# 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..109]--> unknown_A (17) <--[0..1]--> unknown_B (48) <--[6..27]--> unknown_C (18) <--[0..7]--> unknown_D (26) <--[0..1]--> unknown_E (36) <--[0..12]--> unknown_F (100) <--[2..9]--> unknown_G (28) <--[7..16]--> unknown_I (85) <--[0..1]--> unknown_J (63) <--[0..2]--> unknown_K (24) <--[0..17]--> unknown_L (48) <--[0..15]--> unknown_M (15) <--[0..1]--> unknown_N (36) <--[0..1]--> unknown_O (16) <--[7..20]--> unknown_Q (16) <--[0..1]--> unknown_R (53) <--[0..1]--> unknown_S (20) <--[12..29]--> unknown_U (23) <--[0..7]--> unknown_V (41) <--[28..41]--> unknown_Y (26) <--[0..1]--> unknown_Z (20) <--[2..43]--> unknown_AA (51) <--[0..1]--> unknown_AB (19) <--[0..59]--> unknown_AC (16) <--[0..2]--> unknown_AD (19) <--[0..2]--> unknown_AE (16) <--[0..1]--> unknown_AF (73) <--[4..24]--> unknown_AG (21) <--[0..3]--> unknown_AH (53) <--[7..68]--> unknown_AJ (26) <--[5..154]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig284120180911_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 = 23652, name = Contig2841) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig2841	AUGUSTUS	gene	1	16214	0.01	+	.	g1
Contig2841	AUGUSTUS	transcript	1	16214	0.01	+	.	g1.t1
Contig2841	AUGUSTUS	intron	1	2364	0.17	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	2526	2845	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	2988	3126	0.87	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	3278	3494	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	3715	6118	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	6201	9536	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	9721	11162	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	11234	11293	0.61	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	11370	11466	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	11508	12547	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	12638	12758	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	12846	13328	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	13473	14080	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	intron	14234	14467	0.53	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	2365	2525	0.73	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	2365	2525	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	2846	2987	0.95	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	2846	2987	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	3127	3277	0.88	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	3127	3277	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	3495	3714	0.02	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	3495	3714	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	6119	6200	0.01	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	6119	6200	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	9537	9720	0.09	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	9537	9720	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	11163	11233	0.89	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	11163	11233	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	11294	11369	0.6	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	11294	11369	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	11467	11507	0.58	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	11467	11507	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	12548	12637	0.58	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	12548	12637	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	12759	12845	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	12759	12845	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	13329	13472	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	13329	13472	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	14081	14233	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	14081	14233	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	CDS	14468	14656	0.53	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	14468	15477	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	stop_codon	14654	14656	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	15640	15719	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	exon	15898	16214	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2841	AUGUSTUS	tts	16214	16214	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gcaactctaaatggaatagatagtgttcaaaaagtgctagattcctttcgggagcagggcaaatttccagaagtagtgg
# atggatatcatggaacactgataggtcaactggactgtgaaaaaaccttctttacatgtgtggaagttactgctgggaacagactttttcatcatgtg
# gtggattgtgacaaaacaggaactaagatcctcacggaaatgaaccggcttcgcctgccgggagaggtcactctaatgccgcttaataaattggacgg
# caaggaaactcagtatccatctacaaatgatgccattcctatgattagcaaaattaaattcgaacgtccatttgcccgtgcaatgaatcatgtgtttg
# ggaaaaccttaatatgtcgcaatatggagactgcaacccagattgcaagaacacaaaacctggattgcataacattagaaggtgaccaagtgagtcgc
# cgtggagctctgactgggggttattatgacatgcgaaggtcacgacttgatctccagaaaggaaagatggagttcgaaagaaaacttggtgatcaaga
# aaaagaatataacgaacacaaacagaagctagaggaagtggagtccaagatcaacaacctggtcagcgagatgcagaaaatggagaccaggaatagca
# aaaacaaagacacctttgacaagatgagggcagatttgagactcatgacagaggaaaaacaagcaatagaaaaatccatgttatcaaagttggaaggt
# gaaaagaataaattagagaatttgctgcataataacctgatgaaaaaacgagaccgaatcatgcacgacctgcaggaagtttctgtagctgatcggcg
# tcagaagctggaccaataccagacagaactggaccaagaggatgaaaaactagccggttttaaggaacaaaacaaagatttggattctcaacttgaaa
# agatgaataaagaacagaaagaattgcagtccaacttagaaaactggagagcaagcacccagaaaatatggacaccatacacgtatttaaagagtact
# gttgatatattttcttggttagatgatgctaccattgtagatttcacacacgtattagctacagagaagggaaaagaaaaagaatatcaagagaaaat
# ctcagaggatgccaaagatttagagaagatgacaaataaacagagcttgttgttgaaaaagaaagatgaatgcatgaagaaaatcagagaattaggat
# cactgccaagcgatgcatttgaaaagtatcaaagctttaatcttaagcagctctttaaaaaactggagaactgcaaccaagagctaaaaagatacagt
# catgtaaacaagaaagcattggatcagtttgtgaacttctcagatcagaaagagaaacttatcaagaggaaggaggagcttgacagtgctcatcaggt
# gtccaagtactttagtgagatattcagaaaattggccccacaaggtcatgcccagctggtgatgaagaaaggggacgcggaccagaatgatgatgagg
# actcgcaagattccgttcccttggtggaacagttcacaggagtgggaataaaggtttctttcactggaaacaaagcagagatgagagacatgcagcag
# ctctcaggaggacagaagtcactagtagccctgactctgatctttgccattcagaaatgtgaccctgccccattttatctctttgatgaaattgacca
# ggctctggactcaagtcacaggaaagctgtggcaggcaagtattga]
# protein sequence = [ATLNGIDSVQKVLDSFREQGKFPEVVDGYHGTLIGQLDCEKTFFTCVEVTAGNRLFHHVVDCDKTGTKILTEMNRLRL
# PGEVTLMPLNKLDGKETQYPSTNDAIPMISKIKFERPFARAMNHVFGKTLICRNMETATQIARTQNLDCITLEGDQVSRRGALTGGYYDMRRSRLDLQ
# KGKMEFERKLGDQEKEYNEHKQKLEEVESKINNLVSEMQKMETRNSKNKDTFDKMRADLRLMTEEKQAIEKSMLSKLEGEKNKLENLLHNNLMKKRDR
# IMHDLQEVSVADRRQKLDQYQTELDQEDEKLAGFKEQNKDLDSQLEKMNKEQKELQSNLENWRASTQKIWTPYTYLKSTVDIFSWLDDATIVDFTHVL
# ATEKGKEKEYQEKISEDAKDLEKMTNKQSLLLKKKDECMKKIRELGSLPSDAFEKYQSFNLKQLFKKLENCNQELKRYSHVNKKALDQFVNFSDQKEK
# LIKRKEELDSAHQVSKYFSEIFRKLAPQGHAQLVMKKGDADQNDDEDSQDSVPLVEQFTGVGIKVSFTGNKAEMRDMQQLSGGQKSLVALTLIFAIQK
# CDPAPFYLFDEIDQALDSSHRKAVAGKY]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937017X.prfl --predictionStart=0  --predictionEnd=35483  --species=fly ./tmp/Contig284120180911_busco_2432604931_.temp