Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 169)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 42731)	% of Background Sequences with Motif
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e-7	-1.765e+01	0.0000	59.0	34.91%	7332.7	17.16%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e-5	-1.277e+01	0.0005	71.0	42.01%	10978.5	25.69%
SeqBias: CG-repeat	CGCGCGCGCG	1e-4	-1.131e+01	0.0013	106.0	62.72%	19762.4	46.25%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e-4	-9.829e+00	0.0043	59.0	34.91%	9258.8	21.67%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e-3	-8.902e+00	0.0087	28.0	16.57%	3350.4	7.84%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e-3	-8.838e+00	0.0087	68.0	40.24%	11574.9	27.09%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e-3	-8.369e+00	0.0106	58.0	34.32%	9520.6	22.28%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e-3	-8.113e+00	0.0120	14.0	8.28%	1188.5	2.78%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e-3	-7.499e+00	0.0197	43.0	25.44%	6616.5	15.49%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer	MACAGGAAGT	1e-3	-7.390e+00	0.0198	31.0	18.34%	4248.0	9.94%
SeqBias: TA-repeat	TATATATATA	1e-2	-6.789e+00	0.0329	138.0	81.66%	30384.0	71.11%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e-2	-6.764e+00	0.0329	128.0	75.74%	27566.1	64.52%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-2	-6.560e+00	0.0350	57.0	33.73%	9976.5	23.35%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e-2	-6.378e+00	0.0389	105.0	62.13%	21628.7	50.62%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e-2	-6.332e+00	0.0389	110.0	65.09%	22948.8	53.71%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e-2	-6.021e+00	0.0487	37.0	21.89%	5853.9	13.70%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e-2	-5.925e+00	0.0505	47.0	27.81%	8021.6	18.77%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e-2	-5.791e+00	0.0545	90.0	53.25%	18146.7	42.47%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e-2	-5.726e+00	0.0551	122.0	72.19%	26455.4	61.92%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e-2	-5.676e+00	0.0551	106.0	62.72%	22258.9	52.10%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e-2	-5.462e+00	0.0649	138.0	81.66%	31034.9	72.64%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e-2	-5.321e+00	0.0713	30.0	17.75%	4645.3	10.87%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-2	-5.197e+00	0.0772	106.0	62.72%	22527.5	52.72%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e-2	-5.144e+00	0.0781	105.0	62.13%	22300.6	52.19%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e-2	-5.103e+00	0.0781	65.0	38.46%	12478.3	29.20%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e-2	-5.046e+00	0.0794	120.0	71.01%	26296.4	61.55%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e-2	-4.800e+00	0.0979	125.0	73.96%	27787.8	65.04%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e-2	-4.662e+00	0.1083	28.0	16.57%	4457.7	10.43%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e-2	-4.611e+00	0.1100	101.0	59.76%	21592.9	50.54%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e-1	-4.406e+00	0.1306	58.0	34.32%	11210.6	26.24%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e-1	-4.380e+00	0.1306	23.0	13.61%	3533.0	8.27%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e-1	-4.215e+00	0.1483	26.0	15.38%	4202.4	9.84%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e-1	-4.153e+00	0.1529	53.0	31.36%	10187.1	23.84%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e-1	-4.047e+00	0.1649	9.0	5.33%	988.8	2.31%
SeqBias: A/T bias	WWWWWWWWWW	1e-1	-4.025e+00	0.1649	166.0	98.22%	40432.3	94.63%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e-1	-3.992e+00	0.1649	7.0	4.14%	674.1	1.58%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e-1	-3.874e+00	0.1803	24.0	14.20%	3911.1	9.15%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e-1	-3.763e+00	0.1960	12.0	7.10%	1573.8	3.68%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e-1	-3.756e+00	0.1960	41.0	24.26%	7659.4	17.93%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-1	-3.723e+00	0.1960	47.0	27.81%	9041.1	21.16%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e-1	-3.676e+00	0.1982	14.0	8.28%	1970.6	4.61%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e-1	-3.636e+00	0.2015	17.0	10.06%	2567.4	6.01%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e-1	-3.551e+00	0.2142	26.0	15.38%	4458.7	10.44%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-1	-3.466e+00	0.2279	39.0	23.08%	7359.3	