGAGccaaagatgtgtcaaaatactatctgtggccctggcacagagagaagagtctcatccttagggtgctgggccaagcaatatgccacaattccctctttatgcatgacctaggcagaagagtaacattatctgggtgtagggtcccgaaatacagcaaaattcctgttcatgggcactctttagcaacaagacaagagtcacacaacctgaatactgggcttctcaatatctcacagatctctgattgtaaaagcccagacagaagtgagtcaaattacttagattgtgggttcaaagagaggacccaatgtctttagtaggcagggctcaggcaaaaaaagtgaatcatatcacctaggtgttttctttaagtatacgtcacaatttaatgtgtgggaagaaaccaggctgaagtgcctggttcctggttcctggttcccaagatattcacaaatcccccttagaaaaggacccaggcaagagagttacatcacctaggagcaggttcctccctgatgttacaatgctccatgtgggcagcccatgaaggaattcacatcatctaggtgataggcctagagatatgtcacataaccttcttgaaagcatggccctggcaaaagagtaccataacctttgtccctcgtctagcaatatgtcactatacaagtgggcaggtttcaagcaaaagagccatatcatctatataataggccctgtaatatgtcataatattgtcttttatgcatggtcctgggaaaaaaatcatcattacctgtgtgccttgcctatgaatatgtcactctcctgccctgtgtgtagggaccattccagagaggaaagttacatcacctcagtggtggacacataatatgtcacaaggttgtctaggggcagggaacaggcaagaatgtaatgtcacctaagcactgaatccaatgatgtcacaatccttaatgagatcagggcccaggcagaagtgtcacaaaacttcagtgttggcccaggtaaatatcaaaatcctttatgtaggctggaattagtctgaagagtgaaatcacAAAAGTGCATGGAAAAGCTTTATATCACAGTCATGAAAAAATAAAATTCTAGGGATTATTTTAAAATACCACATGTGTC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q panTro2.chrY                                      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i panTro2.chrY          C 0 C 0
e tetNig2.chrUn_random   51494646   957 - 107808587 T
e gasAcu1.chrV            9098936     0 +  12251397 I
e fr2.chrUn             102968626  1519 - 400509343 T
e papHam1.scaffold23501     18711  1367 -     34585 I
e oryLat2.chr4           15868065  1340 -  34636364 T
e xenTro2.scaffold_676     107922   135 -    553874 I

a score=48062.000000
s hg19.chrY               7852379 556 +  59373566 ACTTTTGCTCAAAAATGTGTAAAAACATATATTAAAAAATTTACCCTTCACATTATTTTAATTAAGTCATCATACAAACC-----TTTATTTTCCTGAAATTTATTTTCATGCCAATCATTGAATTTTTGTTTCCTTCATTGTTTAGATTATTACCTGT-------TTTAGAGGCaaaatttaaataaaataatatGCTACACAAATAC-TAACAGATGACACCAATTTATTTAAAATGTAATAGGATTTCTTAAATGAGTAAGTAATTTCAGTAAACTTAG---TTTATGTTACTTGCATAAATTATTTTACATCTTATTCTTAATATTAAGAAAAGATATTTAGGCATGCAATGCACTTG-ACAAATTT---TTAAATTAGGCAACTTAAAACATTGTATTGGACATGATAAGTA--ATACTATTCTCAAATATTTTATTTTAGATGTTAACATACCTGACAATTGATATTCATATTATCTATGAAAGTGACATTATGAACATACTTATATAGTTGCCAAAATTTAGAAGAAAAAATCTATTCTGGTCTTCAGTAGTAATATTTAAAGTTTACAAA
s panTro2.chrY             705764 557 +  23952694 ACTTTTGCTCAAAAATGTGTAAAAACATATATTAAAAATTTTACCCTTCACATTATTTTAATTAAGTCATCATACAAACC----TTTTATTTTCCTGAAATTTATTTTCATGCCAATCATTCAATTTTTGTTTCCTTCATTGTTTAGATTATTACCTGT-------TTTAGAGGCAAAATCTAAATAAAATAATATGCTACACAAATAC-TAACAGATGACATCAATTTATTTAAAATATAATAGGATTTCTTAAATGAGTAAATAATTTCAGTAAACTTAG---TTTATGTTACTTGCATAAATTATTTTACATCTTATTCTTAATATGAAGAAAAGATATTTAGGCATGCAATGCACTTG-ACAAATTT---TTTAATTAGGCAACTTAAAACATTGTATTGGACATGATAAGTA--ATACTATTCTCAAATATTTTATTTTAGATGTTAACACACCTGACAACTGATATTCATATTATCTATGAAAGTGACATTATGAACATACTTATATAGTTGCCAAAATTTAGGAGAAAAAATCTATTCTGGTCTTCAGTAGtaatatttaaaatttataaa
