##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-C00SLm0005K22-CfAGc/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 = 162708, name = C00SLm0005K22.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	27389	34881	0.57	-	.	ID=g1
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	27389	34881	0.57	-	.	ID=g1.t1;Parent=g1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	27389	27391	.	-	0	Parent=g1.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	27516	27631	0.92	-	.	Parent=g1.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	27712	34680	0.84	-	.	Parent=g1.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	27389	27515	0.62	-	1	ID=g1.t1.cds;Parent=g1.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	27632	27711	0.92	-	0	ID=g1.t1.cds;Parent=g1.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	34681	34881	0.85	-	0	ID=g1.t1.cds;Parent=g1.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	34879	34881	.	-	0	Parent=g1.t1
# protein sequence = [MKEEGMGSTCSGSGHFGRKWVMVGGYGVFNVEEGRRVPGKNGENEMGFWGVILTLPENTPGRVVAEKRSKGKHGDGVL
# EFLALIRCRRRKWDDGWRKGGGSLEKMGKTKWDLGGGFDFAGKCSGKGGGRKSMYNK]
# end gene g1
###
# start gene g2
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	104131	105668	0.32	+	.	ID=g2
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	104131	105668	0.32	+	.	ID=g2.t1;Parent=g2
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	104131	104133	.	+	0	Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	104202	104420	0.58	+	.	Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	104560	104751	0.56	+	.	Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	104952	105022	1	+	.	Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	104131	104201	0.58	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	104421	104559	0.91	+	1	ID=g2.t1.cds;Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	104752	104951	0.63	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	105023	105668	1	+	1	ID=g2.t1.cds;Parent=g2.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	105666	105668	.	+	0	Parent=g2.t1
# protein sequence = [MGKRKEQKKVCHRDDEDKEVEGSRFTVNPRRRIRQHNGEVRMGALRTKRKRPWEMILCIYGFPTNVSALQLMLANLKP
# EFATHVNFFSSLLQFEWAWQHPVESRAVRQAAASFKTLGGVANKIKLAYTMLTLPEWQSLNLTVNFFSTKYKMHSAGCPSLPEHMRVHICALDELPCY
# TGIDRDEWENICALDELPSYTGIDRDEWENREECESSEELTDEISTNSNSSFSNQDKDDEQTDWRELDERAGENSTRGREHSYIIIDSPAERLCSIQG
# DFFHIADKKERHQLDDEFGENQANKMYDSLATKNAGLPCDIEVIDVFTPPVRADNKRRRLSASVPEIIDLTDSPVYV]
# end gene g2
###
# start gene g3
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	118717	122864	0.8	+	.	ID=g3
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	118717	122864	0.8	+	.	ID=g3.t1;Parent=g3
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	118717	118719	.	+	0	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	119223	119440	0.96	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	119501	120160	0.95	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	120285	120418	1	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	120488	120584	0.9	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	120684	120895	0.97	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	120963	121623	1	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	121689	121871	1	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	121967	122151	0.99	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	122277	122456	1	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	122558	122777	0.94	+	.	Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	118717	119222	1	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	119441	119500	0.96	+	1	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	120161	120284	1	+	1	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	120419	120487	1	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	120585	120683	0.89	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	120896	120962	1	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	121624	121688	1	+	2	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	121872	121966	1	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	122152	122276	0.99	+	1	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	122457	122557	0.96	+	2	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	122778	122864	0.94	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	122862	122864	.	+	0	Parent=g3.t1
# protein sequence = [MNPSSLLLPINQPPPVNTFRSQFLNPTPLRLTPKFYLKRRIQSTVISSSSASLQHKPTSVNPDVFGGKKELSPIQSLV
# DAMSPPIRIASSALIFAAAIAAGYGLGLRFGGSRNAGLGGAIAFGAAGAGAAYALNSCAPQVAAINLHNYVADFDNPAALNKEDIESIANKYGVSKQN
# EAFNAELRDIYCRYISAVLPASTEELRGDEVDTIIKFKNALGIDDPDAADMHMEIGRRIFRQRLETGDRDGDMEQRRAFQKLIYVSTLVFGESSAFLL
# PWKRVFKVTDAQVDVAVRDNAQRLYASKLKSVGRDIDVNQLISLREAQLAYRLSDELAHEMLKEHARKLVEEIISTAVGILKSRTRATEPTRVIEELD
# KVLSYNNLLISLKNHADASRFAPGIGPVSLVGGEYDGDRKMDDLKLLYRAYVTDSLSSGRMEEDKDNNGYTSRFVCQWKMACAHPLLSITGQE]
# end gene g3
###
# start gene g4
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	123676	130075	0.25	-	.	ID=g4
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	123676	130075	0.25	-	.	ID=g4.t1;Parent=g4
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	123676	123678	.	-	0	Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	124028	125612	0.34	-	.	Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	125663	128252	0.46	-	.	Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	128343	129964	0.47	-	.	Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	123676	124027	0.29	-	1	ID=g4.t1.cds;Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	125613	125662	0.36	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	128253	128342	0.52	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	129965	130075	0.48	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	130073	130075	.	-	0	Parent=g4.t1
# protein sequence = [MEEGQVEMATHLLNQDLINGERKPVQTFEKWGSLYERASRPLSSSGFSGESLLPSAHHFVKFAAPERANPSQRNTGAR
# AGAGCVSDPKAVVHSMVALHRKLSTVDRVQKWGKVGSTDCLLCNDQVEETPEHLFFDCPYSAFIRPFLVKWLDHTRSIGDWNQESNSRPQAGMFGFCC
# TRRLREIAVQVHIEGQRHSIWLAK]
# end gene g4
###
# start gene g5
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	130832	135435	0.46	+	.	ID=g5
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	130832	135435	0.46	+	.	ID=g5.t1;Parent=g5
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	130832	130834	.	+	0	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	130906	131040	0.94	+	.	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	131105	131305	0.97	+	.	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	131523	132584	0.74	+	.	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	132740	133892	0.72	+	.	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	134019	134129	0.95	+	.	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	135096	135192	1	+	.	Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	130832	130905	0.91	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	131041	131104	0.97	+	1	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	131306	131522	0.99	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	132585	132739	0.98	+	2	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	133893	134018	0.7	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	134130	135095	0.97	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	135193	135435	1	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	135433	135435	.	+	0	Parent=g5.t1
# protein sequence = [MWSNSTLWNLGFWVKAGITTDNNIXFLIDDEMVCGSVWSLDRYTRKLAALNQLRNIFGLGKREADTITLDVTSKVYRK
# RLAQAVTSGELEAFESKAAYLQNLCEELIFDPQKALEIHQEIYRQKLQLLVTDGELSDEDMKALERLQVMLCVPKQTVEAAHADICGSLFEKVVKEAI
# ACGIDGYDTETKNAVRKAAYGLRLTRDVAMTIASKAVRKIFITYIQRVRGAGSRTESAKELKKMIAFNSFVASQLVADIKGESSDTPAEETQQEQIQQ
# NEEEDEEWESLQSLRKVKPSKKNLRKDIQTEITLKDDLPERERTELYKTYLLFCLTGQVTKIPFGVQITTKKDDSEYVFLSQLGSILGLTDSEIVGVH
# QGLAEQAFRQQAEVILADGQITKAKMVQLNELQKNVGLPPHYAQNIIKSITTTKLAAALETAVGQGRLSIKEIRELKESSVDINTMISESLRENLFKK
# TLADIFSSGTGEFDEEEVYENVPKDLNINVEKAKKVVHELARSRLSNSLIQAVSLLRQRNHKALVYSLNDLLACDKAVPAIPLSWEVPEELSDLFIVY
# LKSDPPPEKLSRLQYLLGISDSTAETLRTVKDRELPNGAGEEEFVF]
# end gene g5
###
# start gene g6
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	142967	143660	0.62	+	.	ID=g6
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	142967	143660	0.62	+	.	ID=g6.t1;Parent=g6
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	142967	142969	.	+	0	Parent=g6.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	143159	143233	0.79	+	.	Parent=g6.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	143417	143636	0.88	+	.	Parent=g6.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	142967	143158	0.76	+	0	ID=g6.t1.cds;Parent=g6.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	143234	143416	0.69	+	0	ID=g6.t1.cds;Parent=g6.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	143637	143660	0.88	+	0	ID=g6.t1.cds;Parent=g6.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	143658	143660	.	+	0	Parent=g6.t1
# protein sequence = [MIESDILAALKPLLTSIDTLTARVEACGSIQEETFEITTLKVNIADLRKDIDYLESTNFTSLLESEAKIVKEYIDMRE
# AEVYDDLADLEDVMFETVRQTSLRETTMVGSNAAGGAIEVTSGTDAQALYYVDA]
# end gene g6
###
# start gene g7
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	144634	145350	0.46	+	.	ID=g7
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	144634	145350	0.46	+	.	ID=g7.t1;Parent=g7
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	144634	144636	.	+	0	Parent=g7.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	144677	144759	0.53	+	.	Parent=g7.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	intron	144835	145219	0.83	+	.	Parent=g7.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	144634	144676	0.51	+	0	ID=g7.t1.cds;Parent=g7.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	144760	144834	0.89	+	2	ID=g7.t1.cds;Parent=g7.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	145220	145350	0.84	+	2	ID=g7.t1.cds;Parent=g7.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	145348	145350	.	+	0	Parent=g7.t1
# protein sequence = [MRATYGEIMHCIHFWHLSTFVELELAFEASIVNLRTFDNGENQFGNRKEQSTSRLVVPRCIVGSSKVTELKDANGEAE
# RRWS]
# end gene g7
###
# start gene g8
C00SLm0005K22.1	AUGUSTUS_ab_initio	gene	161641	161964	0.61	+	.	ID=g8
C00SLm0005K22.1	AUGUSTUS_ab_initio	transcript	161641	161964	0.61	+	.	ID=g8.t1;Parent=g8
C00SLm0005K22.1	AUGUSTUS_ab_initio	start_codon	161641	161643	.	+	0	Parent=g8.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	CDS	161641	161964	0.61	+	0	ID=g8.t1.cds;Parent=g8.t1
C00SLm0005K22.1	AUGUSTUS_ab_initio	stop_codon	161962	161964	.	+	0	Parent=g8.t1
# protein sequence = [MVRENIDEPPHKRAQCIKINEGRSNPLRRGIQELSPCDRGEGRRPMSDRAASSPQDNLSELQDNHLIYDQEEYKNYRH
# VIEGKEGGPCLTGLLLALRTIYLSFKTTI]
# end gene g8
###
# command line:
# /usr/bin/augustus.real --species=tomato --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00SLm0005K22-CfAGc/AUGUSTUS_ab_initio/seq_with_defline_removed