Extraction of the motifs in a cluster. We generated a motif for every sequence 15 amino acids long and belonging to each cluster/multiple-alignment. In detail, we considered all the amino acids composing each of these sequences ordered by the conservation in the corresponding multiple-alignment (computed in terms of information as shown in Figure 2) . A residue was kept as constant in the motif if it satisfied the first constraint of the bonus round (no more than three consecutive amino acids already present in the training set). The remaining amino acids are less conserved and do not satisfy the constraint of the bonus round; so these residues were allowed to vary within their amino acid group or following the variation patterns in a specific position reported in the multiple-alignment results. The amino acids groups were obtained by clustering amino acids on the basis of the BLOSUM50 matrix. A motif was thus generated for every sequence in the clusters.