We found 36 mutation hotspots in the alignments where mutations occurred near one another (within 20 bp). A perfect match (PM) probe residing in a mutation hotspot may contain mismatches that will have a detrimental effect on its hybridization intensity. To avoid this problem, we designed additional PM probes that contain all possible combinations of mutations found in each mutation hotspot. Thus, if two mutations are found within 20 bp of each other in the alignments, then we need in total four (2 2 ) PM probes to encode them. In general, 2 x PM probes are needed to completely encode a cluster of x mutations that occur within 20 bp of one another in the alignments.