Table 3 Summary of varVAMP designs for qPCR

From: varVAMP: degenerate primer design for tiled full genome sequencing and qPCR

Alignment statistics

varVAMP parameters

varVAMP output

Virus

Subtypes

n sequences

% mean sequence identity

Primer max ambig bases

Probe max ambig bases

Threshold

ΔG cutoff (kcal/mol)

n found schemes

varVAMP version

PV

1

241

86 ± 12

2

1

0.93

−3

3

0.7

PV

2

494

88 ± 8

1

0

0.98

−3

4

0.7

PV

3

209

91 ± 9

2

1

0.93

−3

3

0.7

  1. Important alignment statistics are listed together with varVAMP input parameters and output information, including the varVAMP version. Pairwise sequence identity was calculated with Identity (https://github.com/BioinformaticsToolsmith/Identity). All primers and their respective varVAMP outputs are accessible at: https://github.com/jonas-fuchs/ViralPrimerSchemes.
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