# 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
# --[3..54]--> unknown_A (9) <--[13..34]--> unknown_C (25) <--[6..11]--> unknown_D (32) <--[0..33]--> unknown_E (22) <--[28..123]--> unknown_G (21) <--[0..2]--> unknown_H (12) <--[8..79]--> unknown_J (35) <--[0..29]--> unknown_K (16) <--[0..14]--> unknown_L (10) <--[0..1]--> unknown_M (10) <--[0..2]--> unknown_N (10) <--[0..2]--> unknown_O (12) <--[0..3]--> unknown_P (19) <--[0..2]--> unknown_Q (45) <--[4..27]--> unknown_R (18) <--[10..176]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7842520180911_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 = 9846, name = Contig78425) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig78425	AUGUSTUS	gene	1	4855	0.12	+	.	g1
Contig78425	AUGUSTUS	transcript	1	4855	0.12	+	.	g1.t1
Contig78425	AUGUSTUS	intron	1	210	0.76	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	intron	331	1484	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	intron	1639	2109	0.32	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	intron	2182	3181	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	intron	3300	3758	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	intron	3826	4776	0.66	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	CDS	211	330	0.77	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	CDS	1485	1638	0.66	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	CDS	2110	2181	0.52	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	CDS	3182	3299	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	CDS	3759	3825	0.75	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	CDS	4777	4855	0.66	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig78425	AUGUSTUS	stop_codon	4853	4855	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ttgtttcctggtaaattcggcagaccgaattatccgagtttatgagagcggggaagtcctagcgtgcgggaaagacggt
# gaaccagaaccaatacagaaacttcaggacctcgtcaacaaattgttgtggaagaaatgctgtttttctggagatggggaattcattgtagcagggtc
# tgccagacagcactcactctatgtctgggaaaagagtgttgggaatctcgtgaaaattctccatggaacgaaaggggaactgctgcttgatgtggtgt
# ggcatcctgtgcgtccaatcattgcctcaatatccagtggtctagtgtcaatatgggcacagaatcaagtcgaaaattggagtgcctttgcacccgat
# ttcaaggaattggatgagaatgttgaatatgaggagagagaatctgagtttgatgtcgaagatgaagacaaagaaaaggaggaaacgaaggggccgta
# tgaggaggactcagaagttgatgtgaccaccattgaacccattcaagcttttgtcagcagtgattgggatgaggaagaaaccaggaagctgcttgctc
# taccttcctgttccaccagacacttgaggaaccgacgatga]
# protein sequence = [CFLVNSADRIIRVYESGEVLACGKDGEPEPIQKLQDLVNKLLWKKCCFSGDGEFIVAGSARQHSLYVWEKSVGNLVKI
# LHGTKGELLLDVVWHPVRPIIASISSGLVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDVEDEDKEKEETKGPYEEDSEVDVTTIEPIQAFVS
# SDWDEEETRKLLALPSCSTRHLRNRR]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370YSI.prfl --predictionStart=0  --predictionEnd=21695  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7842520180911_busco_2432604931_.temp