# 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
# --[33..161]--> unknown_A (24) <--[0..2]--> unknown_B (12) <--[0..4]--> unknown_C (65) <--[1..5]--> unknown_D (51) <--[0..17]--> unknown_E (15) <--[0..2]--> unknown_F (67) <--[0..12]--> unknown_G (15) <--[0..21]--> unknown_H (18) <--[0..2]--> unknown_I (10) <--[7..12]--> unknown_K (17) <--[0..6]--> unknown_L (12) <--[0..1]--> unknown_M (15) <--[11..18]--> unknown_O (51) <--[2..8]--> unknown_P (56) <--[0..3]--> unknown_Q (31) <--[0..6]--> unknown_R (23) <--[0..3]--> unknown_S (25) <--[0..6]--> unknown_T (74) <--[0..1]--> unknown_U (82) <--[0..2]--> unknown_V (98) <--[50..460]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3466520180911_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 = 24281, name = Contig34665) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig34665	AUGUSTUS	gene	1	9012	0.05	-	.	g1
Contig34665	AUGUSTUS	transcript	1	9012	0.05	-	.	g1.t1
Contig34665	AUGUSTUS	intron	1	79	0.64	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	intron	288	957	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	intron	965	1226	0.55	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	intron	1400	1986	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	intron	2188	3689	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	intron	3900	4464	0.76	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	intron	4605	8832	0.68	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	80	287	0.28	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	958	964	0.4	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	1227	1399	0.76	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	1987	2187	0.98	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	3690	3899	1	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	4465	4604	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	CDS	8833	9012	0.6	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig34665	AUGUSTUS	start_codon	9010	9012	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagcgtggacgcgtatgccccaaattcccaatccttgactttcctcgagactgaagaggatctcattggggccgaca
# ctcaaggaaccgattatgactatacggatttcaccctaccatcccagacccaatcacagacccaagcttcccaacttgagcatggacaaagtcaaagt
# caggtgaatggcccagaggctcccattcaaaatgggctggataaaggggttgcatcgattgcacagggggtgggggagctcaattttgaggaggagga
# agaagaacagtttatgatgaaagatctccccaagcatgcttgctctcacatcatcaaccatcttgtgagggcaaaggcgaaggaagtgaccctgcaca
# aagatggccccctgggagagactgtcctggagtgctataactgtggctgtcggaatgtcttcctgttaggcttcatcccagccaaggctgactcggtc
# gtcgtcctcctctgtcgccagccctgtgccactctaaccaatttgaaggacatgaactgggaccccagtcagtggcagccgttgatacaggacaggca
# gtttctgtcgtggctcgttaaggttccgtcggaccaggagcagatgaggagtagacaaatcagatcacaaactagaaggaactctggaaggactaacc
# cagaggccacgctggatctagaaaagccaggggtggatgaggaacctacccaagtgttgttaagatacgacgatgcctaccaataccagaacatcttt
# ggaccgctggtgaaattggaggctgactacgacaaaaagctgaaggagtcgcagacccaggacaacattgtagtgcgctgggacgtggggctgaacaa
# gaagaggattgcttatttccatctgcccaaggctaatgatgagatagcgatgcaggcggcgctgaagacgttcgctgtggatgaaacgtctgtgtggg
# gctatatctatcacaagcttctgggacacgaggtggaggacgtggtcattaaatgtcagctccccaagcgattcagtgttcctaacctgcccgagctc
# aaccactcccaggtgtacgccgtcaagaccgtccttcagcgaccgctaagtctgatccag]
# protein sequence = [MSVDAYAPNSQSLTFLETEEDLIGADTQGTDYDYTDFTLPSQTQSQTQASQLEHGQSQSQVNGPEAPIQNGLDKGVAS
# IAQGVGELNFEEEEEEQFMMKDLPKHACSHIINHLVRAKAKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCATLTNLKDMN
# WDPSQWQPLIQDRQFLSWLVKVPSDQEQMRSRQIRSQTRRNSGRTNPEATLDLEKPGVDEEPTQVLLRYDDAYQYQNIFGPLVKLEADYDKKLKESQT
# QDNIVVRWDVGLNKKRIAYFHLPKANDEIAMQAALKTFAVDETSVWGYIYHKLLGHEVEDVVIKCQLPKRFSVPNLPELNHSQVYAVKTVLQRPLSLI
# Q]
# end gene g1
###
# start gene g2
Contig34665	AUGUSTUS	gene	12381	23739	0.02	+	.	g2
