# 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
# --[17..464]--> unknown_A (15) <--[7..32]--> unknown_B (52) <--[4..8]--> unknown_C (13) <--[0..6]--> unknown_D (23) <--[3..25]--> unknown_E (33) <--[1..21]--> unknown_F (41) <--[1..15]--> unknown_G (25) <--[3..14]--> unknown_H (13) <--[2..7]--> unknown_I (39) <--[2..24]--> unknown_J (51) <--[0..2]--> unknown_K (15) <--[1..4]--> unknown_L (16) <--[0..2]--> unknown_M (20) <--[1..33]--> unknown_N (30) <--[2..5]--> unknown_O (21) <--[14..50]--> unknown_Q (18) <--[18..66]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig3048220180911_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 = 5926, name = Contig30482) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig30482	AUGUSTUS	gene	78	5809	0.03	-	.	g1
Contig30482	AUGUSTUS	transcript	78	5809	0.03	-	.	g1.t1
Contig30482	AUGUSTUS	tts	78	78	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	exon	78	416	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	stop_codon	123	125	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	intron	417	2346	0.33	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	intron	2479	3017	0.79	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	intron	3183	3726	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	intron	3745	3814	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	intron	3931	5587	0.13	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	CDS	123	416	0.91	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	CDS	2347	2478	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	exon	2347	2478	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	CDS	3018	3182	0.84	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	exon	3018	3182	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	CDS	3727	3744	0.37	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	exon	3727	3744	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	CDS	3815	3930	0.18	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	exon	3815	3930	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	CDS	5588	5696	0.11	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	exon	5588	5809	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig30482	AUGUSTUS	start_codon	5694	5696	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctggagatcatcatggcgatcaaaaacaacaacataaggaagattcctaactacgaccccgagcacctagaacatc
# tcaagaaagtgaccagaggaatattgagagtttccatggagtcagtggtgggggacgtcagttctcagctgctggagttggcacggaaacagagaatg
# aacacggacatcaggaagaacatcttctgtgtcatcatgtctagtcagctttatataacataccgtgattatattgatgcatttgataagctgctgcg
# cttagggttgaaaaaccaacaggaaagggagataattcacatcattgtagacctgtgtctacaagagaagagctataacccgttctacactctactgc
# tacagaagttctgtctctatcacagaagatttcagatgtccacccagttcctgatgtgggacaaatttaaggatatgaagaaactttctcagtcacag
# agagaccacctcagtgagctcctgtcccagctactctcctccaaagccatgtccctgtccgtcctaaaggtggtagagttcggcaccttggatgtgta
# catgctgagattcctgaaacgccttatgcagagtgttctcttggattatccggaagacgttactcgggcgatgttctatcgaatagcgccgttgtcca
# aacttcatcacctacacgaaggactgaagttattcatgcagcatttcctacagaggaagaaatctaaggatgtggcagacattcctttattaaaagaa
# cgtatagacatggcggataaaattttatcggcaagttcatcgcattcacattcagagttcgatgactga]
# protein sequence = [MLEIIMAIKNNNIRKIPNYDPEHLEHLKKVTRGILRVSMESVVGDVSSQLLELARKQRMNTDIRKNIFCVIMSSQLYI
# TYRDYIDAFDKLLRLGLKNQQEREIIHIIVDLCLQEKSYNPFYTLLLQKFCLYHRRFQMSTQFLMWDKFKDMKKLSQSQRDHLSELLSQLLSSKAMSL
# SVLKVVEFGTLDVYMLRFLKRLMQSVLLDYPEDVTRAMFYRIAPLSKLHHLHEGLKLFMQHFLQRKKSKDVADIPLLKERIDMADKILSASSSHSHSE
# FDD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705YE.prfl --predictionStart=0  --predictionEnd=25810  --species=fly ./tmp/Contig3048220180911_busco_2432604931_.temp