# 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
# --[19..87]--> unknown_B (23) <--[0..1]--> unknown_C (44) <--[14..40]--> unknown_E (29) <--[0..2]--> unknown_F (25) <--[4..13]--> unknown_G (17) <--[1..12]--> unknown_H (29) <--[10..24]--> unknown_I (20) <--[4..9]--> unknown_J (23) <--[1..28]--> unknown_K (27) <--[3..14]--> unknown_L (19) <--[0..1]--> unknown_M (19) <--[0..1]--> unknown_N (30) <--[0..20]--> unknown_O (41) <--[0..1]--> unknown_P (13) <--[0..44]--> unknown_Q (10) <--[0..2]--> unknown_R (17) <--[0..7]--> unknown_S (46) <--[0..213]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2263920180911_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 = 17318, name = Contig22639) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig22639	AUGUSTUS	gene	1	3208	0.29	+	.	g1
Contig22639	AUGUSTUS	transcript	1	3208	0.29	+	.	g1.t1
Contig22639	AUGUSTUS	intron	1	1972	0.54	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22639	AUGUSTUS	intron	2345	2420	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22639	AUGUSTUS	CDS	1973	2344	0.47	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22639	AUGUSTUS	CDS	2421	3208	0.59	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22639	AUGUSTUS	stop_codon	3206	3208	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aagaactagagaccagaatctatccccaatacgaatcagtggcctccgatatccgaaatgagaaagcagatctcgacac
# gaattacgggaaactgaccactactgctgaccaacaaggagatgtcttgcaccgagagatcaccaccattgtcagccaacggaaatctgacattaggg
# agatgaaaagtgaacacctggctgttttagataaacagacagacgacattacaaagaaaatgacggaactcaaacagatcattcaagaactgaagaca
# attctggataccgatgacgtctctctagattctacctatcaatctaggaatgctgagttccgaaagttaccacctaaagtcctagttacatttccaac
# agaagaacatgacgacacaatggcgtcaccagaagctgtatccnnnnnnnnnnnnnnnntcggcgatgaagaagtttggacatctgggacaaataaaa
# tcatgaagctcctcgaccttcagggtaaactactgacatcaatacaaaccgagtccgggaacatgccatgggacatagcggtgacacggagtggcgat
# ctagtttatactgatcctgaggaaagaaccgtaaacctcgtgaagaataaacagacacagaccttgatcagactacagcccgagtggaacccctggaa
# tgtctgcagtacctcctctggtgatctgctggttgtcatggtaaatgatgacctcacacaatccaaagtcgtgcgttacgctggctccacagcgacac
# aaagcattcagtttgatgatcaggataaacctctctattcatctggtactttcatcaaatacatcagtgagaacaagaacctggatatctgtgtggct
# gactatgaagctagagcagtagtggtggtcaatcagtcgggaaaattccgatttaggtacactggtcatcctcctgataccaaggaatcattctatcc
# ttacggcatcactacagacagccaaagtcacatcctaactgcagactgtgacaatggccgcatccacatcctagatcaggacggacagttcctccgct
# acattcagaacttacgtcgtccagtcggtttatgtgtggacatcagagacaacctctttgtggctgacactcccaaagtaaagaaaatccaatacctt
# tga]
# protein sequence = [ELETRIYPQYESVASDIRNEKADLDTNYGKLTTTADQQGDVLHREITTIVSQRKSDIREMKSEHLAVLDKQTDDITKK
# MTELKQIIQELKTILDTDDVSLDSTYQSRNAEFRKLPPKVLVTFPTEEHDDTMASPEAVSXXXXXXGDEEVWTSGTNKIMKLLDLQGKLLTSIQTESG
# NMPWDIAVTRSGDLVYTDPEERTVNLVKNKQTQTLIRLQPEWNPWNVCSTSSGDLLVVMVNDDLTQSKVVRYAGSTATQSIQFDDQDKPLYSSGTFIK
# YISENKNLDICVADYEARAVVVVNQSGKFRFRYTGHPPDTKESFYPYGITTDSQSHILTADCDNGRIHILDQDGQFLRYIQNLRRPVGLCVDIRDNLF
# VADTPKVKKIQYL]
# end gene g1
###
# start gene g2
Contig22639	AUGUSTUS	gene	7225	10582	0.26	-	.	g2
