# 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..942]--> unknown_A (15) <--[0..4]--> unknown_B (16) <--[1..4]--> unknown_C (12) <--[3..6]--> unknown_D (17) <--[0..2]--> unknown_E (13) <--[1..24]--> unknown_F (21) <--[0..26]--> unknown_G (40) <--[0..1]--> unknown_H (15) <--[0..1]--> unknown_I (27) <--[4..29]--> unknown_J (7) <--[0..62]--> unknown_K (23) <--[18..49]--> unknown_N (17) <--[0..5]--> unknown_O (12) <--[0..306]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig3136020180911_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 = 32289, name = Contig31360) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig31360	AUGUSTUS	gene	3096	9645	0.01	-	.	g1
Contig31360	AUGUSTUS	transcript	3096	9645	0.01	-	.	g1.t1
Contig31360	AUGUSTUS	tts	3096	3096	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	3096	3502	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	stop_codon	3191	3193	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	3503	4936	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	5145	6168	0.86	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	6340	6516	0.24	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	6553	6619	0.22	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	6654	6726	0.19	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	6760	6830	0.26	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	6873	6922	0.2	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	7035	7284	0.3	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	7314	7382	0.21	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	intron	7446	7905	0.07	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	3191	3502	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	4937	5144	0.99	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	4937	5144	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	6169	6339	0.31	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	6169	6339	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	6517	6552	0.24	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	6517	6552	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	6620	6653	0.19	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	6620	6653	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	6727	6759	0.19	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	6727	6759	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	6831	6872	0.12	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	6831	6872	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	6923	7034	0.31	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	6923	7034	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	7285	7313	0.2	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	7285	7313	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	7383	7445	0.07	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	7383	7445	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	CDS	7906	7921	0.07	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	7906	7996	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	start_codon	7919	7921	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	8842	9011	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	exon	9545	9645	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig31360	AUGUSTUS	tss	9645	9645	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcattctccacagtctctccaccaatgtcactttctccacaggcacacctctccaccaatgtcatattttccacag
# tctcgccaccaatgtcactttctccaaaggatgagtttgattatatggactgtactttaaaggggcatggacacgttctgaccagaatacagatctgt
# ttcagccatgaagtacacctcaccaaaatgtattcgataatagaatccacaggtaagtctacctcaccaatgtcattctccacaggtaagtctctcac
# caatgtcacattctccacaggtaaactctccaaccgatttcacatctccactaggtcagtctctccaccgatttcacatttctcccacagttcctctc
# caccaatgtcactttctccacaggccacctcttcccggacaatgtcatattttccacaggtaaatctctccaccaatgtcctttctccaaagcgtcag
# ttcttcaccaatggtcacattctctcacaactaagtctcgccaccaatgtcacttttctccaaagagatatgaagtgcgagaacctcctgctggatag
# tgttaataatgtaaagatctcggattttggattttcccggaagttcaagtccggggacgtctgtaagactttctgtggaagtgccgcttatgccgctc
# ccgaaatcctacagggaatcccctaccatggaccagtgcacgatatgtggagcctcggggtggtcctgtatatcatggtatgcgcctcaatgccgttc
# gacgataccaacatcaggaaaatgatcaaggatcaacttggtggaaaagtgaagttttcaaaacccaagaaattaacaattgagtgcaaggacctcat
# acaccaaatcttagaaaacgatgtaaagaggcgggccaccatcgctaccgtgatggaccatccctggatggcggtcaaaaagtccgagtcggataaag
# cgctccagaaagccaaagacagggaaatcaaaatgattccggcgtctgaaaccctcaagtccaaactagccaatctagccaaaggcaaaagttaa]
# protein sequence = [MSFSTVSPPMSLSPQAHLSTNVIFSTVSPPMSLSPKDEFDYMDCTLKGHGHVLTRIQICFSHEVHLTKMYSIIESTGK
# STSPMSFSTGKSLTNVTFSTGKLSNRFHISTRSVSPPISHFSHSSSPPMSLSPQATSSRTMSYFPQVNLSTNVLSPKRQFFTNGHILSQLSLATNVTF
# LQRDMKCENLLLDSVNNVKISDFGFSRKFKSGDVCKTFCGSAAYAAPEILQGIPYHGPVHDMWSLGVVLYIMVCASMPFDDTNIRKMIKDQLGGKVKF
# SKPKKLTIECKDLIHQILENDVKRRATIATVMDHPWMAVKKSESDKALQKAKDREIKMIPASETLKSKLANLAKGKS]
# end gene g1
###
# start gene g2
Contig31360	AUGUSTUS	gene	11386	12820	0.03	+	.	g2
Contig31360	AUGUSTUS	transcript	11386	12820	0.03	+	.	g2.t1
