Primer3 picks primers for PCR reactions, considering as criteria:
- oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities,
- PCR product size,
- positional constraints within the source (template) sequence, and
- possibilities for ectopic priming (amplifying the wrong sequence)
- many other constraints.
All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair.