| Rank | Motif | Name | P-value | log P-pvalue | q-value (Benjamini) | # Target Sequences with Motif | % of Targets Sequences with Motif | # Background Sequences with Motif | % of Background Sequences with Motif | Motif File |
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| 1 |  | CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2096 | -4.828e+03 | 0.0000 | 5406.0 | 13.34% | 303.5 | 0.41% | motif file (matrix) |
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| 2 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-1214 | -2.796e+03 | 0.0000 | 20006.0 | 49.38% | 20291.7 | 27.22% | motif file (matrix) |
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| 3 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-1129 | -2.602e+03 | 0.0000 | 21291.0 | 52.55% | 22971.8 | 30.81% | motif file (matrix) |
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| 4 |  | RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer | 1e-23 | -5.408e+01 | 0.0000 | 15935.0 | 39.33% | 27074.8 | 36.31% | motif file (matrix) |
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| 5 |  | ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer | 1e-6 | -1.408e+01 | 0.0001 | 7665.0 | 18.92% | 13249.6 | 17.77% | motif file (matrix) |
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| 6 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-3 | -8.850e+00 | 0.0092 | 22460.0 | 55.44% | 40499.4 | 54.32% | motif file (matrix) |
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| 7 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-3 | -8.686e+00 | 0.0093 | 3611.0 | 8.91% | 6182.9 | 8.29% | motif file (matrix) |
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| 8 |  | Unknown3/Drosophila-Promoters/Homer | 1e-2 | -6.531e+00 | 0.0705 | 818.0 | 2.02% | 1318.3 | 1.77% | motif file (matrix) |
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| 9 |  | SeqBias: G/A bias | 1e-2 | -6.207e+00 | 0.0867 | 40514.0 | 100.00% | 74537.5 | 99.98% | motif file (matrix) |
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| 10 |  | ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.885e+00 | 0.1077 | 1129.0 | 2.79% | 1872.1 | 2.51% | motif file (matrix) |
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| 11 |  | GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.475e+00 | 0.1474 | 1177.0 | 2.91% | 1966.6 | 2.64% | motif file (matrix) |
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