# 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..70]--> unknown_A (58) <--[5..8]--> unknown_B (56) <--[0..1]--> unknown_C (13) <--[0..1]--> unknown_D (129) <--[0..9]--> unknown_E (25) <--[18..57]--> unknown_H (36) <--[0..7]--> unknown_I (15) <--[1..6]--> unknown_J (14) <--[5..34]--> unknown_K (30) <--[5..60]--> unknown_L (22) <--[1..40]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7126520180911_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 = 13962, name = Contig71265) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig71265	AUGUSTUS	gene	4	2580	0.1	-	.	g1
Contig71265	AUGUSTUS	transcript	4	2580	0.1	-	.	g1.t1
Contig71265	AUGUSTUS	stop_codon	4	6	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig71265	AUGUSTUS	intron	1791	2369	0.49	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig71265	AUGUSTUS	CDS	4	1790	0.71	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig71265	AUGUSTUS	CDS	2370	2580	0.13	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig71265	AUGUSTUS	start_codon	2578	2580	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggatgttcttgtgagtctgaaacatgatgggaagctcagtgattgcctgcataaggcctatacttccaaacatttgt
# gtgatgtaaaagtggtgacttcagaccagtccactttctacacacaccgacttgttttaacagcgttctcggacttcttccagagagaaatcagagga
# cgacaagattcgtacaacatggtcattccaatagatgtggattcagcggtctttaagatacttatagaattcatgtacaccggccagttgtgtgtcac
# tacagaagagaaaatttctctctatcacgcttcagtgattctggagatggatactgcccaagatctcctgcagcaggcgtacatttccagcgagtggc
# cgggtattatgaatgccaaggtcgttaaaaacgtcgctggttccgatcacatcgtcatggttgaaccggattctgaggtcaaggaccagaacattcgt
# tcagtgtgtgatgtcacagacagcaccataaccagtgccacgaggagtaaaatgtcaaatttacattcaacgcaaaagaaaagaggcagaaagaaaaa
# gaaaacagaggtgaaaatcgaggaacctgaggttttcgtacaaccagtgaatgtggctgaaccagagatcggaggtgtcccggaatcagcagacgacg
# gaatgaggaccagaaaccgcgggaaaaggagaccggtcgtggacaatccagacaagaaatgcaggagacaaaagaaggactcgaaagagccgaggaaa
# aacgatcctaaaggaaagaaaaaggggggcattaccaaagacaaatctaaaaaggttgtcaagatctgggttcccaaagcatccaaagtaagatgtga
# tgtctgtgggaaagcactgagctctcacattgcgctgaaaagacacatggttgttcagcacagggagatacctctgaagttcacccaaagtcgtgcca
# tcgtgagcaatattgtaaagggttcaggatccctgcgttattgtacactaacagactacagtaagaagttcatgtgtacaatctgtgcatgtagcttt
# cagttttacagcttgttttacagacacattcaagagaatcatatgccgttctatccgggcgataaacaagggcaattccacaaagtggccaaacacat
# ccagaatatgaaatccatatttaaaaagaaaaacaaaggactaaaatcagttaagaaaacgaggcgattccagccaaacaaagagtatgagaagtgct
# gcttctgtcattcggttctctcaaaagggagaatctatgcaagtcacctcatcaagaaacattatttgagttttgagaaagccaaggaattgaccggg
# taccccaggtaccgtctgcaacagaagtgggagtgtccagactgtaatttaacgttcgtcggaaacaaggctctgaaaagccattttgagggtgtgca
# ccagcttgacgacatgaaatacccttgccccgagtgcgatagctcttactcgnacaaggctctgaaaagccattttgagggtgtacaccagctggatg
# atatgaaatacccttgccccgagtgtgatagctcttactcatccttgggtaccatcaaatcccacttacgatgggttcacaagaagactgccgcggag
# gttctagaggcactgaagaactcggtcgcctgtgaggtggaggggtgtgactacaccacggggaacatgatgaccatgaagctgcacgtcgtgaagga
# acacccccaggttcagtaccgctgccccgagtgtaacttcaccttccatgtgaaaaagacgcttaatcgacacatgatagtcaaacatctccgacgtt
