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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.