# 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..120]--> unknown_A (14) <--[3..33]--> unknown_B (26) <--[0..7]--> unknown_C (28) <--[3..36]--> unknown_D (22) <--[0..7]--> unknown_E (27) <--[4..11]--> unknown_F (19) <--[10..30]--> unknown_H (22) <--[2..22]--> unknown_I (22) <--[1..25]--> unknown_J (17) <--[0..183]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5376020180911_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 = 11293, name = Contig53760) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig53760	AUGUSTUS	gene	1	2547	0.13	+	.	g1
Contig53760	AUGUSTUS	transcript	1	2547	0.13	+	.	g1.t1
Contig53760	AUGUSTUS	intron	199	545	0.26	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	intron	705	1205	0.42	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	intron	1422	2256	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	CDS	1	198	0.44	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	CDS	546	704	0.25	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	CDS	1206	1421	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	CDS	2257	2547	0.73	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53760	AUGUSTUS	stop_codon	2545	2547	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aaaatacaggatctgtttggtggagaagtgatcctcagaatggcccagcagaaggcaggtccagtggtaacagacaatg
# gtaactgtgtgttggactggaagttccccaatccttgtgatgactgggacaattgtaacaccactatcaaattgattccaggtgtggtggaaactggt
# ctcttcatcaaaatggcaaagttttttggaagtgtgagatcgcatgtcacgggccacgatagacagtgcaaaacgatgtccgcaatagaggccagcaa
# aaaagcagcagcatttgcggctgtcgacgaaaatattagaggaacaaccaaaagattggcatcggagtggatcaactgtggggagaaaattgtcgcct
# cctgtgccaaagatcttatcatcattgcagacaacagaaaagactctcaagtgctgggtacaacatacaagaagggaatcccaatagaagttattcat
# atggcatacaaacccgttcagatgaaaatacaggatctgtttggtggagaagtgatcctagaatggcccagcagaaggcaggtccgagtggtaacgac
# aatggagaaaattgtcgcctcctgtgccaaagatcttatcatcattgcagacgacagaaaagatctcgcgtgctgggtagcaacatacaagaagggaa
# tcccaatagaagttattcctatggcatacaaacccgtttcagatgaaaatacaggatctgtttggtggagaagtgccctaagaatggcccagcacaag
# tcaggtccagtggttacagacaatggtaactgtgtgttggactggaagttccccaatccttgtgatgactgggacaattgtaacacactaatcaaatg
# a]
# protein sequence = [KIQDLFGGEVILRMAQQKAGPVVTDNGNCVLDWKFPNPCDDWDNCNTTIKLIPGVVETGLFIKMAKFFGSVRSHVTGH
# DRQCKTMSAIEASKKAAAFAAVDENIRGTTKRLASEWINCGEKIVASCAKDLIIIADNRKDSQVLGTTYKKGIPIEVIHMAYKPVQMKIQDLFGGEVI
# LEWPSRRQVRVVTTMEKIVASCAKDLIIIADDRKDLACWVATYKKGIPIEVIPMAYKPVSDENTGSVWWRSALRMAQHKSGPVVTDNGNCVLDWKFPN
# PCDDWDNCNTLIK]
# end gene g1
###
# start gene g2
Contig53760	AUGUSTUS	gene	4233	10746	0.11	-	.	g2
Contig53760	AUGUSTUS	transcript	4233	10746	0.11	-	.	g2.t1
Contig53760	AUGUSTUS	stop_codon	4233	4235	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	4323	4817	0.75	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	4834	6254	0.34	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	6454	6671	0.59	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	6781	6899	0.81	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	7089	8008	0.85	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	8141	8698	0.98	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	8731	9685	0.96	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	9791	9981	0.69	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	intron	10162	10610	1	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	4233	4322	0.75	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	4818	4833	0.75	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	6255	6453	0.23	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	6672	6780	0.97	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	6900	7088	0.81	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	8009	8140	1	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	8699	8730	0.98	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	9686	9790	0.94	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	9982	10161	0.7	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	CDS	10611	10746	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53760	AUGUSTUS	start_codon	10744	10746	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgctgagtgaatcggttgtccacatactccccattgtaaatcccgatggagcaatggcggcttccccggctggctgca
# atgtcaccacgggcaaaaacaatgctaaaaatgtggacctacttttaaacttctacactgaagaagagaaggtgaagctggtgcagacagagactaaa
# ctgttgatggactggatgatgaaagtgcagcctacattagccttatcactgaggagtggattccagggtgttaccactccaccctatggtaaatgtaa
# tccagtcattagattccagggtgttaccactccaccctatgtgaacctgagccctccagagaagtctgtattggataatttaggcggaaagtttacca
# acatactgtcaacgttagacggagctggaaaagagaagtgtgggaagggtggcgacactttcttcaatagcagtttcctggaatatgcctacagccac
# tgccattctgtcccactagaaatttcaacaggatgttgtcatcgcccaaatgaagatcaactgctgaacatttggcataaactccgagagcctctgtt
# agacatggtgactgaggctaataaaggttttagtggaatcgttaaagacaaggaatcccaaaagaatatggtcaatgccacaatcaaaatccaagggt
# ttagctggactttccatgtgaatgaagaagcaaggttccatatctacctccctccaggaggttaccaaattactgtcagttgtcatggttaccagaat
# ttcaaaaagaacattgtggtaccaaatggtgagctagggagattaaattcagtgatccacttgcagtcagtaagcaccatacttggactatcccatgc
# tgcatttattgttatagcatccatagctgtgatgattgttttgctgatttgtactgtgttgatctgtatgagagccagggccagaaaaacagcgggct
# tctcaaggataaagtttgatgaggaggaggacgaagatttcgaagaatattacgataacggagcaacgaaaaagtttataaataaagaataccatgac
# tatagctcagatgatgaagatatgaaatggtgttaccttgtattgaccgggaagtcttggtcgagacagtgtaacccggacggatacgccattcagat
# ggcgggcgatagaggagttagaccagtctaa]
# protein sequence = [MLSESVVHILPIVNPDGAMAASPAGCNVTTGKNNAKNVDLLLNFYTEEEKVKLVQTETKLLMDWMMKVQPTLALSLRS
# GFQGVTTPPYGKCNPVIRFQGVTTPPYVNLSPPEKSVLDNLGGKFTNILSTLDGAGKEKCGKGGDTFFNSSFLEYAYSHCHSVPLEISTGCCHRPNED
# QLLNIWHKLREPLLDMVTEANKGFSGIVKDKESQKNMVNATIKIQGFSWTFHVNEEARFHIYLPPGGYQITVSCHGYQNFKKNIVVPNGELGRLNSVI
# HLQSVSTILGLSHAAFIVIASIAVMIVLLICTVLICMRARARKTAGFSRIKFDEEEDEDFEEYYDNGATKKFINKEYHDYSSDDEDMKWCYLVLTGKS
# WSRQCNPDGYAIQMAGDRGVRPV]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370U9P.prfl --predictionStart=0  --predictionEnd=22633  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5376020180911_busco_2432604931_.temp