foreach $qbase (@query_sequence [$q_start .. $q_end]) { if ($qbase eq ("n"||"N") && $subj_sequence[$qbase] ne ("n"||"N")) { ++$ncount; } } foreach $sbase (@subj_sequence [$s_start .. $s_end]) { if ($sbase eq ("n"||"N") && $query_sequence[$sbase] ne ("n"||"N")) { ++$ncount; } }