Primer3Plus

Primer3Plus is a web-based tool for designing and evaluating primers from DNA sequences, built around the Primer3 software and presented as a version incorporating features from its developers. It supports several tasks: selecting primer pairs for a template, designing primers for cloning or sequencing, finding primers that distinguish sequences, listing possible primers, and checking primers supplied by the user.

Users can paste a sequence or upload a sequence file, then configure design settings such as primer size, melting temperature, GC content, product length, and salt or oligo concentrations. The interface also allows users to mark target, included, and excluded regions, specify primer locations, and set constraints for probes and primer pairs. Advanced options cover thermodynamic parameters, complementarity, hairpins, mispriming, and sequence quality. Settings can be loaded from or saved to a file, and results may include secondary-structure information and debugging details. Primer3Plus is intended for researchers and other users working with DNA sequence analysis; its browser interface requires JavaScript to run.