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Table 4 Effect of artificial base mismatches in three mismatch sites on the specificity of allele-specific PCR

From: An improved allele-specific PCR primer design method for SNP marker analysis and its application

Mismatch sites closest to the 3’end of primers

Mismatch types

Polymorphism percent of primers

Mismatch types

Polymorphism percent of primers

Mismatch types

Polymorphism percent of primers

Mismatch types

Polymorphism percent of primers

The 2 nd base

TC

26.2%

GA

22.5%

CA

25.7%

AA

23.8%

(17/65)

(16/71)

(19/74)

(15/63)

TG

26.4%

GG

24.2%

CC

26.1%

TT

25.6%

(19/72)

(15/62)

(18/69)

(20/78)

The 3 rd base

TC

32.1%

GA

28.3%

CA

46.8%

AA

30.6%

(26/81)

(17/60)

(37/79)

(26/85)

TG

38.6%

GG

30.4%

CC

23.9%

TT

29.7%

(27/70)

(21/69)

(16/67)

(19/64)

The 4 th base

TC

32.9%

GA

31.7%

CA

28.0%

AA

26.8%

(24/73)

(26/82)

(21/75)

(19/71)

TG

23.3%

GG

25.8%

CC

33.3%

TT

32.4%

(14/60)

(16/62)

(22/66)

(22/68)