Contig22639	AUGUSTUS	transcript	7225	10582	0.26	-	.	g2.t1
Contig22639	AUGUSTUS	stop_codon	7225	7227	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig22639	AUGUSTUS	intron	7579	8027	0.57	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig22639	AUGUSTUS	intron	8265	10501	0.5	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig22639	AUGUSTUS	CDS	7225	7578	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig22639	AUGUSTUS	CDS	8028	8264	0.58	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig22639	AUGUSTUS	CDS	10502	10582	0.67	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig22639	AUGUSTUS	start_codon	10580	10582	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagacgcccacaccggcagggacagcaagcgcaggaactccgggctcagcattccacaaaaaaatcaccatgacaa
# cagctgcggaatatgagaaagatgaagactctggagtcgtacactcctgtctgtacgtggacgcagcaaacggtattggagcacagaaagttcccatc
# ctgcaatccaaattaggagagctgttaacgacatcttgtcggcgatggaagtggcagattgaatcacgatgtggagctgattttgttaaggttcaaca
# gaaacctccatctggagtcacgttgaccgggccagagatgggcacttgctgttggtgggatgattcttgcgaattacgactggatgtggagcaatgga
# aaaagcatacacagatctccccaacaggacagctcaaggtcaaggtcaaagatcgatccgtgatacagaccactgatgcggaaagaaaagccgcaact
# cctcccgggcttcagagcgccattgatgaagctgttgccaagtacgtcagtggccgctcttttgtgagaccgtccgggacggaggatgttgtccgtgt
# ttatgctgaggcggattcccagtcttctgcgacgcgctggccaatgaggtggctgtcctggtctacagaatggcgggcgggatcggggaggagcctcg
# ggtaa]
# protein sequence = [METPTPAGTASAGTPGSAFHKKITMTTAAEYEKDEDSGVVHSCLYVDAANGIGAQKVPILQSKLGELLTTSCRRWKWQ
# IESRCGADFVKVQQKPPSGVTLTGPEMGTCCWWDDSCELRLDVEQWKKHTQISPTGQLKVKVKDRSVIQTTDAERKAATPPGLQSAIDEAVAKYVSGR
# SFVRPSGTEDVVRVYAEADSQSSATRWPMRWLSWSTEWRAGSGRSLG]
# end gene g2
###
# start gene g3
Contig22639	AUGUSTUS	gene	10628	11469	0.8	+	.	g3
Contig22639	AUGUSTUS	transcript	10628	11469	0.8	+	.	g3.t1
Contig22639	AUGUSTUS	start_codon	10628	10630	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig22639	AUGUSTUS	intron	10705	11225	0.9	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig22639	AUGUSTUS	CDS	10628	10704	0.9	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig22639	AUGUSTUS	CDS	11226	11469	0.8	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig22639	AUGUSTUS	stop_codon	11467	11469	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgctaatcatcggattgatagccacgggtttcactgcagaagtgaagggaaaccataagaaaagtggaagatcaaggg
# cagaatatctgaatgtgaaggcaatatggctggtgttctacagtataattttatgttggtgttcattgacagggcggactatatctgatgtgaaggca
# atatggctggtgtttacgggagacttggagaggacacaacggccaggctcaacaatcggacagtggaacgctggaggcatcgggctgagtgggaaacg
# ccaggctcaacgatcggacagggagacgctggaggcatcgatctga]
# protein sequence = [MLIIGLIATGFTAEVKGNHKKSGRSRAEYLNVKAIWLVFYSIILCWCSLTGRTISDVKAIWLVFTGDLERTQRPGSTI
# GQWNAGGIGLSGKRQAQRSDRETLEASI]
# end gene g3
###
# start gene g4
Contig22639	AUGUSTUS	gene	13188	13616	0.44	-	.	g4
Contig22639	AUGUSTUS	transcript	13188	13616	0.44	-	.	g4.t1
