It is an interesting observation that the runtime seems to follow the number of cliques in the set, in contrast to the runtime of the Cliquer that is mainly determined by how interwoven the cliques are. The runtime of our algorithm thus indicates that for these random data sets the runtime is bound by out. Biological data sets are very different in structure from random data sets, which is caused by the clusteredness of their sequences. Since genes are often composites of different functional domains, aligned sequences have a high probability to center around those domains and build groups of 'similar' sequences with respect to the position and length of their alignment to the query.