| 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(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-1092 | -2.516e+03 | 0.0000 | 10921.0 | 47.92% | 19669.0 | 23.24% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-773 | -1.781e+03 | 0.0000 | 11412.0 | 50.07% | 24269.5 | 28.68% | motif file (matrix) |
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| 3 |  | Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer | 1e-10 | -2.369e+01 | 0.0000 | 12387.0 | 54.35% | 43956.3 | 51.94% | motif file (matrix) |
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| 4 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-5 | -1.286e+01 | 0.0003 | 2062.0 | 9.05% | 6853.3 | 8.10% | motif file (matrix) |
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| 5 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-3 | -7.838e+00 | 0.0305 | 3705.0 | 16.26% | 12984.0 | 15.34% | motif file (matrix) |
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| 6 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-3 | -7.508e+00 | 0.0354 | 4536.0 | 19.90% | 16027.4 | 18.94% | motif file (matrix) |
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| 7 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-3 | -6.939e+00 | 0.0536 | 4036.0 | 17.71% | 14246.2 | 16.83% | motif file (matrix) |
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