Diferential primer design

[Tom Knight]

Yoram Gerchman <gerchman from research.haifa.ac.il> writes:

> I am trying to design primer to differentiate via real-time PCR, the
> expression of 4 homologous genes. Does anyone know of a software or
> webpage that will enable me to define the primer search so that the
> primer will bind to sequence 1 but not to sequences 2,3 and 4?

Primers fail to prime if they mismatch at the 3' end, even by a single
base.  You can design the primers you want just by a clustalW
alignment of the homologous genes and searches for locations with
mismatches.