# 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 using config directory /augustus/config/ ...
# Using protein profile unknown
# --[0..405]--> unknown_A (10) <--[0..1]--> unknown_B (12) <--[0..11]--> unknown_C (16) <--[0..1]--> unknown_D (33) <--[3..9]--> unknown_E (61) <--[0..5]--> unknown_F (26) <--[0..1]--> unknown_G (52) <--[0..3]--> unknown_H (8) <--[0..5]--> unknown_I (12) <--[0..12]--> unknown_J (27) <--[0..2]--> unknown_K (9) <--[0..1]--> unknown_L (19) <--[0..6]--> unknown_M (14) <--[0..4]--> unknown_N (8) <--[0..1]--> unknown_O (43) <--[0..2]--> unknown_P (22) <--[0..1]--> unknown_Q (33) <--[0..43]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig330020180911_busco_2432604931_.temp 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 = 8901, name = Contig3300) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig3300	AUGUSTUS	gene	1	8901	0.37	-	.	g1
Contig3300	AUGUSTUS	transcript	1	8901	0.37	-	.	g1.t1
Contig3300	AUGUSTUS	intron	1	41	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	97	633	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	788	1433	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	1601	2602	0.86	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	2669	2812	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	2939	3185	0.94	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	3291	3683	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	3749	3916	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	4051	5997	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	6147	6428	0.81	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	6519	8034	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	intron	8085	8901	0.65	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	42	96	0.95	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	634	787	0.99	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	1434	1600	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	2603	2668	0.94	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	2813	2938	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	3186	3290	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	3684	3748	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	3917	4050	0.95	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	5998	6146	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	6429	6518	0.85	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig3300	AUGUSTUS	CDS	8035	8084	0.99	-	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtattaagaatgctccggctcagctagctattgtgcagaaaagatgcaaaagtacgtatggaccactgaaggatgagga
# cagaatcttcacaaacctctacggccggcatgactggaaactcaagggagccatgtcaaggggagactggtacaaaaccaaggagatcatcctgaagg
# gccatgactggatcttaaaggagatcacggcctcgggacttaggggccggggtggggcagggttccccactggaatgaagtggggctttatgaacaag
# cccagtgatggaaggccaaagtacttggtggtgaatgctgatgagggagagcccggtacttgtaaggacagagaaatcatgagacatgaccctcacaa
# gttagtggagggatgtttagtagctggccgtgccatgggagcaattgctgcatacatctacatcagaggagagttctacaatgaggcctctaatctac
# agctggcaatcaatgaggcctacgcagcaggattgatcggtaaaaatgcatgtggctctggttacgacttcgacgtctttgtacatcgaggggcaggg
# gcctacatctgtggggaagaaacttccctaattgagtcattggagggtaaagctggcaagccacgcttaaagccgccattccctgctgacgttggggt
# gtttggatgtcccacaactgtcgctaatgtcgaaacagtcgccgtggctccagtaatctgcagaagaggtggagagtggtttgctggattcgggcgag
# aacgaaacaggggaaccaaactgttcaacatctctggacaagtcaataacccagtgactgtggaggaggagatgtccatcactctaaaggagctgatc
# gagaggcacgcgggcggagtcatcgggggctgggacaacctcctgggggtcatcccaggggggtcctctacccccatcatacccaagagtgtgtgtac
# ggatttaatgatggactttgatgccttggtccaggctcagacagggctgggtacggctgcggttattgtcatgaataaagatgctgatgtcatcaggt
# gtatctctcgactgatcgagttctacaagcacgagagctgtggccagtgcacaccatgcagagagggagtgggctggatggccaagatcatgaaacgt
# tttg]
# protein sequence = [IKNAPAQLAIVQKRCKSTYGPLKDEDRIFTNLYGRHDWKLKGAMSRGDWYKTKEIILKGHDWILKEITASGLRGRGGA
# GFPTGMKWGFMNKPSDGRPKYLVVNADEGEPGTCKDREIMRHDPHKLVEGCLVAGRAMGAIAAYIYIRGEFYNEASNLQLAINEAYAAGLIGKNACGS
# GYDFDVFVHRGAGAYICGEETSLIESLEGKAGKPRLKPPFPADVGVFGCPTTVANVETVAVAPVICRRGGEWFAGFGRERNRGTKLFNISGQVNNPVT
# VEEEMSITLKELIERHAGGVIGGWDNLLGVIPGGSSTPIIPKSVCTDLMMDFDALVQAQTGLGTAAVIVMNKDADVIRCISRLIEFYKHESCGQCTPC
# REGVGWMAKIMKRF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093708OP.prfl --predictionStart=0  --predictionEnd=26146  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig330020180911_busco_2432604931_.temp