Illustration of the move-set for binding site clustering. Starting from a configuration C with three clusters, the top sequence in the blue cluster is chosen for resampling. It is removed from its cluster to produce configuration C-. Probabilities are then calculated for all configurations that would be obtained by inserting the sequence into any of the clusters or a new cluster (gray sequences), and finally one of these (C') is sampled. In this example the sequence was placed in a new cluster. For illustration purposes we have assumed all sequences in D have precisely the length l of the hypothesized site, so that each sequence can only be aligned in one way with any cluster. In general the sequences in D will be longer than l and one would also sample over all ways that the sequence can be aligned with each of the clusters.