# 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
# --[2..19]--> unknown_A (161) <--[0..1]--> unknown_B (18) <--[0..3]--> unknown_C (40) <--[0..1]--> unknown_D (7) <--[1..4]--> unknown_E (104) <--[5..8]--> unknown_F (29) <--[1..8]--> unknown_G (97) <--[0..39]--> unknown_H (60) <--[2..22]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig524020180911_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 = 11475, name = Contig5240) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig5240	AUGUSTUS	gene	1	9786	0.32	+	.	g1
Contig5240	AUGUSTUS	transcript	1	9786	0.32	+	.	g1.t1
Contig5240	AUGUSTUS	intron	188	444	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	569	1627	0.76	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	1821	2049	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	2214	2450	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	2652	6957	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	7071	7171	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	7378	7620	0.6	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	intron	7762	9639	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	1	187	0.87	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	445	568	0.72	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	1628	1820	0.94	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	2050	2213	0.96	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	2451	2651	0.88	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	6958	7070	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	7172	7377	1	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	7621	7761	0.6	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	CDS	9640	9786	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5240	AUGUSTUS	stop_codon	9784	9786	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tattgtttcagggagtatgatattacaaaggaaagaatagagaagattttagctgctggagcaaatgttattctaacca
# ccggtggaattgacgacttgtgcttaaaatactttgtggaagcaggggccatggctgtcagacggtgtaagaaagtggatctgaagaggattgccaaa
# gccacaggaggtcagctagtgatgaccttggctaaccttgagggagaggaaacatttgaggcctccatgttgggaaatgcggaagaagttgtccaaga
# tcgtgtctgtgatgatgaactcattcttgtgatgggtcctaaggcacgaacagcagcctcaattattctgagaggtgcgaacgactttatgtgcgatg
# aaatggaacgctctgtccacgatgctctgtgtgtagtgaagcgagtcctggagtcgaaatcggtcgtccccggcggtggagcagtggaggcagcattg
# tcgatttatctcgagaacttcgctacatcactgggatcaagggaacagctagctatcgctgagtttgcgcggtctctactagtaatccctaaacagct
# aggaattaatgctgctcaggatgccaccgatttagtggctaagttacgagcctaccacaacatgtctcaaaccaaacaggaacacagggacctcagat
# gggttggattggacttgtatcagggtacagtgagagacaacaagaaggctggggtactggaacctgcaatgtccaaaatcaaatccctcaagtttgcc
# acggaggctgctatcaccattcttagaatagacgacatgataaaacttatagatcaaggtcgaggaggcggcaagacttaccaggacgctttgaacgc
# tggggacgttgtcccatatacacccaaaaagaaatcggatgcattgccatccattgatgccacaaatgatatacaggacccactggattattcatttt
# gtcgactgaataaagtagaggatgcactggaagaggagcccagatcgtctccaaaaaaagatgagtccaatgattctgggaagtctcaaagtcgctgt
# cttcgattaaacaataacagtcttcagtcgattgaacgacttaatgaagtcataaatgccaagtttgataatcccaagaatattgcttggattgactt
# atctttcaatgaactgacaaccattgatccagttttattggagtttactgaacttcaaatactgtacctccatgggaatcagataggagatgttaaag
# aagttgctaagctctctggcctgccgaaattaaggaaagtgactctccatggaaacccacttgagaagaccaagggttacaaattccaagtgatggca
# atggttcctcagattcagacggtggacttcagtcgtgtaacaaagtgtgacagaaaaacatcgcaggtctggaatagcatgaacaatgccccgaagaa
# aaagaagaaaatagaggaggattaa]
# protein sequence = [YCFREYDITKERIEKILAAGANVILTTGGIDDLCLKYFVEAGAMAVRRCKKVDLKRIAKATGGQLVMTLANLEGEETF
# EASMLGNAEEVVQDRVCDDELILVMGPKARTAASIILRGANDFMCDEMERSVHDALCVVKRVLESKSVVPGGGAVEAALSIYLENFATSLGSREQLAI
# AEFARSLLVIPKQLGINAAQDATDLVAKLRAYHNMSQTKQEHRDLRWVGLDLYQGTVRDNKKAGVLEPAMSKIKSLKFATEAAITILRIDDMIKLIDQ
# GRGGGKTYQDALNAGDVVPYTPKKKSDALPSIDATNDIQDPLDYSFCRLNKVEDALEEEPRSSPKKDESNDSGKSQSRCLRLNNNSLQSIERLNEVIN
# AKFDNPKNIAWIDLSFNELTTIDPVLLEFTELQILYLHGNQIGDVKEVAKLSGLPKLRKVTLHGNPLEKTKGYKFQVMAMVPQIQTVDFSRVTKCDRK
# TSQVWNSMNNAPKKKKKIEED]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370762.prfl --predictionStart=0  --predictionEnd=22604  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig524020180911_busco_2432604931_.temp