##gff-version 3
# This output was generated with AUGUSTUS (version 2.3).
# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mstanke@gwdg.de)
# and Oliver Keller (keller@cs.uni-goettingen.de).
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# reading in the file /tmp/bac-submission-temp-C03SLe0111P12-FGCs4/AUGUSTUS_tom_ugs/hints.gff ...
# Setting 1group1gene for E.
# Sources of extrinsic information: M E 
# Have extrinsic information about 1 sequences (in the specified range). 
# Initialising the parameters ...
# tomato version. Use default transition matrix.
# Looks like /tmp/bac-submission-temp-C03SLe0111P12-FGCs4/AUGUSTUS_tom_ugs/seq_with_defline_removed is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 95158, name = C03SLe0111P12.1) -----
#
# Delete group HintGroup SGN-U573936, 21114-26721, mult= 1, priority= 4 16 features
# Delete group HintGroup SGN-U572304, 85059-94963, mult= 1, priority= 4 11 features
# Forced unstranded hint group to the only possible strand for 12 groups.
# Deleted 2 groups because some hint was not satisfiable.

# Predicted genes for sequence number 1 on both strands
# start gene g1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	1311	9444	0.68	-	.	ID=g1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	1311	9444	0.68	-	.	ID=g1.t1;Parent=g1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	1311	1313	.	-	0	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	1389	2231	0.73	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	2379	3918	0.94	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	6034	6106	1	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	6302	7347	1	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	7429	7519	1	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	7610	8114	1	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	8202	9396	1	-	.	Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	1311	1388	0.74	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	2232	2378	0.71	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	3919	6033	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	6107	6301	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	7348	7428	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	7520	7609	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	8115	8201	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	9397	9444	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	9442	9444	.	-	0	Parent=g1.t1
# protein sequence = [MNNVQRNSLGERNVEQAITALKRGSYLLKYGRRGKPKFCPFRLSTDETRLIWYVEKEEKQLQLSQVSRIIPGQRTANF
# LRFPRPEKEYQSFSLLYGKSSLDLICKDKEEAEVWFVALRALTSRVDCQKWTSDIRYDIAYSDGSTSATQRRSHSALSSSSGSSSTPYEDPKKNLLGS
# VPSQSPPRKRLERAFSDYLLYNSAAKCSSHREFATSSFNSRSYGNLDDEIGQSSTDTIRSSFSSAISSSSHGSFANADTLCDILIWGEGIGDGLLGGG
# MCGLGKFETARRDAPLPRTLESALILDAQYVACGSRHAVLITKQGEIFSWGEGLSGRLGHGVESDISSPKLIDSLCGLNVTSAACGDYHTCATTITGD
# LYTWGEGTFNFGLLGHDTGISHWIPKKVRGPLVGKHVSYVSCGPWHSAVITSVGQLFTFGDGTFGALGHGDRSSIGIPREVETLQGLRTVRVACGHWH
# TAAVVELSFDDSSSCNSPPWKLFTWGNGDDGQLGHEDNASRHTPCKVVQLDGINFSRVACGHSITVALTTLGQVYTMGKVDYGQLGIPGSTGKFPSRV
# QGKITDCFIEEIACGSFHVVSLSSNSELYTWGKGGNGQLGHGDNHDRNTPTLVEALKAKKVKDVVCGNNFTAAICLHREVSLADNSICAGCQSPFNLR
# RKRHNCYNCGLVFCTVCTSKRSVRASLAPKMNKPYRVCEDCFTKLNKGLDIGLTCLPPKVTTGSLQKNTGERRKETSPSKQKGLLSRLSSFNSFRSDD
# KRFRKNQKQDSNSENVSPIPNGNTQSEVSQTSSQLLSFSSCPEILSVSFVGSTSHSQAGSPASFESCSSNSVLLRSAFAAQANHEVDLDDSKQTSESL
# KKEISILKEQVDILTQRSLFLEAELEKKSTQLQEKSEEAITETDKNNAAKEVIKSLMTQVKGNTARAPQDGSAENLIHSTMTVP]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 60
# CDS exons: 5/8
#      E:   5 
# CDS introns: 4/7
#      E:   4 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 2
#      E:   2 (SGN-U565504,SGN-U604070)
# end gene g1
###
# start gene g2
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	12529	14596	1	-	.	ID=g2
