Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 3934)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 19830)	% of Background Sequences with Motif
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e-217	-5.011e+02	0.0000	1430.0	36.35%	3113.3	15.70%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e-165	-3.812e+02	0.0000	883.0	22.45%	1619.3	8.16%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e-72	-1.669e+02	0.0000	1907.0	48.47%	6832.7	34.45%
SeqBias: CG-repeat	CGCGCGCGCG	1e-62	-1.432e+02	0.0000	780.0	19.83%	2129.8	10.74%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e-52	-1.206e+02	0.0000	559.0	14.21%	1417.5	7.15%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e-42	-9.849e+01	0.0000	637.0	16.19%	1829.4	9.22%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e-42	-9.775e+01	0.0000	1020.0	25.93%	3408.8	17.19%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e-40	-9.431e+01	0.0000	604.0	15.35%	1726.8	8.71%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e-40	-9.230e+01	0.0000	417.0	10.60%	1039.5	5.24%
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e-39	-9.107e+01	0.0000	546.0	13.88%	1522.7	7.68%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e-37	-8.717e+01	0.0000	394.0	10.02%	981.9	4.95%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e-37	-8.609e+01	0.0000	471.0	11.97%	1267.7	6.39%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e-33	-7.825e+01	0.0000	379.0	9.63%	970.4	4.89%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e-31	-7.175e+01	0.0000	568.0	14.44%	1730.9	8.73%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e-29	-6.832e+01	0.0000	501.0	12.74%	1488.7	7.51%
PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer	NNBCACGTGN	1e-24	-5.602e+01	0.0000	919.0	23.36%	3358.6	16.93%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e-24	-5.551e+01	0.0000	830.0	21.10%	2971.4	14.98%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e-23	-5.445e+01	0.0000	131.0	3.33%	236.3	1.19%
IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer	CACGTGCC	1e-22	-5.269e+01	0.0000	1264.0	32.13%	4969.3	25.06%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e-22	-5.093e+01	0.0000	408.0	10.37%	1241.9	6.26%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e-21	-4.925e+01	0.0000	128.0	3.25%	242.2	1.22%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e-20	-4.738e+01	0.0000	1748.0	44.43%	7357.5	37.10%
SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer	WNBCACGTGA	1e-20	-4.680e+01	0.0000	1029.0	26.16%	3963.4	19.98%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e-19	-4.512e+01	0.0000	391.0	9.94%	1216.1	6.13%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e-19	-4.468e+01	0.0000	318.0	8.08%	932.9	4.70%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e-19	-4.416e+01	0.0000	757.0	19.24%	2774.1	13.99%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e-17	-3.970e+01	0.0000	760.0	19.32%	2840.0	14.32%
KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer	RGKGGGCGKGGC	1e-15	-3.513e+01	0.0000	526.0	13.37%	1868.4	9.42%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e-14	-3.416e+01	0.0000	746.0	18.96%	2848.2	14.36%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e-13	-3.183e+01	0.0000	1327.0	33.73%	5587.3	28.17%
KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer	GGGGGTGTGTCC	1e-13	-3.147e+01	0.0000	237.0	6.02%	708.9	3.57%
ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer	TGGGGAAGGGCM	1e-13	-3.031e+01	0.0000	311.0	7.91%	1012.6	5.11%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer	TBGCACGCAA	1e-13	-2.995e+01	0.0000	993.0	25.24%	4042.2	20.38%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e-11	-2.668e+01	0.0000	314.0	7.98%	1057.4	5.33%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e-11	-2.564e+01	0.0000	2761.0	70.18%	12911.5	65.10%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e-10	-2.387e+01	0.0000	283.0	7.19%	955.9	4.82%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e-10	-2.316e+01	0.0000	149.0	3.79%	426.6	2.15%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e-9	-2.293e+01	0.0000	269.0	6.84%	907.0	4.57%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-9	-2.180e+01	0.0000	436.0	11.08%	1634.2	8.24%
Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer	GCCACRCCCACY	1e-8	-1.994e+01	0.0000	120.0	3.05%	337.1	1.70%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e-8	-1.864e+01	0.0000	58.0	1.47%	125.5	0.63%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e-7	-1.821e+01	0.0000	140.0	3.56%	425.7	2.15%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e-7	-1.787e+01	0.0000	497.0	12.63%	1963.3	9.90%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e-7	-1.621e+01	0.0000	126.0	3.20%	385.7	1.94%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e-6	-1.493e+01	0.0000	183.0	4.65%	627.0	3.16%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e-5	-1.377e+01	0.0000	96.0	2.44%	286.1	1.44%
