To prune matches S' that will eventually not meet the score threshold, we check the score threshold as each position in S' is being considered. If the score for any prefix of S' falls below the score threshold, we can discard S'. In fact, before applying scores over all positions, we first consider the scores for the prefixes of the core positions within the component. This continuous check for the core positions and regular positions leads to very effective pruning. Note that as opposed to previous methods [19-22], our approach does not require the core positions be consecutive so as to find the most conserved parts in the profile.