# 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
# --[4..114]--> unknown_A (21) <--[0..16]--> unknown_B (9) <--[1..28]--> unknown_C (23) <--[4..70]--> unknown_D (17) <--[0..12]--> unknown_E (22) <--[0..9]--> unknown_F (9) <--[0..18]--> unknown_G (11) <--[3..26]--> unknown_H (13) <--[0..37]--> unknown_I (35) <--[0..1]--> unknown_J (15) <--[1..130]--> unknown_K (17) <--[0..1]--> unknown_L (38) <--[0..1]--> unknown_M (9) <--[0..3]--> unknown_N (27) <--[4..28]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3947020180911_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 = 20136, name = Contig39470) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig39470	AUGUSTUS	gene	11466	12236	0.86	-	.	g1
Contig39470	AUGUSTUS	transcript	11466	12236	0.86	-	.	g1.t1
Contig39470	AUGUSTUS	stop_codon	11466	11468	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39470	AUGUSTUS	intron	11707	12120	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39470	AUGUSTUS	CDS	11466	11706	0.98	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig39470	AUGUSTUS	CDS	12121	12236	0.86	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39470	AUGUSTUS	start_codon	12234	12236	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcagttagaggaacatccatcagatttaccgatattcttgttttacagtgtaaggagtggacaggtgagaaatgtgg
# aatcagccagagtatccatggtcgggcagctgaaaagagttgaaacagaagaaactgccacagcagaattagaccatcagtttgaggctggtcctcat
# tcagaaggaaccagcacaatcatggaggaagatgaagacgaaagcaatgctaatccaacaaatgaagaacttcaaccttcagagaaaaatgccaacag
# catgcccacatcagattccagtacacagccagagttcaagactcctgatatccctgttgcctcggtaaccatcattttctaa]
# protein sequence = [MQLEEHPSDLPIFLFYSVRSGQVRNVESARVSMVGQLKRVETEETATAELDHQFEAGPHSEGTSTIMEEDEDESNANP
# TNEELQPSEKNANSMPTSDSSTQPEFKTPDIPVASVTIIF]
# end gene g1
###
# start gene g2
Contig39470	AUGUSTUS	gene	12648	13397	0.99	-	.	g2
Contig39470	AUGUSTUS	transcript	12648	13397	0.99	-	.	g2.t1
Contig39470	AUGUSTUS	stop_codon	12648	12650	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig39470	AUGUSTUS	intron	12895	13164	0.99	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig39470	AUGUSTUS	CDS	12648	12894	0.99	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig39470	AUGUSTUS	CDS	13165	13397	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig39470	AUGUSTUS	start_codon	13395	13397	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggtaaggcaaaagccaggtaaaaaaagcaaagccacagccacagacaaggttgagcaaaccgggcgacgccttgtac
# atccgtgtggggtaaagcgggacaccggaagcgcgagcacagacatggccaatccggacgggcaggggaggcagggggcacacgggggagcggaacaa
# cacggagagccgacaacaaaggggccggccagggaggcagcagaagacagggcacgagggcaaggtggaggaagaggggaaacaagaagaaaaacggc
# cacagcaggaaggatgaccagcaggggaggcggggccgcaggcagaaggaaaccagcacaagcaggaggaagggaagaccgaaagcaaggcgaaagca
# acaatgaggaagaacggcaacggcagagaaaaaggccaacagcagggcccgacagcagagccatgannnnnnnnnnnnnnnnnnnnnnnnntttcatc
# agaaattga]
# protein sequence = [MVRQKPGKKSKATATDKVEQTGRRLVHPCGVKRDTGSASTDMANPDGQGRQGAHGGAEQHGEPTTKGPAREAAEDRAR
# GQGGGRGETRRKTATAGRMTSRGGGAAGRRKPAQAGGREDRKQGESNNEEERQRQRKRPTAGPDSRAMXXXXXXXXXFIRN]
# end gene g2
###
# start gene g3
Contig39470	AUGUSTUS	gene	13673	14698	0.95	-	.	g3
