# 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
# --[2..160]--> unknown_A (35) <--[0..37]--> unknown_B (43) <--[3..45]--> unknown_C (67) <--[1..47]--> unknown_D (13) <--[5..87]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig9282920180911_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 = 18922, name = Contig92829) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig92829	AUGUSTUS	gene	77	18921	0.01	+	.	g1
Contig92829	AUGUSTUS	transcript	77	18921	0.01	+	.	g1.t1
Contig92829	AUGUSTUS	exon	77	372	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	1037	1094	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	2589	2671	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	7987	9141	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	11012	11158	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	start_codon	11084	11086	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	intron	11159	12471	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	intron	12577	12762	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	intron	12869	17791	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	intron	17871	18350	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	intron	18491	18799	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	CDS	11084	11158	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	CDS	12472	12576	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	12472	12576	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	CDS	12763	12868	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	12763	12868	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	CDS	17792	17870	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	17792	17870	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	CDS	18351	18490	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	18351	18490	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	CDS	18800	18882	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	exon	18800	18921	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	stop_codon	18880	18882	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	tts	18921	18921	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	11117	11158	2.42	+	0	target "unknown_A[1..14]"; target_start 11; transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	12472	12534	3.71	+	0	target "unknown_A[15..35]"; target_start 11; transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	12535	12576	4.1	+	0	target "unknown_B[1..14]"; target_start 46; transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	12763	12849	7.84	+	0	target "unknown_B[15..43]"; target_start 46; transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	17803	17870	10.2	+	0	target "unknown_C[1..23]"; target_start 99; transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	18351	18483	8.2	+	1	target "unknown_C[23..67]"; target_start 99; transcript_id "g1.t1"; gene_id "g1";
Contig92829	AUGUSTUS	protein_match	18802	18840	6.63	+	0	target "unknown_D[1..13]"; target_start 169; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcagatttaggagagagctcagcaccttcacccccaggggctgtacaacagttattcagaagattgggagagtcga
# aacaaaaccttctggacaaggccacaccatacacaactttcagatgggtctttacagttgttttatttctaatatatggactcagagtttatttgcta
# cagggctggtatatagtcacatacgccttggggatttttcaactaaatcagtttattgcctttttaacaccgaaagttgacccagcttttcaggagca
# agatgatgatgaggacgggccttctctcccgacaaagtctaatgaagaattcagaccgtttatgaggcgattaccagaattcaagttttggtatagtg
# caagtaaagccgttgtcgtggcaatgatatgcacattttttgaagccctgaatattccagttttctggcctattttagttatgtacttcatcatcctg
# tttgtgataaccatgaaacgacaaattagggtaatgaataagtaccgttacgtcccattttctcacggcaagcgtcgataccaggggaaagaggacag
# tggaaaagtggtatcttaa]
# protein sequence = [MADLGESSAPSPPGAVQQLFRRLGESKQNLLDKATPYTTFRWVFTVVLFLIYGLRVYLLQGWYIVTYALGIFQLNQFI
# AFLTPKVDPAFQEQDDDEDGPSLPTKSNEEFRPFMRRLPEFKFWYSASKAVVVAMICTFFEALNIPVFWPILVMYFIILFVITMKRQIRVMNKYRYVP
# FSHGKRRYQGKEDSGKVVS]
# sequence of block unknown_A    11 [PPGAVQQLFRRLGESKQNLLDKATPYTTFRWVFTV] 46
# sequence of block unknown_B    46 [VLFLIYGLRVYLLQGWYIVTYALGIFQLNQFIAFLTPKVDPAF] 89
# sequence of block unknown_C    99 [SLPTKSNEEFRPFMRRLPEFKFWYSASKAVVVAMICTFFEALNIPVFWPILVMYFIILFVITMKRQI] 166
# sequence of block unknown_D   169 [NKYRYVPFSHGKR] 182
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370XO6.prfl --predictionStart=0  --predictionEnd=38483  --species=fly ./tmp/Contig9282920180911_busco_2432604931_.temp