Ranked Mismatch Matrix ( RMM ) composition at different Dice dissimilarity thresholds for PFGE clustering. The RMMs for the comparison of emm type with PFGE clusterings have dimensions p × 2, where p depends on the number of PFGE clusters and the two columns correspond to isolate pairs with the same or with different emm type. The PFGE intercluster distance rank is represented in the horizontal axis. The isolate pairs with the same emm type are represented with full lines while for pairs with different emm type a dashed line was used. The frequencies plotted in the vertical axis are relative, meaning that the content of each RMM element was divided by the sum of all RMM elements. It corresponds to the fraction of isolate pairs contributing for the respective RMM element. RMM composition was studied at three different thresholds (T = 21, 29 and 41) because, 21 is an optimal threshold for RAR but not for HA, 29 is an optimal threshold for both measures and 41 is a slightly sub-optimal threshold for HA (it is at the end of the maximal plateau of HA in Figure 3) and a bad threshold for RAR. The frequency distributions of isolate pairs with the same emm type are similar for the three thresholds. This is not the case for isolate pairs with different emm type. Here, as the threshold increases, the frequency peaks become larger and occur at lower cluster distance ranks, contributing in this way for a weaker agreement.