# 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..84]--> unknown_A (23) <--[0..1]--> unknown_B (79) <--[4..16]--> unknown_C (75) <--[4..63]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig8654720180911_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 = 6322, name = Contig86547) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig86547	AUGUSTUS	gene	1165	5245	0.01	-	.	g1
Contig86547	AUGUSTUS	transcript	1165	5245	0.01	-	.	g1.t1
Contig86547	AUGUSTUS	tts	1165	1165	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	1165	1454	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	stop_codon	1423	1425	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	intron	1455	2330	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	intron	2520	3251	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	intron	3307	3712	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	intron	3861	4484	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	intron	4569	4745	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	intron	4795	5113	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	1423	1454	0.01	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	2331	2519	0.01	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	2331	2519	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	3252	3306	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	3252	3306	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	3713	3860	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	3713	3860	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	4485	4568	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	4485	4568	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	4746	4794	0.01	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	4746	4794	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	CDS	5114	5162	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	exon	5114	5245	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	start_codon	5160	5162	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	tss	5245	5245	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	1441	1454	1.19	-	2	target "unknown_C[71..75]"; target_start 121; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	2331	2519	4.31	-	2	target "unknown_C[8..71]"; target_start 121; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	3252	3273	1.42	-	0	target "unknown_C[1..8]"; target_start 121; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	3298	3306	2.98	-	0	target "unknown_B[77..79]"; target_start 34; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	3713	3860	8.51	-	1	target "unknown_B[27..76]"; target_start 34; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	4485	4564	5.59	-	0	target "unknown_B[1..27]"; target_start 34; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	4565	4568	12.6	-	1	target "unknown_A[22..23]"; target_start 11; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	4746	4794	3.59	-	2	target "unknown_A[6..22]"; target_start 11; transcript_id "g1.t1"; gene_id "g1";
Contig86547	AUGUSTUS	protein_match	5114	5129	1.41	-	0	target "unknown_A[1..6]"; target_start 11; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatgttatcaatgcttgcctccaattttatatgctttattggcaattcattttattatgtgttaactggtaaaggaa
# caaggatagattttggttggttctttgaacaaacatctccttacctgtgggcttcgttaggagttacttttgccatttccttctcagttgttggtgct
# gcatgggggatattcacaactggtgctagtatcttaggagggggtgtgaaggctcctcgtatcaagaccaagaacctgattagcatcatcttctgtga
# ggctgtagctatttacggaatcatcatggccatcatcataggacagagcattggagcattcgacaaagaaaaggattctccacaagtaatcagagaca
# gctatgatgcaggcttccgtatgtttgcggctggactgagcgtcggggtgtccaatgttgcgtgtgggatcactgtaggaattgtcggctccggagca
# gctctggcagacgcacagaattctacactgtttgtcaaaattctgatccttgaaatctttgccagtgtcattggtttggtgttattggttggaatttt
# acagggccccaaccatgcaaattttttttctgcatga]
# protein sequence = [MMLSMLASNFICFIGNSFYYVLTGKGTRIDFGWFFEQTSPYLWASLGVTFAISFSVVGAAWGIFTTGASILGGGVKAP
# RIKTKNLISIIFCEAVAIYGIIMAIIIGQSIGAFDKEKDSPQVIRDSYDAGFRMFAAGLSVGVSNVACGITVGIVGSGAALADAQNSTLFVKILILEI
# FASVIGLVLLVGILQGPNHANFFSA]
# sequence of block unknown_C   121 [IRDSYDAGFRMFAAGLSVGVSNVACGITVGIVGSGAALADAQNSTLFVKILILEIFASVIGLVLLVGILQGPNHA] 196
# sequence of block unknown_B    34 [FEQTSPYLWASLGVTFAISFSVVGAAWGIFTTGASILGGGVKAPRIKTKNLISIIFCEAVAIYGIIMAIIIGQSIGAFD] 113
# sequence of block unknown_A    11 [CFIGNSFYYVLTGKGTRIDFGWF] 34
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370WYG.prfl --predictionStart=0  --predictionEnd=23859  --species=fly ./tmp/Contig8654720180911_busco_2432604931_.temp