# 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
# --[11..114]--> unknown_B (23) <--[0..1]--> unknown_C (43) <--[0..38]--> unknown_D (23) <--[0..1]--> unknown_E (6) <--[0..40]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig2115620180911_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 = 22750, name = Contig21156) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig21156	AUGUSTUS	gene	1726	4193	0.01	+	.	g1
Contig21156	AUGUSTUS	transcript	1726	4193	0.01	+	.	g1.t1
Contig21156	AUGUSTUS	exon	1726	2061	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	start_codon	1806	1808	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	intron	2062	2622	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	CDS	1806	2061	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	CDS	2623	2753	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	exon	2623	2757	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	stop_codon	2751	2753	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	exon	3587	4193	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	tts	4193	4193	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	protein_match	1902	1970	4.47	+	0	target "unknown_B[1..23]"; target_start 32; transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	protein_match	1971	2061	9.35	+	0	target "unknown_C[1..31]"; target_start 55; transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	protein_match	2623	2660	8.15	+	2	target "unknown_C[31..43]"; target_start 55; transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	protein_match	2664	2732	8.09	+	0	target "unknown_D[1..23]"; target_start 99; transcript_id "g1.t1"; gene_id "g1";
Contig21156	AUGUSTUS	protein_match	2733	2750	7.98	+	0	target "unknown_E[1..6]"; target_start 122; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagtaaacgaggaggagatacaagtgtttcggcaaagtcagtgccgtcagaaaaccttgtgacggtgctgaagaaat
# tttacgatgagtacatgacatccacgtccaaaaggctgaaaatcgtcgatgcttacctcgtttacattttgcttaccggtgtcgctcagtttgtctac
# tgtgccatcgtcgggacatttccattcaattcctttctttctgggtttatatcaaccgttggttcttttgttttagctgtttgtttgagactccaagt
# caacccccaaaacaagacagattttgttggaattagtccagaaagagcctttgcagacttcatatttgcacatgttattctgcatttagtcgtcatca
# atttcattggttaa]
# protein sequence = [MSKRGGDTSVSAKSVPSENLVTVLKKFYDEYMTSTSKRLKIVDAYLVYILLTGVAQFVYCAIVGTFPFNSFLSGFIST
# VGSFVLAVCLRLQVNPQNKTDFVGISPERAFADFIFAHVILHLVVINFIG]
# sequence of block unknown_B    32 [TSTSKRLKIVDAYLVYILLTGVA] 55
# sequence of block unknown_C    55 [QFVYCAIVGTFPFNSFLSGFISTVGSFVLAVCLRLQVNPQNKT] 98
# sequence of block unknown_D    99 [FVGISPERAFADFIFAHVILHLV] 122
# sequence of block unknown_E   122 [VINFIG] 128
# end gene g1
###
# start gene g2
Contig21156	AUGUSTUS	gene	12476	20452	0.01	+	.	g2
Contig21156	AUGUSTUS	transcript	12476	20452	0.01	+	.	g2.t1
Contig21156	AUGUSTUS	tss	12476	12476	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	exon	12476	12830	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	start_codon	12536	12538	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	intron	12831	13000	0.39	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	intron	13489	15001	0.41	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	intron	15482	18163	0.43	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	intron	18195	19046	0.42	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	CDS	12536	12830	0.24	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	CDS	13001	13488	0.68	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	exon	13001	13488	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	CDS	15002	15481	0.62	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	exon	15002	15481	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	CDS	18164	18194	0.42	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	exon	18164	18194	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	CDS	19047	19216	0.64	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	exon	19047	20452	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	stop_codon	19214	19216	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig21156	AUGUSTUS	tts	20452	20452	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgcgcccaggactgacagatgaccttcaggtcatggatgatgctcgaaaaacagcagtgattgatcgtgaactgcaca
# gactgaacatcgacatagcagccctgcaggaaacgcgactcccagataagggatccctgaaggaggaacactataccttcttctggcaaggaaaaggc
# actgaggaagtaagggaacacggtgttggatttgcagtacgccatacaatgcttcgcatgattgaaccaacaggcggcacagagagaatttttacgct
# acgcctgtcatccatgcagggatgtatacatccggtgaaccttgtttgcgtctacgccccaacacggcaagattcggctgaagtaaaggaccaattct
# acgagtcactagacaccgttgtcagcaagatcccaaagcagagcatatctaccttctttgcgacttcaacgcgcgagtcggtgcagaccgagaatcac
# ggcataggaaagatgaatgagaacggtcagaggcttcttgaactctgctgctaccgcaggctctgcgtgacgaacacctactttcagaacaaggcatg
# tcacaaggtatcctggagacatccgaggtcaaaacactggtatcagctggacatgatcatcaccaaacgtgattccttgaacaacgtttgcaacacca
# ggtcctatcaaagagctgattgcgacaccgatcactccattattgccacaaaggtgaaactgaaaccacgaagtttcatcactcaaagagaaagggtc
# agcctaggatcaacatcagatgtcccctctccaccagcaattcacattgacaacgaggagctagaagtcacagatcacttcacatacccgggctcaac
# catcaccagcaacctctcacttgacgcagaattagacaagcgcgtcgccaaagctgccgccgtcatggcacaactgagcaagagagtgtggaccaaca
# agcaactcactttgaacaccaaactcaaagtctaccaggcgtgcgtactcagtagcctactgtacggcagtgaatcctggacaacatacgccacacaa
# gaaaaccgtctggaaagcttccacattcgctgtctacgacgaattctctgcatcaagtggcaggacaaggtcaccaacaccgaggtgctagaaaaagc
# aagttccctcagcatgcatctcgtgcttcttgccagcgacgtttgtgatggctcggtcacgtacataggatggacggtgggcgcatacccaaagacat
# catgtatgactgtcattttcgtactagatgtgacgactgtaaatgtggaagacctggtgtacttctacagtaatagggacatgcccatgcagggtggg
# aaatcgatacctgttagctacatcgatacctttgtcatgggaaatcagcttcaacagtcatcatacaaggtcaagatgtcagaaaactacctaatact
# cggagtctcgtag]
# protein sequence = [MRPGLTDDLQVMDDARKTAVIDRELHRLNIDIAALQETRLPDKGSLKEEHYTFFWQGKGTEEVREHGVGFAVRHTMLR
# MIEPTGGTERIFTLRLSSMQGCIHPVNLVCVYAPTRQDSAEVKDQFYESLDTVVSKIPKQSISTFFATSTRESVQTENHGIGKMNENGQRLLELCCYR
# RLCVTNTYFQNKACHKVSWRHPRSKHWYQLDMIITKRDSLNNVCNTRSYQRADCDTDHSIIATKVKLKPRSFITQRERVSLGSTSDVPSPPAIHIDNE
# ELEVTDHFTYPGSTITSNLSLDAELDKRVAKAAAVMAQLSKRVWTNKQLTLNTKLKVYQACVLSSLLYGSESWTTYATQENRLESFHIRCLRRILCIK
# WQDKVTNTEVLEKASSLSMHLVLLASDVCDGSVTYIGWTVGAYPKTSCMTVIFVLDVTTVNVEDLVYFYSNRDMPMQGGKSIPVSYIDTFVMGNQLQQ
# SSYKVKMSENYLILGVS]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937129K.prfl --predictionStart=0  --predictionEnd=22750  --species=fly ./tmp/Contig2115620180911_busco_2432604931_.temp