# 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..64]--> unknown_A (10) <--[1..2]--> unknown_B (11) <--[0..11]--> unknown_C (19) <--[13..26]--> unknown_E (25) <--[0..20]--> unknown_F (30) <--[0..4]--> unknown_G (26) <--[0..1]--> unknown_H (14) <--[0..9]--> unknown_I (10) <--[8..25]--> unknown_J (20) <--[28..59]--> unknown_L (36) <--[12..53]--> unknown_N (16) <--[2..27]--> unknown_O (31) <--[3..72]--> unknown_P (34) <--[0..5]--> unknown_Q (23) <--[5..24]--> unknown_R (27) <--[0..21]--> unknown_S (31) <--[10..57]--> unknown_T (25) <--[8..92]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5213120180911_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 = 23310, name = Contig52131) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig52131	AUGUSTUS	gene	271	4722	0.09	-	.	g1
Contig52131	AUGUSTUS	transcript	271	4722	0.09	-	.	g1.t1
Contig52131	AUGUSTUS	stop_codon	271	273	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	438	491	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	602	1096	0.91	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	1192	1451	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	1674	2084	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	2325	2450	0.88	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	2658	3130	0.26	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	intron	3272	4569	0.26	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	271	437	0.86	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	492	601	0.96	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	1097	1191	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	1452	1673	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	2085	2324	0.88	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	2451	2657	0.42	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	3131	3271	0.38	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	CDS	4570	4722	0.87	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52131	AUGUSTUS	start_codon	4720	4722	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggtggtgattagacgagaaagaaagagcaacagctggatggaaaccatggggagaagcaaaaacagctgtaaaagac
# tgggctatgtggaggaaaacagctgcaaaagactgggctatgtggagggagctaaaaacagctgtaaaagaccgctcaaatccgaggcaaacactgaa
# ccccggaaaaaattccacaccttggcgcgtatcaaaaaggccctgttttatgcggaggaatttggaggtctttgtgacagttcaaagtgtgacgcccg
# gaccaagctagagagtcaattgatctttttttttcgcagaactatttatgagaagctgggcagtgctttcaccgaagatgttcaacagttgtatctac
# agcaggtggaggagatcacccccaatattcgctactgtgcctacaatatcggggaccagtccgctattgatgaattaaaacagctcaggcgaaaagga
# ggagaggaccagcttacatcacatttagacgatcttctctcacaaaccagagagaaacagacagccaccttatcagaggttaagtggcaaggtcgggt
# ggtgccggtgaagaatgaacccgtgcggttgtttctgttgaatttacaagatagcaccaaagagattgagtctgctgagagcgtcgatagcaaaatct
# ctatctatgaaagtgtactaaagcaatgcattgatgctctacaagtgctgaaggacactctccaagatgatcagaatttcaaattagcggtgagaggg
# caggaagtggaaggcaaaatctccaaccaacattatctgcatagctacctgacctttatacgactgagcaaaactatagagcggaacctgctgttgat
# agaaatgatgaagaactatctaccgggcaaaaaagtggaggaggggcacaagatcaccaaacctcaggaccttgtgaggctctatgacatcatcatac
# agaatctgaatgagatccctaatctaacaggggtagaaggggacagcaatctgtcggaagaaacggcagtcagagtgctaggatacaaagcatttaga
# gaaaccatggcccttgcaccaagccaaacgctacaacctgccgcaacgcatacgacacgggcaatgatccagacagatctggcagagccggaagatgt
# gcatccaccaggaaggagaaggactcctcgggtatgcacgtggaacggtccatgcggagctattaaacacatgggtcgatgccaatatggaagcggtg
# gaacagggacccagatgacctggaagcagtgtgacgagaggatcggaaagactggaaactctcaacaacccaacccatga]
# protein sequence = [MVVIRRERKSNSWMETMGRSKNSCKRLGYVEENSCKRLGYVEGAKNSCKRPLKSEANTEPRKKFHTLARIKKALFYAE
# EFGGLCDSSKCDARTKLESQLIFFFRRTIYEKLGSAFTEDVQQLYLQQVEEITPNIRYCAYNIGDQSAIDELKQLRRKGGEDQLTSHLDDLLSQTREK
# QTATLSEVKWQGRVVPVKNEPVRLFLLNLQDSTKEIESAESVDSKISIYESVLKQCIDALQVLKDTLQDDQNFKLAVRGQEVEGKISNQHYLHSYLTF
# IRLSKTIERNLLLIEMMKNYLPGKKVEEGHKITKPQDLVRLYDIIIQNLNEIPNLTGVEGDSNLSEETAVRVLGYKAFRETMALAPSQTLQPAATHTT
# RAMIQTDLAEPEDVHPPGRRRTPRVCTWNGPCGAIKHMGRCQYGSGGTGTQMTWKQCDERIGKTGNSQQPNP]
# end gene g1
###
# start gene g2
Contig52131	AUGUSTUS	gene	14716	22011	0.01	+	.	g2
