Primer3 picks primers for PCR reactions, considering as criteria:
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.
- oligonucleotide melting temperature, size, GC content,
and primer-dimer possibilities,
- PCR product size,
- positional constraints within the source sequence, and
- miscellaneous other constraints.