# 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
# --[2..45]--> unknown_A (26) <--[0..22]--> unknown_B (7) <--[0..2]--> unknown_C (17) <--[6..8]--> unknown_D (13) <--[14..49]--> unknown_F (19) <--[0..3]--> unknown_G (68) <--[11..40]--> unknown_H (56) <--[0..26]--> unknown_I (21) <--[35..198]--> unknown_K (13) <--[2..18]--> unknown_L (36) <--[10..16]--> unknown_M (22) <--[30..449]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig3941420180911_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 = 29360, name = Contig39414) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig39414	AUGUSTUS	gene	4846	20513	0.01	+	.	g1
Contig39414	AUGUSTUS	transcript	4846	20513	0.01	+	.	g1.t1
Contig39414	AUGUSTUS	tss	4846	4846	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	exon	4846	5255	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	exon	6584	6708	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	exon	10293	10444	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	start_codon	10309	10311	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	10445	18206	0.06	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	18337	18537	0.11	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	18640	18699	0.12	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	10309	10444	0.1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	18207	18336	0.09	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	exon	18207	18336	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	18538	18639	0.1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	exon	18538	18639	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	18700	18781	0.1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	exon	18700	20513	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	stop_codon	18779	18781	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	tts	20513	20513	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtttctcatcagactaagtctgaaaaagctactggaagaattgaaggatactcctgacttccggtggtggatagatg
# atcccaatcacaggtttagccactgcaagctcttcgtccgtcttgttctgattctctcctctgatattacacacatccagtatgtcttaattcttatc
# actaaaagcacctgtgccaacaccttgtccccaaaccttgaacttttcttcatcaacgtacatttatcaatgattctgagatctacttggttccctga
# aattcaatgctcccattccaaaaatacaacactgtcggatcactcacttcctgctgctgctgccttcttcactggttctttgagggtcataaaagttc
# gaggagactgggtaaggaatggggaccacagtcacacccatgtccctcagatcctgagcagtgacatacttgattga]
# protein sequence = [MFLIRLSLKKLLEELKDTPDFRWWIDDPNHRFSHCKLFVRLVLILSSDITHIQYVLILITKSTCANTLSPNLELFFIN
# VHLSMILRSTWFPEIQCSHSKNTTLSDHSLPAAAAFFTGSLRVIKVRGDWVRNGDHSHTHVPQILSSDILD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SYK.prfl --predictionStart=0  --predictionEnd=29589  --species=fly ./tmp/Contig3941420180911_busco_2432604931_.temp