# 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..143]--> unknown_A (33) <--[0..26]--> unknown_B (15) <--[0..2]--> unknown_C (30) <--[1..18]--> unknown_D (10) <--[0..2]--> unknown_E (16) <--[1..652]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig1726520180911_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 = 28100, name = Contig17265) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig17265	AUGUSTUS	gene	28765	45046	0.01	+	.	g1
Contig17265	AUGUSTUS	transcript	28765	45046	0.01	+	.	g1.t1
Contig17265	AUGUSTUS	tss	28765	28765	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	exon	28765	28910	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	start_codon	28858	28860	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	intron	28911	39717	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	intron	39829	41306	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	intron	41329	41879	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	intron	41978	43727	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	CDS	28858	28910	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	CDS	39718	39828	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	exon	39718	39828	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	CDS	41307	41328	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	exon	41307	41328	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	CDS	41880	41977	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	exon	41880	41977	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	CDS	43728	43881	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	exon	43728	44093	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	stop_codon	43879	43881	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	exon	44529	45046	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	tts	45046	45046	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	28900	28910	1.48	+	0	target "unknown_A[1..4]"; target_start 14; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	39718	39805	3.59	+	1	target "unknown_A[4..33]"; target_start 14; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	41311	41328	4.21	+	0	target "unknown_B[1..6]"; target_start 56; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	41880	41906	4.43	+	0	target "unknown_B[7..15]"; target_start 56; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	41913	41977	7.84	+	0	target "unknown_C[1..22]"; target_start 73; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	43728	43752	5.75	+	1	target "unknown_C[22..30]"; target_start 73; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	43756	43785	3.99	+	0	target "unknown_D[1..10]"; target_start 104; transcript_id "g1.t1"; gene_id "g1";
Contig17265	AUGUSTUS	protein_match	43786	43833	2.76	+	0	target "unknown_E[1..16]"; target_start 114; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggacttagcttgccaacatccacatcgtgtcgggcgggggcattctctgttaaccaactgtccgaattagaatatc
# acacagtcgccgatgagacgatggaatctctcactgaggtgtttgaagatctaccagagacagtgcctttggcatatatctggataaacatagatgcc
# caatactcgagtggtgtacttacagtaaaaatcagtgatgaatttgggacatacgtcatcaacaagcaacccagcaacctacagatctggctctcctc
# tccagtcagtggtccttttcgctatgacttcctggaaggaacgtggatttacaaaagaacctcacacactctccatggccttctgtctgatgaagtgt
# ctaaagctctcaatgcctctgtagactttaccaagtgtacctatggctgtcgaaaggaaagttag]
# protein sequence = [MGLSLPTSTSCRAGAFSVNQLSELEYHTVADETMESLTEVFEDLPETVPLAYIWINIDAQYSSGVLTVKISDEFGTYV
# INKQPSNLQIWLSSPVSGPFRYDFLEGTWIYKRTSHTLHGLLSDEVSKALNASVDFTKCTYGCRKES]
# sequence of block unknown_A    14 [AFSVNQLSELEYHTVADETMESLTEVFEDLPET] 47
# sequence of block unknown_B    56 [IDAQYSSGVLTVKIS] 71
# sequence of block unknown_C    73 [FGTYVINKQPSNLQIWLSSPVSGPFRYDFL] 103
# sequence of block unknown_D   104 [GTWIYKRTSH] 114
# sequence of block unknown_E   114 [TLHGLLSDEVSKALNA] 130
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093713HJ.prfl --predictionStart=21880  --predictionEnd=61975  --species=fly ./tmp/Contig1726520180911_busco_2432604931_.temp