Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 4422)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 21022)	% of Background Sequences with Motif
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e-231	-5.330e+02	0.0000	1522.0	34.42%	3100.8	14.75%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e-197	-4.556e+02	0.0000	980.0	22.16%	1613.6	7.68%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e-72	-1.659e+02	0.0000	2087.0	47.20%	7157.0	34.05%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e-57	-1.321e+02	0.0000	585.0	13.23%	1368.4	6.51%
SeqBias: CG-repeat	CGCGCGCGCG	1e-51	-1.195e+02	0.0000	786.0	17.77%	2144.4	10.20%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e-44	-1.021e+02	0.0000	430.0	9.72%	978.9	4.66%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e-43	-1.009e+02	0.0000	430.0	9.72%	983.6	4.68%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e-43	-9.906e+01	0.0000	662.0	14.97%	1805.0	8.59%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e-42	-9.794e+01	0.0000	435.0	9.84%	1012.7	4.82%
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e-42	-9.751e+01	0.0000	576.0	13.03%	1502.9	7.15%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e-40	-9.317e+01	0.0000	669.0	15.13%	1866.0	8.88%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e-40	-9.252e+01	0.0000	1087.0	24.58%	3506.2	16.68%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e-39	-9.130e+01	0.0000	493.0	11.15%	1241.9	5.91%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e-34	-8.043e+01	0.0000	606.0	13.70%	1711.7	8.14%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e-31	-7.231e+01	0.0000	901.0	20.38%	2923.8	13.91%
PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer	NNBCACGTGN	1e-30	-6.953e+01	0.0000	990.0	22.39%	3312.7	15.76%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e-30	-6.941e+01	0.0000	2076.0	46.95%	8078.4	38.44%
IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer	CACGTGCC	1e-28	-6.473e+01	0.0000	1347.0	30.46%	4874.2	23.19%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e-23	-5.474e+01	0.0000	508.0	11.49%	1517.6	7.22%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e-23	-5.464e+01	0.0000	420.0	9.50%	1188.0	5.65%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e-23	-5.390e+01	0.0000	805.0	18.20%	2703.3	12.86%
SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer	WNBCACGTGA	1e-23	-5.351e+01	0.0000	1102.0	24.92%	3951.6	18.80%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e-22	-5.182e+01	0.0000	358.0	8.10%	978.4	4.66%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e-22	-5.104e+01	0.0000	133.0	3.01%	237.1	1.13%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e-21	-4.898e+01	0.0000	826.0	18.68%	2840.3	13.51%
KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer	RGKGGGCGKGGC	1e-17	-3.972e+01	0.0000	551.0	12.46%	1812.7	8.62%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e-17	-3.956e+01	0.0000	132.0	2.99%	270.8	1.29%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e-16	-3.815e+01	0.0000	408.0	9.23%	1262.1	6.00%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e-14	-3.424e+01	0.0000	795.0	17.98%	2883.5	13.72%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e-14	-3.339e+01	0.0000	1421.0	32.13%	5639.4	26.83%
ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer	TGGGGAAGGGCM	1e-13	-3.182e+01	0.0000	319.0	7.21%	971.0	4.62%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e-13	-3.075e+01	0.0000	337.0	7.62%	1049.5	4.99%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e-13	-3.053e+01	0.0000	2982.0	67.44%	13043.2	62.06%
KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer	GGGGGTGTGTCC	1e-12	-2.822e+01	0.0000	240.0	5.43%	700.0	3.33%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer	TBGCACGCAA	1e-12	-2.796e+01	0.0000	1022.0	23.11%	3957.1	18.83%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e-11	-2.635e+01	0.0000	159.0	3.60%	418.8	1.99%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e-10	-2.510e+01	0.0000	151.0	3.41%	397.8	1.89%
Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer	GCCACRCCCACY	1e-10	-2.325e+01	0.0000	130.0	2.94%	335.0	1.59%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e-9	-2.214e+01	0.0000	496.0	11.22%	1783.7	8.49%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e-8	-2.036e+01	0.0000	62.0	1.40%	124.4	0.59%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-8	-2.014e+01	0.0000	448.0	10.13%	1609.3	7.66%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e-8	-1.886e+01	0.0000	290.0	6.56%	976.2	4.64%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e-8	-1.860e+01	0.0000	1615.0	36.52%	6831.0	32.50%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e-7	-1.825e+01	0.0000	104.0	2.35%	271.8	1.29%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e-7	-1.762e+01	0.0000	194.0	4.39%	609.6	2.90%
SeqBias: TA-repeat	TATATATATA	1e-7	-1.748e+01	0.0000	3935.0	88.99%	18124.1	86.23%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e-7	-1.645e+01	0.0000	272.0	6.15%	931.0	4.43%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e-6	-1.515e+01	0.0000	504.0	11.40%	1921.8	9.14%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e-6	-1.459e+01	0.0000	202.0	4.57%	669.1	3.18%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e-6	-1.455e+01	0.0000	1431.0	32.36%	6090.0	28.98%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e-5	-1.335e+01	0.0000	127.0	2.87%	388.0	1.85%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e-5	-1.232e+01	0.0000	91.0	2.06%	261.6	1.24%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-5	-1.163e+01	0.0001	774.0	17.50%	3181.7	15.14%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e-4	-1.113e+01	0.0001	223.0	5.04%	794.4	3.78%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e-4	-1.083e+01	0.0001	127.0	2.87%	410.9	1.95%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e-4	-1.076e+01	0.0001	573.0	12.96%	2307.3	10.98%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e-4	-1.015e+01	0.0003	1008.0	22.80%	4279.8	20.36%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e-4	-9.903e+00	0.0003	43.0	0.97%	105.8	0.50%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e-4	-9.698e+00	0.0004	830.0	18.77%	3484.4	16.58%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e-4	-9.490e+00	0.0005	692.0	15.65%	2869.0	13.65%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e-3	-9.164e+00	0.0007	273.0	6.17%	1033.5	4.92%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e-3	-8.606e+00	0.0011	69.0	1.56%	206.7	0.98%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e-3	-8.606e+00	0.0011	69.0	1.56%	206.7	0.98%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e-3	-8.491e+00	0.0012	78.0	1.76%	241.7	1.15%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e-3	-8.137e+00	0.0017	277.0	6.26%	1068.6	5.08%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e-3	-8.116e+00	0.0018	87.0	1.97%	279.4	1.33%
Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer	GGGAAAAMCCCG	1e-3	-7.484e+00	0.0032	207.0	4.68%	780.0	3.71%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e-3	-7.345e+00	0.0037	180.0	4.07%	668.8	3.18%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e-3	-7.345e+00	0.0037	475.0	10.74%	1954.8	9.30%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e-3	-7.293e+00	0.0038	559.0	12.64%	2331.3	11.09%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e-2	-6.650e+00	0.0071	41.0	0.93%	116.5	0.55%
ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer	GAGSCCGAGC	1e-2	-6.458e+00	0.0084	49.0	1.11%	147.4	0.70%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e-2	-6.285e+00	0.0099	109.0	2.46%	387.8	1.85%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e-2	-5.920e+00	0.0140	199.0	4.50%	773.0	3.68%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e-2	-5.896e+00	0.0142	245.0	5.54%	973.7	4.63%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e-2	-5.888e+00	0.0142	30.0	0.68%	81.4	0.39%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e-2	-5.718e+00	0.0165	339.0	7.67%	1391.7	6.62%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e-2	-5.375e+00	0.0230	41.0	0.93%	125.5	0.60%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer	GGGGGAATCCCC	1e-2	-5.363e+00	0.0230	37.0	0.84%	110.1	0.52%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e-2	-5.354e+00	0.0230	482.0	10.90%	2042.6	9.72%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e-2	