# 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..17]--> unknown_A (15) <--[12..83]--> unknown_C (22) <--[1..32]--> unknown_D (11) <--[0..2]--> unknown_E (11) <--[0..16]--> unknown_F (10) <--[1..74]--> unknown_G (20) <--[0..1]--> unknown_H (7) <--[3..15]--> unknown_I (17) <--[0..3]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig305020180911_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 = 7656, name = Contig3050) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig3050	AUGUSTUS	gene	1214	4550	0.01	+	.	g1
Contig3050	AUGUSTUS	transcript	1214	4550	0.01	+	.	g1.t1
Contig3050	AUGUSTUS	exon	1214	1364	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	start_codon	1269	1271	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	intron	1365	2193	0.11	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	intron	2342	3248	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	intron	3335	4336	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	CDS	1269	1364	0.23	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	CDS	2194	2341	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	exon	2194	2341	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	CDS	3249	3334	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	exon	3249	3334	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	CDS	4337	4435	0.09	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	exon	4337	4550	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	stop_codon	4433	4435	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	tts	4550	4550	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	1275	1319	5.74	+	0	target "unknown_A[1..15]"; target_start 2; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	2206	2271	6.44	+	0	target "unknown_C[1..22]"; target_start 36; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	2275	2307	8.7	+	0	target "unknown_D[1..11]"; target_start 59; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	2308	2340	7.84	+	0	target "unknown_E[1..11]"; target_start 70; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	3251	3280	8.4	+	0	target "unknown_F[1..10]"; target_start 82; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	3284	3334	7.12	+	0	target "unknown_G[1..17]"; target_start 93; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	4337	4345	7.32	+	0	target "unknown_G[18..20]"; target_start 93; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	4346	4366	9.77	+	0	target "unknown_H[1..7]"; target_start 113; transcript_id "g1.t1"; gene_id "g1";
Contig3050	AUGUSTUS	protein_match	4376	4426	5.46	+	0	target "unknown_I[1..17]"; target_start 123; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcgggtaactactactttgtgatggtcggacacttggacaatccgatatttgagatggaattttgtccaccaaaca
# gggccaatgaacccaagaaggatgaccatcgtcacctgaaccagtttgtcgctcatgaggctctggacctggtcgatgaacaggtgtggacgaccaac
# aacatgtaccttaagattgtggacaaattcaatgagtggtttgtgtcagcttttgtcacagcaagtcgaatgagattcatgatgttacatgatgtgaa
# aaacgaagatggtatcaagaatttcttcacggaaacttacgaaatgtacatcaagcattccatgaacccattctatgaaatcaacaaaccaattgtat
# cgcctgcttttgagaaaaaagttcagacatttggacgaaagtacctaacaggataa]
# protein sequence = [MSGNYYFVMVGHLDNPIFEMEFCPPNRANEPKKDDHRHLNQFVAHEALDLVDEQVWTTNNMYLKIVDKFNEWFVSAFV
# TASRMRFMMLHDVKNEDGIKNFFTETYEMYIKHSMNPFYEINKPIVSPAFEKKVQTFGRKYLTG]
# sequence of block unknown_A     2 [GNYYFVMVGHLDNPI] 17
# sequence of block unknown_C    36 [RHLNQFVAHEALDLVDEQVWTT] 58
# sequence of block unknown_D    59 [NMYLKIVDKFN] 70
# sequence of block unknown_E    70 [EWFVSAFVTAS] 81
# sequence of block unknown_F    82 [MRFMMLHDVK] 92
# sequence of block unknown_G    93 [EDGIKNFFTETYEMYIKHSM] 113
# sequence of block unknown_H   113 [NPFYEIN] 120
# sequence of block unknown_I   123 [VSPAFEKKVQTFGRKYL] 140
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370X1T.prfl --predictionStart=0  --predictionEnd=23337  --species=fly ./tmp/Contig305020180911_busco_2432604931_.temp