##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-C04SLf0138K20-bebm1/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-C04SLf0138K20-bebm1/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 = 19776, name = C04SLf0138K20.1) -----
#
# Set orientation to reverse for hint group HintGroup SGN-U313160, 521-1896, priority= 4 5 features
# Set orientation to reverse for hint group HintGroup SGN-U313162, 521-1980, 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
###
C04SLf0138K20.1	AUGUSTUS_tom_ugs	gene	513	1834	1	-	.	ID=g1
C04SLf0138K20.1	AUGUSTUS_tom_ugs	transcript	513	1834	.	-	.	ID=g1.t1;Parent=g1
C04SLf0138K20.1	AUGUSTUS_tom_ugs	CDS	513	684	.	-	2	ID=g1.t1.cds;Parent=g1.t1
C04SLf0138K20.1	AUGUSTUS_tom_ugs	CDS	1569	1716	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C04SLf0138K20.1	AUGUSTUS_tom_ugs	CDS	1802	1834	.	-	0	ID=g1.t1.cds;Parent=g1.t1
C04SLf0138K20.1	AUGUSTUS_tom_ugs	start_codon	1832	1834	.	-	0	Parent=g1.t1
# protein sequence = [MATPQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF
# NFKENTVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVR]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 83.3
# CDS exons: 3/3
#      E:   3 
# CDS introns: 2/3
#      E:   2 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 1
#      E:   1 (SGN-U313161)
# incompatible hint groups: 2
#      E:   2 (SGN-U313160,SGN-U313162)
###
# command line:
# /usr/bin/augustus.real --species=human --hintsfile=/tmp/bac-submission-temp-C04SLf0138K20-bebm1/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C04SLf0138K20-bebm1/AUGUSTUS_tom_ugs/seq_with_defline_removed