# 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..129]--> unknown_A (15) <--[3..6]--> unknown_B (23) <--[0..16]--> unknown_C (30) <--[6..13]--> unknown_D (11) <--[13..24]--> unknown_E (21) <--[3..19]--> unknown_F (33) <--[0..1]--> unknown_G (21) <--[1..17]--> unknown_H (25) <--[1..15]--> unknown_I (36) <--[1..9]--> unknown_J (25) <--[0..16]--> unknown_K (18) <--[0..2]--> unknown_L (19) <--[0..1]--> unknown_M (28) <--[0..3]--> unknown_N (31) <--[0..1]--> unknown_O (19) <--[0..19]--> unknown_P (13) <--[9..18]--> unknown_R (14) <--[0..20]--> unknown_S (15) <--[10..25]--> unknown_U (17) <--[44..183]--> unknown_X (45) <--[1..5]--> unknown_Y (22) <--[0..6]--> unknown_Z (8) <--[5..12]--> unknown_AA (17) <--[0..14]--> unknown_AB (33) <--[1..76]--> unknown_AC (26) <--[0..3]--> unknown_AD (18) <--[23..230]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig2883520180911_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 = 35077, name = Contig28835) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig28835	AUGUSTUS	gene	35773	38349	0.04	+	.	g1
Contig28835	AUGUSTUS	transcript	35773	38349	0.04	+	.	g1.t1
Contig28835	AUGUSTUS	tss	35773	35773	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig28835	AUGUSTUS	exon	35773	35936	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig28835	AUGUSTUS	exon	36246	38349	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig28835	AUGUSTUS	start_codon	36253	36255	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig28835	AUGUSTUS	CDS	36253	38136	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig28835	AUGUSTUS	stop_codon	38134	38136	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig28835	AUGUSTUS	tts	38349	38349	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaggttcctgtaataggaattgatcttggaacaacttattcgtgtgtgggtgttttccagcatgggaaagtagaaa
# taatcgccaatgaccaaggcaacagaacaacgccaagttatgtagcctttacggacaccgagcgcattatcggagatgctgcaaaaaaccaagtggct
# atgaatcctaaaaatactatttttgacgccaaaagacttattggacgaaaatttgaagagccgtctgtccaaagtgacatgaaacattggcctttcaa
# agtcactaacaagcagggaaaaccaataatacaagttgaatacaagaatgaaataaaatcctttagtcctgaggaggttagttcgatggtactgacca
# aaatgcgcgagacggcggaagcgtttctaggagagaaagtgaccaaggcagtcatcaccgtcccggcgtactttaacgactcacagcgccaagcaaca
# aaagacgcgggcatcatcgcaggattagaggtattacgaattgtaaacgaacctacggctgcagccctagcatacgggcttgacaagaatttatcggg
# ggaaaagaatgttttaatttacgatctaggcgggggcacattcgatgtatcgattcttaacatcgacgaaggttcagtgtttgaagtacagtctacag
# ctggtgacacccatcttggaggagaggattttgacaacagaatggtggattactttgtaaaagaatttaagaggaaataccagaaggaaataacttca
# aacaatcgagcgcttagaagacttagaactgcatgtgaaagagccaagaggaccttgtccagcagcacagaggctagtatagaaatagattccctttg
# cgacggggttgacttctacacaaaaataactcgcgccagattcgaggaactgtgttctgacttgttcaaaagtaccatggaacctgtggaaagagcaa
# taaaagatgccaaattagacaagtctaaaatccacgatatcgttctggttggcggatcaacacgaataccaaagatacaaaaactactttctgatttc
# atgggaggaaaagacttgaaccgttctattaatccagatgaggctgtagcctatggcgctgccgttcaggccgccattttatcgggtgattccagtga
# tgttatcaaagacttgcttttgatcgatgttgctcctttatcccttggaatagagacggcgggtggtgtcatgacaaatcttattgatagaaatagcc
# gaattccgtgtaaaattagcaaaactttcacgacgtactctgataaccaaccaggcgtccatattcaagtttttgaaggagaacgcgccatgacaaag
# gacaaccacaaactcggaaatttcgatcttacgggcattcctccagcgcctagaggtgttccgcaaatcgacgttgaatttgatttggatgccaactg
# cattttaaatgtttctgcagtagacaagagcacgggcaagtctaataaagtgaccatcacgaacgacaaaggccggcttagcaaaactgaaattgatc
# gaatggtttcggacgctgaaaaatacaaggaggcggacgaaaaacagaagcaacgtgtacaaagtaagaaccagttagaaaactacatttacggcatc
# cgcaatgcggtggaagaggaaaagggcaaacttcagccctcggagaagacagaagcactgaatgcctgcgaggaagctttgaaatggttggatcttaa
# cgccgaagcagaaacgtctgaatatgaaggtaaattgaagatggtccaggagacttgtagtccgattatgacaaagcttcacagcgaacagaaggaaa
# gtagtacggcagatggaccaaaggtggaagaagtagattaa]
# protein sequence = [MKVPVIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERIIGDAAKNQVAMNPKNTIFDAKRLIGRKFE
# EPSVQSDMKHWPFKVTNKQGKPIIQVEYKNEIKSFSPEEVSSMVLTKMRETAEAFLGEKVTKAVITVPAYFNDSQRQATKDAGIIAGLEVLRIVNEPT
# AAALAYGLDKNLSGEKNVLIYDLGGGTFDVSILNIDEGSVFEVQSTAGDTHLGGEDFDNRMVDYFVKEFKRKYQKEITSNNRALRRLRTACERAKRTL
# SSSTEASIEIDSLCDGVDFYTKITRARFEELCSDLFKSTMEPVERAIKDAKLDKSKIHDIVLVGGSTRIPKIQKLLSDFMGGKDLNRSINPDEAVAYG
# AAVQAAILSGDSSDVIKDLLLIDVAPLSLGIETAGGVMTNLIDRNSRIPCKISKTFTTYSDNQPGVHIQVFEGERAMTKDNHKLGNFDLTGIPPAPRG
# VPQIDVEFDLDANCILNVSAVDKSTGKSNKVTITNDKGRLSKTEIDRMVSDAEKYKEADEKQKQRVQSKNQLENYIYGIRNAVEEEKGKLQPSEKTEA
# LNACEEALKWLDLNAEAETSEYEGKLKMVQETCSPIMTKLHSEQKESSTADGPKVEEVD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093707VQ.prfl --predictionStart=16268  --predictionEnd=57353  --species=fly ./tmp/Contig2883520180911_busco_2432604931_.temp