# 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..174]--> unknown_A (14) <--[2..7]--> unknown_B (22) <--[0..1]--> unknown_C (10) <--[0..2]--> unknown_D (19) <--[1..39]--> unknown_E (20) <--[6..46]--> unknown_F (37) <--[27..249]--> unknown_H (11) <--[10..42]--> unknown_I (18) <--[2..23]--> unknown_J (14) <--[1..5]--> unknown_K (12) <--[6..150]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig4251920180911_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 = 15456, name = Contig42519) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig42519	AUGUSTUS	gene	6146	15068	0.01	+	.	g1
Contig42519	AUGUSTUS	transcript	6146	15068	0.01	+	.	g1.t1
Contig42519	AUGUSTUS	tss	6146	6146	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	exon	6146	6436	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	exon	12786	15068	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	start_codon	12984	12986	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	CDS	12984	13862	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	stop_codon	13860	13862	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	tts	15068	15068	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	12996	13037	4.28	+	0	target "unknown_A[1..14]"; target_start 4; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13053	13118	8.64	+	0	target "unknown_B[1..22]"; target_start 23; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13122	13151	3.59	+	0	target "unknown_C[1..10]"; target_start 46; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13152	13208	7.59	+	0	target "unknown_D[1..19]"; target_start 56; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13212	13271	6.49	+	0	target "unknown_E[1..20]"; target_start 76; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13290	13400	3.23	+	0	target "unknown_F[1..37]"; target_start 102; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13554	13586	2.18	+	0	target "unknown_H[1..11]"; target_start 190; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13626	13679	4.11	+	0	target "unknown_I[1..18]"; target_start 214; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13695	13736	4.35	+	0	target "unknown_J[1..14]"; target_start 237; transcript_id "g1.t1"; gene_id "g1";
Contig42519	AUGUSTUS	protein_match	13740	13775	5.04	+	0	target "unknown_K[1..12]"; target_start 252; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggacgcatcagcagaaatggaacaatttttcggtgtatatttactgtataatattaacccacagtataaaggcagga
# cttatattggcttcacagtgaacccaaacaggcgaattcagcagcataacaaaggcaaacaggctggcggagcctggaggacgcatggtcggggaccg
# tgggaaatggtgctcgtcattcacggatttccaaatgagatctcagccttacgattcgagtgggcgtggcaaaatccaaagaagtctagaaggttgaa
# gcatttacctgcaaaaacgaagaaagagactcagtttcagtataaattccgaattgtctctgtcatgttgaatacgtgcccatggtgcaggtttgcat
# taaccgttaggtggttaaaacagcagtacattcaggacttttccttggagtttagtccgccatcacacatgcctatagcatacggccccgttaggata
# aaaaagaatgcaacaaataacaaaagaagcagaacgagggcggtgtcagacagccaagatgatgatgacgacgaattactgcatctcctcaggaaaaa
# cgtgaaacacatcaggtgcagtatttgtagagagcgtttgaaggccagtgacagtactctgaagtgtgttcacccaaagtgttcaatgcaggcccaca
# taatatgcctggccaagcggtttcttacaaaccagccgggacaaatcattccagttgatgggaaatgccctttgtgtagggcagtaatcctgtgggga
# gatctgatccgcgccaaacaaggctgctatcagaacttggaggaatgtacgagtacagaagaggacacaggagaagaggactggactgaagagctgca
# gagtcaggtcacctga]
# protein sequence = [MDASAEMEQFFGVYLLYNINPQYKGRTYIGFTVNPNRRIQQHNKGKQAGGAWRTHGRGPWEMVLVIHGFPNEISALRF
# EWAWQNPKKSRRLKHLPAKTKKETQFQYKFRIVSVMLNTCPWCRFALTVRWLKQQYIQDFSLEFSPPSHMPIAYGPVRIKKNATNNKRSRTRAVSDSQ
# DDDDDELLHLLRKNVKHIRCSICRERLKASDSTLKCVHPKCSMQAHIICLAKRFLTNQPGQIIPVDGKCPLCRAVILWGDLIRAKQGCYQNLEECTST
# EEDTGEEDWTEELQSQVT]
# sequence of block unknown_A     4 [AEMEQFFGVYLLYN] 18
# sequence of block unknown_B    23 [KGRTYIGFTVNPNRRIQQHNKG] 45
# sequence of block unknown_C    46 [QAGGAWRTHG] 56
# sequence of block unknown_D    56 [RGPWEMVLVIHGFPNEISA] 75
# sequence of block unknown_E    76 [RFEWAWQNPKKSRRLKHLPA] 96
# sequence of block unknown_F   102 [QFQYKFRIVSVMLNTCPWCRFALTVRWLKQQYIQDFS] 139
# sequence of block unknown_H   190 [VKHIRCSICRE] 201
# sequence of block unknown_I   214 [PKCSMQAHIICLAKRFLT] 232
# sequence of block unknown_J   237 [IIPVDGKCPLCRAV] 251
# sequence of block unknown_K   252 [LWGDLIRAKQGC] 264
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370R67.prfl --predictionStart=0  --predictionEnd=33769  --species=fly ./tmp/Contig4251920180911_busco_2432604931_.temp