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Table 3 Characteristics of VNTR markers and sequence of the PCR primers

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

   
  1. a Position on the chromosome expressed in kbp
  2. b Expected size for a truly 2U amplicon is 312 bp long
  3. c Additional large alleles probably contain an IS element
  4. d Hunter Gaston Diversity index