17.22%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e-1	-3.369e+00	0.2457	66.0	39.05%	13736.3	32.15%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e-1	-3.304e+00	0.2563	53.0	31.36%	10683.7	25.00%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer	CTGTTTAC	1e-1	-3.224e+00	0.2717	108.0	63.91%	24340.6	56.97%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e-1	-3.221e+00	0.2717	54.0	31.95%	10972.0	25.68%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e-1	-3.206e+00	0.2717	2.0	1.18%	80.4	0.19%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e-1	-3.171e+00	0.2717	30.0	17.75%	5499.4	12.87%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e-1	-3.144e+00	0.2717	31.0	18.34%	5734.8	13.42%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e-1	-3.113e+00	0.2744	18.0	10.65%	2946.2	6.90%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e-1	-3.111e+00	0.2744	71.0	42.01%	15131.3	35.41%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e-1	-3.055e+00	0.2802	55.0	32.54%	11319.9	26.49%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e-1	-3.054e+00	0.2802	15.0	8.88%	2352.6	5.51%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e-1	-3.026e+00	0.2802	38.0	22.49%	7375.7	17.26%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e-1	-3.025e+00	0.2802	10.0	5.92%	1379.2	3.23%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e-1	-3.010e+00	0.2802	103.0	60.95%	23219.0	54.34%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e-1	-2.976e+00	0.2802	50.0	29.59%	10190.2	23.85%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e-1	-2.966e+00	0.2802	9.0	5.33%	1206.6	2.82%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e-1	-2.965e+00	0.2802	24.0	14.20%	4282.3	10.02%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e-1	-2.952e+00	0.2802	68.0	40.24%	14518.9	33.98%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e-1	-2.918e+00	0.2802	81.0	47.93%	17740.0	41.52%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e-1	-2.917e+00	0.2802	20.0	11.83%	3443.8	8.06%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e-1	-2.913e+00	0.2802	124.0	73.37%	28776.6	67.35%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e-1	-2.902e+00	0.2802	144.0	85.21%	34224.5	80.10%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e-1	-2.806e+00	0.2897	43.0	25.44%	8663.7	20.28%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e-1	-2.796e+00	0.2897	155.0	91.72%	37435.5	87.62%
SeqBias: CA-repeat	CACACACACA	1e-1	-2.713e+00	0.3087	168.0	99.41%	41625.4	97.42%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e-1	-2.697e+00	0.3091	53.0	31.36%	11095.7	25.97%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e-1	-2.629e+00	0.3262	41.0	24.26%	8313.8	19.46%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e-1	-2.619e+00	0.3262	17.0	10.06%	2928.4	6.85%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e-1	-2.600e+00	0.3266	102.0	60.36%	23302.6	54.54%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e-1	-2.566e+00	0.3334	66.0	39.05%	14333.6	33.55%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e-1	-2.547e+00	0.3351	21.0	12.43%	3823.8	8.95%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e-1	-2.532e+00	0.3357	8.0	4.73%	1124.7	2.63%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e-1	-2.492e+00	0.3448	44.0	26.04%	9110.8	21.32%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e-1	-2.481e+00	0.3448	95.0	56.21%	21624.4	50.61%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e-1	-2.479e+00	0.3448	16.0	9.47%	2773.9	6.49%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e-1	-2.478e+00	0.3448	39.0	23.08%	7948.4	18.60%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e-1	-2.473e+00	0.3448	83.0	49.11%	18610.2	43.56%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e-1	-2.463e+00	0.3448	8.0	4.73%	1143.0	2.68%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer	TBGCACGCAA	1e-1	-2.434e+00	0.3448	47.0	27.81%	9862.8	23.08%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e-1	-2.385e+00	0.3519	22.0	13.02%	4124.5	9.65%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e-1	-2.369e+00	0.3532	14.0	8.28%	2393.9	5.60%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e-1	-2.365e+00	0.3532	75.0	44.38%	16717.7	39.13%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e-1	-2.316e+00	0.3641	9.0	5.33%	1380.1	3.23%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e0	-2.227e+00	0.3934	161.0	95.27%	39529.3	92.52%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-2.223e+00	0.3934	56.0	33.14%	12189.9	28.53%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e0	