q panTro2.chrY                                    00000000000000000000000000000000000000000000000000000000000000000000000000000000----000000000000000000000000000000000000000000000000000000000000000000000000000-------0000000000000000000000000000000000000000000-000000000000000000000000000000000000000000000000000000000000000000000000---00000000000000000000000000000000000000000000000000000000000000000000000000000-00000000---0000000000000000000000000000000000000000000--000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s danRer6.chr3            5031920 517 +  60907308 acattttcctcaaaatattt-----cctggattaaaacact---ctctaatatcattttaa-aaatacatcctattaaaatatgttttatcatc----aaaatattcccacacaagcta-caaataggtgttt-ctcccctgttca-ataaatgtgtgtgtaagtcttgagtggccgattctacatgtcat-gtgtgcagcgtgatcatgtctCTGATTGCTTACATTT-----------------ATCTCTCAA----------TATTTTAATGAATTAAGTGTTTTATATTAT-----TATACTAATCCCAAATTCAGTTTTACTGCAAAATAAAGCGTTTGCGTCTCTTCAAGAGTTTACACAAGCTTATGTTCAGTTAAACAGTCAA--------TATTCAATATAATCAGCATTAAACTACCTCTTAGTGAATGA-ATTAGATGGAGACACAAATGAAA---GGTGTCCAGATAACCCGCGAGTAAGACATTACAAGAGTGTTTACAGCGTAGCATCGAGCTAAAAACAAGAGAGTATATTAGCATTGAGCACATATGTTAAAGCGGTTCAAA
i danRer6.chr3          N 0 N 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936   0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=6261.000000
s hg19.chrY               7852935 87 +  59373566 -----------AATGAGATTAAATTTACTGCCTGCATTACCCACCAAAACTCAAACAGATTCATTTACTTGTTCTTTATCTTTCAGTATCTGAAAAAA
s panTro2.chrY             706321 87 +  23952694 -----------aatgagattaaatttactgcctgcattacccaccaaaactcaaacagattcatttacttgttctttatctttcagtatgtgaaaaaa
q panTro2.chrY                                   -----------000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
i panTro2.chrY          C 0 C 0
s danRer6.chr4            9846924 86 -  71658100 ccagagtttcgagtaag--cagtcttgtagactagattatttac-------tgcacaattatgtgaaattattctgt-tctctcattcagagaaaa--
i danRer6.chr4          N 0 C 0
e tetNig2.chrUn_random   51494646 957 - 107808587 T
e gasAcu1.chrV            9098936  0 +  12251397 I
e fr2.chrUn             102968626 1519 - 400509343 T
e papHam1.scaffold23501     18711 1367 -     34585 I
e oryLat2.chr4           15868065 1340 -  34636364 T
e xenTro2.scaffold_676     107922 135 -    553874 I

a score=15476.000000
s hg19.chrY                 7853022 146 +  59373566 TATTACCAACATTACTGGGTTTTACTA-CTGGCAGAAGCCGGGTTTTCATGGAGCCTGATGCAACATAACCACTCTTTATGTATCAGTAAACTGCCCAAAATCTACCCAGAACTGAAGACAcattgaaacctccccacctcccggtt
s panTro2.chrY               706408 129 +  23952694 tattaccaacattactgggttttacta-ctggcAGAAGCCGGGTTTTCATGGAGCCTGATGCAACATAACCACT-----------------CTGCCCAAAATCTACCCAGAACTGAAGACAcattgaaacctccccacctcccgatt
q panTro2.chrY                                      000000000000000000000000000-0000000000000000000000000000000000000000000000-----------------00000000000000000000000000000000000000000000000000000000
