# 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
# --[5..66]--> unknown_A (14) <--[2..16]--> unknown_B (21) <--[0..1]--> unknown_C (23) <--[0..4]--> unknown_D (88) <--[0..1]--> unknown_E (32) <--[0..5]--> unknown_F (30) <--[8..15]--> unknown_G (20) <--[2..12]--> unknown_H (16) <--[5..7]--> unknown_I (14) <--[0..1]--> unknown_J (13) <--[0..1]--> unknown_K (10) <--[0..21]--> unknown_L (37) <--[0..39]--> unknown_M (79) <--[0..2]--> unknown_N (16) <--[0..4]--> unknown_O (49) <--[0..5]--> unknown_P (15) <--[0..8]--> unknown_Q (45) <--[0..2]--> unknown_R (51) <--[0..17]--> unknown_S (56) <--[0..4]--> unknown_T (30) <--[0..4]--> unknown_U (20) <--[0..1]--> unknown_V (22) <--[1..22]--> unknown_W (56) <--[0..6]--> unknown_X (22) <--[0..2]--> unknown_Y (15) <--[1..4]--> unknown_Z (27) <--[1..3]--> unknown_AA (18) <--[10..24]--> unknown_AB (36) <--[0..1]--> unknown_AC (22) <--[0..6]--> unknown_AD (13) <--[9..14]--> unknown_AE (12) <--[1..88]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig1073120180911_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 = 10602, name = Contig10731) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig10731	AUGUSTUS	gene	2644	10425	0.03	+	.	g1
Contig10731	AUGUSTUS	transcript	2644	10425	0.03	+	.	g1.t1
Contig10731	AUGUSTUS	exon	2644	2799	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	start_codon	2668	2670	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	2800	4508	0.39	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	4625	4722	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	4838	7364	0.57	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	7524	7895	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	8097	8209	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	8349	8441	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	8546	8675	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	8754	8889	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	9047	9185	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	9350	9693	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	9934	10066	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	intron	10253	10349	0.75	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	2668	2799	0.34	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	4509	4624	0.5	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	4509	4624	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	4723	4837	0.83	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	4723	4837	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	7365	7523	0.9	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	7365	7523	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	7896	8096	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	7896	8096	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	8210	8348	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	8210	8348	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	8442	8545	0.95	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	8442	8545	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	8676	8753	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	8676	8753	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	8890	9046	0.6	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	8890	9046	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	9186	9349	0.99	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	9186	9349	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	9694	9933	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	9694	9933	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	10067	10252	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	10067	10252	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	CDS	10350	10382	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	exon	10350	10425	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	stop_codon	10380	10382	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig10731	AUGUSTUS	tts	10425	10425	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgccacccataacaatgaattcggttaacctctcggaggaagcagccaagcttctggacttcagtcagaagctggaca
# tcaacctgctggataatgttgtcaccatgatgtacacaggaaatggaccacagattttgaaatatgaatggcccagaaattggccatcattcatcagt
# gacattgtaggagctagtaaaacaaatgaatcattgtgtcagaataatttgactattctcaaattactcagtgaagaggtcttcgacttcagcagtgg
# tcaaatgacacaggcaaaagctaagcatttaaaggacagcatgtgtagtgaattttcctctatcttccagctgtgccaatttgtcatgatgttgcctt
# tggaaacaaatttgaaagaagcgtatcagaaagggacagatgatgaacagaaatttatacagaacctcagtttgttcctgtgtacgtatctcaaggaa
# cacggtcagctgatcgagaggaaacaagacctgcacagtgttctattggaggcccttcactacctgatcctgatatcagaagtggaggaggtggaaat
# ctttaagattgcgctggagtactggaacacactggctgctgatctctacagagagagtccattttcttccaacacatcccccctactcataggaaaac
# cgcaccacaatgatgtgcctgccagaagacagctctatacgcaagtcctatctagggtacgacgagttatgatatcgagaatggctaagccagaggaa
# gtcctaattgtcgagaatgaacagggagaggtggtcagggaattccttaaagacacagactccattaatctgtacaaaaacatgagagaaacattagt
# gtacctgactcacttggattataatgacacagaatcaatcatgacagaaaaacttcatcatcaggtggatggtacagaatggtcgtggaaaaacctta
# acacattatgctgggccattggatccatcagtggagccatgcatgaggacgacgaaaaaagatttcttgtcactgttatcaaggatttgttggggttg
# tgtgagcagaagagagggaaggacaacaaggccattgtagcctctaacatcatgtatgtagtgggacagtatcctcgatttctgcgggcccactggag
# gttcctcaaaacagttgtcaacaagctcttcgagttcatgcatgagacacatgatggtgtacaagacatggcatgtgatactttcatcaagattgccc
# agaagtgcaggcgacattttgtacaggttcaggtgggagaagtaatgccattcatagaggaaattctgaacggaataaacacgatcatctgtgatcta
# caaccacaacaggtgcacacgttctacgaggcagtggggatgatgatcagtgcacagaacgaccaggtagctcaggagcatctgatagaacgatatct
# gttgttaccaaaccaagtctgggatggaatcattaaccaggccacacagaatgtggaagtactgaaggaccctgatgctgtcaaacaactaggaaaca
# ttctcaagacaaatgttcgagcttgcaaagcactgggccatccttatgtagtgcagttaggaagaatttatttggacatgctgaatgtgtacaaagtg
# atgagtgagaacatcagcagtgccatagcaacaaacggcgagaccgtgacaaagcagccgctcatacgcagcatgaggaccgtgaagaaggagaccct
# gaagctgatatcaggctgggtcagtcgttccacggatcctcagatgatactgttaaatcatttattttcatgggtttaa]
# protein sequence = [MPPITMNSVNLSEEAAKLLDFSQKLDINLLDNVVTMMYTGNGPQILKYEWPRNWPSFISDIVGASKTNESLCQNNLTI
# LKLLSEEVFDFSSGQMTQAKAKHLKDSMCSEFSSIFQLCQFVMMLPLETNLKEAYQKGTDDEQKFIQNLSLFLCTYLKEHGQLIERKQDLHSVLLEAL
# HYLILISEVEEVEIFKIALEYWNTLAADLYRESPFSSNTSPLLIGKPHHNDVPARRQLYTQVLSRVRRVMISRMAKPEEVLIVENEQGEVVREFLKDT
# DSINLYKNMRETLVYLTHLDYNDTESIMTEKLHHQVDGTEWSWKNLNTLCWAIGSISGAMHEDDEKRFLVTVIKDLLGLCEQKRGKDNKAIVASNIMY
# VVGQYPRFLRAHWRFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIEEILNGINTIICDLQPQQVHTFYEAVGMMISAQ
# NDQVAQEHLIERYLLLPNQVWDGIINQATQNVEVLKDPDAVKQLGNILKTNVRACKALGHPYVVQLGRIYLDMLNVYKVMSENISSAIATNGETVTKQ
# PLIRSMRTVKKETLKLISGWVSRSTDPQMILLNHLFSWV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937018Z.prfl --predictionStart=0  --predictionEnd=30243  --species=fly ./tmp/Contig1073120180911_busco_2432604931_.temp