General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

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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