# 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..191]--> unknown_A (9) <--[4..23]--> unknown_B (22) <--[9..12]--> unknown_D (13) <--[0..11]--> unknown_E (20) <--[0..3]--> unknown_F (11) <--[7..119]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig1602320180911_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 = 13568, name = Contig16023) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig16023	AUGUSTUS	gene	1256	4964	0.07	+	.	g1
Contig16023	AUGUSTUS	transcript	1256	4964	0.07	+	.	g1.t1
Contig16023	AUGUSTUS	tss	1256	1256	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig16023	AUGUSTUS	exon	1256	1312	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig16023	AUGUSTUS	exon	2315	4964	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig16023	AUGUSTUS	start_codon	2323	2325	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig16023	AUGUSTUS	CDS	2323	4344	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig16023	AUGUSTUS	stop_codon	4342	4344	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig16023	AUGUSTUS	tts	4964	4964	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcaacccttgaaagaggacattgagaggatgaggggtaagcaggaaaatctggctttctggcagagaagacggcgtt
# tcctgacggttcattggaacaagttcccccgcgaggacctcgttagcctgtcgtactgctacagcagtgtaatggtgtatagctgccggtatccccag
# gctatgatggacaaactgtatggtcttgctctagaagtggctgataacctccacaaggaagaaagcatggcgcttccgcgggaaatccgcagaaagtg
# gaacgaggctatgacggaaccagaaaccctggggcagattgagctttacaagatggaggaagagactggagagtctgcagatgatgaaggggacacaa
# tggatgtagcaggttacactgaacaaggacagccaaacatggaggagaaagcaataaaggaccttgatgaaaaagagcaaactccattgattaatcaa
# tcctcacagaagttactcccagagaacctttctaaggttccatatccatctgatgaagtactccctcttgcatgcaatgggccggaacaaaagatgct
# gaacaaccaactaaagagccctccattatgtggactgaacaaccaaacaaacacctcactgaaaagtagagctgcagtgattacaagtaatcaactcc
# caaaagaggaatctgaacatcatcatctagcttcctgtgagccgcaattgagtttgctacagcaacaaaaatcttatcttcaaaaatcttcgcaaaag
# tcccaacacactagtgctgttgatgttaaagtgaaacatcataacagaaaatccaatgtcctattgggaacaggaaggtcacatttgtcagaagtcga
# gcgatctcccggagtgaaggagagacatcaccagatgcacagcgatataaacaaattaaaacagttttacaattcaacaagttacaaagaagtgcgat
# acaaaaagaatgaaccaatgccatctgaatgccctcatcctccaccaactaaagcttgtgctgtagaacagatgccagaagtgcagcgggatggagag
# cacttagggaaaagggggtcacccagtacagcgaacgttctcaaaaagaaacacaatttactgacaaaaaaggttgaacattgtgagaaaatttctac
# taccaagaccagtgttttaaggaagagtaagcaggaagattttggtagaaaggataaatgtggaacttctcaagagcagactactccgtatgacaagg
# ctatagtgcatgaaaggagagaacatgggacatgccataaatctgtgtctactaggagtcatgtggttggtaaagatgacacaataacaaacattaaa
# tcagaaaacaaaaggaagggtgttagggaattgtccacatcaaagtgtgttacacttcacagtcaaggtcaaactggaggggcattttacagaaaaga
# gggaatccaaacccatgttcaaggtcaacctggaaatggatttttcaaaaaggagggaacccaatactatggtcaaagtcaaggtggattttacacca
# aagagggagcccagaccctgaccaaagggaattacccgagctccaaatcagtccaaaacctggcagcatctggaagcagtggtgatatcaagcagagg
# aaagcatcagataacactgaaggagcccagaaaaagtccagggtgatttatccctcccactctagcaaatcttcctcctcgtttaccagaaacaaaat
# ggatgcaaagaatggagaaaaaatagttaaaccagtacagagcaacttctccaagagtcatcttcccaagtcacaagagagcgtagagaaaccagtac
# agagcaacttctccaagagtcatcatcccaagtcacaagagagcgtagagaaacccagatgggcagaacatggcgccaggtctctccatggaccaact
# gcatacaagtcaaacaagtttcctttgaaaaatttctttcaaggtctctttcagaaagccagaaactcctttgactgttag]
# protein sequence = [MQPLKEDIERMRGKQENLAFWQRRRRFLTVHWNKFPREDLVSLSYCYSSVMVYSCRYPQAMMDKLYGLALEVADNLHK
# EESMALPREIRRKWNEAMTEPETLGQIELYKMEEETGESADDEGDTMDVAGYTEQGQPNMEEKAIKDLDEKEQTPLINQSSQKLLPENLSKVPYPSDE
# VLPLACNGPEQKMLNNQLKSPPLCGLNNQTNTSLKSRAAVITSNQLPKEESEHHHLASCEPQLSLLQQQKSYLQKSSQKSQHTSAVDVKVKHHNRKSN
# VLLGTGRSHLSEVERSPGVKERHHQMHSDINKLKQFYNSTSYKEVRYKKNEPMPSECPHPPPTKACAVEQMPEVQRDGEHLGKRGSPSTANVLKKKHN
# LLTKKVEHCEKISTTKTSVLRKSKQEDFGRKDKCGTSQEQTTPYDKAIVHERREHGTCHKSVSTRSHVVGKDDTITNIKSENKRKGVRELSTSKCVTL
# HSQGQTGGAFYRKEGIQTHVQGQPGNGFFKKEGTQYYGQSQGGFYTKEGAQTLTKGNYPSSKSVQNLAASGSSGDIKQRKASDNTEGAQKKSRVIYPS
# HSSKSSSSFTRNKMDAKNGEKIVKPVQSNFSKSHLPKSQESVEKPVQSNFSKSHHPKSQESVEKPRWAEHGARSLHGPTAYKSNKFPLKNFFQGLFQK
# ARNSFDC]
# end gene g1
###
# start gene g2
Contig16023	AUGUSTUS	gene	6329	12605	0.01	-	.	g2
