##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 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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 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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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00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 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 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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--GTAATGAAACAGGCATGAGATCCATATAATCTAAATGCTGTGGCAGAAATCTTCcaatattcttttttggcaaatttctagaagaaaaatcacataactttggggctacgcccgaatgtatgagacaacaccccttgtgggcagtgtttgacagaagagGAGAGAAATATTAAATAAATGGTAGGTTCAGAGATAAGTTATAGTGGTAACTTGTTGAAAGGACCAGGCAAGAAAATCATATCATTTAAATGCAGTCCTTAGAAATACTACAATCTCCAGTGGAAGTAGAATCCAGGCGGGACATGCTAGTGAGGcacctagattgagggtccagagacatgttacaaagcttcctgaagatactgttaagccaggagagtcaaatcaccaaagtgcttagctgagatatatgtccaaatctcaattgtgtgctgcacctcggcagGATTACTAAATCACTCAGGGGATGGGCAAAAGTATATGTCACTATAACACTAGTGGAAAATTCCAGGAATAGGAGTCACCATCATGCCTATGACCTGGCTCTAGGTTTAAGAGTCATGATTAGTCCTCTTATctgatctcagttatatgggacaatatcccttgtgagcgcagaggaagcaaaatatcacatcacctaggtggatgttggtccagtgagatgtcacaatcatcgtgggcagaattctggaagaagggtcacatcacctggatgctggtttaactgacttagcaaaattccccttttgggctgggcttagaaaggagaggggactcacttcacctaggcaattggtgtacatatgtgtcacaatggccactgtgtgcaggacaaatgtttggaagagatcacaacttggtgctggatttagccatatgtcacaatctcccttgtggtcagcgcagggcaagagaggaaaaacatcacctaggtgctgtgctgagccaagttatgtgttacaaagctttctgatggcaaaacccaaaatgcagtcacatcacttggcagcagtaccctgttatgtgtaacaatgcaccattaatgcagggccaagggattagaattggataacatcacttacatgatgaacccagacataagccac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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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gcatggcagtagaagggagtcacatcacttacatgatgaacgtagatataagccataatgccttttataggcaggtataaggcaaataattcacatcacatgggtgctggtcccagtaatatgtaaaattgccctttatatgcacacccaggcaCCTACGCTTAGGTGTACGATGGTCAAATTATTCAGGCACTCAGCTAACTTTTATGTCCTAATTACATGCTAGGAAATATTTAGAAATAAGTTTCCCAGTACCACACAAGTCctggatttgtgtatgtgagtcaacacttcctgtgagttgggtcaaagcagaggagtcacagtctcatcaatgggcaagattcatgcataagatgcccaattttacttgaagattgtgttccaatagacgagtcacaaccccacaggtgtgctgaatcATGCATCACCAAACTAACCATATAGGAGAGGAGCAATTTTAACCTTTGACTGCTCTGTTtatgaggtttaacaccttatttctaggccctgttcttgtgagagaatgaatactggatcagctggctgcacattcaagagtcacaatcgtacttctttcctgttccctgttataacactgtttttaccactcagactttatatactatgtcagagtgtcataatcctctgtgaaatttaggccattgggagacctagtactttacttgtggctataagactggctataagaatcaaaatatctctctgattctacatatgacacttatatttgtgcatgtgagctgaacccagttatatgtcataacttaacctgtgagcagaagcaaggggggagagtctcatcacctggattctgaactcaggatacattgtaatctcctttgcaggcagggccaagtcagaagtgtcacatcacctgggtactacagcaagtaatatggcatcatgtccactgtagacaggtttgaagaaaaagaggagagtcacaccacctaggtgatgggctcagcaatatataataattacctcatttggctgactccagtataaggaggagagttgcattacctaggttgtgtactcagctgtatgtcgcaattcattcagtggtcagggtctaggcaggagacaagcatcacatttccAGATACTACTTCAAgagatgtcataattttccttggggatagagcacaggcaaaataaagaaatcagctagttgataggctcagagatctgtgataatatacattttggggcaaagcccaggcagaggagtcatattattatgattctaaaccaatgatatatcacaatgcAAACATGGGAAAAAATTTATGCAAGTTTTAACACCTGGGTAATAGGACCAGAGATAAGACACAATCTCCTTATCCTtgagagtgacacctttaactgttagcttggtgtgtatatgagtcacaatgtcacatattgtgtgctggctcatcctatgacaccctctagaatgtctgagggctttatatggcttgcatgagagttgcaaactactctgaggcccacatgcgtatattaaatcacaatctcatatattgcattacacacaggtatgatagcaaacatctctcatttaggctgatatcaggaatcagacttattttatacctgtgagcttggtcaaaagtgagtcacaatcatacctgtggccagatccatatatgagagccacaattttatctTTACATTATCTTCAGTtgttaaactcagtacaccaacagtgggcttggtaaatgtgaaatagtgatatcttttactttcacctgggtgtttaattgagagtcacaatcttaactttttgctgggccttgttttgaaactctgtatcccccaaatagtttatacaagataaactagtgctgtaaacttccatgagctttgtacaaatttccaacccagaattttacctattgcctcaagactagcaacaagaggcaaaatatcttctcttgcctgaatcctaatataagtgaccatcatacctttaagctgaaccaaggtatatgtcataatcccatttgtgggccaaaaaaatagggaaaagagtaacatcacatagctgatatggcaattaacatgtcacaatgtcctctctaggcagaacctaggaaaaaggcttacattaactgggtgctggaaccggtaatattacagaattctgcatatgaaaaaacttagccaaggggtaagagccaaaacacctATGGAATAAACAAAAGATATGTCAGAATACTTCCTGTGGCTCTGTCATGTAATATTACAGAATTCCACATATGAAAAATCTTAGCAAAGGGGTAAGAGCCAAAACAACTACAGAATAAAACAAAGATATATCAAAATACTTCCTGTGGCTCTGTCACAGGCATGACAGTAGCATCATCAGGGTGATCggcccaccatctgcaataattttctctttattcaggactctggcaaaaaagtaacatcatctgagtccaataggtcataatttctttctggtcatggttcagaaaaaagaatagagtcacatgatgttaatgttgggctcagcaatatgtcacaatcctgccattttaaaggccctggcagaagagagtcatattacttaggtcatgggctcagagatgtatcccaatgtccctagtaggcagggctcaggcggtcaaggagattcatatcatatgcatgtttcccacggaatatgtcacaatgtaacaagtgggcagaaaatagacaggagagccacatcaattgggtactgcgtcctgagatatttcacaagtctctcttaggacatcaaccagacagtggagttacatcacctacatgcagtttctcggcttatgccacattgctccatgtgggtagtatcaaaggaggaagtcacttcaccaaggtgatagggccaaagatatgtcacaatatcctctatgaagcatagccctggcaaaagagtaccatcacctctgtgcctggccttgaaatatgtcatgctgcaagttggcagtgcccaagcaggagagccacataaccagagatatttcaaaatcctgtcttttgggcatggctttggcaaaagagtagcctcacctgttttcttggccttgaatcatgtcactaccttttctttgttcaaggcccattccagagagaagagttacattgcttATGAGGTGGACACATAAATATTTCACAATAATTTTGGTGGGTGTGCTGCAGGCAAGAATGTAATATAACATGGGTGCTAGATCCAGTGATATATCACCATTCTTACTGTTAATAGGGTCCAGACAGGAGAGTAATATCACCTTGAGGTAGGACTAGGTAGATATCACAACCCCATATATGGACTGGAAACATTCTGGAGAGTCGAATTACACAGGTTGTTGAAAAAAATCTATAAAACATTCGCACTGTCAGAAAATTCCAAAGATGAGATTTAGAATACTACACATGACCTGTTTTCACATGTGACAATGGCATCAtccatgtgagatgatgacaatccttactatcagctgggtgtgcaaagaagactcacaatttcacctgtgtgctgagccctgctttgactcagtctgtataagccaaagacttagtaaaatatgtgtgagtgttataaacatttctgatgtttgcacaagaagctgatgcaggatgtcatgcgtgtctctaaacatacttatgagagtatgtttagatacttttgagagtatgtttagataataggggatacttatgagagtatccactattagctgagtccacatatgagagtcattatcattgctgtggcctgtgcctaagtatatgttacaattccctctgtggttatgaagcaggaagaatggccacatcacataaatgctgggccagaaatattccaatattgtctttatactaagtttcctgtcagaaatgtcacataccttgtgtgttaggtttagctctgtggcacaatgtcccttgtaggcagtgtccagggagaagaggagagtcatatcacataaatgatgggctccataatatgtcacaatgactcctgttggcaaagccaacaggcaaggtattaatatcatttggatgcagtgtttagaaaagctacaattaccaaaggaagcagggtacagacagaagaggagagtcatgtaacctaaatactagatccagaaatatgttacaatccccccaaggacatttttaagatagcacagtcaaatcatcagggtacttggctcaagtatttgttaaaatctcatctgtgggctatacctaggcagaattattaaatcactcaggagctgggcaaagttgtaagtcacaattagacttgtgggaaggtgtaagaataagagtcaccacactgaatattaggtttggttatgttctcaggtatatggcacaatatcacctgtagccagagagaaggcaagaaagtcacatcaactatgtatgtgtgggtctagtaaaatgtcacaatacactttgtggtaggacactggcagaagagccatatcacctgcatgctgctttcagtgatatatcaaaatccactatgagggcaggactttggaaagaaaggagactcacttagcttagtcaactcgcccaagtatatgtcacaatggcccttatatgcagtaccgagtctggggagtgaccttaacttcatgctgtgtgcagcaatacatcactatttccctgtggtcaggacccaggaaaaattgaagaagcatcacctaggtgctgagccaaatgatatgttccaattcttcctgtttgcagagctcaaaaacaagaatctcgtcacctgggtgcagtacccagttatgtgtcatatagcagtgtaagtgcagggccaaggcagtagaagggactcacataacttatgtgatatgcctagatttaagacacaattctccttgtaggcagttttcaggcagataacttacatcacttgggcgattgtcccagtgacatataaaagtgccctttgCAATGGG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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