# 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/Contig4925220180911_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 = 6880, name = Contig49252) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig49252	AUGUSTUS	gene	556	4586	0.01	+	.	g1
Contig49252	AUGUSTUS	transcript	556	4586	0.01	+	.	g1.t1
Contig49252	AUGUSTUS	tss	556	556	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig49252	AUGUSTUS	exon	556	568	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig49252	AUGUSTUS	exon	2853	4586	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig49252	AUGUSTUS	start_codon	3231	3233	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig49252	AUGUSTUS	CDS	3231	4214	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig49252	AUGUSTUS	stop_codon	4212	4214	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig49252	AUGUSTUS	tts	4586	4586	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaaactgtaaatcagctcaatacacagcagctgccgaaaacgagttttgccaagagaagctggcagaagttgaaga
# atttgttgtccaagtataggcgagatcggagagtttcccgcaagtttaaaaatggattagtgaacttcaagaatgcaacaaaactgaacaagtatgac
# atcacactagggcatttactgggaacgggtgggttcggatctgtctataagggagccttcagacaacgaaatgtggcggtgaaaataatgcatcaaaa
# atgcaaaaacgtagcggcccagttagaaagttttaaggccgagcttcacgttatggaatttgaccaccagaatattgttcgaactcttgcggccactt
# ccattaaggaattccacgaaggagcctggatagtgatggaatacgtcggaaataaaacacttcagactatgattaacctggaagagttaggacgggaa
# atgagaatcaagttcgcccttcagttatcggatgctctccagtatctccatggtaatcacgtgatacatatggacctgaaacccgccaatattctcgt
# ttctgtggatggggatgtaaaactcgccgacttcggatgttcacggaaagcggagatgaacactggacttatcagtcctaccgagcggtcctacctga
# cgggcacctttgcttaccgtgccccggaacttctaaagggtcagataccgtcctgtaaagctgatatttatgccctaggtgtgacgttgtggcagatg
# cttacgcagaaaaacccgtacggacatgaggatcagcatgttgtgatattcagtgttgtggcgtacgggcatcgccccgcccacccggaaattgagct
# ggatccattggaggagtgttaccgagatctttactcgcagtgctggtcagcgaccgaaagagaccgaccctccgcagacgacgtttacgaaacgctta
# aaatctgggcagaacacgtgtag]
# protein sequence = [MKTVNQLNTQQLPKTSFAKRSWQKLKNLLSKYRRDRRVSRKFKNGLVNFKNATKLNKYDITLGHLLGTGGFGSVYKGA
# FRQRNVAVKIMHQKCKNVAAQLESFKAELHVMEFDHQNIVRTLAATSIKEFHEGAWIVMEYVGNKTLQTMINLEELGREMRIKFALQLSDALQYLHGN
# HVIHMDLKPANILVSVDGDVKLADFGCSRKAEMNTGLISPTERSYLTGTFAYRAPELLKGQIPSCKADIYALGVTLWQMLTQKNPYGHEDQHVVIFSV
# VAYGHRPAHPEIELDPLEECYRDLYSQCWSATERDRPSADDVYETLKIWAEHV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GHM.prfl --predictionStart=0  --predictionEnd=24022  --species=fly ./tmp/Contig4925220180911_busco_2432604931_.temp