INPUT: We want to find a novel motif of length 10 bps We have 20 sequences of length 100 bps The novel motif will be represented as a Position weight matrix M: 1 2 ... 10 A 0.7 ... C 0.1 ... G 0.1 ... T 0.1 ... The matrix will be the estimation of the distribution of nucleotides for the novel motif The background will be represented as a Position weight matrix B: A 0.2 C 0.3 G 0.2 T 0.3 The background matrix will be the estimation of the distribution of nucleotides for the positions in the sequences that do not belong to the motif