##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
# No extrinsic information on sequences given.
# Initialising the parameters ...
# tomato version. Use default transition matrix.
# Looks like /tmp/bac-submission-temp-C00SLm0121I03-UIgCS/AUGUSTUS_ab_initio/seq_with_defline_removed is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 41082, name = C00SLm0121I03.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C00SLm0121I03.1	AUGUSTUS_ab_initio	gene	169	6101	0.36	+	.	ID=g1
C00SLm0121I03.1	AUGUSTUS_ab_initio	transcript	169	6101	0.36	+	.	ID=g1.t1;Parent=g1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	1	168	0.96	+	.	Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	221	401	0.96	+	.	Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	530	898	0.75	+	.	Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	1013	4713	0.61	+	.	Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	4865	5765	0.88	+	.	Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	169	220	0.96	+	1	ID=g1.t1.cds;Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	402	529	0.94	+	0	ID=g1.t1.cds;Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	899	1012	0.59	+	1	ID=g1.t1.cds;Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	4714	4864	0.88	+	1	ID=g1.t1.cds;Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	5766	6101	0.93	+	0	ID=g1.t1.cds;Parent=g1.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	stop_codon	6099	6101	.	+	0	Parent=g1.t1
# protein sequence = [LLNPSTFAGWFGRSLFHAIVVFVITIHAYAFEKSEMEEASMVALSGCIWLQAFVVALETKSYTIFFLTLIRREQAHQQ
# VGHRDVSVLDGRGLGLERYGSFTILQHIAIWGNLVAFYVINWIVSAFPSSGLYTIMFRLCRQPSYWITIFIIVAAGMGPVLALKYFRYTYRSSKINIL
# QQAERMGGPILSLGNIEPQLRSLDKDVAPLSISQPKNRTSVYEPLLSDSPSATRRSFGPGAPFDFFQPQARLSSNYTRNCKDN]
# end gene g1
###
# start gene g2
C00SLm0121I03.1	AUGUSTUS_ab_initio	gene	9619	13351	0.75	-	.	ID=g2
C00SLm0121I03.1	AUGUSTUS_ab_initio	transcript	9619	13351	0.75	-	.	ID=g2.t1;Parent=g2
C00SLm0121I03.1	AUGUSTUS_ab_initio	stop_codon	9619	9621	.	-	0	Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	9901	10857	0.99	-	.	Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	11005	11402	1	-	.	Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	11696	12945	0.96	-	.	Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	13007	13174	1	-	.	Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	9619	9900	0.94	-	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	10858	11004	1	-	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	11403	11695	0.82	-	2	ID=g2.t1.cds;Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	12946	13006	1	-	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	13175	13351	0.98	-	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	start_codon	13349	13351	.	-	0	Parent=g2.t1
# protein sequence = [MLMIQSTISLPLQKSVLVPAKIATSGSKNGCFLDLNGRCGSKSASYHFPRRPIKGNSIQLKIYARKSESLPILLSEKV
# DELPEMLLNGGDITISSGEILSLSAFSCGSIFWLTSGQVALASEGVRVNMVYEVGELFELGIQLTYLLLLLALLGVGSFFVIRQVLVRRELDLSAKEL
# QEQVRSGDASATELFELGAVMLRRKFYPAATKYLLQAVEKWDGDDQDLAQVYNALGVSYVLDGKIDKGIAQFENAVKVQPGYVTAWNNLGDAYEKTKD
# LTSALNAFEEVLLFDPNNKIARPRRDALKDKVTMYKGVSVKSKKS]
# end gene g2
###
# start gene g3
C00SLm0121I03.1	AUGUSTUS_ab_initio	gene	24966	26222	0.86	+	.	ID=g3
C00SLm0121I03.1	AUGUSTUS_ab_initio	transcript	24966	26222	0.86	+	.	ID=g3.t1;Parent=g3
