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) |