Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 3670)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 45188)	% of Background Sequences with Motif
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e-871	-2.008e+03	0.0000	1686.0	45.94%	3362.0	7.44%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e-815	-1.878e+03	0.0000	1833.0	49.95%	4511.9	9.98%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e-622	-1.433e+03	0.0000	2157.0	58.77%	8517.4	18.84%
Ptf1a(HLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e-403	-9.292e+02	0.0000	2107.0	57.41%	10899.2	24.11%
Tal1	CATCTG	1e-377	-8.686e+02	0.0000	1572.0	42.83%	6521.8	14.43%
SCL(HLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e-234	-5.396e+02	0.0000	2580.0	70.30%	19684.2	43.54%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e-212	-4.894e+02	0.0000	896.0	24.41%	3451.0	7.63%
Ap4(HLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e-189	-4.371e+02	0.0000	1066.0	29.05%	5052.7	11.18%
Tcf12(HLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e-183	-4.229e+02	0.0000	903.0	24.60%	3873.8	8.57%
MyoG(HLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e-180	-4.162e+02	0.0000	947.0	25.80%	4250.4	9.40%
E2A(HLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e-176	-4.069e+02	0.0000	1123.0	30.60%	5742.1	12.70%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e-170	-3.929e+02	0.0000	734.0	20.00%	2820.8	6.24%
MyoD(HLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e-149	-3.433e+02	0.0000	732.0	19.95%	3083.7	6.82%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e-90	-2.081e+02	0.0000	317.0	8.64%	998.0	2.21%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e-76	-1.759e+02	0.0000	801.0	21.83%	5022.4	11.11%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e-75	-1.734e+02	0.0000	916.0	24.96%	6124.5	13.55%
Fox:Ebox(Forkhead:HLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e-61	-1.426e+02	0.0000	694.0	18.91%	4432.0	9.80%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e-60	-1.396e+02	0.0000	628.0	17.11%	3871.6	8.56%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e-58	-1.347e+02	0.0000	273.0	7.44%	1070.0	2.37%
E2A-nearPU.1(HLH)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e-41	-9.513e+01	0.0000	734.0	20.00%	5479.5	12.12%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e-41	-9.479e+01	0.0000	1645.0	44.82%	15383.0	34.03%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer	CTGTTTAC	1e-34	-8.009e+01	0.0000	972.0	26.49%	8221.6	18.19%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e-33	-7.791e+01	0.0000	1963.0	53.49%	19635.8	43.44%
RBPJ:Ebox/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e-30	-7.128e+01	0.0000	223.0	6.08%	1139.1	2.52%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e-28	-6.514e+01	0.0000	353.0	9.62%	2307.9	5.11%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e-28	-6.510e+01	0.0000	610.0	16.62%	4774.2	10.56%
RFX1/HOCOMOCO	GTTGCYAGGGAA	1e-27	-6.235e+01	0.0000	93.0	2.53%	288.2	0.64%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e-25	-5.811e+01	0.0000	1466.0	39.95%	14343.1	31.73%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e-24	-5.745e+01	0.0000	1353.0	36.87%	13056.2	28.88%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-21	-5.006e+01	0.0000	291.0	7.93%	1949.6	4.31%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e-20	-4.695e+01	0.0000	962.0	26.21%	8960.4	19.82%
RFX2/HOCOMOCO	KGTTGCYAGGSAA	1e-19	-4.580e+01	0.0000	67.0	1.83%	206.2	0.46%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e-19	-4.448e+01	0.0000	729.0	19.86%	6483.2	14.34%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e-18	-4.275e+01	0.0000	402.0	10.95%	3129.7	6.92%
HNF4a(NR/DR1)/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e-18	-4.215e+01	0.0000	230.0	6.27%	1506.8	3.33%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e-17	-4.082e+01	0.0000	414.0	11.28%	3287.3	7.27%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e-16	-3.905e+01	0.0000	970.0	26.43%	9303.6	20.58%
