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Table 1 The mismatches at the 3' end and the second mismatches at the third or other position from the 3' end in an allele-specific primer

From: BatchPrimer3: A high throughput web application for PCR and sequencing primer design

IUB/IUPAC Code of a SNP

Alleles of a SNP

Mismatch at the 3' end (forward/reverse)

Mismatch strength at the 3' end

Second mismatch at the third or other position from the 3' end

R

G/A

G/T

Weak

G/A, T/C

  

A/C

Weak

A/G, C/T

Y

T/C

G/T

Weak

G/A, T/C

  

A/C

Weak

A/G, C/T

S

G/C

G/G

Medium

C/C, A/A, G/G, T/T

  

C/C

Medium

C/C, A/A, G/G, T/T

W

A/T

A/A

Medium

C/C, A/A, G/G, T/T

  

T/T

Medium

C/C, A/A, G/G, T/T

K

G/T

G/A

Strong

G/T, A/C

  

T/C

Strong

T/G, C/A

M

A/C

G/A

Strong

G/T, A/C

  

T/C

Strong

T/G, C/A