##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-C04HBa0021K21-4fg9A/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-C04HBa0021K21-4fg9A/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 = 122627, name = C04HBa0021K21.1) -----
#
# Constraints/Hints:
C04HBa0021K21.1	AUGUSTUS_tom_ugs_hint	ep	12374	12429	0	.	.	grp=SGN-U332989;pri=4;src=E "100;1;0:0"
C04HBa0021K21.1	AUGUSTUS_tom_ugs_hint	ep	31013	31022	0	.	.	grp=SGN-U342126;pri=4;src=E "100;1;0:0"
C04HBa0021K21.1	AUGUSTUS_tom_ugs_hint	ep	93454	93468	0	.	.	grp=SGN-U321136;pri=4;src=E "100;1;0:0"
# Predicted genes for sequence number 1 on both strands
###
C04HBa0021K21.1	AUGUSTUS_tom_ugs	gene	202	11103	1	-	.	ID=g1
C04HBa0021K21.1	AUGUSTUS_tom_ugs	transcript	202	11103	.	-	.	ID=g1.t1;Parent=g1
C04HBa0021K21.1	AUGUSTUS_tom_ugs	CDS	202	408	.	-	2	ID=g1.t1.cds;Parent=g1.t1
C04HBa0021K21.1	AUGUSTUS_tom_ugs	CDS	11067	11103	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0021K21.1	AUGUSTUS_tom_ugs	start_codon	11101	11103	.	-	0	Parent=g1.t1
# protein sequence = [MTFDQYGPLVDYTPAALATLSATSSCCPRDPLRCQLSQQQQHCPCNPLRRQSRSSITALATLSLIASNAAAAVASAVP
# PSP]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/2
# 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
###
###
C04HBa0021K21.1	AUGUSTUS_tom_ugs	gene	44525	45343	1	-	.	ID=g2
C04HBa0021K21.1	AUGUSTUS_tom_ugs	transcript	44525	45343	.	-	.	ID=g2.t1;Parent=g2
C04HBa0021K21.1	AUGUSTUS_tom_ugs	stop_codon	44525	44527	.	-	0	Parent=g2.t1
C04HBa0021K21.1	AUGUSTUS_tom_ugs	CDS	44525	45343	.	-	0	ID=g2.t1.cds;Parent=g2.t1
C04HBa0021K21.1	AUGUSTUS_tom_ugs	start_codon	45341	45343	.	-	0	Parent=g2.t1
# protein sequence = [MHPEIVTEEFEAKLQVKEDEPKIDLEEEDDDEENDHEIELVDATEEDFSFVCGVLTSPVAAAEAFDNGQIRPFFPLFN
# QDLLLSDIDFQHLKKRAPVNKVFIETDNSNNPPITTSDEEISGPYCEWSKKTTNINNSAENKSTCKKSNSTGFSKLWRFRDFMNRSNSDGRDAFVYLN
# NNSSTTRSSMSNVNKKEDKVVVTEKKEKSSGDGVVKLVTQNKKNIKKSEAVLAHEVYMRSKAKHEERRRSYLPYRPDLVGFFTNVNGGLTRNVHPF]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/1
# CDS introns: 0/0
# 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-C04HBa0021K21-4fg9A/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C04HBa0021K21-4fg9A/AUGUSTUS_tom_ugs/seq_with_defline_removed