where X k = (1/N ) N n=1 X nk and Y k are the respective means of column k, and X nk are elements of X. Note that Matthews correlation coefficient (M CC) applies to the two categories (K = 2) base paired (i bp j) and not base paired (i ¬bp j) for any pair of bases (N = M (M − 1)/2 where M is length of sequence). Correction for sliding base pairing is not used.