# ccgagcacctaaaaaaacagtgcgattcgtgcggacggaggtttagcaagaattcccagctccacgtccatcagtttatcaaacacggcatctaccac
# gacgagatgaaggtacgtctgcttgtagagtgcttagtacgtctgcctggtgtgtga]
# protein sequence = [MDVLVSLKHDGKLSDCLHKAYTSKHLCDVKVVTSDQSTFYTHRLVLTAFSDFFQREIRGRQDSYNMVIPIDVDSAVFK
# ILIEFMYTGQLCVTTEEKISLYHASVILEMDTAQDLLQQAYISSEWPGIMNAKVVKNVAGSDHIVMVEPDSEVKDQNIRSVCDVTDSTITSATRSKMS
# NLHSTQKKRGRKKKKTEVKIEEPEVFVQPVNVAEPEIGGVPESADDGMRTRNRGKRRPVVDNPDKKCRRQKKDSKEPRKNDPKGKKKGGITKDKSKKV
# VKIWVPKASKVRCDVCGKALSSHIALKRHMVVQHREIPLKFTQSRAIVSNIVKGSGSLRYCTLTDYSKKFMCTICACSFQFYSLFYRHIQENHMPFYP
# GDKQGQFHKVAKHIQNMKSIFKKKNKGLKSVKKTRRFQPNKEYEKCCFCHSVLSKGRIYASHLIKKHYLSFEKAKELTGYPRYRLQQKWECPDCNLTF
# VGNKALKSHFEGVHQLDDMKYPCPECDSSYSXKALKSHFEGVHQLDDMKYPCPECDSSYSSLGTIKSHLRWVHKKTAAEVLEALKNSVACEVEGCDYT
# TGNMMTMKLHVVKEHPQVQYRCPECNFTFHVKKTLNRHMIVKHLRRSEHLKKQCDSCGRRFSKNSQLHVHQFIKHGIYHDEMKVRLLVECLVRLPGV]
# end gene g1
###
# start gene g2
Contig71265	AUGUSTUS	gene	10738	13962	0.05	+	.	g2
Contig71265	AUGUSTUS	transcript	10738	13962	0.05	+	.	g2.t1
Contig71265	AUGUSTUS	start_codon	10738	10740	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	intron	10782	10934	0.93	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	intron	11070	11750	0.81	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	intron	11827	11884	0.11	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	intron	11944	13162	0.11	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	intron	13283	13450	0.67	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	intron	13548	13962	0.52	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	CDS	10738	10781	0.76	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	CDS	10935	11069	1	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	CDS	11751	11826	0.82	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	CDS	11885	11943	0.11	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	CDS	13163	13282	0.65	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig71265	AUGUSTUS	CDS	13451	13547	0.79	+	1	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatttctccctcgcagaaacacccaagacgacaaatctcatattgtgttgcgaatgcggcacagagatcgagccca
# atgcctccaacatgtgtgtgtcatgtatcagaacacaagtggatatcaccgagggaatccctaaacaggctgtactgtatttctgcagaaactgcaac
# aggttggttgatgctggatttgtgtggactgaaccgcactccatgagaatcaaagtcaagctcactgtacagaaagagatcactcttcaaaactttgc
# aggaataacaaatgcttacatgattgcgctttgtagaaggatggcagaaagtatgtcacagtatgatttgtctttttcagacggattggactttttct
# actctcaaaaacaagatgctcgtaaactggttgattttctggtgaatgttgtgccctgcaggtatcaatcggcacaagaattggtttcccatgatgtc
# cggaataacacctttacgtacaaatacacgttctccgtggagattgtcccgatttgtaag]
# protein sequence = [MDFSLAETPKTTNLILCCECGTEIEPNASNMCVSCIRTQVDITEGIPKQAVLYFCRNCNRLVDAGFVWTEPHSMRIKV
# KLTVQKEITLQNFAGITNAYMIALCRRMAESMSQYDLSFSDGLDFFYSQKQDARKLVDFLVNVVPCRYQSAQELVSHDVRNNTFTYKYTFSVEIVPIC
# K]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937085E.prfl --predictionStart=0  --predictionEnd=33960  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7126520180911_busco_2432604931_.temp