RFX1..5_RFXANK_RFXAP.p2/SwissRegulon	CSGTCGCCATGGCAACVG	1e-16	-3.806e+01	0.0000	127.0	3.46%	675.4	1.49%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e-15	-3.496e+01	0.0000	315.0	8.58%	2422.9	5.36%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e-14	-3.449e+01	0.0000	1000.0	27.25%	9804.8	21.69%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e-14	-3.321e+01	0.0000	62.0	1.69%	234.1	0.52%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e-14	-3.319e+01	0.0000	626.0	17.06%	5694.3	12.60%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e-14	-3.250e+01	0.0000	54.0	1.47%	187.9	0.42%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e-13	-3.197e+01	0.0000	626.0	17.06%	5731.2	12.68%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e-13	-3.135e+01	0.0000	113.0	3.08%	626.3	1.39%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e-13	-3.045e+01	0.0000	462.0	12.59%	4022.6	8.90%
RFX3/HOCOMOCO	BGTTGCCATGGTAA	1e-13	-3.027e+01	0.0000	71.0	1.93%	313.7	0.69%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e-10	-2.531e+01	0.0000	75.0	2.04%	380.4	0.84%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e-10	-2.491e+01	0.0000	411.0	11.20%	3637.2	8.05%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e-10	-2.479e+01	0.0000	1082.0	29.48%	11148.6	24.66%
Isl2-mouse/Jaspar	MHMAATYAATTAAKWT	1e-10	-2.430e+01	0.0000	723.0	19.70%	7067.4	15.63%
ETS:E-box/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e-9	-2.260e+01	0.0000	62.0	1.69%	303.4	0.67%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e-9	-2.126e+01	0.0000	124.0	3.38%	841.5	1.86%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e-8	-2.072e+01	0.0000	97.0	2.64%	608.5	1.35%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e-8	-2.021e+01	0.0000	861.0	23.46%	8811.2	19.49%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e-8	-1.996e+01	0.0000	216.0	5.89%	1749.7	3.87%
PDX1/HOCOMOCO	RGTAATTAG	1e-8	-1.969e+01	0.0000	260.0	7.08%	2202.9	4.87%
TR4(NR/DR1)/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e-8	-1.851e+01	0.0000	56.0	1.53%	291.1	0.64%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e-8	-1.847e+01	0.0000	748.0	20.38%	7599.0	16.81%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e-7	-1.710e+01	0.0000	725.0	19.75%	7402.6	16.37%
RXR(NR/DR1)/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e-7	-1.708e+01	0.0000	397.0	10.82%	3734.4	8.26%
BMYB(HTH)/Hela-BMYB-ChIPSeq(GSE27030)/Homer	NHAACBGYYV	1e-6	-1.578e+01	0.0000	643.0	17.52%	6531.7	14.45%
PAX5(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e-6	-1.539e+01	0.0000	130.0	3.54%	995.1	2.20%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e-6	-1.511e+01	0.0000	99.0	2.70%	705.2	1.56%
MA0069.1_PAX6/Jaspar	TTCACGCWTGANTT	1e-6	-1.507e+01	0.0000	59.0	1.61%	349.8	0.77%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e-6	-1.420e+01	0.0000	55.0	1.50%	325.3	0.72%
Pax8(Paired/Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e-5	-1.363e+01	0.0000	117.0	3.19%	903.3	2.00%
SeqBias: TA-repeat	TATATATATA	1e-5	-1.351e+01	0.0000	1484.0	40.44%	16576.5	36.67%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e-5	-1.325e+01	0.0000	616.0	16.78%	6350.2	14.05%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e-5	-1.299e+01	0.0000	729.0	19.86%	7664.3	16.95%
PPARE(NR/DR1)/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e-5	-1.282e+01	0.0000	327.0	8.91%	3127.4	6.92%
pax6-mouse/Jaspar	TGAYTAATTAATTNAC	1e-5	-1.274e+01	0.0000	279.0	7.60%	2609.0	5.77%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e-5	-1.176e+01	0.0000	257.0	7.00%	2405.2	5.32%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e-5	-1.174e+01	0.0000	877.0	23.90%	9466.4	20.94%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e-5	-1.155e+01	0.0000	144.0	3.92%	1219.4	2.70%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e-4	-1.121e+01	0.0001	977.0	26.62%	10681.4	23.63%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e-4	-1.112e+01	0.0001	576.0	15.69%	6007.3	13.29%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e-4	-1.094e+01	0.0001	60.0	1.63%	411.0	0.91%