Contig22639	AUGUSTUS	stop_codon	13188	13190	.	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig22639	AUGUSTUS	CDS	13188	13616	0.44	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig22639	AUGUSTUS	start_codon	13614	13616	.	-	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgattcttgcgaattacgactgggatgtggagcaatggaacaaagcatacacagatctccccaacaggcagctcaagg
# tcaaggtcaaagatcgatccgtgatacagaccactgatgcggaaagaaaagccgcaactcctcccgggcttcagagcgccattgatgaagctgttgcc
# aagtacgtcagtggccgctcttttgtgagaccgtccgggacggaggatgttgtccgtgtttatgctgaggcggattcccagtcttctgcggacgcgct
# ggccaatgaggtggctgtcctggtctacagaatggcgggcgggataggggaggagcctcgggtactcgattgggggggggggggctcagcggtaactc
# gcaggattcgggaagggggctcagcggaacacgattgggaggagcctcagcagtaa]
# protein sequence = [MILANYDWDVEQWNKAYTDLPNRQLKVKVKDRSVIQTTDAERKAATPPGLQSAIDEAVAKYVSGRSFVRPSGTEDVVR
# VYAEADSQSSADALANEVAVLVYRMAGGIGEEPRVLDWGGGGSAVTRRIREGGSAEHDWEEPQQ]
# end gene g4
###
# start gene g5
Contig22639	AUGUSTUS	gene	14217	16900	0.22	-	.	g5
Contig22639	AUGUSTUS	transcript	14217	16900	0.22	-	.	g5.t1
Contig22639	AUGUSTUS	stop_codon	14217	14219	.	-	0	transcript_id "g5.t1"; gene_id "g5";
Contig22639	AUGUSTUS	intron	14989	16760	0.73	-	.	transcript_id "g5.t1"; gene_id "g5";
Contig22639	AUGUSTUS	CDS	14217	14988	0.41	-	1	transcript_id "g5.t1"; gene_id "g5";
Contig22639	AUGUSTUS	CDS	16761	16900	0.63	-	0	transcript_id "g5.t1"; gene_id "g5";
Contig22639	AUGUSTUS	start_codon	16898	16900	.	-	0	transcript_id "g5.t1"; gene_id "g5";
# coding sequence = [atgattagcataaagagtgggacgcgcagggaccccgcgacggtggcgatgtgtaggatgaggacgccccacaccggca
# gggacagcaagcgcaggaaactccgggactcagcattccacaaaaaaatcaccatgacaataaaaatggattttgatgacgtgcaagttactggtgaa
# aaaaactatccgaaacgagatgaaatacccattcagtacggcaccgccgggtttagaaccaaaggaaatcgcttggagcatgttatctacaggatggg
# ggtcctggcggccattcgttctgcgtgcaaaaatggcgcggctataggagttatgatcacggcgtctcacaatcccgaggaggataatggcgtgaaat
# tgatggatcctatgggggaaatgctgggtccagactgggaaaagtatgcctctgatgttgcaaatgttcctggtaatgaactagggtcgcttttccag
# actttggtgaaaaatcttggagtgactactcttcaaaatagtctagtcgtgtttgcccgagacacgagaccgagtagccctgttctggcagaagcttt
# agaggcgggcattaaagcagctggtgcccagtttcagaacttcggactccttactacaccacaactgcactatattgttcgttgtatgaacacaaatg
# ggcagtacggaaagccgaccgaggagggctactttgaaaaactgactgatgcttttatcaagctgcggaatatgantggaaaaccgaccgaggaggga
# tattttgaaaaacttactgatgcttttatcaggctgcggaatatgagaaagatgaagactctggagtcgtacaactcctgtctgtacgtggacgcagc
# aaacggtaattggagcacagaaagttcccatcctgcaatccaaaattag]
# protein sequence = [MISIKSGTRRDPATVAMCRMRTPHTGRDSKRRKLRDSAFHKKITMTIKMDFDDVQVTGEKNYPKRDEIPIQYGTAGFR
# TKGNRLEHVIYRMGVLAAIRSACKNGAAIGVMITASHNPEEDNGVKLMDPMGEMLGPDWEKYASDVANVPGNELGSLFQTLVKNLGVTTLQNSLVVFA
# RDTRPSSPVLAEALEAGIKAAGAQFQNFGLLTTPQLHYIVRCMNTNGQYGKPTEEGYFEKLTDAFIKLRNMXGKPTEEGYFEKLTDAFIRLRNMRKMK
# TLESYNSCLYVDAANGNWSTESSHPAIQN]
# end gene g5
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370B1L.prfl --predictionStart=0  --predictionEnd=34918  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2263920180911_busco_2432604931_.temp