# 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..774]--> unknown_A (45) <--[4..25]--> unknown_B (73) <--[0..1]--> unknown_C (14) <--[0..2]--> unknown_D (17) <--[0..2]--> unknown_E (18) <--[4..26]--> unknown_F (10) <--[0..1]--> unknown_G (18) <--[10..34]--> unknown_I (10) <--[1..7]--> unknown_J (26) <--[2..9]--> unknown_K (24) <--[1..8]--> unknown_L (9) <--[0..5]--> unknown_M (11) <--[0..22]--> unknown_N (38) <--[0..3]--> unknown_O (60) <--[10..62]--> unknown_Q (22) <--[0..1]--> unknown_R (23) <--[8..14]--> unknown_T (41) <--[9..22]--> unknown_U (21) <--[0..3]--> unknown_V (13) <--[0..356]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4701420180911_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 = 19105, name = Contig47014) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig47014	AUGUSTUS	gene	1	18615	0.02	-	.	g1
Contig47014	AUGUSTUS	transcript	1	18615	0.02	-	.	g1.t1
Contig47014	AUGUSTUS	intron	1	160	0.89	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	293	2911	0.32	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	2992	3351	0.76	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	3486	4078	0.93	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	4197	5315	0.61	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	5412	8290	0.36	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	8319	10231	0.62	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	10246	12589	0.66	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	12757	13114	0.42	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	13330	15855	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	16060	17555	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	intron	17673	18409	0.81	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	161	292	0.79	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	2912	2991	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	3352	3485	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	4079	4196	0.93	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	5316	5411	0.55	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	8291	8318	0.64	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	10232	10245	0.7	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	12590	12756	0.53	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	13115	13329	0.43	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	15856	16059	0.77	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	17556	17672	0.83	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	CDS	18410	18615	0.86	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47014	AUGUSTUS	start_codon	18613	18615	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtggcccttgggcctcttgtttgaaatcttattgtttattgttggtaatcttattcatttcctgtcaaaagctcaca
# aaggaagcctcaacagaggaagttcagtcggccaaagaatcgtggaggaccggcaaatcaaagtgtccaaagcccagggagaggaaacaccccatgta
# tgtctaatccagcagttcatgtcaaagtgattacccaaaacgggggagaggaatcttttgatcaccagtgctctcccttatgtaaacaacgttcctca
# ccttggaaacatcattggctgtgttctcagtgctgatgtcttctctaggtactgtaaactcaggaactataactgtctgtacatttgtggaacagatg
# agtatggaactgcgacagagacgaaagccattgaggagggactcacccccaaggagatctgcgacaaatacaacaaaatccacaacgaaatctacgag
# tggttcaatatttcctttgataagtttggtcgtacctcagttccggaacaaactaggttccttgctgaccgcttcgttgagggcacctgtcctctttg
# tggctatgacgacgcccgtggtgaccagtgtgatgggtgtggtaaactactgaatgccgtggacctgaaagaccccaagtgtaaagtgtgtcagggaa
# tccccatggtcaaatcctcaagacacttgttcctagatttacccaaagtaagatggggcaagagacacggtcaatagagtaaactccagactcacctg
# aataaagagtttagtcgaggactatggacaaacaatgctcgcgtcattaccaactcctggttacgagacggactgaagcctcggtgtattagccgtga
# tctcaagtggggcatcccggtacccctggagggattcaaagataaagaggagtctaacttttgggtgacagtggcggatccaggatttgtgttttatg
# tttggtatgatgccccaattggatacatatcagcgaccgcatgttacaccgaccaatgggagcaatggtggaaaaatcccaaacaggtggaactgtat
# aatttcctgggtaaggacaatgtacccttccactcggtgatatttccctgcaccttactgggagctgatgataattacaccgtagtcaaccatatgtc
# agctacagagtacttgaactatgaggatacaaagttctccaaaagccgggggaccggtgtgtttggtcatcaggccagggagacgggtatcccagctg
# atgtgtaccgattctacctcttgtatgtacggccagagtcacaggatagtagttttagctgggacgattttcaactgaaaaacaacagtgagctctta
# aataacctgggaaacttcatcaacagggctttgatgtttgtcagtaatcattttgggggagagattcaggagatgaatttgacagcggaagacttcca
# cctgctggccctagtgaacagagagctccgcacctacatagacaacatggaacaagtcaa]
# protein sequence = [MWPLGLLFEILLFIVGNLIHFLSKAHKGSLNRGSSVGQRIVEDRQIKVSKAQGEETPHVCLIQQFMSKXLPKTGERNL
# LITSALPYVNNVPHLGNIIGCVLSADVFSRYCKLRNYNCLYICGTDEYGTATETKAIEEGLTPKEICDKYNKIHNEIYEWFNISFDKFGRTSVPEQTR
# FLADRFVEGTCPLCGYDDARGDQCDGCGKLLNAVDLKDPKCKVCQGIPMVKSSRHLFLDLPKVRWGKRHGQXSKLQTHLNKEFSRGLWTNNARVITNS
# WLRDGLKPRCISRDLKWGIPVPLEGFKDKEESNFWVTVADPGFVFYVWYDAPIGYISATACYTDQWEQWWKNPKQVELYNFLGKDNVPFHSVIFPCTL
# LGADDNYTVVNHMSATEYLNYEDTKFSKSRGTGVFGHQARETGIPADVYRFYLLYVRPESQDSSFSWDDFQLKNNSELLNNLGNFINRALMFVSNHFG
# GEIQEMNLTAEDFHLLALVNRELRTYIDNMEQV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093709BZ.prfl --predictionStart=0  --predictionEnd=37674  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4701420180911_busco_2432604931_.temp