Contig31360	AUGUSTUS	tss	11386	11386	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig31360	AUGUSTUS	exon	11386	12820	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig31360	AUGUSTUS	start_codon	11486	11488	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31360	AUGUSTUS	CDS	11486	12541	0.59	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31360	AUGUSTUS	stop_codon	12539	12541	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31360	AUGUSTUS	tts	12820	12820	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgcctccgagtaataagaaactgaagtgtgcaatggctgagaaccccttagattctcagaatttgcaacaagagctgg
# aagtactgcaaggagaagtggaagcggtagagattcgtcgttcatcaacggagaggtgcgaaacaataaaatatcgccccacctaccgcgccatcctg
# gccaaaaaggggtttttagtcaagcagaccctaggaagtggaagctactccaaagtaaagttcgcctatagtctcaaggatggcaaaggcggtgtggt
# cgcggtcaaaattgtagatcgaaacaaagccccaaaagattttcaacatcgatttttgccacgggaaatcaaaatttggccacagctaaatcatccac
# acatcgtcaagctcctggatatttttgaggactataggcgcgtatacatggtgctagaatacggagaaaagggcgatgttctacgatacattcagcgc
# gtgggtgctatcaaggaaggaatggcgagaaattggacaaaacaaatttgtgacgccgtgcgctacctccatgagcaaaacatcactcatcgagatct
# aaaactggagaatctgcttctagacaacaactacaatatcaaaatctgcgatttcggatttgtcaaattggatcccgatcgacagcttagcaaaacct
# actgtggctctaaatcttatgcggctccagaaattttgagaggggaaccctatgatacccagaaagctgatatctgggctataggcgtcattttatac
# atttttgtcaccgggaaaatgccatttgacgagagtaaaggaaaccatggtgtattagaggagcacagaaaattaaattttccctggcacaagattaa
# aaagaacgtatcggaagaatgccgcgctctgatcttatggtgcttcaagtacagtttttctgagcggccagacatttatgatgttttaggaagcttgt
# ggttgaaagcaggggccaaagtggaaaacccagaaaacgcgtgtatcgaaggaccaaaacccatcacagggaaagcggacacttctagcacatag]
# protein sequence = [MPPSNKKLKCAMAENPLDSQNLQQELEVLQGEVEAVEIRRSSTERCETIKYRPTYRAILAKKGFLVKQTLGSGSYSKV
# KFAYSLKDGKGGVVAVKIVDRNKAPKDFQHRFLPREIKIWPQLNHPHIVKLLDIFEDYRRVYMVLEYGEKGDVLRYIQRVGAIKEGMARNWTKQICDA
# VRYLHEQNITHRDLKLENLLLDNNYNIKICDFGFVKLDPDRQLSKTYCGSKSYAAPEILRGEPYDTQKADIWAIGVILYIFVTGKMPFDESKGNHGVL
# EEHRKLNFPWHKIKKNVSEECRALILWCFKYSFSERPDIYDVLGSLWLKAGAKVENPENACIEGPKPITGKADTSST]
# end gene g2
###
# start gene g3
Contig31360	AUGUSTUS	gene	18170	30885	0.01	-	.	g3
Contig31360	AUGUSTUS	transcript	18170	30885	0.01	-	.	g3.t1
Contig31360	AUGUSTUS	tts	18170	18170	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	18170	18357	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	18732	18839	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	stop_codon	18732	18734	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	intron	18840	19988	0.02	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	intron	20085	20212	0.02	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	intron	20294	26564	0.01	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	intron	26756	29800	0.96	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	intron	29904	30076	0.64	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	CDS	18732	18839	0.03	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	CDS	19989	20084	0.02	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	19989	20084	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	CDS	20213	20293	0.03	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	20213	20293	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	CDS	26565	26755	0.92	-	2	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	26565	26755	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	CDS	29801	29903	0.64	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	29801	29903	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	CDS	30077	30190	0.97	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	30077	30194	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	start_codon	30188	30190	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	exon	30637	30885	.	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig31360	AUGUSTUS	tss	30885	30885	.	-	.	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggaagaagaggagaaggaagagaaagaagaagttgtgatatctcagaaaacgagtcgccgagtgtctcgagccaact
# cgcgagcttccaggctttctacagcacctgtacaggttgatactcagaaacagaaggcgcttctagatgaaattacggcaaaagtagaaggagtggaa
# ctagagaaaaccgaagacttgtctgatgataaattagaagaagagatcaagaatgatgatagtgaggagaagagagatgaagagaaatcggaggatgg
# tctgacgaagggggaatctgatgaggaggagattgaggaggaggaggagacgactaagtacatcactgaggtgtacgccccggtccttgtatccgtac
# atcaggactcctacatccgattctggacaatggaggcctacaatcatcacctggaaagttttaacactgcggacaaaaaccagggtgctgtgtttagg
# gccttgcccgtctatcgaataaaaactccaaagaaagtgacaattccagaaccgagctacaaaattccaatggaagacgaatcacagagttacctctt
# tggaaacaccagcaaggtcaccccaaggaagccccaatatgtgccccacatgacccgcatctatcaggccttgaaggccgaccccaaactcagatacc
# cccgtctgagaagcagaagacgctag]
# protein sequence = [MEEEEKEEKEEVVISQKTSRRVSRANSRASRLSTAPVQVDTQKQKALLDEITAKVEGVELEKTEDLSDDKLEEEIKND
# DSEEKRDEEKSEDGLTKGESDEEEIEEEEETTKYITEVYAPVLVSVHQDSYIRFWTMEAYNHHLESFNTADKNQGAVFRALPVYRIKTPKKVTIPEPS
# YKIPMEDESQSYLFGNTSKVTPRKPQYVPHMTRIYQALKADPKLRYPRLRSRRR]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GHM.prfl --predictionStart=0  --predictionEnd=32289  --species=fly ./tmp/Contig3136020180911_busco_2432604931_.temp