-2.154e+00	0.4139	26.0	15.38%	5156.7	12.07%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-2.152e+00	0.4139	19.0	11.24%	3578.8	8.38%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e0	-2.144e+00	0.4139	106.0	62.72%	24746.9	57.92%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-2.132e+00	0.4139	86.0	50.89%	19679.4	46.06%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	-2.123e+00	0.4139	12.0	7.10%	2067.8	4.84%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e0	-2.108e+00	0.4139	9.0	5.33%	1446.4	3.39%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e0	-2.107e+00	0.4139	7.0	4.14%	1044.0	2.44%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e0	-2.107e+00	0.4139	7.0	4.14%	1044.0	2.44%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	-2.104e+00	0.4139	42.0	24.85%	8927.2	20.89%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e0	-2.031e+00	0.4253	55.0	32.54%	12114.0	28.35%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e0	-2.019e+00	0.4264	16.0	9.47%	2981.4	6.98%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e0	-1.982e+00	0.4381	35.0	20.71%	7365.4	17.24%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e0	-1.971e+00	0.4384	59.0	34.91%	13144.8	30.76%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e0	-1.917e+00	0.4584	82.0	48.52%	18892.8	44.22%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e0	-1.914e+00	0.4584	16.0	9.47%	3034.4	7.10%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e0	-1.895e+00	0.4594	9.0	5.33%	1520.1	3.56%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e0	-1.888e+00	0.4594	49.0	28.99%	10789.9	25.25%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e0	-1.855e+00	0.4695	134.0	79.29%	32329.3	75.67%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-1.840e+00	0.4720	8.0	4.73%	1330.1	3.11%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e0	-1.838e+00	0.4720	40.0	23.67%	8668.2	20.29%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-1.803e+00	0.4811	41.0	24.26%	8938.4	20.92%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-1.769e+00	0.4929	34.0	20.12%	7295.2	17.07%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e0	-1.741e+00	0.5027	75.0	44.38%	17330.9	40.56%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e0	-1.726e+00	0.5059	9.0	5.33%	1585.5	3.71%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e0	-1.721e+00	0.5059	73.0	43.20%	16853.2	39.44%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e0	-1.717e+00	0.5059	134.0	79.29%	32460.4	75.97%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e0	-1.666e+00	0.5231	27.0	15.98%	5721.8	13.39%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e0	-1.645e+00	0.5296	9.0	5.33%	1618.7	3.79%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e0	-1.642e+00	0.5296	23.0	13.61%	4800.7	11.24%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-1.627e+00	0.5300	24.0	14.20%	5045.4	11.81%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-1.546e+00	0.5703	100.0	59.17%	23855.7	55.83%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	-1.490e+00	0.5978	45.0	26.63%	10203.3	23.88%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-1.480e+00	0.5989	59.0	34.91%	13653.0	31.95%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e0	-1.469e+00	0.6007	28.0	16.57%	6117.1	14.32%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e0	-1.462e+00	0.6007	14.0	8.28%	2832.8	6.63%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e0	-1.435e+00	0.6114	19.0	11.24%	4012.6	9.39%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan et al.)/Homer	CCATATATGGNM	1e0	-1.426e+00	0.6123	25.0	14.79%	5438.1	12.73%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-1.422e+00	0.6123	105.0	62.13%	25280.4	59.17%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-1.403e+00	0.6163	78.0	46.15%	18476.3	43.24%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-1.370e+00	0.6322	102.0	60.36%	24582.8	57.54%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e0	-1.313e+00	0.6644	68.0	40.24%	16091.4	37.66%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-1.255e+00	0.6987	28.0	16.57%	6311.9	14.77%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-1.215e+00	0.7217	18.0	10.65%	3942.1	9.23%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-1.212e+00	0.7217	6.0	3.55%	1140.6	2.67%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e0	-1.201e+00	0.7217	12.0	7.10%	2531.0	5.92%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-1.190e+00	0.7236	10.0	5.92%	2070.7	4.85%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e0	