Core Genome MLST Target Definer

Core genome MLST Target Definer

Resulting Targets:

2952 targets were defined for MLST+ (2884626 bases)

1699 targets were used as Accessory targets (1431581 bases)

553 targets were discarded

Reference Genome:

* GenBank entry NC_002695.1, 5498450 bases, 5204 genes (Escherichia coli O157:H7 str. Sakai chromosome, complete genome.)

Query Genomes (10):

* GenBank entry NC_017626.1, 5241977 bases, 4793 genes (Escherichia coli 042, complete genome.)

* GenBank entry NC_013364.1, 5371077 bases, 4968 genes (Escherichia coli O111:H- str. 11128, complete genome.)

* GenBank entry NC_011601.1, 4965553 bases, 4548 genes (Escherichia coli O127:H6 str. E2348/69 chromosome, complete genome.)

* GenBank entry NC_011353.1, 5572075 bases, 5315 genes (Escherichia coli O157:H7 str. EC4115 chromosome, complete genome.)

* GenBank entry NC_002655.2, 5528445 bases, 5286 genes (Escherichia coli O157:H7 str. EDL933 chromosome, complete genome.)

* GenBank entry NC_013008.1, 5528136 bases, 5253 genes (Escherichia coli O157:H7 str. TW14359 chromosome, complete genome.)

* GenBank entry NC_013361.1, 5697240 bases, 5360 genes (Escherichia coli O26:H11 str. 11368 chromosome, complete genome.)

* GenBank entry NC_013941.1, 5386352 bases, 5010 genes (Escherichia coli O55:H7 str. CB9615 chromosome, complete genome.)

* GenBank entry NC_017656.1, 5263980 bases, 4912 genes (Escherichia coli O55:H7 str. RM12579 chromosome, complete genome.)

* GenBank entry NC_017646.1, 5313531 bases, 5009 genes (Escherichia coli O7:K1 str. CE10 chromosome, complete genome.)

Reference Genome Filters:

* Minimum length filter

* Start Codon Filter

* Stop Codon Filter

* Homologous Gene Filter

* Gene overlap filter

* Excluded Sequences Filter

Query Genomes Filters:

* Stop Codon Percentage Filter

Query Genome Blast Search Settings:

* Identity %: 90.0

* Aligned %: 100.0

* Word size: 11

* Mismatch penalty: -1

* Match reward: 1

* Gap open costs: 5

* Gap extension costs: 2

Progress:

* MLST+ target search start at Aug 22, 2014 1:27 PM

* 4333 targets after filtering GenBank entry NC_002695.1, 5498450 bases, 5204 genes (Escherichia coli O157:H7 str. Sakai chromosome, complete genome.).

* 3493 targets after blasting against GenBank entry NC_017626.1, 5241977 bases, 4793 genes (Escherichia coli 042, complete genome.)

* 3266 targets after blasting against GenBank entry NC_013364.1, 5371077 bases, 4968 genes (Escherichia coli O111:H- str. 11128, complete genome.)

* 3031 targets after blasting against GenBank entry NC_011601.1, 4965553 bases, 4548 genes (Escherichia coli O127:H6 str. E2348/69 chromosome, complete genome.)

* 3021 targets after blasting against GenBank entry NC_011353.1, 5572075 bases, 5315 genes (Escherichia coli O157:H7 str. EC4115 chromosome, complete genome.)

* 3019 targets after blasting against GenBank entry NC_002655.2, 5528445 bases, 5286 genes (Escherichia coli O157:H7 str. EDL933 chromosome, complete genome.)

* 3019 targets after blasting against GenBank entry NC_013008.1, 5528136 bases, 5253 genes (Escherichia coli O157:H7 str. TW14359 chromosome, complete genome.)

* 3006 targets after blasting against GenBank entry NC_013361.1, 5697240 bases, 5360 genes (Escherichia coli O26:H11 str. 11368 chromosome, complete genome.)

* 3001 targets after blasting against GenBank entry NC_013941.1, 5386352 bases, 5010 genes (Escherichia coli O55:H7 str. CB9615 chromosome, complete genome.)

* 3001 targets after blasting against GenBank entry NC_017656.1, 5263980 bases, 4912 genes (Escherichia coli O55:H7 str. RM12579 chromosome, complete genome.)

* 2958 targets after blasting against GenBank entry NC_017646.1, 5313531 bases, 5009 genes (Escherichia coli O7:K1 str. CE10 chromosome, complete genome.)

* MLST+ target search ended at Aug 22, 2014 1:29 PM

MLST+ Genome Coverage:

* 52.5% of Reference genome (GenBank entry NC_002695.1) bases covered by MLST+ targets

* 55.0% of Query genome (GenBank entry NC_017626.1) bases covered by MLST+ targets

* 53.7% of Query genome (GenBank entry NC_013364.1) bases covered by MLST+ targets

* 58.1% of Query genome (GenBank entry NC_011601.1) bases covered by MLST+ targets

* 51.8% of Query genome (GenBank entry NC_011353.1) bases covered by MLST+ targets

* 52.2% of Query genome (GenBank entry NC_002655.2) bases covered by MLST+ targets

* 52.2% of Query genome (GenBank entry NC_013008.1) bases covered by MLST+ targets

* 50.6% of Query genome (GenBank entry NC_013361.1) bases covered by MLST+ targets

* 53.6% of Query genome (GenBank entry NC_013941.1) bases covered by MLST+ targets

* 54.8% of Query genome (GenBank entry NC_017656.1) bases covered by MLST+ targets

* 54.3% of Query genome (GenBank entry NC_017646.1) bases covered by MLST+ targets

Targets Discarded by Reference Genome Filter:

* Stop Codon Filter: 4

* Homologous Gene Filter: 550