##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-C10HBa0306E10-JCcni/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 = 147507, name = C10HBa0306E10.1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
C10HBa0306E10.1	AUGUSTUS_ab_initio	gene	33515	35715	0.21	-	.	ID=g1
C10HBa0306E10.1	AUGUSTUS_ab_initio	transcript	33515	35715	0.21	-	.	ID=g1.t1;Parent=g1
C10HBa0306E10.1	AUGUSTUS_ab_initio	stop_codon	33515	33517	.	-	0	Parent=g1.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	33767	34064	0.23	-	.	Parent=g1.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	34680	35697	0.95	-	.	Parent=g1.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	33515	33766	0.26	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	34065	34679	0.79	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	35698	35715	0.95	-	0	ID=g1.t1.cds;Parent=g1.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	start_codon	35713	35715	.	-	0	Parent=g1.t1
# protein sequence = [MSRVAAVEERGTDARRNLLKISSNGKSLLRNVNTTTAYVAAVLRRDRIEVDSGCFYGWCPNLKSRYSISTGANKITVD
# LIELQTERNKPDLISFDRPIQSEDIPSNNGEVFDSRKLKEEEAMAAWCLFKDKAGDSVDVPSIHGTTKDVAREFKGLPLAIIIVAGARKRKIKPSWED
# SLRKLRRAEARNIHGVYEKVYKCLRRSYDHLGENENVKFLCLFDCDLVTHLSKRTHEVIKFPNLYYLELGHLGCLTHICSDNVERIEFPPLQTMFFFE
# LPEFQNFTPTANNSNHLFDE]
# end gene g1
###
# start gene g2
C10HBa0306E10.1	AUGUSTUS_ab_initio	gene	43059	44403	0.27	-	.	ID=g2
C10HBa0306E10.1	AUGUSTUS_ab_initio	transcript	43059	44403	0.27	-	.	ID=g2.t1;Parent=g2
C10HBa0306E10.1	AUGUSTUS_ab_initio	stop_codon	43059	43061	.	-	0	Parent=g2.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	43273	43505	0.57	-	.	Parent=g2.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	43641	44374	0.29	-	.	Parent=g2.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	43059	43272	0.99	-	1	ID=g2.t1.cds;Parent=g2.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	43506	43640	0.55	-	1	ID=g2.t1.cds;Parent=g2.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	44375	44403	0.79	-	0	ID=g2.t1.cds;Parent=g2.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	start_codon	44401	44403	.	-	0	Parent=g2.t1
# protein sequence = [MQIAKFELTNFDHISSPCWLHSQEFGACVVPPQVPSKEVRISALSKSTGKPTVQCSFAVTHNGDNQGDETAGNGDSLN
# EQEYRRTIELEAEERKLEGTLEYQRQMENDAKLKHLAEQTKRTAKTC]
# end gene g2
###
# start gene g3
C10HBa0306E10.1	AUGUSTUS_ab_initio	gene	68754	70759	0.94	-	.	ID=g3
C10HBa0306E10.1	AUGUSTUS_ab_initio	transcript	68754	70759	0.94	-	.	ID=g3.t1;Parent=g3
C10HBa0306E10.1	AUGUSTUS_ab_initio	stop_codon	68754	68756	.	-	0	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	68792	68873	0.98	-	.	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	69193	69286	1	-	.	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	69333	70128	0.98	-	.	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	70201	70315	1	-	.	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	70443	70523	0.99	-	.	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	70629	70713	1	-	.	Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	68754	68791	0.97	-	2	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	68874	69192	1	-	0	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	69287	69332	1	-	1	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	70129	70200	0.98	-	1	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	70316	70442	1	-	2	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	70524	70628	0.99	-	2	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	70714	70759	1	-	0	ID=g3.t1.cds;Parent=g3.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	start_codon	70757	70759	.	-	0	Parent=g3.t1
# protein sequence = [MSIAYGIQGQLLEVTVVACNKLKDTEWISRQDPYVCLEYGSSKFRTRTCTDGGKNPTFQEKFVFKLIEGLREINVVVW
# NSNTVNSDDFIGSGKVQLQKVLSQGFDDTAWPLQRKNGRHAGEVRLIMHYANTNKPATSHAQSGPPFVTPTPGSYPYSVAPPHVASHPTPSGYPAPSP
# YSTASPPSAFYPASPYSTVPPPPAAYHSTSLYPPQSAAYPSPYSSSAYLPQPYPPQGYSYPPGQYPGVYPPRSY]
# end gene g3
###
# start gene g4
C10HBa0306E10.1	AUGUSTUS_ab_initio	gene	93911	97208	0.59	-	.	ID=g4