Contig39470	AUGUSTUS	transcript	13673	14698	0.95	-	.	g3.t1
Contig39470	AUGUSTUS	stop_codon	13673	13675	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig39470	AUGUSTUS	CDS	13673	14698	0.95	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig39470	AUGUSTUS	start_codon	14696	14698	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggcacatgaggtcaaggaggggaacacgaggacgcaaaagcgagaaaggacggaacggaaagggtgcaaacgggggg
# agcaccagagcagagagggtccgccagcggcgggcggggggcgagaggagaggagaaggggaggaccggagagcggacgaggaagagcgatagaggaa
# cggagagaagaaagtaagcggagagagggcgggaggcagggaagcaccgagacgacagggaaaacgcagcaaggcggcggcgcgagaggaaagagacc
# ggcgaaaagctgccgagccggagagcacgccgaaaaaagagaagaaggagggagcagaagagagacaaaacaaaagagggcaggagacggacgggggg
# gcagacgggagcgaaaagcacgtcaagtgggcggtaaaaggggaaccaagagaagcggcgcggagatgggagccgggaaagaaaggaaggagagcggg
# ggaacggaagaaggcgggaggcaggagggcgcgggcagagaggggggggtaaagggccgggggaaaacagagcaaggaaaggacacgacagaggcaga
# ccgcggagcacgagacaggcaggaggaggcggaaggaaaaagggcagggaaggcacaccggcggagggagaaggggaaaggggagaggaggccgggag
# agaggaacggggaggagggggaagcagaagagggggaaggcgcccggaagatggggagggaagcagcgggctcgggggagggacgtcaggggaacgca
# gagggccaaatcccggcaggcagaaaggagggagggagcaccaaaggaccggagagacaaggacaggggggaccaaggcaggaaggccaaagggcacc
# gagaacagagaggaagaagagggcagcggaggagcggagactcgcgcaaagccaggaaaggcaagggcaccgaggaacaaggaccgcaggggaaaaga
# gagggaaggcgggaggcaacgagggcgggaacagaggaggggaagcaaagaaagaacgaaactaa]
# protein sequence = [MAHEVKEGNTRTQKRERTERKGCKRGEHQSREGPPAAGGGREERRRGGPESGRGRAIEERREESKRREGGRQGSTETT
# GKTQQGGGARGKRPAKSCRAGEHAEKREEGGSRRETKQKRAGDGRGGRRERKARQVGGKRGTKRSGAEMGAGKERKESGGTEEGGRQEGAGREGGVKG
# RGKTEQGKDTTEADRGARDRQEEAEGKRAGKAHRRREKGKGERRPGERNGEEGEAEEGEGARKMGREAAGSGEGRQGNAEGQIPAGRKEGGSTKGPER
# QGQGGPRQEGQRAPRTERKKRAAEERRLAQSQERQGHRGTRTAGEKRGKAGGNEGGNRGGEAKKERN]
# end gene g3
###
# start gene g4
Contig39470	AUGUSTUS	gene	14907	18001	0.43	-	.	g4
Contig39470	AUGUSTUS	transcript	14907	18001	0.43	-	.	g4.t1
Contig39470	AUGUSTUS	stop_codon	14907	14909	.	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	intron	15927	16179	0.56	-	.	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	intron	16780	16852	0.6	-	.	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	intron	17690	17899	0.81	-	.	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	CDS	14907	15926	0.56	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	CDS	16180	16779	0.6	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	CDS	16853	17689	0.5	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	CDS	17900	18001	0.82	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig39470	AUGUSTUS	start_codon	17999	18001	.	-	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgccagggccacaaacacaaagagagcagccagaaagaggagcaacaaaagaagcgcggcgagggcaaacgggcgcga