-1.189e+00	0.7236	50.0	29.59%	11777.6	27.56%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e0	-1.187e+00	0.7236	71.0	42.01%	17010.4	39.81%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-1.183e+00	0.7236	54.0	31.95%	12777.9	29.91%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-1.156e+00	0.7267	13.0	7.69%	2797.4	6.55%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-1.155e+00	0.7267	14.0	8.28%	3035.2	7.10%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e0	-1.148e+00	0.7267	13.0	7.69%	2803.7	6.56%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e0	-1.124e+00	0.7346	39.0	23.08%	9141.9	21.40%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-1.106e+00	0.7424	21.0	12.43%	4757.6	11.13%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e0	-1.076e+00	0.7602	15.0	8.88%	3335.1	7.81%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-1.073e+00	0.7602	3.0	1.78%	523.0	1.22%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e0	-1.071e+00	0.7602	76.0	44.97%	18433.3	43.14%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e0	-1.049e+00	0.7647	6.0	3.55%	1216.6	2.85%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e0	-1.044e+00	0.7647	68.0	40.24%	16466.1	38.54%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-1.036e+00	0.7647	47.0	27.81%	11235.7	26.30%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e0	-1.029e+00	0.7651	81.0	47.93%	19756.5	46.24%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e0	-1.025e+00	0.7651	13.0	7.69%	2894.5	6.77%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e0	-9.919e-01	0.7832	91.0	53.85%	22337.3	52.28%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-9.780e-01	0.7890	43.0	25.44%	10320.1	24.15%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-9.767e-01	0.7890	93.0	55.03%	22867.9	53.52%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e0	-9.709e-01	0.7890	15.0	8.88%	3423.1	8.01%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e0	-9.631e-01	0.7890	24.0	14.20%	5636.0	13.19%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-9.527e-01	0.7890	36.0	21.30%	8615.7	20.16%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e0	-9.424e-01	0.7917	60.0	35.50%	14618.7	34.21%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e0	-9.327e-01	0.7944	15.0	8.88%	3457.2	8.09%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e0	-9.182e-01	0.8010	12.0	7.10%	2737.6	6.41%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-9.158e-01	0.8010	7.0	4.14%	1527.3	3.57%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e0	-9.153e-01	0.8010	21.0	12.43%	4948.7	11.58%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e0	-9.132e-01	0.8010	22.0	13.02%	5197.5	12.16%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e0	-9.085e-01	0.8010	28.0	16.57%	6687.3	15.65%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-9.026e-01	0.8010	105.0	62.13%	26027.2	60.92%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-8.780e-01	0.8037	9.0	5.33%	2037.8	4.77%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e0	-8.720e-01	0.8037	79.0	46.75%	19511.9	45.67%
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e0	-8.641e-01	0.8052	15.0	8.88%	3521.3	8.24%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e0	-8.389e-01	0.8209	33.0	19.53%	8024.0	18.78%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e0	-8.303e-01	0.8232	10.0	5.92%	2319.7	5.43%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-8.216e-01	0.8255	12.0	7.10%	2820.7	6.60%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-8.113e-01	0.8292	80.0	47.34%	19872.7	46.51%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e0	-8.075e-01	0.8292	18.0	10.65%	4323.9	10.12%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e0	-7.893e-01	0.8379	52.0	30.77%	12863.4	30.11%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e0	-7.882e-01	0.8379	10.0	5.92%	2354.8	5.51%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-7.877e-01	0.8379	96.0	56.80%	23954.5	56.06%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e0	-7.712e-01	0.8387	38.0	22.49%	9376.6	21.95%