ISL1/HOCOMOCO	SYTAATG	1e-4	-1.037e+01	0.0001	581.0	15.83%	6108.4	13.51%
Pax6-mouse/UniProbe	TGAYTAATTAATTNAC	1e-4	-1.032e+01	0.0001	257.0	7.00%	2458.8	5.44%
GATA-DR8(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e-4	-1.014e+01	0.0002	44.0	1.20%	278.1	0.62%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e-4	-1.007e+01	0.0002	157.0	4.28%	1394.3	3.08%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e-4	-9.471e+00	0.0003	444.0	12.10%	4589.1	10.15%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson et al.)/Homer	GYCATCMATCAT	1e-4	-9.371e+00	0.0003	56.0	1.53%	397.9	0.88%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e-3	-8.987e+00	0.0005	548.0	14.93%	5811.2	12.85%
PAX6/SwissRegulon	TTCACGCTTGATTT	1e-3	-8.971e+00	0.0005	90.0	2.45%	734.2	1.62%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e-3	-8.940e+00	0.0005	344.0	9.37%	3484.8	7.71%
Unknown-ESC-element/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e-3	-8.843e+00	0.0005	222.0	6.05%	2133.9	4.72%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e-3	-8.543e+00	0.0007	286.0	7.79%	2853.5	6.31%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-3	-8.528e+00	0.0007	253.0	6.89%	2487.5	5.50%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e-3	-8.528e+00	0.0007	675.0	18.39%	7319.9	16.19%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e-3	-8.231e+00	0.0009	95.0	2.59%	802.2	1.77%
NPAS2(HLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e-3	-8.167e+00	0.0010	358.0	9.75%	3682.1	8.14%
PAX5/long/HOCOMOCO	VDGDGCASYSAAGCGTGAC	1e-3	-8.082e+00	0.0011	75.0	2.04%	605.0	1.34%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e-3	-8.007e+00	0.0011	335.0	9.13%	3430.5	7.59%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e-3	-7.972e+00	0.0012	87.0	2.37%	727.6	1.61%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e-3	-7.965e+00	0.0012	254.0	6.92%	2523.9	5.58%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-3	-7.956e+00	0.0012	277.0	7.55%	2780.4	6.15%
Pax7(Paired/Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e-3	-7.938e+00	0.0012	59.0	1.61%	450.8	1.00%
Lmx1a-mouse/Jaspar	CGAWTTAATTAAAAAYY	1e-3	-7.868e+00	0.0012	150.0	4.09%	1389.0	3.07%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e-3	-7.738e+00	0.0014	206.0	5.61%	2002.4	4.43%
SeqBias: CG bias	SSSSSSSSSS	1e-3	-7.735e+00	0.0014	2034.0	55.42%	23810.7	52.67%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e-3	-7.689e+00	0.0014	256.0	6.98%	2558.4	5.66%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e-3	-7.401e+00	0.0019	45.0	1.23%	326.1	0.72%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e-3	-7.338e+00	0.0020	107.0	2.92%	950.2	2.10%
Lmx1b-mouse/Jaspar	VRWWWTTAATTAATWHB	1e-3	-7.270e+00	0.0021	71.0	1.93%	582.9	1.29%
GATA-IR4(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e-3	-6.987e+00	0.0028	47.0	1.28%	352.3	0.78%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e-2	-6.412e+00	0.0049	538.0	14.66%	5872.0	12.99%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e-2	-6.387e+00	0.0050	84.0	2.29%	737.4	1.63%
BMAL1(HLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e-2	-6.037e+00	0.0070	618.0	16.84%	6842.6	15.14%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e-2	-6.020e+00	0.0071	36.0	0.98%	264.6	0.59%
Max(HLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e-2	-6.001e+00	0.0071	203.0	5.53%	2046.5	4.53%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e-2	-5.962e+00	0.0074	1305.0	35.56%	15080.1	33.36%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e-2	-5.936e+00	0.0075	248.0	6.76%	2556.3	5.65%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer	ATTTTCCATT	1e-2	-5.691e+00	0.0095	377.0	10.27%	4050.6	8.96%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e-2	-5.636e+00	0.0099	282.0	7.68%	2960.5	6.55%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e-2	-5.555e+00	0.0107	320.0	8.72%	3401.9	7.53%
SeqBias: G/A bias	RRRRRRRRRR	1e-2	-5.252e+00	0.0143	3661.0	99.75%	44962.7	99.46%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e-2	-5.176e+00	0.0153	172.0	4.69%	1739.6	3.85%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e-2	-4.920e+00	0.0197	7.0	0.19%	28.0	0.06%
SeqBias: polyC-repeat	CCCCCCCCCC	1e-2	-4.917e+00	0.0197	3482.0	94.88%	42459.8	93.92%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e-1	-4.526e+00	0.0286	187.0	5.10%	1942.4	4.30%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e-1	-4.485e+00	0.0296	133.0	3.62%	1336.5	2.96%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e-1	-4.466e+00	0.0299	422.0	11.50%	4669.4	10.33%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e-1	-4.448e+00	0.0303	233.0	6.35%	2472.9	5.47%
PAX6/HOCOMOCO	TCAWGCGTGAA	1e-1	-4.431e+00	0.0305	44.0	1.20%	375.7	0.83%
Lmx1b-mouse/UniProbe	VRWWWTTAATTAATWHB	1e-1	-4.330e+00	0.0335	59.0	1.61%	534.8	1.18%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e-1	-4.312e+00	0.0338	251.0	6.84%	2688.7	5.95%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e-1	-4.269e+00	0.0350	431.0	11.74%	4793.0	10.60%
TRa(NR)/C17.2-TRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e-1	-4.026e+00	0.0443	118.0	3.22%	1190.4	2.63%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e-1	-3.962e+00	0.0469	1677.0	45.69%	19882.7	43.98%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e-1	-3.948e+00	0.0472	280.0	7.63%	3050.0	6.75%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e-1	-3.921e+00	0.0481	483.0	13.16%	5439.9	12.03%
PAX3:FKHR-fusion(Paired/Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e-1	-3.916e+00	0.0481	91.0	2.48%	895.8	1.98%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e-1	-3.878e+00	0.0495	189.0	5.15%	2003.6	4.43%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e-1	-3.715e+00	0.0578	80.0	2.18%	782.2	1.73%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e-1	-3.685e+00	0.0591	481.0	13.11%	5439.3	12.03%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e-1	-3.659e+00	0.0603	197.0	5.37%	2109.4	4.67%
GATA-IR3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e-1	-3.636e+00	0.0613	65.0	1.77%	621.3	1.37%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e-1	-3.502e+00	0.0696	84.0	2.29%	835.8	1.85%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e-1	-3.499e+00	0.0696	151.0	4.11%	1591.1	3.52%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e-1	-3.466e+00	0.0711	197.0	5.37%	2122.3	4.69%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer	TBGCACGCAA	1e-1	-3.282e+00	0.0848	159.0	4.33%	1696.1	3.75%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e-1	-3.265e+00	0.0857	491.0	13.38%	5603.7	12.40%
Tbox:Smad/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e-1	-3.261e+00	0.0857	67.0	1.83%	657.2	1.45%
SeqBias: A/T bias	WWWWWWWWWW	1e-1	-3.252e+00	0.0857	3337.0	90.93%	40708.3	90.05%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e-1	-3.252e+00	0.0857	409.0	11.14%	4629.4	10.24%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e-1	-3.125e+00	0.0959	949.0	25.86%	11133.4	24.63%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer	MACAGGAAGT	1e-1	-3.101e+00	0.0975	103.0	2.81%	1067.9	2.36%
NF1:FOXA1/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e-1	-3.032e+00	0.1038	23.0	0.63%	193.5	0.43%
ISRE(IRF)/ThioMac-LPS-exp(GSE23622)/HOMER	AGTTTCASTTTC	1e-1	-2.898e+00	0.1180	23.0	0.63%	196.2	0.43%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-1	-2.859e+00	0.1218	248.0	6.76%	2765.0	6.12%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e-1	-2.798e+00	0.1287	22.0	0.60%	188.3	0.42%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e-1	-2.704e+00	0.1404	28.0	0.76%	253.9	0.56%
GATA:SCL/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e-1	-2.691e+00	0.1413	43.0	1.17%	415.8	0.92%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e-1	-2.631e+00	0.1490	241.0	6.57%	2702.8	5.98%
Oct2(POU/Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e-1	-2.629e+00	0.1490	128.0	3.49%	1381.7	3.06%
SeqBias: CA-repeat	CACACACACA	1e-1	-2.600e+00	0.1519	1801.0	49.07%	21640.4	47.87%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e-1	-2.598e+00	0.1519	65.0	1.77%	663.4	1.47%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e-1	-2.578e+00	0.1533	318.0	8.66%	3619.6	8.01%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e-1	-2.510e+00	0.1630	248.0	6.76%	2796.8	6.19%
PAX2-long/HOCOMOCO	GHTCAGTCATGCGTGACA	1e-1	-2.472e+00	0.1682	38.0	1.04%	368.9	0.82%
Srebp2(HLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e-1	-2.416e+00	0.1769	38.0	1.04%	370.1	0.82%
PAX5-shortForm(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e-1	-2.389e+00	0.1806	28.0	0.76%	262.5	0.58%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e-1	-2.380e+00	0.1812	748.0	20.38%	8815.9	19.50%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e-1	-2.329e+00	0.1895	200.0	5.45%	2246.7	4.97%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-2.302e+00	0.1936	7.0	0.19%	48.1	0.11%
SeqBias: GA-repeat	GAGAGAGAGA	1e0	-2.287e+00	0.1953	2121.0	57.79%	25650.4	56.74%
GRE(NR/IR3)/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-2.283e+00	0.1953	40.0	1.09%	397.6	0.88%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-2.283e+00	0.1953	30.0	0.82%	287.8	0.64%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan et al.)/Homer	CCATATATGGNM	1e0	-2.213e+00	0.2067	111.0	3.02%	1212.5	2.68%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	-2.201e+00	0.2078	614.0	16.73%	7222.3	15.98%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e0	-2.154e+00	0.2166	52.0	1.42%	537.1	1.19%
NFkB-p65-Rel(RHD)/LPS-exp(GSE23622)/Homer	GGAAATTCCC	1e0	-2.139e+00	0.2186	21.0	0.57%	194.9	0.43%
GRE/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e0	-2.134e+00	0.2186	76.0	2.07%	812.2	1.80%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-2.126e+00	0.2190	3650.0	99.46%	44881.1	99.28%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-2.119e+00	0.2192	279.0	7.60%	3205.5	7.09%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529/Homer	CYAAAAATAG	1e0	-2.116e+00	0.2192	171.0	4.66%	1923.6	4.26%
LXRE(NR/DR4)/BLRP(RAW)-LXRb-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-2.053e+00	0.2316	16.0	0.44%	143.6	0.32%
n-Myc(HLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e0	-2.045e+00	0.2321	179.0	4.88%	2024.9	4.48%
Pax7-long(Paired/Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-1.988e+00	0.2444	13.0	0.35%	113.1	0.25%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	-1.961e+00	0.2496	43.0	1.17%	444.4	0.98%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e0	-1.942e+00	0.2533	85.0	2.32%	928.3	2.05%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e0	-1.902e+00	0.2621	20.0	0.54%	190.9	0.42%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-1.866e+00	0.2701	152.0	4.14%	1721.3	3.81%
GATA-DR4(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-1.844e+00	0.2746	36.0	0.98%	370.5	0.82%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e0	-1.839e+00	0.2746	1417.0	38.61%	17087.0	37.80%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-1.819e+00	0.2787	479.0	13.05%	5652.0	12.50%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-1.780e+00	0.2883	112.0	3.05%	1256.9	2.78%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e0	-1.696e+00	0.3118	60.0	1.63%	653.2	1.44%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e0	-1.667e+00	0.3177	28.0	0.76%	287.3	0.64%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e0	-1.667e+00	0.3177	28.0	0.76%	287.3	0.64%
NFAT:AP1/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-1.641e+00	0.3243	61.0	1.66%	668.6	1.48%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-1.626e+00	0.3276	627.0	17.08%	7481.6	16.55%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-1.570e+00	0.3448	35.0	0.95%	371.5	0.82%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e0	-1.494e+00	0.3698	59.0	1.61%	654.1	1.45%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e0	-1.473e+00	0.3759	69.0	1.88%	773.4	1.71%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-1.448e+00	0.3836	16.0	0.44%	160.3	0.35%
CLOCK(HLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e0	-1.416e+00	0.3938	126.0	3.43%	1456.0	3.22%
NRF1/Promoter/Homer	STGCGCATGCGC	1e0	-1.413e+00	0.3938	19.0	0.52%	195.7	0.43%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e0	-1.402e+00	0.3957	102.0	2.78%	1170.5	2.59%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e0	-1.387e+00	0.3995	206.0	5.61%	2419.4	5.35%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e0	-1.384e+00	0.3995	299.0	8.15%	3543.1	7.84%
FXR(NR/IR1)/Liver-FXR-ChIP-Seq(Chong et al.)/Homer	AGGTCANTGACCTB	1e0	-1.336e+00	0.4161	103.0	2.81%	1188.8	2.63%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e0	-1.330e+00	0.4169	146.0	3.98%	1704.5	3.77%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer	GCTGTGGTTW	1e0	-1.300e+00	0.4273	233.0	6.35%	2757.4	6.10%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e0	-1.292e+00	0.4286	316.0	8.61%	3764.1	8.33%
Oct4:Sox17/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-1.290e+00	0.4286	60.0	1.63%	680.7	1.51%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	-1.264e+00	0.4367	239.0	6.51%	2835.7	6.27%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-1.245e+00	0.4428	192.0	5.23%	2269.1	5.02%
Usf2(HLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e0	-1.244e+00	0.4428	76.0	2.07%	874.4	1.93%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e0	-1.242e+00	0.4428	345.0	9.40%	4125.5	9.13%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e0	-1.240e+00	0.4428	592.0	16.13%	7136.8	15.79%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-1.235e+00	0.4428	3655.0	99.59%	44986.8	99.51%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-1.218e+00	0.4442	145.0	3.95%	1705.9	3.77%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e0	-1.218e+00	0.4442	121.0	3.30%	1416.6	3.13%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e0	-1.215e+00	0.4442	97.0	2.64%	1128.1	2.50%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e0	-1.168e+00	0.4609	218.0	5.94%	2595.9	5.74%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e0	-1.142e+00	0.4706	83.0	2.26%	967.2	2.14%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e0	-1.134e+00	0.4725	237.0	6.46%	2831.2	6.26%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e0	-1.098e+00	0.4877	9.0	0.25%	92.5	0.20%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e0	-1.084e+00	0.4920	41.0	1.12%	469.9	1.04%
c-Myc/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e0	-1.074e+00	0.4948	125.0	3.41%	1481.3	3.28%
Oct4(POU/Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e0	-1.022e+00	0.5189	194.0	5.29%	2326.2	5.15%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e0	-1.018e+00	0.5189	424.0	11.55%	5134.0	11.36%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e0	-1.004e+00	0.5239	292.0	7.96%	3524.5	7.80%
FOXA1:AR/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e0	-9.826e-01	0.5327	22.0	0.60%	249.7	0.55%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e0	-9.815e-01	0.5327	57.0	1.55%	669.4	1.48%
E-box(HLH)/Promoter/Homer	SSGGTCACGTGA	1e0	-9.751e-01	0.5327	12.0	0.33%	131.8	0.29%
CEBP(bZIP)/CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e0	-9.720e-01	0.5327	244.0	6.65%	2945.0	6.51%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e0	-9.672e-01	0.5327	53.0	1.44%	622.3	1.38%
HIF-1a(HLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e0	-9.574e-01	0.5345	55.0	1.50%	647.7	1.43%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-9.423e-01	0.5403	251.0	6.84%	3035.1	6.71%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	-9.385e-01	0.5403	234.0	6.38%	2828.1	6.26%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-9.339e-01	0.5403	87.0	2.37%	1037.6	2.30%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e0	-9.229e-01	0.5439	43.0	1.17%	505.2	1.12%
ZNF711(Zf)/SH-SY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e0	-9.185e-01	0.5439	465.0	12.67%	5660.3	12.52%
CTCF-SatelliteElement/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-8.810e-01	0.5624	5.0	0.14%	52.5	0.12%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-8.340e-01	0.5870	83.0	2.26%	1000.1	2.21%
USF1(HLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e0	-8.000e-01	0.6047	95.0	2.59%	1151.3	2.55%
Pax7-longest(Paired/Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-7.835e-01	0.6123	10.0	0.27%	115.3	0.26%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e0	-7.473e-01	0.6322	17.0	0.46%	202.1	0.45%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-7.452e-01	0.6322	6.0	0.16%	68.3	0.15%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e0	-7.257e-01	0.6407	70.0	1.91%	854.7	1.89%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-7.009e-01	0.6541	265.0	7.22%	3258.5	7.21%
OCT4-SOX2-TCF-NANOG((POU/Homeobox/HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-6.958e-01	0.6548	74.0	2.02%	907.5	2.01%
CHR/Cell-Cycle-Exp/Homer	SRGTTTCAAA	1e0	-6.936e-01	0.6548	250.0	6.81%	3075.4	6.80%
PRDM1/BMI1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-6.919e-01	0.6548	170.0	4.63%	2090.1	4.62%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e0	-6.784e-01	0.6582	61.0	1.66%	749.2	1.66%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e0	-6.603e-01	0.6675	49.0	1.34%	603.9	1.34%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e0	-6.545e-01	0.6688	107.0	2.92%	1320.6	2.92%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-6.322e-01	0.6811	801.0	21.83%	9886.4	21.87%
Egr2/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e0	-5.811e-01	0.7140	25.0	0.68%	314.0	0.69%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-5.498e-01	0.7338	29.0	0.79%	366.4	0.81%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e0	-5.438e-01	0.7353	106.0	2.89%	1327.9	2.94%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e0	-5.316e-01	0.7415	60.0	1.63%	756.0	1.67%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-5.259e-01	0.7428	79.0	2.15%	994.8	2.20%
c-Myc(HLH)/LNCAP-cMyc-ChIP-Seq(unpublished)/Homer	VCCACGTG	1e0	-5.175e-01	0.7462	74.0	2.02%	933.9	2.07%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e0	-5.105e-01	0.7485	1374.0	37.44%	17011.5	37.63%
Srebp1a(HLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e0	-5.035e-01	0.7509	54.0	1.47%	685.9	1.52%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e0	-4.726e-01	0.7715	323.0	8.80%	4041.2	8.94%
HIF2a(HLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e0	-4.657e-01	0.7739	67.0	1.83%	854.9	1.89%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e0	-4.408e-01	0.7904	2.0	0.05%	28.0	0.06%
EBNA1(EBV virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	-4.364e-01	0.7908	3.0	0.08%	42.0	0.09%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e0	-4.319e-01	0.7914	347.0	9.46%	4354.9	9.63%
ERE(NR/IR3)/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e0	-4.031e-01	0.8114	62.0	1.69%	802.4	1.77%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-3.762e-01	0.8304	106.0	2.89%	1363.7	3.02%
STAT6/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-3.676e-01	0.8345	188.0	5.12%	2395.3	5.30%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-3.655e-01	0.8345	139.0	3.79%	1781.1	3.94%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e0	-3.563e-01	0.8377	72.0	1.96%	938.6	2.08%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e0	-3.528e-01	0.8377	31.0	0.84%	415.1	0.92%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e0	-3.495e-01	0.8377	47.0	1.28%	621.5	1.37%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e0	-3.489e-01	0.8377	74.0	2.02%	965.4	2.14%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-3.266e-01	0.8504	26.0	0.71%	354.2	0.78%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e0	-3.188e-01	0.8539	45.0	1.23%	601.4	1.33%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-3.148e-01	0.8543	15.0	0.41%	211.3	0.47%
E2F(E2F)/Cell-Cycle-Exp/Homer	TTSGCGCGAAAA	1e0	-3.014e-01	0.8627	4.0	0.11%	62.6	0.14%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-2.919e-01	0.8677	122.0	3.32%	1589.0	3.51%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-2.900e-01	0.8677	87.0	2.37%	1145.1	2.53%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e0	-2.797e-01	0.8721	37.0	1.01%	505.9	1.12%
