# 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
# --[13..161]--> unknown_B (29) <--[0..13]--> unknown_C (51) <--[0..85]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig11833620180911_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 = 5575, name = Contig118336) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig118336	AUGUSTUS	gene	633	5515	0.01	-	.	g1
Contig118336	AUGUSTUS	transcript	633	5515	0.01	-	.	g1.t1
Contig118336	AUGUSTUS	tts	633	633	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	exon	633	830	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	stop_codon	740	742	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	intron	831	1832	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	intron	1905	5114	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	intron	5249	5399	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	CDS	740	830	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	CDS	1833	1904	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	exon	1833	1904	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	CDS	5115	5248	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	exon	5115	5248	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	CDS	5400	5444	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	exon	5400	5515	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	start_codon	5442	5444	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	tss	5515	5515	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	protein_match	755	830	9.92	-	1	target "unknown_C[26..51]"; target_start 58; transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	protein_match	1833	1904	11.1	-	1	target "unknown_C[2..26]"; target_start 58; transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	protein_match	5115	5119	13.5	-	0	target "unknown_C[1..2]"; target_start 58; transcript_id "g1.t1"; gene_id "g1";
Contig118336	AUGUSTUS	protein_match	5120	5206	7.4	-	0	target "unknown_B[1..29]"; target_start 29; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcacgagcattgtttacctattgtgaatgctgtttctctcttgatggtgaccaaatagacatcttaccagctgatc
# aggctagtcaacctgtggagccgcaaaagagaatcactacaccatacctgacaaaatatgaacgtgctcgggtattaggaacaagagctttgcaaata
# gcgatgtgtgcaccagtgatggtggaactcgagggagaaacggatcctttgctgattgcaatgaaggaacttaaagccaggaagattcccatcatcat
# tcggaggtacctaccggacggcagttttgaggactgggggatagatgaactgctgatgacagaatga]
# protein sequence = [MARALFTYCECCFSLDGDQIDILPADQASQPVEPQKRITTPYLTKYERARVLGTRALQIAMCAPVMVELEGETDPLLI
# AMKELKARKIPIIIRRYLPDGSFEDWGIDELLMTE]
# sequence of block unknown_C    58 [IAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSFEDWGIDEL] 109
# sequence of block unknown_B    29 [QPVEPQKRITTPYLTKYERARVLGTRALQ] 58
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093712Q6.prfl --predictionStart=0  --predictionEnd=25188  --species=fly ./tmp/Contig11833620180911_busco_2432604931_.temp