# 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..93]--> unknown_A (64) <--[0..1]--> unknown_B (61) <--[0..33]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig4343120180911_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 = 31400, name = Contig43431) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig43431	AUGUSTUS	gene	7949	17545	0.01	-	.	g1
Contig43431	AUGUSTUS	transcript	7949	17545	0.01	-	.	g1.t1
Contig43431	AUGUSTUS	tts	7949	7949	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	exon	7949	8271	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	stop_codon	8149	8151	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	intron	8272	9952	0.12	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	intron	10094	11250	0.9	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	intron	11427	15657	0.45	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	CDS	8149	8271	0.12	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	CDS	9953	10093	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	exon	9953	10093	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	CDS	11251	11426	0.75	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	exon	11251	11426	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	CDS	15658	15703	0.59	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	exon	15658	15715	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	start_codon	15701	15703	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	exon	17475	17545	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	tss	17545	17545	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	protein_match	8200	8271	5.73	-	0	target "unknown_B[38..61]"; target_start 84; transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	protein_match	9953	10063	8.98	-	0	target "unknown_B[1..37]"; target_start 84; transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	protein_match	10067	10093	10.8	-	0	target "unknown_A[56..64]"; target_start 19; transcript_id "g1.t1"; gene_id "g1";
Contig43431	AUGUSTUS	protein_match	11251	11415	10.2	-	0	target "unknown_A[1..55]"; target_start 19; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtccaggagttatcgccaatcagaaaggatgacgacagtgcaaggcctgaagatgaagttcaacaagatggtatctt
# cctcgaggaggaaaaatagaaagcgccatttcaatgctccctcgcacatccgcaggaagatgatgagttctcccctgtctaaagaacttcgtcagaaa
# tacaatgtcaggagtatgccaatcagaaaggatgacgaagtgcaggttgtccgaggtcactacaaggggcagcaagtaggaaaaattgtccaagtgta
# ccgtaaaaagtttgtggtgtacattgagagaatccagagggaaaaggccaacggagcatctgtccacgtgggaatccatccctccaaggttgttctcg
# tcaaattaaagattgataaggaccgcaaaagaattttggaccgcaaagccaggtcaagacaagttgctgataagggcaagcacaccgaagaaagcatt
# gctatggactcgtaa]
# protein sequence = [MSRSYRQSERMTTVQGLKMKFNKMVSSSRRKNRKRHFNAPSHIRRKMMSSPLSKELRQKYNVRSMPIRKDDEVQVVRG
# HYKGQQVGKIVQVYRKKFVVYIERIQREKANGASVHVGIHPSKVVLVKLKIDKDRKRILDRKARSRQVADKGKHTEESIAMDS]
# sequence of block unknown_B    84 [VGKIVQVYRKKFVVYIERIQREKANGASVHVGIHPSKVVLVKLKIDKDRKRILDRKARSRQ] 145
# sequence of block unknown_A    19 [KFNKMVSSSRRKNRKRHFNAPSHIRRKMMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQ] 83
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937133J.prfl --predictionStart=0  --predictionEnd=31400  --species=fly ./tmp/Contig4343120180911_busco_2432604931_.temp