# gtgcggcgccggggacgcggcaatgcccaagaataaaggcggcacagggcggaggagcaaacggcagaggccaacaggcgaacacaccgcgggacaca
# gggcacaaggaacgcacgccgcgcgcggccagcggggaaagccaggggggacacagcgcgagcaaaaaggccagcgcgggagggagggccgagagggt
# gaaggcgcaaggaggagcaaaaccgacacacaccgcacggccggcgggccacgcagcacagccagagggaggccgggggcaggcaggccagagcagcg
# ggagggggggcaagcgaagcgaggggcggggaaaacgagaagaaaaaagcgggcggagggaacagacagcgctcagggcagggaacggggtgggggtg
# gcggcagggggaacgaaagcggaaggcgagagggaggggggcaacaatggaaagaggggaacagggggcgaacacaaggcagcaagggaggagcgtag
# caaaaaggtaaagagaaggaataaggggaggcaggggaaagagggagcgggagagaaaagacggggggaccgggagcaagggcccaggcgggcgggag
# ggaagggagcacggggaccaacccggagcagccgaaaagaggggaaaggagagcgcaggcggaaaagagacaggagggaggaggcgagggatgacaac
# gggggacgggaggagagagggagagggacagtgaggggagtaggcgagggcgaagacaggggacgggaggggagaggacaggagggggagggagcgag
# gggagaccacgagacggggaggggaagaggaagggacaaggaggaggagcgagggcgagtaccacggacggggagggagggaggagcgaggcgagaca
# ggggacggagggagagagggggagaggacagaggggaggagctgagggcgagaccggggacgggaggagagagagggagagggacaggaggggaggag
# cgagggcgagacaacgggacggggagggggagatgtgggagagggacaggagggaggagcgaggtgcgagacacgggacggagggagagaggaaggac
# aggagggaggagcgaggcgagacacgggacgggaggagagagggggaggggacaggaggggaggaagcgagggcgagacacggacgggagggagaagg
# ggagagggacaggaggggaggagcgagggcgagacacggggacggggagggatggggaggacagtgaggaggagagcgtagggcgagacacgggacgg
# gagggggagaggggagagggacaggaggggaggagcgagggcgagacacgggacggagggaggacagggggagagggacaggaggggaggagcgaggg
# cgagacacgggggacgggagggaagagggagaggacaggagggaggagcaccgatgacacggaacgggaggagaggagagggacaggagagaccacgc
# gaggcggaggcgcacagacgaaggcggagacggcaaaacggcagggaggaacgagacaggacacgaccaggggaggaggcaggaagaggagaagggac
# acgcacaggggaggagggcaggagaggaggaagggacacgcacagggggggagggcaggaagggagaagggaccgcacagggtgggggggaggagggc
# agggaagggagagaagggacacgcacaggggggaggtgagggcagggaagggggaagaagggacacgggcacaggggggaggagggcaggcggaaggg
# agaagggacacgccacaggggggagggagggcagggaagggagaagggacacgcacagggggggggaggagggagggaagggagacaggacactcaca
# ggggggggagagagggaaggagaagggacgcgcatcagggggggaggagggcagggaaggggagaagggacacggacaggggggaggaggggcaggaa
# ggggcagaaggacacgcacaggggggaggagggcagaaggagaagggacacgcacaggggggggggaggagggcaggggaagggagaagggacacgca
# agggagggcaggtaagggagaagggacgcgcacagggaggagggagggaaggcggagaagggacacgcacagggggggaggagggcagggagggagaa
# gggacacgcaacaggcgggagggagggagaggaaacagcaaggacgccgcaggaggaggcaggcggggcggaagggaaggacaggagggggaaagcgc
# gagaacagggaatggaaggggggaggaagagggggcggggggcggacggcgggcaggaggaggcgcgcgagcaacagaggcggacccagaaggggcac
# ggggcggccagccagcggggcgggcggccggccgccgggccagcaacagaggaggaacacgaaacgcaaaaccgagacacgggacagagcgaacgggg
# ggtacacgggggaacagagggagagggtag]
# protein sequence = [MPGPQTQREQPERGATKEARRGQTGASAAPGTRQCPRIKAAQGGGANGRGQQANTPRDTGHKERTPRAASGESQGGHS
# ASKKASAGGRAERVKAQGGAKPTHTARPAGHAAQPEGGRGQAGQSSGRGGKRSEGRGKREEKSGRREQTALRAGNGVGVAAGGTKAEGEREGGNNGKR
# GTGGEHKAAREERSKKVKRRNKGRQGKEGAGEKRRGDREQGPRRAGGKGARGPTRSSRKEGKGERRRKRDRREEARDDNGGREERGRGTVRGVGEGED
