# 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..194]--> unknown_A (12) <--[1..32]--> unknown_B (56) <--[0..60]--> unknown_C (61) <--[12..92]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig4559320180911_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 = 16659, name = Contig45593) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig45593	AUGUSTUS	gene	5255	16265	0.01	-	.	g1
Contig45593	AUGUSTUS	transcript	5255	16265	0.01	-	.	g1.t1
Contig45593	AUGUSTUS	tts	5255	5255	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	5255	5955	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	stop_codon	5834	5836	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	intron	5956	7904	0.03	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	intron	8034	8287	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	intron	8341	11014	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	intron	11055	13655	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	intron	13731	15501	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	intron	15579	16137	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	5834	5955	0.05	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	7905	8033	0.03	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	7905	8033	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	8288	8340	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	8288	8340	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	11015	11054	0.01	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	11015	11054	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	13656	13730	0.01	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	13656	13730	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	15502	15578	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	15502	15578	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	CDS	16138	16160	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	exon	16138	16265	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	start_codon	16158	16160	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	tss	16265	16265	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	5903	5955	4.71	-	2	target "unknown_C[44..61]"; target_start 89; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	7905	8033	7.62	-	2	target "unknown_C[1..44]"; target_start 89; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	8288	8288	1	-	0	target "unknown_C[1..1]"; target_start 89; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	8289	8340	10.5	-	1	target "unknown_B[39..56]"; target_start 33; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	11015	11054	14.4	-	2	target "unknown_B[26..39]"; target_start 33; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	13656	13730	10.9	-	2	target "unknown_B[1..26]"; target_start 33; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	15502	15502	1	-	0	target "unknown_B[1..1]"; target_start 33; transcript_id "g1.t1"; gene_id "g1";
Contig45593	AUGUSTUS	protein_match	15506	15541	6.48	-	0	target "unknown_A[1..12]"; target_start 20; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacccctgggggtacattgggaattgagagtaaacatgaggtgacaatattgggcggactcaatgaattcatcgtta
# aatttcatggtccacagggaactccatacgaaggaggggtgtggaaagtccgagtagatctgccagagaaatacccattcaagtcaccctctataggt
# ttcatgaataggatataccaccccaacatagatgaagtatccggtaccgtttgcttagatgtaatcaaccaagcatggacagcaatttatgatctggc
# caatatttttgaggctttcctgccacagcttctgacatatcctaatccaatagacccgttgaatggcgatgctgccgccatgtatctccataagcctg
# aggactacaaaaagaaagtcctagagtatgtgaagaagtatgccacggaggaagcattgcgtgagcatgatgaccagcacagttcctccagcgagtcc
# agtatgagtgacttttctgaggatgaggctcaggacatggagctataa]
# protein sequence = [MTPGGTLGIESKHEVTILGGLNEFIVKFHGPQGTPYEGGVWKVRVDLPEKYPFKSPSIGFMNRIYHPNIDEVSGTVCL
# DVINQAWTAIYDLANIFEAFLPQLLTYPNPIDPLNGDAAAMYLHKPEDYKKKVLEYVKKYATEEALREHDDQHSSSSESSMSDFSEDEAQDMEL]
# sequence of block unknown_C    89 [DLANIFEAFLPQLLTYPNPIDPLNGDAAAMYLHKPEDYKKKVLEYVKKYATEEALREHDDQ] 150
# sequence of block unknown_B    33 [TPYEGGVWKVRVDLPEKYPFKSPSIGFMNRIYHPNIDEVSGTVCLDVINQAWTAIY] 89
# sequence of block unknown_A    20 [LNEFIVKFHGPQ] 32
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UID.prfl --predictionStart=0  --predictionEnd=33755  --species=fly ./tmp/Contig4559320180911_busco_2432604931_.temp