# 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..141]--> unknown_A (13) <--[2..15]--> unknown_B (10) <--[4..32]--> unknown_C (15) <--[0..22]--> unknown_D (30) <--[0..11]--> unknown_E (17) <--[2..19]--> unknown_F (13) <--[0..4]--> unknown_G (12) <--[0..2]--> unknown_H (14) <--[0..8]--> unknown_I (18) <--[0..4]--> unknown_J (80) <--[3..11]--> unknown_K (37) <--[4..9]--> unknown_L (23) <--[1..17]--> unknown_M (24) <--[5..11]--> unknown_N (33) <--[0..1]--> unknown_O (83) <--[3..20]--> unknown_P (26) <--[1..6]--> unknown_Q (28) <--[1..14]--> unknown_R (25) <--[0..11]--> unknown_S (47) <--[5..11]--> unknown_T (68) <--[7..16]--> unknown_U (20) <--[1..6]--> unknown_V (15) <--[0..21]--> unknown_W (48) <--[0..1]--> unknown_X (14) <--[12..132]--> unknown_Y (89) <--[0..15]--> unknown_Z (48) <--[1..24]--> unknown_AA (82) <--[0..17]--> unknown_AB (23) <--[7..82]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6235620180911_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 = 17110, name = Contig62356) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig62356	AUGUSTUS	gene	133	16492	0.01	+	.	g1
Contig62356	AUGUSTUS	transcript	133	16492	0.01	+	.	g1.t1
Contig62356	AUGUSTUS	start_codon	133	135	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	188	591	0.83	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	730	2643	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	2765	4488	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	4641	5038	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	5215	6818	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	6930	8009	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	8136	8663	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	8770	9921	0.28	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	9967	12277	0.22	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	12379	12468	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	12607	13015	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	13134	13428	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	13626	14971	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	15116	16029	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	intron	16128	16461	0.23	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	133	187	0.83	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	592	729	0.98	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	2644	2764	0.94	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	4489	4640	0.98	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	5039	5214	0.9	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	6819	6929	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	8010	8135	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	8664	8769	0.52	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	9922	9966	0.41	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	12278	12378	0.99	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	12469	12606	0.95	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	13016	13133	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	13429	13625	0.94	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	14972	15115	0.72	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	16030	16127	0.45	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	CDS	16462	16492	0.23	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig62356	AUGUSTUS	stop_codon	16490	16492	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggatgtgtggcatacgtccttcgacacagctttggtacgtcacaaggcaaactgaacaaaagatcctaagaggaacc
# gctacaagctgtttttggagtgtacgttgattctgacgtctgtggtaccgccggagctgccgatagaactgtcgctagctgttaataccagtctcctg
# gctttgaccaaactatatgtgtactgtaccgagccgttcagaataccttttgctggtaaagtggacatctgctgcttcgacaaaacagggacactgac
# agcagacgacttagtagtggagggaatcactggtctcaacgggaaggagatgatgtcagccactgaagtccctattgggacggcccatgtcttggcta
# catgtcatgctctggtgcacttggatgatgaattggtgggggatcccctggagaaggcaacactgaaagcagtggagtggaaccttactaaaggagag
# tcagttgtaccacagaagaggaagacccatggcttgaagatttatcatcgtttccattttgccagtgccctgaagagaatgtcggtcattgctggaca
# cacggccccaggctctgtagaaaccgagtatatagctactgttaaaggggcaccagagactctcaaacctatgtttaaagagatgccagctgactatg
# acgatgtgtatatggagatgtcaaggagaggggctagagttctggcccttggctgtaggaacctggggaacctaactcatcaacaggtgagagaaatg
# gctcgagaagaggtggagaaggacctcagcttttgtggctttgtcatcatctcctgtcccctcaaatcggactccaagtctgttgtcaaggaaatcat
# tcaggcctcccatcatattgtgatgataactggagacaacccgctgaccgcctgccatgtggccaaagaactcagaatgaccaggaaagaaatgctga
# ttctggagaagccgaatcatttagagtccaccataatcatgcatatggtctacccatcggacaaaggtggtgttgctttgcttgcaaatgccccagag
# agaccaatggaaagaaggaaaaagaaagaaaaaactgatgaggtagactttgaatctgaagttcacaatcttggaagttccgtagatggggaagctac
# ttcctccaatgacagagtaatgccccctggtatgaaaagttctggtaaatttgctggccgtgctgctaaggccagggctgtggcaaggggagataatt
# tagctccatcacagaaaaagttggccaacatgctgaaggagatagaggaagaagagaaagctcagatcgtgaagttgggggacgccagtatagcctct
# cccttcacctccaagctgtccactaccacgtgtgtatgccatatcattaagcagggcaggtgtacccttgtgaccaccctgcagatgttcaagatcct
# tgccttaaatgctttgatcctggcctacagccagagtgtcctatatttagatgggatcaagttcagtgacagtcaggccactatgcagggcctgctgt
# tggctggatgtttcttgtttatttctagatcaaagggagagccattcatggagagtttatttaacaacaaaccattgctgtacagcttggctttctct
# gccaccgcaatcacagggctagctagcggtgttatacccgagatagcagagcagtttgaaatagttccattaccaacagaggacattgtgatatggag
# actgaagacacccaagccttttttaactcagcatgtgattgtgtatttctcatccgagggtaaagctcagatgaatttaagagcacaggcttggacca
# aaaagatgttataa]
# protein sequence = [MDVWHTSFDTALVRHKANXTKDPKRNRYKLFLECTLILTSVVPPELPIELSLAVNTSLLALTKLYVYCTEPFRIPFAG
# KVDICCFDKTGTLTADDLVVEGITGLNGKEMMSATEVPIGTAHVLATCHALVHLDDELVGDPLEKATLKAVEWNLTKGESVVPQKRKTHGLKIYHRFH
# FASALKRMSVIAGHTAPGSVETEYIATVKGAPETLKPMFKEMPADYDDVYMEMSRRGARVLALGCRNLGNLTHQQVREMAREEVEKDLSFCGFVIISC
# PLKSDSKSVVKEIIQASHHIVMITGDNPLTACHVAKELRMTRKEMLILEKPNHLESTIIMHMVYPSDKGGVALLANAPERPMERRKKKEKTDEVDFES
# EVHNLGSSVDGEATSSNDRVMPPGMKSSGKFAGRAAKARAVARGDNLAPSQKKLANMLKEIEEEEKAQIVKLGDASIASPFTSKLSTTTCVCHIIKQG
# RCTLVTTLQMFKILALNALILAYSQSVLYLDGIKFSDSQATMQGLLLAGCFLFISRSKGEPFMESLFNNKPLLYSLAFSATAITGLASGVIPEIAEQF
# EIVPLPTEDIVIWRLKTPKPFLTQHVIVYFSSEGKAQMNLRAQAWTKKML]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093701EE.prfl --predictionStart=0  --predictionEnd=34755  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6235620180911_busco_2432604931_.temp