# 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
# --[6..53]--> unknown_A (37) <--[2..34]--> unknown_B (54) <--[0..2]--> unknown_C (14) <--[0..223]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig570520180911_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 = 8091, name = Contig5705) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig5705	AUGUSTUS	gene	206	6533	0.01	+	.	g1
Contig5705	AUGUSTUS	transcript	206	6533	0.01	+	.	g1.t1
Contig5705	AUGUSTUS	tss	206	206	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	exon	206	530	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	start_codon	528	530	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	intron	531	876	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	intron	974	1619	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	intron	1820	2085	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	CDS	528	530	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	CDS	877	973	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	exon	877	973	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	CDS	1620	1819	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	exon	1620	1819	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	CDS	2086	2142	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	exon	2086	2220	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	stop_codon	2140	2142	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	exon	2977	3089	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	exon	6149	6533	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	tts	6533	6533	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	protein_match	898	973	5.33	+	0	target "unknown_A[1..26]"; target_start 8; transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	protein_match	1620	1654	6.92	+	2	target "unknown_A[26..37]"; target_start 8; transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	protein_match	1661	1819	11.4	+	0	target "unknown_B[1..53]"; target_start 47; transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	protein_match	2086	2088	8.62	+	0	target "unknown_B[54..54]"; target_start 47; transcript_id "g1.t1"; gene_id "g1";
Contig5705	AUGUSTUS	protein_match	2092	2133	9.32	+	0	target "unknown_C[1..14]"; target_start 102; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtctcactttaaagacaccaaggctccacaagaggaagctcccattcacagaattcgcatcacgttgaccatcagga
# atgtgaaaagtctggaaaaggtgtgtgctgatttgatcaaaggagctaaagagaaatctctgaaggtgaaaggacctgtgcgtatgcccacaaaggtc
# ttgcgaatcaccaccaggaaaaccccttgtggagagggttcaaagacatgggacaggtaccagatgagaatccacaaacgtctcattgatcttcacag
# tccatctgagattgtaaaacagattacatcaatcagtatcgaacccggagtagaggtcgaggttactatcgctgatgcatga]
# protein sequence = [MSHFKDTKAPQEEAPIHRIRITLTIRNVKSLEKVCADLIKGAKEKSLKVKGPVRMPTKVLRITTRKTPCGEGSKTWDR
# YQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA]
# sequence of block unknown_A     8 [APQEEAPIHRIRITLTIRNVKSLEKVCADLIKGAKEK] 45
# sequence of block unknown_B    47 [KVKGPVRMPTKVLRITTRKTPCGEGSKTWDRYQMRIHKRLIDLHSPSEIVKQIT] 101
# sequence of block unknown_C   102 [ISIEPGVEVEVTIA] 116
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09371431.prfl --predictionStart=0  --predictionEnd=26182  --species=fly ./tmp/Contig570520180911_busco_2432604931_.temp