# 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..109]--> unknown_A (17) <--[0..1]--> unknown_B (48) <--[6..27]--> unknown_C (18) <--[0..7]--> unknown_D (26) <--[0..1]--> unknown_E (36) <--[0..12]--> unknown_F (100) <--[2..9]--> unknown_G (28) <--[7..16]--> unknown_I (85) <--[0..1]--> unknown_J (63) <--[0..2]--> unknown_K (24) <--[0..17]--> unknown_L (48) <--[0..15]--> unknown_M (15) <--[0..1]--> unknown_N (36) <--[0..1]--> unknown_O (16) <--[7..20]--> unknown_Q (16) <--[0..1]--> unknown_R (53) <--[0..1]--> unknown_S (20) <--[12..29]--> unknown_U (23) <--[0..7]--> unknown_V (41) <--[28..41]--> unknown_Y (26) <--[0..1]--> unknown_Z (20) <--[2..43]--> unknown_AA (51) <--[0..1]--> unknown_AB (19) <--[0..59]--> unknown_AC (16) <--[0..2]--> unknown_AD (19) <--[0..2]--> unknown_AE (16) <--[0..1]--> unknown_AF (73) <--[4..24]--> unknown_AG (21) <--[0..3]--> unknown_AH (53) <--[7..68]--> unknown_AJ (26) <--[5..154]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig5652120180911_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 = 12123, name = Contig56521) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig56521	AUGUSTUS	gene	770	11432	0.01	+	.	g1
Contig56521	AUGUSTUS	transcript	770	11432	0.01	+	.	g1.t1
Contig56521	AUGUSTUS	exon	770	793	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	start_codon	772	774	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	intron	794	4793	0.55	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	intron	4934	5239	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	intron	5320	7902	0.07	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	intron	7964	8129	0.24	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	intron	8211	8299	0.32	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	CDS	772	793	0.56	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	CDS	4794	4933	0.91	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	4794	4933	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	CDS	5240	5319	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	5240	5319	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	CDS	7903	7963	0.25	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	7903	7963	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	CDS	8130	8210	0.32	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	8130	8210	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	CDS	8300	8485	0.33	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	8300	9246	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	stop_codon	8483	8485	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	9742	9886	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	exon	10895	11432	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56521	AUGUSTUS	tts	11432	11432	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaggtttcatcacaggagactatccagttcgtcctttctgatgaattcaatcatcttagacccgaacagaggcaag
# ctcttcttcatgaaggaacaggtccaagggttatttcagcctttgtggagatcatatttgacaattcagataacaggataccaattgacaaagatgaa
# gtggtactcagacgtgtaattggatccaagaaagaccagtactttttagacaagaaaatggtcacatctttagaatataccattcatgaccatgagct
# gagagacaccaggaaaaaactagatgagctgcaagagaaacgagataatagtggtgctatgacccaaaagattcgagacaaacagcagtccactgttg
# accgagttaagtccataactcgagaactccgagacctgaagactaaaatgcagggagtgatggaagagaaagaaaatatgaactctgacaaccaagaa
# gtgacgaagcgcagagccaagctggagttgatgatcaaggacattcaagatgagctagagggggacaaaagtgctagggtaatagactttgtattgta
# a]
# protein sequence = [MKVSSQETIQFVLSDEFNHLRPEQRQALLHEGTGPRVISAFVEIIFDNSDNRIPIDKDEVVLRRVIGSKKDQYFLDKK
# MVTSLEYTIHDHELRDTRKKLDELQEKRDNSGAMTQKIRDKQQSTVDRVKSITRELRDLKTKMQGVMEEKENMNSDNQEVTKRRAKLELMIKDIQDEL
# EGDKSARVIDFVL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937017X.prfl --predictionStart=0  --predictionEnd=26834  --species=fly ./tmp/Contig5652120180911_busco_2432604931_.temp