# 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
# --[0..42]--> unknown_A (23) <--[0..20]--> unknown_B (6) <--[0..1]--> unknown_C (30) <--[0..1]--> unknown_D (15) <--[0..1]--> unknown_E (38) <--[0..35]--> unknown_F (43) <--[0..45]--> unknown_G (51) <--[0..4]--> unknown_H (22) <--[0..2]--> unknown_I (22) <--[0..34]--> unknown_J (27) <--[1..7]--> unknown_K (13) <--[0..11]--> unknown_L (16) <--[0..2]--> unknown_M (15) <--[0..1]--> unknown_N (28) <--[0..3]--> unknown_O (10) <--[0..4]--> unknown_P (16) <--[0..9]--> unknown_Q (29) <--[0..26]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig16220180911_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 = 27925, name = Contig162) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig162	AUGUSTUS	gene	27409	49064	0.01	+	.	g1
Contig162	AUGUSTUS	transcript	27409	49064	0.01	+	.	g1.t1
Contig162	AUGUSTUS	start_codon	27409	27411	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	27443	27499	0.31	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	27550	28988	0.28	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	29139	29190	0.38	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	29533	34254	0.13	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	34319	40185	0.28	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	40549	47401	0.05	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	intron	47758	47993	0.8	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	27409	27442	0.59	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	27409	27442	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	27500	27549	0.3	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	27500	27549	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	28989	29138	0.28	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	28989	29138	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	29191	29532	0.16	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	29191	29532	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	34255	34318	0.17	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	34255	34318	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	40186	40548	0.16	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	40186	40548	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	47402	47757	0.19	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	47402	47757	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	CDS	47994	48818	0.69	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	exon	47994	49064	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	stop_codon	48816	48818	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig162	AUGUSTUS	tts	49064	49064	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtggacctgtcttgacaggtgctccaagatagggctgttgggtgctggttggaacattacctcagttttctttgtgc
# ttattgttctcgaagatggaaacaaatctccgtcctttgcagttacaaatggcgtgaagcaaggctgtgtgctggctccgactctgttcagtatgatg
# ttcaccgctttgctgttggacgcattcacagaacaagatccaggcgttgatatagagaccaaagttcactaccaaaggataagggaccttttctttgc
# tgatgactgtgccttgaatgcccatacacaatcagacatgcaacatagcctcaacaagttttcaactgcgtgcgacaactttggacttacaataagca
# caaagaaaactgaggtaatgttccaaccagcacccaacagcccctacacagagccagttgtctacatcaagtctgagcgactcaatcctgtggagaaa
# tttacctatcttggaagcaccctgtcaagacaggtccacattgacgacgaggtcaactcccgcacagcaaaagcaagttctgcatttggtcgactgaa
# gaagtctgaagtcggcggtactttgggtggttcccagggtagcaaggtagacaagattgagactacaccccgacatggcactggaatgggtcgcggcg
# ctaggattggaattgggacgcagtgctgggattgggacgcggagctgggatcaggacgcggcgctgggattgggattctgggattgagacatgaaact
# gggattgggacgcggcgctgggatcgggacgcggagctgggattgggattttgtgatgagacatggagcttggattgggacgcggagctgggatcaga
# acgcgaagcgggaatcgggacgcggcgctgggtggggtgcagagttgggattgggacgcggcgcgggatcgggaaagaacccgggtctcccgactttg
# atgcaagatgcgtgtacatgatgtcagaaggtatgaatgaaggcagtaagtatgtaccacgagcagtactcttggacttggaacctgcaaccatggac
# gcagtcagatccggaccatacggcgaacttttccgtccggacaattttgtttttggacattccggcgccgggaacaactgggcgaaaggacactacac
# cgagggagccgagttagtggacactgtcctggacgttctgaggagagaggcagaagcctgcgattgtcttcaaggctttcagatggctcacagtctcg
# ggggtgggacggggtctggtatgggaactctcctcattagcaaaatgaaagaggaatatcccgatagaatcatgacaaccttttccgttttaccttca
# ccaaaggtttcagacgcggttgtggaaccttataacgcgactttgtctgttcaccaactggtcgaaaacacggacgaaacattctgcattgataacga
# ggctctttacgatatatgtttccggaccctcaaattggccacgcccacatacggggatcttaatcacctgctctcagcaactatgtccggcgtaacaa
# cgtgcctccggtttcctggacagcttaacgcagacttaagaaaacttgctgtaaatatggtgccatttcctagactacatttctttataacggggttt
# agccctttaacatccagagggtgtcaacagtatcgaacaatttctgttcccgagcttacacaacaaatgttcgattccaaaaacatgatggccgcctg
# cgatccgcgacatggacgatacctcacagtagctgccatgttcagaggtcgaatgtcgatgaaagaagttgatgaacaaatgttaaacgtccaaaaca
# aaaacacctcatattttgttgaatggattccaaataatgtgaaaattgctgtctgtgacattccccctcgaggattgaaaatgtctgcaacttttatt
# ggaaattcaacttcaattcaggaaatttttaagagaatttcagagcagtttgcagccatgtttagacgcaaagctttcttgcattggtacacagggga
# aggtatggacgaaatggagtttatggaggcagagtccaacatgaatgaccttgtatctgagtaccaacagtaccaggatgcaacggtggaggacgaag
# tagatgattttaacgaggagttagaagaagaagaggaagaatattaa]
# protein sequence = [MWTCLDRCSKIGLLGAGWNITSVFFVLIVLEDGNKSPSFAVTNGVKQGCVLAPTLFSMMFTALLLDAFTEQDPGVDIE
# TKVHYQRIRDLFFADDCALNAHTQSDMQHSLNKFSTACDNFGLTISTKKTEVMFQPAPNSPYTEPVVYIKSERLNPVEKFTYLGSTLSRQVHIDDEVN
# SRTAKASSAFGRLKKSEVGGTLGGSQGSKVDKIETTPRHGTGMGRGARIGIGTQCWDWDAELGSGRGAGIGILGLRHETGIGTRRWDRDAELGLGFCD
# ETWSLDWDAELGSEREAGIGTRRWVGCRVGIGTRRGIGKEPGSPDFDARCVYMMSEGMNEGSKYVPRAVLLDLEPATMDAVRSGPYGELFRPDNFVFG
# HSGAGNNWAKGHYTEGAELVDTVLDVLRREAEACDCLQGFQMAHSLGGGTGSGMGTLLISKMKEEYPDRIMTTFSVLPSPKVSDAVVEPYNATLSVHQ
# LVENTDETFCIDNEALYDICFRTLKLATPTYGDLNHLLSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFITGFSPLTSRGCQQYRTISVPEL
# TQQMFDSKNMMAACDPRHGRYLTVAAMFRGRMSMKEVDEQMLNVQNKNTSYFVEWIPNNVKIAVCDIPPRGLKMSATFIGNSTSIQEIFKRISEQFAA
# MFRRKAFLHWYTGEGMDEMEFMEAESNMNDLVSEYQQYQDATVEDEVDDFNEELEEEEEEY]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370ADO.prfl --predictionStart=27386  --predictionEnd=68740  --species=fly ./tmp/Contig16220180911_busco_2432604931_.temp