Contig16023	AUGUSTUS	transcript	6329	12605	0.01	-	.	g2.t1
Contig16023	AUGUSTUS	tts	6329	6329	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	exon	6329	7057	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	exon	8864	9169	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	stop_codon	9107	9109	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	intron	9170	9273	0.01	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	intron	9401	10242	0.01	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	intron	10317	12014	0.01	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	CDS	9107	9169	0.01	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	CDS	9274	9400	0.01	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	exon	9274	9400	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	CDS	10243	10316	0.01	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	exon	10243	10316	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	CDS	12015	12062	0.01	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	exon	12015	12069	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	start_codon	12060	12062	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	exon	12549	12605	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	tss	12605	12605	.	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	9140	9169	8.64	-	0	target "unknown_F[2..11]"; target_start 82; transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	9274	9276	6.34	-	0	target "unknown_F[1..1]"; target_start 82; transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	9280	9339	6.05	-	0	target "unknown_E[1..20]"; target_start 61; transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	9343	9381	6.94	-	0	target "unknown_D[1..13]"; target_start 47; transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	10254	10316	8.54	-	0	target "unknown_B[2..22]"; target_start 15; transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	12015	12017	6.94	-	0	target "unknown_B[1..1]"; target_start 15; transcript_id "g2.t1"; gene_id "g2";
Contig16023	AUGUSTUS	protein_match	12036	12062	9.51	-	0	target "unknown_A[1..9]"; target_start 0; transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgttgtatccaaaggaagataacgaaacaaggactatgttgttagcttgcagaaactgtgattaccaagaagaagcca
# ccaatccatgtatttatgtcaacaaaatcacacatgaagtcgatgagctgacccaaattattggagacgtgatagcagaccctaccttgccccgcact
# gaagaccatccgtgtcccaaatgttcccacaaagagtccgttttcttccaatctcacagtaccaaagctgaggaaggtatgcgactctactatgtttg
# caccaattcgcaatgtattcatcgatggaccgagtag]
# protein sequence = [MLYPKEDNETRTMLLACRNCDYQEEATNPCIYVNKITHEVDELTQIIGDVIADPTLPRTEDHPCPKCSHKESVFFQSH
# STKAEEGMRLYYVCTNSQCIHRWTE]
# sequence of block unknown_F    82 [EEGMRLYYVCT] 93
# sequence of block unknown_E    61 [HPCPKCSHKESVFFQSHSTK] 81
# sequence of block unknown_D    47 [GDVIADPTLPRTE] 60
# sequence of block unknown_B    15 [ACRNCDYQEEATNPCIYVNKIT] 37
# sequence of block unknown_A     0 [MLYPKEDNE] 9
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093710JH.prfl --predictionStart=0  --predictionEnd=29399  --species=fly ./tmp/Contig1602320180911_busco_2432604931_.temp