Why do some designs fall into low-level multiplexes?
The design software checks for primer compatibility between assays, and cases where there is a high likelihood of false priming potential or dimerization are separated into different multiplexes. Also the extension product masses in one multiplex must be sufficiently separated to allow the genotypes to be discerned. The software can add, up to a point, non-genomic 5′ bases to an extension primer to change extension product size, allowing more flexibility in any given multiplex. Our experience however is that for any given set of sequences, a few will fall into one or more low-level multiplexes.
