| 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-10193 | -2.347e+04 | 0.0000 | 31506.0 | 58.79% | 3990.0 | 5.43% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-9851 | -2.268e+04 | 0.0000 | 33644.0 | 62.78% | 6031.4 | 8.20% | motif file (matrix) |
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| 3 |  | CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-304 | -7.007e+02 | 0.0000 | 3292.0 | 6.14% | 1527.9 | 2.08% | motif file (matrix) |
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| 4 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-91 | -2.113e+02 | 0.0000 | 9809.0 | 18.30% | 10338.4 | 14.06% | motif file (matrix) |
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| 5 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-58 | -1.345e+02 | 0.0000 | 25021.0 | 46.69% | 30975.1 | 42.12% | motif file (matrix) |
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| 6 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-33 | -7.826e+01 | 0.0000 | 11480.0 | 21.42% | 13709.3 | 18.64% | motif file (matrix) |
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| 7 |  | Unknown3/Drosophila-Promoters/Homer | 1e-17 | -4.030e+01 | 0.0000 | 1205.0 | 2.25% | 1162.6 | 1.58% | motif file (matrix) |
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| 8 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-12 | -2.831e+01 | 0.0000 | 5009.0 | 9.35% | 6031.6 | 8.20% | motif file (matrix) |
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| 9 |  | SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer | 1e-6 | -1.529e+01 | 0.0000 | 40313.0 | 75.22% | 54395.2 | 73.97% | motif file (matrix) |
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| 10 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.397e+01 | 0.0000 | 12354.0 | 23.05% | 16116.8 | 21.92% | motif file (matrix) |
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| 11 |  | E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.338e+01 | 0.0001 | 17501.0 | 32.66% | 23103.1 | 31.42% | motif file (matrix) |
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| 12 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-3 | -8.567e+00 | 0.0061 | 4792.0 | 8.94% | 6157.9 | 8.37% | motif file (matrix) |
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| 13 |  | SeqBias: G/A bias | 1e-3 | -7.704e+00 | 0.0134 | 53590.0 | 100.00% | 73514.1 | 99.97% | motif file (matrix) |
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