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Table 2 Composition of the 4 multiplex PCR according to the size range and the different dye label compatibility.

From: Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis

 

Locus

Repeat units

Fragment size range (bps)

Number of alleles

New alleles

HDGI index (total n = 67)*

Primer conc. (μM)

Multiplex A

CG3 a

5

153–158

2

 

0.50

0.30

 

bams44 a

39

339–417

2

 

0.21

0.30

 

bams3 a

15

474–609

7

1

0.51

0.30

 

vrrB 2 c

9

135–171

4

 

0.27

0.15

 

bams5 c

39

229–385

5

2

0.49

0.30

 

bams15 c

9

409–616

10

5

0.62

0.60

 

bams1 b

21

380–485

5

 

0.54

0.15

 

vrrC1 b

9

517–616

4

 

0.42

0.30

Multiplex B

bams13 a

39

337–868

13

4

0.61

0.30

 

vrrB1 b

9

193–256

4

 

0.36

0,10

 

bams28 b

24

373–493

4

1

0.35

0.15

 

vrrC2 b

18

532–604

3

 

0.40

0.10

 

bams53 c

12

212–236

2

 

0.21

0.60

 

bams31 c

9

331–952

8

4

0.58

0.60

Multiplex C

vrrA a

12

290–326

4

 

0.40

0.06

 

bams25 a

15

376–391

2

 

0.11

0.15

 

bams21 a

45

541–676

3

 

0.09

0.30

 

bams34 c

39

238–581

5

 

0.40

0.30

 

bams24 b

42

469–637

6

3

0.27

0.30

Multiplex D

bams51 b

45

358–538

4

 

0.33

0.60

 

bams22 b

36

555–735

5

1

0.34

0.15

 

bams23 c

42

399–651

5

2

0.40

0.30

 

bams30 a

9

268–916

12

4

0.71

0.30

 

pXO1 b

3

123–135

5

 

0.77

0.15

 

pXO2 a

2

132–145

8

 

0.58

0.15

  1. The number of diverse allele and new allele are described for the 25 markers. Primer concentration for each set of marker in the multiplex is also reported.
  2. * HGDI (Hunter-Gaston Diversity Index) calculated as in [36]
  3. The alleles are identified with the number of repeats versus the former nomenclature [12]. Locusa, locusb, locuscare loci amplified by a forward primer respectively labeled with cy5.5, cy5 and WellRed dyeD2.