##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-C04HBa0204I09-GnK0o/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-C04HBa0204I09-GnK0o/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 = 139577, name = C04HBa0204I09.1) -----
#
# Set orientation to forward for hint group HintGroup SGN-U312463, 38539-41704, priority= 4 7 features
# Delete group HintGroup SGN-U333592, 38567-38707, priority= 4 2 features
# Forced unstranded hint group to the only possible strand for 1 groups.
# Deleted 1 groups because some hint was not satisfiable.

# Constraints/Hints:
# Predicted genes for sequence number 1 on both strands
###
C04HBa0204I09.1	AUGUSTUS_tom_ugs	gene	38621	41720	1	+	.	ID=g1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	transcript	38621	41720	.	+	.	ID=g1.t1;Parent=g1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	start_codon	38621	38623	.	+	0	Parent=g1.t1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	CDS	38621	38717	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	CDS	39611	39681	.	+	2	ID=g1.t1.cds;Parent=g1.t1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	CDS	39871	39990	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	CDS	41598	41720	.	+	0	ID=g1.t1.cds;Parent=g1.t1
C04HBa0204I09.1	AUGUSTUS_tom_ugs	stop_codon	41718	41720	.	+	0	Parent=g1.t1
# protein sequence = [MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSN
# DRDRVVEARDELHRMLNEDELRDVVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHW]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 4/4
#      E:   4 
# CDS introns: 3/3
#      E:   3 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 1
#      E:   1 (SGN-U333587)
# incompatible hint groups: 1
#      E:   1 (SGN-U312463)
###
# command line:
# /usr/bin/augustus.real --species=human --hintsfile=/tmp/bac-submission-temp-C04HBa0204I09-GnK0o/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C04HBa0204I09-GnK0o/AUGUSTUS_tom_ugs/seq_with_defline_removed