Validation of the conservation scores obtained when applying FastCompare to D. melanogaster and D. pseudoobscura. (a) Distributions of conservation scores for actual (red) and randomized (black) data, showing that high conservation scores are unlikely to be obtained from randomized data. Conservation scores for certain known regulatory elements are also indicated. Both distributions were constructed using bin sizes of 5, and the top portion of the figure is not shown for the purpose of presentation. (b, c) Proportion of 7-mers supported by different types of independent biological data (using windows of size 100, see Materials and methods) as a function of the conservation score rank, obtained when applying FastCompare to D. melanogaster and D. pseudoobscura. (b, c) strongly indicate that the frequency of support increases with conservation score as calculated by FastCompare.