# 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
# --[14..112]--> unknown_B (17) <--[1..4]--> unknown_C (21) <--[86..536]--> unknown_D (33) <--[0..9]--> unknown_E (13) <--[0..1]--> unknown_F (8) <--[0..6]--> unknown_G (27) <--[2..5]--> unknown_H (14) <--[0..5]--> unknown_I (58) <--[0..29]--> unknown_J (20) <--[4..18]--> unknown_K (24) <--[2..12]--> unknown_L (46) <--[0..163]--> unknown_M (108) <--[0..3]--> unknown_N (27) <--[0..1]--> unknown_O (31) <--[2..20]--> unknown_P (27) <--[12..95]--> unknown_R (16) <--[3..8]--> unknown_S (18) <--[0..5]--> unknown_T (32) <--[0..30]--> unknown_U (32) <--[9..50]--> unknown_V (8) <--[5..11]--> unknown_W (13) <--[0..15]--> unknown_X (21) <--[0..2]--> unknown_Y (8) <--[6..23]--> unknown_Z (13) <--[0..11]--> unknown_AA (16) <--[8..132]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig5355720180911_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 = 12907, name = Contig53557) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig53557	AUGUSTUS	gene	3043	10155	0.01	-	.	g1
Contig53557	AUGUSTUS	transcript	3043	10155	0.01	-	.	g1.t1
Contig53557	AUGUSTUS	tts	3043	3043	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	exon	3043	3816	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	exon	4159	4678	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	stop_codon	4542	4544	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	intron	4679	7107	0.32	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	intron	8342	8428	0.44	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	CDS	4542	4678	0.32	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	CDS	7108	8341	0.3	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	exon	7108	8341	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	CDS	8429	10027	0.22	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	exon	8429	10155	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	start_codon	10025	10027	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig53557	AUGUSTUS	tss	10155	10155	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtccgatttctgtggaaaagaggacattaagaaaaagacaaaatacataccattaactgaatatgagaggaagaaaa
# tgtataaggactcacttgaagataaaatttctgaactagaagctcaaaaaatagagtttggaaactctgttcaggatatcaaagacgacatcttaaag
# tttgagggtgttataattaaacaagaagacattgatcaacttctcagaagatatgaaatagaatattccagactggagcaagcgctacctatctatgc
# acagcgcactcgaatagtcaataccgttttagaaaaccaggtgtgtgttcttcttggagagacggggtcaggaaaaagcacgcagttgacccagtatt
# tgctgcagtctaaaatggcctgtgagggtcgtatagtctgcacacaaccaagaaaagttgcagctgctagtcttgcgcaacgagttgcaagtgaaatg
# aagtctaatgtggctgatatagttggctatcagtgtggaattcagaagaaagtttcagatcacacaaaagtggtgtatatgaccgaccatacactcct
# gaacgaatgcctaaaagatcctcttttaaatgactattcctgtataataattgatgaagcacatgagcgaagtatatacactgatctgttgcttggaa
# tgataaagaaatgcttgcaccagcgatcagatattcacgtcattgtgacatctgcaacaattgacccggaagtgtttgtgcgatatttcgaagactgc
# ccagttcttaaagtttcaggtagaatgtatcctgttgacatcgaatgggagcctgtcgagagtgatgaaattttagaaaattatgacaggagggcagt
# tgaaaaaacgttagaaattcatgataaggaacctacgggtgacattctgctgtttctcacagggcaaatggaaattgaaaaatgcattgacaacctac
# gctgggaacttgagggtaaaacggaccatttgatattgccactacatggtaaacttcaaacggaagaacaaaacagaattttcaaagaaacaccacaa
