MLST+ Target Definer Results Aug 14, 2013 9:37 AM Ridom SeqSphere+ 1.0.0-rc41_(2013-08) Resulting Targets: 1241 targets were defined for MLST+ (1195420 bases) 676 targets were excluded Reference Genome: * GenBank file NC_008767.1.gb, 2194961 bases, 1917 genes (Neisseria meningitidis FAM18 chromosome, complete genome.) Query Genomes (13): * GenBank file NC_003112.2.gb, 2272360 bases, 2063 genes (Neisseria meningitidis MC58 chromosome, complete genome.) * GenBank file NC_003116.1.gb, 2184406 bases, 1909 genes (Neisseria meningitidis Z2491 chromosome, complete genome.) * GenBank file NC_010120.1.gb, 2153416 bases, 2020 genes (Neisseria meningitidis 053442 chromosome, complete genome.) * GenBank file NC_013016.1.gb, 2145295 bases, 1872 genes (Neisseria meningitidis alpha14 chromosome, complete genome.) * GenBank file NC_017501.1.gb, 2277550 bases, 1913 genes (Neisseria meningitidis 8013, complete genome.) * GenBank file NC_017505.1.gb, 2242947 bases, 2017 genes (Neisseria meningitidis alpha710 chromosome, complete genome.) * GenBank file NC_017512.1.gb, 2227255 bases, 1941 genes (Neisseria meningitidis WUE 2594, complete genome.) * GenBank file NC_017513.1.gb, 2184862 bases, 1971 genes (Neisseria meningitidis G2136 chromosome, complete genome.) * GenBank file NC_017514.1.gb, 2223518 bases, 1985 genes (Neisseria meningitidis M01-240149 chromosome, complete genome.) * GenBank file NC_017515.1.gb, 2250449 bases, 2022 genes (Neisseria meningitidis M04-240196 chromosome, complete genome.) * GenBank file NC_017516.1.gb, 2240883 bases, 2025 genes (Neisseria meningitidis H44/76 chromosome, complete genome.) * GenBank file NC_017517.1.gb, 2287777 bases, 2023 genes (Neisseria meningitidis M01-240355 chromosome, complete genome.) * GenBank file NC_017518.1.gb, 2248966 bases, 2014 genes (Neisseria meningitidis NZ-05/33 chromosome, complete genome.) Reference Genome Filters: * Minimum length filter * Start Codon Filter * Stop Codon Filter * Multi Copy Filter * Gene overlap 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 14, 2013 9:35 AM * 1662 targets after filtering GenBank file NC_008767.1.gb, 2194961 bases, 1917 genes (Neisseria meningitidis FAM18 chromosome, complete genome.). * 1451 targets after blasting against GenBank file NC_003112.2.gb, 2272360 bases, 2063 genes (Neisseria meningitidis MC58 chromosome, complete genome.) * 1363 targets after blasting against GenBank file NC_003116.1.gb, 2184406 bases, 1909 genes (Neisseria meningitidis Z2491 chromosome, complete genome.) * 1335 targets after blasting against GenBank file NC_010120.1.gb, 2153416 bases, 2020 genes (Neisseria meningitidis 053442 chromosome, complete genome.) * 1285 targets after blasting against GenBank file NC_013016.1.gb, 2145295 bases, 1872 genes (Neisseria meningitidis alpha14 chromosome, complete genome.) * 1278 targets after blasting against GenBank file NC_017501.1.gb, 2277550 bases, 1913 genes (Neisseria meningitidis 8013, complete genome.) * 1272 targets after blasting against GenBank file NC_017505.1.gb, 2242947 bases, 2017 genes (Neisseria meningitidis alpha710 chromosome, complete genome.) * 1267 targets after blasting against GenBank file NC_017512.1.gb, 2227255 bases, 1941 genes (Neisseria meningitidis WUE 2594, complete genome.) * 1262 targets after blasting against GenBank file NC_017513.1.gb, 2184862 bases, 1971 genes (Neisseria meningitidis G2136 chromosome, complete genome.) * 1259 targets after blasting against GenBank file NC_017514.1.gb, 2223518 bases, 1985 genes (Neisseria meningitidis M01-240149 chromosome, complete genome.) * 1254 targets after blasting against GenBank file NC_017515.1.gb, 2250449 bases, 2022 genes (Neisseria meningitidis M04-240196 chromosome, complete genome.) * 1253 targets after blasting against GenBank file NC_017516.1.gb, 2240883 bases, 2025 genes (Neisseria meningitidis H44/76 chromosome, complete genome.) * 1249 targets after blasting against GenBank file NC_017517.1.gb, 2287777 bases, 2023 genes (Neisseria meningitidis M01-240355 chromosome, complete genome.) * 1249 targets after blasting against GenBank file NC_017518.1.gb, 2248966 bases, 2014 genes (Neisseria meningitidis NZ-05/33 chromosome, complete genome.) * MLST+ target search ended at Aug 14, 2013 9:37 AM Genome Coverage: * 54.5% of Reference genome (GenBank file NC_008767.1.gb) bases covered by MLST+ targets * 52.6% of Query genome (GenBank file NC_003112.2.gb) bases covered by MLST+ targets * 54.7% of Query genome (GenBank file NC_003116.1.gb) bases covered by MLST+ targets * 55.5% of Query genome (GenBank file NC_010120.1.gb) bases covered by MLST+ targets * 55.7% of Query genome (GenBank file NC_013016.1.gb) bases covered by MLST+ targets * 52.5% of Query genome (GenBank file NC_017501.1.gb) bases covered by MLST+ targets * 53.3% of Query genome (GenBank file NC_017505.1.gb) bases covered by MLST+ targets * 53.7% of Query genome (GenBank file NC_017512.1.gb) bases covered by MLST+ targets * 54.7% of Query genome (GenBank file NC_017513.1.gb) bases covered by MLST+ targets * 53.8% of Query genome (GenBank file NC_017514.1.gb) bases covered by MLST+ targets * 53.1% of Query genome (GenBank file NC_017515.1.gb) bases covered by MLST+ targets * 53.3% of Query genome (GenBank file NC_017516.1.gb) bases covered by MLST+ targets * 52.3% of Query genome (GenBank file NC_017517.1.gb) bases covered by MLST+ targets * 53.2% of Query genome (GenBank file NC_017518.1.gb) bases covered by MLST+ targets Targets Excluded by Reference Genome Filter: * Start Codon Filter: 1 * Stop Codon Filter: 34 * Multi Copy Filter: 136 * Gene overlap filter: 84 Targets Excluded by Query Genome Blast Search: * No Hits: 369 * Multiple Hits: 44 Targets Excluded by Other Reason: * Stop Codon Percentage Filter: >10 query genomes with erroneous stop codons: 8