# 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..75]--> unknown_A (23) <--[0..25]--> unknown_B (11) <--[0..6]--> unknown_C (38) <--[0..41]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig14320180911_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 = 30270, name = Contig143) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig143	AUGUSTUS	gene	9860	15555	0.01	-	.	g1
Contig143	AUGUSTUS	transcript	9860	15555	0.01	-	.	g1.t1
Contig143	AUGUSTUS	tts	9860	9860	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	exon	9860	10268	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	stop_codon	10064	10066	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	intron	10269	15320	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	CDS	10064	10268	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	CDS	15321	15397	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	exon	15321	15555	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	start_codon	15395	15397	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	tss	15555	15555	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	protein_match	10118	10231	7.02	-	0	target "unknown_C[1..38]"; target_start 38; transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	protein_match	10235	10267	5.31	-	0	target "unknown_B[1..11]"; target_start 26; transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	protein_match	10268	10268	1	-	1	target "unknown_A[23..23]"; target_start 3; transcript_id "g1.t1"; gene_id "g1";
Contig143	AUGUSTUS	protein_match	15321	15388	2.82	-	0	target "unknown_A[1..23]"; target_start 3; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacggctgtaaacgaagcacagatgaagctgttcactgatctcgaaattgaaatgactgcagatatgtataataaaa
# tgacggcttgttgtctgcaaaaatgtataccacccaagtacaaagaggcggaactgtctaaaggggaggcagtgtgcctggacagatgtgtcgccaaa
# tacatggaaatccacgacagaatcggtaaaaaactaactcagctgtcacaggaggacgagagtcgagtgaaacaaatgcaagcacatctccagcagca
# gtcatag]
# protein sequence = [MTAVNEAQMKLFTDLEIEMTADMYNKMTACCLQKCIPPKYKEAELSKGEAVCLDRCVAKYMEIHDRIGKKLTQLSQED
# ESRVKQMQAHLQQQS]
# sequence of block unknown_C    38 [KYKEAELSKGEAVCLDRCVAKYMEIHDRIGKKLTQLSQ] 76
# sequence of block unknown_B    26 [MTACCLQKCIP] 37
# sequence of block unknown_A     3 [VNEAQMKLFTDLEIEMTADMYNK] 26
# end gene g1
###
# start gene g2
Contig143	AUGUSTUS	gene	15946	26059	0.02	+	.	g2
Contig143	AUGUSTUS	transcript	15946	26059	0.02	+	.	g2.t1
Contig143	AUGUSTUS	tss	15946	15946	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	exon	15946	16021	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	exon	18587	18787	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	start_codon	18598	18600	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	intron	18788	19240	0.97	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	intron	19411	19967	0.86	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	CDS	18598	18787	0.6	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	CDS	19241	19410	0.91	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	exon	19241	19410	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	CDS	19968	20096	0.35	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	exon	19968	20269	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	stop_codon	20094	20096	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	exon	24989	26059	.	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig143	AUGUSTUS	tts	26059	26059	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgttctatatactacaggaacatatgattgttttgaccagaaccacgggacagaaattgctctttgagggacgccatg
# agcaggccgtgccagcagctatgcagtccctgcgatttgccattgacgtgcatggcttagccagtattgagctggtcccctcttacctaattcttgga
# gaagccagcataggacttggtcgattaaatcaagctgaggaatatctagcacaagcgcagtggaccgtccttaaaacacctgaatgttcaaatgcaat
# aaaatccaaactgtacagaaacctgggacttttgtacgccgctaagggagagtacgaggaagcactgaggcagctcgctgatgatatataccactcct
# cagaagagtgtggcacgggcgacataaggacttcgggtggatactttcacatggctaacgttttcttccgacaaggacgcatggatgtcgcagattct
# ttgtacagtgaagtatga]
# protein sequence = [MFYILQEHMIVLTRTTGQKLLFEGRHEQAVPAAMQSLRFAIDVHGLASIELVPSYLILGEASIGLGRLNQAEEYLAQA
# QWTVLKTPECSNAIKSKLYRNLGLLYAAKGEYEEALRQLADDIYHSSEECGTGDIRTSGGYFHMANVFFRQGRMDVADSLYSEV]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093718EG.prfl --predictionStart=0  --predictionEnd=30270  --species=fly ./tmp/Contig14320180911_busco_2432604931_.temp