##gff-version 3
## sequence-region Contig1 1 37450
Contig1	confirmed	transcript	1001	2000	42	+	.	ID=Transcript:trans-1;Gene=abc-1;Gene=xyz-2;Note=function+unknown
Contig1	confirmed	exon	1001	1100	.	+	.	ID=Transcript:trans-1
Contig1	confirmed	exon	1201	1300	.	+	.	ID=Transcript:trans-1
Contig1	confirmed	exon	1401	1450	.	+	.	ID=Transcript:trans-1
Contig1	confirmed	CDS	1051	1100	.	+	0	ID=Transcript:trans-1
Contig1	confirmed	CDS	1201	1300	.	+	2	ID=Transcript:trans-1
Contig1	confirmed	CDS	1401	1440	.	+	0	ID=Transcript:trans-1
Contig1	est	similarity	1001	1100	96	.	.	Target=EST:CEESC13F 1 100 +
Contig1	est	similarity	1201	1300	99	.	.	Target=EST:CEESC13F 101 200 +
Contig1	est	similarity	1401	1450	99	.	.	Target=EST:CEESC13F 201 250 +
Contig1	tc1	transposon	5001	6000	.	+	.	ID=Transposon:c128.1
Contig1	tc1	transposon	8001	9000	.	-	.	ID=Transposon:c128.2
Contig1	confirmed	transcript	30001	31000	.	-	.	ID=Transcript:trans-2;Gene=xyz-2;Note=Terribly+interesting
Contig1	confirmed	exon	30001	30100	.	-	.	ID=Transcript:trans-2;Gene=abc-1;Note=function+unknown
Contig1	confirmed	exon	30701	30800	.	-	.	ID=Transcript:trans-2
Contig1	confirmed	exon	30801	31000	.	-	.	ID=Transcript:trans-2

## sequence-region Contig2 1 37450
Contig2	clone	Component	1	2000	.	.	.	Target=Clone:AL12345.1 1 2000 +;Note=Terribly+interesting
Contig2	clone	Component	2001	5000	.	.	.	Target=Clone:AL11111.1 6000 3001 +
Contig2	clone	Component	5001	20000	.	.	.	Target=Clone:AC13221.2 1 15000 +
Contig2	clone	Component	2001	37450	.	.	.	Target=Clone:M7.3 1001 36450 +
Contig2	predicted	transcript	2501	4500	.	+	.	ID=Transcript:trans-3;Alias=trans-18
Contig2	predicted	transcript	5001	8001	.	-	.	ID=Transcript:trans-4


#processed_transcript
Contig3	clone	Component	1	50000	.	.	.	ID=Clone:AL12345.2
Contig3	confirmed	mRNA	32000	35000	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	UTR	32000	32100	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	CDS	32101	33000	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	CDS	34000	34500	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	CDS	34600	34900	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	UTR	34901	35000	.	+	.	ID=mRNA:trans-8

## preferred group assignments
Contig4	clone	Component	1	50000	.	.	.	ID=Clone:ABC123
Contig4	confirmed	gene	32000	35000	.	+	.	ID=Misc:thing1;gene=gene-9
Contig4	confirmed	mRNA	32000	35000	.	+	.	ID=Misc:thing2;mRNA=trans-9;gene=gene-9
Contig4	confirmed	CDS	32000	35000	.	+	.	ID=Misc:thing3;mRNA=trans-9

##gff-version 3
##sequence-region test01 1 400
test01	RANDOM	contig	1	400	.	+	.	ID=test01;Note=this is test
test01	.	mRNA	3	14	.	+	.	ID=mrna01short;Name=testmRNA;Note=this is test mRNA
test01	.	mRNA	101	230	.	+	.	ID=mrna01;Name=testmRNA;Note=this is test mRNA
test01	.	mRNA	101	280	.	+	.	ID=mrna01a;Name=testmRNAalterative;Note=test of alternative splicing variant
test01	.	exon	101	160	.	+	.	ID=exon01;Name=exon01;Alias=exon 1;Parent=mrna01,mrna01a
test01	.	exon	201	230	.	+	.	ID=exon02;Name=exon02;Alias=exon 2;Parent=mrna01
test01	.	exon	251	280	.	+	.	ID=exon02a;Name=exon02a;Alias=exon 2a;Parent=mrna01a
test01	.	CDS	3	14	.	+	.	ID=cds_short;Name=testmRNA;Parent=mrna01short;Note=this is test mRNA
test01	.	CDS	192	200	.	+	.	ID=cds1;Parent=mrna01a
test01	.	CDS	164	190	.	+	.	ID=cds1;Parent=mrna01a
test01	.	CDS	192	200	.	+	.	ID=cds2;Parent=mrna01a
test01	.	Match	101	123	.	.	.	ID=match01;Name=match01;Target=EST101 1 21;Gap=M8 D3 M6 I1 M6
##FASTA
>test01
ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
>test02
ACGACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGACAAAAAA