| 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 | |
| 1 | | CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-105 | -2.423e+02 | 0.0000 | 2197.0 | 6.45% | 18608.5 | 3.86% | motif file (matrix) | |
| 2 | | SeqBias: GA-repeat | 1e-14 | -3.334e+01 | 0.0000 | 30130.0 | 88.45% | 419851.1 | 87.00% | motif file (matrix) | |
| 3 | | SeqBias: CG bias | 1e-5 | -1.338e+01 | 0.0002 | 32525.0 | 95.48% | 458024.1 | 94.91% | motif file (matrix) | |
| 4 | | SUT1?/SacCer-Promoters/Homer | 1e-4 | -1.050e+01 | 0.0027 | 28813.0 | 84.58% | 404164.5 | 83.75% | motif file (matrix) | |
| 5 | | ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -6.766e+00 | 0.0892 | 938.0 | 2.75% | 11976.6 | 2.48% | motif file (matrix) | |
| 6 | | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -6.635e+00 | 0.0892 | 5273.0 | 15.48% | 71779.3 | 14.87% | motif file (matrix) | |
| 7 | | SeqBias: CA-repeat | 1e-2 | -5.665e+00 | 0.1916 | 27339.0 | 80.25% | 384350.1 | 79.64% | motif file (matrix) |