##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-C03HBa0013A17-4qf6j/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 = 161619, name = C03HBa0013A17.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C03HBa0013A17.1	AUGUSTUS_ab_initio	gene	2482	22337	0.14	-	.	ID=g1
C03HBa0013A17.1	AUGUSTUS_ab_initio	transcript	2482	22337	0.14	-	.	ID=g1.t1;Parent=g1
C03HBa0013A17.1	AUGUSTUS_ab_initio	stop_codon	2482	2484	.	-	0	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	2667	8229	0.84	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	8315	8714	0.66	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	8768	9611	0.67	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	9829	13406	0.51	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	13504	19495	0.5	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	19580	19657	0.99	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	19780	22112	0.94	-	.	Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	2482	2666	0.92	-	2	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	8230	8314	0.86	-	0	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	8715	8767	0.69	-	2	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	9612	9828	0.88	-	0	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	13407	13503	0.92	-	1	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	19496	19579	0.53	-	1	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	19658	19779	1	-	0	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	22113	22337	0.72	-	0	ID=g1.t1.cds;Parent=g1.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	start_codon	22335	22337	.	-	0	Parent=g1.t1
# protein sequence = [MATSLQNLVPPFSCRRTTYTSPCTPIAIFRGGRRRNARKMLRVCRAMVEKTVQGASSTFAKEMERLSAKESLLLAFKD
# AGGFEALVTGKTTDVQCIDVNERIISLEKLNPTPRPSTSPNLEGRWNFEWFGAGSPVLLLAKIFFGRIPPTLANLSKLDVLIKDGCGTATAQVKILNS
# IENKFIISTKYSVEGPLRMKEEYVEGEFESPKVDEEAVPEQLRGAFGQAFNTLQQLPVPIRDAVSSGMKVSLSGTFQRLILISYLDDEILIIRNTAGE
# PEVLTRLEAGPDPQNITEYESHANRLGDDEIEQRSSQGRPIDLERPPRHPPVGFGEIWASNRDIPSVSNKNWSSKFKFGWA]
# end gene g1
###
# start gene g2
C03HBa0013A17.1	AUGUSTUS_ab_initio	gene	64685	65005	0.68	-	.	ID=g2
C03HBa0013A17.1	AUGUSTUS_ab_initio	transcript	64685	65005	0.68	-	.	ID=g2.t1;Parent=g2
C03HBa0013A17.1	AUGUSTUS_ab_initio	stop_codon	64685	64687	.	-	0	Parent=g2.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	64685	65005	0.68	-	0	ID=g2.t1.cds;Parent=g2.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	start_codon	65003	65005	.	-	0	Parent=g2.t1
# protein sequence = [MSSSGGRKDAKRVSCWCFLLLQPYEDMDEGRTMKRGRVLPIRSMYLDVSEAQFLTPMFTPFGIKSVGEIVVLGVIDAV
# EIIVYHRACIAALSHVSLLRSFTLGLLE]
# end gene g2
###
# start gene g3
C03HBa0013A17.1	AUGUSTUS_ab_initio	gene	76731	77168	0.83	+	.	ID=g3
C03HBa0013A17.1	AUGUSTUS_ab_initio	transcript	76731	77168	0.83	+	.	ID=g3.t1;Parent=g3
C03HBa0013A17.1	AUGUSTUS_ab_initio	start_codon	76731	76733	.	+	0	Parent=g3.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	76731	77168	0.83	+	0	ID=g3.t1.cds;Parent=g3.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	stop_codon	77166	77168	.	+	0	Parent=g3.t1
# protein sequence = [MGTGKKKIEMEKITKKSCRMVTFSKRRNGLFKKNEELESLTGSQVSSVVLSPAGRIYTYGDVNTAINMHFSKIDCMRQ
# SDSDVVVSSGSSELRSSSKSLRDWLEDIDVEQCQNLNQLLLLKEQLEGTKKKIVSIEDSKSFQALFM]
# end gene g3
###
# start gene g4
C03HBa0013A17.1	AUGUSTUS_ab_initio	gene	79854	87287	0.05	-	.	ID=g4
C03HBa0013A17.1	AUGUSTUS_ab_initio	transcript	79854	87287	0.05	-	.	ID=g4.t1;Parent=g4
C03HBa0013A17.1	AUGUSTUS_ab_initio	stop_codon	79854	79856	.	-	0	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	79915	82520	0.46	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	82580	82700	0.84	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	82842	82927	1	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	83064	83225	0.98	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	83303	83641	0.45	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	83748	83871	0.62	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	83922	84095	0.71	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	84189	85922	0.72	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	86055	86566	0.6	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	86708	87185	0.54	-	.	Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	79854	79914	0.75	-	1	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	82521	82579	0.69	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	82701	82841	0.96	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	82928	83063	1	-	1	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	83226	83302	0.83	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	83642	83747	0.41	-	1	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	83872	83921	0.72	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	84096	84188	0.99	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	85923	86054	0.58	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	86567	86707	0.59	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	87186	87287	0.69	-	0	ID=g4.t1.cds;Parent=g4.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	start_codon	87285	87287	.	-	0	Parent=g4.t1
# protein sequence = [MLAAHRLVDSTIVFIMLQPRSAQSYHVSALETTLVSDIELAVQVENNQNLLRTEAFNWSFSLLFSPALSFVSLPTKSF
# FMPGNIRKINFCQFCGGPNKHEIPDGEEKVRAICTHCGKITYENPKMIDEWSVSWETRSHNSSQSRRYTRSELTLSRHAQGITVNPEYVLVGDSRFLL
# GLCNSEVKETIETLFCFMLYFGIMVWELAKLQVVGCLIEHDKKILMCRRKIHPSYGLWTLPAGYMEIGESAAEGAIRETWEEANAEVEVQSLFAQLDI
# PLIGQTYMIFLAKLKNPHFSPGPESSECQLFELDDIPFDSLAFSSMLVSLNLYIEDIKVGRPKFHYGVINKRPGTSPSDIHAYTLDFHMQS]
# end gene g4
###
# start gene g5
C03HBa0013A17.1	AUGUSTUS_ab_initio	gene	88054	88684	0.46	+	.	ID=g5
C03HBa0013A17.1	AUGUSTUS_ab_initio	transcript	88054	88684	0.46	+	.	ID=g5.t1;Parent=g5
C03HBa0013A17.1	AUGUSTUS_ab_initio	start_codon	88054	88056	.	+	0	Parent=g5.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	intron	88225	88513	0.53	+	.	Parent=g5.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	88054	88224	0.84	+	0	ID=g5.t1.cds;Parent=g5.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	CDS	88514	88684	0.52	+	0	ID=g5.t1.cds;Parent=g5.t1
C03HBa0013A17.1	AUGUSTUS_ab_initio	stop_codon	88682	88684	.	+	0	Parent=g5.t1
# protein sequence = [MKSPQMGKDEGQRRQSLCSELGGAGPLTFNLESPNLGCDAGEGGLRCTQQRTSKDQEPIFPTHEKSEEEEAIVKNPEI
# SEIPQPWEDSGMQESAMLKSEENNSSLTTFEMQYL]
# end gene g5
###
# command line:
# /usr/bin/augustus.real --species=tomato --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C03HBa0013A17-4qf6j/AUGUSTUS_ab_initio/seq_with_defline_removed