ETS:RUNX/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e0	-2.704e-01	0.8771	19.0	0.52%	270.6	0.60%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-2.491e-01	0.8928	186.0	5.07%	2415.7	5.34%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e0	-2.465e-01	0.8928	386.0	10.52%	4931.0	10.91%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e0	-2.369e-01	0.8975	2.0	0.05%	36.1	0.08%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e0	-2.321e-01	0.8986	10.0	0.27%	153.2	0.34%
VDR(NR/DR3)/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-2.258e-01	0.9011	43.0	1.17%	595.6	1.32%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e0	-2.204e-01	0.9028	34.0	0.93%	478.1	1.06%
LMX1B/HOCOMOCO	WKGMTGTTAATTATTKGYTTC	1e0	-2.055e-01	0.9132	29.0	0.79%	415.1	0.92%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-1.761e-01	0.9372	324.0	8.83%	4199.9	9.29%
bZIP:IRF/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-1.460e-01	0.9625	131.0	3.57%	1766.8	3.91%
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e0	-1.426e-01	0.9625	24.0	0.65%	363.7	0.80%
PAX8/HOCOMOCO	KTVAYTSRMGCRKR	1e0	-1.380e-01	0.9636	9.0	0.25%	153.5	0.34%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-1.231e-01	0.9747	246.0	6.70%	3254.3	7.20%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-1.221e-01	0.9747	208.0	5.67%	2770.7	6.13%
NFkB-p50,p52(RHD)/p50-ChIP-Chip(Schreiber et al.)/Homer	GGGGGAATCCCC	1e0	-1.214e-01	0.9747	14.0	0.38%	229.3	0.51%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e0	-1.198e-01	0.9747	96.0	2.62%	1328.8	2.94%
GFY-Staf/Promoters/Homer	RACTACAATTCCCAGAAKGC	1e0	-1.188e-01	0.9747	4.0	0.11%	80.9	0.18%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-1.055e-01	0.9753	418.0	11.39%	5453.3	12.06%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-1.044e-01	0.9753	200.0	5.45%	2683.3	5.94%
 Ik-1	NHTTGGGAATRCC	1e0	-8.118e-02	0.9927	3670.0	100.00%	45207.2	100.00%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e0	-7.502e-02	0.9955	22.0	0.60%	359.8	0.80%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e0	-7.027e-02	0.9970	21.0	0.57%	347.9	0.77%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e0	-4.635e-02	1.0000	13.0	0.35%	242.9	0.54%
bHLHE40(HLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e0	-4.567e-02	1.0000	44.0	1.20%	687.9	1.52%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-4.197e-02	1.0000	27.0	0.74%	451.7	1.00%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e0	-3.235e-02	1.0000	3.0	0.08%	85.1	0.19%
GLI3(Zf)/GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-2.887e-02	1.0000	18.0	0.49%	331.3	0.73%
Reverb(NR/DR2)/BLRP(RAW)-Reverba-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e0	-2.784e-02	1.0000	21.0	0.57%	377.4	0.83%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-2.480e-02	1.0000	3644.0	99.29%	44988.8	99.52%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-2.476e-02	1.0000	364.0	9.92%	4931.8	10.91%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-9.337e-03	1.0000	224.0	6.10%	3195.4	7.07%
Mouse_Recombination_Hotspot/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-6.889e-03	1.0000	12.0	0.33%	273.8	0.61%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e0	-6.887e-03	1.0000	24.0	0.65%	464.3	1.03%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e0	-6.153e-03	1.0000	3.0	0.08%	111.1	0.25%
SeqBias: CG-repeat	CGCGCGCGCG	1e0	-5.597e-03	1.0000	68.0	1.85%	1114.5	2.47%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-5.455e-03	1.0000	45.0	1.23%	785.9	1.74%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-2.000e-05	1.0000	2.0	0.05%	166.4	0.37%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e0	0.000e+00	1.0000	0.0	0.00%	5.9	0.01%
T1ISRE(IRF)/Ifnb-Exp/Homer	ACTTTCGTTTCT	1e0	0.000e+00	1.0000	0.0	0.00%	55.0	0.12%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e0	0.000e+00	1.0000	0.0	0.00%	21.1	0.05%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e0	0.000e+00	1.0000	0.0	0.00%	7.3	0.02%
LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer	CARTGGAGCGCRYTTGCATT	1e0	0.000e+00	1.0000	0.0	0.00%	6.3	0.01%
LMX1A/UniProbe	NNTAATWWNN	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%