# RGREGRGQEGEGARGDHETGRGRGRDKEEERGRVPRTGREGGARRDRGRRERGGEDRGEELRARPGTGGERGRGTGGEERGRDNGTGRGRCGRGTGGR
# SEVRDTGRRERGRTGGRSEARHGTGGERGRGQEGRKRGRDTDGREKGRGTGGEERGRDTGTGRDGEDSEEESVGRDTGREGERGEGQEGRSEGETRDG
# GRTGGEGQEGRSEGETRGTGGKRERTGGRSTDDTEREERRGTGETTRGGGAQTKAETAKRQGGTRQDTTRGGGRKRRRDTHRGGGQERRKGHAQGGRA
# GREKGPHRVGGRRAGKGEKGHAQGGGEGREGGRRDTGTGGRRAGGREKGHATGGREGREGRRDTHRGGEEGGKGDRTLTGGGEREGEGTRIRGGGGQG
# RGEGTRTGGRRGRKGQKDTHRGEEGRRRRDTHRGGGGGQGKGEGTRKGGQVREKGRAQGGGREGGEGTRTGGEEGREGEGTRNRREGGRGNSKDAAGG
# GRRGGREGQEGESARTGNGRGEEEGAGGGRRAGGGARATEADPEGARGGQPAGRAAGRRASNRGGTRNAKPRHGTERTGGTRGNRGRG]
# end gene g4
###
# start gene g5
Contig39470	AUGUSTUS	gene	18168	19460	0.23	-	.	g5
Contig39470	AUGUSTUS	transcript	18168	19460	0.23	-	.	g5.t1
Contig39470	AUGUSTUS	stop_codon	18168	18170	.	-	0	transcript_id "g5.t1"; gene_id "g5";
Contig39470	AUGUSTUS	intron	18869	19048	0.48	-	.	transcript_id "g5.t1"; gene_id "g5";
Contig39470	AUGUSTUS	CDS	18168	18868	0.48	-	2	transcript_id "g5.t1"; gene_id "g5";
Contig39470	AUGUSTUS	CDS	19049	19460	0.4	-	0	transcript_id "g5.t1"; gene_id "g5";
Contig39470	AUGUSTUS	start_codon	19458	19460	.	-	0	transcript_id "g5.t1"; gene_id "g5";
# coding sequence = [atgagcgcgacagaaagccataggaggacggggggcgagagcgtggggaccacaatgaggtgccaaagcgggagagaga
# gagggcggcggggggagcgggggaaagaggggggagcaggggaagcggagggggcgcagcagcaggggaagcaggtgaggggggcagggagcaaggcc
# gggcaagtgcagaaatggggggcgcgagggagcggcaggacagcggaggccacccgggaaaggggaggggcagacaaagcggtcgcgggaggccagac
# catgtgcagccgtgggaaagggaaaggaagccaggtacgcaggcgaagccaggggaaaggaaaggaagggaaagaggaccacacagagggccgcagga
# caacaggcgaagagagagacgggggaaagaggaagcgaggcagcgaggaagagaaggcggaagacggaggaaaaggagctaaccgggaaccgactggg
# gcaacggagaggcagaacgcacagcgggaccgctgggaccccagagagagagagcgggaaggaggcggaggcagagggaaagggaggaaatgcaggga
# ccggagggaaggagggcccgagccggggcggaagggaaagagggaaagccgggaacgaaggcagaaagggcagaggccagaaggcacgagggcaagag
# gcgaggagcacacaacgagcaggaaagacataggggaagggacggtgcaggggcacaagccgaagggggcgcggggggggggaacggcggcaagcgcg
# ccgcgggcgccccgccggggggaaagaggacgacggcaaacaaacaacaaagcgaaaaaggcggagggggaaagagaaaggaaagtaaaagaggtccg
# ggatagagcgggagggagaaaggaagcgggaacgcgggctgagggcgaggaaagggagggaaggcgggtaccggaggaaagtagggcccgcgccaagg
# ggcggaaagaggaaagccctgtggtaacgcaggcagaaaggccagaggccagaaagcaccgtgcaggcaaggcccgcgagaaggggcaacagagggcc
# acaagcgggcggaggaagatagggaaaaggaggggaccgggacgacggggctaa]
# protein sequence = [MSATESHRRTGGESVGTTMRCQSGRERGRRGERGKEGGAGEAEGAQQQGKQVRGAGSKAGQVQKWGARGSGRTAEATR
# ERGGADKAVAGGQTMCSRGKGKGSQVRRRSQGKGKEGKEDHTEGRRTTGEERDGGKRKRGSEEEKAEDGGKGANREPTGATERQNAQRDRWDPRERER
# EGGGGRGKGRKCRDRREGGPEPGRKGKRESRERRQKGQRPEGTRARGEEHTTSRKDIGEGTVQGHKPKGARGGGTAASAPRAPRRGERGRRQTNNKAK
# KAEGERERKVKEVRDRAGGRKEAGTRAEGEEREGRRVPEESRARAKGRKEESPVVTQAERPEARKHRAGKAREKGQQRATSGRRKIGKRRGPGRRG]
# end gene g5
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370PLC.prfl --predictionStart=4544  --predictionEnd=44642  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3947020180911_busco_2432604931_.temp