C00SLm0121I03.1	AUGUSTUS_ab_initio	start_codon	24966	24968	.	+	0	Parent=g3.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	24966	26222	0.86	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	stop_codon	26220	26222	.	+	0	Parent=g3.t1
# protein sequence = [MSSMKVGGNTLPVTVDEHGHVRYDTIARQAENSQKIVYCHYNDLVPKFVKDHDQDLEQEKKKLIDETTRETKAILLQK
# IGTQQSWDSMESLKFIKYKPCKQQQGSRLVKMVEKAVDPMEPPKFKHKKVPRASGSPPVPVMHSPPRPVTVKDQQDWKIPPCISNWKNPKGYTIPLDK
# RLAADGSRGIDEVKINDDFPKLAEALYVATEKATEAIAMRSKVQREIILKEMELQELARNARAEIAAGLKNDGDDYEGRLWREKISKERHQERRLLEA
# KEGAAMKRRKIKTRDGDRDISEKVALGMASTSRGCGEATMYDQRLFNQEKGIDSGFAADDAYNLYDNILFTAQCTLYRPKKDVDCDTYGEQQQEKITH
# SKPDNAFAGTSERTDPRDRPVEFEADPFGLDQFMTGVKNNMANYGN]
# end gene g3
###
# start gene g4
C00SLm0121I03.1	AUGUSTUS_ab_initio	gene	27991	31687	0.11	-	.	ID=g4
C00SLm0121I03.1	AUGUSTUS_ab_initio	transcript	27991	31687	0.11	-	.	ID=g4.t1;Parent=g4
C00SLm0121I03.1	AUGUSTUS_ab_initio	stop_codon	27991	27993	.	-	0	Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	28133	28245	0.66	-	.	Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	28469	29708	0.71	-	.	Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	29944	30848	0.41	-	.	Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	31020	31321	0.87	-	.	Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	27991	28132	0.32	-	1	ID=g4.t1.cds;Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	28246	28468	0.83	-	2	ID=g4.t1.cds;Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	29709	29943	0.28	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	30849	31019	0.95	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	31322	31687	0.87	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	start_codon	31685	31687	.	-	0	Parent=g4.t1
# protein sequence = [MEIQQFSPFTITPCHFHPIPNSNHHPVLVSPLKQQRNLLKLSPLFCSSSHSNPVVQDPILQQGNGSLGKSRDTHYKNS
# RKKRVFFLDVNPICYKGSIPSLQSFAHWISIFFSQVSLTDPVIAVIDGERGNEYRRQLLPSYKASRRKYWHQLQGAVKSPRSTIERSHRLILDVLQSC
# NVPVVKIESHEADDVIATLVEQVLQRGHRVVVASPDKDFKQLISDDVQIVMPVPEFNRWSFYTLKHYVAQYNCDPRSDLSLRCILGDEVDGVPGIQHV
# VPGFGRKTALKLLKKHGTLENLLNAASVRSVGRQYAQDALIKYADYLRRNYEVLSLKRDVSIHIEEQWLNERDARNDSLVLSNFVTSLEDSRNLNLEK
# RSHSIG]
# end gene g4
###
# start gene g5
C00SLm0121I03.1	AUGUSTUS_ab_initio	gene	32518	33552	0.43	-	.	ID=g5
C00SLm0121I03.1	AUGUSTUS_ab_initio	transcript	32518	33552	0.43	-	.	ID=g5.t1;Parent=g5
C00SLm0121I03.1	AUGUSTUS_ab_initio	stop_codon	32518	32520	.	-	0	Parent=g5.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	32749	32838	0.98	-	.	Parent=g5.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	intron	32932	33471	0.98	-	.	Parent=g5.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	32518	32748	1	-	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	32839	32931	0.98	-	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	CDS	33472	33552	0.44	-	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0121I03.1	AUGUSTUS_ab_initio	start_codon	33550	33552	.	-	0	Parent=g5.t1
# protein sequence = [MLPLFCTEVNDDANFATTAACDIQLLQALSRRIHYGKFVAEVKFRDSIDEYKPFILAQDRDALMKLLTFEAVEEMVKK
# RVAKKAKVFGQEVSLNDNAEEVKGKIDPLLVSRLYDEWVMPLTKLVEVEYLLRRLD]
# end gene g5
###
# command line:
# /usr/bin/augustus.real --species=tomato --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00SLm0121I03-UIgCS/AUGUSTUS_ab_initio/seq_with_defline_removed