Overview of the FastCompare approach. (a) Determination of orthologous pairs of ORFs, and extraction of the associated upstream regions (data not shown). (b) For each k-mer (here CACGTGA), determination of the sets of ORFs that contain it in their upstream regions, in each species separately. The conservation score (hypergeometric p-values to assess the overlap between both sets) is then calculated. (c) Ranking of all k-mers on the basis of their conservation scores.