From: Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing
Name | R6 positiona | Locus | Motif bp | Percent matches | R6 amplicon | PCR primers | No of alleles | Allele size range (units) | HGDId (56 strains) | |
---|---|---|---|---|---|---|---|---|---|---|
size bp | repeats | |||||||||
Spneu15 | 1579 | BOX | 45 | 94 | 507 | 7 | TCCAACACGACCTTTATCCA | 10 | 1–12 | 0.827 |
AGCCTTGCTCCTCATCTTGA | ||||||||||
Spneu17 | 1783 | BOX | 45 | 86 | 167 | 3 | TCGAAAATCTCTGCAAACCA | 12 | 1–13 | 0.883 |
CGGACTAGGCGGCTGATTA | ||||||||||
Spneu19 | 1925 | pcpA | 60 | 98 | 663 | 10 | TCGGGTGTAGTCGTGTTTACT | 5 | 7–10 | 0.749 |
AACTGATGTAGCTAAACCTAAAAAGAA | ||||||||||
Spneu25 | 101 | BOX | 45 | 96 | 423 | 4 | TCGCCTTTGCTAATCAAACA | 7 | 1–6c | 0.744 |
GACTGGGTAACAATTCCATT | ||||||||||
Spneu26 | 185 | intergenic | 51 | 65 | 492 | 6 | ATGGAACAGAAGGCGAATTG | 7 | 1–9 | 0.688 |
AACAAGGCCAGGATTTTCGT | ||||||||||
Spneu27 | 257 | BOX | 45 | 95 | 347 | 3 | TCAGGAACAGCTATTATCCC | 5 | 0.5–4 | 0.575 |
CCAACCTCCTTTTCGTTTCA | ||||||||||
Spneu31 | 557 | BOX | 45 | 98 | 594 | 9 | CTGGAATAGTCCATCGAGCTT | 9 | 1–9 | 0.763 |
CGAAGGTAAATGTGAACAAAC | ||||||||||
Spneu32 | 571 | BOX | 45 | 86 | 280 | 2 | AAAGCAAAATAATGCGCTCCT | 4 | 1–4 | 0.629 |
ACTACCAAAGCCCAAGTGGT | ||||||||||
Spneu33 | 698 | BOX | 45 | 95 | 407 | 2 | CAGCTGAACATGATGGCAAA | 10 | 1–10c | 0.858 |
CATCACTTCTCCCTTCTAATC | ||||||||||
Spneu34 | 1082 | BOX | 45 | 97 | 239 | 1 | CTCGGTAAAGACGAGGTTCAA | 6 | 1–11 | 0.598 |
CATCGTGCAGGGATTTTCTAA | ||||||||||
Spneu35 | 1166 | intergenic | 49 | 100 | 349 | 4 | ACAATCTCAGCTACGCCCTA | 5 | 1–5 | 0.561 |
ACGGGATGACATTAAAAACC | ||||||||||
Spneu36 | 1209 | trzA | 45 | 86 | 320 | 2 | GAAATCTTGATCACAAGTCAC | 10 | 1–10 | 0.866 |
AAAAAGTTGCCTTCGAGTGAC | ||||||||||
Spneu37 | 1350 | BOX | 45 | 91 | 501 | 7 | ATGCGCAAATCGATTAAGGA | 11 | 2–12 | 0.876 |
CGATGTGCTTCACTCACTCC | ||||||||||
Spneu38 | 1911 | BOX | 45 | 84 | 297 | 1.5b | TCAGGAGTAGGTTCCTGACCA | 6 | 0.1–4 | 0.616 |
AACCCGAGAAGAAGTGCAAG | ||||||||||
Spneu39 | 1915 | BOX | 45 | 83 | 275 | 2 | CCTTGGACTACCACCTCGTT | 14 | 2–17 | 0.862 |
GCCGTGACAGACTTCTGGAA | ||||||||||
Spneu40 | 1611 | BOX | 45 | 88 | 376 | 3 | AGTAGTCTGCAATCGCAGCT | 7 | 2–8 | 0.832 |
GGGCCTTAAGTCGCTTTGAT | ||||||||||
Spneu41 | 394 | intergenic | 14 | 100 | 166 | 2 | ACCGTAATGGGACTTCATCT | 5 | 1–4 | 0.484 |
ATCTGCACCTAAGACAATCG | ||||||||||
Spneu42 | 1036 | intergenic | 12 | 91 | 120 | 3 | TGCTCCCTCTGAAAAGTCAT | 6 | 0.1–4 | 0.739 |
CTTTATATTATATCATGCCTTC |