##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-C12HBa0079F24-qtQJ5/AUGUSTUS_tom_cdna/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-C12HBa0079F24-qtQJ5/AUGUSTUS_tom_cdna/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 = 21211, name = C12HBa0079F24.1) -----
#
# Set orientation to forward for hint group HintGroup SGN-E300172, 9560-13917, priority= 4 5 features
# Delete group HintGroup SGN-E693559, 16090-16193, priority= 4 3 features
# Delete group HintGroup SGN-E376267, 16201-18833, priority= 4 3 features
# Delete group HintGroup SGN-E556125, 16201-18839, priority= 4 4 features
# Delete group HintGroup SGN-E257293, 16201-18855, priority= 4 5 features
# Forced unstranded hint group to the only possible strand for 1 groups.
# Deleted 4 groups because some hint was not satisfiable.

# Constraints/Hints:
# Predicted genes for sequence number 1 on both strands
###
C12HBa0079F24.1	AUGUSTUS_tom_cdna	gene	8667	8709	1	+	.	ID=g1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	transcript	8667	8709	.	+	.	ID=g1.t1;Parent=g1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	8667	8709	.	+	1	ID=g1.t1.cds;Parent=g1.t1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	stop_codon	8707	8709	.	+	0	Parent=g1.t1
# protein sequence = [NFIHIYIYIYIYI]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 50
# CDS exons: 1/1
#      E:   1 
# CDS introns: 0/1
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 9
#      E:   9 (SGN-E395261,SGN-E304225,SGN-E556571,SGN-E331059,SGN-E721523,SGN-E718293,SGN-E375161,...)
# incompatible hint groups: 0
###
###
C12HBa0079F24.1	AUGUSTUS_tom_cdna	gene	9929	16282	1	+	.	ID=g2
C12HBa0079F24.1	AUGUSTUS_tom_cdna	transcript	9929	16282	.	+	.	ID=g2.t1;Parent=g2
C12HBa0079F24.1	AUGUSTUS_tom_cdna	start_codon	9929	9931	.	+	0	Parent=g2.t1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	9929	9943	.	+	0	ID=g2.t1.cds;Parent=g2.t1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	13658	13681	.	+	0	ID=g2.t1.cds;Parent=g2.t1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	16097	16282	.	+	0	ID=g2.t1.cds;Parent=g2.t1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	stop_codon	16280	16282	.	+	0	Parent=g2.t1
# protein sequence = [MADLQVYILTCFPLLMLKDLLLLDLTYLLYLCIFLMQAIQNLISSKKKKKKRKKEKEKIEDLCGHLCFSGLHGM]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 60
# CDS exons: 2/3
#      E:   2 
# CDS introns: 1/2
#      E:   1 
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 27
#      E:  27 (SGN-E234767,SGN-E549930,SGN-E229205,SGN-E374230,SGN-E546707,SGN-E744922,SGN-E736354,...)
# incompatible hint groups: 2
#      E:   2 (SGN-E300172,SGN-E311278)
###
# command line:
# /usr/bin/augustus.real --species=human --hintsfile=/tmp/bac-submission-temp-C12HBa0079F24-qtQJ5/AUGUSTUS_tom_cdna/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C12HBa0079F24-qtQJ5/AUGUSTUS_tom_cdna/seq_with_defline_removed