| 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 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-6 | -1.510e+01 | 0.0001 | 141.0 | 14.57% | 66.9 | 7.38% | motif file (matrix) |
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| 2 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-5 | -1.369e+01 | 0.0002 | 92.0 | 9.50% | 36.2 | 3.99% | motif file (matrix) |
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| 3 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-5 | -1.156e+01 | 0.0012 | 24.0 | 2.48% | 2.5 | 0.27% | motif file (matrix) |
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| 4 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-4 | -1.110e+01 | 0.0015 | 147.0 | 15.19% | 80.3 | 8.86% | motif file (matrix) |
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| 5 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-4 | -9.962e+00 | 0.0037 | 15.0 | 1.55% | 0.0 | 0.00% | motif file (matrix) |
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| 6 |  | Unknown6/Drosophila-Promoters/Homer | 1e-2 | -6.781e+00 | 0.0732 | 58.0 | 5.99% | 27.2 | 3.00% | motif file (matrix) |
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| 7 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-2 | -6.712e+00 | 0.0732 | 65.0 | 6.71% | 32.6 | 3.59% | motif file (matrix) |
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| 8 |  | CHR(?)/Hela-CellCycle-Expression/Homer | 1e-2 | -6.632e+00 | 0.0732 | 44.0 | 4.55% | 18.1 | 1.99% | motif file (matrix) |
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| 9 |  | SeqBias: TA-repeat | 1e-2 | -6.551e+00 | 0.0732 | 247.0 | 25.52% | 178.6 | 19.69% | motif file (matrix) |
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| 10 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.022e+00 | 0.0939 | 36.0 | 3.72% | 14.1 | 1.55% | motif file (matrix) |
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| 11 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-2 | -5.856e+00 | 0.1007 | 151.0 | 15.60% | 101.8 | 11.23% | motif file (matrix) |
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| 12 |  | Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer | 1e-2 | -5.347e+00 | 0.1536 | 136.0 | 14.05% | 91.8 | 10.13% | motif file (matrix) |
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| 13 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.264e+00 | 0.1541 | 13.0 | 1.34% | 2.8 | 0.31% | motif file (matrix) |
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| 14 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-2 | -5.215e+00 | 0.1541 | 61.0 | 6.30% | 33.7 | 3.72% | motif file (matrix) |
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| 15 |  | E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.839e+00 | 0.2042 | 18.0 | 1.86% | 5.2 | 0.58% | motif file (matrix) |
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| 16 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-2 | -4.780e+00 | 0.2042 | 66.0 | 6.82% | 38.7 | 4.26% | motif file (matrix) |
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| 17 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-2 | -4.666e+00 | 0.2142 | 38.0 | 3.93% | 18.8 | 2.08% | motif file (matrix) |
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