C10HBa0306E10.1	AUGUSTUS_ab_initio	transcript	93911	97208	0.59	-	.	ID=g4.t1;Parent=g4
C10HBa0306E10.1	AUGUSTUS_ab_initio	stop_codon	93911	93913	.	-	0	Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	93961	94897	0.73	-	.	Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	95274	95551	0.93	-	.	Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	95645	96236	0.86	-	.	Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	96441	96517	0.98	-	.	Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	96730	96832	0.99	-	.	Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	93911	93960	0.74	-	2	ID=g4.t1.cds;Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	94898	95273	0.79	-	0	ID=g4.t1.cds;Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	95552	95644	0.94	-	0	ID=g4.t1.cds;Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	96237	96440	0.97	-	0	ID=g4.t1.cds;Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	96518	96729	0.99	-	2	ID=g4.t1.cds;Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	96833	97208	0.99	-	0	ID=g4.t1.cds;Parent=g4.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	start_codon	97206	97208	.	-	0	Parent=g4.t1
# protein sequence = [MSQQETSKRTKKAKKKTFAKPGSLSFLANKKRLLLTTNEIIKEIECEKGHLLKLIGAEQSVAPQSEAKRQSVEKLPFE
# NQPIEELPVVQPVEELPLEQHGKDFTFEDQVQMNSFTPRTNDQPKEQGRTQMHDVHARKERKLIILNSQNQPVGPTDDVVIELSSFLGTLARNATLCP
# FDILDWRSMDTKKDLWYHTKGKYIIPEVAYHWAMVKIRDAWRRHRSNLKLNYYDPYDNDTIRMAKKPGHIPECQFRELLKYWNSEKFKKMSETNAMNR
# KKLMNPHTAGKKSFALVRNKLPEMEEIQKQISINDEYVDAFSSVMGHEHPGRLTLYGAGVTKTTLKKKVGNLESILSATTDGMQQMQEKMQKMEKQME
# EQKKIVRQEVIVDVIAQLKHAGLIYPNILEALSTPSPRESTFVQGAKQGDEIEEGDESSSEDLT]
# end gene g4
###
# start gene g5
C10HBa0306E10.1	AUGUSTUS_ab_initio	gene	97809	98117	0.97	-	.	ID=g5
C10HBa0306E10.1	AUGUSTUS_ab_initio	transcript	97809	98117	0.97	-	.	ID=g5.t1;Parent=g5
C10HBa0306E10.1	AUGUSTUS_ab_initio	stop_codon	97809	97811	.	-	0	Parent=g5.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	97809	98117	0.97	-	0	ID=g5.t1.cds;Parent=g5.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	start_codon	98115	98117	.	-	0	Parent=g5.t1
# protein sequence = [MWKIRLRKNVYYGRNKVPVDLYDLEEENCPNIEETFLREPNDDFGSSERLVDVDVRWSREDLPVDIIDALSIAQHSPD
# EAMETSEEEDDFDDTDWDWMEVDY]
# end gene g5
###
# start gene g6
C10HBa0306E10.1	AUGUSTUS_ab_initio	gene	102383	103944	0.77	+	.	ID=g6
C10HBa0306E10.1	AUGUSTUS_ab_initio	transcript	102383	103944	0.77	+	.	ID=g6.t1;Parent=g6
C10HBa0306E10.1	AUGUSTUS_ab_initio	start_codon	102383	102385	.	+	0	Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	102514	102737	1	+	.	Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	102780	102858	1	+	.	Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	102968	103713	0.92	+	.	Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	intron	103793	103876	0.78	+	.	Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	102383	102513	1	+	0	ID=g6.t1.cds;Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	102738	102779	1	+	1	ID=g6.t1.cds;Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	102859	102967	1	+	1	ID=g6.t1.cds;Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	103714	103792	0.79	+	0	ID=g6.t1.cds;Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	CDS	103877	103944	0.79	+	2	ID=g6.t1.cds;Parent=g6.t1
C10HBa0306E10.1	AUGUSTUS_ab_initio	stop_codon	103942	103944	.	+	0	Parent=g6.t1
# protein sequence = [MTTTIAIEDVRREVKILRALTGHRNLVQFYDAYEDEENVYIVMELCKGGELLDWILARGGKYSEDDAKAVMVQLLSVV
# SYCHLQQVVHRDLKPENFLFVSKDENSPLKDIDFILSDYVKPYERLNDIVGSELCVTVYAYSDS]
# end gene g6
###
# command line:
# /usr/bin/augustus.real --species=tomato --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C10HBa0306E10-JCcni/AUGUSTUS_ab_initio/seq_with_defline_removed