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e0	-7.536e-01	0.8488	35.0	20.71%	8650.1	20.25%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e0	-7.441e-01	0.8521	13.0	7.69%	3143.2	7.36%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e0	-7.145e-01	0.8728	4.0	2.37%	914.0	2.14%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-6.887e-01	0.8907	1.0	0.59%	176.6	0.41%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e0	-6.830e-01	0.8909	7.0	4.14%	1691.8	3.96%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-6.793e-01	0.8909	6.0	3.55%	1441.9	3.37%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-6.786e-01	0.8909	36.0	21.30%	9024.6	21.12%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-6.785e-01	0.8909	67.0	39.64%	16851.1	39.44%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e0	-6.654e-01	0.8909	158.0	93.49%	39811.3	93.18%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e0	-6.652e-01	0.8909	36.0	21.30%	9047.5	21.18%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-6.593e-01	0.8909	48.0	28.40%	12091.7	28.30%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-6.452e-01	0.8909	17.0	10.06%	4266.4	9.99%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-6.184e-01	0.9103	69.0	40.83%	17483.2	40.92%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e0	-5.816e-01	0.9394	19.0	11.24%	4864.9	11.39%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	-5.800e-01	0.9394	1.0	0.59%	207.1	0.48%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e0	-5.712e-01	0.9395	3.0	1.78%	743.4	1.74%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-5.707e-01	0.9395	1.0	0.59%	210.2	0.49%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e0	-5.662e-01	0.9395	52.0	30.77%	13295.2	31.12%
SeqBias: CG bias	SSSSSSSSSS	1e0	-5.532e-01	0.9419	162.0	95.86%	40917.4	95.77%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e0	-5.444e-01	0.9454	12.0	7.10%	3115.9	7.29%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-5.334e-01	0.9510	96.0	56.80%	24494.2	57.33%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e0	-5.239e-01	0.9553	148.0	87.57%	37511.2	87.79%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e0	-5.130e-01	0.9609	21.0	12.43%	5487.7	12.84%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e0	-5.037e-01	0.9651	93.0	55.03%	23813.0	55.73%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-4.948e-01	0.9689	44.0	26.04%	11421.2	26.73%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e0	-4.816e-01	0.9769	62.0	36.69%	16036.0	37.53%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-4.811e-01	0.9769	7.0	4.14%	1881.1	4.40%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e0	-4.720e-01	0.9769	5.0	2.96%	1355.7	3.17%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e0	-4.671e-01	0.9769	41.0	24.26%	10719.2	25.09%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e0	-4.656e-01	0.9769	95.0	56.21%	24416.0	57.14%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e0	-4.548e-01	0.9793	16.0	9.47%	4288.2	10.04%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e0	-4.535e-01	0.9793	64.0	37.87%	16617.8	38.89%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e0	-4.518e-01	0.9793	3.0	1.78%	826.2	1.93%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e0	-4.470e-01	0.9793	25.0	14.79%	6645.1	15.55%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e0	-4.469e-01	0.9793	8.0	4.73%	2188.3	5.12%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e0	-4.421e-01	0.9793	51.0	30.18%	13339.0	31.22%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e0	-4.393e-01	0.9793	86.0	50.89%	22223.4	52.01%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e0	-4.328e-01	0.9793	15.0	8.88%	4063.4	9.51%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-4.236e-01	0.9793	8.0	4.73%	2218.3	5.19%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-4.204e-01	0.9793	2.0	1.18%	566.7	1.33%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-4.176e-01	0.9793	4.0	2.37%	1134.7	2.66%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e0	-4.074e-01	0.9793	73.0	43.20%	19031.5	44.54%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e0	-4.052e-01	0.9793	1.0	0.59%	277.9	0.65%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e0	-4.032e-01	0.9793	28.0	16.57%	7520.0	17.60%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e0	-3.932e-01	0.9793	32.0	18.93%	8581.5	20.08%
