%Written for MATLAB.
%This script uses our previous calculations to compute the score according to
% the MATCH program's formula (Kel et al., NAR 2003 v31 pp3576-3579).
% We're using a pseudocount of one here!
info_vector = sum(Frequency .* LogoddsACGT);
info_matrix = [info_vector; info_vector; info_vector; info_vector];
MatchACGT = info_matrix .* Frequency; %match-like scoring matrix.
ScoresACGTmatch = BineAlignACGT*MatchACGT(:);