I wonder if this would be useful for sorting out the subsequence issues that we've seen in Bio::Search::SearchUtils::tile_hsps, Bio::Search::Hit::GenericHit::length_aln, et al. (e.g. Bug 2476 <http://bugzilla.open-bio.org/show_bug.cgi?id=2476> ). Not for release 1.6, but a 1.6.x point release perhaps. Dave