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	12529	14596	1	-	.	ID=g2.t1;Parent=g2
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	12529	12531	.	-	0	Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	12595	12731	1	-	.	Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	12976	14144	1	-	.	Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	14268	14360	1	-	.	Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	14388	14525	1	-	.	Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	12529	12594	1	-	0	ID=g2.t1.cds;Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	12732	12975	1	-	1	ID=g2.t1.cds;Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	14145	14267	1	-	1	ID=g2.t1.cds;Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	14361	14387	1	-	1	ID=g2.t1.cds;Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	14526	14596	1	-	0	ID=g2.t1.cds;Parent=g2.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	14594	14596	.	-	0	Parent=g2.t1
# protein sequence = [MGGSGGGIVSLLKVIISNFDVLAGPVVSLVYPLYASIRAIETKSPVDDQQWLTYWILYSMITLFELTFAKLIEWLPFW
# SYAKLIATCWLVIPYFNGAAYVYEHYIRTYIVQRKAVNIWYVPRKKDVFSKPDDILTAAEKYIKEHGTQAFEEMIHKADGERKTHTSNYVFYDDDYRY]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 5/5
#      E:   5 
# CDS introns: 4/4
#      E:   4 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 1
#      E:   1 (SGN-U584349)
# end gene g2
###
# start gene g3
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	17070	19830	1	-	.	ID=g3
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	17070	19830	1	-	.	ID=g3.t1;Parent=g3
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	17070	17072	.	-	0	Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	17481	17875	1	-	.	Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	18004	18130	1	-	.	Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	18250	19762	1	-	.	Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	17070	17480	1	-	0	ID=g3.t1.cds;Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	17876	18003	1	-	2	ID=g3.t1.cds;Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	18131	18249	1	-	1	ID=g3.t1.cds;Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	19763	19830	1	-	0	ID=g3.t1.cds;Parent=g3.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	19828	19830	.	-	0	Parent=g3.t1
# protein sequence = [MDTENPAPIVEKDTTDAETSLDSSHLRKKIQKKVPKRIHKAEREKMKREHLNELFLGLADALELSEQMNGKASVLSEA
# ARFVKDMLSQIKHMRTENTTLLSESQYLSVEKKELEDENTVLEAEISKLQNEVKAREAETSLDLNLAPPEIHHTEFASQTNYMRLPASEHGFQQSQMM
# NPVYVFPLSSNPQAYPAPDAADPMAMPSSTVKKPQPRYPTPNDVWPSQILEKRPQLLRQEVQDGA]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 4/4
#      E:   4 
# CDS introns: 3/3
#      E:   3 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 1
#      E:   1 
# incompatible hint groups: 2
#      E:   2 (SGN-U579828,SGN-U580216)
# end gene g3
###
# start gene g4
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	23406	26517	0.29	-	.	ID=g4
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	23406	26517	0.29	-	.	ID=g4.t1;Parent=g4
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	23406	23408	.	-	0	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	23568	24435	0.74	-	.	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	24550	24647	1	-	.	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	24737	24838	0.93	-	.	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	24880	25109	1	-	.	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	25175	25260	1	-	.	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	25428	26405	1	-	.	Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	23406	23567	0.35	-	0	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	24436	24549	0.98	-	0	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	24648	24736	0.93	-	2	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	24839	24879	0.99	-	1	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	25110	25174	1	-	0	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	25261	25427	1	-	2	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	26406	26517	0.96	-	0	ID=g4.t1.cds;Parent=g4.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	26515	26517	.	-	0	Parent=g4.t1
# protein sequence = [MVRVRNYCSISKPAIWIWLISALTFYLLFLMANRNSREWSISNAEQRSRLYEKMEKDLEDHGATFLKQGETTQSLSLS
# DLFILKDGVVTPVLKPANPPVRANVLYLNPEYSVPIADAVRSIFSPHFDKAIWFQNSSLYHFSMFHGSHHITAVPASESEIEAEANAVRAVSESICPL
# KITLDRVVLTSTGVLVGCWQVDSGSDPVTIRQKLRNALPHAPAKQLVRAKQTFSALHLSEDAYVFALQPLGAN]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 69.2
# CDS exons: 5/7
#      E:   5 
# CDS introns: 4/6
#      E:   4 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 3
#      E:   3 
# incompatible hint groups: 1
#      E:   1 (SGN-U589321)
# end gene g4
###
# start gene g5
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	37513	38824	1	-	.	ID=g5
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	37513	38824	1	-	.	ID=g5.t1;Parent=g5
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	37513	37515	.	-	0	Parent=g5.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	38446	38527	1	-	.	Parent=g5.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	37513	38445	1	-	0	ID=g5.t1.cds;Parent=g5.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	38528	38824	1	-	0	ID=g5.t1.cds;Parent=g5.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	38822	38824	.	-	0	Parent=g5.t1
# protein sequence = [MDGGGDDHLHQRHQHNHRSIATFPFQLLEKKEDEACSSSSNAAAAYTTSLAISNTDNTHTNPNNTPRSTISTLQISAS
# GADTSKKPPPKRTSTKDRHTKVDGRGRRIRMPALCAARVFQLTRELGHKSDGETIEWLLQQAEPAVIAATGTGTIPANFTSLNISLRSSGSSMSVPSQ
# LRSSYFNPNFSLSQRRGLFPPGIGLSTDTSATTLLNFQSANLSSNIQLQTKPELRDNSIDLTESSPAEDNLSRKRRSDLDLEQQQHQQQQQQMGSYLL
# QSSTGTMPTSHSSIPANFWMVTNPIPSNQVMGGDPIWPFQSVSNSGALYRGTMPSGLQFMNFPTSVALLPSQQLGGGSSGGGGGNNGLGEGQLGMFAG
# LNPYRGGGGVSESQASGSHSHHGGGTDDRHDTTSHHS]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 2/2
#      E:   2 
# CDS introns: 1/1
#      E:   1 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 2
#      E:   2 (SGN-U571327,SGN-U574962)
# end gene g5
###
# start gene g6
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	50590	50892	1	-	.	ID=g6
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	50590	50892	1	-	.	ID=g6.t1;Parent=g6
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	50590	50592	.	-	0	Parent=g6.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	50590	50892	1	-	0	ID=g6.t1.cds;Parent=g6.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	50890	50892	.	-	0	Parent=g6.t1
# protein sequence = [MARRVGEDEIDTSQTYSTAYGSLRFRLIHAKRKMEGEERGVVGVCRSRSVFLGFCREGRERASVGETRERGKERMKEG
# GRVGRKERGFWGIGFSGFLSGN]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/1
# CDS introns: 0/0
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 0
# end gene g6
###
# start gene g7
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	52811	65245	0.17	+	.	ID=g7
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	52811	65245	0.17	+	.	ID=g7.t1;Parent=g7
