Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 3816)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 4016)	% of Background Sequences with Motif
ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer	WDNCTGGGCA	1e-14	-3.234e+01	0.0000	298.0	7.81%	152.6	3.80%
PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer	HAATAAAGNN	1e-11	-2.588e+01	0.0000	643.0	16.85%	462.8	11.51%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e-10	-2.526e+01	0.0000	341.0	8.93%	204.2	5.08%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e-10	-2.412e+01	0.0000	296.0	7.75%	171.6	4.27%
FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer	WWTRTAAACAVG	1e-10	-2.398e+01	0.0000	260.0	6.81%	143.3	3.56%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e-9	-2.110e+01	0.0000	756.0	19.81%	588.1	14.62%
FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer	TRTTTACTTW	1e-9	-2.080e+01	0.0000	273.0	7.15%	162.7	4.04%
SeqBias: TA-repeat	TATATATATA	1e-8	-1.933e+01	0.0000	1115.0	29.21%	943.8	23.47%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e-6	-1.413e+01	0.0000	410.0	10.74%	305.0	7.58%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e-5	-1.380e+01	0.0000	200.0	5.24%	124.5	3.10%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e-5	-1.335e+01	0.0001	69.0	1.81%	26.8	0.67%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e-5	-1.307e+01	0.0001	268.0	7.02%	184.2	4.58%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e-5	-1.303e+01	0.0001	62.0	1.62%	22.9	0.57%
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e-5	-1.195e+01	0.0002	83.0	2.17%	38.4	0.96%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e-4	-1.045e+01	0.0008	319.0	8.36%	241.2	6.00%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e-4	-1.032e+01	0.0008	57.0	1.49%	23.0	0.57%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e-4	-1.031e+01	0.0008	140.0	3.67%	86.7	2.16%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e-4	-1.023e+01	0.0008	46.0	1.21%	16.7	0.42%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e-4	-1.003e+01	0.0009	72.0	1.89%	34.3	0.85%
Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer	TTRAGTGSYK	1e-4	-9.838e+00	0.0010	477.0	12.50%	391.0	9.72%
PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer	NNBCACGTGN	1e-4	-9.784e+00	0.0010	211.0	5.53%	148.5	3.69%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e-4	-9.376e+00	0.0015	804.0	21.06%	711.2	17.68%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e-4	-9.375e+00	0.0015	243.0	6.37%	178.1	4.43%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e-3	-8.747e+00	0.0026	41.0	1.07%	15.7	0.39%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e-3	-8.674e+00	0.0026	57.0	1.49%	26.9	0.67%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e-3	-8.467e+00	0.0031	78.0	2.04%	42.3	1.05%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e-3	-8.153e+00	0.0041	136.0	3.56%	90.1	2.24%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e-3	-7.939e+00	0.0049	36.0	0.94%	13.1	0.33%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e-3	-7.929e+00	0.0049	196.0	5.13%	143.7	3.57%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e-3	-7.909e+00	0.0049	42.0	1.10%	17.8	0.44%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e-3	-7.803e+00	0.0051	68.0	1.78%	36.4	0.91%
Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	TATGCWAATBAV	1e-3	-7.747e+00	0.0052	82.0	2.15%	47.4	1.18%
IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer	CACGTGCC	1e-3	-7.596e+00	0.0059	221.0	5.79%	167.2	4.16%
KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer	RGKGGGCGKGGC	1e-3	-7.159e+00	0.0089	203.0	5.32%	153.8	3.82%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e-3	-7.016e+00	0.0099	99.0	2.59%	63.8	1.59%
SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer	WNBCACGTGA	1e-2	-6.846e+00	0.0114	161.0	4.22%	117.3	2.92%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e-2	-6.776e+00	0.0119	250.0	6.55%	198.7	4.94%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e-2	-6.771e+00	0.0119	214.0	5.61%	165.5	4.12%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e-2	-6.700e+00	0.0122	36.0	0.94%	15.4	0.38%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e-2	-6.542e+00	0.0139	85.0	2.23%	53.1	1.32%
Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer	WATGCAAATGAG	1e-2	-6.529e+00	0.0139	91.0	2.38%	58.7	1.46%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-2	-6.493e+00	0.0139	167.0	4.38%	124.3	3.09%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e-2	-6.422e+00	0.0146	71.0	1.86%	42.3	1.05%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e-2	-6.209e+00	0.0177	143.0	3.75%	104.3	2.59%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e-2	-6.017e+00	0.0210	142.0	3.72%	104.9	2.61%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e-2	-5.997e+00	0.0210	90.0	2.36%	59.1	1.47%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer	CTGTTTAC	1e-2	-5.931e+00	0.0219	287.0	7.52%	238.4	5.93%
Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer	GCCACRCCCACY	1e-2	-5.929e+00	0.0219	34.0	0.89%	15.6	0.39%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e-2	-5.919e+00	0.0219	15.0	0.39%	3.1	0.08%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e-2	-5.901e+00	0.0219	147.0	3.85%	109.9	2.73%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e-2	-5.437e+00	0.0330	24.0	0.63%	9.1	0.23%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e-2	-5.402e+00	0.0335	200.0	5.24%	160.5	3.99%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e-2	-5.259e+00	0.0380	120.0	3.14%	88.3	2.19%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e-2	-4.977e+00	0.0494	415.0	10.87%	369.8	9.20%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e-2	-4.886e+00	0.0531	27.0	0.71%	13.0	0.32%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e-2	-4.734e+00	0.0608	106.0	2.78%	78.8	1.96%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e-2	-4.713e+00	0.0610	32.0	0.84%	16.2	0.40%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e-2	-4.660e+00	0.0631	25.0	0.65%	11.8	0.29%
ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer	TGGGGAAGGGCM	1e-1	-4.566e+00	0.0682	79.0	2.07%	55.4	1.38%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e-1	-4.444e+00	0.0758	204.0	5.34%	170.6	4.24%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e-1	-4.424e+00	0.0761	189.0	4.95%	156.4	3.89%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e-1	-4.317e+00	0.0833	36.0	0.94%	20.8	0.52%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e-1	-4.298e+00	0.0835	12.0	0.31%	3.1	0.08%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-1	-3.974e+00	0.1137	93.0	2.44%	70.7	1.76%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e-1	-3.899e+00	0.1206	148.0	3.88%	121.1	3.01%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e-1	-3.791e+00	0.1324	73.0	1.91%	53.7	1.33%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e-1	-3.778e+00	0.1324	116.0	3.04%	92.8	2.31%
DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer	YDGHTACAWTGTADC	1e-1	-3.739e+00	0.1354	45.0	1.18%	29.2	0.73%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e-1	-3.715e+00	0.1354	14.0	0.37%	5.9	0.15%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e-1	-3.715e+00	0.1354	14.0	0.37%	5.9	0.15%
LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer	ADAAATATCT	1e-1	-3.711e+00	0.1354	245.0	6.42%	215.1	5.35%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e-1	-3.633e+00	0.1421	41.0	1.07%	26.8	0.67%
Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer	GGGGCTYGKCTGGGA	1e-1	-3.581e+00	0.1477	18.0	0.47%	8.7	0.22%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e-1	-3.510e+00	0.1564	15.0	0.39%	6.4	0.16%
DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer	TWGHWACAWTGTWDC	1e-1	-3.385e+00	0.1748	54.0	1.41%	38.5	0.96%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-1	-3.385e+00	0.1748	82.0	2.15%	63.4	1.58%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e-1	-3.153e+00	0.2148	73.0	1.91%	56.5	1.40%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e-1	-3.120e+00	0.2190	27.0	0.71%	16.7	0.41%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e-1	-3.091e+00	0.2227	193.0	5.06%	171.0	4.25%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e-1	-3.087e+00	0.2227	40.0	1.05%	27.7	0.69%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e-1	-3.015e+00	0.2344	50.0	1.31%	37.0	0.92%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e-1	-2.913e+00	0.2563	6.0	0.16%	1.8	0.04%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e-1	-2.886e+00	0.2601	109.0	2.86%	91.5	2.28%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e-1	-2.879e+00	0.2601	4.0	0.10%	0.7	0.02%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e-1	-2.849e+00	0.2636	12.0	0.31%	5.4	0.13%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e-1	-2.847e+00	0.2636	57.0	1.49%	44.0	1.09%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e-1	-2.833e+00	0.2636	26.0	0.68%	16.7	0.41%
SeqBias: CG bias	SSSSSSSSSS	1e-1	-2.816e+00	0.2636	1376.0	36.05%	1381.3	34.35%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e-1	-2.726e+00	0.2846	111.0	2.91%	94.1	2.34%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e-1	-2.724e+00	0.2846	35.0	0.92%	24.8	0.62%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e-1	-2.720e+00	0.2846	64.0	1.68%	50.0	1.24%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e-1	-2.701e+00	0.2846	13.0	0.34%	6.7	0.17%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e-1	-2.696e+00	0.2846	54.0	1.41%	41.2	1.02%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e-1	-2.557e+00	0.3194	7.0	0.18%	2.8	0.07%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e-1	-2.502e+00	0.3337	240.0	6.29%	222.6	5.54%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e-1	-2.472e+00	0.3403	69.0	1.81%	56.4	1.40%
