The region chosen for the 77-nt rotavirus probe, positions 112-178 in the alignment, was analyzed using the haplotype function of ConSortß, which decomposes highly variable stretches into a small number of less variable stretches (haplotypes). This resulted in two major haplotypes and probes which potentially covered all rotavirus group A variations recorded in GenBank. The two haplotype probes contained 14 and 8 dInosines, respectively, in combination with four degenerations. They were called Ino14_w4 and Ino8_w4 ( Figure 5C , Inosine as yellow and wobbles as light grey boxes). Two additional probes with fewer dInosines and more degenerations were also created: Ino11_w7 and Ino5_w7 ( Figure 5C ). The consensus sequence and the pattern of variation of the region chosen for the probe are shown in Figure 5A . The sequences of the four probes are shown in Supplementary  Table S4A and B and (schematically) in Figure 5C .