Source sequence (up to 1,000 bases)

Position of SNP from start of sequence

Allele 1

Allele 2

Optimum primer size

Maximum primer size

Minimum primer size

Optimum product size

Maximum product size

Minimum product size

Optimum primer Tm

Maximum primer Tm

Minimum primer Tm

Maximum primer GC%

Minimum primer GC%

Maximum complementarity

Maximum 3' complementarity

Salt concentration (mM)

Annealing primer concentration (nM)

Number of bases for mismatches on either side of SNP

Number of primer pairs


For any questions or comments, please contact xke@soton.ac.uk

Please cite the following paper in your resulting publications of using this program:

Xiayi Ke, Andrew Collins and Shu Ye
PIRA PCR designer for restriction analysis of single nucleotide polymorphisms.
Bioinformatics, 2001, Vol.17, No.9, Pages 838-839