| 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-701 | -1.616e+03 | 0.0000 | 8674.0 | 39.49% | 14992.1 | 20.08% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-582 | -1.342e+03 | 0.0000 | 9283.0 | 42.27% | 17872.2 | 23.94% | motif file (matrix) |
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| 3 |  | CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-284 | -6.555e+02 | 0.0000 | 1280.0 | 5.83% | 928.6 | 1.24% | motif file (matrix) |
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| 4 |  | YY1(Zf)/Promoter/Homer | 1e-5 | -1.178e+01 | 0.0007 | 560.0 | 2.55% | 1534.1 | 2.05% | motif file (matrix) |
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| 5 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-4 | -9.750e+00 | 0.0045 | 3519.0 | 16.02% | 11163.4 | 14.95% | motif file (matrix) |
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| 6 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-3 | -8.884e+00 | 0.0089 | 1413.0 | 6.43% | 4305.8 | 5.77% | motif file (matrix) |
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| 7 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-3 | -7.699e+00 | 0.0251 | 1445.0 | 6.58% | 4451.5 | 5.96% | motif file (matrix) |
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| 8 |  | Unknown3/Drosophila-Promoters/Homer | 1e-3 | -7.124e+00 | 0.0390 | 481.0 | 2.19% | 1382.0 | 1.85% | motif file (matrix) |
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| 9 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -6.406e+00 | 0.0710 | 1992.0 | 9.07% | 6295.5 | 8.43% | motif file (matrix) |
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| 10 |  | Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer | 1e-2 | -6.147e+00 | 0.0829 | 11847.0 | 53.94% | 39451.8 | 52.84% | motif file (matrix) |
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| 11 |  | ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -6.119e+00 | 0.0829 | 378.0 | 1.72% | 1081.8 | 1.45% | motif file (matrix) |
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