# 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..42]--> unknown_A (23) <--[0..20]--> unknown_B (6) <--[0..1]--> unknown_C (30) <--[0..1]--> unknown_D (15) <--[0..1]--> unknown_E (38) <--[0..35]--> unknown_F (43) <--[0..45]--> unknown_G (51) <--[0..4]--> unknown_H (22) <--[0..2]--> unknown_I (22) <--[0..34]--> unknown_J (27) <--[1..7]--> unknown_K (13) <--[0..11]--> unknown_L (16) <--[0..2]--> unknown_M (15) <--[0..1]--> unknown_N (28) <--[0..3]--> unknown_O (10) <--[0..4]--> unknown_P (16) <--[0..9]--> unknown_Q (29) <--[0..26]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig3577420180911_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 = 24039, name = Contig35774) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig35774	AUGUSTUS	gene	36	9615	0.01	-	.	g1
Contig35774	AUGUSTUS	transcript	36	9615	0.01	-	.	g1.t1
Contig35774	AUGUSTUS	tts	36	36	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	exon	36	2125	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	stop_codon	1310	1312	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	intron	2126	5885	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	intron	6173	6763	0.32	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	intron	6834	8644	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	CDS	1310	2125	0.51	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	CDS	5886	6172	0.34	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	exon	5886	6172	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	CDS	6764	6833	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	exon	6764	6833	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	CDS	8645	8728	0.9	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	exon	8645	8753	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	start_codon	8726	8728	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	exon	9512	9615	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35774	AUGUSTUS	tss	9615	9615	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggatcgaccctactgggacctaccatggtgactcagacttgcagctcgaaagaatcaatgtttactacaacgaggc
# aactggttagatttaggttacagtggtacattctaaatcccaaactactgctcttagtgaagcagcttgtctcaggtccattcggtcagatatttcgt
# ccagacaactttgtgtttggtcagagtggtgctggaaataactgggccaaaggtcactacacagagggcgctgaattggtagactcagtgatggacgt
# ggtgcgtaaggagtcggagaactgcgactgtctgcaggggttccagatgacacactctctggggggcgggaccgggtcaggaatgggaacgctactca
# tctccaaaatccgggaggaatatccagacagaatcatgaacacattctccgtcgtcccctcacccaaggtgtccgatacagtagtagaaccatacaac
# gccacactctctgttcatcagctggtagaaaacacagacgagacatactgcattgataacgaggctttgtatgacatttgcttcaggacgctgaagct
# ctccacaccaacctatggtgaccttaatcacctggtgtctgccacaatgtcaggggtcacgacctgtcttagattccccggacagttgaacgctgacc
# tcaggaaactggccgttaacatggttcctttcccccgtcttcacttctttatgccagggttcgctccccttacctcccgaggcagtcaacaataccga
# gccctgtctgtacccgagctcactcaacagatgttcgattccaaaaatatgatggcagcctgtgatccccgccatggccgttacctgacagtcgccgc
# catattccggggtcgcatgtccatgaaggaggtagatgagcaaatgttaaatgtccagaacaagaacagcagctacttcgtagagtggatccctaaca
# atgtcaagacggccgtctgcgacattcctccaaggggtctcaaaatgtccgccactttcatcggaaacagtaccgctattcaggaactcttcaagaga
# atctccgagcagtttacggctatgttccgtcgtaaggctttcttgcattggtacactggcgagggtatggatgagatggaattcaccgaggccgaatc
# gaatatgaacgacttggtgtcggaatatcagcaataccaggaagccactgcggatgaagaggcggaatttgatgaagaggaggagcccgaggaagtat
# ga]
# protein sequence = [MGSTLLGPTMVTQTCSSKESMFTTTRQLVRFRLQWYILNPKLLLLVKQLVSGPFGQIFRPDNFVFGQSGAGNNWAKGH
# YTEGAELVDSVMDVVRKESENCDCLQGFQMTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCID
# NEALYDICFRTLKLSTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALSVPELTQQMFDSKNMMA
# ACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYT
# GEGMDEMEFTEAESNMNDLVSEYQQYQEATADEEAEFDEEEEPEEV]
# end gene g1
###
# start gene g2
Contig35774	AUGUSTUS	gene	11086	22852	0.01	+	.	g2
