"Primer3 is a complete rewrite of the original PRIMER program
(Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric
Lander.  See DIFFERENCES FROM EARLIER VERSIONS for a discussion
of how Primer3 differs from its predecessors, Primer 0.5 and
Primer v2.

Primer3 picks primers for PCR reactions, considering as criteria:

o oligonucleotide melting temperature, size, GC content,
  and primer-dimer possibilities,
o PCR product size,
o positional constraints within the source sequence, and
o miscellaneous 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."
- from the README file

WWW: http://www-genome.wi.mit.edu/genome_software/other/primer3.html

--
Tony Maher <tonym@biolateral.com.au>
