For FMDV, MPP predicted six nondegenerate multiplex compatible primers to amplify all targets. GreeneSCPrimer generated a number of candidates, and manual inspection identified that the best of those primer combinations would require 6 primers, one of which had 2-fold and another had 3-fold degeneracy, totaling 9 actual priming sequences in a reaction (Supplementary Data). This compares with two primers each with 4-fold degeneracy using HYDEN (eight priming sequences in a reaction), to amplify 98% (183 of 187) targets. Again, the small number of signatures predicted by HYDEN is desirable for some applications, although the degeneracy is high and these must be supplemented to pick up the few outlying sequences