# This output was generated with AUGUSTUS (version 2.7).
# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.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 ...
# human version. Using default transition matrix.
# Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat 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 = HS04636) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
HS04636	AUGUSTUS	gene	966	6903	1	+	.	g1
HS04636	AUGUSTUS	transcript	966	6903	.	+	.	g1.t1
HS04636	AUGUSTUS	intron	1018	1817	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	1935	2054	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	2199	2851	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	2996	3425	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	3608	4339	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	4424	4542	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	4790	5071	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	5359	5859	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	intron	6008	6493	.	+	.	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	966	1017	.	+	0	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	transcript_id "g1.t1"; gene_id "g1";
HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
# end gene g1
###
#
# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 2 on both strands
# start gene g2
HS08198	AUGUSTUS	gene	445	1848	1	+	.	g2
HS08198	AUGUSTUS	transcript	445	1848	.	+	.	g2.t1
HS08198	AUGUSTUS	intron	583	811	.	+	.	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	intron	895	1052	.	+	.	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	intron	1124	1207	.	+	.	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	intron	1316	1586	.	+	.	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	intron	1689	1771	.	+	.	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	CDS	445	582	.	+	0	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	CDS	812	894	.	+	0	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	transcript_id "g2.t1"; gene_id "g2";
HS08198	AUGUSTUS	CDS	1772	1848	.	+	2	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
# ggcgtggtga]
# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
# HVLDGECTAGASMAAW]
# end gene g2
###
# command line:
# augustus --strand=both --noInFrameStop=false --gff3=off --protein=on --introns=on --start=off --stop=off --cds=on --codingseq=on --singlestrand=false /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat --UTR=off --genemodel=complete --species=human