##gff-version 3
##sequence-region Contig1 1 37450
# #index-subfeatures 0
Contig1	confirmed	transcript	1001	2000	42	+	.	ID=trans-1;Name=abc-1;Alias=xyz-2;Note=function+unknown
Contig1	confirmed	exon	1001	1100	.	+	.	Parent=trans-1
Contig1	confirmed	exon	1201	1300	.	+	.	Parent=trans-1
Contig1	confirmed	exon	1401	1450	.	+	.	Parent=trans-1
Contig1	confirmed	CDS	1051	1100	.	+	0	Parent=trans-1
Contig1	confirmed	CDS	1201	1300	.	+	2	Parent=trans-1
Contig1	confirmed	CDS	1401	1440	.	+	0	Parent=trans-1
Contig1	est	match	1001	1100	96	.	.	Target=CEESC13F 1 100 +;Name=match1
Contig1	est	match	1201	1300	99	.	.	Target=CEESC13F 101 200 +;Name=match2
Contig1	est	match	1401	1450	99	.	.	Target=CEESC13F 201 250 +;Name=match3
Contig1	tc1	transposable_element	5001	6000	.	+	.	ID=c128.1;Name=c128.1
Contig1	tc1	transposable_element	8001	9000	.	-	.	ID=c128.2;Name=c128.2
Contig1	confirmed	transcript	30001	31000	.	-	.	ID=trans-2;Name=trans-2;Alias=xyz-2;Note=Terribly+interesting
Contig1	confirmed	exon	30001	30100	.	-	.	Parent=trans-2;Alias=abc-1;Note=function+unknown;index=1
Contig1	confirmed	exon	30701	30800	.	-	.	Parent=trans-2
Contig1	confirmed	exon	30801	31000	.	-	.	Parent=trans-2

##sequence-region Contig2 1 37450
Contig2	clone	assembly_component	1	2000	.	.	.	Target=AL12345.1 1 2000 +;Name=match4;Note=Terribly+interesting
Contig2	clone	assembly_component	2001	5000	.	.	.	Target=AL11111.1 6000 3001 +;Name=match5
Contig2	clone	assembly_component	5001	20000	.	.	.	Target=AC13221.2 1 15000 +;Name=match6
Contig2	clone	assembly_component	2001	37450	.	.	.	Target=M7.3 1001 36450 +;Name=match7
Contig2	predicted	transcript	2501	4500	.	+	.	ID=trans-3;Name=trans-3;Alias=trans-18
Contig2	predicted	transcript	5001	8001	.	-	.	ID=trans-4;Name=trans-4

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

# associative attributes
# these are not intended to have any implied parent/child relationship, but their attributes can be
# used to group them arbitrarily.
Contig4	clone	assembly_component	1	50000	.	.	.	ID=ABC123
Contig4	confirmed	gene	32000	35000	.	+	.	ID=thing1;gene=gene-9
Contig4	confirmed	mRNA	32000	35000	.	+	.	ID=thing2;mRNA=trans-9;gene=gene-9
Contig4	confirmed	CDS	32000	35000	.	+	.	ID=thing3;mRNA=trans-9

# three-tiered gene
Contig1	confirmed	gene	2000	3000	.	.	.	ID=tier0;Name=gene3;expressed=yes;in_process=1
Contig1	confirmed	mRNA	2000	3000	.	+	.	Parent=tier0;ID=tier0.1;expressed=yes;Name=gene3.a;index=1
Contig1	confirmed	mRNA	2500	3000	.	+	.	Parent=tier0;ID=tier0.2;Name=gene3.b
Contig1	confirmed	five_prime_UTR	2000	2100	.	+	.	Parent=tier0.1
Contig1	confirmed	CDS	2101	2200	.	+	0	Parent=tier0.1
Contig1	confirmed	CDS	2500	2800	.	+	0	Parent=tier0.1
Contig1	confirmed	three_prime_UTR	2801	2900	.	+	.	Parent=tier0.1
Contig1	confirmed	three_prime_UTR	2910	3000	.	+	.	Parent=tier0.1

Contig1	confirmed	five_prime_UTR	2500	2510	.	+	.	Parent=tier0.2
Contig1	confirmed	CDS	2511	2520	.	+	0	Parent=tier0.2
Contig1	confirmed	CDS	2300	2400	.	+	0	Parent=tier0.2,tier0.1;Name=shared_exon
Contig1	confirmed	CDS	2500	2800	.	+	0	Parent=tier0.2
Contig1	confirmed	three_prime_UTR	2801	2900	.	+	.	Parent=tier0.2;ID=utr1
Contig1	confirmed	three_prime_UTR	2910	3000	.	+	.	Parent=tier0.2;ID=utr1

ctgA	est	EST_match	5410	5500	.	-	.	ID=Match2;Name=agt830.3;Target=agt830.3 505 595
ctgA	est	EST_match	7000	7503	.	-	.	ID=Match2;Name=agt830.3;Target=agt830.3 1 504 
ctgA	est	EST_match	1050	1500	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 451
ctgA	est	EST_match	3000	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 452 654

# test multiple parentage handling
Contig1	test	gparent	2500	2550	.	+	.	ID=gparent1;Name=gparent1
Contig1	test	parent	2500	2550	.	+	.	ID=parent1;Name=parent1;Parent=gparent1
Contig1	test	parent	2501	2551	.	+	.	ID=parent2;Name=parent2;Parent=gparent1
Contig1	test	child	2500	2550	.	+	0	ID=child1;Parent=parent1,parent2;Name=child1
Contig1	test	child	2501	2551	.	+	1	ID=child2;Parent=parent1,parent2;Name=child2

# test out DNA loading
>Contig1
[encoded data, 38064 characters]
cgtattgtgc
>Contig2
[encoded data, 38064 characters]
tgacggtctg
>CEESC13F
ttgcgttcggctaaagattgcgacccttgtatctgttttgtgtcatctcgcttggtgcta
gggtgatgtctctactctggagtgtatacgacgcaagcccttgcaggctaactacggact
gctgcacactctaattcgaccgaactcgagtacgactgcgattataaatgcaacaagtcc
ggggaagcctccgacaccaagacgcgacgctcgcaccatctttcccgtcgctatcccagc
tcggtaagtctcgctcccgcccggcttaccaaaacaacacactcctcggcaatcgaatga
gcgtcttgtgccgataatactttccaaacccgagttttttcctaattgtttggggaacgc
cagtgaggtcagaacgcctacatcagaaggcggacgagagcctcacgattactcgacctg
cttttgtggcacattgagtgccccctggagtcagaacactccgtggctggtacaaaaatg
gtgttagttcttcgacaattagatcatatcaggcggttttagccactattaccgaccatc
cacgcacacctagcaactcaactttttatcacgctggcaagtaagtggaaggccctgctg
ccgttaaacggcaggctcatcgcggtatccacatcaattgcggtgaccggggtctcgctt
tagaaaagccgatatggtccaggacgtcgtggtgcgcaggaacccttagaatttagtatg
cggcgcgcgacgcgctgagagtcatcggcgccttagacggagttactccgcgaagcgctc
