# 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
# --[9..1248]--> unknown_A (15) <--[20..79]--> unknown_D (18) <--[6..9]--> unknown_E (52) <--[0..4]--> unknown_F (55) <--[2..7]--> unknown_G (32) <--[5..8]--> unknown_H (23) <--[12..25]--> unknown_I (25) <--[1..30]--> unknown_J (10) <--[0..6]--> unknown_K (13) <--[59..442]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig26920180911_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 = 21565, name = Contig269) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig269	AUGUSTUS	gene	5	3893	0.07	+	.	g1
Contig269	AUGUSTUS	transcript	5	3893	0.07	+	.	g1.t1
Contig269	AUGUSTUS	start_codon	5	7	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	55	428	0.46	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	550	643	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	797	1445	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	1565	1977	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	2083	2224	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	2304	2487	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	2608	2757	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	3105	3242	0.78	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	intron	3324	3784	0.33	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	5	54	0.37	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	429	549	0.98	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	644	796	0.91	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	1446	1564	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	1978	2082	0.82	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	2225	2303	0.97	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	2488	2607	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	2758	3104	0.74	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	3243	3323	0.72	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	CDS	3785	3893	0.33	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig269	AUGUSTUS	stop_codon	3891	3893	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgtccatgcccctttaactgtgactacaagccccccgcagactacaaacctcctattgttcgtgtgaatgacaaag
# taatgataccacaggacgaccatcccgagattaattttgtcggtctcctgattggaccaagaggaaacacactaaagaacttggaaaaagatactgga
# gcaaaaattatcatccgaggtaaaggttctgtgaaagaggggaagataggaagaaaggacggccagcctcttcctggtgaggacgaacccctgcatgc
# ctacgtgacggcaaacaatccagaaaatgtcaaaaaagccgtggaaaagatcaaagaaattattcaacaaggtatagaggttcccgaaggacaaaatg
# acttgcgacgccagcagctcagagaactggccttgttaaacgggactttacgagaaaatgatgggcttgcgaaactcaaacagttgcagcaggcccaa
# aacattatcacaaataccattatctgttcattgtgtggaggtactggccatatagctcaagactgtaaatcaaaaaaacctggcgactcattcaaaaa
# ttatccacagactgccaaccccgtgtctcaggctgacaaagctaaaatggacagtgagtatatgtccctaatggcggaacttggagaaggtcctcctc
# cacccaagagtcagacgcagcccacacaggccgtgcagtccttcagaccgtcgttcagtcaaccgccgcctaatcctatggcggtgaatccaccctgg
# caacagcaggctcgcccccctcccccacaagtggtctccaacatcagtctcagcacacctgtacagacctcacaggtacagagtacctcccagccccc
# cgtcagctacaatatacagggtgtacagcccccaatgggtatacccaccagtatccagcagccggtgggcatgcagcagcccggacacatgcacatgc
