Properties of the motif pair (M1, M2). We refer only to occurrences in which the distance between the two motifs is <100. (A) Alignment of the 59 occurrences of M1 → M2 with gap length 19. The motifs are enclosed in red boxes. Several positions flanking the two motifs are conserved. In contrast, the gap between them is highly variable. The alignment for gap length 16 exhibits the same features (data not shown). (B) Number of occurrences of each of the possible arrangements of the two motifs. (C) The distribution of the distance between the two motifs for the M1 → M2 arrangement. The two motifs are almost always 16–20 bases apart. The graph shows all gaps of length 1–50; only four occurrences have a gap of length 51–99.
