If we search with 1 motif (PSSM, position-specific scoring matrix), MAST lists e.g. 10 hits of that single motif. If we do the search with 2 motifs by adding a second PSSM to the first one, we get a much longer list of results. Surprisingly, there are more than those 10 hits that feature _only_ motif 1 from the first query. We have no explanation for this surpising behaviour. Do you have any idea? How can we make sure to receive all matching subsequences, including the ones we get if we search with a second motif, when searching with only one PSSM? Any help would be very much appreciated. Gregor Warsow ______________________________________________________________________________ "Ein Herz für Kinder" - Ihre Spende hilft! Aktion: www.deutschlandsegelt.de Unser Dankeschön: Ihr Name auf dem Segel der 1. deutschen America's Cup-Yacht!