# ggaaaaaggaagattgtgatttccactaatctggcggagacttctgtaacaatacctggggtgaagtacgtcattgatactgggcttgcaaaagaaat
# gctgtatgatcccgagaagaaagtgagctctttaagagtagtcaaaataaccaaaagttcagcggatcaaagaaaaggaagagcaggaagaacggcac
# caggaaagtgttaccgattttattccaaggaagattacgataacatgaaagcatcatctgttccagaaattcggagaattcatgtaggacatgctatt
# ttgaaaattttgcaactgaatttgaatccccttgaatttgattttgtagaaccacctccacataattcgatggaggcagctttccagcaattagtcaa
# acttggcgcagttgaggatggaagaatcacaaaattaggcaaatggatatcacagcttccactggaaccaaatctgggagtccttgttcatgatggca
# ttgaaaagaaaatcggactagaagctatgatcattgccgcatcttgcgctggggaccatttcacatttttaagcgtctttaaaaaatggcatattgtt
# ccagaaaaggagaaagcccagtggtgtttggataattctatcaatggaagggcaatgagaaacatccgggacactgttaaagaaatttcattcaattt
# gagaaaaagtatgaacatttttataaaatttgaattggcagaaggaagtcggaatgaaaaggctttgcaaagtcttttattcaaagcttttcagagca
# acctttgttactttcttggacatgaaaaggctggctattatttcattgacaaagatcaacataggactgttcatccgtctgcgtctttccaatctctt
# gcattgtatccaaaatgggttatcgttgagaaagttttgaacacctctcgagaatatgctgtaaatgtaacggaggttaatgaaaatgacgtacaaga
# ggccttgaaacggaaggagctagactttgatatggcaagaatacaaagaaaaagagtggagccaatttatagagaatatgtaggtccagaacttcaca
# ggcagtttgttggtccccgatggaagaacgcaaaagatatcgaaaaacaattgaaaagccaaaatgcagattctgttttcgtaattgatgctgacagg
# gacaagggcgaaatttcaatttttgctccagaagacaaggacgaatcatcaattaaagcattcaaaatggccatcgacccgaaaagggaaagcataag
# gaatgaaacagtaaacttcccaatcttccctagatgctacaatgtcaatgtatcacttggaccaggtggattgatacaagatatgttgtgcgaagatg
# attataactctgtgtatgtatattgttccgaggatgaatgctattcggatgaaaaattaaaagaatggttgaaacaattcggtgacattaaaaaattt
# gtgaagaaatcgccagcaaatacctctttgaaataccgtggcgaagcagtgtttgaaagcagcgaatctgcgaagaaagcagtcgcagcaacacgtgg
# taaatcttcaaagatttttgtaaaacctcctgcttggaggactgatgactccgatgcctttaaagcgaaaatatcatggtgtcgaagaaaaccgaagg
# catatgggtttgttcagataataaatccagaaacgttggaaactatactagaaatttgtactttaaccaaaatatcggtcggtggatgtccagtgacg
# attagccgtgacaataggctcacagtgggtgtgcccggtcgacagaggatgcttactcctcctagacacctgatctcacctctggtgtatccgtgttt
# accacgctcttattttgtgaccggtcagcagaggacgcttactccatga]
# protein sequence = [MSDFCGKEDIKKKTKYIPLTEYERKKMYKDSLEDKISELEAQKIEFGNSVQDIKDDILKFEGVIIKQEDIDQLLRRYE
# IEYSRLEQALPIYAQRTRIVNTVLENQVCVLLGETGSGKSTQLTQYLLQSKMACEGRIVCTQPRKVAAASLAQRVASEMKSNVADIVGYQCGIQKKVS
# DHTKVVYMTDHTLLNECLKDPLLNDYSCIIIDEAHERSIYTDLLLGMIKKCLHQRSDIHVIVTSATIDPEVFVRYFEDCPVLKVSGRMYPVDIEWEPV
# ESDEILENYDRRAVEKTLEIHDKEPTGDILLFLTGQMEIEKCIDNLRWELEGKTDHLILPLHGKLQTEEQNRIFKETPQGKRKIVISTNLAETSVTIP
# GVKYVIDTGLAKEMLYDPEKKVSSLRVVKITKSSADQRKGRAGRTAPGKCYRFYSKEDYDNMKASSVPEIRRIHVGHAILKILQLNLNPLEFDFVEPP
# PHNSMEAAFQQLVKLGAVEDGRITKLGKWISQLPLEPNLGVLVHDGIEKKIGLEAMIIAASCAGDHFTFLSVFKKWHIVPEKEKAQWCLDNSINGRAM
# RNIRDTVKEISFNLRKSMNIFIKFELAEGSRNEKALQSLLFKAFQSNLCYFLGHEKAGYYFIDKDQHRTVHPSASFQSLALYPKWVIVEKVLNTSREY
# AVNVTEVNENDVQEALKRKELDFDMARIQRKRVEPIYREYVGPELHRQFVGPRWKNAKDIEKQLKSQNADSVFVIDADRDKGEISIFAPEDKDESSIK
# AFKMAIDPKRESIRNETVNFPIFPRCYNVNVSLGPGGLIQDMLCEDDYNSVYVYCSEDECYSDEKLKEWLKQFGDIKKFVKKSPANTSLKYRGEAVFE
# SSESAKKAVAATRGKSSKIFVKPPAWRTDDSDAFKAKISWCRRKPKAYGFVQIINPETLETILEICTLTKISVGGCPVTISRDNRLTVGVPGRQRMLT
# PPRHLISPLVYPCLPRSYFVTGQQRTLTP]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937060I.prfl --predictionStart=0  --predictionEnd=29793  --species=fly ./tmp/Contig5355720180911_busco_2432604931_.temp