SeqBias: TA-repeat	TATATATATA	1e-5	-1.362e+01	0.0000	3473.0	88.28%	16997.1	85.70%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e-5	-1.318e+01	0.0000	671.0	17.06%	2855.0	14.40%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e-5	-1.316e+01	0.0000	1312.0	33.35%	5937.0	29.94%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e-5	-1.247e+01	0.0000	280.0	7.12%	1075.9	5.43%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e-5	-1.201e+01	0.0000	129.0	3.28%	432.6	2.18%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e-5	-1.158e+01	0.0001	440.0	11.18%	1814.2	9.15%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e-5	-1.154e+01	0.0001	532.0	13.52%	2241.9	11.30%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e-4	-1.147e+01	0.0001	474.0	12.05%	1973.6	9.95%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e-4	-1.131e+01	0.0001	489.0	12.43%	2046.5	10.32%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e-4	-1.047e+01	0.0002	1503.0	38.21%	6963.6	35.11%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e-4	-9.815e+00	0.0004	94.0	2.39%	310.0	1.56%
Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer	GGGAAAAMCCCG	1e-4	-9.754e+00	0.0004	202.0	5.13%	770.4	3.88%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e-4	-9.717e+00	0.0004	944.0	24.00%	4251.3	21.44%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e-3	-9.156e+00	0.0007	205.0	5.21%	792.7	4.00%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-3	-9.130e+00	0.0007	690.0	17.54%	3047.6	15.37%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e-3	-9.113e+00	0.0007	773.0	19.65%	3445.9	17.37%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e-3	-8.851e+00	0.0009	172.0	4.37%	651.1	3.28%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e-3	-8.806e+00	0.0009	78.0	1.98%	253.6	1.28%
Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer	CCTGCTGAGH	1e-3	-8.321e+00	0.0014	382.0	9.71%	1614.6	8.14%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e-3	-8.235e+00	0.0016	50.0	1.27%	147.5	0.74%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e-3	-8.048e+00	0.0018	89.0	2.26%	305.2	1.54%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e-3	-7.845e+00	0.0022	82.0	2.08%	278.5	1.40%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e-3	-7.832e+00	0.0022	43.0	1.09%	123.6	0.62%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e-3	-7.797e+00	0.0023	44.0	1.12%	127.3	0.64%
Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer	RGAGAGAG	1e-3	-7.687e+00	0.0025	1538.0	39.10%	7244.5	36.53%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-3	-7.548e+00	0.0028	736.0	18.71%	3316.2	16.72%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e-3	-7.500e+00	0.0029	1235.0	31.39%	5752.7	29.01%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e-3	-7.387e+00	0.0032	192.0	4.88%	762.9	3.85%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e-2	-6.790e+00	0.0058	529.0	13.45%	2347.4	11.84%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e-2	-6.244e+00	0.0099	171.0	4.35%	687.7	3.47%
ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer	GTGGGCCCCA	1e-2	-5.841e+00	0.0146	48.0	1.22%	157.8	0.80%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e-2	-5.836e+00	0.0146	40.0	1.02%	125.3	0.63%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-2	-5.797e+00	0.0149	556.0	14.13%	2508.8	12.65%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e-2	-5.769e+00	0.0151	170.0	4.32%	691.4	3.49%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e-2	-5.387e+00	0.0219	101.0	2.57%	388.2	1.96%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e-2	-5.358e+00	0.0222	156.0	3.97%	635.0	3.20%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e-2	-5.315e+00	0.0229	242.0	6.15%	1032.3	5.21%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e-2	-5.174e+00	0.0261	315.0	8.01%	1378.9	6.95%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e-2	-5.140e+00	0.0267	46.0	1.17%	155.3	0.78%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e-2	-4.871e+00	0.0345	95.0	2.41%	369.5	1.86%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e-2	-4.859e+00	0.0345	112.0	2.85%	445.6	2.25%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e-2	-4.848e+00	0.0345	451.0	11.46%	2036.8	10.27%
ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer	GAGSCCGAGC	1e-2	-4.772e+00	0.0368	49.0	1.25%	171.2	0.86%
ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer	ARGAGGMCAAAATGW	1e-2	-4.651e+00	0.0411	148.0	3.76%	612.8	3.09%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e-1	-4.523e+00	0.0462	310.0	7.88%	1373.1	6.92%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e-1	-4.293e+00	0.0575	28.0	0.71%	89.3	0.45%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e-1	-4.214e+00	0.0615	700.0	17.79%	3269.2	16.48%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e-1	-4.142e+00	0.0654	296.0	7.52%	1318.4	6.65%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e-1	-4.060e+00	0.0703	2.0	0.05%	1.4	0.01%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e-1	-3.995e+00	0.0735	57.0	1.45%	214.4	1.08%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e-1	-3.995e+00	0.0735	57.0	1.45%	214.4	1.08%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e-1	-3.973e+00	0.0743	241.0	6.13%	1062.1	5.36%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e-1	-3.918e+00	0.0777	166.0	4.22%	711.1	3.59%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e-1	-3.492e+00	0.1178	112.0	2.85%	470.4	2.37%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e-1	-3.417e+00	0.1257	62.0	1.58%	244.9	1.23%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	MACAGGAAGT	1e-1	-3.315e+00	0.1379	184.0	4.68%	811.6	4.09%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e-1	-3.237e+00	0.1475	54.0	1.37%	211.2	1.07%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer	GGGGGAATCCCC	1e-1	-3.233e+00	0.1475	32.0	0.81%	116.0	0.58%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e-1	-3.091e+00	0.1675	47.0	1.19%	182.8	0.92%
Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)	NNAYTTCCTGHN	1e-1	-3.051e+00	0.1727	647.0	16.45%	3067.3	15.47%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e-1	-2.951e+00	0.1892	605.0	15.38%	2866.5	14.45%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e-1	-2.908e+00	0.1955	1054.0	26.79%	5089.8	25.66%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e-1	-2.818e+00	0.2121	17.0	0.43%	56.9	0.29%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e-1	-2.714e+00	0.2332	35.0	0.89%	134.3	0.68%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e-1	-2.662e+00	0.2433	28.0	0.71%	104.2	0.53%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e-1	-2.653e+00	0.2435	179.0	4.55%	807.4	4.07%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e-1	-2.645e+00	0.2435	420.0	10.68%	1975.2	9.96%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e-1	-2.641e+00	0.2435	113.0	2.87%	494.3	2.49%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e-1	-2.633e+00	0.2435	107.0	2.72%	466.5	2.35%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e-1	-2.627e+00	0.2435	410.0	10.42%	1927.3	9.72%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e-1	-2.625e+00	0.2435	218.0	5.54%	995.9	5.02%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e-1	-2.592e+00	0.2457	140.0	3.56%	623.0	3.14%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e-1	-2.515e+00	0.2630	845.0	21.48%	4078.6	20.56%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e-1	-2.487e+00	0.2682	419.0	10.65%	1978.7	9.98%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-1	-2.408e+00	0.2879	474.0	12.05%	2252.0	11.36%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e-1	-2.365e+00	0.2980	455.0	11.57%	2161.2	10.90%
HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer	VCAGCTGBNN	1e0	-2.300e+00	0.3153	819.0	20.82%	3964.7	19.99%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e0	-2.274e+00	0.3212	33.0	0.84%	131.7	0.66%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e0	-2.095e+00	0.3812	175.0	4.45%	807.3	4.07%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-2.086e+00	0.3815	177.0	4.50%	817.0	4.12%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e0	-2.054e+00	0.3907	995.0	25.29%	4859.5	24.50%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e0	-2.033e+00	0.3958	32.0	0.81%	130.8	0.66%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e0	-1.966e+00	0.4202	1053.0	26.77%	5156.4	26.00%
Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer	GCTATTTTTAGC	1e0	-1.952e+00	0.4228	336.0	8.54%	1599.1	8.06%
ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer	AACATCTGGA	1e0	-1.923e+00	0.4317	224.0	5.69%	1052.1	5.30%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e0	-1.918e+00	0.4317	91.0	2.31%	409.7	2.07%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e0	-1.906e+00	0.4328	13.0	0.33%	47.6	0.24%
Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer	SCTGTCAVTCAV	1e0	-1.867e+00	0.4465	118.0	3.00%	540.5	2.73%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e0	-1.777e+00	0.4851	875.0	22.24%	4284.2	21.60%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-1.744e+00	0.4974	1042.0	26.49%	5121.2	25.82%
ZNF528(Zf)/HEK293-ZNF528.GFP-ChIP-Seq(GSE58341)/Homer	AGAAATGACTTCCCT	1e0	-1.732e+00	0.4998	7.0	0.18%	23.4	0.12%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e0	-1.716e+00	0.5043	76.0	1.93%	343.6	1.73%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e0	-1.686e+00	0.5159	878.0	22.32%	4307.8	21.72%
ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer	TGGAACAGMA	1e0	-1.660e+00	0.5258	600.0	15.25%	2924.8	14.75%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e0	-1.647e+00	0.5290	97.0	2.47%	446.0	2.25%
ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer	SMCAGTCWGAKGGAGGAGGC	1e0	-1.623e+00	0.5378	11.0	0.28%	41.1	0.21%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e0	-1.584e+00	0.5554	204.0	5.19%	970.2	4.89%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e0	-1.561e+00	0.5642	116.0	2.95%	541.1	2.73%
EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	-1.502e+00	0.5941	8.0	0.20%	29.8	0.15%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e0	-1.498e+00	0.5941	3078.0	78.24%	15414.5	77.72%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-1.474e+00	0.6030	60.0	1.53%	273.1	1.38%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e0	-1.454e+00	0.6108	535.0	13.60%	2617.7	13.20%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e0	-1.402e+00	0.6394	422.0	10.73%	2059.7	10.39%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-1.385e+00	0.6461	42.0	1.07%	189.3	0.95%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e0	-1.372e+00	0.6500	747.0	18.99%	3682.3	18.57%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e0	-1.329e+00	0.6743	580.0	14.74%	2852.9	14.38%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e0	-1.258e+00	0.7186	129.0	3.28%	617.9	3.12%
DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer	TWGHWACAWTGTWDC	1e0	-1.226e+00	0.7377	315.0	8.01%	1540.4	7.77%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-1.223e+00	0.7377	71.0	1.80%	334.7	1.69%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-1.199e+00	0.7476	13.0	0.33%	55.4	0.28%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e0	-1.184e+00	0.7541	121.0	3.08%	581.4	2.93%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	-1.052e+00	0.8558	74.0	1.88%	355.6	1.79%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e0	-1.032e+00	0.8675	107.0	2.72%	519.5	2.62%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-1.009e+00	0.8815	138.0	3.51%	674.5	3.40%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e0	-9.981e-01	0.8860	1001.0	25.44%	4998.9	25.21%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e0	-9.760e-01	0.9001	646.0	16.42%	3218.2	16.23%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-9.727e-01	0.9001	207.0	5.26%	1020.0	5.14%
LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer	CARTGGAGCGCRYTTGCATT	1e0	-9.075e-01	0.9522	5.0	0.13%	21.5	0.11%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e0	-9.040e-01	0.9522	31.0	0.79%	148.2	0.75%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-8.966e-01	0.9522	95.0	2.41%	466.2	2.35%
PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer	AAGAACATWHTGTTC	1e0	-8.477e-01	0.9928	200.0	5.08%	994.6	5.01%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e0	-8.377e-01	0.9968	29.0	0.74%	140.7	0.71%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e0	-8.283e-01	1.0000	1337.0	33.99%	6714.9	33.86%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	-7.776e-01	1.0000	15.0	0.38%	72.8	0.37%
DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer	YDGHTACAWTGTADC	1e0	-7.673e-01	1.0000	228.0	5.80%	1141.1	5.75%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e0	-7.411e-01	1.0000	119.0	3.02%	596.0	3.01%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e0	-7.323e-01	1.0000	256.0	6.51%	1285.5	6.48%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e0	-7.124e-01	1.0000	365.0	9.28%	1836.4	9.26%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-7.013e-01	1.0000	50.0	1.27%	250.4	1.26%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-6.880e-01	1.0000	322.0	8.19%	1622.7	8.18%
ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer	GAGCCTGGTACTGWGCCTGR	1e0	-6.744e-01	1.0000	46.0	1.17%	231.1	1.17%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-6.618e-01	1.0000	216.0	5.49%	1090.5	5.50%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e0	-6.493e-01	1.0000	61.0	1.55%	308.1	1.55%
PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	GGAAGTGAAAST	1e0	-6.458e-01	1.0000	167.0	4.25%	844.8	4.26%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e0	-6.437e-01	1.0000	13.0	0.33%	65.1	0.33%
PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer	NGTGTTCAVTSAAGCGKAAA	1e0	-6.296e-01	1.0000	76.0	1.93%	385.7	1.94%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-6.248e-01	1.0000	795.0	20.21%	4017.3	20.26%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e0	-6.091e-01	1.0000	73.0	1.86%	371.5	1.87%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-6.019e-01	1.0000	1.0	0.03%	5.0	0.03%
SeqBias: G/A bias	RRRRRRRRRR	1e0	-5.951e-01	1.0000	3934.0	100.00%	19829.7	99.98%
Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer	NAACAGCTGG	1e0	-5.771e-01	1.0000	375.0	9.53%	1903.4	9.60%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-5.697e-01	1.0000	130.0	3.30%	663.3	3.34%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e0	-5.623e-01	1.0000	86.0	2.19%	440.4	2.22%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e0	-5.555e-01	1.0000	1193.0	30.33%	6039.9	30.45%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e0	-5.332e-01	1.0000	118.0	3.00%	605.1	3.05%
SeqBias: A/T bias	WWWWWWWWWW	1e0	-5.305e-01	1.0000	3929.0	99.87%	19806.4	99.87%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e0	-5.143e-01	1.0000	455.0	11.57%	2317.4	11.68%
OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	ATGAATATTCATGAG	1e0	-4.541e-01	1.0000	9.0	0.23%	49.4	0.25%
OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATWATTCATGA	1e0	-4.414e-01	1.0000	31.0	0.79%	165.8	0.84%
ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer	RGGGCACTAACY	1e0	-4.201e-01	1.0000	494.0	12.56%	2531.2	12.76%
ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer	GTCWGCTGTYYCTCT	1e0	-4.065e-01	1.0000	41.0	1.04%	219.2	1.11%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e0	-4.054e-01	1.0000	36.0	0.92%	193.0	0.97%
IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	CTTTCANTATGACTV	1e0	-4.045e-01	1.0000	143.0	3.63%	745.7	3.76%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e0	-3.846e-01	1.0000	876.0	22.27%	4476.3	22.57%
ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer	CCTCATGGTGYCYTWYTCCCTTGTG	1e0	-3.590e-01	1.0000	14.0	0.36%	79.7	0.40%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e0	-3.495e-01	1.0000	683.0	17.36%	3506.2	17.68%
FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer	WWTRTAAACAVG	1e0	-3.145e-01	1.0000	1305.0	33.17%	6669.0	33.63%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-3.035e-01	1.0000	48.0	1.22%	263.8	1.33%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e0	-3.016e-01	1.0000	1534.0	38.99%	7830.0	39.48%
ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer	AAGGKGRCGCAGGCA	1e0	-3.002e-01	1.0000	22.0	0.56%	125.4	0.63%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-2.980e-01	1.0000	79.0	2.01%	426.4	2.15%
Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer	GGGGCTYGKCTGGGA	1e0	-2.935e-01	1.0000	21.0	0.53%	120.8	0.61%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-2.857e-01	1.0000	291.0	7.40%	1522.3	7.68%
ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer	GARTGGTCATCGCCC	1e0	-2.782e-01	1.0000	44.0	1.12%	244.7	1.23%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e0	-2.548e-01	1.0000	597.0	15.18%	3095.0	15.61%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-2.426e-01	1.0000	155.0	3.94%	829.4	4.18%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e0	-2.384e-01	1.0000	18.0	0.46%	107.1	0.54%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-2.327e-01	1.0000	628.0	15.96%	3259.0	16.43%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e0	-2.144e-01	1.0000	36.0	0.92%	207.3	1.05%
RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer	TGCATGCA	1e0	-2.136e-01	1.0000	1531.0	38.92%	7850.3	39.58%
ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer	WDNCTGGGCA	1e0	-2.116e-01	1.0000	376.0	9.56%	1976.6	9.97%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-2.108e-01	1.0000	208.0	5.29%	1110.6	5.60%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-1.984e-01	1.0000	3934.0	100.00%	19832.8	100.00%
 Ik-1	NHTTGGGAATRCC	1e0	-1.984e-01	1.0000	3934.0	100.00%	19832.8	100.00%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer	CCATATATGGNM	1e0	-1.584e-01	1.0000	377.0	9.58%	1998.8	10.08%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-1.411e-01	1.0000	174.0	4.42%	950.4	4.79%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-1.282e-01	1.0000	3933.0	99.97%	19829.8	99.98%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e0	-1.196e-01	1.0000	1546.0	39.30%	7979.2	40.23%
Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer	AGGVNCCTTTGT	1e0	-1.123e-01	1.0000	739.0	18.78%	3879.6	19.56%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e0	-1.065e-01	1.0000	352.0	8.95%	1890.9	9.53%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-8.681e-02	1.0000	526.0	13.37%	2801.6	14.13%
Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATATTC	1e0	-6.907e-02	1.0000	154.0	3.91%	870.4	4.39%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-6.881e-02	1.0000	284.0	7.22%	1556.4	7.85%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e0	-6.727e-02	1.0000	670.0	17.03%	3558.5	17.94%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-6.285e-02	1.0000	120.0	3.05%	691.1	3.48%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-6.162e-02	1.0000	64.0	1.63%	387.9	1.96%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e0	-6.090e-02	1.0000	1124.0	28.57%	5889.3	29.69%
Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer	RAACAATGGN	1e0	-5.108e-02	1.0000	1339.0	34.04%	6996.6	35.28%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e0	-4.979e-02	1.0000	894.0	22.72%	4728.0	23.84%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-4.958e-02	1.0000	405.0	10.29%	2203.4	11.11%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-4.725e-02	1.0000	592.0	15.05%	3176.6	16.02%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e0	-4.691e-02	1.0000	292.0	7.42%	1614.2	8.14%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-4.240e-02	1.0000	181.0	4.60%	1030.9	5.20%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-4.236e-02	1.0000	408.0	10.37%	2227.0	11.23%
SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer	TWCCAWWTWTGG	1e0	-3.488e-02	1.0000	654.0	16.62%	3513.4	17.72%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-3.367e-02	1.0000	84.0	2.14%	511.8	2.58%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e0	-3.326e-02	1.0000	190.0	4.83%	1086.5	5.48%
ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer	GNCTGTASTRNTGBCTCHTT	1e0	-3.316e-02	1.0000	14.0	0.36%	109.6	0.55%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e0	-3.303e-02	1.0000	373.0	9.48%	2055.0	10.36%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e0	-3.040e-02	1.0000	105.0	2.67%	630.0	3.18%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer	CTGTTTAC	1e0	-2.952e-02	1.0000	1650.0	41.94%	8612.1	43.42%
FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer	TRTTTACTTW	1e0	-2.909e-02	1.0000	1208.0	30.71%	6367.4	32.11%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-2.906e-02	1.0000	16.0	0.41%	123.9	0.62%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-2.824e-02	1.0000	136.0	3.46%	800.8	4.04%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-2.735e-02	1.0000	288.0	7.32%	1614.6	8.14%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e0	-2.622e-02	1.0000	578.0	14.69%	3134.2	15.80%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer	GYCATCMATCAT	1e0	-2.491e-02	1.0000	124.0	3.15%	738.5	3.72%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-2.362e-02	1.0000	1920.0	48.81%	9991.8	50.38%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e0	-2.295e-02	1.0000	317.0	8.06%	1774.4	8.95%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-1.694e-02	1.0000	417.0	10.60%	2313.2	11.66%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	ATTTTCCATT	1e0	-1.593e-02	1.0000	1200.0	30.50%	6363.3	32.08%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e0	-1.295e-02	1.0000	301.0	7.65%	1710.3	8.62%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e0	-1.126e-02	1.0000	1141.0	29.00%	6081.6	30.66%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-1.035e-02	1.0000	183.0	4.65%	1083.5	5.46%
ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer	GRTGMTRGAGCC	1e0	-1.000e-02	1.0000	214.0	5.44%	1252.1	6.31%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-9.846e-03	1.0000	196.0	4.98%	1155.4	5.83%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-9.375e-03	1.0000	166.0	4.22%	993.7	5.01%
Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer	KBCTACCTGW	1e0	-9.003e-03	1.0000	294.0	7.47%	1685.9	8.50%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-7.754e-03	1.0000	80.0	2.03%	519.6	2.62%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-5.886e-03	1.0000	303.0	7.70%	1747.2	8.81%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e0	-5.811e-03	1.0000	761.0	19.34%	4156.1	20.96%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-5.719e-03	1.0000	276.0	7.02%	1603.6	8.09%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer	AGGTCANTGACCTB	1e0	-4.554e-03	1.0000	154.0	3.91%	945.7	4.77%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-4.102e-03	1.0000	465.0	11.82%	2621.2	13.22%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-3.690e-03	1.0000	210.0	5.34%	1258.5	6.35%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e0	-3.491e-03	1.0000	609.0	15.48%	3385.5	17.07%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-3.448e-03	1.0000	6.0	0.15%	74.1	0.37%
SeqBias: CG bias	SSSSSSSSSS	1e0	-3.001e-03	1.0000	3310.0	84.14%	16992.8	85.68%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	GCTGTGGTTW	1e0	-2.693e-03	1.0000	416.0	10.57%	2376.2	11.98%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-2.127e-03	1.0000	963.0	24.48%	5248.6	26.46%
Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer	GCTATTTTTGGM	1e0	-2.103e-03	1.0000	1177.0	29.92%	6351.0	32.02%
ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer	YTKGATAHAGTATTCTWGGTNGGCA	1e0	-1.709e-03	1.0000	80.0	2.03%	546.6	2.76%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e0	-1.660e-03	1.0000	335.0	8.52%	1958.6	9.88%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	AGGTCAAGGTCA	1e0	-1.606e-03	1.0000	33.0	0.84%	264.4	1.33%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-1.565e-03	1.0000	2.0	0.05%	44.1	0.22%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-1.339e-03	1.0000	446.0	11.34%	2559.9	12.91%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e0	-8.110e-04	1.0000	523.0	13.29%	2985.5	15.05%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e0	-7.810e-04	1.0000	721.0	18.33%	4030.5	20.32%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-7.160e-04	1.0000	67.0	1.70%	483.7	2.44%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e0	-6.050e-04	1.0000	79.0	2.01%	557.7	2.81%
Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	TATGCWAATBAV	1e0	-5.870e-04	1.0000	345.0	8.77%	2042.8	10.30%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e0	-5.040e-04	1.0000	865.0	21.99%	4799.9	24.20%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e0	-3.730e-04	1.0000	197.0	5.01%	1241.9	6.26%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-3.300e-04	1.0000	712.0	18.10%	4014.2	20.24%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e0	-2.550e-04	1.0000	522.0	13.27%	3017.4	15.21%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-1.780e-04	1.0000	44.0	1.12%	360.5	1.82%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e0	-1.780e-04	1.0000	884.0	22.47%	4937.6	24.90%
ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer	NGNTCTAGAACCNGV	1e0	-1.580e-04	1.0000	208.0	5.29%	1321.5	6.66%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-1.510e-04	1.0000	608.0	15.46%	3491.1	17.60%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-1.420e-04	1.0000	586.0	14.90%	3376.9	17.03%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e0	-5.700e-05	1.0000	1604.0	40.77%	8687.4	43.80%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-5.500e-05	1.0000	3931.0	99.92%	19831.3	99.99%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-3.000e-05	1.0000	381.0	9.68%	2316.4	11.68%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-2.800e-05	1.0000	635.0	16.14%	3686.9	18.59%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e0	-2.600e-05	1.0000	151.0	3.84%	1031.6	5.20%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-2.300e-05	1.0000	320.0	8.13%	1987.9	10.02%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e0	-1.200e-05	1.0000	1304.0	33.15%	7210.9	36.36%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-8.000e-06	1.0000	1415.0	35.97%	7792.9	39.29%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-8.000e-06	1.0000	586.0	14.90%	3459.2	17.44%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e0	-5.000e-06	1.0000	352.0	8.95%	2199.7	11.09%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-5.000e-06	1.0000	1644.0	41.79%	8981.1	45.28%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-3.000e-06	1.0000	890.0	22.62%	5100.5	25.72%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-3.000e-06	1.0000	438.0	11.13%	2684.8	13.54%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e0	-2.000e-06	1.0000	913.0	23.21%	5229.6	26.37%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-2.000e-06	1.0000	174.0	4.42%	1210.1	6.10%
Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer	BTBRAGTGSN	1e0	-2.000e-06	1.0000	1306.0	33.20%	7286.0	36.74%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-1.000e-06	1.0000	23.0	0.58%	265.1	1.34%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e0	-1.000e-06	1.0000	1163.0	29.56%	6562.6	33.09%
Tal1	CATCTG	1e0	-1.000e-06	1.0000	830.0	21.10%	4822.0	24.31%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e0	-1.000e-06	1.0000	580.0	14.74%	3489.5	17.59%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e0	-1.000e-06	1.0000	1520.0	38.64%	8410.5	42.41%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-1.000e-06	1.0000	1525.0	38.76%	8444.8	42.58%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e0	-0.000e+00	1.0000	1832.0	46.57%	10013.2	50.49%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e0	-0.000e+00	1.0000	1993.0	50.66%	10832.6	54.62%
Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer	WATGCAAATGAG	1e0	-0.000e+00	1.0000	442.0	11.24%	2765.9	13.95%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-0.000e+00	1.0000	615.0	15.63%	3713.5	18.72%
Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer	TTRAGTGSYK	1e0	-0.000e+00	1.0000	1464.0	37.21%	8168.1	41.18%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-0.000e+00	1.0000	292.0	7.42%	1939.4	9.78%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e0	-0.000e+00	1.0000	1011.0	25.70%	5838.6	29.44%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-0.000e+00	1.0000	1117.0	28.39%	6403.2	32.29%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e0	-0.000e+00	1.0000	379.0	9.63%	2444.7	12.33%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e0	-0.000e+00	1.0000	1374.0	34.93%	7750.2	39.08%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e0	-0.000e+00	1.0000	68.0	1.73%	614.5	3.10%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-0.000e+00	1.0000	942.0	23.95%	5532.5	27.90%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-0.000e+00	1.0000	1843.0	46.85%	10180.0	51.33%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e0	-0.000e+00	1.0000	125.0	3.18%	994.3	5.01%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e0	-0.000e+00	1.0000	750.0	19.06%	4518.0	22.78%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e0	-0.000e+00	1.0000	1329.0	33.78%	7575.5	38.20%
Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer	NNYTAATTAR	1e0	-0.000e+00	1.0000	1546.0	39.30%	8697.5	43.85%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-0.000e+00	1.0000	478.0	12.15%	3049.6	15.38%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e0	-0.000e+00	1.0000	768.0	19.52%	4634.4	23.37%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e0	-0.000e+00	1.0000	1653.0	42.02%	9249.0	46.64%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e0	-0.000e+00	1.0000	603.0	15.33%	3744.1	18.88%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e0	-0.000e+00	1.0000	1506.0	38.28%	8517.6	42.95%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-0.000e+00	1.0000	917.0	23.31%	5461.0	27.54%
HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer	TTTTATKRGG	1e0	-0.000e+00	1.0000	1503.0	38.21%	8530.9	43.01%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e0	-0.000e+00	1.0000	1107.0	28.14%	6489.9	32.72%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-0.000e+00	1.0000	583.0	14.82%	3684.5	18.58%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e0	-0.000e+00	1.0000	1909.0	48.53%	10613.8	53.52%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e0	-0.000e+00	1.0000	2669.0	67.84%	14397.7	72.60%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e0	-0.000e+00	1.0000	739.0	18.78%	4588.5	23.14%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e0	-0.000e+00	1.0000	1314.0	33.40%	7640.2	38.52%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e0	-0.000e+00	1.0000	1542.0	39.20%	8817.6	44.46%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-0.000e+00	1.0000	1236.0	31.42%	7237.8	36.49%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e0	-0.000e+00	1.0000	1342.0	34.11%	7795.6	39.31%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	-0.000e+00	1.0000	945.0	24.02%	5720.4	28.84%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e0	-0.000e+00	1.0000	251.0	6.38%	1865.6	9.41%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e0	-0.000e+00	1.0000	1902.0	48.35%	10684.1	53.87%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e0	-0.000e+00	1.0000	1822.0	46.31%	10287.2	51.87%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-0.000e+00	1.0000	679.0	17.26%	4323.4	21.80%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e0	-0.000e+00	1.0000	1163.0	29.56%	6957.1	35.08%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e0	-0.000e+00	1.0000	2197.0	55.85%	12294.2	61.99%
LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer	ADAAATATCT	1e0	-0.000e+00	1.0000	1590.0	40.42%	9256.8	46.67%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-0.000e+00	1.0000	232.0	5.90%	1861.6	9.39%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e0	-0.000e+00	1.0000	1703.0	43.29%	9864.5	49.74%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-0.000e+00	1.0000	1992.0	50.64%	11343.6	57.20%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-0.000e+00	1.0000	1587.0	40.34%	9287.2	46.83%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e0	0.000e+00	1.0000	819.0	20.82%	5721.3	28.85%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	RGGTCADNNAGAGGTCAV	1e0	0.000e+00	1.0000	0.0	0.00%	13.8	0.07%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	0.000e+00	1.0000	1900.0	48.30%	11061.4	55.77%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	0.000e+00	1.0000	1037.0	26.36%	6784.4	34.21%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e0	0.000e+00	1.0000	2110.0	53.63%	12282.7	61.93%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e0	0.000e+00	1.0000	2091.0	53.15%	11897.4	59.99%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e0	0.000e+00	1.0000	2979.0	75.72%	17565.6	88.57%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e0	0.000e+00	1.0000	1796.0	45.65%	10558.7	53.24%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e0	0.000e+00	1.0000	2935.0	74.61%	16887.1	85.15%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e0	0.000e+00	1.0000	2904.0	73.82%	17247.0	86.96%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e0	0.000e+00	1.0000	1920.0	48.81%	11981.9	60.41%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	0.000e+00	1.0000	454.0	11.54%	3288.5	16.58%
Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer	YTGWCADY	1e0	0.000e+00	1.0000	2125.0	54.02%	12278.8	61.91%
Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer	TGTCANYT	1e0	0.000e+00	1.0000	2248.0	57.14%	12677.5	63.92%
ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer	GGGTTTTGAAGGATGARTAGGAGTT	1e0	0.000e+00	1.0000	0.0	0.00%	1.1	0.01%
ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer	MACCTTCYATGGCTCCCTAKTGCCY	1e0	0.000e+00	1.0000	0.0	0.00%	1.5	0.01%
SeqBias: CA-repeat	CACACACACA	1e0	0.000e+00	1.0000	2912.0	74.02%	16251.5	81.94%
SeqBias: polyC-repeat	CCCCCCCCCC	1e0	0.000e+00	1.0000	3895.0	99.01%	19825.2	99.96%
SeqBias: GA-repeat	GAGAGAGAGA	1e0	0.000e+00	1.0000	3363.0	85.49%	17847.4	89.99%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e0	0.000e+00	1.0000	1174.0	29.84%	7361.1	37.12%
KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer	ARGAATAWWN	1e0	0.000e+00	1.0000	1940.0	49.31%	11235.7	56.65%
PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer	HAATAAAGNN	1e0	0.000e+00	1.0000	2420.0	61.51%	13555.4	68.35%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	0.000e+00	1.0000	868.0	22.06%	5563.8	28.05%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e0	0.000e+00	1.0000	1789.0	45.48%	10715.5	54.03%