Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 3000)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 2519)	% of Background Sequences with Motif
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e-440	-1.013e+03	0.0000	1953.0	65.10%	221.9	8.81%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e-362	-8.341e+02	0.0000	1652.0	55.07%	161.9	6.43%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e-309	-7.116e+02	0.0000	1369.0	45.63%	100.0	3.97%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e-295	-6.806e+02	0.0000	1316.0	43.87%	94.2	3.74%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e-146	-3.371e+02	0.0000	550.0	18.33%	5.1	0.20%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e-103	-2.381e+02	0.0000	594.0	19.80%	58.3	2.32%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e-102	-2.361e+02	0.0000	585.0	19.50%	57.0	2.26%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e-58	-1.336e+02	0.0000	498.0	16.60%	94.7	3.76%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e-23	-5.508e+01	0.0000	754.0	25.13%	357.6	14.20%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e-22	-5.187e+01	0.0000	100.0	3.33%	3.9	0.15%
Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer	NAACAGCTGG	1e-18	-4.303e+01	0.0000	295.0	9.83%	95.1	3.78%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e-18	-4.271e+01	0.0000	217.0	7.23%	55.2	2.19%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e-18	-4.231e+01	0.0000	267.0	8.90%	81.3	3.23%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e-15	-3.531e+01	0.0000	313.0	10.43%	118.2	4.69%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e-14	-3.312e+01	0.0000	487.0	16.23%	232.7	9.24%
SeqBias: polyA-repeat	AAAAAAAAAA	1e-13	-3.180e+01	0.0000	2921.0	97.37%	2342.4	93.03%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e-13	-3.165e+01	0.0000	341.0	11.37%	142.7	5.67%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e-12	-2.981e+01	0.0000	465.0	15.50%	226.8	9.01%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e-12	-2.963e+01	0.0000	206.0	6.87%	67.4	2.68%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e-12	-2.915e+01	0.0000	383.0	12.77%	174.9	6.95%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e-12	-2.900e+01	0.0000	259.0	8.63%	98.1	3.90%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e-12	-2.824e+01	0.0000	621.0	20.70%	338.5	13.45%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e-12	-2.808e+01	0.0000	1075.0	35.83%	677.2	26.90%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e-12	-2.802e+01	0.0000	181.0	6.03%	57.0	2.26%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e-11	-2.617e+01	0.0000	212.0	7.07%	76.5	3.04%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e-11	-2.593e+01	0.0000	111.0	3.70%	24.9	0.99%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e-11	-2.583e+01	0.0000	173.0	5.77%	56.0	2.22%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	GCTGTGGTTW	1e-11	-2.534e+01	0.0000	166.0	5.53%	53.0	2.10%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e-10	-2.523e+01	0.0000	175.0	5.83%	57.1	2.27%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e-10	-2.395e+01	0.0000	212.0	7.07%	80.0	3.18%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-10	-2.350e+01	0.0000	170.0	5.67%	57.9	2.30%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e-9	-2.286e+01	0.0000	381.0	12.70%	189.0	7.51%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e-9	-2.171e+01	0.0000	203.0	6.77%	79.6	3.16%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-9	-2.128e+01	0.0000	181.0	6.03%	68.0	2.70%
HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer	VCAGCTGBNN	1e-8	-2.036e+01	0.0000	420.0	14.00%	223.3	8.87%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e-8	-1.953e+01	0.0000	222.0	7.40%	95.3	3.78%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e-8	-1.906e+01	0.0000	86.0	2.87%	20.1	0.80%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e-7	-1.811e+01	0.0000	150.0	5.00%	55.3	2.20%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e-7	-1.663e+01	0.0000	672.0	22.40%	420.6	16.71%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e-7	-1.660e+01	0.0000	291.0	9.70%	147.8	5.87%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e-7	-1.656e+01	0.0000	236.0	7.87%	111.9	4.44%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e-6	-1.563e+01	0.0000	297.0	9.90%	154.0	6.12%
ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer	AACATCTGGA	1e-6	-1.547e+01	0.0000	138.0	4.60%	53.4	2.12%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e-6	-1.504e+01	0.0000	86.0	2.87%	25.7	1.02%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e-6	-1.458e+01	0.0000	173.0	5.77%	76.9	3.05%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e-6	-1.456e+01	0.0000	192.0	6.40%	88.0	3.50%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e-6	-1.450e+01	0.0000	315.0	10.50%	170.2	6.76%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-6	-1.398e+01	0.0000	148.0	4.93%	62.2	2.47%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e-5	-1.331e+01	0.0000	85.0	2.83%	27.9	1.11%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e-5	-1.267e+01	0.0000	255.0	8.50%	135.0	5.36%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e-5	-1.252e+01	0.0000	28.0	0.93%	2.0	0.08%
SeqBias: A/T bias	WWWWWWWWWW	1e-5	-1.231e+01	0.0000	2152.0	71.73%	1665.3	66.14%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e-4	-1.113e+01	0.0001	256.0	8.53%	141.1	5.61%
Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)	NNAYTTCCTGHN	1e-4	-1.046e+01	0.0002	158.0	5.27%	77.8	3.09%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e-4	-1.043e+01	0.0002	50.0	1.67%	13.5	0.54%
SeqBias: polyC-repeat	CCCCCCCCCC	1e-4	-1.041e+01	0.0002	2718.0	90.60%	2194.6	87.16%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e-4	-1.041e+01	0.0002	27.0	0.90%	3.8	0.15%
Tal1	CATCTG	1e-4	-1.007e+01	0.0003	340.0	11.33%	205.5	8.16%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e-4	-9.302e+00	0.0006	51.0	1.70%	15.2	0.60%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e-3	-9.154e+00	0.0007	15.0	0.50%	0.4	0.02%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e-3	-8.980e+00	0.0008	200.0	6.67%	110.5	4.39%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	MACAGGAAGT	1e-3	-8.634e+00	0.0011	69.0	2.30%	26.6	1.06%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e-3	-8.472e+00	0.0013	65.0	2.17%	24.0	0.95%
Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer	CCTGCTGAGH	1e-3	-8.471e+00	0.0013	114.0	3.80%	54.9	2.18%
SeqBias: GA-repeat	GAGAGAGAGA	1e-3	-8.468e+00	0.0013	1052.0	35.07%	769.8	30.57%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e-3	-8.178e+00	0.0016	46.0	1.53%	15.0	0.60%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e-3	-7.799e+00	0.0024	205.0	6.83%	118.5	4.71%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-3	-7.618e+00	0.0028	118.0	3.93%	59.1	2.35%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer	CTGTTTAC	1e-3	-7.599e+00	0.0028	287.0	9.57%	178.9	7.11%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e-3	-7.551e+00	0.0029	62.0	2.07%	24.2	0.96%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer	CCATATATGGNM	1e-3	-7.239e+00	0.0039	47.0	1.57%	16.1	0.64%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e-3	-7.181e+00	0.0041	18.0	0.60%	2.7	0.11%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e-3	-7.146e+00	0.0042	180.0	6.00%	103.2	4.10%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-2	-6.778e+00	0.0060	66.0	2.20%	28.8	1.14%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e-2	-6.764e+00	0.0060	61.0	2.03%	25.4	1.01%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e-2	-6.737e+00	0.0060	735.0	24.50%	529.8	21.04%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e-2	-6.302e+00	0.0092	61.0	2.03%	26.6	1.06%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e-2	-6.166e+00	0.0104	191.0	6.37%	115.3	4.58%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e-2	-6.099e+00	0.0110	10.0	0.33%	0.3	0.01%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e-2	-5.994e+00	0.0121	13.0	0.43%	1.5	0.06%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e-2	-5.774e+00	0.0148	118.0	3.93%	65.7	2.61%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e-2	-5.711e+00	0.0156	260.0	8.67%	169.0	6.71%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e-2	-5.190e+00	0.0260	175.0	5.83%	108.4	4.30%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e-2	-4.911e+00	0.0339	259.0	8.63%	172.2	6.84%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e-2	-4.829e+00	0.0364	100.0	3.33%	56.6	2.25%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e-1	-4.575e+00	0.0464	65.0	2.17%	33.6	1.34%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e-1	-4.471e+00	0.0509	28.0	0.93%	10.8	0.43%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e-1	-4.312e+00	0.0589	24.0	0.80%	8.6	0.34%
ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer	TGGAACAGMA	1e-1	-4.241e+00	0.0626	101.0	3.37%	59.2	2.35%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e-1	-4.240e+00	0.0626	115.0	3.83%	69.2	2.75%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e-1	-4.194e+00	0.0641	12.0	0.40%	2.7	0.11%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e-1	-4.178e+00	0.0645	540.0	18.00%	397.7	15.80%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e-1	-4.144e+00	0.0660	255.0	8.50%	174.3	6.92%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer	GYCATCMATCAT	1e-1	-3.815e+00	0.0908	19.0	0.63%	6.8	0.27%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e-1	-3.723e+00	0.0984	11.0	0.37%	2.7	0.11%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e-1	-3.703e+00	0.0994	95.0	3.17%	57.4	2.28%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e-1	-3.697e+00	0.0994	736.0	24.53%	560.2	22.25%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e-1	-3.634e+00	0.1043	22.0	0.73%	8.3	0.33%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e-1	-3.589e+00	0.1080	162.0	5.40%	107.9	4.29%