SeqBias: GA-repeat	GAGAGAGAGA	1e0	-3.811e-01	0.9833	168.0	99.41%	42437.0	99.32%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e0	-3.698e-01	0.9900	23.0	13.61%	6291.1	14.72%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-3.586e-01	0.9968	11.0	6.51%	3126.0	7.32%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson et al.)/Homer	GYCATCMATCAT	1e0	-3.582e-01	0.9968	5.0	2.96%	1479.1	3.46%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e0	-3.567e-01	0.9968	45.0	26.63%	12039.1	28.18%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	-3.509e-01	0.9968	77.0	45.56%	20222.4	47.33%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e0	-3.429e-01	0.9968	9.0	5.33%	2609.2	6.11%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e0	-3.401e-01	0.9968	18.0	10.65%	5038.2	11.79%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e0	-3.400e-01	0.9968	45.0	26.63%	12090.1	28.30%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong et al.)/Homer	AGGTCANTGACCTB	1e0	-3.378e-01	0.9968	26.0	15.38%	7157.0	16.75%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e0	-3.350e-01	0.9968	109.0	64.50%	28306.8	66.25%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-3.310e-01	0.9968	2.0	1.18%	636.4	1.49%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e0	-3.286e-01	0.9968	93.0	55.03%	24330.4	56.94%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber et al.)/Homer	GGGGGAATCCCC	1e0	-3.196e-01	0.9968	12.0	7.10%	3470.8	8.12%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-3.106e-01	0.9968	60.0	35.50%	16039.1	37.54%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e0	-3.066e-01	0.9968	19.0	11.24%	5384.2	12.60%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e0	-2.947e-01	1.0000	3.0	1.78%	977.7	2.29%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-2.930e-01	1.0000	20.0	11.83%	5686.2	13.31%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-2.922e-01	1.0000	30.0	17.75%	8337.5	19.51%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-2.916e-01	1.0000	10.0	5.92%	2978.4	6.97%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-2.843e-01	1.0000	44.0	26.04%	12016.2	28.12%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-2.710e-01	1.0000	2.0	1.18%	695.6	1.63%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-2.678e-01	1.0000	34.0	20.12%	9467.8	22.16%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e0	-2.638e-01	1.0000	3.0	1.78%	1016.9	2.38%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-2.631e-01	1.0000	13.0	7.69%	3868.5	9.05%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e0	-2.562e-01	1.0000	141.0	83.43%	36386.6	85.16%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e0	-2.552e-01	1.0000	40.0	23.67%	11082.0	25.94%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-2.494e-01	1.0000	169.0	100.00%	42663.7	99.85%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-2.488e-01	1.0000	76.0	44.97%	20355.4	47.64%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-2.479e-01	1.0000	26.0	15.38%	7421.9	17.37%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e0	-2.334e-01	1.0000	79.0	46.75%	21182.0	49.58%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer	ATTTTCCATT	1e0	-2.302e-01	1.0000	59.0	34.91%	16102.0	37.69%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e0	-2.296e-01	1.0000	35.0	20.71%	9870.4	23.10%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e0	-2.226e-01	1.0000	155.0	91.72%	39753.4	93.04%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e0	-2.192e-01	1.0000	11.0	6.51%	3424.7	8.02%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e0	-2.182e-01	1.0000	30.0	17.75%	8592.9	20.11%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e0	-2.177e-01	1.0000	45.0	26.63%	12538.2	29.35%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-2.147e-01	1.0000	25.0	14.79%	7271.0	17.02%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-2.132e-01	1.0000	26.0	15.38%	7544.3	17.66%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e0	-2.119e-01	1.0000	66.0	39.05%	17980.9	42.08%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-2.074e-01	1.0000	10.0	5.92%	3173.5	7.43%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e0	-1.981e-01	1.0000	49.0	28.99%	13669.4	31.99%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e0	-1.949e-01	1.0000	35.0	20.71%	10015.0	23.44%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e0	-1.913e-01	1.0000	71.0	42.01%	19359.6	45.31%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e0	-1.881e-01	1.0000	25.0	14.79%	7374.4	17.26%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e0	-1.736e-01	1.0000	23.0	13.61%	6893.9	16.13%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e0	-1.728e-01	1.0000	66.0	39.05%	18184.8	42.56%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e0	-1.690e-01	1.0000	6.0	3.55%	2108.8	4.94%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e0	-1.568e-01	1.0000	17.0	10.06%	5313.3	12.44%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-1.564e-01	1.0000	11.0	6.51%	3617.2	8.47%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e0	-1.436e-01	1.0000	124.0	73.37%	32768.0	76.69%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e0	-1.395e-01	1.0000	30.0	17.75%	8956.4	