# 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..145]--> unknown_A (24) <--[0..5]--> unknown_B (24) <--[0..1]--> unknown_C (24) <--[0..6]--> unknown_D (9) <--[0..3]--> unknown_E (69) <--[0..1]--> unknown_F (16) <--[4..209]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig33420180911_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 = 22259, name = Contig334) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig334	AUGUSTUS	gene	5786	7755	0.01	-	.	g1
Contig334	AUGUSTUS	transcript	5786	7755	0.01	-	.	g1.t1
Contig334	AUGUSTUS	exon	5786	6007	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	stop_codon	5799	5801	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	intron	6008	6648	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	intron	6843	7474	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	CDS	5799	6007	0.01	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	CDS	6649	6842	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	exon	6649	6842	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	CDS	7475	7623	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	exon	7475	7755	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	start_codon	7621	7623	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	tss	7755	7755	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	5853	5900	3.67	-	0	target "unknown_F[1..16]"; target_start 150; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	5901	6007	5.25	-	2	target "unknown_E[34..69]"; target_start 81; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	6649	6748	8.88	-	0	target "unknown_E[1..34]"; target_start 81; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	6749	6775	5.53	-	0	target "unknown_D[1..9]"; target_start 72; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	6776	6842	6.95	-	1	target "unknown_C[2..24]"; target_start 48; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	7475	7479	15.9	-	0	target "unknown_C[1..2]"; target_start 48; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	7480	7551	4.82	-	0	target "unknown_B[1..24]"; target_start 24; transcript_id "g1.t1"; gene_id "g1";
Contig334	AUGUSTUS	protein_match	7552	7623	8.58	-	0	target "unknown_A[1..24]"; target_start 0; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgggacttggagcaatgtgatccaaagaaatgcagtggcaggaagctagggcgcctggggtatgtgaagacactcc
# gtctccaacagaggtttaatgggctgatactgtcgccaatgggaatcaaatgtgtgtctccagaagatagggaagtggtggctcaacatggtgtggca
# gtgatagactgctcttgggcccgtctggaggacacaccattttccagaatgagagggggacaccctcggttattaccttacctagtggctacaaaccc
# aatcaactacggaaagccatgcacactgtcatgtgttgaggcatatgctgcagccttttacataacaggatatgaagaactgggtgaaatactgctgc
# agaagttcaaatgggggcatacattttatgaagtcaataaagaattgttggaaaagtatgccaagtgtaaagacagcgcagaggtggtggctacacag
# aaagagtacctggagcagttagagctggaacacaacaaaccaaaacaaggtagggtagcaaccttcatttgcatgctctag]
# protein sequence = [MWDLEQCDPKKCSGRKLGRLGYVKTLRLQQRFNGLILSPMGIKCVSPEDREVVAQHGVAVIDCSWARLEDTPFSRMRG
# GHPRLLPYLVATNPINYGKPCTLSCVEAYAAAFYITGYEELGEILLQKFKWGHTFYEVNKELLEKYAKCKDSAEVVATQKEYLEQLELEHNKPKQGRV
# ATFICML]
# sequence of block unknown_F   150 [AEVVATQKEYLEQLEL] 166
# sequence of block unknown_E    81 [RLLPYLVATNPINYGKPCTLSCVEAYAAAFYITGYEELGEILLQKFKWGHTFYEVNKELLEKYAKCKDS] 150
# sequence of block unknown_D    72 [FSRMRGGHP] 81
# sequence of block unknown_C    48 [DREVVAQHGVAVIDCSWARLEDTP] 72
# sequence of block unknown_B    24 [TLRLQQRFNGLILSPMGIKCVSPE] 48
# sequence of block unknown_A     0 [MWDLEQCDPKKCSGRKLGRLGYVK] 24
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370S0F.prfl --predictionStart=0  --predictionEnd=26829  --species=fly ./tmp/Contig33420180911_busco_2432604931_.temp