Designing primers that do not bind at multiple places in your template

The default settings for Primer3 do not actually check for whether a primer will bind at multiple places in the template. To turn this on use the PRIMER vs PRODUCT setting in the PRIMER BINDING tab (the Primer3 parameter is “PRIMER_MAX_TEMPLATE_MISPRIMING”). The default value is -1, which means do not check. Change this to 1 to start checking, or increase the number to increase stringency.

This should now find any duplicate alignments.

Incidentally an upcoming release will have a special “QuickPrimer” tool for checking such issues as well as the Primer3 tool.

Primer3 Primer2Product

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