# 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
# --[1..876]--> unknown_A (14) <--[2..34]--> unknown_B (14) <--[0..1]--> unknown_C (12) <--[2..15]--> unknown_D (12) <--[6..12]--> unknown_E (13) <--[2..4]--> unknown_F (19) <--[8..35]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig171820180911_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 = 10619, name = Contig1718) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig1718	AUGUSTUS	gene	368	6306	0.04	+	.	g1
Contig1718	AUGUSTUS	transcript	368	6306	0.04	+	.	g1.t1
Contig1718	AUGUSTUS	exon	368	760	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	start_codon	498	500	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	intron	761	3515	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	intron	3661	4913	0.41	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	intron	5013	5185	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	intron	5461	5732	0.61	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	CDS	498	760	0.32	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	CDS	3516	3660	0.51	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	exon	3516	3660	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	CDS	4914	5012	0.41	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	exon	4914	5012	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	CDS	5186	5460	0.82	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	exon	5186	5460	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	CDS	5733	5829	0.61	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	exon	5733	6306	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	stop_codon	5827	5829	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	tts	6306	6306	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5198	5239	3.25	+	0	target "unknown_A[1..14]"; target_start 173; transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5246	5287	2.17	+	0	target "unknown_B[1..14]"; target_start 189; transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5288	5323	7.1	+	0	target "unknown_C[1..12]"; target_start 203; transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5351	5386	4.37	+	0	target "unknown_D[1..12]"; target_start 224; transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5411	5449	4.84	+	0	target "unknown_E[1..13]"; target_start 244; transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5459	5460	1	+	0	target "unknown_F[1..1]"; target_start 260; transcript_id "g1.t1"; gene_id "g1";
Contig1718	AUGUSTUS	protein_match	5733	5787	3.45	+	1	target "unknown_F[1..19]"; target_start 260; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaacatgaacagttcgtcctctgaagatgagagctcttctgatgaagaattgaaagaagtagccatgaatcttagtg
# aaagtatctcaaaacagatatcgctgaaaagacaagaacagtgcacaggagttgaaactgaaagctccctgtttgttttggacagaaaaccacaaacc
# actgtgaagtcaccgcggggaaatcaaaaggcagaaaattcaaagagtaaagaaaataacaagaaaaccaagaagaaaaagaactatgatggtttatc
# ttcatatattcactccaacattaatctaatggatccaacatctttcaaacaaaatgcatccaaaaaaggaacttcaaacaagaaacagaagagtggaa
# ataaagaagctagcaagtctgatagtactgtacaagaaattatgaaaaagagtgtcatcacaccagattttgaaaaacaagattcacttgaaccatac
# gaggaaagtctaaggaaactgaagcagaaaagaaggaaagagcgagccatgacgaaggggaagggctggtttggtatgtcagcaccagaaatgactga
# tgatgccaaaatgaatctggagatgttgagaatgagaaaagccctggatcccaaaagattctacaagggaaatgatatgaagggtctacccaagttct
# ttcagtttggaaaagttgtcgaatcagcagcagatttctaccactctaggattccaaagaaacaacgaaaagcaaaccttgttcaggagctgttagct
# gatgcagaatttaggagatacaataaaagaaaatatgtggaggttcaggaggccaagatgaaaggagaaggaccttataaacgaatgaaaagagtgaa
# gaaaaagaaaaaataa]
# protein sequence = [MNMNSSSSEDESSSDEELKEVAMNLSESISKQISLKRQEQCTGVETESSLFVLDRKPQTTVKSPRGNQKAENSKSKEN
# NKKTKKKKNYDGLSSYIHSNINLMDPTSFKQNASKKGTSNKKQKSGNKEASKSDSTVQEIMKKSVITPDFEKQDSLEPYEESLRKLKQKRRKERAMTK
# GKGWFGMSAPEMTDDAKMNLEMLRMRKALDPKRFYKGNDMKGLPKFFQFGKVVESAADFYHSRIPKKQRKANLVQELLADAEFRRYNKRKYVEVQEAK
# MKGEGPYKRMKRVKKKKK]
# sequence of block unknown_A   173 [MTKGKGWFGMSAPE] 187
# sequence of block unknown_B   189 [DDAKMNLEMLRMRK] 203
# sequence of block unknown_C   203 [ALDPKRFYKGND] 215
# sequence of block unknown_D   224 [FGKVVESAADFY] 236
# sequence of block unknown_E   244 [RKANLVQELLADA] 257
# sequence of block unknown_F   260 [RYNKRKYVEVQEAKMKGEG] 279
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370ZI7.prfl --predictionStart=0  --predictionEnd=25461  --species=fly ./tmp/Contig171820180911_busco_2432604931_.temp