# 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..249]--> unknown_A (14) <--[0..8]--> unknown_B (21) <--[0..1]--> unknown_C (22) <--[0..15]--> unknown_D (15) <--[0..1]--> unknown_E (16) <--[1..48]--> unknown_F (28) <--[0..20]--> unknown_G (40) <--[30..46]--> unknown_K (19) <--[0..25]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig1570220180911_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 = 21139, name = Contig15702) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig15702	AUGUSTUS	gene	1	4381	0.28	+	.	g1
Contig15702	AUGUSTUS	transcript	1	4381	0.28	+	.	g1.t1
Contig15702	AUGUSTUS	intron	1	1030	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	intron	1152	1338	0.9	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	intron	1414	1702	0.49	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	intron	1770	3493	0.4	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	intron	3572	4244	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	CDS	1031	1151	0.89	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	CDS	1339	1413	0.69	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	CDS	1703	1769	0.42	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	CDS	3494	3571	0.89	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	CDS	4245	4381	0.84	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig15702	AUGUSTUS	stop_codon	4379	4381	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ttaccagttcaaccccatgcatttccagacgacggtagcatgccagattttactcaaagctctcaccaatatgccgcac
# acagacttcactttgtgtaaatgcttgattgatgcagtcaagcatgacgaggagccaacagcacaggtcatgaatctagcacacttactggaaacctg
# tcagttcagagaattctggggggctttgagaacaaatcctgacttgacatccaacatcagaggatttgatgattcagttagaaaatttgtttgtcatg
# tgatagcagctacataccaaactataccttcagatgtgttaaaagaattactgggagatattccagaggatcaggttcaacagtggattactaaatac
# ggctggaaacatcaggaggatggaaacgttttcatcgtcaatcaggaggagaatatcaaaacaaagaacatcacagagaaaatcacgtttgatagtga
# gtactag]
# protein sequence = [YQFNPMHFQTTVACQILLKALTNMPHTDFTLCKCLIDAVKHDEEPTAQVMNLAHLLETCQFREFWGALRTNPDLTSNI
# RGFDDSVRKFVCHVIAATYQTIPSDVLKELLGDIPEDQVQQWITKYGWKHQEDGNVFIVNQEENIKTKNITEKITFDSEY]
# end gene g1
###
# start gene g2
Contig15702	AUGUSTUS	gene	8727	19801	0.01	-	.	g2
Contig15702	AUGUSTUS	transcript	8727	19801	0.01	-	.	g2.t1
Contig15702	AUGUSTUS	stop_codon	8727	8729	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	intron	8859	12528	0.28	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	intron	12682	13649	0.7	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	intron	13787	14594	0.46	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	intron	14734	17914	0.24	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	intron	18157	19227	0.58	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	intron	19370	19741	0.43	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	8727	8858	0.4	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	12529	12681	0.98	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	13650	13786	0.87	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	14595	14733	0.4	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	17915	18156	0.4	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	19228	19369	0.89	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	CDS	19742	19801	0.36	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig15702	AUGUSTUS	start_codon	19799	19801	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaagcatcctaacagcacgattatgttggttttcggcaagtcgtatcatgacagaaggaataacccagaaaaacttt
# tgcacctgaagaacatatgtaccattctgcaagacagaggacttagaggtggatacaaagactactcatgtctacctccaatagtgcagtggtttgat
# gtgctggagagtagtctcattgtagatgatccttttaagacgaactttggagccagtaactacacagtactagtgcctcatgtgctgcagttatttgc
# gattctgtttcctgaccagaagagatgtcccagccataaacactcctcaattcctggccgaggaaccaaacaagtttatagaacctcatatggagggt
# actgtagattccttatcttacatgagtactttatattgcgagttgattctacaccgtcaaattgtgagaacgatgtacctaagcagaaatcaaccaca
# gtaactgaacacatgaagcagacggacattttatgtaaggcgtatcacggcttggtgttttatgtggaatggacagtggccagaaacaagagccagag
# actgagagatttaggtgaccagctggatgacgatgtgagtgaaaactttgaggacttcatgcgatcctccgcagacaaggcccttaacttcttcgatg
# ttctgagagacatacccggagtgtgggacatttttataacaaagcaagtggagatgttggagtactatgataggctggaggaagcagaaggcgtgtta
# caggcatacaaacagcagaacggggacaatccaaatacgcacaagtacctgtatcacttcgcagtccgccatcactggtcgacatcatccaaagtcag
# tctgctcaagataccgattttcttaggagtgttaaggtctgtgctgttcttatcagaggaagaggacaattatcatcaacagagaaaagatgtgcaga
# tttgtcggagtcaaacgtggacgagcgatttcgatgtcatctga]
# protein sequence = [MKHPNSTIMLVFGKSYHDRRNNPEKLLHLKNICTILQDRGLRGGYKDYSCLPPIVQWFDVLESSLIVDDPFKTNFGAS
# NYTVLVPHVLQLFAILFPDQKRCPSHKHSSIPGRGTKQVYRTSYGGYCRFLILHEYFILRVDSTPSNCENDVPKQKSTTVTEHMKQTDILCKAYHGLV
# FYVEWTVARNKSQRLRDLGDQLDDDVSENFEDFMRSSADKALNFFDVLRDIPGVWDIFITKQVEMLEYYDRLEEAEGVLQAYKQQNGDNPNTHKYLYH
# FAVRHHWSTSSKVSLLKIPIFLGVLRSVLFLSEEEDNYHQQRKDVQICRSQTWTSDFDVI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UG9.prfl --predictionStart=0  --predictionEnd=21139  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig1570220180911_busco_2432604931_.temp