# 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..25]--> unknown_A (29) <--[2..6]--> unknown_B (29) <--[0..1]--> unknown_C (25) <--[0..2]--> unknown_D (25) <--[0..4]--> unknown_E (14) <--[1..18]--> unknown_F (14) <--[0..37]--> unknown_G (24) <--[0..1]--> unknown_H (27) <--[0..1]--> unknown_I (19) <--[0..1]--> unknown_J (11) <--[0..3]--> unknown_K (10) <--[0..831]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5572620180911_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 = 23378, name = Contig55726) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig55726	AUGUSTUS	gene	1	4431	0.04	+	.	g1
Contig55726	AUGUSTUS	transcript	1	4431	0.04	+	.	g1.t1
Contig55726	AUGUSTUS	intron	1	621	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	intron	653	2181	0.2	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	intron	2251	2551	0.54	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	intron	2667	3462	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	intron	3599	4333	0.41	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	CDS	622	652	0.51	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	CDS	2182	2250	0.47	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	CDS	2552	2666	0.98	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	CDS	3463	3598	0.73	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	CDS	4334	4431	0.41	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig55726	AUGUSTUS	stop_codon	4429	4431	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gttatataaggggtgaatatgtagatctcagtcgtggtgcaaactatttgacacaggtattgctcaggccaggtgcttc
# cgatctgacaggaagttttaggttgtacaagaaagaagtcttacagaagctggtgaactcctgtatatctaaaggctatgtgttccagatggagatga
# tcgtcagagcacgacagtttggttacagcattggagagtatggtcatttgaacaacacgaacaagccagatgccgagctaaatatggggttaggaaga
# tggggcagggaagaggggccggcagggtggggcagggaagagaaggcagggtgggggcagggaagaggggtgcgagttaggattaaatacagaccgtg
# gatattggcctgggtagctcagtggttagagctcctgactagtaatgcaggggtcagattcctggtccagccataa]
# protein sequence = [YIRGEYVDLSRGANYLTQVLLRPGASDLTGSFRLYKKEVLQKLVNSCISKGYVFQMEMIVRARQFGYSIGEYGHLNNT
# NKPDAELNMGLGRWGREEGPAGWGREEKAGWGQGRGVRVRIKYRPWILAWVAQWLELLTSNAGVRFLVQP]
# end gene g1
###
# start gene g2
Contig55726	AUGUSTUS	gene	7419	8132	0.91	-	.	g2
Contig55726	AUGUSTUS	transcript	7419	8132	0.91	-	.	g2.t1
Contig55726	AUGUSTUS	stop_codon	7419	7421	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55726	AUGUSTUS	CDS	7419	8132	0.91	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55726	AUGUSTUS	start_codon	8130	8132	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggcatggagtttagcagtgaaaagcaaagtcatggataacagcgaaaacaacacccttgctcatatatccatgaacg
# gacaacagctaaaggaagtggacgccttcaaatatctcggcgccacactaacgaaacacagtcgatccaccaccgaaatcaagaccagaatcgccatc
# gcaacggccaccatatcaaaactcacacagaaacagcaaaacaacgaaatccaattccttccaaacataaacctttacaaagccctggtcctttccat
# cctcctctacggctgcgagagctggaccatgacagcagagatgatcaggagagtccaaacgtttgagaccaaatgctacagacgtatcctcgggatct
# cttggtcagaccagatgaccaacgaatatgttcgtgccaaagttacagcactggcaggtccccaagtattccttctaacaatcgtgaaaaagaggaaa
# ctgtcgtggttcggccatgttacccgccacaataccctatccaagacagtcctacaagggaccctggaaggtgggcggagacgaggaagacaagttaa
# gagctggatggataacttcaaagactggacacgaatggacagccccaccatgatcaggaaagcagaggatcgaactggttggcgctccctggcacaca
# agtcgtccctcatgtcgcctctacggccttcgcggtcaggagaatga]
# protein sequence = [MAWSLAVKSKVMDNSENNTLAHISMNGQQLKEVDAFKYLGATLTKHSRSTTEIKTRIAIATATISKLTQKQQNNEIQF
# LPNINLYKALVLSILLYGCESWTMTAEMIRRVQTFETKCYRRILGISWSDQMTNEYVRAKVTALAGPQVFLLTIVKKRKLSWFGHVTRHNTLSKTVLQ
# GTLEGGRRRGRQVKSWMDNFKDWTRMDSPTMIRKAEDRTGWRSLAHKSSLMSPLRPSRSGE]
# end gene g2
###
# start gene g3
Contig55726	AUGUSTUS	gene	8478	9341	0.93	-	.	g3
Contig55726	AUGUSTUS	transcript	8478	9341	0.93	-	.	g3.t1