SeqBias: G/A bias	RRRRRRRRRR	1e-1	-3.570e+00	0.1090	2936.0	97.87%	2442.8	97.02%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e-1	-3.451e+00	0.1215	458.0	15.27%	339.0	13.47%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e-1	-3.430e+00	0.1229	126.0	4.20%	81.1	3.22%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e-1	-3.359e+00	0.1306	79.0	2.63%	47.2	1.87%
FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer	WWTRTAAACAVG	1e-1	-3.346e+00	0.1311	101.0	3.37%	63.5	2.52%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e-1	-3.308e+00	0.1348	21.0	0.70%	8.9	0.35%
ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer	YTKGATAHAGTATTCTWGGTNGGCA	1e-1	-3.262e+00	0.1398	10.0	0.33%	2.9	0.12%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e-1	-3.236e+00	0.1423	167.0	5.57%	113.5	4.51%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e-1	-3.206e+00	0.1451	19.0	0.63%	7.5	0.30%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e-1	-3.165e+00	0.1499	2939.0	97.97%	2447.2	97.20%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e-1	-3.115e+00	0.1561	42.0	1.40%	22.2	0.88%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e-1	-3.105e+00	0.1563	36.0	1.20%	18.9	0.75%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e-1	-2.999e+00	0.1722	40.0	1.33%	21.2	0.84%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e-1	-2.913e+00	0.1860	155.0	5.17%	106.3	4.22%
PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	GGAAGTGAAAST	1e-1	-2.882e+00	0.1903	18.0	0.60%	7.8	0.31%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e-1	-2.857e+00	0.1933	11.0	0.37%	3.5	0.14%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e-1	-2.850e+00	0.1933	69.0	2.30%	42.9	1.70%
SeqBias: CG bias	SSSSSSSSSS	1e-1	-2.844e+00	0.1933	1294.0	43.13%	1032.4	41.00%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e-1	-2.765e+00	0.2066	56.0	1.87%	33.4	1.33%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e-1	-2.689e+00	0.2209	19.0	0.63%	8.4	0.33%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e-1	-2.629e+00	0.2328	25.0	0.83%	12.9	0.51%
Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer	GGGGCTYGKCTGGGA	1e-1	-2.625e+00	0.2328	28.0	0.93%	14.5	0.58%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e-1	-2.557e+00	0.2459	12.0	0.40%	4.3	0.17%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e-1	-2.556e+00	0.2459	78.0	2.60%	50.0	1.99%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e-1	-2.530e+00	0.2485	145.0	4.83%	101.7	4.04%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	ATTTTCCATT	1e-1	-2.512e+00	0.2511	75.0	2.50%	48.2	1.92%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e-1	-2.504e+00	0.2512	83.0	2.77%	54.4	2.16%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e-1	-2.485e+00	0.2540	39.0	1.30%	22.9	0.91%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e-1	-2.438e+00	0.2621	4.0	0.13%	0.9	0.04%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e-1	-2.438e+00	0.2621	4.0	0.13%	0.5	0.02%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e-1	-2.377e+00	0.2765	24.0	0.80%	12.5	0.50%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e-1	-2.364e+00	0.2777	44.0	1.47%	26.4	1.05%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e0	-2.218e+00	0.3190	32.0	1.07%	18.1	0.72%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-2.201e+00	0.3220	11.0	0.37%	4.3	0.17%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-2.186e+00	0.3244	29.0	0.97%	16.6	0.66%
ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer	GTCWGCTGTYYCTCT	1e0	-2.117e+00	0.3452	17.0	0.57%	8.6	0.34%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-2.070e+00	0.3589	325.0	10.83%	248.7	9.88%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e0	-2.005e+00	0.3803	21.0	0.70%	11.6	0.46%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e0	-2.001e+00	0.3803	12.0	0.40%	5.6	0.22%
Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer	RAACAATGGN	1e0	-1.992e+00	0.3803	96.0	3.20%	67.1	2.67%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e0	-1.987e+00	0.3803	105.0	3.50%	74.5	2.96%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e0	-1.965e+00	0.3847	503.0	16.77%	394.4	15.66%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e0	-1.961e+00	0.3847	7.0	0.23%	2.9	0.11%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e0	-1.961e+00	0.3847	7.0	0.23%	2.5	0.10%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e0	-1.944e+00	0.3847	206.0	6.87%	154.7	6.14%
FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer	TRTTTACTTW	1e0	-1.942e+00	0.3847	111.0	3.70%	79.3	3.15%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-1.906e+00	0.3940	64.0	2.13%	43.5	1.73%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e0	-1.869e+00	0.4064	109.0	3.63%	78.0	3.10%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-1.868e+00	0.4064	215.0	7.17%	162.3	6.45%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e0	-1.859e+00	0.4064	5.0	0.17%	1.7	0.07%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e0	-1.859e+00	0.4064	5.0	0.17%	1.7	0.07%
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e0	-1.850e+00	0.4064	16.0	0.53%	8.1	0.32%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e0	-1.813e+00	0.4156	23.0	0.77%	13.1	0.52%
LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer	ADAAATATCT	1e0	-1.776e+00	0.4282	175.0	5.83%	131.6	5.23%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e0	-1.758e+00	0.4330	132.0	4.40%	97.4	3.87%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer	TBGCACGCAA	1e0	-1.743e+00	0.4368	47.0	1.57%	31.3	1.24%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-1.743e+00	0.4368	279.0	9.30%	215.6	8.56%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-1.711e+00	0.4453	87.0	2.90%	62.2	2.47%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e0	-1.687e+00	0.4534	140.0	4.67%	104.9	4.17%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e0	-1.684e+00	0.4534	21.0	0.70%	12.8	0.51%
ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer	TGGGGAAGGGCM	1e0	-1.679e+00	0.4534	70.0	2.33%	49.7	1.97%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e0	-1.635e+00	0.4687	33.0	1.10%	21.3	0.85%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e0	-1.598e+00	0.4835	15.0	0.50%	8.7	0.35%
ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer	RGGGCACTAACY	1e0	-1.585e+00	0.4868	55.0	1.83%	38.3	1.52%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-1.558e+00	0.4969	47.0	1.57%	32.9	1.31%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e0	-1.524e+00	0.5109	31.0	1.03%	20.0	0.79%
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e0	-1.491e+00	0.5248	40.0	1.33%	27.5	1.09%
DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer	YDGHTACAWTGTADC	1e0	-1.476e+00	0.5294	20.0	0.67%	12.5	0.50%
KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer	RGKGGGCGKGGC	1e0	-1.465e+00	0.5322	141.0	4.70%	107.8	4.28%
RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer	TGCATGCA	1e0	-1.426e+00	0.5503	254.0	8.47%	199.2	7.91%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e0	-1.425e+00	0.5503	46.0	1.53%	32.0	1.27%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-1.408e+00	0.5537	42.0	1.40%	29.6	1.17%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	-1.408e+00	0.5537	21.0	0.70%	13.3	0.53%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-1.399e+00	0.5537	104.0	3.47%	78.5	3.12%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e0	-1.399e+00	0.5537	4.0	0.13%	1.5	0.06%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e0	-1.393e+00	0.5537	56.0	1.87%	40.9	1.62%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-1.390e+00	0.5537	75.0	2.50%	55.9	2.22%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e0	-1.379e+00	0.5537	110.0	3.67%	83.4	3.31%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-1.317e+00	0.5826	31.0	1.03%	21.1	0.84%
Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer	GGGAAAAMCCCG	1e0	-1.281e+00	0.5936	15.0	0.50%	9.1	0.36%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e0	-1.281e+00	0.5936	15.0	0.50%	9.6	0.38%
ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer	AAGGKGRCGCAGGCA	1e0	-1.281e+00	0.5936	15.0	0.50%	9.8	0.39%
Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer	AGGVNCCTTTGT	1e0	-1.268e+00	0.5983	70.0	2.33%	52.2	2.07%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e0	-1.238e+00	0.6134	24.0	0.80%	17.0	0.67%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e0	-1.219e+00	0.6185	2.0	0.07%	0.4	0.02%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e0	-1.219e+00	0.6185	2.0	0.07%	0.7	0.03%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e0	-1.213e+00	0.6185	140.0	4.67%	109.9	4.36%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e0	-1.190e+00	0.6260	25.0	0.83%	17.4	0.69%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e0	-1.190e+00	0.6260	25.0	0.83%	17.4	0.69%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e0	-1.159e+00	0.6427	35.0	1.17%	25.1	1.00%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e0	-1.107e+00	0.6730	93.0	3.10%	72.7	2.89%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-1.093e+00	0.6794	37.0	1.23%	27.3	1.08%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e0	-1.064e+00	0.6956	33.0	1.10%	24.4	0.97%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e0	-1.059e+00	0.6957	6.0	0.20%	3.8	0.15%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-1.021e+00	0.7185	55.0	1.83%	43.0	1.71%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e0	-9.921e-01	0.7321	11.0	0.37%	7.7	0.31%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-9.921e-01	0.7321	11.0	0.37%	7.7	0.31%
IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer	CACGTGCC	1e0	-9.895e-01	0.7321	128.0	4.27%	102.3	4.06%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-9.745e-01	0.7376	36.0	1.20%	27.2	1.08%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e0	-9.700e-01	0.7376	31.0	1.03%	23.5	0.93%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e0	-9.655e-01	0.7376	3.0	0.10%	1.7	0.07%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e0	-9.637e-01	0.7376	113.0	3.77%	90.7	3.60%
PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer	NNBCACGTGN	1e0	-9.502e-01	0.7408	131.0	4.37%	105.4	4.19%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e0	-9.375e-01	0.7466	70.0	2.33%	55.0	2.19%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-9.225e-01	0.7541	38.0	1.27%	29.9	1.19%
Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer	GCCACRCCCACY	1e0	-8.910e-01	0.7745	18.0	0.60%	13.4	0.53%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-8.877e-01	0.7745	13.0	0.43%	9.1	0.36%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-8.785e-01	0.7766	237.0	7.90%	194.7	7.73%
Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer	GCTATTTTTAGC	1e0	-8.558e-01	0.7906	19.0	0.63%	14.5	0.58%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	RGGTCADNNAGAGGTCAV	1e0	-8.465e-01	0.7942	4.0	0.13%	2.8	0.11%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e0	-8.461e-01	0.7942	205.0	6.83%	168.3	6.68%
SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer	WNBCACGTGA	1e0	-8.368e-01	0.7943	82.0	2.73%	66.4	2.64%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e0	-8.310e-01	0.7952	339.0	11.30%	280.7	11.15%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e0	-8.208e-01	0.7996	89.0	2.97%	72.8	2.89%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-8.113e-01	0.8035	26.0	0.87%	20.3	0.81%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e0	-7.586e-01	0.8430	40.0	1.33%	32.7	1.30%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-7.456e-01	0.8500	95.0	3.17%	78.8	3.13%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e0	-7.201e-01	0.8680	30.0	1.00%	24.7	0.98%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-7.195e-01	0.8680	128.0	4.27%	106.8	4.24%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-7.028e-01	0.8751	105.0	3.50%	87.8	3.49%
DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer	TWGHWACAWTGTWDC	1e0	-6.923e-01	0.8803	19.0	0.63%	15.7	0.62%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-6.892e-01	0.8803	2790.0	93.00%	2340.6	92.96%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e0	-6.860e-01	0.8803	13.0	0.43%	10.8	0.43%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-6.747e-01	0.8838	7.0	0.23%	6.0	0.24%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-6.693e-01	0.8847	20.0	0.67%	16.9	0.67%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-6.588e-01	0.8900	14.0	0.47%	11.2	0.45%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-6.402e-01	0.9028	8.0	0.27%	6.2	0.24%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e0	-6.092e-01	0.9028	1.0	0.03%	0.0	0.00%
ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer	MACCTTCYATGGCTCCCTAKTGCCY	1e0	-6.092e-01	0.9028	1.0	0.03%	0.3	0.01%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e0	-6.092e-01	0.9028	1.0	0.03%	0.0	0.00%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e0	-6.092e-01	0.9028	1.0	0.03%	0.0	0.00%
ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer	CCTCATGGTGYCYTWYTCCCTTGTG	1e0	-6.092e-01	0.9028	1.0	0.03%	0.0	0.00%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e0	-6.092e-01	0.9028	1.0	0.03%	0.0	0.00%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e0	-6.092e-01	0.9028	1.0	0.03%	0.7	0.03%
EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	-6.092e-01	0.9028	1.0	0.03%	0.0	0.00%
Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer	TGTCANYT	1e0	-6.089e-01	0.9028	496.0	16.53%	418.6	16.63%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-6.058e-01	0.9028	30.0	1.00%	25.7	1.02%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-5.700e-01	0.9234	2.0	0.07%	1.4	0.06%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-5.681e-01	0.9234	224.0	7.47%	190.8	7.58%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-5.633e-01	0.9234	11.0	0.37%	9.4	0.37%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e0	-5.633e-01	0.9234	11.0	0.37%	10.0	0.40%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e0	-5.434e-01	0.9326	12.0	0.40%	10.3	0.41%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-5.418e-01	0.9326	3.0	0.10%	2.2	0.09%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e0	-5.397e-01	0.9326	20.0	0.67%	17.9	0.71%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e0	-5.378e-01	0.9326	42.0	1.40%	36.4	1.45%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-5.325e-01	0.9326	204.0	6.80%	174.9	6.95%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e0	-5.282e-01	0.9326	105.0	3.50%	90.1	3.58%
ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer	ARGAGGMCAAAATGW	1e0	-5.253e-01	0.9326	13.0	0.43%	11.5	0.46%
Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer	YTGWCADY	1e0	-5.251e-01	0.9326	458.0	15.27%	389.4	15.47%
KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer	GGGGGTGTGTCC	1e0	-5.122e-01	0.9326	37.0	1.23%	32.2	1.28%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e0	-5.105e-01	0.9326	22.0	0.73%	19.4	0.77%
ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer	GTGGGCCCCA	1e0	-5.088e-01	0.9326	14.0	0.47%	12.9	0.51%
Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer	SCTGTCAVTCAV	1e0	-5.088e-01	0.9326	14.0	0.47%	12.3	0.49%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e0	-5.050e-01	0.9326	45.0	1.50%	39.1	1.55%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-4.997e-01	0.9326	5.0	0.17%	4.0	0.16%
ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer	GRTGMTRGAGCC	1e0	-4.976e-01	0.9326	53.0	1.77%	46.9	1.86%
PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer	AAGAACATWHTGTTC	1e0	-4.795e-01	0.9358	16.0	0.53%	14.7	0.58%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e0	-4.664e-01	0.9445	17.0	0.57%	15.7	0.62%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-4.454e-01	0.9609	59.0	1.97%	52.8	2.10%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-4.318e-01	0.9703	20.0	0.67%	18.8	0.74%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e0	-4.243e-01	0.9738	386.0	12.87%	332.3	13.20%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e0	-4.152e-01	0.9789	63.0	2.10%	56.8	2.26%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e0	-3.936e-01	0.9965	24.0	0.80%	22.1	0.88%
Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer	GCTATTTTTGGM	1e0	-3.932e-01	0.9965	74.0	2.47%	66.1	2.63%
SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer	TWCCAWWTWTGG	1e0	-3.771e-01	1.0000	26.0	0.87%	24.9	0.99%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e0	-3.515e-01	1.0000	39.0	1.30%	36.5	1.45%
SeqBias: CA-repeat	CACACACACA	1e0	-3.503e-01	1.0000	647.0	21.57%	557.1	22.13%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e0	-3.360e-01	1.0000	100.0	3.33%	90.5	3.59%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e0	-3.359e-01	1.0000	21.0	0.70%	20.9	0.83%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e0	-3.334e-01	1.0000	51.0	1.70%	47.1	1.87%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e0	-3.295e-01	1.0000	22.0	0.73%	21.2	0.84%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-3.285e-01	1.0000	33.0	1.10%	31.9	1.27%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e0	-3.241e-01	1.0000	70.0	2.33%	64.5	2.56%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-3.217e-01	1.0000	6.0	0.20%	6.0	0.24%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-3.203e-01	1.0000	7.0	0.23%	7.7	0.31%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-3.146e-01	1.0000	9.0	0.30%	9.5	0.38%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e0	-3.110e-01	1.0000	10.0	0.33%	10.9	0.43%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-2.954e-01	1.0000	76.0	2.53%	70.9	2.82%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e0	-2.902e-01	1.0000	29.0	0.97%	28.3	1.12%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e0	-2.874e-01	1.0000	2.0	0.07%	2.2	0.09%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-2.874e-01	1.0000	2.0	0.07%	2.3	0.09%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-2.874e-01	1.0000	2.0	0.07%	2.9	0.11%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-2.853e-01	1.0000	30.0	1.00%	30.0	1.19%
Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer	NNYTAATTAR	1e0	-2.826e-01	1.0000	96.0	3.20%	88.9	3.53%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e0	-2.671e-01	1.0000	45.0	1.50%	43.1	1.71%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e0	-2.654e-01	1.0000	21.0	0.70%	21.7	0.86%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e0	-2.500e-01	1.0000	25.0	0.83%	25.5	1.01%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e0	-2.358e-01	1.0000	29.0	0.97%	29.4	1.17%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e0	-2.290e-01	1.0000	31.0	1.03%	32.0	1.27%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e0	-2.226e-01	1.0000	10.0	0.33%	11.2	0.44%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-2.198e-01	1.0000	8.0	0.27%	9.4	0.37%
ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer	GAGCCTGGTACTGWGCCTGR	1e0	-2.078e-01	1.0000	21.0	0.70%	22.9	0.91%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e0	-2.009e-01	1.0000	64.0	2.13%	62.8	2.49%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e0	-1.929e-01	1.0000	4.0	0.13%	5.8	0.23%
ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer	GNCTGTASTRNTGBCTCHTT	1e0	-1.929e-01	1.0000	4.0	0.13%	5.7	0.23%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e0	-1.929e-01	1.0000	4.0	0.13%	5.9	0.24%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer	AGGTCANTGACCTB	1e0	-1.857e-01	1.0000	31.0	1.03%	32.6	1.30%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-1.749e-01	1.0000	36.0	1.20%	37.7	1.50%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e0	-1.548e-01	1.0000	27.0	0.90%	29.9	1.19%
IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	CTTTCANTATGACTV	1e0	-1.541e-01	1.0000	9.0	0.30%	11.2	0.45%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-1.535e-01	1.0000	28.0	0.93%	30.9	1.23%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e0	-1.444e-01	1.0000	7.0	0.23%	9.7	0.38%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-1.439e-01	1.0000	89.0	2.97%	87.3	3.47%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	-1.397e-01	1.0000	38.0	1.27%	40.9	1.62%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e0	-1.235e-01	1.0000	24.0	0.80%	28.0	1.11%
Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	TATGCWAATBAV	1e0	-1.235e-01	1.0000	24.0	0.80%	27.1	1.07%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e0	-1.234e-01	1.0000	65.0	2.17%	66.5	2.64%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-1.194e-01	1.0000	14.0	0.47%	17.3	0.69%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e0	-1.179e-01	1.0000	33.0	1.10%	36.6	1.45%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-9.993e-02	1.0000	69.0	2.30%	71.3	2.83%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e0	-9.971e-02	1.0000	1.0	0.03%	2.1	0.09%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-9.554e-02	1.0000	25.0	0.83%	29.4	1.17%
Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer	WATGCAAATGAG	1e0	-9.474e-02	1.0000	31.0	1.03%	35.9	1.43%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e0	-9.404e-02	1.0000	33.0	1.10%	38.0	1.51%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer	GGGGGAATCCCC	1e0	-8.774e-02	1.0000	6.0	0.20%	9.6	0.38%
SeqBias: CG-repeat	CGCGCGCGCG	1e0	-8.621e-02	1.0000	47.0	1.57%	51.5	2.05%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e0	-8.167e-02	1.0000	12.0	0.40%	16.2	0.64%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e0	-7.728e-02	1.0000	60.0	2.00%	64.6	2.56%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-7.454e-02	1.0000	32.0	1.07%	37.5	1.49%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-7.413e-02	1.0000	27.0	0.90%	32.6	1.29%
HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer	TTTTATKRGG	1e0	-6.173e-02	1.0000	99.0	3.30%	102.1	4.05%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-5.861e-02	1.0000	34.0	1.13%	40.5	1.61%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e0	-5.519e-02	1.0000	3.0	0.10%	6.3	0.25%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e0	-4.487e-02	1.0000	552.0	18.40%	508.6	20.20%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	-4.442e-02	1.0000	29.0	0.97%	36.7	1.46%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-4.423e-02	1.0000	1.0	0.03%	3.1	0.12%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e0	-4.399e-02	1.0000	28.0	0.93%	35.6	1.41%
ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer	NGNTCTAGAACCNGV	1e0	-4.239e-02	1.0000	25.0	0.83%	32.4	1.29%
PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer	NGTGTTCAVTSAAGCGKAAA	1e0	-3.910e-02	1.0000	2.0	0.07%	5.3	0.21%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e0	-3.910e-02	1.0000	2.0	0.07%	5.5	0.22%
Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer	KBCTACCTGW	1e0	-2.588e-02	1.0000	18.0	0.60%	26.4	1.05%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e0	-2.333e-02	1.0000	47.0	1.57%	57.7	2.29%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-2.225e-02	1.0000	39.0	1.30%	50.0	1.98%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-2.088e-02	1.0000	6.0	0.20%	12.1	0.48%
ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer	WDNCTGGGCA	1e0	-2.005e-02	1.0000	151.0	5.03%	159.0	6.31%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e0	-1.992e-02	1.0000	1.0	0.03%	4.7	0.18%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-1.990e-02	1.0000	2.0	0.07%	6.5	0.26%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e0	-1.291e-02	1.0000	4.0	0.13%	10.7	0.43%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-1.291e-02	1.0000	4.0	0.13%	10.6	0.42%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e0	-1.268e-02	1.0000	25.0	0.83%	36.9	1.47%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-1.004e-02	1.0000	2.0	0.07%	7.2	0.29%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	AGGTCAAGGTCA	1e0	-9.870e-03	1.0000	5.0	0.17%	12.6	0.50%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e0	-6.267e-03	1.0000	24.0	0.80%	37.8	1.50%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e0	-6.148e-03	1.0000	64.0	2.13%	80.2	3.18%
ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer	GAGSCCGAGC	1e0	-5.667e-03	1.0000	5.0	0.17%	13.2	0.53%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e0	-5.563e-03	1.0000	321.0	10.70%	324.4	12.89%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-5.525e-03	1.0000	191.0	6.37%	204.0	8.10%
Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATATTC	1e0	-5.027e-03	1.0000	2.0	0.07%	8.1	0.32%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e0	-5.027e-03	1.0000	2.0	0.07%	8.3	0.33%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e0	-4.211e-03	1.0000	262.0	8.73%	272.1	10.81%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-3.975e-03	1.0000	4.0	0.13%	12.9	0.51%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	-3.631e-03	1.0000	44.0	1.47%	61.9	2.46%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e0	-3.118e-03	1.0000	15.0	0.50%	28.7	1.14%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-2.648e-03	1.0000	81.0	2.70%	101.0	4.01%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e0	-2.428e-03	1.0000	245.0	8.17%	260.1	10.33%
Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer	TTRAGTGSYK	1e0	-1.398e-03	1.0000	238.0	7.93%	257.3	10.22%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-1.382e-03	1.0000	28.0	0.93%	46.5	1.85%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-7.500e-04	1.0000	42.0	1.40%	64.4	2.56%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-4.960e-04	1.0000	152.0	5.07%	180.5	7.17%
ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer	SMCAGTCWGAKGGAGGAGGC	1e0	-3.870e-04	1.0000	1.0	0.03%	10.0	0.40%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-3.320e-04	1.0000	4.0	0.13%	16.3	0.65%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e0	-3.240e-04	1.0000	160.0	5.33%	190.9	7.58%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e0	-3.170e-04	1.0000	119.0	3.97%	149.1	5.92%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-1.980e-04	1.0000	92.0	3.07%	123.4	4.90%
Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer	BTBRAGTGSN	1e0	-4.700e-05	1.0000	199.0	6.63%	238.9	9.49%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e0	-4.300e-05	1.0000	51.0	1.70%	83.5	3.32%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-2.000e-05	1.0000	77.0	2.57%	115.8	4.60%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e0	-1.800e-05	1.0000	83.0	2.77%	122.8	4.88%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e0	-1.000e-06	1.0000	24.0	0.80%	58.2	2.31%
Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer	RGAGAGAG	1e0	-0.000e+00	1.0000	255.0	8.50%	338.8	13.45%
PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer	HAATAAAGNN	1e0	-0.000e+00	1.0000	79.0	2.63%	149.0	5.92%
SeqBias: TA-repeat	TATATATATA	1e0	-0.000e+00	1.0000	208.0	6.93%	324.7	12.90%
KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer	ARGAATAWWN	1e0	-0.000e+00	1.0000	64.0	2.13%	144.6	5.74%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-0.000e+00	1.0000	0.0	0.00%	1.2	0.05%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e0	-0.000e+00	1.0000	0.0	0.00%	2.0	0.08%
OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATWATTCATGA	1e0	-0.000e+00	1.0000	0.0	0.00%	1.7	0.07%
ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer	GARTGGTCATCGCCC	1e0	0.000e+00	1.0000	0.0	0.00%	0.3	0.01%
OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	ATGAATATTCATGAG	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer	GGGTTTTGAAGGATGARTAGGAGTT	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%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
 Ik-1	NHTTGGGAATRCC	1e0	0.000e+00	1.0000	3000.0	100.00%	2517.8	100.00%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
ZNF528(Zf)/HEK293-ZNF528.GFP-ChIP-Seq(GSE58341)/Homer	AGAAATGACTTCCCT	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e0	0.000e+00	1.0000	22.0	0.73%	81.2	3.23%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	0.000e+00	1.0000	0.0	0.00%	4.8	0.19%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e0	0.000e+00	1.0000	0.0	0.00%	6.6	0.26%