20.96%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e0	-1.316e-01	1.0000	29.0	17.16%	8731.4	20.44%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e0	-1.315e-01	1.0000	57.0	33.73%	16127.9	37.75%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e0	-1.265e-01	1.0000	101.0	59.76%	27277.6	63.84%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e0	-1.114e-01	1.0000	25.0	14.79%	7763.7	18.17%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e0	-1.109e-01	1.0000	91.0	53.85%	24915.3	58.31%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e0	-1.006e-01	1.0000	4.0	2.37%	1688.2	3.95%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e0	-9.645e-02	1.0000	75.0	44.38%	21017.1	49.19%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-9.618e-02	1.0000	26.0	15.38%	8142.1	19.06%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e0	-9.190e-02	1.0000	51.0	30.18%	14876.8	34.82%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-9.082e-02	1.0000	49.0	28.99%	14361.3	33.61%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e0	-7.950e-02	1.0000	2.0	1.18%	1058.7	2.48%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e0	-7.926e-02	1.0000	13.0	7.69%	4576.4	10.71%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-7.517e-02	1.0000	169.0	100.00%	42707.9	99.96%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e0	-7.408e-02	1.0000	85.0	50.30%	23760.2	55.61%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-6.463e-02	1.0000	4.0	2.37%	1850.1	4.33%
 Ik-1	NHTTGGGAATRCC	1e0	-6.330e-02	1.0000	169.0	100.00%	42710.1	99.96%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e0	-4.813e-02	1.0000	20.0	11.83%	6900.0	16.15%
Tal1	CATCTG	1e0	-4.668e-02	1.0000	73.0	43.20%	21101.5	49.39%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-4.659e-02	1.0000	1.0	0.59%	774.9	1.81%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e0	-4.607e-02	1.0000	8.0	4.73%	3311.9	7.75%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	-3.497e-02	1.0000	34.0	20.12%	11036.9	25.83%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-3.326e-02	1.0000	35.0	20.71%	11344.9	26.55%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e0	-2.507e-02	1.0000	39.0	23.08%	12624.8	29.55%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e0	-2.465e-02	1.0000	26.0	15.38%	9013.6	21.10%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e0	-2.352e-02	1.0000	59.0	34.91%	17996.7	42.12%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e0	-2.350e-02	1.0000	60.0	35.50%	18257.6	42.73%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e0	-1.683e-02	1.0000	48.0	28.40%	15313.8	35.84%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-1.543e-02	1.0000	4.0	2.37%	2346.5	5.49%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-1.324e-02	1.0000	1.0	0.59%	1081.9	2.53%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e0	-1.319e-02	1.0000	5.0	2.96%	2774.5	6.49%
SeqBias: G/A bias	RRRRRRRRRR	1e0	-1.187e-02	1.0000	169.0	100.00%	42723.5	99.99%
SeqBias: polyC-repeat	CCCCCCCCCC	1e0	-7.911e-03	1.0000	169.0	100.00%	42724.2	99.99%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e0	-5.748e-03	1.0000	94.0	55.62%	27664.4	64.75%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-4.280e-03	1.0000	59.0	34.91%	19046.6	44.58%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e0	-3.991e-03	1.0000	47.0	27.81%	15892.8	37.20%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-3.955e-03	1.0000	169.0	100.00%	42725.1	100.00%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-4.840e-04	1.0000	100.0	59.17%	30234.1	70.76%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e0	-3.450e-04	1.0000	94.0	55.62%	28978.0	67.82%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer	GCTGTGGTTW	1e0	-2.500e-05	1.0000	49.0	28.99%	18750.8	43.89%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-1.500e-05	1.0000	49.0	28.99%	18951.1	44.35%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-5.000e-06	1.0000	50.0	29.59%	19614.3	45.91%
EBNA1(EBV virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	0.000e+00	1.0000	0.0	0.00%	234.4	0.55%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e0	0.000e+00	1.0000	0.0	0.00%	252.7	0.59%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e0	0.000e+00	1.0000	0.0	0.00%	142.3	0.33%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	0.000e+00	1.0000	0.0	0.00%	1012.7	2.37%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e0	0.000e+00	1.0000	0.0	0.00%	165.7	0.39%
LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer	CARTGGAGCGCRYTTGCATT	1e0	0.000e+00	1.0000	0.0	0.00%	60.5	0.14%