| 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-11340 | -2.611e+04 | 0.0000 | 33831.0 | 61.80% | 3895.0 | 5.29% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-10456 | -2.408e+04 | 0.0000 | 35226.0 | 64.35% | 6042.6 | 8.20% | motif file (matrix) |
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| 3 |  | CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-946 | -2.179e+03 | 0.0000 | 4235.0 | 7.74% | 622.1 | 0.84% | motif file (matrix) |
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| 4 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-78 | -1.798e+02 | 0.0000 | 9505.0 | 17.36% | 9981.3 | 13.55% | motif file (matrix) |
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| 5 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-42 | -9.810e+01 | 0.0000 | 25092.0 | 45.83% | 30929.3 | 41.98% | motif file (matrix) |
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| 6 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-30 | -7.113e+01 | 0.0000 | 11662.0 | 21.30% | 13760.0 | 18.68% | motif file (matrix) |
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| 7 |  | Unknown3/Drosophila-Promoters/Homer | 1e-15 | -3.683e+01 | 0.0000 | 1188.0 | 2.17% | 1139.5 | 1.55% | motif file (matrix) |
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| 8 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-14 | -3.358e+01 | 0.0000 | 5017.0 | 9.16% | 5843.2 | 7.93% | motif file (matrix) |
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| 9 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-9 | -2.152e+01 | 0.0000 | 12141.0 | 22.18% | 15292.2 | 20.76% | motif file (matrix) |
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| 10 |  | E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-7 | -1.683e+01 | 0.0000 | 17270.0 | 31.55% | 22216.2 | 30.16% | motif file (matrix) |
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| 11 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-5 | -1.223e+01 | 0.0002 | 4803.0 | 8.77% | 5952.9 | 8.08% | motif file (matrix) |
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| 12 |  | SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer | 1e-4 | -1.034e+01 | 0.0010 | 40516.0 | 74.01% | 53788.6 | 73.01% | motif file (matrix) |
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| 13 |  | SeqBias: polyC-repeat | 1e-2 | -6.311e+00 | 0.0541 | 54725.0 | 99.96% | 73613.2 | 99.92% | motif file (matrix) |
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| 14 |  | SeqBias: G/A bias | 1e-2 | -5.346e+00 | 0.1318 | 54744.0 | 100.00% | 73657.1 | 99.98% | motif file (matrix) |
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