SeqBias: GA-repeat	GAGAGAGAGA	1e-1	-2.441e+00	0.3474	1270.0	33.27%	1279.6	31.82%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e-1	-2.406e+00	0.3561	37.0	0.97%	27.8	0.69%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e-1	-2.338e+00	0.3772	108.0	2.83%	94.4	2.35%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e-1	-2.337e+00	0.3772	84.0	2.20%	71.4	1.78%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e-1	-2.331e+00	0.3772	8.0	0.21%	3.0	0.08%
ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer	GNCTGTASTRNTGBCTCHTT	1e-1	-2.327e+00	0.3772	5.0	0.13%	1.4	0.03%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e-1	-2.327e+00	0.3772	5.0	0.13%	1.0	0.03%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e-1	-2.314e+00	0.3772	41.0	1.07%	31.0	0.77%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e0	-2.281e+00	0.3772	123.0	3.22%	109.7	2.73%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-2.258e+00	0.3819	131.0	3.43%	118.0	2.93%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e0	-2.232e+00	0.3880	103.0	2.70%	90.5	2.25%
ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer	AAGGKGRCGCAGGCA	1e0	-2.227e+00	0.3880	13.0	0.34%	7.0	0.17%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e0	-2.209e+00	0.3898	47.0	1.23%	37.2	0.92%
OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	ATGAATATTCATGAG	1e0	-2.159e+00	0.4025	3.0	0.08%	0.0	0.00%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e0	-2.159e+00	0.4025	3.0	0.08%	0.0	0.00%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e0	-2.118e+00	0.4155	147.0	3.85%	134.7	3.35%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e0	-2.103e+00	0.4181	41.0	1.07%	33.0	0.82%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e0	-2.090e+00	0.4199	959.0	25.12%	964.5	23.98%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-2.041e+00	0.4373	130.0	3.41%	118.8	2.95%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-2.039e+00	0.4373	294.0	7.70%	282.4	7.02%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e0	-2.015e+00	0.4410	150.0	3.93%	138.5	3.44%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e0	-2.014e+00	0.4410	34.0	0.89%	26.4	0.66%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-2.011e+00	0.4410	250.0	6.55%	239.0	5.94%
SeqBias: polyC-repeat	CCCCCCCCCC	1e0	-1.935e+00	0.4659	3036.0	79.54%	3158.9	78.55%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-1.925e+00	0.4666	84.0	2.20%	74.5	1.85%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-1.886e+00	0.4812	63.0	1.65%	54.2	1.35%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-1.833e+00	0.5033	74.0	1.94%	65.9	1.64%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-1.797e+00	0.5176	253.0	6.63%	244.4	6.08%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e0	-1.790e+00	0.5176	792.0	20.75%	798.1	19.85%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-1.781e+00	0.5176	3643.0	95.44%	3818.7	94.96%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e0	-1.778e+00	0.5176	231.0	6.05%	222.0	5.52%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e0	-1.765e+00	0.5176	288.0	7.55%	280.2	6.97%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e0	-1.761e+00	0.5176	104.0	2.72%	95.6	2.38%
Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer	GGGAAAAMCCCG	1e0	-1.755e+00	0.5176	24.0	0.63%	18.9	0.47%
Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer	GCTATTTTTGGM	1e0	-1.752e+00	0.5176	194.0	5.08%	185.8	4.62%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e0	-1.743e+00	0.5176	521.0	13.65%	519.7	12.92%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e0	-1.666e+00	0.5500	94.0	2.46%	86.9	2.16%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e0	-1.622e+00	0.5704	33.0	0.86%	27.3	0.68%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e0	-1.618e+00	0.5704	19.0	0.50%	14.4	0.36%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-1.610e+00	0.5704	203.0	5.32%	196.4	4.88%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e0	-1.590e+00	0.5759	70.0	1.83%	63.5	1.58%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	AGGTCAAGGTCA	1e0	-1.576e+00	0.5797	21.0	0.55%	16.0	0.40%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e0	-1.573e+00	0.5797	80.0	2.10%	73.3	1.82%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-1.569e+00	0.5797	83.0	2.17%	76.5	1.90%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	GCTGTGGTTW	1e0	-1.561e+00	0.5797	92.0	2.41%	85.8	2.13%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e0	-1.501e+00	0.6076	483.0	12.65%	485.5	