Contig55726	AUGUSTUS	stop_codon	8478	8480	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig55726	AUGUSTUS	CDS	8478	9341	0.93	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig55726	AUGUSTUS	start_codon	9339	9341	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgctagccaacaaaagtgtgagacacaagatgagagaagccaaagaacagtggatagacaaacagtgccaagacatcg
# agaaacacgctgaacaaggcaacagcaaaagaanacaagggaacagcaaaagagtgtgcgagaccctgaatacgctcactaggacccagcaaaacaat
# tcagttgtgattgaggacaaagacggtgagctactgaccgagaactccgcaatgctggccagatggacagagtactgtgagggactttacaactaccc
# catacaaccagacaccagcgtgatagatggggagacaaaaccacagaaagatccctcaccactacatgtcatgagggaagaagtagaggaggccatcc
# gcagccttccagcaggcaagtcatcaggagcagacaatataccagcagagctgctcaagcacggagggagctgcttggtcactgtgataacatcactc
# tgtcagaagatctgggagaccaagcagtggccgacagagtggacaagatcactcatccccctccccaaaaaaggaaacttgtgtctgtaccaaaacta
# ccggacaattganacaagatcactcatccccctccccaaaaaagaaaacttgcgtctgtaccaaaactacaggacaattggcctaattaaccacacca
# gcaagatcatgctacgagtgatcctcaacagattgaagaaagaagccgaggaacatttggcagaagaacaggcgggatttagggcaggccgaagcacc
# gtcgaacagattttcaactgccgcatcatgatggaaaagcatctccaacaccagaaagaacttttccacaatttcagacttcaagaaagccttcaata
# g]
# protein sequence = [MLANKSVRHKMREAKEQWIDKQCQDIEKHAEQGNSKRXQGNSKRVCETLNTLTRTQQNNSVVIEDKDGELLTENSAML
# ARWTEYCEGLYNYPIQPDTSVIDGETKPQKDPSPLHVMREEVEEAIRSLPAGKSSGADNIPAELLKHGGSCLVTVITSLCQKIWETKQWPTEWTRSLI
# PLPKKGNLCLYQNYRTIXTRSLIPLPKKENLRLYQNYRTIGLINHTSKIMLRVILNRLKKEAEEHLAEEQAGFRAGRSTVEQIFNCRIMMEKHLQHQK
# ELFHNFRLQESLQ]
# end gene g3
###
# start gene g4
Contig55726	AUGUSTUS	gene	9541	12259	0.22	+	.	g4
Contig55726	AUGUSTUS	transcript	9541	12259	0.22	+	.	g4.t1
Contig55726	AUGUSTUS	start_codon	9541	9543	.	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig55726	AUGUSTUS	intron	9589	10555	0.6	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig55726	AUGUSTUS	intron	10781	12100	0.3	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig55726	AUGUSTUS	CDS	9541	9588	0.62	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig55726	AUGUSTUS	CDS	10556	10780	0.72	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig55726	AUGUSTUS	CDS	12101	12259	0.92	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig55726	AUGUSTUS	stop_codon	12257	12259	.	+	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgatatcgtcttctaaagtccaaacaaatgttccccgaaaacgactcacaagggtgtgtgatgtatttgtctctcttg
# gatatgttggtgtgtgtgagacaacagcgcaaggtcgtccgcaaagtccagatcttctagggttgagaaaggctccagcggatccccttggagagtct
# tctgttgtccttcgcatacccatcgatgaccaattgaatagtactgcagacatcacacacccttgtctaactcccgtttacatcaaaaaaggtgttat
# ggggagacaagacacagaagagccctcaccactacatgccatgagggaagaagtagaggaggccatccgcagccttcagcaggcaagtcataaggagg
# cagacaacataccagcagagctgctcaaagcacggagggagctgcctggtcactgttga]
# protein sequence = [MISSSKVQTNVPRKRLTRVCDVFVSLGYVGVCETTAQGRPQSPDLLGLRKAPADPLGESSVVLRIPIDDQLNSTADIT
# HPCLTPVYIKKGVMGRQDTEEPSPLHAMREEVEEAIRSLQQASHKEADNIPAELLKARRELPGHC]
# end gene g4
###
# start gene g5
Contig55726	AUGUSTUS	gene	12408	12692	0.76	+	.	g5
Contig55726	AUGUSTUS	transcript	12408	12692	0.76	+	.	g5.t1
Contig55726	AUGUSTUS	start_codon	12408	12410	.	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig55726	AUGUSTUS	CDS	12408	12692	0.76	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig55726	AUGUSTUS	stop_codon	12690	12692	.	+	0	transcript_id "g5.t1"; gene_id "g5";
# coding sequence = [atgctacgagtgatcctcaacagattggaagaagaagcgaggaacattttggcagaagaacaggcgggatttggcgcag
# gccgaagcaccgtcgaacagatttttcaactgccgcatcatgatggaaaagcatctccaacaccagaagaacttttccacaatttcaatagacttcag
# gaaagcctttcaatgggtgtgggacgcaggactatggcacgtactgaagagacttcggcatccgaggagggactagtcagacaaccagtcactgtaca
# acactgctag]
# protein sequence = [MLRVILNRLEEEARNILAEEQAGFGAGRSTVEQIFQLPHHDGKASPTPEELFHNFNRLQESLSMGVGRRTMARTEETS
# ASEEGLVRQPVTVQHC]
# end gene g5
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370M9E.prfl --predictionStart=0  --predictionEnd=23378  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5572620180911_busco_2432604931_.temp