i panTro2.chrY            C 0 C 0
s pteVam1.scaffold_4947       43844 115 +    113242 -AATACCAGTCTTACTGGGCCTTAATATTTGGTGGAAGCTGGGTTCCCTTAGGACCCAATGAACTATAACTGCTCTTAACATAACACCCAGTTGCCCAGAACCTATACAGAAATAA-------------------------------
q pteVam1.scaffold_4947                             -9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-------------------------------
i pteVam1.scaffold_4947   N 0 N 0
s turTru1.scaffold_103361     93685 120 +    263644 ----ACCAGTCTTATGGCACCCTACTA-ATGGCAGAAGCAAGGTTACCTCAGGACCCAATGCAATATAACGGCTCTCAACATAAGCCGCAACTGCCCAGAATCTACCCAGAAATAATGGCTGATT----------------------
q turTru1.scaffold_103361                           ----99999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----------------------
i turTru1.scaffold_103361 N 0 N 0
s danRer6.chr4              9847010 120 -  71658100 ---------cattacaatgatctacat-tttgt------taagtttgttttgggt---------gaTCTCAGCTGTATGTGTGAGTGACAATT-CTTATGAATAATTCACACCTGAGAGACAACAGACACTCCCCCACTCACCCAT-
i danRer6.chr4            C 0 C 0
e tetNig2.chrUn_random     51494646 957 - 107808587 T
e gasAcu1.chrV              9098936   0 +  12251397 I
e fr2.chrUn               102968626 1519 - 400509343 T
e papHam1.scaffold23501       18711 1367 -     34585 I
e oryLat2.chr4             15868065 1340 -  34636364 T
e xenTro2.scaffold_676       107922 135 -    553874 I

a score=17919.000000
s hg19.chrY                7853168 224 +  59373566 tcaagtgattctcctgcctcagcctcccgagtagcttggattgcaggcgcccaccactacacccaaatattttttttgttgttgtatttttagtagagatcgggtttcagtatattggcctagctgatctcgaacccctggtatctggtgatccacctgc----ctcagcctcccaaattgctgagatttcagatgtgagccaccacacc---cAAACCAAAGAATGCTTT
s tarSyr1.scaffold_34017       270 195 +     17213 tccggcgatccttccacctcaaccttccgagtagctggaactacaggcgtaagctaccacaccaggct-catttt---------gatttattgtagagatgaggtctcgccaagttgcccaggcgggtctcgaacccgcagactcaggcaatccactcac----ctcagcctcccaaaggcacgggattacaggc-taagccactgagcc---------------------
q tarSyr1.scaffold_34017                           99999999999999999999999999999999999999999999999999999999999999999999-999999---------9999999999999999999999999999999999999999999999999999999999999999999999999999----9999999999999999999999999999999-99999999999999---------------------
i tarSyr1.scaffold_34017 N 0 N 0
s panTro2.chrY              706537 223 +  23952694 tcaagtgattctcctgcctcagcctcccgagtagcttggattgcaggcgcccaccactacaccccaat-ttttttttttttttgtatttttagtagagatcgggtttcagtatattggcctagctgatctcgaacccctggtatctggtgatccacctgc----ctcagcctcccaaattgctgagatttcagatgtgagccaccacacc---cAAACCAAAGAATGCTTT
q panTro2.chrY                                     00000000000000000000000000000000000000000000000000000000000000000000-0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000----0000000000000000000000000000000000000000000000---000000000000000000
i panTro2.chrY           C 0 C