##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-C07HBa0103N02-hOaws/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-C07HBa0103N02-hOaws/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 = 17802, name = C07HBa0103N02.1) -----
#
# Set orientation to reverse for hint group HintGroup SGN-U315903, 235-5947, priority= 4 21 features
# Set orientation to forward for hint group HintGroup SGN-U320751, 15029-17351, priority= 4 5 features
# Forced unstranded hint group to the only possible strand for 2 groups.

# Constraints/Hints:
# Predicted genes for sequence number 1 on both strands
###
C07HBa0103N02.1	AUGUSTUS_tom_ugs	gene	457	5742	1	-	.	ID=g1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	transcript	457	5742	.	-	.	ID=g1.t1;Parent=g1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	stop_codon	457	459	.	-	0	Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	457	717	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	1206	1263	.	-	1	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	1540	1640	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	2603	2743	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	3334	3462	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	3624	3728	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	3889	3990	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	4487	4644	.	-	2	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	4761	4890	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	5156	5289	.	-	2	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	5634	5742	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	start_codon	5740	5742	.	-	0	Parent=g1.t1
# protein sequence = [MYNTRPKRNPQGHIIKHDLQSKELPSTRIQPDRRWFGNTRVVNQKELEFFREELQTRLSSNYNVILKERKLPMSLLND
# HQKQVKVHLLDNEPFADAFGPKTKRKRPKLMALDYEALVKKVDVSHDDFEDKHGASTSMDENADGFRDLVRHTMFEKGQSKRIWSELYKVIDSSDVVI
# QVLDARDPCGTRCYHLEKHLKENCKHKHMVLLLNKCDLVPAWATKGWLRVLSREYPTLAFHASVTKSFGKGSLLSVLRQFSRLKSDKQAISVGFIGYP
# NVGKSSVINTLRTKNVCKVAPIPGETKVWQYITLTKRIFLIDCPGVVYQNHDSETDIVLKGVVRVTNLPDASEHISEVLNRVKKEHLKRAYKIENWVD
# EYDFLQQLCKSSGKLLKGGEPDYNTAAKMVLHDWQRGNIPFFVPPPKLDDEPNELVAEADTAVDNDQATAALKAIADVVSSQQLKEVPVQEELFSKAE
# LLGEN]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 11/11
#      E:  11 
# CDS introns: 10/10
#      E:  10 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 1
#      E:   1 (SGN-U335500)
# incompatible hint groups: 2
#      E:   2 (SGN-U315903,SGN-U327157)
###
###
C07HBa0103N02.1	AUGUSTUS_tom_ugs	gene	9905	11712	1	-	.	ID=g2
C07HBa0103N02.1	AUGUSTUS_tom_ugs	transcript	9905	11712	.	-	.	ID=g2.t1;Parent=g2
C07HBa0103N02.1	AUGUSTUS_tom_ugs	stop_codon	9905	9907	.	-	0	Parent=g2.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	9905	10089	.	-	2	ID=g2.t1.cds;Parent=g2.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	10649	10700	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	11324	11374	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	CDS	11593	11712	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C07HBa0103N02.1	AUGUSTUS_tom_ugs	start_codon	11710	11712	.	-	0	Parent=g2.t1
# protein sequence = [MMENQSLCDDNMEEAEYVLLDLDDLPCEVYIPPNAPYVLSGLDTLNPILTIDGKIKLIGQYDETIGTCLVFDEKDTPP
# EEAGPSEANLCPGRPTLDPKQTKSKQVKPVTQLQKILKFKLLQNSETEDAREKPKED]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/4
# CDS introns: 0/3
# 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-C07HBa0103N02-hOaws/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C07HBa0103N02-hOaws/AUGUSTUS_tom_ugs/seq_with_defline_removed