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	52811	52813	.	+	0	Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	52838	53844	0.53	+	.	Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	53986	54609	0.46	+	.	Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	55393	63877	0.57	+	.	Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	64068	65177	0.64	+	.	Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	52811	52837	0.75	+	0	ID=g7.t1.cds;Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	53845	53985	0.54	+	0	ID=g7.t1.cds;Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	54610	55392	0.34	+	0	ID=g7.t1.cds;Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	63878	64067	0.73	+	0	ID=g7.t1.cds;Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	65178	65245	0.86	+	2	ID=g7.t1.cds;Parent=g7.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	65243	65245	.	+	0	Parent=g7.t1
# protein sequence = [MFTWMSLVRMSSQFLHFKMVTQAPDILRVWWGNLKECQKREISIYLGHLPSIMDFKLQGLAEPSQTSPLDNYEFYLSI
# RKFPIHTTRDAWAKVFYNLKEGDIQWVLPSFRSQMIAAQGAKLPFLVLPGIRGSRPYNPTRVMRQFGKVQTIPAQGDASSFIVDYNGKDKIPFAKIIL
# QEWAGRVNMKWEVTEDRYGAGYVDEYKTWLHKDLRGVVDPTPRTSQKIEDVETRLQIYAYHFQQEWDRREQEFHKKEQEFQQRDQAYQLQELENQRLL
# AVTSQELADTRTCLIRLDTILDEQMNTLQAVPTSSKAAFAEPYNTKILGFSGVAFGYEEQFKSWESSFVLAVRRRNIGLVFRLCSWFACGSLFRSRSS
# LPVRCLKKEGHKGLISSIKSSHEVDEQIPS]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 22.2
# CDS exons: 2/5
#      E:   2 
# CDS introns: 0/4
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 2
#      E:   2 (SGN-U579247,SGN-U602315)
# end gene g7
###
# start gene g8
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	70341	71911	0.63	-	.	ID=g8
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	70341	71911	0.63	-	.	ID=g8.t1;Parent=g8
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	70341	70343	.	-	0	Parent=g8.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	70626	70899	0.93	-	.	Parent=g8.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	71222	71765	0.97	-	.	Parent=g8.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	70341	70625	0.97	-	0	ID=g8.t1.cds;Parent=g8.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	70900	71221	0.92	-	1	ID=g8.t1.cds;Parent=g8.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	71766	71911	0.69	-	0	ID=g8.t1.cds;Parent=g8.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	71909	71911	.	-	0	Parent=g8.t1
# protein sequence = [MNCSPLPGAPFPAGYNRKPNPSYEFAEYLVMLHPGSTFNVFPPNHPQLQEVMGDLFNQFAKIGAILESILSESLGLPP
# SILQEFNNERNSDVLTALYYLPATENEKMGINSHRDVGCITFVLQDEVGGLEVQKDGNWIPVTPNKGALVVNIGIVLQVLTNDKYKSPNHRAMRPNGR
# SRNSFSFFYNVSGEKWLEPLPHFTKQIDEKPNYKGFIYSDYLQKRNENKLKRAAGLEEDLGLSHFSLTRSIENH]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/3
# CDS introns: 0/2
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 0
# end gene g8
###
# start gene g9
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	72801	73248	0.52	-	.	ID=g9
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	72801	73248	0.52	-	.	ID=g9.t1;Parent=g9
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	72801	72803	.	-	0	Parent=g9.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	73071	73161	1	-	.	Parent=g9.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	72801	73070	1	-	0	ID=g9.t1.cds;Parent=g9.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	73162	73248	0.52	-	0	ID=g9.t1.cds;Parent=g9.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	73246	73248	.	-	0	Parent=g9.t1
# protein sequence = [MKLKALRFLKMTIAPSKDKLIVNIGDVIQVLSNNKFKSATHRAANPSETDRYSYAFFYNVQGSKWVEPLPQFTEEIGE
# SPKYRGFLFEEYLQLRIKNRSHPPARPEDLIHITHYSISN]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 2/2
#      E:   2 
# CDS introns: 1/1
#      E:   1 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 1
#      E:   1 (SGN-U574082)
# end gene g9
###
# start gene g10
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	74581	75693	1	-	.	ID=g10
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	74581	75693	1	-	.	ID=g10.t1;Parent=g10
