# 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..34]--> unknown_A (16) <--[1..17]--> unknown_B (13) <--[1..5]--> unknown_C (35) <--[8..29]--> unknown_D (23) <--[1..11]--> unknown_E (20) <--[8..12]--> unknown_G (7) <--[0..5]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig2206520180911_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 = 34126, name = Contig22065) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig22065	AUGUSTUS	gene	406	14447	0.01	+	.	g1
Contig22065	AUGUSTUS	transcript	406	14447	0.01	+	.	g1.t1
Contig22065	AUGUSTUS	tss	406	406	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	exon	406	585	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	exon	827	1032	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	start_codon	960	962	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	intron	1033	2952	0.04	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	intron	3037	4210	0.08	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	intron	4386	14020	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	CDS	960	1032	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	CDS	2953	3036	0.04	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	exon	2953	3036	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	CDS	4211	4385	0.62	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	exon	4211	4385	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	CDS	14021	14138	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	exon	14021	14447	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	stop_codon	14136	14138	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	tts	14447	14447	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	963	1010	5.54	+	0	target "unknown_A[1..16]"; target_start 1; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	1020	1032	11.6	+	0	target "unknown_B[1..5]"; target_start 20; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	2953	2978	6.25	+	2	target "unknown_B[5..13]"; target_start 20; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	2988	3036	5.78	+	0	target "unknown_C[1..17]"; target_start 36; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	4211	4266	6.4	+	2	target "unknown_C[17..35]"; target_start 36; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	4294	4362	6.89	+	0	target "unknown_D[1..23]"; target_start 80; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	4381	4385	3.37	+	0	target "unknown_E[1..2]"; target_start 109; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	14021	14075	7.4	+	1	target "unknown_E[2..20]"; target_start 109; transcript_id "g1.t1"; gene_id "g1";
Contig22065	AUGUSTUS	protein_match	14103	14123	5.25	+	0	target "unknown_G[1..7]"; target_start 138; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcgggggtgttgttcgaagatatttttgatgtgaaggatattgatccagaaggcaagaagtttgatcgagtgtcca
# gacttttttgtgagtctgagtccttcaaaatggacttgatcttagatatcaatacacagatgtaccctgtagacttgggtgacaaattccgtatggtt
# ttagcgaagacgctgagggaagatggtaccccagatgacggtgaatataaccctacagacactggtccctccagagccgacagttttgagtacgtaat
# gcacgggaaggtataccgcattgagggggatgacacaggaccggactccagtcgactggcagcttatgtgtcatatggaggcctgctgatgagactac
# aaggtgatgccaacaatctacatggttttgaagttgattcctttgtttatcttcttataaagaagctagctttttaa]
# protein sequence = [MAGVLFEDIFDVKDIDPEGKKFDRVSRLFCESESFKMDLILDINTQMYPVDLGDKFRMVLAKTLREDGTPDDGEYNPT
# DTGPSRADSFEYVMHGKVYRIEGDDTGPDSSRLAAYVSYGGLLMRLQGDANNLHGFEVDSFVYLLIKKLAF]
# sequence of block unknown_A     1 [AGVLFEDIFDVKDIDP] 17
# sequence of block unknown_B    20 [KFDRVSRLFCESE] 33
# sequence of block unknown_C    36 [MDLILDINTQMYPVDLGDKFRMVLAKTLREDGTPD] 71
# sequence of block unknown_D    80 [GPSRADSFEYVMHGKVYRIEGDD] 103
# sequence of block unknown_E   109 [RLAAYVSYGGLLMRLQGDAN] 129
# sequence of block unknown_G   138 [FVYLLIK] 145
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370YCN.prfl --predictionStart=0  --predictionEnd=34126  --species=fly ./tmp/Contig2206520180911_busco_2432604931_.temp