12.07%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-1.475e+00	0.6193	6.0	0.16%	3.8	0.09%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	MACAGGAAGT	1e0	-1.420e+00	0.6448	37.0	0.97%	32.5	0.81%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e0	-1.420e+00	0.6448	37.0	0.97%	32.4	0.81%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e0	-1.403e+00	0.6514	41.0	1.07%	36.8	0.92%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-1.363e+00	0.6737	62.0	1.62%	57.6	1.43%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e0	-1.358e+00	0.6737	82.0	2.15%	77.7	1.93%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e0	-1.327e+00	0.6892	24.0	0.63%	20.0	0.50%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-1.314e+00	0.6930	9.0	0.24%	6.9	0.17%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e0	-1.297e+00	0.7003	543.0	14.23%	552.7	13.74%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e0	-1.285e+00	0.7046	10.0	0.26%	7.9	0.20%
Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer	RAACAATGGN	1e0	-1.278e+00	0.7048	159.0	4.17%	156.9	3.90%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e0	-1.263e+00	0.7109	40.0	1.05%	36.0	0.90%
Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer	GCTATTTTTAGC	1e0	-1.254e+00	0.7126	47.0	1.23%	43.7	1.09%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-1.252e+00	0.7126	50.0	1.31%	46.2	1.15%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-1.233e+00	0.7185	128.0	3.35%	126.0	3.13%
ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer	CCTCATGGTGYCYTWYTCCCTTGTG	1e0	-1.227e+00	0.7185	3.0	0.08%	1.4	0.03%
ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer	YTKGATAHAGTATTCTWGGTNGGCA	1e0	-1.190e+00	0.7401	16.0	0.42%	13.3	0.33%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e0	-1.151e+00	0.7650	68.0	1.78%	65.6	1.63%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	RGGTCADNNAGAGGTCAV	1e0	-1.141e+00	0.7650	4.0	0.10%	2.7	0.07%
ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer	SMCAGTCWGAKGGAGGAGGC	1e0	-1.141e+00	0.7650	4.0	0.10%	2.5	0.06%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e0	-1.141e+00	0.7650	4.0	0.10%	2.4	0.06%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e0	-1.141e+00	0.7650	4.0	0.10%	2.5	0.06%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e0	-1.138e+00	0.7650	28.0	0.73%	25.7	0.64%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e0	-1.133e+00	0.7650	32.0	0.84%	29.5	0.73%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-1.130e+00	0.7650	38.0	1.00%	35.9	0.89%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e0	-1.130e+00	0.7650	38.0	1.00%	35.7	0.89%
Tal1	CATCTG	1e0	-1.126e+00	0.7650	214.0	5.61%	215.1	5.35%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e0	-1.107e+00	0.7650	97.0	2.54%	95.1	2.37%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e0	-1.102e+00	0.7650	169.0	4.43%	169.8	4.22%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-1.093e+00	0.7650	5.0	0.13%	3.4	0.08%
Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)	NNAYTTCCTGHN	1e0	-1.062e+00	0.7736	113.0	2.96%	112.4	2.80%
ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer	GARTGGTCATCGCCC	1e0	-1.043e+00	0.7792	7.0	0.18%	5.8	0.15%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-1.043e+00	0.7792	7.0	0.18%	6.0	0.15%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-1.018e+00	0.7946	9.0	0.24%	7.9	0.20%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-1.011e+00	0.7953	122.0	3.20%	122.4	3.04%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-1.003e+00	0.7974	118.0	3.09%	118.5	2.95%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e0	-9.991e-01	0.7974	34.0	0.89%	32.9	0.82%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-9.952e-01	0.7974	13.0	0.34%	11.9	0.30%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e0	-9.877e-01	0.7974	17.0	0.45%	15.6	0.39%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-9.877e-01	0.7974	17.0	0.45%	15.7	0.39%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e0	-9.868e-01	0.7974	22.0	0.58%	20.1	0.50%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e0	-9.864e-01	0.7974	20.0	0.52%	18.1	0.45%
RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer	TGCATGCA	1e0	-9.823e-01	0.7974	342.0	8.96%	351.8	8.75%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	-9.313e-01	0.8198	289.0	7.57%	297.5	7.40%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e0	-9.184e-01	0.8261	187.0	4.90%	191.7	4.77%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e0	-9.087e-01	0.8297	77.0	2.02%	77.4	1.92%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e0	-8.878e-01	0.8427	97.0	2.54%	98.9	2.46%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-8.646e-01	0.8580	88.0	2.31%	89.3	2.22%
