# 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..101]--> unknown_A (13) <--[0..2]--> unknown_B (16) <--[24..208]--> unknown_D (20) <--[2..6]--> unknown_E (14) <--[5..18]--> unknown_F (16) <--[0..5]--> unknown_G (16) <--[0..51]--> unknown_H (12) <--[0..1]--> unknown_I (18) <--[0..12]--> unknown_J (18) <--[0..9]--> unknown_K (10) <--[12..217]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig5015920180911_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 = 6634, name = Contig50159) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig50159	AUGUSTUS	gene	826	4023	0.02	+	.	g1
Contig50159	AUGUSTUS	transcript	826	4023	0.02	+	.	g1.t1
Contig50159	AUGUSTUS	exon	826	1055	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	start_codon	855	857	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	intron	1056	1452	0.15	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	CDS	855	1055	0.13	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	CDS	1453	2208	0.03	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	exon	1453	4023	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	stop_codon	2206	2208	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	tts	4023	4023	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	939	977	5.64	+	0	target "unknown_A[1..13]"; target_start 28; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	981	1028	5.23	+	0	target "unknown_B[1..16]"; target_start 42; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1570	1629	3.63	+	0	target "unknown_D[1..20]"; target_start 106; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1636	1677	2.65	+	0	target "unknown_E[1..14]"; target_start 128; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1699	1746	3.18	+	0	target "unknown_F[1..16]"; target_start 149; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1750	1797	1.66	+	0	target "unknown_G[1..16]"; target_start 166; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1813	1848	3.54	+	0	target "unknown_H[1..12]"; target_start 187; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1852	1905	2.74	+	0	target "unknown_I[1..18]"; target_start 200; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1915	1968	4.02	+	0	target "unknown_J[1..18]"; target_start 221; transcript_id "g1.t1"; gene_id "g1";
Contig50159	AUGUSTUS	protein_match	1969	1998	3.79	+	0	target "unknown_K[1..10]"; target_start 239; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagtgaaaaaagaggaaagaaacgacccaagtcatactacataaaatgtgccaacaagaaaccaaagagagatgttt
# ggaagctagaggcagggatgaggggattcctcattacttgtaacaacaatgagaaaggggctgttcgagaggcatacaacatcctgaatgagtatgct
# gataaactctatggcccagagaaggatacaccagacacaaagaatgacgaagacttgtcagaagaggaggaggaggaggaggaagacattgaaaaggc
# gatgatgaaggaggtgaaggaaatcaaggagaccaagcttgcacagagacgatttcaaaacaccaatacaagagcaaagaactgcatcttcattagga
# ccaccctaccagatcctagccagttagctcactccatactctctgatctgtccgaaaaaaaggtacaaaaatccaggtacgccattcgtctgcttccg
# atagcaggtagttgtagagcagaggaaagtgaagtgaaaaagcttgggaaagaactattcactccaatctttgagactccagttggaaagggatattc
# tttcagtataattgtgaaaatcaggaacaataatgggcttgggcgagattcagttattcctgccttggctggtatcataaaagagttgaatccgttac
# atcgagtgaatcatgatagaccagattatgttatactggtggaagtgattcaatctgtgtgttgtttggggatagcagaggacttcttcaaattcaaa
# aagtacaacttgcaagagataataaagaaaagcactgagagcaaagcagtgccagtagaattaaacatggaagaaactgttcaagccccaaaggacaa
# tgaggaagaaagtgtacaagcctcaaagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccagaggataa]
# protein sequence = [MSEKRGKKRPKSYYIKCANKKPKRDVWKLEAGMRGFLITCNNNEKGAVREAYNILNEYADKLYGPEKDTPDTKNDEDL
# SEEEEEEEEDIEKAMMKEVKEIKETKLAQRRFQNTNTRAKNCIFIRTTLPDPSQLAHSILSDLSEKKVQKSRYAIRLLPIAGSCRAEESEVKKLGKEL
# FTPIFETPVGKGYSFSIIVKIRNNNGLGRDSVIPALAGIIKELNPLHRVNHDRPDYVILVEVIQSVCCLGIAEDFFKFKKYNLQEIIKKSTESKAVPV
# ELNMEETVQAPKDNEEESVQASKXXXXXXXXXXXXXXXXXXXRG]
# sequence of block unknown_A    28 [LEAGMRGFLITCN] 41
# sequence of block unknown_B    42 [NEKGAVREAYNILNEY] 58
# sequence of block unknown_D   106 [QRRFQNTNTRAKNCIFIRTT] 126
# sequence of block unknown_E   128 [DPSQLAHSILSDLS] 142
# sequence of block unknown_F   149 [RYAIRLLPIAGSCRAE] 165
# sequence of block unknown_G   166 [SEVKKLGKELFTPIFE] 182
# sequence of block unknown_H   187 [GYSFSIIVKIRN] 199
# sequence of block unknown_I   200 [NGLGRDSVIPALAGIIKE] 218
# sequence of block unknown_J   221 [LHRVNHDRPDYVILVEVI] 239
# sequence of block unknown_K   239 [QSVCCLGIAE] 249
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SO4.prfl --predictionStart=0  --predictionEnd=21992  --species=fly ./tmp/Contig5015920180911_busco_2432604931_.temp