##gff-version 3
# This output was generated with AUGUSTUS (version 2.3.1).
# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mstanke@gwdg.de)
# and Oliver Keller (keller@cs.uni-goettingen.de).
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# myOrg version. Use default transition matrix.
# Looks like example2.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 9453, name = Contig4636) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig4636	AUGUSTUS	gene	836	7001	1	+	.	ID=g1
Contig4636	AUGUSTUS	transcript	836	7001	.	+	.	ID=g1.t1;Parent=g1
Contig4636	AUGUSTUS	transcription_start_site	836	836	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	exon	836	1017	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	start_codon	966	968	.	+	0	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	966	1017	.	+	0	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	CDS	1818	1934	.	+	2	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	1818	1934	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	2055	2198	.	+	2	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	2055	2198	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	2852	2995	.	+	2	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	2852	2995	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	3426	3607	.	+	2	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	3426	3607	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	4340	4423	.	+	0	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	4340	4423	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	4543	4789	.	+	0	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	4543	4789	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	5072	5358	.	+	2	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	5072	5358	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	5860	6007	.	+	0	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	5860	6007	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	CDS	6494	6903	.	+	2	ID=g1.t1.cds;Parent=g1.t1
Contig4636	AUGUSTUS	exon	6494	7001	.	+	.	Parent=g1.t1
Contig4636	AUGUSTUS	stop_codon	6901	6903	.	+	0	Parent=g1.t1
Contig4636	AUGUSTUS	transcription_end_site	7001	7001	.	+	.	Parent=g1.t1
# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
# end gene g1
###
#
# ----- prediction on sequence number 2 (length = 2344, name = Contig8198) -----
#
# Predicted genes for sequence number 2 on both strands
# start gene g2
Contig8198	AUGUSTUS	gene	421	2105	1	+	.	ID=g2
Contig8198	AUGUSTUS	transcript	421	2105	.	+	.	ID=g2.t1;Parent=g2
Contig8198	AUGUSTUS	exon	421	582	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	start_codon	445	447	.	+	0	Parent=g2.t1
Contig8198	AUGUSTUS	CDS	445	582	.	+	0	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	CDS	758	894	.	+	0	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	exon	758	894	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	CDS	1053	1123	.	+	1	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	exon	1053	1123	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	CDS	1208	1315	.	+	2	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	exon	1208	1315	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	CDS	1587	1688	.	+	2	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	exon	1587	1688	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	CDS	1772	1810	.	+	2	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	exon	1772	1810	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	CDS	1890	1903	.	+	2	ID=g2.t1.cds;Parent=g2.t1
Contig8198	AUGUSTUS	exon	1890	2105	.	+	.	Parent=g2.t1
Contig8198	AUGUSTUS	stop_codon	1901	1903	.	+	0	Parent=g2.t1
Contig8198	AUGUSTUS	transcription_end_site	2105	2105	.	+	.	Parent=g2.t1
# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVA
# PQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTE
# DQIFYFPKYGFCEAADQFHVLDEVRR]
# end gene g2
###
# command line:
# ./augustus --gff3=on --UTR=on --species=myOrg example2.fa --AUGUSTUS_CONFIG_PATH=/home/augustus/augustus/config/