Contig52131	AUGUSTUS	transcript	14716	22011	0.01	+	.	g2.t1
Contig52131	AUGUSTUS	start_codon	14716	14718	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	intron	14742	15421	0.2	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	intron	15543	15721	0.22	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	intron	15977	16048	0.41	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	intron	16231	21681	0.4	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	intron	21737	21900	0.24	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	CDS	14716	14741	0.2	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	CDS	15422	15542	0.2	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	CDS	15722	15976	0.15	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	CDS	16049	16230	0.58	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	CDS	21682	21736	0.4	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	CDS	21901	22011	0.13	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig52131	AUGUSTUS	stop_codon	22009	22011	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagtatttggggcacattttaagctgtaaaagacggcgctatgtggagggagctaaaacactgcaaagaccgggct
# atgtggaggaaaacagctgtaaaagaccgggctatgtggaggaaaacagcgtaaaagcagccggctatactgggctatgtggagggagcaaaaacagc
# tgtaaaagaccgggctatgtggaggaagcaaaaacagctgtaaaagaccgggctatgtggaggaagctaaaacagctgcaaaagactgggctatgtgg
# aggaactaaacagctggtaaaagatcggggcctatgtggaggagctaaaacagctgtaaaagaccgggatatgttggaggaagctaaaacgctgccaa
# aaccgggcatgtggagggagctaacagctacgggctatgtggaggaagctaaaacagctgcaaaagaccgcggctatgtggagggagctaaaacagct
# gtaaaagatcgagctatgtggaggaaaacagctgcctacaaaagaccgggctatgtggaggaagaagtgttgaggccttgtgtgtcacttggcatgaa
# gaggataggtaacagcgtaatggatgagatgaagaaagtgatgagagttatattgggcatcatttttaagctgtttaaaaagactgggcatgtggagg
# atgaacacgctgaaaagactggcgctatgtggaaggaagctaaaacagctgtaaaagaccgggctatgtggaggaaggcataa]
# protein sequence = [MEYLGHILSCKRRRYVEGAKTLQRPGYVEENSCKRPGYVEENSVKAAGYTGLCGGSKNSCKRPGYVEEAKTAVKDRAM
# WRKLKQLQKTGLCGGTKQLVKDRGLCGGAKTAVKDRDMLEEAKTLPKPGMWRELTATGYVEEAKTAAKDRGYVEGAKTAVKDRAMWRKTAAYKRPGYV
# EEEVLRPCVSLGMKRIGNSVMDEMKKVMRVILGIIFKLFKKTGHVEDEHAEKTGAMWKEAKTAVKDRAMWRKA]
# end gene g2
###
# start gene g3
Contig52131	AUGUSTUS	gene	22646	23003	0.69	+	.	g3
Contig52131	AUGUSTUS	transcript	22646	23003	0.69	+	.	g3.t1
Contig52131	AUGUSTUS	start_codon	22646	22648	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig52131	AUGUSTUS	intron	22793	22868	0.78	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig52131	AUGUSTUS	CDS	22646	22792	0.78	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig52131	AUGUSTUS	CDS	22869	23003	0.73	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig52131	AUGUSTUS	stop_codon	23001	23003	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgagcgactgggttctagtggtggtgcacacgatagaatctattatctgtctaaaagaccggggcttagtgttggagg
# aagctaaaacagctgtaaaaaagacaggggctattgtggaggaaaacagcgcaaaggatcgggctatggtgtgtttatgcgtccgcgatgaggaggct
# aaaacagcatgcgtggtatgctatataagcattctcctcggtgtgacggctatgagagcgcaagtgaccagtttggttcgccgtctcgccctcgtggc
# ggtatga]
# protein sequence = [MSDWVLVVVHTIESIICLKDRGLVLEEAKTAVKKTGAIVEENSAKDRAMVCLCVRDEEAKTACVVCYISILLGVTAMR
# AQVTSLVRRLALVAV]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093707B7.prfl --predictionStart=0  --predictionEnd=23310  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5213120180911_busco_2432604931_.temp