# ctcccggacagatgccagcccccgtggccccgccctctcattacacgtcatccacaggcccagttccacccccgtggcagtccaatacaatgacgtct
# caaaactgtgctgtgtcgtctgcaggaggcggtaagagttcctcctccatctttgttgtcggctccaccaccgccaccaccaagcagccagcctccca
# catcatggatgcagcaagctataaatattaccacaaagcacatgggaagtccttggggtctaatctaaggaagataggagctatttcacaaatttcag
# gggaacgatgtgatgattctttgcattag]
# protein sequence = [MCPCPFNCDYKPPADYKPPIVRVNDKVMIPQDDHPEINFVGLLIGPRGNTLKNLEKDTGAKIIIRGKGSVKEGKIGRK
# DGQPLPGEDEPLHAYVTANNPENVKKAVEKIKEIIQQGIEVPEGQNDLRRQQLRELALLNGTLRENDGLAKLKQLQQAQNIITNTIICSLCGGTGHIA
# QDCKSKKPGDSFKNYPQTANPVSQADKAKMDSEYMSLMAELGEGPPPPKSQTQPTQAVQSFRPSFSQPPPNPMAVNPPWQQQARPPPPQVVSNISLST
# PVQTSQVQSTSQPPVSYNIQGVQPPMGIPTSIQQPVGMQQPGHMHMPPGQMPAPVAPPSHYTSSTGPVPPPWQSNTMTSQNCAVSSAGGGKSSSSIFV
# VGSTTATTKQPASHIMDAASYKYYHKAHGKSLGSNLRKIGAISQISGERCDDSLH]
# end gene g1
###
# start gene g2
Contig269	AUGUSTUS	gene	4184	4681	0.77	-	.	g2
Contig269	AUGUSTUS	transcript	4184	4681	0.77	-	.	g2.t1
Contig269	AUGUSTUS	stop_codon	4184	4186	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig269	AUGUSTUS	intron	4435	4620	0.81	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig269	AUGUSTUS	CDS	4184	4434	0.81	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig269	AUGUSTUS	CDS	4621	4681	0.78	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig269	AUGUSTUS	start_codon	4679	4681	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaaggtcaacacatcagttcatttttactacacatatccattcagaacagcaaataatgtattcactgtagatattg
# ttctcaacttggaggtggaggtgggggagctccaagcatgcccagcgtattcatatcaaatgctcccgggggtgggggaggaggtaccgccatggggt
# tgtagccttgctgtccagggggaggtggtggagggggtgcaacaccacttggcattggtggtggagcttgttgccatggtggcatgttgtttggagga
# ggcggtgccggttgccatggtgatgctgatgtactag]
# protein sequence = [MKVNTSVHFYYTYPFRTANNVFTVDIVLNLEVEVGELQACPAYSYQMLPGVGEEVPPWGCSLAVQGEVVEGVQHHLAL
# VVELVAMVACCLEEAVPVAMVMLMY]
# end gene g2
###
# start gene g3
Contig269	AUGUSTUS	gene	14203	16144	0.4	-	.	g3
Contig269	AUGUSTUS	transcript	14203	16144	0.4	-	.	g3.t1
Contig269	AUGUSTUS	stop_codon	14203	14205	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig269	AUGUSTUS	intron	14675	15968	0.9	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig269	AUGUSTUS	CDS	14203	14674	0.87	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig269	AUGUSTUS	CDS	15969	16144	0.42	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig269	AUGUSTUS	start_codon	16142	16144	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgggaccgcttctgtgtctggctttcatcaacgaccttccagatgccgtcagttctcctgtaaagttgtttgcagatg
# actgcttcatttatcgttccatcaactctgctggagacaacatcatctttcaacaagacctcgcggcacttgagacatgggagaaagaatggcagata
# tcttctcaagtcctactaaagacagcagtgacagaggtatacagttcaggaatggagcagaatgtcgagcaaactgttaacatcatgtttaacgaggg
# gtcacaacgatcatttatcaaccaaaagttggcatctgaactccagcttgagatgattggaaaggaagtaatcaatgctgcaggattcgtatcaaaga
# aaactgaagtccgtcaccttgacaaagtacaattgtccatcatcggcgaaggaaaccagtccatacctatagatgtacttgtcgttccacaaattggt
# gttccaattcaaacccactcagcagaaataaaacaacttccacacctgcgtcatttgaatttagcacatgccagtccaagtgatcaaccatttgaaat
# agagatacttattggagcagattactacagggacttcatcatgaaccatgtaatacgaggcaatggacaaccgctataa]
# protein sequence = [MGPLLCLAFINDLPDAVSSPVKLFADDCFIYRSINSAGDNIIFQQDLAALETWEKEWQISSQVLLKTAVTEVYSSGME
# QNVEQTVNIMFNEGSQRSFINQKLASELQLEMIGKEVINAAGFVSKKTEVRHLDKVQLSIIGEGNQSIPIDVLVVPQIGVPIQTHSAEIKQLPHLRHL
# NLAHASPSDQPFEIEILIGADYYRDFIMNHVIRGNGQPL]
# end gene g3
###
# start gene g4
Contig269	AUGUSTUS	gene	16550	17029	0.5	-	.	g4
