Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 4260)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 21022)	% of Background Sequences with Motif
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e-213	-4.925e+02	0.0000	1447.0	33.97%	3100.8	14.75%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e-181	-4.183e+02	0.0000	941.0	22.09%	1655.3	7.88%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e-74	-1.720e+02	0.0000	2008.0	47.14%	7045.4	33.52%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e-53	-1.221e+02	0.0000	561.0	13.17%	1383.9	6.58%
SeqBias: CG-repeat	CGCGCGCGCG	1e-45	-1.043e+02	0.0000	747.0	17.54%	2172.4	10.34%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e-41	-9.530e+01	0.0000	1046.0	24.55%	3450.3	16.41%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e-40	-9.342e+01	0.0000	627.0	14.72%	1777.5	8.46%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e-39	-9.062e+01	0.0000	397.0	9.32%	953.4	4.54%
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e-38	-8.867e+01	0.0000	551.0	12.93%	1518.8	7.23%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e-36	-8.482e+01	0.0000	404.0	9.48%	1004.8	4.78%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e-36	-8.431e+01	0.0000	385.0	9.04%	940.0	4.47%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e-35	-8.116e+01	0.0000	619.0	14.53%	1825.0	8.68%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e-33	-7.608e+01	0.0000	1992.0	46.76%	7921.3	37.69%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e-31	-7.328e+01	0.0000	455.0	10.68%	1249.0	5.94%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e-26	-6.102e+01	0.0000	555.0	13.03%	1715.0	8.16%
IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer	CACGTGCC	1e-26	-6.088e+01	0.0000	1296.0	30.42%	4886.6	23.25%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e-26	-6.036e+01	0.0000	503.0	11.81%	1515.7	7.21%
SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer	WNBCACGTGA	1e-24	-5.608e+01	0.0000	1054.0	24.74%	3865.3	18.39%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e-23	-5.495e+01	0.0000	123.0	2.89%	207.1	0.99%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e-21	-5.050e+01	0.0000	822.0	19.30%	2919.0	13.89%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e-20	-4.777e+01	0.0000	768.0	18.03%	2716.8	12.93%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e-20	-4.621e+01	0.0000	327.0	7.68%	935.3	4.45%
PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer	NNBCACGTGN	1e-19	-4.575e+01	0.0000	914.0	21.46%	3372.3	16.04%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e-19	-4.521e+01	0.0000	398.0	9.34%	1215.5	5.78%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e-18	-4.306e+01	0.0000	131.0	3.08%	265.9	1.26%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e-18	-4.231e+01	0.0000	384.0	9.01%	1182.7	5.63%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e-16	-3.861e+01	0.0000	770.0	18.08%	2830.7	13.47%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e-13	-3.168e+01	0.0000	1351.0	31.71%	5566.9	26.48%
KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer	RGKGGGCGKGGC	1e-12	-2.983e+01	0.0000	522.0	12.25%	1867.7	8.89%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer	TBGCACGCAA	1e-12	-2.779e+01	0.0000	990.0	23.24%	3969.6	18.89%
KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer	GGGGGTGTGTCC	1e-10	-2.523e+01	0.0000	229.0	5.38%	707.1	3.36%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e-10	-2.500e+01	0.0000	725.0	17.02%	2819.6	13.41%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e-10	-2.459e+01	0.0000	497.0	11.67%	1825.0	8.68%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e-10	-2.333e+01	0.0000	316.0	7.42%	1074.4	5.11%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e-10	-2.318e+01	0.0000	2848.0	66.85%	13061.5	62.14%
ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer	TGGGGAAGGGCM	1e-9	-2.275e+01	0.0000	289.0	6.78%	969.4	4.61%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e-9	-2.185e+01	0.0000	149.0	3.50%	426.0	2.03%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e-8	-2.052e+01	0.0000	1560.0	36.62%	6787.2	32.29%
SeqBias: TA-repeat	TATATATATA	1e-8	-2.039e+01	0.0000	3774.0	88.59%	17965.0	85.47%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e-8	-1.987e+01	0.0000	286.0	6.71%	986.4	4.69%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e-8	-1.969e+01	0.0000	147.0	3.45%	432.4	2.06%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e-7	-1.818e+01	0.0000	63.0	1.48%	140.3	0.67%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-7	-1.706e+01	0.0000	422.0	9.91%	1602.9	7.63%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e-7	-1.645e+01	0.0000	258.0	6.06%	907.5	4.32%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e-6	-1.533e+01	0.0000	1356.0	31.83%	5947.4	28.29%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e-6	-1.489e+01	0.0000	454.0	10.66%	1777.7	8.46%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e-6	-1.384e+01	0.0000	675.0	15.85%	2795.3	13.30%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e-5	-1.311e+01	0.0000	75.0	1.76%	206.4	0.98%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e-5	-1.311e+01	0.0000	75.0	1.76%	206.4	0.98%
Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer	GCCACRCCCACY	1e-5	-1.294e+01	0.0000	116.0	2.72%	363.5	1.73%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e-5	-1.266e+01	0.0000	121.0	2.84%	385.5	1.83%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-5	-1.254e+01	0.0000	737.0	17.30%	3110.6	14.80%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e-5	-1.253e+01	0.0000	181.0	4.25%	630.5	3.00%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e-5	-1.221e+01	0.0000	209.0	4.91%	751.1	3.57%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e-5	-1.218e+01	0.0000	128.0	3.00%	417.1	1.98%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e-5	-1.196e+01	0.0000	122.0	2.86%	395.3	1.88%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e-5	-1.173e+01	0.0001	807.0	18.94%	3456.0	16.44%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e-5	-1.167e+01	0.0001	968.0	22.72%	4211.6	20.04%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e-4	-1.071e+01	0.0001	92.0	2.16%	287.3	1.37%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e-4	-1.070e+01	0.0001	84.0	1.97%	256.4	1.22%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e-4	-1.061e+01	0.0002	562.0	13.19%	2349.7	11.18%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e-4	-1.040e+01	0.0002	181.0	4.25%	655.9	3.12%
Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer	RGAGAGAG	1e-3	-8.974e+00	0.0008	1597.0	37.49%	7313.7	34.79%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e-3	-8.480e+00	0.0013	269.0	6.31%	1067.7	5.08%
ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer	GAGSCCGAGC	1e-3	-7.962e+00	0.0021	53.0	1.24%	157.7	0.75%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e-3	-7.842e+00	0.0023	44.0	1.03%	124.5	0.59%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e-3	-7.758e+00	0.0025	330.0	7.75%	1355.6	6.45%
Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer	CCTGCTGAGH	1e-3	-7.313e+00	0.0038	384.0	9.01%	1611.7	7.67%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e-3	-7.223e+00	0.0041	40.0	0.94%	113.6	0.54%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e-3	-7.190e+00	0.0042	77.0	1.81%	259.0	1.23%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e-2	-6.750e+00	0.0064	83.0	1.95%	287.6	1.37%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e-2	-6.513e+00	0.0080	209.0	4.91%	836.1	3.98%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e-2	-6.379e+00	0.0090	538.0	12.63%	2350.8	11.18%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e-2	-6.352e+00	0.0091	463.0	10.87%	2001.4	9.52%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e-2	-6.044e+00	0.0122	122.0	2.86%	461.7	2.20%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e-2	-6.008e+00	0.0125	168.0	3.94%	663.4	3.16%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e-2	-5.953e+00	0.0131	175.0	4.11%	695.9	3.31%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e-2	-5.612e+00	0.0181	40.0	0.94%	124.7	0.59%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e-2	-5.587e+00	0.0183	1240.0	29.11%	5730.0	27.26%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-2	-5.533e+00	0.0191	577.0	13.54%	2561.9	12.19%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e-2	-5.477e+00	0.0200	480.0	11.27%	2107.9	10.03%
Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer	GGGAAAAMCCCG	1e-2	-5.448e+00	0.0203	197.0	4.62%	803.8	3.82%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e-2	-5.325e+00	0.0227	190.0	4.46%	774.6	3.68%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e-2	-5.039e+00	0.0299	96.0	2.25%	363.9	1.73%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e-2	-4.994e+00	0.0309	29.0	0.68%	86.8	0.41%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e-2	-4.752e+00	0.0388	119.0	2.79%	469.0	2.23%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e-1	-4.330e+00	0.0586	127.0	2.98%	511.3	2.43%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e-1	-4.325e+00	0.0586	1032.0	24.23%	4788.9	22.78%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e-1	-4.273e+00	0.0606	246.0	5.77%	1054.2	5.02%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e-1	-4.182e+00	0.0656	80.0	1.88%	306.1	1.46%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e-1	-4.145e+00	0.0674	66.0	1.55%	246.5	1.17%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e-1	-4.076e+00	0.0714	247.0	5.80%	1064.7	5.07%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e-1	-4.057e+00	0.0720	440.0	10.33%	1968.0	9.36%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e-1	-3.848e+00	0.0878	48.0	1.13%	173.6	0.83%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer	GGGGGAATCCCC	1e-1	-3.827e+00	0.0887	34.0	0.80%	115.7	0.55%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e-1	-3.771e+00	0.0928	38.0	0.89%	132.4	0.63%
Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)	NNAYTTCCTGHN	1e-1	-3.765e+00	0.0928	660.0	15.49%	3027.9	14.41%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e-1	-3.610e+00	0.1068	1292.0	30.33%	6091.0	28.98%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e-1	-3.399e+00	0.1306	444.0	10.42%	2013.5	9.58%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e-1	-3.294e+00	0.1436	317.0	7.44%	1416.8	6.74%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	MACAGGAAGT	1e-1	-3.281e+00	0.1440	180.0	4.23%	776.3	3.69%
EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e-1	-3.279e+00	0.1440	11.0	0.26%	29.6	0.14%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e-1	-3.240e+00	0.1472	686.0	16.10%	3178.2	15.12%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e-1	-3.217e+00	0.1491	141.0	3.31%	599.0	2.85%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e-1	-3.183e+00	0.1528	19.0	0.45%	60.5	0.29%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e-1	-3.057e+00	0.1717	30.0	0.70%	106.2	0.51%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-1	-2.844e+00	0.2105	503.0	11.81%	2320.3	11.04%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-1	-2.837e+00	0.2105	710.0	16.67%	3316.6	15.78%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e-1	-2.652e+00	0.2503	160.0	3.76%	701.2	3.34%
Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer	GCTATTTTTAGC	1e-1	-2.610e+00	0.2587	371.0	8.71%	1700.3	8.09%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e-1	-2.519e+00	0.2809	36.0	0.85%	138.0	0.66%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e-1	-2.449e+00	0.2984	1074.0	25.21%	5108.8	24.30%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e-1	-2.438e+00	0.2991	52.0	1.22%	210.2	1.00%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e-1	-2.428e+00	0.2996	17.0	0.40%	58.8	0.28%
OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	ATGAATATTCATGAG	1e-1	-2.404e+00	0.3041	15.0	0.35%	50.8	0.24%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e-1	-2.402e+00	0.3041	904.0	21.22%	4284.5	20.38%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e-1	-2.387e+00	0.3041	3281.0	77.02%	16004.1	76.14%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e-1	-2.362e+00	0.3092	129.0	3.03%	565.7	2.69%
Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer	GGGGCTYGKCTGGGA	1e-1	-2.357e+00	0.3092	30.0	0.70%	114.9	0.55%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e-1	-2.345e+00	0.3092	35.0	0.82%	136.2	0.65%
DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer	TWGHWACAWTGTWDC	1e0	-2.192e+00	0.3571	343.0	8.05%	1586.5	7.55%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e0	-2.168e+00	0.3628	104.0	2.44%	454.8	2.16%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e0	-2.094e+00	0.3876	44.0	1.03%	180.7	0.86%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e0	-2.058e+00	0.3985	548.0	12.86%	2581.3	12.28%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e0	-2.024e+00	0.4089	104.0	2.44%	458.7	2.18%
ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer	GTGGGCCCCA	1e0	-1.985e+00	0.4218	46.0	1.08%	191.0	0.91%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e0	-1.919e+00	0.4473	40.0	0.94%	165.8	0.79%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e0	-1.839e+00	0.4808	420.0	9.86%	1976.6	9.40%
DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer	YDGHTACAWTGTADC	1e0	-1.738e+00	0.5276	253.0	5.94%	1177.9	5.60%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e0	-1.704e+00	0.5415	76.0	1.78%	336.7	1.60%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-1.697e+00	0.5415	625.0	14.67%	2980.9	14.18%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-1.648e+00	0.5645	146.0	3.43%	669.0	3.18%
ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer	RGGGCACTAACY	1e0	-1.637e+00	0.5659	527.0	12.37%	2508.7	11.93%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e0	-1.528e+00	0.6269	87.0	2.04%	393.7	1.87%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e0	-1.527e+00	0.6269	132.0	3.10%	607.2	2.89%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e0	-1.520e+00	0.6269	460.0	10.80%	2191.3	10.42%
ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer	TGGAACAGMA	1e0	-1.435e+00	0.6728	595.0	13.97%	2855.4	13.58%
ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer	ARGAGGMCAAAATGW	1e0	-1.375e+00	0.7092	133.0	3.12%	618.5	2.94%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-1.368e+00	0.7092	40.0	0.94%	176.4	0.84%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e0	-1.355e+00	0.7132	887.0	20.82%	4291.0	20.41%
ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer	CCTCATGGTGYCYTWYTCCCTTGTG	1e0	-1.354e+00	0.7132	19.0	0.45%	79.9	0.38%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e0	-1.333e+00	0.7190	746.0	17.51%	3602.4	17.14%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e0	-1.325e+00	0.7194	166.0	3.90%	779.0	3.71%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e0	-1.284e+00	0.7439	413.0	9.69%	1980.0	9.42%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e0	-1.284e+00	0.7439	88.0	2.07%	406.9	1.94%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-1.189e+00	0.8076	198.0	4.65%	941.5	4.48%
HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer	VCAGCTGBNN	1e0	-1.185e+00	0.8076	828.0	19.44%	4019.7	19.12%
Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer	SCTGTCAVTCAV	1e0	-1.162e+00	0.8183	119.0	2.79%	560.2	2.67%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e0	-1.097e+00	0.8673	407.0	9.55%	1966.9	9.36%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e0	-1.082e+00	0.8748	1053.0	24.72%	5136.0	24.43%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e0	-1.081e+00	0.8748	1065.0	25.00%	5195.4	24.72%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e0	-1.061e+00	0.8808	53.0	1.24%	246.2	1.17%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-1.051e+00	0.8847	232.0	5.45%	1115.4	5.31%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e0	-1.021e+00	0.9054	117.0	2.75%	557.9	2.65%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e0	-1.012e+00	0.9075	31.0	0.73%	142.1	0.68%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-1.007e+00	0.9075	1038.0	24.37%	5072.6	24.13%
Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer	RAACAATGGN	1e0	-9.776e-01	0.9274	1451.0	34.06%	7109.5	33.82%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e0	-9.729e-01	0.9274	272.0	6.38%	1316.8	6.26%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e0	-9.578e-01	0.9340	89.0	2.09%	425.0	2.02%
LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer	CARTGGAGCGCRYTTGCATT	1e0	-9.540e-01	0.9340	3.0	0.07%	11.7	0.06%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer	CCATATATGGNM	1e0	-9.488e-01	0.9340	421.0	9.88%	2048.1	9.74%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e0	-9.105e-01	0.9611	915.0	21.48%	4480.1	21.31%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e0	-8.406e-01	1.0000	204.0	4.79%	993.2	4.73%
ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer	AACATCTGGA	1e0	-8.170e-01	1.0000	224.0	5.26%	1093.7	5.20%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-8.108e-01	1.0000	4260.0	100.00%	21015.8	99.98%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e0	-8.039e-01	1.0000	381.0	8.94%	1866.8	8.88%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-7.989e-01	1.0000	833.0	19.55%	4092.1	19.47%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-7.942e-01	1.0000	49.0	1.15%	236.2	1.12%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-7.861e-01	1.0000	1.0	0.02%	3.6	0.02%
ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer	GAGCCTGGTACTGWGCCTGR	1e0	-7.819e-01	1.0000	44.0	1.03%	212.0	1.01%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e0	-7.601e-01	1.0000	32.0	0.75%	154.0	0.73%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-7.267e-01	1.0000	245.0	5.75%	1205.0	5.73%
PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	GGAAGTGAAAST	1e0	-7.134e-01	1.0000	177.0	4.15%	870.1	4.14%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	RGGTCADNNAGAGGTCAV	1e0	-7.127e-01	1.0000	3.0	0.07%	13.2	0.06%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e0	-6.819e-01	1.0000	263.0	6.17%	1297.7	6.17%
OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATWATTCATGA	1e0	-6.655e-01	1.0000	36.0	0.85%	177.2	0.84%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-6.564e-01	1.0000	63.0	1.48%	311.9	1.48%
ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer	GTCWGCTGTYYCTCT	1e0	-6.511e-01	1.0000	48.0	1.13%	237.6	1.13%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e0	-6.253e-01	1.0000	18.0	0.42%	89.2	0.42%
PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer	NGTGTTCAVTSAAGCGKAAA	1e0	-6.237e-01	1.0000	80.0	1.88%	397.1	1.89%
SeqBias: G/A bias	RRRRRRRRRR	1e0	-6.081e-01	1.0000	4260.0	100.00%	21016.6	99.99%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-5.986e-01	1.0000	64.0	1.50%	319.3	1.52%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-5.906e-01	1.0000	137.0	3.22%	682.6	3.25%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-5.700e-01	1.0000	92.0	2.16%	460.5	2.19%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-5.386e-01	1.0000	10.0	0.23%	51.0	0.24%
ZNF528(Zf)/HEK293-ZNF528.GFP-ChIP-Seq(GSE58341)/Homer	AGAAATGACTTCCCT	1e0	-5.347e-01	1.0000	3.0	0.07%	15.7	0.07%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e0	-5.019e-01	1.0000	317.0	7.44%	1585.4	7.54%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e0	-4.818e-01	1.0000	38.0	0.89%	195.5	0.93%
Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer	NAACAGCTGG	1e0	-4.723e-01	1.0000	385.0	9.04%	1927.9	9.17%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e0	-4.380e-01	1.0000	638.0	14.98%	3189.2	15.17%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e0	-4.312e-01	1.0000	648.0	15.21%	3240.1	15.41%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e0	-4.184e-01	1.0000	221.0	5.19%	1118.4	5.32%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e0	-4.009e-01	1.0000	118.0	2.77%	604.9	2.88%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e0	-3.930e-01	1.0000	97.0	2.28%	499.6	2.38%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-3.426e-01	1.0000	159.0	3.73%	817.3	3.89%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e0	-3.360e-01	1.0000	57.0	1.34%	301.2	1.43%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e0	-3.171e-01	1.0000	11.0	0.26%	64.0	0.30%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-3.138e-01	1.0000	528.0	12.39%	2669.5	12.70%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-2.918e-01	1.0000	311.0	7.30%	1589.7	7.56%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e0	-2.916e-01	1.0000	569.0	13.36%	2879.4	13.70%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e0	-2.723e-01	1.0000	922.0	21.64%	4642.8	22.09%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-2.658e-01	1.0000	83.0	1.95%	441.8	2.10%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e0	-2.563e-01	1.0000	68.0	1.60%	365.9	1.74%
Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATATTC	1e0	-2.425e-01	1.0000	175.0	4.11%	913.5	4.35%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-2.389e-01	1.0000	4253.0	99.84%	20991.1	99.86%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e0	-2.389e-01	1.0000	813.0	19.08%	4111.2	19.56%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e0	-2.324e-01	1.0000	1670.0	39.20%	8366.9	39.81%
 Ik-1	NHTTGGGAATRCC	1e0	-2.027e-01	1.0000	4260.0	100.00%	21019.6	100.00%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-2.020e-01	1.0000	202.0	4.74%	1058.6	5.04%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e0	-1.967e-01	1.0000	463.0	10.87%	2376.4	11.31%
Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer	AGGVNCCTTTGT	1e0	-1.901e-01	1.0000	754.0	17.70%	3835.7	18.25%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-1.847e-01	1.0000	19.0	0.45%	114.4	0.54%
PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer	AAGAACATWHTGTTC	1e0	-1.841e-01	1.0000	190.0	4.46%	1001.5	4.76%
IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	CTTTCANTATGACTV	1e0	-1.832e-01	1.0000	150.0	3.52%	797.3	3.79%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e0	-1.737e-01	1.0000	359.0	8.43%	1860.8	8.85%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-1.686e-01	1.0000	2044.0	47.98%	10246.3	48.75%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-1.611e-01	1.0000	204.0	4.79%	1079.0	5.13%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e0	-1.409e-01	1.0000	353.0	8.29%	1841.4	8.76%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e0	-1.386e-01	1.0000	1426.0	33.47%	7206.2	34.28%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	ATTTTCCATT	1e0	-1.372e-01	1.0000	1238.0	29.06%	6273.1	29.84%
ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer	WDNCTGGGCA	1e0	-1.365e-01	1.0000	375.0	8.80%	1954.8	9.30%
ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer	AAGGKGRCGCAGGCA	1e0	-1.364e-01	1.0000	20.0	0.47%	124.5	0.59%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-1.350e-01	1.0000	142.0	3.33%	767.3	3.65%
Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer	GCTATTTTTGGM	1e0	-1.220e-01	1.0000	1304.0	30.61%	6611.9	31.46%
ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer	SMCAGTCWGAKGGAGGAGGC	1e0	-1.195e-01	1.0000	4.0	0.09%	32.5	0.15%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-1.162e-01	1.0000	605.0	14.20%	3123.0	14.86%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-1.148e-01	1.0000	286.0	6.71%	1511.0	7.19%
ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer	YTKGATAHAGTATTCTWGGTNGGCA	1e0	-1.101e-01	1.0000	107.0	2.51%	593.0	2.82%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e0	-1.072e-01	1.0000	677.0	15.89%	3490.3	16.60%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e0	-9.939e-02	1.0000	1150.0	27.00%	5861.3	27.89%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-9.560e-02	1.0000	423.0	9.93%	2216.1	10.54%
RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer	TGCATGCA	1e0	-9.483e-02	1.0000	1564.0	36.71%	7923.0	37.69%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-9.452e-02	1.0000	307.0	7.21%	1627.3	7.74%
SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer	TWCCAWWTWTGG	1e0	-8.968e-02	1.0000	697.0	16.36%	3602.1	17.14%
FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer	WWTRTAAACAVG	1e0	-8.928e-02	1.0000	1421.0	33.36%	7218.8	34.34%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer	GYCATCMATCAT	1e0	-8.253e-02	1.0000	140.0	3.29%	773.0	3.68%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e0	-7.702e-02	1.0000	106.0	2.49%	597.9	2.84%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-6.918e-02	1.0000	299.0	7.02%	1600.9	7.62%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer	AGGTCANTGACCTB	1e0	-6.496e-02	1.0000	165.0	3.87%	911.4	4.34%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e0	-5.997e-02	1.0000	759.0	17.82%	3939.3	18.74%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e0	-5.801e-02	1.0000	107.0	2.51%	610.6	2.91%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e0	-5.651e-02	1.0000	1639.0	38.47%	8336.6	39.66%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-5.575e-02	1.0000	69.0	1.62%	408.1	1.94%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer	CTGTTTAC	1e0	-5.482e-02	1.0000	1740.0	40.85%	8839.1	42.05%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-4.854e-02	1.0000	243.0	5.70%	1326.7	6.31%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e0	-4.243e-02	1.0000	29.0	0.68%	192.6	0.92%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-3.989e-02	1.0000	321.0	7.54%	1736.7	8.26%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e0	-3.812e-02	1.0000	373.0	8.76%	2005.2	9.54%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-3.796e-02	1.0000	9.0	0.21%	74.1	0.35%
ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer	GARTGGTCATCGCCC	1e0	-3.751e-02	1.0000	38.0	0.89%	245.4	1.17%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-3.085e-02	1.0000	44.0	1.03%	282.2	1.34%
SeqBias: A/T bias	WWWWWWWWWW	1e0	-2.746e-02	1.0000	4251.0	99.79%	20996.0	99.89%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-2.702e-02	1.0000	596.0	13.99%	3159.1	15.03%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e0	-2.687e-02	1.0000	719.0	16.88%	3783.3	18.00%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-2.653e-02	1.0000	423.0	9.93%	2277.2	10.83%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-2.570e-02	1.0000	231.0	5.42%	1286.2	6.12%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-2.404e-02	1.0000	147.0	3.45%	846.8	4.03%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e0	-2.154e-02	1.0000	382.0	8.97%	2075.1	9.87%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-2.138e-02	1.0000	86.0	2.02%	521.4	2.48%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-1.989e-02	1.0000	65.0	1.53%	407.2	1.94%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-1.940e-02	1.0000	491.0	11.53%	2639.5	12.56%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-1.910e-02	1.0000	121.0	2.84%	713.7	3.40%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	-1.869e-02	1.0000	12.0	0.28%	100.7	0.48%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-1.812e-02	1.0000	4259.0	99.98%	21019.6	100.00%
ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer	GRTGMTRGAGCC	1e0	-1.668e-02	1.0000	204.0	4.79%	1158.2	5.51%
ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer	GNCTGTASTRNTGBCTCHTT	1e0	-1.590e-02	1.0000	13.0	0.31%	108.6	0.52%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e0	-1.381e-02	1.0000	315.0	7.39%	1745.1	8.30%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e0	-1.287e-02	1.0000	596.0	13.99%	3194.7	15.20%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	GCTGTGGTTW	1e0	-1.281e-02	1.0000	417.0	9.79%	2276.4	10.83%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e0	-1.121e-02	1.0000	1173.0	27.54%	6118.2	29.11%
Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	TATGCWAATBAV	1e0	-9.664e-03	1.0000	373.0	8.76%	2059.4	9.80%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e0	-9.572e-03	1.0000	791.0	18.57%	4200.8	19.99%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-9.315e-03	1.0000	88.0	2.07%	549.3	2.61%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-9.188e-03	1.0000	3.0	0.07%	42.5	0.20%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e0	-7.723e-03	1.0000	1684.0	39.53%	8690.9	41.35%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-6.950e-03	1.0000	482.0	11.31%	2635.8	12.54%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e0	-6.240e-03	1.0000	754.0	17.70%	4032.1	19.18%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-6.090e-03	1.0000	644.0	15.12%	3472.7	16.52%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-5.236e-03	1.0000	724.0	17.00%	3887.7	18.50%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e0	-3.485e-03	1.0000	912.0	21.41%	4861.3	23.13%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-3.066e-03	1.0000	177.0	4.15%	1059.7	5.04%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-2.890e-03	1.0000	186.0	4.37%	1109.8	5.28%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-2.636e-03	1.0000	71.0	1.67%	476.9	2.27%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-2.473e-03	1.0000	390.0	9.15%	2194.1	10.44%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e0	-1.400e-03	1.0000	537.0	12.61%	2978.2	14.17%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-1.236e-03	1.0000	154.0	3.62%	954.4	4.54%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e0	-7.280e-04	1.0000	170.0	3.99%	1053.7	5.01%
FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer	TRTTTACTTW	1e0	-6.350e-04	1.0000	1289.0	30.26%	6841.1	32.55%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e0	-5.980e-04	1.0000	378.0	8.87%	2175.0	10.35%
Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer	WATGCAAATGAG	1e0	-5.180e-04	1.0000	493.0	11.57%	2782.8	13.24%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e0	-4.560e-04	1.0000	530.0	12.44%	2979.8	14.18%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e0	-4.380e-04	1.0000	204.0	4.79%	1250.8	5.95%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-2.510e-04	1.0000	346.0	8.12%	2028.0	9.65%
Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer	KBCTACCTGW	1e0	-2.320e-04	1.0000	271.0	6.36%	1628.7	7.75%
SeqBias: CG bias	SSSSSSSSSS	1e0	-1.840e-04	1.0000	3452.0	81.03%	17466.5	83.10%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e0	-1.440e-04	1.0000	84.0	1.97%	596.3	2.84%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-1.110e-04	1.0000	395.0	9.27%	2310.4	10.99%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-4.800e-05	1.0000	650.0	15.26%	3674.7	17.48%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-4.700e-05	1.0000	1806.0	42.39%	9533.5	45.36%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e0	-4.100e-05	1.0000	840.0	19.72%	4662.4	22.18%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-4.100e-05	1.0000	584.0	13.71%	3334.3	15.86%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e0	-3.400e-05	1.0000	1349.0	31.67%	7260.5	34.54%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	AGGTCAAGGTCA	1e0	-2.700e-05	1.0000	27.0	0.63%	262.3	1.25%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-1.500e-05	1.0000	257.0	6.03%	1612.1	7.67%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-1.400e-05	1.0000	943.0	22.14%	5227.5	24.87%
Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer	BTBRAGTGSN	1e0	-1.300e-05	1.0000	1341.0	31.48%	7253.6	34.51%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e0	-1.300e-05	1.0000	1086.0	25.49%	5960.8	28.36%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-9.000e-06	1.0000	1947.0	45.70%	10293.4	48.97%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e0	-9.000e-06	1.0000	1569.0	36.83%	8413.0	40.02%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e0	-9.000e-06	1.0000	151.0	3.54%	1027.2	4.89%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e0	-8.000e-06	1.0000	1910.0	44.84%	10114.2	48.12%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e0	-7.000e-06	1.0000	802.0	18.83%	4522.4	21.52%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e0	-6.000e-06	1.0000	883.0	20.73%	4942.1	23.51%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e0	-5.000e-06	1.0000	670.0	15.73%	3845.8	18.30%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-4.000e-06	1.0000	1468.0	34.46%	7931.9	37.74%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e0	-3.000e-06	1.0000	843.0	19.79%	4758.6	22.64%
ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer	NGNTCTAGAACCNGV	1e0	-3.000e-06	1.0000	199.0	4.67%	1321.9	6.29%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e0	-2.000e-06	1.0000	2085.0	48.94%	11025.6	52.45%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e0	-2.000e-06	1.0000	614.0	14.41%	3573.7	17.00%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-2.000e-06	1.0000	1669.0	39.18%	8968.2	42.67%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e0	-1.000e-06	1.0000	1936.0	45.45%	10304.1	49.02%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e0	-1.000e-06	1.0000	403.0	9.46%	2460.8	11.71%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-1.000e-06	1.0000	167.0	3.92%	1156.4	5.50%
Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer	NNYTAATTAR	1e0	-0.000e+00	1.0000	1711.0	40.16%	9228.0	43.90%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e0	-0.000e+00	1.0000	75.0	1.76%	618.4	2.94%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-0.000e+00	1.0000	40.0	0.94%	397.9	1.89%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e0	-0.000e+00	1.0000	1975.0	46.36%	10564.9	50.26%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-0.000e+00	1.0000	507.0	11.90%	3068.1	14.60%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e0	-0.000e+00	1.0000	1247.0	29.27%	6940.8	33.02%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-0.000e+00	1.0000	436.0	10.23%	2702.0	12.85%
Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer	TTRAGTGSYK	1e0	-0.000e+00	1.0000	1498.0	35.16%	8214.5	39.08%
Tal1	CATCTG	1e0	-0.000e+00	1.0000	839.0	19.69%	4844.1	23.05%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-0.000e+00	1.0000	934.0	21.92%	5341.2	25.41%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e0	-0.000e+00	1.0000	929.0	21.81%	5318.0	25.30%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e0	-0.000e+00	1.0000	1428.0	33.52%	7887.0	37.52%
HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer	TTTTATKRGG	1e0	-0.000e+00	1.0000	1625.0	38.15%	8921.3	42.44%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e0	-0.000e+00	1.0000	274.0	6.43%	1852.9	8.81%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e0	-0.000e+00	1.0000	1202.0	28.22%	6795.5	32.33%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-0.000e+00	1.0000	610.0	14.32%	3705.8	17.63%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e0	-0.000e+00	1.0000	1378.0	32.35%	7718.3	36.72%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-0.000e+00	1.0000	964.0	22.63%	5598.9	26.64%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-0.000e+00	1.0000	947.0	22.23%	5524.2	26.28%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e0	-0.000e+00	1.0000	1431.0	33.59%	8018.5	38.15%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e0	-0.000e+00	1.0000	1289.0	30.26%	7300.5	34.73%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-0.000e+00	1.0000	1094.0	25.68%	6310.0	30.02%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e0	-0.000e+00	1.0000	1593.0	37.39%	8852.7	42.12%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-0.000e+00	1.0000	269.0	6.31%	1886.8	8.98%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-0.000e+00	1.0000	540.0	12.68%	3403.2	16.19%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e0	-0.000e+00	1.0000	2859.0	67.11%	15055.5	71.63%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e0	-0.000e+00	1.0000	1687.0	39.60%	9377.5	44.61%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e0	-0.000e+00	1.0000	1640.0	38.50%	9150.5	43.53%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-0.000e+00	1.0000	2170.0	50.94%	11778.6	56.04%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e0	-0.000e+00	1.0000	1368.0	32.11%	7788.9	37.06%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e0	-0.000e+00	1.0000	1976.0	46.38%	10842.4	51.58%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e0	-0.000e+00	1.0000	2208.0	51.83%	12038.6	57.27%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-0.000e+00	1.0000	1246.0	29.25%	7244.2	34.46%
PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer	HAATAAAGNN	1e0	-0.000e+00	1.0000	2686.0	63.05%	14362.8	68.33%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-0.000e+00	1.0000	247.0	5.80%	1848.3	8.79%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-0.000e+00	1.0000	718.0	16.85%	4486.4	21.34%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e0	-0.000e+00	1.0000	1872.0	43.94%	10434.5	49.64%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e0	-0.000e+00	1.0000	2309.0	54.20%	12627.0	60.07%
KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer	ARGAATAWWN	1e0	-0.000e+00	1.0000	2126.0	49.91%	11746.7	55.88%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-0.000e+00	1.0000	643.0	15.09%	4148.5	19.74%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	-0.000e+00	1.0000	927.0	21.76%	5680.2	27.02%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-0.000e+00	1.0000	1662.0	39.01%	9473.9	45.07%
Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer	TGTCANYT	1e0	-0.000e+00	1.0000	2354.0	55.26%	12885.9	61.30%
SeqBias: GA-repeat	GAGAGAGAGA	1e0	-0.000e+00	1.0000	3571.0	83.83%	18503.5	88.03%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e0	0.000e+00	1.0000	838.0	19.67%	5778.8	27.49%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	0.000e+00	1.0000	2042.0	47.93%	11444.3	54.45%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	0.000e+00	1.0000	1111.0	26.08%	6949.7	33.06%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e0	0.000e+00	1.0000	2314.0	54.32%	12841.7	61.09%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e0	0.000e+00	1.0000	3231.0	75.85%	18391.6	87.50%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e0	0.000e+00	1.0000	1887.0	44.30%	10691.9	50.87%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e0	0.000e+00	1.0000	3195.0	75.00%	17713.8	84.27%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e0	0.000e+00	1.0000	3094.0	72.63%	17992.9	85.60%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e0	0.000e+00	1.0000	0.0	0.00%	1.2	0.01%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e0	0.000e+00	1.0000	1961.0	46.03%	12217.3	58.12%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	0.000e+00	1.0000	448.0	10.52%	3288.6	15.65%
Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer	YTGWCADY	1e0	0.000e+00	1.0000	2259.0	53.03%	12477.2	59.36%
ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer	GGGTTTTGAAGGATGARTAGGAGTT	1e0	0.000e+00	1.0000	0.0	0.00%	0.9	0.00%
ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer	MACCTTCYATGGCTCCCTAKTGCCY	1e0	0.000e+00	1.0000	0.0	0.00%	1.2	0.01%
SeqBias: CA-repeat	CACACACACA	1e0	0.000e+00	1.0000	3074.0	72.16%	16784.1	79.85%
SeqBias: polyC-repeat	CCCCCCCCCC	1e0	0.000e+00	1.0000	4199.0	98.57%	20976.1	99.79%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e0	0.000e+00	1.0000	1314.0	30.85%	7767.2	36.95%
LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer	ADAAATATCT	1e0	0.000e+00	1.0000	1701.0	39.93%	9717.8	46.23%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	0.000e+00	1.0000	964.0	22.63%	5989.3	28.49%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e0	0.000e+00	1.0000	1947.0	45.70%	11107.9	52.85%