# 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..140]--> unknown_A (8) <--[5..22]--> unknown_B (33) <--[5..44]--> unknown_C (15) <--[4..95]--> unknown_D (13) <--[3..42]--> unknown_E (13) <--[18..81]--> unknown_F (16) <--[0..3]--> unknown_G (19) <--[1..17]--> unknown_H (9) <--[10..26]--> unknown_J (19) <--[0..4]--> unknown_K (316) <--[0..7]--> unknown_L (103) <--[0..1]--> unknown_M (137) <--[0..1]--> unknown_N (124) <--[0..11]--> unknown_O (101) <--[0..3]--> unknown_P (12) <--[4..752]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6209620180911_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 = 21225, name = Contig62096) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig62096	AUGUSTUS	gene	1	14079	0.07	-	.	g1
Contig62096	AUGUSTUS	transcript	1	14079	0.07	-	.	g1.t1
Contig62096	AUGUSTUS	intron	1	47	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	234	827	0.93	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	1007	1509	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	1693	2344	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	2567	8392	0.18	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	8538	9940	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	10009	10880	0.54	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	10930	13541	0.42	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	intron	13646	13977	0.55	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	48	233	0.9	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	828	1006	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	1510	1692	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	2345	2566	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	8393	8537	0.51	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	9941	10008	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	10881	10929	0.43	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	13542	13645	0.54	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	CDS	13978	14079	0.91	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig62096	AUGUSTUS	start_codon	14077	14079	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagaattgcttcgagctactggagcattctgaaggccaccaagaaggccatccgcaggggccactgtcaatacttcg
# gttatatcgccaaaagctattggagatggagtgttgaaaatcactatccttcatgtttgaatacatcgagagatgggcaggacatataccgcgtggct
# ccacttcttggaggatgtttgatggacagtaacagggcagagggcgcgtatttggtgtctcggggcaggaagggggtggcgttttatgggatctttga
# ggaatgcgtttggattggtccagccaaaattctacaatatgcccacagaaaaattgttgtgtgtcgtagtcagggactggcctcagtgagacactttg
# ctcgtgttttgactcggggactggtctccgtgaggagaatttgttttgattgtactttgggactgatctcgagatttactcggagattggcctcactg
# gtggataccacagtagagattgccaataaagtgggagcagctgagattatccagagaattgtagatgatttgaaggatgaagctgaacagtacagaaa
# gatggtgatggagactattgagaagatcatggggaatctgggagctgccgacattgactcgcgtctggaggaacagcttattgatggtatcctttatg
# ccttccaggaacagaccacagaggatgtggtgatgttgaatggctttggtacagtggtgaatgccctgggtaagcgggtcaagccatacctccctcag
# atctgtggtaccattctgtggcgtctcaacaacaagtccgccaaagtacgtcaacaggcagccgatctcatctccagaatcgccatcgtcatgaaaac
# ctgccaggaggaacggttgatgggacacttgggggtggtgctgtacgagtacctgggagaggaataccccgaagtcttgggaagtatcctaggtgccc
# tgaaggccattgttaatgtcatcggaatgaccaagatgactcccccgattaaagatctgcttcctcgtctcactccaatcctcaaaaacagacatgag
# aaggtgcaggagaactgtatagatctggtagggaggattgctgaccggggggcagagtatgtctcagccagggagtggatgagaatctgcttcgagct
# actggagcttctgaaggcgcacaagaaggccatccgcagggccactgtcaataccttcggttatatcgccaaagctattgg]
# protein sequence = [MRIASSYWSILKATKKAIRRGHCQYFGYIAKSYWRWSVENHYPSCLNTSRDGQDIYRVAPLLGGCLMDSNRAEGAYLV
# SRGRKGVAFYGIFEECVWIGPAKILQYAHRKIVVCRSQGLASVRHFARVLTRGLVSVRRICFDCTLGLISRFTRRLASLVDTTVEIANKVGAAEIIQR
# IVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDSRLEEQLIDGILYAFQEQTTEDVVMLNGFGTVVNALGKRVKPYLPQICGTILWRLNNKSAKVRQQ
# AADLISRIAIVMKTCQEERLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVIGMTKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRIADRGAE
# YVSAREWMRICFELLELLKAHKKAIRRATVNTFGYIAKAI]
# end gene g1
###
# start gene g2
Contig62096	AUGUSTUS	gene	16494	21156	0.13	-	.	g2
Contig62096	AUGUSTUS	transcript	16494	21156	0.13	-	.	g2.t1
Contig62096	AUGUSTUS	stop_codon	16494	16496	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	intron	16565	16675	0.31	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	intron	16830	17522	1	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	intron	17671	18573	0.51	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	intron	18699	21054	0.52	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	CDS	16494	16564	0.31	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	CDS	16676	16829	0.84	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	CDS	17523	17670	0.83	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	CDS	18574	18698	0.56	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	CDS	21055	21156	0.89	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig62096	AUGUSTUS	start_codon	21154	21156	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggacgctgagtatgccaactactacaccagggaagtcatgctcatcttaaagagagagttccagtctcctgatgagg
# aaatgaagaaaatcgtgctaaaggtggtgaaaacagtgttgtgcacagatgctgtggcactcaaatacatcaaggacgaaatcctgcccccatttttc
# aacatttctggaatcaggagaatggtttggatagacggattacagacagggatgaagctgaacagttacagcaaagatggtgatggaggactattgag
# aagcatcatggggaatctgtggagttgccgacatgactccgtcttggaggaacagcttattgattggtatcctttatgctttccaggacagaccacag
# agtggatgaatgccctgggaagcgggtcagccatacctcccttcagatctgttggtaccattcctgtggcgtctcaaacaagtacgcccaaagtacgt
# tcacaggcagccgattctcattctccagaatcgcctcgtcatgaaaacctgccagagagtggctcagtggtagagctctcatctcatgctcaggcacc
# cggccacagcaaacttaagacagtaaaatag]
# protein sequence = [MDAEYANYYTREVMLILKREFQSPDEEMKKIVLKVVKTVLCTDAVALKYIKDEILPPFFNISGIRRMVWIDGLQTGMK
# LNSYSKDGDGGLLRSIMGNLWSCRHDSVLEEQLIDWYPLCFPGQTTEWMNALGSGSAIPPFRSVGTIPVASQTSTPKVRSQAADSHSPESPRHENLPE
# SGSVVELSSHAQAPGHSKLKTVK]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937019B.prfl --predictionStart=0  --predictionEnd=41198  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6209620180911_busco_2432604931_.temp