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. 2008 Aug 6;36(16):5221–5231. doi: 10.1093/nar/gkn488

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© 2008 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — Resolution of inferred binding sites. (A) Distribution of the distance between SISSRs-inferred binding site and the middle of the nearest canonical motif occurrence. The red curve is for all binding sites, and the blue curve is for high-scoring binding sites. About 75% of all CTCF, NRSF and STAT1 sites were within 18, 27 and 51 bp of the nearest consensus motif, respectively (90% within 31, 52 and 73 bp, respectively). The resolution is much higher for high-scoring binding sites (90% within 20, 19 and 45 bp, respectively). (B) Distribution of the number of canonical motifs within the 200-bp region centered on identified binding sites. The coloring scheme is the same as that used in A. (C) A 200-bp region centered on a CTCF binding site (highlighted in black) with high tag density. Nine instances of core CTCF motif (10⁻⁸ < P < 0.0025) are highlighted in yellow.