Contig35774	AUGUSTUS	transcript	11086	22852	0.01	+	.	g2.t1
Contig35774	AUGUSTUS	tss	11086	11086	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	11086	11132	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	13939	14305	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	17322	18263	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	start_codon	17422	17424	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	intron	18264	18613	0.81	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	intron	18786	20020	0.32	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	intron	20176	20263	0.46	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	CDS	17422	18263	0.59	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	CDS	18614	18785	0.76	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	18614	18785	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	CDS	20021	20175	0.35	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	20021	20175	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	CDS	20264	20294	0.49	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	20264	20317	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	stop_codon	20292	20294	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	exon	22553	22852	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig35774	AUGUSTUS	tts	22852	22852	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatgaaagcgatggatccaacagcactgaagagcagggatcattttcctttggtacggaggtggttctttttctgg
# acgacgacggcaatgagaatcacttcatcgtcggcccaggggtgtaccaaaattgtgagacatcttcaagtttgaacgatggttcaaaagtgatttta
# gaaaatgatatcaaagttatttcaagtgaagtagagaaattgatatcgaacacagagaagctgagcagcgatcatggagggaccattaatgccgaaga
# tgggagtacagacaatttcagtgctttaccaagggagataattttaaagatttttagttttttttctgctgtggaactgagtctgtgcgtgacaccgg
# tttgtaaacgttggtacgaagtcggacatgacccaagcttatggaaagagctagatttcagccgccattgtgaacttccgtccagcacattatgtaga
# gctatctgtcgagccacattgctcagaaagctgaacttaatgggaagagttgacctgagcactgccgaggtggcagtcttttcccaatacattccact
# gctggaatcggtcaatttaggattctgtgctgatgttaatagaacagtgatcgagtacttcgtcaggaactgtcctcgacttacggaactgaacgtgg
# aagggtgtcatttagtggacgacaacgtcacggccgctttaccttgggggaagagactggagaggtttaacttttctcactgtaacctgacggacagc
# agcatcgttcttatgtcctctgctgtgagaaatatcgtgtcccttaatattgatggaatttcttggatttctgacagtgccattgtcacgcttgtgga
# ccaccagcacgagaatctggaggagttcttcctggatggagctgaactctcggacaaaagtgtccaccatattgccaggtgtgccaaacttcacaaac
# tacacatgtccttctgtgaagggctgactgaccaatccctcaggtatatacagaatctgactcacctgaagatgaggaagggtgtgtacttcagtact
# gagggcttgctctctctattcacctgtcagtcaatgtcacggttggtggagctcgacttctccgaaagcacgaattttgtcgacgaatgtgttataca
# aatgaccaagtggtcatttgaaataaaatgcaatcagagttga]
# protein sequence = [MDESDGSNSTEEQGSFSFGTEVVLFLDDDGNENHFIVGPGVYQNCETSSSLNDGSKVILENDIKVISSEVEKLISNTE
# KLSSDHGGTINAEDGSTDNFSALPREIILKIFSFFSAVELSLCVTPVCKRWYEVGHDPSLWKELDFSRHCELPSSTLCRAICRATLLRKLNLMGRVDL
# STAEVAVFSQYIPLLESVNLGFCADVNRTVIEYFVRNCPRLTELNVEGCHLVDDNVTAALPWGKRLERFNFSHCNLTDSSIVLMSSAVRNIVSLNIDG
# ISWISDSAIVTLVDHQHENLEEFFLDGAELSDKSVHHIARCAKLHKLHMSFCEGLTDQSLRYIQNLTHLKMRKGVYFSTEGLLSLFTCQSMSRLVELD
# FSESTNFVDECVIQMTKWSFEIKCNQS]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370ADO.prfl --predictionStart=0  --predictionEnd=26278  --species=fly ./tmp/Contig3577420180911_busco_2432604931_.temp