##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-C00HBa0205L07-2MrjM/AUGUSTUS_tom_cdna/hints.gff ...
# Setting 1group1gene for E.
# Sources of extrinsic information: M E 
# Have extrinsic information about 0 sequences (in the specified range). 
# Initialising the parameters ...
# tomato version. Use default transition matrix.
# Looks like /tmp/bac-submission-temp-C00HBa0205L07-2MrjM/AUGUSTUS_tom_cdna/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 = 88677, name = C00HBa0205L07.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C00HBa0205L07.1	AUGUSTUS_tom_cdna	gene	73682	73918	0.82	+	.	ID=g1
C00HBa0205L07.1	AUGUSTUS_tom_cdna	transcript	73682	73918	0.82	+	.	ID=g1.t1;Parent=g1
C00HBa0205L07.1	AUGUSTUS_tom_cdna	start_codon	73682	73684	.	+	0	Parent=g1.t1
C00HBa0205L07.1	AUGUSTUS_tom_cdna	CDS	73682	73918	0.82	+	0	ID=g1.t1.cds;Parent=g1.t1
C00HBa0205L07.1	AUGUSTUS_tom_cdna	stop_codon	73916	73918	.	+	0	Parent=g1.t1
# protein sequence = [MNSISAREQRKPVKRKSYKDKDNMSWFLGFFLNVPLNYANNFAAEEPAIIVQMALRWRNIAPKDIGIHLERPPHFSPV]
# 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 g1
###
# command line:
# /usr/bin/augustus.real --species=tomato --hintsfile=/tmp/bac-submission-temp-C00HBa0205L07-2MrjM/AUGUSTUS_tom_cdna/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00HBa0205L07-2MrjM/AUGUSTUS_tom_cdna/seq_with_defline_removed