| 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 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-6 | -1.509e+01 | 0.0001 | 249.0 | 17.09% | 155.0 | 10.64% | motif file (matrix) |
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| 2 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-5 | -1.277e+01 | 0.0006 | 97.0 | 6.66% | 44.7 | 3.07% | motif file (matrix) |
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| 3 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-5 | -1.173e+01 | 0.0010 | 101.0 | 6.93% | 49.1 | 3.37% | motif file (matrix) |
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| 4 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-5 | -1.155e+01 | 0.0010 | 79.0 | 5.42% | 34.3 | 2.35% | motif file (matrix) |
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| 5 |  | DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer | 1e-4 | -1.022e+01 | 0.0028 | 18.0 | 1.24% | 1.8 | 0.12% | motif file (matrix) |
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| 6 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-4 | -9.499e+00 | 0.0048 | 115.0 | 7.89% | 65.6 | 4.50% | motif file (matrix) |
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| 7 |  | CHR(?)/Hela-CellCycle-Expression/Homer | 1e-4 | -9.311e+00 | 0.0050 | 58.0 | 3.98% | 24.3 | 1.67% | motif file (matrix) |
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| 8 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.799e+00 | 0.0198 | 19.0 | 1.30% | 3.6 | 0.25% | motif file (matrix) |
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| 9 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-3 | -7.358e+00 | 0.0274 | 89.0 | 6.11% | 51.9 | 3.56% | motif file (matrix) |
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| 10 |  | DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer | 1e-3 | -7.235e+00 | 0.0279 | 22.0 | 1.51% | 5.2 | 0.35% | motif file (matrix) |
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| 11 |  | SeqBias: TA-repeat | 1e-3 | -7.044e+00 | 0.0307 | 415.0 | 28.48% | 340.1 | 23.34% | motif file (matrix) |
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| 12 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-2 | -6.259e+00 | 0.0617 | 250.0 | 17.16% | 193.3 | 13.26% | motif file (matrix) |
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| 13 |  | EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer | 1e-2 | -5.057e+00 | 0.1895 | 12.0 | 0.82% | 2.5 | 0.17% | motif file (matrix) |
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| 14 |  | Unknown6/Drosophila-Promoters/Homer | 1e-2 | -4.995e+00 | 0.1895 | 88.0 | 6.04% | 58.5 | 4.02% | motif file (matrix) |
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| 15 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-2 | -4.721e+00 | 0.2299 | 101.0 | 6.93% | 70.3 | 4.82% | motif file (matrix) |
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| 16 |  | PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -4.674e+00 | 0.2299 | 29.0 | 1.99% | 13.6 | 0.93% | motif file (matrix) |
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