SeqBias: G/A bias	RRRRRRRRRR	1e0	-8.508e-01	0.8653	3733.0	97.80%	3929.8	97.72%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e0	-8.085e-01	0.8980	137.0	3.59%	141.5	3.52%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-7.800e-01	0.9192	36.0	0.94%	36.7	0.91%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e0	-7.784e-01	0.9192	8.0	0.21%	7.9	0.20%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-7.775e-01	0.9192	103.0	2.70%	106.5	2.65%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e0	-7.662e-01	0.9192	6.0	0.16%	5.3	0.13%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e0	-7.538e-01	0.9244	30.0	0.79%	30.8	0.77%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-7.517e-01	0.9244	73.0	1.91%	75.5	1.88%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-7.432e-01	0.9244	3.0	0.08%	3.0	0.07%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e0	-7.432e-01	0.9244	3.0	0.08%	2.4	0.06%
EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	-7.330e-01	0.9244	2.0	0.05%	1.4	0.03%
ZNF528(Zf)/HEK293-ZNF528.GFP-ChIP-Seq(GSE58341)/Homer	AGAAATGACTTCCCT	1e0	-7.330e-01	0.9244	2.0	0.05%	2.0	0.05%
ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer	GGGTTTTGAAGGATGARTAGGAGTT	1e0	-7.195e-01	0.9284	1.0	0.03%	0.0	0.00%
HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer	TTTTATKRGG	1e0	-7.157e-01	0.9284	198.0	5.19%	207.8	5.17%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-6.812e-01	0.9553	90.0	2.36%	95.0	2.36%
ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer	RGGGCACTAACY	1e0	-6.793e-01	0.9553	53.0	1.39%	55.3	1.38%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-6.787e-01	0.9553	17.0	0.45%	17.4	0.43%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e0	-6.749e-01	0.9553	88.0	2.31%	92.6	2.30%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-6.716e-01	0.9553	69.0	1.81%	72.4	1.80%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e0	-6.246e-01	0.9868	11.0	0.29%	11.2	0.28%
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e0	-6.129e-01	0.9937	10.0	0.26%	11.0	0.27%
PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	GGAAGTGAAAST	1e0	-6.002e-01	1.0000	22.0	0.58%	24.0	0.60%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-5.922e-01	1.0000	80.0	2.10%	85.9	2.14%
SeqBias: CG-repeat	CGCGCGCGCG	1e0	-5.899e-01	1.0000	95.0	2.49%	101.6	2.53%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e0	-5.688e-01	1.0000	7.0	0.18%	8.0	0.20%
ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer	GTCWGCTGTYYCTCT	1e0	-5.688e-01	1.0000	7.0	0.18%	7.5	0.19%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e0	-5.671e-01	1.0000	18.0	0.47%	19.9	0.50%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e0	-5.391e-01	1.0000	39.0	1.02%	42.3	1.05%
ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer	GAGSCCGAGC	1e0	-5.375e-01	1.0000	15.0	0.39%	17.0	0.42%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e0	-5.277e-01	1.0000	63.0	1.65%	68.2	1.70%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e0	-5.265e-01	1.0000	5.0	0.13%	5.8	0.14%
ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer	GAGCCTGGTACTGWGCCTGR	1e0	-5.033e-01	1.0000	22.0	0.58%	24.0	0.60%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer	GGGGGAATCCCC	1e0	-5.015e-01	1.0000	12.0	0.31%	13.5	0.34%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e0	-4.976e-01	1.0000	4.0	0.10%	4.1	0.10%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e0	-4.976e-01	1.0000	4.0	0.10%	4.5	0.11%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-4.946e-01	1.0000	21.0	0.55%	23.1	0.57%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-4.946e-01	1.0000	21.0	0.55%	23.3	0.58%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-4.946e-01	1.0000	21.0	0.55%	23.2	0.58%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer	TBGCACGCAA	1e0	-4.387e-01	1.0000	55.0	1.44%	61.2	1.52%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e0	-4.328e-01	1.0000	15.0	0.39%	17.9	0.44%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e0	-4.231e-01	1.0000	74.0	1.94%	82.3	2.05%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-4.170e-01	1.0000	108.0	2.83%	119.8	2.98%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-4.131e-01	1.0000	225.0	5.89%	245.0	6.09%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e0	-4.085e-01	1.0000	322.0	8.44%	349.6	8.69%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-4.038e-01	1.0000	2.0	0.05%	2.7	0.07%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e0	-3.923e-01	1.0000	77.0	2.02%	86.8	2.16%
ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer	TGGAACAGMA	1e0	-3.848e-01	1.0000	86.0	2.25%	96.6	2.40%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-3.777e-01	1.0000	11.0	0.29%	13.4	0.33%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e0	-3.743e-01	1.0000	25.0	0.65%	29.5	0.73%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e0	-3.625e-01	1.0000	136.0	3.56%	151.5	3.77%
Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer	AGGVNCCTTTGT	1e0	-3.485e-01	1.0000	86.0	2.25%	97.2	2.42%
SeqBias: CA-repeat	CACACACACA	1e0	-3.406e-01	1.0000	841.0	22.03%	906.8	22.55%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e0	-3.364e-01	1.0000	28.0	0.73%	33.4	0.83%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e0	-3.299e-01	1.0000	336.0	8.80%	368.3	9.16%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e0	-3.283e-01	1.0000	80.0	2.10%	91.2	2.27%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-3.198e-01	1.0000	13.0	0.34%	16.1	0.40%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-3.128e-01	1.0000	25.0	0.65%	30.3	0.75%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e0	-3.054e-01	1.0000	12.0	0.31%	15.2	0.38%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e0	-3.033e-01	1.0000	134.0	3.51%	151.3	3.76%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e0	-2.903e-01	1.0000	88.0	2.31%	101.6	2.53%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e0	-2.901e-01	1.0000	11.0	0.29%	14.1	0.35%
KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer	GGGGGTGTGTCC	1e0	-2.803e-01	1.0000	42.0	1.10%	50.4	1.25%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e0	-2.705e-01	1.0000	91.0	2.38%	105.2	2.62%
ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer	ARGAGGMCAAAATGW	1e0	-2.622e-01	1.0000	14.0	0.37%	18.5	0.46%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-2.491e-01	1.0000	13.0	0.34%	17.6	0.44%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-2.406e-01	1.0000	49.0	1.28%	59.7	1.48%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e0	-2.383e-01	1.0000	98.0	2.57%	114.0	2.83%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	-2.356e-01	1.0000	97.0	2.54%	113.6	2.82%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e0	-2.328e-01	1.0000	105.0	2.75%	122.2	3.04%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e0	-2.222e-01	1.0000	26.0	0.68%	33.7	0.84%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer	AGGTCANTGACCTB	1e0	-2.222e-01	1.0000	26.0	0.68%	33.3	0.83%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e0	-2.155e-01	1.0000	4.0	0.10%	6.8	0.17%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-2.148e-01	1.0000	25.0	0.65%	32.2	0.80%
ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer	NGNTCTAGAACCNGV	1e0	-2.096e-01	1.0000	36.0	0.94%	45.3	1.13%
Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATATTC	1e0	-2.046e-01	1.0000	14.0	0.37%	19.4	0.48%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e0	-1.953e-01	1.0000	192.0	5.03%	220.8	5.49%
HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer	VCAGCTGBNN	1e0	-1.925e-01	1.0000	221.0	5.79%	252.7	6.28%
IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	CTTTCANTATGACTV	1e0	-1.925e-01	1.0000	13.0	0.34%	18.9	0.47%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e0	-1.915e-01	1.0000	89.0	2.33%	107.0	2.66%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e0	-1.845e-01	1.0000	111.0	2.91%	131.1	3.26%
PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer	AAGAACATWHTGTTC	1e0	-1.764e-01	1.0000	25.0	0.65%	33.9	0.84%
Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer	KBCTACCTGW	1e0	-1.764e-01	1.0000	48.0	1.26%	61.0	1.52%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e0	-1.644e-01	1.0000	110.0	2.88%	131.2	3.26%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e0	-1.620e-01	1.0000	134.0	3.51%	158.1	3.93%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-1.534e-01	1.0000	7.0	0.18%	11.7	0.29%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e0	-1.534e-01	1.0000	7.0	0.18%	11.9	0.30%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e0	-1.474e-01	1.0000	13.0	0.34%	19.7	0.49%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e0	-1.474e-01	1.0000	13.0	0.34%	19.0	0.47%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e0	-1.450e-01	1.0000	1.0	0.03%	2.6	0.06%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e0	-1.433e-01	1.0000	58.0	1.52%	73.4	1.83%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e0	-1.301e-01	1.0000	2.0	0.05%	4.4	0.11%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e0	-1.301e-01	1.0000	2.0	0.05%	4.3	0.11%
Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer	CCTGCTGAGH	1e0	-1.279e-01	1.0000	72.0	1.89%	90.0	2.24%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e0	-1.245e-01	1.0000	11.0	0.29%	17.8	0.44%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-1.228e-01	1.0000	70.0	1.83%	88.1	2.19%
Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer	NAACAGCTGG	1e0	-1.200e-01	1.0000	82.0	2.15%	102.8	2.56%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e0	-1.198e-01	1.0000	248.0	6.50%	288.7	7.18%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e0	-1.154e-01	1.0000	61.0	1.60%	78.7	1.96%
Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer	NNYTAATTAR	1e0	-1.096e-01	1.0000	228.0	5.97%	267.3	6.65%
PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer	NGTGTTCAVTSAAGCGKAAA	1e0	-1.078e-01	1.0000	7.0	0.18%	12.5	0.31%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e0	-1.074e-01	1.0000	47.0	1.23%	62.4	1.55%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	ATTTTCCATT	1e0	-1.015e-01	1.0000	114.0	2.99%	140.2	3.49%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e0	-1.007e-01	1.0000	15.0	0.39%	23.0	0.57%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e0	-1.007e-01	1.0000	15.0	0.39%	23.0	0.57%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e0	-9.912e-02	1.0000	331.0	8.67%	382.3	9.51%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e0	-9.149e-02	1.0000	6.0	0.16%	11.3	0.28%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e0	-8.647e-02	1.0000	36.0	0.94%	50.2	1.25%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-7.604e-02	1.0000	29.0	0.76%	42.0	1.05%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-7.465e-02	1.0000	5.0	0.13%	10.1	0.25%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e0	-7.094e-02	1.0000	65.0	1.70%	86.9	2.16%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e0	-7.064e-02	1.0000	531.0	13.91%	606.4	15.08%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e0	-6.978e-02	1.0000	17.0	0.45%	27.1	0.67%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-6.965e-02	1.0000	154.0	4.03%	189.7	4.72%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e0	-6.649e-02	1.0000	3.0	0.08%	7.9	0.20%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e0	-6.649e-02	1.0000	3.0	0.08%	7.7	0.19%
Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer	TGTCANYT	1e0	-6.563e-02	1.0000	433.0	11.34%	500.0	12.43%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-6.498e-02	1.0000	3567.0	93.45%	3790.2	94.25%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	-6.218e-02	1.0000	100.0	2.62%	128.7	3.20%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e0	-5.743e-02	1.0000	4.0	0.10%	9.3	0.23%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e0	-5.383e-02	1.0000	151.0	3.96%	188.2	4.68%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e0	-5.217e-02	1.0000	14.0	0.37%	24.7	0.61%
ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer	GTGGGCCCCA	1e0	-5.146e-02	1.0000	7.0	0.18%	14.4	0.36%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-4.740e-02	1.0000	32.0	0.84%	48.7	1.21%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-3.746e-02	1.0000	90.0	2.36%	120.3	2.99%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e0	-3.617e-02	1.0000	4.0	0.10%	10.6	0.26%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e0	-3.457e-02	1.0000	24.0	0.63%	39.1	0.97%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e0	-3.400e-02	1.0000	45.0	1.18%	66.8	1.66%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e0	-3.231e-02	1.0000	15.0	0.39%	28.0	0.70%
Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer	YTGWCADY	1e0	-3.213e-02	1.0000	378.0	9.90%	449.7	11.18%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e0	-3.144e-02	1.0000	20.0	0.52%	34.2	0.85%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-2.850e-02	1.0000	173.0	4.53%	219.7	5.46%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e0	-2.844e-02	1.0000	71.0	1.86%	99.5	2.47%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e0	-2.668e-02	1.0000	104.0	2.72%	139.1	3.46%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e0	-2.603e-02	1.0000	131.0	3.43%	171.6	4.27%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-2.174e-02	1.0000	231.0	6.05%	288.3	7.17%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-2.012e-02	1.0000	21.0	0.55%	37.8	0.94%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-1.834e-02	1.0000	96.0	2.52%	132.8	3.30%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e0	-1.827e-02	1.0000	284.0	7.44%	351.0	8.73%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e0	-1.716e-02	1.0000	9.0	0.24%	20.7	0.52%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-1.651e-02	1.0000	151.0	3.96%	198.8	4.94%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-1.566e-02	1.0000	7.0	0.18%	17.7	0.44%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-1.499e-02	1.0000	14.0	0.37%	28.4	0.71%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e0	-1.170e-02	1.0000	9.0	0.24%	21.6	0.54%
Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer	SCTGTCAVTCAV	1e0	-1.075e-02	1.0000	14.0	0.37%	29.2	0.73%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e0	-9.372e-03	1.0000	1.0	0.03%	6.9	0.17%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e0	-8.534e-03	1.0000	88.0	2.31%	127.9	3.18%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-8.410e-03	1.0000	3.0	0.08%	11.0	0.27%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-7.386e-03	1.0000	12.0	0.31%	27.3	0.68%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-7.157e-03	1.0000	57.0	1.49%	89.2	2.22%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e0	-6.412e-03	1.0000	98.0	2.57%	141.6	3.52%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer	GYCATCMATCAT	1e0	-6.008e-03	1.0000	8.0	0.21%	22.0	0.55%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e0	-5.745e-03	1.0000	91.0	2.38%	133.6	3.32%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-5.344e-03	1.0000	40.0	1.05%	68.5	1.70%
KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer	ARGAATAWWN	1e0	-4.134e-03	1.0000	221.0	5.79%	291.7	7.25%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-3.337e-03	1.0000	23.0	0.60%	46.9	1.17%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e0	-3.093e-03	1.0000	738.0	19.33%	877.7	21.82%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e0	-2.882e-03	1.0000	22.0	0.58%	45.1	1.12%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e0	-2.443e-03	1.0000	32.0	0.84%	60.9	1.51%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-1.520e-03	1.0000	9.0	0.24%	26.5	0.66%
ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer	AACATCTGGA	1e0	-1.221e-03	1.0000	31.0	0.81%	61.8	1.54%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e0	-1.133e-03	1.0000	92.0	2.41%	143.5	3.57%
SeqBias: A/T bias	WWWWWWWWWW	1e0	-1.061e-03	1.0000	2824.0	73.98%	3094.9	76.96%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e0	-1.005e-03	1.0000	555.0	14.54%	686.9	17.08%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e0	-9.390e-04	1.0000	287.0	7.52%	380.3	9.46%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-4.760e-04	1.0000	269.0	7.05%	364.6	9.07%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e0	-3.300e-04	1.0000	56.0	1.47%	101.8	2.53%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e0	-2.050e-04	1.0000	122.0	3.20%	191.0	4.75%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e0	-1.960e-04	1.0000	22.0	0.58%	53.0	1.32%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e0	-7.100e-05	1.0000	121.0	3.17%	194.7	4.84%
ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer	GRTGMTRGAGCC	1e0	-4.500e-05	1.0000	19.0	0.50%	52.7	1.31%
SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer	TWCCAWWTWTGG	1e0	-2.200e-05	1.0000	41.0	1.07%	89.1	2.22%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-7.000e-06	1.0000	251.0	6.58%	370.8	9.22%
Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer	BTBRAGTGSN	1e0	-6.000e-06	1.0000	193.0	5.06%	298.0	7.41%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer	CCATATATGGNM	1e0	-3.000e-06	1.0000	17.0	0.45%	55.6	1.38%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e0	-1.000e-06	1.0000	8.0	0.21%	39.5	0.98%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-0.000e+00	1.0000	3490.0	91.43%	3791.1	94.27%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e0	-0.000e+00	1.0000	147.0	3.85%	256.5	6.38%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	-0.000e+00	1.0000	62.0	1.62%	138.6	3.45%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e0	-0.000e+00	1.0000	116.0	3.04%	226.3	5.63%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e0	-0.000e+00	1.0000	294.0	7.70%	469.3	11.67%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e0	-0.000e+00	1.0000	223.0	5.84%	378.5	9.41%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-0.000e+00	1.0000	116.0	3.04%	244.8	6.09%
Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer	RGAGAGAG	1e0	-0.000e+00	1.0000	203.0	5.32%	400.6	9.96%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-0.000e+00	1.0000	111.0	2.91%	248.5	6.18%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	-0.000e+00	1.0000	38.0	1.00%	124.8	3.10%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer	CARTGGAGCGCRYTTGCATT	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer	MACCTTCYATGGCTCCCTAKTGCCY	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
 Ik-1	NHTTGGGAATRCC	1e0	0.000e+00	1.0000	3817.0	100.00%	4021.6	100.00%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e0	0.000e+00	1.0000	0.0	0.00%	0.9	0.02%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e0	0.000e+00	1.0000	0.0	0.00%	2.3	0.06%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e0	0.000e+00	1.0000	0.0	0.00%	10.8	0.27%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	0.000e+00	1.0000	0.0	0.00%	1.5	0.04%
OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATWATTCATGA	1e0	0.000e+00	1.0000	0.0	0.00%	5.3	0.13%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e0	0.000e+00	1.0000	0.0	0.00%	6.3	0.16%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	0.000e+00	1.0000	0.0	0.00%	11.7	0.29%