# 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..14]--> unknown_A (48) <--[0..2]--> unknown_B (65) <--[0..24]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig3152820180911_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 = 5405, name = Contig31528) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig31528	AUGUSTUS	gene	40	3944	0.01	+	.	g1
Contig31528	AUGUSTUS	transcript	40	3944	0.01	+	.	g1.t1
Contig31528	AUGUSTUS	exon	40	122	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	start_codon	96	98	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	123	220	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	241	427	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	457	773	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	794	849	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	864	1093	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	1140	2841	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	intron	2967	3581	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	96	122	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	221	240	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	221	240	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	428	456	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	428	456	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	774	793	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	774	793	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	850	863	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	850	863	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	1094	1139	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	1094	1139	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	2842	2966	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	2842	2966	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	CDS	3582	3702	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	exon	3582	3944	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	stop_codon	3700	3702	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	tts	3944	3944	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	224	240	0.865	+	0	target "unknown_A[1..6]"; target_start 10; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	428	456	1.23	+	0	target "unknown_A[7..16]"; target_start 9; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	774	793	1	+	1	target "unknown_A[16..23]"; target_start 9; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	850	863	0.615	+	2	target "unknown_A[23..27]"; target_start 9; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	1094	1139	5.23	+	0	target "unknown_A[28..43]"; target_start 9; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	2842	2859	3.58	+	0	target "unknown_A[43..48]"; target_start 10; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	2860	2966	5.32	+	0	target "unknown_B[1..36]"; target_start 58; transcript_id "g1.t1"; gene_id "g1";
Contig31528	AUGUSTUS	protein_match	3582	3669	4.62	+	1	target "unknown_B[36..65]"; target_start 58; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagtatgagaccagtttacatcaagtattctacaattcttcaaaatgggaacctaataaatacatttgatgctcttt
# ttacttcatatgttactttgttttgtaaacaacaacagctggatgcccaatttaatgaaaattccctagtaaaagaggagctcgatcgtgtggaagac
# ctagacagtgtatacaaaatgattggtccagtattggtcaaacaagatgtgacagaagctaaacagaacgtccagaaaaggatagactacattaatgg
# agaaattaaaagacatgatggtgtaataaaagatttagaaaagaaacaagagagccagagagaggccctgactaaacttcagcatcaattacagcagc
# aacaggtcaaagctgctgcccggtcgtag]
# protein sequence = [MSMRPVYIKYSTILQNGNLINTFDALFTSYVTLFCKQQQLDAQFNENSLVKEELDRVEDLDSVYKMIGPVLVKQDVTE
# AKQNVQKRIDYINGEIKRHDGVIKDLEKKQESQREALTKLQHQLQQQQVKAAARS]
# sequence of block unknown_A    10 [STILQNGNLINTFDALFTSYVTLFCKQQQLDAQFNENSLVKEELDRVE] 58
# sequence of block unknown_B    58 [DLDSVYKMIGPVLVKQDVTEAKQNVQKRIDYINGEIKRHDGVIKDLEKKQESQREALTKLQHQLQ] 123
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093719IK.prfl --predictionStart=0  --predictionEnd=22967  --species=fly ./tmp/Contig3152820180911_busco_2432604931_.temp