The cause of variation however, is unknown. It could be due to mutational drift under the influence of selection. There may also be gene-specific effects. The simplest weight matrix is for the consensus sequence. A match to the consensus nucleotide produces a score.
Partial matches produce scores intermediate to the maximum.
A major drawback is that rarely will an actual sequence motif perfectly match the consensus sequence. No known sigma-70 promoter matches the consensus at all 12 nucleotides. This is equivalent to a maximum likelihood approach. If the individual activities of a group of motif sequences are equal, the maximum likelihood weight matrix elements are logarithms of observed frequencies for each nucleotide at a position divided by the probability that the nucleotide occurs by chance. The weight element for a T at this position, .