| 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 |  | REB1/SacCer-Promoters/Homer | 1e-20 | -4.682e+01 | 0.0000 | 73.0 | 11.32% | 1393.9 | 3.09% | motif file (matrix) |
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| 2 |  | ABF1/SacCer-Promoters/Homer | 1e-17 | -4.141e+01 | 0.0000 | 100.0 | 15.50% | 2634.0 | 5.83% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-7 | -1.728e+01 | 0.0000 | 130.0 | 20.16% | 5653.4 | 12.52% | motif file (matrix) |
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| 4 |  | SeqBias: TA-repeat | 1e-6 | -1.501e+01 | 0.0000 | 390.0 | 60.47% | 22844.8 | 50.61% | motif file (matrix) |
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| 5 |  | SeqBias: GA-repeat | 1e-5 | -1.295e+01 | 0.0002 | 408.0 | 63.26% | 24500.0 | 54.27% | motif file (matrix) |
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| 6 |  | TATA-box/SacCer-Promoters/Homer | 1e-4 | -1.140e+01 | 0.0007 | 128.0 | 19.84% | 6196.1 | 13.73% | motif file (matrix) |
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| 7 |  | SUT1?/SacCer-Promoters/Homer | 1e-4 | -9.892e+00 | 0.0028 | 278.0 | 43.10% | 16072.5 | 35.60% | motif file (matrix) |
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| 8 |  | SeqBias: CG bias | 1e-4 | -9.698e+00 | 0.0030 | 432.0 | 66.98% | 26887.2 | 59.56% | motif file (matrix) |
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| 9 |  | SFP1/SacCer-Promoters/Homer | 1e-4 | -9.509e+00 | 0.0032 | 36.0 | 5.58% | 1245.4 | 2.76% | motif file (matrix) |
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| 10 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -9.483e+00 | 0.0032 | 101.0 | 15.66% | 4837.1 | 10.71% | motif file (matrix) |
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| 11 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-3 | -8.531e+00 | 0.0069 | 76.0 | 11.78% | 3494.3 | 7.74% | motif file (matrix) |
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| 12 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-3 | -7.610e+00 | 0.0160 | 299.0 | 46.36% | 18006.5 | 39.89% | motif file (matrix) |
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| 13 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-2 | -6.605e+00 | 0.0403 | 14.0 | 2.17% | 378.9 | 0.84% | motif file (matrix) |
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| 14 |  | PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer | 1e-2 | -5.979e+00 | 0.0700 | 11.0 | 1.71% | 277.4 | 0.61% | motif file (matrix) |
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| 15 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-2 | -5.888e+00 | 0.0715 | 26.0 | 4.03% | 993.1 | 2.20% | motif file (matrix) |
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| 16 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.630e+00 | 0.0868 | 51.0 | 7.91% | 2401.5 | 5.32% | motif file (matrix) |
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| 17 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.564e+00 | 0.0873 | 23.0 | 3.57% | 863.2 | 1.91% | motif file (matrix) |
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| 18 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.021e+00 | 0.1418 | 72.0 | 11.16% | 3742.8 | 8.29% | motif file (matrix) |
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| 19 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-2 | -4.887e+00 | 0.1537 | 37.0 | 5.74% | 1686.9 | 3.74% | motif file (matrix) |
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| 20 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-2 | -4.867e+00 | 0.1537 | 86.0 | 13.33% | 4634.4 | 10.27% | motif file (matrix) |
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| 21 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-2 | -4.806e+00 | 0.1537 | 20.0 | 3.10% | 765.3 | 1.70% | motif file (matrix) |
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| 22 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -4.783e+00 | 0.1537 | 13.0 | 2.02% | 419.0 | 0.93% | motif file (matrix) |
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| 23 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-2 | -4.743e+00 | 0.1537 | 170.0 | 26.36% | 10075.4 | 22.32% | motif file (matrix) |
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| 24 |  | TOD6?/SacCer-Promoters/Homer | 1e-2 | -4.664e+00 | 0.1537 | 19.0 | 2.95% | 724.8 | 1.61% | motif file (matrix) |
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