(A) The position-specific scoring matrix is represented as a sequence logo [9], in which the height of each letter is proportional to the information content at that position. The CTCF model is from [2]. (B) The 20 top-scoring occurrences of the CTCF binding site in human chromosome 21. Coordinates of the starting position of each occurrence are given with respect to human genome assembly NCBI 36.1. (C) A histogram of scores produced by scanning a shuffled version of human chromosome 21 with the CTCF motif. (D) This panel zooms in on the right tail of the distribution shown in panel (C). The blue histogram corresponds to the observed score distribution from scanning a shuffled chromosome, and the grey line corresponds to the analytic distribution. The p-value associated with an observed score of 17 is equal to the area under the curve to the right of 17. (E) The FDR is estimated from the empirical null distribution for a score threshold of 17.00. There are 35 null scores > 17 and 519 observed scores > 17, leading to an estimate of 6.7%. This procedure assumes that the number of observed scores equals the number of null scores.