##gff-version 3
# This output was generated with AUGUSTUS (version 2.0.2).
# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mstanke@gwdg.de).
# Please cite: Mario Stanke and Stephan Waack (2003) "Gene prediction with a hidden Markov model and
# a new intron submodel", Bioinformatics, Vol. 19 Suppl. 2, ii215-ii225
# reading in the file /tmp/bac-submission-temp-C04HBa0006E18-8eiFj/AUGUSTUS_tom_ugs/hints.gff ...
# Sources of extrinsic information: M E 
# Have extrinsic information about 1 sequences (in the specified range). 
# Initialising the parameters ...
# human version. Use default transition matrix.
# Looks like /tmp/bac-submission-temp-C04HBa0006E18-8eiFj/AUGUSTUS_tom_ugs/seq_with_defline_removed is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 120037, name = C04HBa0006E18.1) -----
#
# Set orientation to forward for hint group HintGroup SGN-U316570, 69933-72514, priority= 4 7 features
# Set orientation to forward for hint group HintGroup SGN-U316571, 72210-74826, priority= 4 3 features
# Forced unstranded hint group to the only possible strand for 2 groups.

# Constraints/Hints:
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	ep	69934	70224	0	+	.	grp=SGN-U316570;pri=4;src=E "100;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	ep	71850	72228	0	.	.	grp=SGN-U335736;pri=4;src=E "65.7933;1;0:1"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	ep	72201	72515	0	+	.	grp=SGN-U316570;pri=4;src=E "100;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	ep	72211	73166	0	+	.	grp=SGN-U316571;pri=4;src=E "100;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	ep	74397	74827	0	+	.	grp=SGN-U316571;pri=4;src=E "100;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	exon	70309	70986	0	+	.	grp=SGN-U316570;pri=4;src=E "1000;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	exon	71151	71306	0	+	.	grp=SGN-U316570;pri=4;src=E "1000;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	intron	70225	70308	0	+	.	grp=SGN-U316570;pri=4;src=E "10411.3;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	intron	70987	71150	0	+	.	grp=SGN-U316570;pri=4;src=E "10818.8;1;0:0"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	intron	71307	72200	0	+	.	grp=SGN-U316570;pri=4;src=E "6393.6;1;0:1"
C04HBa0006E18.1	AUGUSTUS_tom_ugs_hint	intron	73167	74396	0	+	.	grp=SGN-U316571;pri=4;src=E "18044.5;1;0:0"
# Predicted genes for sequence number 1 on both strands
###
C04HBa0006E18.1	AUGUSTUS_tom_ugs	gene	70018	74438	1	+	.	ID=g1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	transcript	70018	74438	.	+	.	ID=g1.t1;Parent=g1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	start_codon	70018	70020	.	+	0	Parent=g1.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	70018	70224	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	70309	70986	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	71151	71306	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	72201	73166	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	74397	74438	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	stop_codon	74436	74438	.	+	0	Parent=g1.t1
# protein sequence = [MDSSRRAVESYWRSRMIDGATSDEDKVTPVYKLEEICELLRSSHSSIVKEVSEFILKRLQHKSPIVKQKALRVIKYAV
# GKSCPEFTREMQRNSVAIRQLIHYKGQPDPLKADALNKAVRETAQEALSALFSSQDTKPPTENLNLGGRIQGFGNTSYEIHDDKRSFLSDVVGATIKQ
# GLNTLTQSPPLKKNDTGTYTSPNLQSSLTTQPDTSHNHTSRFSTNPASATWTHTETTTKPHSAEKTREDRLLETIATSGGVRLQPTRDALQVFLLEAS
# KLDALALTHALESKLQSPSWQVRVKAICVLEAILRKKDDAHFGTMASYFTENRDVVVKCYESPQASLREKANKVLSLLNDGQTADAVAHVDRSANACN
# PVVQMPDLIDTDNSDYLFGTDNLTNMQSSEGIKIASTSATPLMDDLFGDKSGSSFSSSQKKNDDDPFADVSFHISNEKAPEADLFSGMTVDKSDATEI
# HSVNNRNGPELFDIFGSSVEVPREPNNSRKDVPDLMNSLSLNGNESSMEQNGSSGATPYQNIFQEPTIDPCHHASNDVMNSILSSQAGGVNANPMFPL
# GSMQYNLPPGFVLNPSFAPQALNYNAMGNIFAQQQLLATLSSYQQLGSMHSSTSASHAADSAEVYGSALPDIFNASISKQTPTSLMNTSKKEGTKAFD
# FISDHLAAARDPKRVI]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 5/5
#      E:   5 
# CDS introns: 4/4
#      E:   4 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 3
#      E:   3 (SGN-U316570,SGN-U335736,SGN-U316571)
###
###
C04HBa0006E18.1	AUGUSTUS_tom_ugs	gene	83170	83899	1	-	.	ID=g2
C04HBa0006E18.1	AUGUSTUS_tom_ugs	transcript	83170	83899	.	-	.	ID=g2.t1;Parent=g2
C04HBa0006E18.1	AUGUSTUS_tom_ugs	stop_codon	83170	83172	.	-	0	Parent=g2.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	83170	83400	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	83556	83711	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	CDS	83852	83899	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C04HBa0006E18.1	AUGUSTUS_tom_ugs	start_codon	83897	83899	.	-	0	Parent=g2.t1
# protein sequence = [MHPEHQLGVDINLEVEILAAIGDRRQASAAVVPAPAPALQVQPPPVHVAAPPDLEVREMPLRDKKMFKEWWRTYQESR
# PVRSPPICWREFSESFLARFMPQSVRDRLSDQISRLELGFMTVSKYEVRFHELSQHVTMILPTEER]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/3
# CDS introns: 0/2
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 0
###
# command line:
# /usr/bin/augustus.real --species=human --hintsfile=/tmp/bac-submission-temp-C04HBa0006E18-8eiFj/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C04HBa0006E18-8eiFj/AUGUSTUS_tom_ugs/seq_with_defline_removed