Contig269	AUGUSTUS	transcript	16550	17029	0.5	-	.	g4.t1
Contig269	AUGUSTUS	stop_codon	16550	16552	.	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig269	AUGUSTUS	CDS	16550	17029	0.5	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig269	AUGUSTUS	start_codon	17027	17029	.	-	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgcgagacatcattagacctgaggcaaagcagaacccgaagaagttatggtccttcctaaaggggaagaagcaagaaa
# catccggtgttgcaccactccataacccagatggcctcatccacagcgactctgggactaaagccaacatattgaaggcccggttcaagtcagtcttt
# acaaaaagggacctaagcagcatgccggacaaaggcccctgttcatacaacgatatggagcccatcaccatcactactcccggcgtggaaaaactgct
# gcaaactcttcagccccataaagccacaggaccagacaaaattccatctcgacttctaaaggaactctcttgcgaactggcaccagcacttactcata
# tctaccagacctccctgaatgcaggaattgtcccaaatgactggaatatggcgcacgttgtcccaatcttcaagaagggcgacaagtcaaaggcgtcc
# aactactga]
# protein sequence = [MRDIIRPEAKQNPKKLWSFLKGKKQETSGVAPLHNPDGLIHSDSGTKANILKARFKSVFTKRDLSSMPDKGPCSYNDM
# EPITITTPGVEKLLQTLQPHKATGPDKIPSRLLKELSCELAPALTHIYQTSLNAGIVPNDWNMAHVVPIFKKGDKSKASNY]
# end gene g4
###
# start gene g5
Contig269	AUGUSTUS	gene	17189	21011	0.77	+	.	g5
Contig269	AUGUSTUS	transcript	17189	21011	0.77	+	.	g5.t1
Contig269	AUGUSTUS	start_codon	17189	17191	.	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig269	AUGUSTUS	intron	17259	17954	0.99	+	.	transcript_id "g5.t1"; gene_id "g5";
Contig269	AUGUSTUS	intron	18164	20714	0.97	+	.	transcript_id "g5.t1"; gene_id "g5";
Contig269	AUGUSTUS	CDS	17189	17258	0.8	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig269	AUGUSTUS	CDS	17955	18163	0.99	+	2	transcript_id "g5.t1"; gene_id "g5";
Contig269	AUGUSTUS	CDS	20715	21011	0.99	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig269	AUGUSTUS	stop_codon	21009	21011	.	+	0	transcript_id "g5.t1"; gene_id "g5";
# coding sequence = [atgcctagagcgggtaaaattgtttggaacatgaatgtccatcaggctcatgaggttgtctctgaaggatagatgagcc
# caagtgtggctcacgagcctctctgctctaatgtatcgtccaacggattgttaagatcatggggaaagattgctcgccacttactcgtcatacgcgac
# gtcataacatatcgccccactgggatgcctgtccatttcaactccgagcaagagcgaagacacggaaagttgatagaagacagtgaaagaagtcgatc
# tgatgtaggacccaacagcaacctcatccccaaaacgacaagagtgtctggaaccacaaaaccttcgaagacagtgaaagaacacatcattggtaatc
# ttccaaagatcaataacaaaattccggaggactcagaatatcaggttgttcataacaatgccgaaccagcattattgtggcacagagagcctgttaaa
# caataccgtagtctcttcattggacggtcgctgcctttcaaacttcgtaatgtcttcagacagagaccagacatctcggccactggaggcgtcctaat
# gctgtaa]
# protein sequence = [MPRAGKIVWNMNVHQAHEVVSEGXMSPSVAHEPLCSNVSSNGLLRSWGKIARHLLVIRDVITYRPTGMPVHFNSEQER
# RHGKLIEDSERSRSDVGPNSNLIPKTTRVSGTTKPSKTVKEHIIGNLPKINNKIPEDSEYQVVHNNAEPALLWHREPVKQYRSLFIGRSLPFKLRNVF
# RQRPDISATGGVLML]
# end gene g5
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CIV.prfl --predictionStart=0  --predictionEnd=21565  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig26920180911_busco_2432604931_.temp