# 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
# --[3..245]--> unknown_A (69) <--[7..12]--> unknown_C (11) <--[6..16]--> unknown_D (11) <--[5..47]--> unknown_E (12) <--[0..9]--> unknown_F (65) <--[0..326]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig8110720180911_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 = 7358, name = Contig81107) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig81107	AUGUSTUS	gene	9	1177	0.01	+	.	g1
Contig81107	AUGUSTUS	transcript	9	1177	0.01	+	.	g1.t1
Contig81107	AUGUSTUS	start_codon	9	11	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	intron	22	417	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	CDS	9	21	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	exon	9	21	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	CDS	418	1103	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	exon	418	1177	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	stop_codon	1101	1103	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	tts	1177	1177	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	protein_match	480	686	3.4	+	0	target "unknown_A[1..69]"; target_start 25; transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	protein_match	708	740	2.99	+	0	target "unknown_C[1..11]"; target_start 101; transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	protein_match	759	791	4.01	+	0	target "unknown_D[1..11]"; target_start 118; transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	protein_match	810	845	3.53	+	0	target "unknown_E[1..12]"; target_start 135; transcript_id "g1.t1"; gene_id "g1";
Contig81107	AUGUSTUS	protein_match	858	1052	4.85	+	0	target "unknown_F[1..65]"; target_start 151; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtaccaaaattgtcaacacaatgatacaccagaagacaaggccttgaaacaaccagattttttcaaagtgagagaaa
# tggtggatatgcatgccttgtacaagaacagagtttacttcggtcatcatcaaggctgccgacatccctttatggtaccctttctctatggagtccgc
# caagacacagatataattgatatagataaaactttacctcgtttacactcggccctgaattttattgcccatatagtgtacagaggagggattgtgct
# gtttatgtcgagaagtgcacagcacatgcctctggtagaaaaaacttctcaaaactgtggggaatactcccattgtcgcttctggaaagggggtcttc
# ttaccaatattgaaagactgttcagcaatctgacgaggtatcctgatgtcgtgatttttgttcacacacaaaacagcatcggtaatgaacacactgct
# gtgacagagtgtgcgaaaatgctaatcccgaccgtaggaatagtagactcgaactgtgatccaacattcattacctatcccattcctgggaacgatga
# ttcacctgacgcagtgaaactgtactgtagactgtttgagcaaaccattttacgtgccaaagaatacagaaaaagagatgggctggattccattgatg
# aaagtcaagctaaagaaaaggttgttaattag]
# protein sequence = [MYQNCQHNDTPEDKALKQPDFFKVREMVDMHALYKNRVYFGHHQGCRHPFMVPFLYGVRQDTDIIDIDKTLPRLHSAL
# NFIAHIVYRGGIVLFMSRSAQHMPLVEKTSQNCGEYSHCRFWKGGLLTNIERLFSNLTRYPDVVIFVHTQNSIGNEHTAVTECAKMLIPTVGIVDSNC
# DPTFITYPIPGNDDSPDAVKLYCRLFEQTILRAKEYRKRDGLDSIDESQAKEKVVN]
# sequence of block unknown_A    25 [EMVDMHALYKNRVYFGHHQGCRHPFMVPFLYGVRQDTDIIDIDKTLPRLHSALNFIAHIVYRGGIVLFM] 94
# sequence of block unknown_C   101 [PLVEKTSQNCG] 112
# sequence of block unknown_D   118 [FWKGGLLTNIE] 129
# sequence of block unknown_E   135 [TRYPDVVIFVHT] 147
# sequence of block unknown_F   151 [GNEHTAVTECAKMLIPTVGIVDSNCDPTFITYPIPGNDDSPDAVKLYCRLFEQTILRAKEYRKRD] 216
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OS5.prfl --predictionStart=0  --predictionEnd=20989  --species=fly ./tmp/Contig8110720180911_busco_2432604931_.temp