##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-C10HBa0057G01-2ToRM/AUGUSTUS_tom_cdna/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-C10HBa0057G01-2ToRM/AUGUSTUS_tom_cdna/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 = 61868, name = C10HBa0057G01.2) -----
#
# Forced unstranded hint group to the only possible strand for 6 groups.

# Predicted genes for sequence number 1 on both strands
# start gene g1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	gene	41341	47718	0.96	-	.	ID=g1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	transcript	41341	47718	0.96	-	.	ID=g1.t1;Parent=g1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	stop_codon	41341	41343	.	-	0	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	41422	41518	0.96	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	41596	41683	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	41791	41881	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	41995	42085	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	42400	42488	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	42790	42864	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	43087	44062	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	44303	44397	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	44488	44567	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	45110	47459	1	-	.	Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	41341	41421	0.96	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	41519	41595	1	-	2	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	41684	41790	1	-	1	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	41882	41994	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	42086	42399	1	-	2	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	42489	42789	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	42865	43086	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	44063	44302	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	44398	44487	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	44568	45109	1	-	2	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	47460	47718	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	start_codon	47716	47718	.	-	0	Parent=g1.t1
# protein sequence = [MPPKSVRKTASGSGSKRGGRTPRGTPKSQAKSVKVEEPMEVQDKDKAVEEVSEEKPELKITQSEPEEPAETALNVNAV
# GKGAVSEKKKDNLKESVDHYEKGERLDLGDNDPEYEPEEYGTVDYDENGIEHDGVQEEGNEIEEEPEEADVGEEEEGDMAEEDVEDVHEENEGDEEDE
# HAEMADAAEEEEHHEVVDERRKRKEFEIFVGGLDKDATEEDLRKVFSKVGEITEVRLLMNSQTKKNKGFAFLRFATVEQAKRACTELKTPVINGKQCG
# VSPSQDNDTLFLGNICKTWTKEALKEKLKHYGVHNIEDLTLVEDTNNEGMNRGFAFLEFSSRSEAMDAFKRLQKRDIVFGVDRPAKVSFEDSFIDPGD
# EIMSQVKTVFIDGLAVSWNEDHVRELLKEYGKIRKVELARNRPSAKRKDFGFVTFDTHEAAVTCAKSINNEEFGEGDNKVKVRARLSRPLHMGRGKYG
# GRGEFRPWRMPMHGSHAPWGRTVPYSRSIRGTRVSTRMPPVVSRGFKRPTALRDRHAEMALSPRGRSMASPPRRSYDRRPPVSSYPKSNFKRDYGRRE
# EISPSRSRAIPEYPSRVHSDRRISYRDEYSSRGSGYPELPRGTHSAARRSYVDDGYGQRFERPPPSYREGRGREYDSVSGSKRPYMAVDDVHPHYAMA
# GVRHSRARLDYELGSASGSHYGDAYGDSRLGRSNLGYGGNRSSISRQDSHGIYSSRQGMDYGGGSYGGSDVGGLYSSSYGGDYMSRGSDVGSSVYSSR
# GMGGSGYMGSGGSGSYY]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 85.7
# CDS exons: 10/11
#      E:  10 
# CDS introns: 8/10
#      E:   8 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 7
#      E:   7 (SGN-E731946,SGN-E738479,SGN-E342955,SGN-E738452,SGN-E271196)
# incompatible hint groups: 3
#      E:   3 (SGN-E365794,SGN-E322085,SGN-E331699)
# end gene g1
###
# start gene g2
C10HBa0057G01.2	AUGUSTUS_tom_cdna	gene	56386	57279	0.65	+	.	ID=g2
C10HBa0057G01.2	AUGUSTUS_tom_cdna	transcript	56386	57279	0.65	+	.	ID=g2.t1;Parent=g2
C10HBa0057G01.2	AUGUSTUS_tom_cdna	start_codon	56386	56388	.	+	0	Parent=g2.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	intron	56508	57068	0.69	+	.	Parent=g2.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	56386	56507	0.84	+	0	ID=g2.t1.cds;Parent=g2.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	CDS	57069	57279	0.72	+	1	ID=g2.t1.cds;Parent=g2.t1
C10HBa0057G01.2	AUGUSTUS_tom_cdna	stop_codon	57277	57279	.	+	0	Parent=g2.t1
# protein sequence = [MKLKIMTVLSDSKSHRNYSDVWLFTGLLCEWGLSKMAPRRRVFWVVVFWLDLAIGRNVGSGSGGIPVACFGLAVGVGG
# CWRSGLLEKRAKMKGDFGVYGLWTHRKLAELR]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/2
# CDS introns: 0/1
# 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 g2
###
# command line:
# /usr/bin/augustus.real --species=tomato --hintsfile=/tmp/bac-submission-temp-C10HBa0057G01-2ToRM/AUGUSTUS_tom_cdna/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C10HBa0057G01-2ToRM/AUGUSTUS_tom_cdna/seq_with_defline_removed