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	74581	74583	.	-	0	Parent=g10.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	74851	74937	1	-	.	Parent=g10.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	75260	75358	1	-	.	Parent=g10.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	74581	74850	1	-	0	ID=g10.t1.cds;Parent=g10.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	74938	75259	1	-	1	ID=g10.t1.cds;Parent=g10.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	75359	75693	1	-	0	ID=g10.t1.cds;Parent=g10.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	75691	75693	.	-	0	Parent=g10.t1
# protein sequence = [MASFDIPTIDVSPFFKSDENEGAKKQAIEQIREACVSYGFFQIVNHGIPSDLLSRTIDMYKTFFGCSDEEKLCLPDNY
# LKSTPNSAETFEHLWFRFPFSGFNNCRSITPHFKKVLEEIVSHFTKLGVVLEGIISECLGLPPDFLSNYRNGRSRDSLMGLHYFPATEDDNTGKPAHE
# DPGCFTILYQDEIGGLQVHKDDHWIPIPPSKDKLVVNIGDVIQVLSNNKFKSATHKVVRPIETNRYSYVFFYNVEGDKWIEPLPQFTKEIGESPKYRG
# FVFEEYHELRFRNRSHPPARPEDLIHITHYSISN]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 3/3
#      E:   3 
# CDS introns: 2/2
#      E:   2 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 1
#      E:   1 (SGN-U574083)
# end gene g10
###
# start gene g11
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	76433	77554	0.99	-	.	ID=g11
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	76433	77554	0.99	-	.	ID=g11.t1;Parent=g11
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	76433	76435	.	-	0	Parent=g11.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	76703	76788	1	-	.	Parent=g11.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	77111	77216	1	-	.	Parent=g11.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	76433	76702	1	-	0	ID=g11.t1.cds;Parent=g11.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	76789	77110	1	-	1	ID=g11.t1.cds;Parent=g11.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	77217	77554	0.99	-	0	ID=g11.t1.cds;Parent=g11.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	77552	77554	.	-	0	Parent=g11.t1
# protein sequence = [MASFDIPTIDVSPFITSEENEEGKKKAIEQMREACVNYGFFQIANHGIPLDLLSRIMDMYKTFFACSDEEKLSVPSDN
# YFKSTKKSAGTYEQLLFHLSSSGFNVCPENPPRFKQVLEEMASHFTNLGFVLGRIISECLGIPPNFLANYRNDQAKDFLLGIHYSPATEAENVGKSAH
# KDPGCITILYQPEVGGLQVQKDEQWIPIAPSKDKLVVNIGDVIQVLSNNKFKSATHRVIRPRETNRYSCAFFYNVQGDKWVEPLPQCTKEIGESPKYR
# GFIFKEYVQRRRRDETHPPARPEDLFNISHYSIST]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 3/3
#      E:   3 
# CDS introns: 2/2
#      E:   2 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 1
#      E:   1 (SGN-U587850)
# end gene g11
###
# start gene g12
C03SLe0111P12.1	AUGUSTUS_tom_ugs	gene	83919	85149	0.06	+	.	ID=g12
C03SLe0111P12.1	AUGUSTUS_tom_ugs	transcript	83919	85149	0.06	+	.	ID=g12.t1;Parent=g12
C03SLe0111P12.1	AUGUSTUS_tom_ugs	start_codon	83919	83921	.	+	0	Parent=g12.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	intron	83957	84890	0.48	+	.	Parent=g12.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	83919	83956	0.43	+	0	ID=g12.t1.cds;Parent=g12.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	CDS	84891	85149	0.12	+	1	ID=g12.t1.cds;Parent=g12.t1
C03SLe0111P12.1	AUGUSTUS_tom_ugs	stop_codon	85147	85149	.	+	0	Parent=g12.t1
# protein sequence = [MSRKLTGDSLGFLGKRVKRRSLNDDARIGKRVVDDSDGDSAPRSKEEIRNGNMKVVEDDARGEVSGHGCLPLGITGML
# VWWFSLRQSNLISLVVWVNY]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 33.3
# CDS exons: 1/2
#      E:   1 
# CDS introns: 0/1
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 1
#      E:   1 (SGN-U575059)
# incompatible hint groups: 0
# end gene g12
###
# command line:
# /usr/bin/augustus.real --species=tomato --hintsfile=/tmp/bac-submission-temp-C03SLe0111P12-FGCs4/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C03SLe0111P12-FGCs4/AUGUSTUS_tom_ugs/seq_with_defline_removed