##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-C00SLm0078A08-kQyks/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 = 168571, name = C00SLm0078A08.2) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C00SLm0078A08.2	AUGUSTUS_ab_initio	gene	50192	51082	0.65	+	.	ID=g1
C00SLm0078A08.2	AUGUSTUS_ab_initio	transcript	50192	51082	0.65	+	.	ID=g1.t1;Parent=g1
C00SLm0078A08.2	AUGUSTUS_ab_initio	start_codon	50192	50194	.	+	0	Parent=g1.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	50358	50603	0.65	+	.	Parent=g1.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	50192	50357	0.99	+	0	ID=g1.t1.cds;Parent=g1.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	50604	51082	0.65	+	2	ID=g1.t1.cds;Parent=g1.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	stop_codon	51080	51082	.	+	0	Parent=g1.t1
# protein sequence = [MAGNPADERFRPPDPPLGTGNPIVQSKIHEVAEESLSTSSQATVEAEIDASHHNLETGIAQQEQRNRDGQQQQGHRPV
# QNPQSIPNLKKEKEITQQFQRPTRIQDSREAVHLAKNSHPAMHSSELAIRSDNGQGNTSLPNFNSKNDGVLKEIDRTTAEHDYHNNFPKVSSNFDRPV
# SKKVNEKNDQPPNNNFNKKDHIPEPAPYTIVQTYADRL]
# end gene g1
###
# start gene g2
C00SLm0078A08.2	AUGUSTUS_ab_initio	gene	51806	52819	0.94	+	.	ID=g2
C00SLm0078A08.2	AUGUSTUS_ab_initio	transcript	51806	52819	0.94	+	.	ID=g2.t1;Parent=g2
C00SLm0078A08.2	AUGUSTUS_ab_initio	start_codon	51806	51808	.	+	0	Parent=g2.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	52181	52537	1	+	.	Parent=g2.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	51806	52180	0.94	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	52538	52819	1	+	0	ID=g2.t1.cds;Parent=g2.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	stop_codon	52817	52819	.	+	0	Parent=g2.t1
# protein sequence = [MEKNKPRKDTAQNVNAELQIHKDKDNGRSDAEYNQQRHHQVDNQHQVIQQEWLTEKRRSGNQQVRFSNDRTVVHQQQP
# QTGMVPIPTKNTYIDLEVQEYNTTGDGMEAYTQQRQEQSQTYVEGIQIIKETNFDEYRKPDSEDEYDVDTHSLGDGIEPGEEITTSDQIQKGPLLSTS
# NVDEILEVSGKQGLSPRGRKLSKSIKNPSTSKPNTRARSRGN]
# end gene g2
###
# start gene g3
C00SLm0078A08.2	AUGUSTUS_ab_initio	gene	62642	68857	0.04	+	.	ID=g3
C00SLm0078A08.2	AUGUSTUS_ab_initio	transcript	62642	68857	0.04	+	.	ID=g3.t1;Parent=g3
C00SLm0078A08.2	AUGUSTUS_ab_initio	start_codon	62642	62644	.	+	0	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	62951	64174	0.45	+	.	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	64244	64323	0.45	+	.	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	64420	65679	0.71	+	.	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	65728	66178	0.72	+	.	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	66251	67450	0.35	+	.	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	67629	68744	0.37	+	.	Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	62642	62950	1	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	64175	64243	0.45	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	64324	64419	0.99	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	65680	65727	0.72	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	66179	66250	0.9	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	67451	67628	0.33	+	0	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	68745	68857	0.25	+	2	ID=g3.t1.cds;Parent=g3.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	stop_codon	68855	68857	.	+	0	Parent=g3.t1
# protein sequence = [MRTKTVVAAGFFLLLILTTSSGFQSDELLVDDEEFGLEGGIRSRSRSDPNNVNAATPQSIRKRLVSDSDSKIQFPLEH
# AFGDSNFSRAGTFTARLKSSSHGSQMQTLTKLRFSRNAFIGPEKEDFEKLLKGDDFYKIRVPSNVLNLSGREYVVSSVKARCLPRDGLEEHFLIHMDG
# VNILAVNYGSPGACQYPRQLKFVICLLIKLTSWMAYLATLHANHLHNIITLSILLKKWEFASLPSFQRLMGIRLLPYFKIMDHLLMEEAFGDEPTRTV
# SSDLARPIFQYLGPWGQFTR]
# end gene g3
###
# start gene g4
C00SLm0078A08.2	AUGUSTUS_ab_initio	gene	70362	73180	0.17	-	.	ID=g4
C00SLm0078A08.2	AUGUSTUS_ab_initio	transcript	70362	73180	0.17	-	.	ID=g4.t1;Parent=g4
C00SLm0078A08.2	AUGUSTUS_ab_initio	stop_codon	70362	70364	.	-	0	Parent=g4.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	70558	72719	0.3	-	.	Parent=g4.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	72754	73107	0.32	-	.	Parent=g4.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	70362	70557	0.32	-	1	ID=g4.t1.cds;Parent=g4.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	72720	72753	0.47	-	2	ID=g4.t1.cds;Parent=g4.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	73108	73180	0.42	-	0	ID=g4.t1.cds;Parent=g4.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	start_codon	73178	73180	.	-	0	Parent=g4.t1
# protein sequence = [MASASSPLARGEARPPCHSPLRRGDYCKMPSVFTVLESATYERGDTTIGPEVAADDREPPLEVKTKAETGHVPGHVGA
# KVDPDLSIQGTGVACCVEDIVK]
# end gene g4
###
# start gene g5
C00SLm0078A08.2	AUGUSTUS_ab_initio	gene	76956	80649	0.29	+	.	ID=g5
C00SLm0078A08.2	AUGUSTUS_ab_initio	transcript	76956	80649	0.29	+	.	ID=g5.t1;Parent=g5
C00SLm0078A08.2	AUGUSTUS_ab_initio	start_codon	76956	76958	.	+	0	Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	77006	79693	0.6	+	.	Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	79782	79859	0.98	+	.	Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	intron	80001	80529	0.58	+	.	Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	76956	77005	0.6	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	79694	79781	0.71	+	1	ID=g5.t1.cds;Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	79860	80000	0.75	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	CDS	80530	80649	0.54	+	0	ID=g5.t1.cds;Parent=g5.t1
C00SLm0078A08.2	AUGUSTUS_ab_initio	stop_codon	80647	80649	.	+	0	Parent=g5.t1
# protein sequence = [MYRLCKADSISRIELPXTPIFSEAVVGENAEGDEVQPPERSFWAKYWMYLIPLGLIVMNAMTQAMNMAEEQTSGQAGA
# QGQQAIGAQRAQNTVVVSSLLVSVFRVIMVQGHVCFEKRIDDCSPNSWCVRLER]
# end gene g5
###
# command line:
# /usr/bin/augustus.real --species=tomato --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C00SLm0078A08-kQyks/AUGUSTUS_ab_initio/seq_with_defline_removed