The approach in which you are interested has susscessfully
been used in the field of diagnosis of viral pathogens
using PCR. This references may be useful for you:
Dopazo & Sobrino (1993) A computer program for the design
of PCR primers for diagnosis of highly variable genomes. J.
Virol. Methods 41:157-166
Dopazo et al., (1993) Design of primers for PCR
amplification of highly variable genomes. CABIOS 9:123-125.
Rodriguez et al. (1992) Primer design for specific
diagnosis by PCR of highly variable RNA viruses: typing
foot-and-mouth disease virus. Virology 189:363-367.
In brief you will find information about the algorithms and
the programs in our Web page at:
If you do not have access to some of this journals I can
send a copy to you.