##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-C00SLm0132P07-KRTV8/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 = 108711, name = C00SLm0132P07.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C00SLm0132P07.1	AUGUSTUS_ab_initio	gene	54927	57161	0.6	-	.	ID=g1
C00SLm0132P07.1	AUGUSTUS_ab_initio	transcript	54927	57161	0.6	-	.	ID=g1.t1;Parent=g1
C00SLm0132P07.1	AUGUSTUS_ab_initio	stop_codon	54927	54929	.	-	0	Parent=g1.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	55342	56235	0.96	-	.	Parent=g1.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	54927	55341	0.96	-	1	ID=g1.t1.cds;Parent=g1.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	56236	57161	0.6	-	0	ID=g1.t1.cds;Parent=g1.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	start_codon	57159	57161	.	-	0	Parent=g1.t1
# protein sequence = [MTNKYLNLRFKFGGILVSEVGPVYVGGRTEYVENGDEDHLSIIELADYAKPFGISKLGKTYASPSLGGDLVELKNDMG
# ICSMALFMHDGDTIDIYVCDSTILDDVGPSEGQNSQILSQVVESFNSHGESLTAKPKKSDLGLGSSSSFPATERLENDGVARVEQESDDDYSSLDWTD
# TEEEVEPTVQQGTEPSIQQEVEPITQENVDEDIDSDSVCSDQSIDYRSDVHEELRIVKEDVRKLRESRRRNKKEKPKGFFLGKVGFDEGYEDIEKGKK
# NFKVSSQRRSHTMTVLTVIVFKVMKKNLFLMMNLKSRAFAETWTDGIFPMAMMVFNTNVTRSMQCNIEWNGDVGFEVLEGVYKHTANLGQQKCSCRSW
# ELKGIPCAQAIAAMNHLNMDASQAISSWYRKDTYMKTYSHFIQPVPNMEIWPESRNPMVEPPEARQMPGRPPKN]
# end gene g1
###
# start gene g2
C00SLm0132P07.1	AUGUSTUS_ab_initio	gene	83923	97618	0.08	+	.	ID=g2
C00SLm0132P07.1	AUGUSTUS_ab_initio	transcript	83923	97618	0.08	+	.	ID=g2.t1;Parent=g2
C00SLm0132P07.1	AUGUSTUS_ab_initio	start_codon	83923	83925	.	+	0	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	84319	86399	0.74	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	86627	86757	0.92	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	87125	89908	0.34	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	89991	92904	0.45	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	93039	93215	0.5	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	93261	93371	0.73	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	93519	94900	0.71	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	95039	95127	0.95	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	95162	97439	0.45	+	.	Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	83923	84318	0.92	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	86400	86626	0.99	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	86758	87124	0.47	+	1	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	89909	89990	0.42	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	92905	93038	0.44	+	2	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	93216	93260	0.72	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	93372	93518	0.8	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	94901	95038	0.81	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	95128	95161	0.94	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	97440	97618	0.51	+	2	ID=g2.t1.cds;Parent=g2.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	stop_codon	97616	97618	.	+	0	Parent=g2.t1
# protein sequence = [MNSPATLRYLSTSSSFRKPNFFAKQLVFNDKLPSSCKFPPNHKSFKLITANTFFRTKIPVRSNRIRTSSNDSQSVQQQ
# GSFVEFITSERVKVVAMLALSLALCNADRVVMSVAIVPLSLSHGWRQSFAGVVQSSFLWGYLISPIAGGTLVDYYGGKLVMAWGVALWSMATLLTPWA
# AEVSLWALLAMRMLLGIAEGVALPCMNNMIARWFPPTERSRAVGLAMAGFQLGSAIGLTFSPILMSQGGLFGPFVIFGLSGFLWVLVWVSATSSTPEH
# SRQISIHELRYIQNKGQIHNIVEGKSKSSKGIPPFRRLLSKLPTWSIIVANAMHSWPCKACHFVWHFDPPDLLPRPFEVLNATVSCYDSEIDDVWVLY
# GRRNRRKEKKFSGSLAYIVVRASDCANLQEGFFVILSWMPIYFKTIYHVDLRQAAWFSAVPWSMMALTGYFAGFLSDMMIQRGISVTLTRKVMQSVGF
# FGPGFSLIGLTTAPSPSIASAWLTLAVGLKAFSHCGFLVNLQEIAPQYSGVLHVHQIVAGMILQLLLFFACNPASSQLYKASAILPGMTYEMFLSLRN
# RLYNWPVTLHWRNK]
# end gene g2
###
# start gene g3
C00SLm0132P07.1	AUGUSTUS_ab_initio	gene	100776	101704	0.31	-	.	ID=g3
C00SLm0132P07.1	AUGUSTUS_ab_initio	transcript	100776	101704	0.31	-	.	ID=g3.t1;Parent=g3
C00SLm0132P07.1	AUGUSTUS_ab_initio	stop_codon	100776	100778	.	-	0	Parent=g3.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	intron	101006	101580	0.53	-	.	Parent=g3.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	100776	101005	0.6	-	2	ID=g3.t1.cds;Parent=g3.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	CDS	101581	101704	0.33	-	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0132P07.1	AUGUSTUS_ab_initio	start_codon	101702	101704	.	-	0	Parent=g3.t1
# protein sequence = [MSGLHVTWRKSFLYPINEVPNMENLKLILGGEVGALPTTYLGNLETLFPDINTLVLRQQNTIVELWTSHGWNNIFRRH
# LNDWAIPRVTEFFSVIEQFSGLETGKDILQWLREQYWDC]
# end gene g3
###
# command line:
# /usr/bin/augustus.real --species=tomato --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00SLm0132P07-KRTV8/AUGUSTUS_ab_initio/seq_with_defline_removed