# 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..40]--> unknown_A (37) <--[0..8]--> unknown_B (18) <--[4..14]--> unknown_C (23) <--[25..302]--> unknown_G (34) <--[3..93]--> unknown_H (22) <--[8..12]--> unknown_J (37) <--[5..13]--> unknown_K (14) <--[0..2]--> unknown_L (41) <--[0..1]--> unknown_M (19) <--[2..4]--> unknown_N (12) <--[0..2]--> unknown_O (22) <--[0..1]--> unknown_P (42) <--[0..80]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig14220180911_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 = 20616, name = Contig142) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig142	AUGUSTUS	gene	43825	47660	0.08	+	.	g1
Contig142	AUGUSTUS	transcript	43825	47660	0.08	+	.	g1.t1
Contig142	AUGUSTUS	tss	43825	43825	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig142	AUGUSTUS	exon	43825	43934	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig142	AUGUSTUS	exon	45389	47660	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig142	AUGUSTUS	start_codon	45399	45401	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig142	AUGUSTUS	CDS	45399	46226	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig142	AUGUSTUS	stop_codon	46224	46226	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig142	AUGUSTUS	tts	47660	47660	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcaagcggtttgagtatgtctaaaacggctgtaaaaagaattaagcagagcgaacttcagctgaattcgactatcc
# acaaaatcaactcctcgttggcagaaagccttcatcaaatcgaacacaatgtgcgaaaaattgagcaggaacatgggcaacagaaaggagagtacctg
# ccctattaccttcggcgacgaccctccattgaacagattgtggaatccgacacagccttcccgctaaacaacgagctccgcgagagagcaagcagtgt
# cggcagcaacccaacaacgacaggcaaacaacaaagtcttagcagctccgcatccaaagaatcggtgtcgtctgacggaagtacgggaagacgtgacg
# tcagtccccagagaccaacgttcaggaaaagtgaaactgctgacgtcaaacttccgtccaatttatcccagttctaccaattcggccgaaggagagaa
# tctagaaggaattcattgccgatgagttttagtctccaaaattctcatgactttcacgggcacagcaaagacgcgcacgtcaaagacgcgcacagcaa
# agacgcacacagtaaagaaggaatcactgttcgtctccggcgcgtggaacatgaacttgctcaaagaaagccaaagagcagacgacaacttatcacct
# caagcatgacgtcaattgatgagagaaaagagcacgagagattggaggacgagaaaagacaacaggccgctgaggaatatgtaaattctattgaggaa
# tgcagttacctccgaaccaaaacgcaaccagaattaactgtaacggaagtcttccagaaataa]
# protein sequence = [MSSGLSMSKTAVKRIKQSELQLNSTIHKINSSLAESLHQIEHNVRKIEQEHGQQKGEYLPYYLRRRPSIEQIVESDTA
# FPLNNELRERASSVGSNPTTTGKQQSLSSSASKESVSSDGSTGRRDVSPQRPTFRKSETADVKLPSNLSQFYQFGRRRESRRNSLPMSFSLQNSHDFH
# GHSKDAHVKDAHSKDAHSKEGITVRLRRVEHELAQRKPKSRRQLITSSMTSIDERKEHERLEDEKRQQAAEEYVNSIEECSYLRTKTQPELTVTEVFQ
# K]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E8S.prfl --predictionStart=28180  --predictionEnd=68293  --species=fly ./tmp/Contig14220180911_busco_2432604931_.temp