# 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..33]--> unknown_A (108) <--[0..9]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig4036520180911_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 = 9519, name = Contig40365) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig40365	AUGUSTUS	gene	1006	8016	0.01	+	.	g1
Contig40365	AUGUSTUS	transcript	1006	8016	0.01	+	.	g1.t1
Contig40365	AUGUSTUS	tss	1006	1006	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	exon	1006	1119	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	exon	1493	1664	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	exon	3498	3722	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	start_codon	3671	3673	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	intron	3723	3974	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	intron	3999	6153	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	intron	6321	7657	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	CDS	3671	3722	0.02	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	CDS	3975	3998	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	exon	3975	3998	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	CDS	6154	6320	0.03	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	exon	6154	6320	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	CDS	7658	7747	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	exon	7658	8016	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	stop_codon	7745	7747	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	tts	8016	8016	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	protein_match	3671	3722	14.5	+	0	target "unknown_A[1..18]"; target_start 0; transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	protein_match	3975	3998	8.88	+	1	target "unknown_A[18..26]"; target_start 0; transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	protein_match	6154	6320	14.5	+	1	target "unknown_A[26..82]"; target_start 0; transcript_id "g1.t1"; gene_id "g1";
Contig40365	AUGUSTUS	protein_match	7658	7738	11.7	+	0	target "unknown_A[82..108]"; target_start 0; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcaaagcatcacccagatcttattttctgcagaaaacagcctggcgtagctattggtagagtttgtgaaaaatgtg
# atggtaaatgtgtgatatgtgactcctacgtccggccctgtacattggtgcggatctgtgacgagtgtaattatggctcttatcaaggtcgctgtgtc
# atctgtggaggtccgggagtctcagacgcttactactgcaaagagtgtaccatcatggagaaggatagggatggatgtccaaaaattgtaaacttagg
# aagtgcaaagactgatttgttttatgagagaaagaaatatggatttaagaagagatga]
# protein sequence = [MAKHHPDLIFCRKQPGVAIGRVCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIM
# EKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR]
# sequence of block unknown_A     0 [MAKHHPDLIFCRKQPGVAIGRVCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIMEKDRDGCPKIVNLGSAKTDLFYERKKYGFK] 108
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093711E9.prfl --predictionStart=0  --predictionEnd=27723  --species=fly ./tmp/Contig4036520180911_busco_2432604931_.temp