Contig34665	AUGUSTUS	transcript	12381	23739	0.02	+	.	g2.t1
Contig34665	AUGUSTUS	start_codon	12381	12383	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	12650	13622	0.8	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	13744	15024	0.25	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	15089	16609	0.13	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	16677	16767	0.68	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	16845	18898	0.78	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	18934	19612	0.79	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	19744	19941	0.76	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	intron	19987	23570	0.42	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	12381	12649	0.6	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	13623	13743	0.57	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	15025	15088	0.25	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	16610	16676	0.68	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	16768	16844	0.99	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	18899	18933	0.8	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	19613	19743	0.79	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	19942	19986	0.74	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	CDS	23571	23739	0.28	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig34665	AUGUSTUS	stop_codon	23737	23739	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggacaggagacttttctatcgtggatccccgatgtatcctgattctcaccgtctgccgcagtttaatccggttattc
# gcttctcacgtatcgtacaacatcagcaaactttctttcacgcacagcctcagtaccagctacaaccaaactggccgaatttccaagtgaatgttaga
# tacccccacactgacaacagggaaagaatccgacaaaatattctctctcaaatacacaacaaagaacccagccatcatcagcaatcccgcaagagatc
# tgcagattccctcccaggttcctccagcagtaagaagcacaagagtgaccacgcaactattaatgtcatcaaagatgtgcctgtccctcccgcgggat
# acaaccccacacacaatgttgaccagaaacgagaagctccagaaattttgtaccaaatccagaaatctctgtttcgatgtagttttgtgagggagtca
# atggttatcagagcaaaggtcccgattctgcgttttaacgattttatcagtaaagcacaggtagatctgaatgtcaataacagtgttgggattcgaaa
# tactcatctactcaaatattactgcttgaggcaggaggcatcccacttgtttcttctcatgattctgacggagagtgagtactcattggttctgtaca
# taagaaatgggctcgattccacgatatcaacgacgccagcaaagcgatccatctcaagttactcactctgtctcatgttgattcatttacttacagta
# tgcctgttcaccgtcaccttccttccctccaaaagctccatccaggcaaaatacatgggcaaagccaacacacgcgaccagattttcatcttcaaccg
# gaacaggtatgaatggcgcaatttgatttggggcgatggccttggaagtcaaagcgcgatgatggaaggcttagaaactcgactaaaatctgccaagg
# ggagagatgatgagtaa]
# protein sequence = [MDRRLFYRGSPMYPDSHRLPQFNPVIRFSRIVQHQQTFFHAQPQYQLQPNWPNFQVNVRYPHTDNRERIRQNILSQIH
# NKEPSHHQQSRKRSADSLPGSSSSKKHKSDHATINVIKDVPVPPAGYNPTHNVDQKREAPEILYQIQKSLFRCSFVRESMVIRAKVPILRFNDFISKA
# QVDLNVNNSVGIRNTHLLKYYCLRQEASHLFLLMILTESEYSLVLYIRNGLDSTISTTPAKRSISSYSLCLMLIHLLTVCLFTVTFLPSKSSIQAKYM
# GKANTRDQIFIFNRNRYEWRNLIWGDGLGSQSAMMEGLETRLKSAKGRDDE]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093701S0.prfl --predictionStart=0  --predictionEnd=24281  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3466520180911_busco_2432604931_.temp