| 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 |  | HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson et al.)/Homer | 1e-4 | -1.035e+01 | 0.0079 | 155.0 | 0.99% | 153.8 | 0.71% | motif file (matrix) |
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| 2 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.879e+00 | 0.1265 | 462.0 | 2.94% | 554.4 | 2.54% | motif file (matrix) |
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| 3 |  | Unknown-ESC-element/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -6.823e+00 | 0.1265 | 800.0 | 5.09% | 996.2 | 4.57% | motif file (matrix) |
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| 4 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -6.782e+00 | 0.1265 | 1650.0 | 10.50% | 2129.6 | 9.77% | motif file (matrix) |
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| 5 |  | RXR(NR/DR1)/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -6.215e+00 | 0.1265 | 1505.0 | 9.58% | 1943.4 | 8.92% | motif file (matrix) |
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| 6 |  | HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer | 1e-2 | -6.070e+00 | 0.1265 | 1859.0 | 11.84% | 2422.2 | 11.12% | motif file (matrix) |
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| 7 |  | Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer | 1e-2 | -5.204e+00 | 0.1931 | 749.0 | 4.77% | 947.6 | 4.35% | motif file (matrix) |
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