# 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
# --[1..438]--> unknown_A (15) <--[0..6]--> unknown_B (19) <--[0..1]--> unknown_C (70) <--[6..12]--> unknown_E (12) <--[1..21]--> unknown_F (36) <--[3..20]--> unknown_G (16) <--[0..4]--> unknown_H (14) <--[0..4]--> unknown_I (59) <--[0..21]--> unknown_J (28) <--[0..33]--> unknown_K (17) <--[0..11]--> unknown_L (19) <--[0..1]--> unknown_M (53) <--[0..1]--> unknown_N (28) <--[0..3]--> unknown_O (99) <--[0..4]--> unknown_P (31) <--[0..7]--> unknown_Q (29) <--[0..192]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig102420180911_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 = 14330, name = Contig1024) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig1024	AUGUSTUS	gene	1	14330	0.11	+	.	g1
Contig1024	AUGUSTUS	transcript	1	14330	0.11	+	.	g1.t1
Contig1024	AUGUSTUS	intron	1	1252	0.39	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	intron	1460	6156	0.42	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	intron	6398	7347	0.54	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	intron	7431	8590	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	intron	8744	10236	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	intron	10435	10932	0.85	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	intron	11026	14330	0.29	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	CDS	1253	1459	0.43	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	exon	1253	1459	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	CDS	6157	6397	0.37	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	exon	6157	6397	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	CDS	7348	7430	0.64	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	exon	7348	7430	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	CDS	8591	8743	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	exon	8591	8743	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	CDS	10237	10434	0.85	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	exon	10237	10434	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	CDS	10933	11025	0.72	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig1024	AUGUSTUS	exon	10933	11025	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atacacattctggagaacggtgatgttcacatctacagcaggaactcagagaacaataccagtaagtacccagacatca
# tcgctcggatcccgaaggtgaaggcggataccgtcacttcctgtgtcatcgactcagaagccgtcgcgtgggacgcggagaaaaaacagatccaacca
# ttccaggtgctcagccacaggaaacggaaggatgctgatgctgcggacattaagatccaggtgtgtgtgtatgcgtttgatctcttgtacctcaatgg
# acaatctctggtgaaagagccgttcaggaagagacgggaactcctccactcgtcattcacggaaatcgagggagaattcgtgttcgccaaatccatga
# tttcttccaacactgatgagatcgcggaattcctggacgactccatcaaaggtaccggagagcggtattttcattgaaactgcgagggcctaatggtg
# aaaactttggatgtagatgccacctatgaaattgccaagcggtctcacaactggctcaagctgaagaaggattacttggatggtgtgggtgacacgtt
# ggatctgctggtgatggggggtttcctcgggacaggaaagagaaccggacggtacggaggattcctcttggcctgttacgacgaggagaatgaagagt
# tccaatctatatgcaagattggaactggtttcactgatgcgtcgttagagacacatgctagcttctttaaggaccatgtgacggagaagccgaagccg
# tactaccggtttgactcctcggtggaaccggaccactggtttgatgcggtgcaggtttgggaggtgaaatgtgccgacctctccatctcacccacaca
# catggctgcagctggaattgtggatccagagaaagggatatccctgaggtttccccgatttttgcggattagagatgacaagaaaccggaggaggcga
# cctcagcttcacag]
# protein sequence = [IHILENGDVHIYSRNSENNTSKYPDIIARIPKVKADTVTSCVIDSEAVAWDAEKKQIQPFQVLSHRKRKDADAADIKI
# QVCVYAFDLLYLNGQSLVKEPFRKRRELLHSSFTEIEGEFVFAKSMISSNTDEIAEFLDDSIKGTGERYFHXNCEGLMVKTLDVDATYEIAKRSHNWL
# KLKKDYLDGVGDTLDLLVMGGFLGTGKRTGRYGGFLLACYDEENEEFQSICKIGTGFTDASLETHASFFKDHVTEKPKPYYRFDSSVEPDHWFDAVQV
# WEVKCADLSISPTHMAAAGIVDPEKGISLRFPRFLRIRDDKKPEEATSASQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937091Y.prfl --predictionStart=0  --predictionEnd=31037  --species=fly ./tmp/Contig102420180911_busco_2432604931_.temp