# 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..190]--> unknown_A (89) <--[9..20]--> unknown_B (13) <--[3..22]--> unknown_C (43) <--[12..69]--> unknown_F (15) <--[1..17]--> unknown_G (35) <--[2..40]--> unknown_H (17) <--[0..56]--> unknown_I (14) <--[0..5]--> unknown_J (24) <--[8..45]--> unknown_K (21) <--[18..112]--> unknown_N (32) <--[0..3]--> unknown_O (23) <--[0..53]--> unknown_P (29) <--[1..29]--> unknown_Q (11) <--[17..65]--> unknown_R (35) <--[41..252]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig1860020180911_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 = 16185, name = Contig18600) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig18600	AUGUSTUS	gene	1	375	0.8	+	.	g1
Contig18600	AUGUSTUS	transcript	1	375	0.8	+	.	g1.t1
Contig18600	AUGUSTUS	intron	1	111	0.8	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig18600	AUGUSTUS	CDS	112	375	0.8	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig18600	AUGUSTUS	stop_codon	373	375	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gagtcgcagatgtatctggcccggctgaaccagtgtttgtcacgagcattgagtctcattaaatcccacgtggttaaca
# ttctgcaatcctccaccaggcaggtccaggagaaacaggtaggtacaatctgggtggcagacccggtggtgtgtaggtacatatctgggtggcagacc
# cggtgttgtcgtagcgtacgaatctggtgtgcagacccggtgttgtgtagtgttacaatctcggtggcaggacccgcggttgtgtag]
# protein sequence = [ESQMYLARLNQCLSRALSLIKSHVVNILQSSTRQVQEKQVGTIWVADPVVCRYISGWQTRCCRSVRIWCADPVLCSVT
# ISVAGPAVV]
# end gene g1
###
# start gene g2
Contig18600	AUGUSTUS	gene	447	1294	0.68	-	.	g2
Contig18600	AUGUSTUS	transcript	447	1294	0.68	-	.	g2.t1
Contig18600	AUGUSTUS	stop_codon	447	449	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig18600	AUGUSTUS	intron	836	1284	0.68	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig18600	AUGUSTUS	CDS	447	835	0.8	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig18600	AUGUSTUS	CDS	1285	1294	0.69	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig18600	AUGUSTUS	start_codon	1292	1294	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggtaaaaataatatttgatttcaacacaaccactgggtctgccaccagattgcacctacaggaccagctagattctg
# ccacgcagattgcacctaacagcaccagtggggtctgccaccagattgtaccttacacgaatcactgggctgcaccagatattacctacacaaccacc
# gaggtctgccaccagattgtactacacaaccaccgggtctgcaccaagattgtacctacacaacacccgcggtctgccacagataattacacacacgc
# cacgggtctgcaccagattgtacctaacacaaccagcggtgcttgcaccaaatttcctacacaaccagcggatctgccaccagatctgtacctacaac
# aaccagcgggtctgccaccagattga]
# protein sequence = [MVKIIFDFNTTTGSATRLHLQDQLDSATQIAPNSTSGVCHQIVPYTNHWAAPDITYTTTEVCHQIVLHNHRVCTKIVP
# TQHPRSATDNYTHATGLHQIVPNTTSGACTKFPTQPADLPPDLYLQQPAGLPPD]
# end gene g2
###
# start gene g3
Contig18600	AUGUSTUS	gene	2572	13119	0.23	+	.	g3
Contig18600	AUGUSTUS	transcript	2572	13119	0.23	+	.	g3.t1
Contig18600	AUGUSTUS	start_codon	2572	2574	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	2610	2802	0.94	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	2930	3111	0.99	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	3204	3944	0.98	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	4085	4387	0.79	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	4549	6368	0.82	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	6517	6833	0.44	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	7017	7398	0.95	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	intron	7514	12914	0.81	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	2572	2609	0.99	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	2803	2929	0.94	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	3112	3203	0.99	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	3945	4084	0.99	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	4388	4548	0.78	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	6369	6516	0.44	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	6834	7016	0.64	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	7399	7513	1	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	CDS	12915	13119	0.98	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig18600	AUGUSTUS	stop_codon	13117	13119	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggagcagttagaaatccggctggataaaagtcctgaatataatcaggctttagtggattgtcatcagtgctacttca
# gtcagcgagaattacttcttgggcctagcattacttctacaatcaatgatttggccacaaaacatgttcgtgatcattgcgcgctgatgagaagtgga
# tgtgcgtttatggtgcatgtgtgtgaggatgagtaccagctgtactatcatttcttcaccagacacgcccccctcttagatgagatgttggaacgact
# ctgtaacagcctgtatgatgtctttcgtcccctcatcattcatgtcaatcatctggaaaccttggcagaactctgttccatcatgaaagtggaaatgt
# tggaggagcatgcacaagctaatgctcaggaattgtcctccttcagtaatgtctgccatcagatgttaatggacatgcaagagcgcctagtttaccga
# acctatatttacattcgctcggacattctacagtattcagcagcacaaggagatctggcctatccagagaaattggaaatgatgcagagcattgctga
# aagcataagagctggggagacaaagggccacacccgaaccccctcatcatcttctttaaagggtcactccagatctccttcaaatgcctccagtacca
# gccaggaggtggctgaactaacagaggcaggaaaaaatgccacgctacctaacactaatccagccacgctacctaacactaatccagccacgctacta
# acactaatccagccacgctacctaacactaatccagccacgctacctaacactaatccagccacgctacctaaacactaatccagccacgctacctaa
# cacaatccagctgaaatcaatatattagatgaagagcatcaccagtacaatgcctatgtctccagccgaccttcatggaatgtggtacccaacagtga
# ggaggacactggtgaccttatctaactgtaccggtgtattgatagcattgctaaagcataagagctggggagacaaagggccacacccgaaccccctc
# atcatcttctttaaagggtgcctcccagcctccttcaaatgcctccagttaccagccaggagggtggctgaactaacagagcagagaaaaatgtgtac
# atactctgcagatattcactgtcatccacatccatcacgctaccaacactaa]
# protein sequence = [MEQLEIRLDKSPEYNQALVDCHQCYFSQRELLLGPSITSTINDLATKHVRDHCALMRSGCAFMVHVCEDEYQLYYHFF
# TRHAPLLDEMLERLCNSLYDVFRPLIIHVNHLETLAELCSIMKVEMLEEHAQANAQELSSFSNVCHQMLMDMQERLVYRTYIYIRSDILQYSAAQGDL
# AYPEKLEMMQSIAESIRAGETKGHTRTPSSSSLKGHSRSPSNASSTSQEVAELTEAGKNATLPNTNPATLPNTNPATLLTLIQPRYLTLIQPRYLTLI
# QPRYLNTNPATLPNTIQLKSIYXMKSITSTMPMSPADLHGMWYPTVRRTLVTLSNCTGVLIALLKHKSWGDKGPHPNPLIIFFKGCLPASFKCLQLPA
# RRVAELTEQRKMCTYSADIHCHPHPSRYQH]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703DY.prfl --predictionStart=0  --predictionEnd=20243  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig1860020180911_busco_2432604931_.temp