# 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
# --[2..210]--> unknown_A (15) <--[0..20]--> unknown_B (18) <--[10..79]--> unknown_D (14) <--[0..7]--> unknown_E (31) <--[0..120]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig278620180911_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 = 12924, name = Contig2786) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig2786	AUGUSTUS	gene	3349	8306	0.01	+	.	g1
Contig2786	AUGUSTUS	transcript	3349	8306	0.01	+	.	g1.t1
Contig2786	AUGUSTUS	exon	3349	3449	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	start_codon	3421	3423	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	intron	3450	6863	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	intron	6960	7030	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	intron	7080	7684	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	CDS	3421	3449	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	CDS	6864	6959	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	exon	6864	6959	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	CDS	7031	7079	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	exon	7031	7079	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	CDS	7685	7861	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	exon	7685	8306	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	stop_codon	7859	7861	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	tts	8306	8306	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	protein_match	3439	3449	0.92	+	0	target "unknown_A[1..4]"; target_start 6; transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	protein_match	6864	6897	9.74	+	1	target "unknown_A[4..15]"; target_start 6; transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	protein_match	6901	6954	5.7	+	0	target "unknown_B[1..18]"; target_start 22; transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	protein_match	7712	7753	4.63	+	0	target "unknown_D[1..14]"; target_start 67; transcript_id "g1.t1"; gene_id "g1";
Contig2786	AUGUSTUS	protein_match	7754	7846	5.07	+	0	target "unknown_E[1..31]"; target_start 81; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtctacagtgaatacatcacagaaatgtcgctgtatgatgtacggctttggggacgacaggaatccatacacagaaa
# gtgttgaactgctagacgatctagtcattgaatacatcacagaaattgttgagatggctagacgatctagttcatgtgaatacatcacagaaatgaca
# aagaaggcaatggaggttgggcgcccaggcagaatttctgtggaagacatcatcttcctgatccgaaaagaccccaagaaatactcgcgtgtgaaaga
# gcttctcatgatgaatgaggaactgaggaaagctagaaaggctttcgatgaaattaaatatgctgccactaaatga]
# protein sequence = [MSTVNTSQKCRCMMYGFGDDRNPYTESVELLDDLVIEYITEIVEMARRSSSCEYITEMTKKAMEVGRPGRISVEDIIF
# LIRKDPKKYSRVKELLMMNEELRKARKAFDEIKYAATK]
# sequence of block unknown_A     6 [SQKCRCMMYGFGDDR] 21
# sequence of block unknown_B    22 [PYTESVELLDDLVIEYIT] 40
# sequence of block unknown_D    67 [PGRISVEDIIFLIR] 81
# sequence of block unknown_E    81 [KDPKKYSRVKELLMMNEELRKARKAFDEIKY] 112
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937122Q.prfl --predictionStart=0  --predictionEnd=27834  --species=fly ./tmp/Contig278620180911_busco_2432604931_.temp