# 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..38]--> unknown_A (16) <--[0..19]--> unknown_B (10) <--[4..6]--> unknown_C (10) <--[0..2]--> unknown_D (23) <--[3..36]--> unknown_E (40) <--[0..8]--> unknown_F (8) <--[0..2]--> unknown_G (16) <--[0..6]--> unknown_H (7) <--[0..7]--> unknown_I (10) <--[1..27]--> unknown_J (36) <--[26..84]--> unknown_L (23) <--[44..267]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig5793820180911_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 = 4332, name = Contig57938) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig57938	AUGUSTUS	gene	1	4278	0.01	-	.	g1
Contig57938	AUGUSTUS	transcript	1	4278	0.01	-	.	g1.t1
Contig57938	AUGUSTUS	tts	1	1	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	exon	1	756	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	stop_codon	496	498	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	intron	757	2925	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	intron	3131	3621	0.02	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	CDS	496	756	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	CDS	2926	3130	0.02	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	exon	2926	3130	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	CDS	3622	4271	0.03	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	exon	3622	4278	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	start_codon	4269	4271	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	2932	3000	2.91	-	0	target "unknown_L[1..23]"; target_start 260; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	3633	3740	3.77	-	0	target "unknown_J[1..36]"; target_start 177; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	3774	3803	2.3	-	0	target "unknown_I[1..10]"; target_start 156; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	3804	3824	5.87	-	0	target "unknown_H[1..7]"; target_start 149; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	3831	3878	4.62	-	0	target "unknown_G[1..16]"; target_start 131; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	3879	3902	2.85	-	0	target "unknown_F[1..8]"; target_start 123; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	3903	4022	3.69	-	0	target "unknown_E[1..40]"; target_start 83; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	4047	4115	4.08	-	0	target "unknown_D[1..23]"; target_start 52; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	4116	4145	3.92	-	0	target "unknown_C[1..10]"; target_start 42; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	4158	4187	3.79	-	0	target "unknown_B[1..10]"; target_start 28; transcript_id "g1.t1"; gene_id "g1";
Contig57938	AUGUSTUS	protein_match	4188	4235	4.54	-	0	target "unknown_A[1..16]"; target_start 12; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaatgagccagaaattttgacagaggtaccagggacgctgaaacggctgattcgattggttgtccgtggattctaca
# gtctggaacatgcaatgatcatcgaccttctagtgcggaatccttgcatgaaagaagatgatatcgtagagatactcaagtttgaaagaaaacaactc
# cgagctctgataaacacactgaaaacagaaaaatttgtaaaaactcgaatgaaaatggaaactgatgccgagaacaaatccactcgccagacatacta
# ctttattaattatcaagtgtttgtcaatattgtcaaatataaactcgaccatatccgcagaaagattgagatggaagagatgcacaacactagcaggg
# cctcgttcaggtgtctcacgtgtcaaaagactttcaccgacctggaagtgaatgagttgtttgacatgatgagtgggacgtttcgttgtacgttctgt
# gagaatgaggtagaggaagatggtggagcttcatcagtccaagactcccggacattactggctaaattcaacgaacagatacagccagtgtacgacct
# gctacagaagtgtgatgacattaaattagctccggagctactggaaccagaacccactgatctcaacaaaattcacaacaggtcacattcatcaaaga
# cagccaatgcagaccgggaagtttggagtggagacaagaatcgggccgtcaattataacctgggaaacaatgccactgtcaccattagtatgggaggg
# gagggagagacaaataaacaagaggcagtgaaaaaggtccccgtatggatgtcccagagcacagtggagggggcacaggaggacagcaggagctcctt
# tgttaatgaggactccaaacctaaccacatggatgcagccaatcgttcagcggtcaacagtgaaatagaaacaatcctgtacattcatgagaagaaag
# gtggggcaccaggggctgcccttcctggacagaaaaacgaaagctccagcagtgactcggaagatgaaacacccaaattttccaccccgtcacaaaat
# ttaggtatgctatactccaaatttatactgaaagtaaggatacaaacctataagtga]
# protein sequence = [MNEPEILTEVPGTLKRLIRLVVRGFYSLEHAMIIDLLVRNPCMKEDDIVEILKFERKQLRALINTLKTEKFVKTRMKM
# ETDAENKSTRQTYYFINYQVFVNIVKYKLDHIRRKIEMEEMHNTSRASFRCLTCQKTFTDLEVNELFDMMSGTFRCTFCENEVEEDGGASSVQDSRTL
# LAKFNEQIQPVYDLLQKCDDIKLAPELLEPEPTDLNKIHNRSHSSKTANADREVWSGDKNRAVNYNLGNNATVTISMGGEGETNKQEAVKKVPVWMSQ
# STVEGAQEDSRSSFVNEDSKPNHMDAANRSAVNSEIETILYIHEKKGGAPGAALPGQKNESSSSDSEDETPKFSTPSQNLGMLYSKFILKVRIQTYK]
# sequence of block unknown_L   260 [KQEAVKKVPVWMSQSTVEGAQED] 283
# sequence of block unknown_J   177 [AKFNEQIQPVYDLLQKCDDIKLAPELLEPEPTDLNK] 213
# sequence of block unknown_I   156 [CENEVEEDGG] 166
# sequence of block unknown_H   149 [GTFRCTF] 156
# sequence of block unknown_G   131 [CQKTFTDLEVNELFDM] 147
# sequence of block unknown_F   123 [RASFRCLT] 131
# sequence of block unknown_E    83 [NKSTRQTYYFINYQVFVNIVKYKLDHIRRKIEMEEMHNTS] 123
# sequence of block unknown_D    52 [KFERKQLRALINTLKTEKFVKTR] 75
# sequence of block unknown_C    42 [MKEDDIVEIL] 52
# sequence of block unknown_B    28 [EHAMIIDLLV] 38
# sequence of block unknown_A    12 [TLKRLIRLVVRGFYSL] 28
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CK6.prfl --predictionStart=0  --predictionEnd=24259  --species=fly ./tmp/Contig5793820180911_busco_2432604931_.temp