This website was planned to be shut off on or after 1st June 2024. However a number of people have contacted us to say it is vital to their research so we are working on moving it to new hosting instead. For more information, or feedback, contact Christopher Gutteridge at totl@soton.ac.uk.

PIRA-PCR

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

Help

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