-5.245e+00	0.0252	114.0	2.58%	422.7	2.01%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e-2	-5.180e+00	0.0266	330.0	7.46%	1365.5	6.50%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e-2	-4.913e+00	0.0343	39.0	0.88%	121.8	0.58%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e-2	-4.910e+00	0.0343	118.0	2.67%	444.3	2.11%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e-2	-4.832e+00	0.0363	70.0	1.58%	245.4	1.17%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e-2	-4.661e+00	0.0425	486.0	10.99%	2083.2	9.91%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e-1	-4.499e+00	0.0495	503.0	11.37%	2166.4	10.31%
Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer	RGAGAGAG	1e-1	-4.296e+00	0.0599	1628.0	36.82%	7401.6	35.22%
HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer	VCAGCTGBNN	1e-1	-4.244e+00	0.0624	851.0	19.24%	3775.2	17.96%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e-1	-4.121e+00	0.0698	1290.0	29.17%	5825.5	27.72%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e-1	-4.106e+00	0.0701	38.0	0.86%	124.9	0.59%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e-1	-4.071e+00	0.0718	100.0	2.26%	381.3	1.81%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e-1	-4.026e+00	0.0743	20.0	0.45%	56.5	0.27%
Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer	CCTGCTGAGH	1e-1	-3.883e+00	0.0848	378.0	8.55%	1620.9	7.71%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e-1	-3.855e+00	0.0863	946.0	21.39%	4235.6	20.15%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-1	-3.724e+00	0.0973	582.0	13.16%	2558.7	12.17%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e-1	-3.656e+00	0.1031	443.0	10.02%	1924.5	9.16%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e-1	-3.583e+00	0.1098	51.0	1.15%	182.6	0.87%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e-1	-3.534e+00	0.1141	96.0	2.17%	373.5	1.78%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-1	-3.418e+00	0.1268	521.0	11.78%	2291.4	10.90%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e-1	-3.399e+00	0.1280	1339.0	30.28%	6098.7	29.02%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e-1	-3.388e+00	0.1281	60.0	1.36%	222.3	1.06%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e-1	-3.322e+00	0.1356	1085.0	24.54%	4913.0	23.38%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e-1	-3.192e+00	0.1529	156.0	3.53%	644.0	3.06%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e-1	-3.058e+00	0.1731	449.0	10.15%	1976.2	9.40%
DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer	TWGHWACAWTGTWDC	1e-1	-3.016e+00	0.1789	367.0	8.30%	1602.3	7.62%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e-1	-3.009e+00	0.1789	1153.0	26.07%	5251.7	24.99%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e-1	-2.950e+00	0.1876	109.0	2.46%	441.6	2.10%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e-1	-2.936e+00	0.1884	699.0	15.81%	3137.3	14.93%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e-1	-2.849e+00	0.2036	580.0	13.12%	2590.9	12.33%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e-1	-2.839e+00	0.2038	15.0	0.34%	45.6	0.22%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-1	-2.810e+00	0.2081	739.0	16.71%	3330.7	15.85%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e-1	-2.730e+00	0.2233	121.0	2.74%	499.1	2.37%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e-1	-2.624e+00	0.2462	61.0	1.38%	238.5	1.13%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e-1	-2.609e+00	0.2477	42.0	0.95%	157.3	0.75%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e-1	-2.562e+00	0.2573	231.0	5.22%	999.0	4.75%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e-1	-2.511e+00	0.2684	302.0	6.83%	1325.8	6.31%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e-1	-2.498e+00	0.2698	35.0	0.79%	129.9	0.62%
ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer	GTGGGCCCCA	1e-1	-2.399e+00	0.2954	49.0	1.11%	190.4	0.91%
Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer	GCTATTTTTAGC	1e-1	-2.355e+00	0.3062	384.0	8.68%	1709.2	8.13%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e0	-2.302e+00	0.3199	185.0	4.18%	799.1	3.80%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e0	-2.262e+00	0.3303	162.0	3.66%	696.6	3.31%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-2.260e+00	0.3303	229.0	5.18%	1001.3	4.76%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e0	-2.245e+00	0.3307	130.0	2.94%	552.1	2.63%
Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer	GGGGCTYGKCTGGGA	1e0	-2.218e+00	0.3368	32.0	0.72%	120.2	0.57%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e0	-2.203e+00	0.3394	3439.0	77.77%	16180.1	76.98%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	-2.173e+00	0.3468	82.0	1.85%	339.5	1.62%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e0	-2.165e+00	0.3468	158.0	3.57%	681.1	3.24%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e0	-2.065e+00	0.3805	435.0	9.84%	1960.3	9.33%
ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer	ARGAGGMCAAAATGW	1e0	-2.040e+00	0.3870	143.0	3.23%	617.9	2.94%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e0	-1.964e+00	0.4146	971.0	21.96%	4473.3	21.28%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-1.885e+00	0.4450	655.0	14.81%	2997.8	14.26%
IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	CTTTCANTATGACTV	1e0	-1.867e+00	0.4497	187.0	4.23%	824.2	3.92%
LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer	CARTGGAGCGCRYTTGCATT	1e0	-1.842e+00	0.4579	7.0	0.16%	21.3	0.10%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e0	-1.818e+00	0.4656	102.0	2.31%	438.3	2.09%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	MACAGGAAGT	1e0	-1.812e+00	0.4656	185.0	4.18%	817.8	3.89%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e0	-1.783e+00	0.4748	410.0	9.27%	1860.5	8.85%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e0	-1.737e+00	0.4936	26.0	0.59%	101.9	0.48%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e0	-1.719e+00	0.4991	143.0	3.23%	628.6	2.99%
OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	ATGAATATTCATGAG	1e0	-1.620e+00	0.5468	13.0	0.29%	47.2	0.22%
ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer	RGGGCACTAACY	1e0	-1.498e+00	0.6138	533.0	12.05%	2454.5	11.68%
ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer	GTCWGCTGTYYCTCT	1e0	-1.464e+00	0.6306	55.0	1.24%	235.9	1.12%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e0	-1.461e+00	0.6306	115.0	2.60%	509.4	2.42%
Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer	NAACAGCTGG	1e0	-1.441e+00	0.6359	419.0	9.48%	1924.3	9.16%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e0	-1.422e+00	0.6438	585.0	13.23%	2705.0	12.87%
EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	-1.406e+00	0.6495	7.0	0.16%	24.8	0.12%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e0	-1.368e+00	0.6704	455.0	10.29%	2098.2	9.98%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e0	-1.346e+00	0.6807	36.0	0.81%	152.5	0.73%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e0	-1.343e+00	0.6807	124.0	2.80%	555.8	2.64%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e0	-1.318e+00	0.6905	103.0	2.33%	459.7	2.19%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e0	-1.243e+00	0.7393	676.0	15.29%	3148.2	14.98%
ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer	CCTCATGGTGYCYTWYTCCCTTGTG	1e0	-1.197e+00	0.7691	20.0	0.45%	83.2	0.40%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e0	-1.128e+00	0.8191	1542.0	34.87%	7258.1	34.53%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-1.111e+00	0.8277	148.0	3.35%	677.6	3.22%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-1.109e+00	0.8277	4418.0	99.91%	20990.2	99.87%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-1.093e+00	0.8316	259.0	5.86%	1198.4	5.70%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-1.052e+00	0.8553	4422.0	100.00%	21012.0	99.97%
SeqBias: G/A bias	RRRRRRRRRR	1e0	-1.052e+00	0.8553	4422.0	100.00%	21012.3	99.97%
FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer	WWTRTAAACAVG	1e0	-1.024e+00	0.8743	1540.0	34.83%	7263.1	34.56%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-1.022e+00	0.8743	2.0	0.05%	6.4	0.03%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e0	-1.018e+00	0.8743	43.0	0.97%	192.3	0.92%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e0	-9.941e-01	0.8840	1092.0	24.69%	5143.6	24.47%
Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)	NNAYTTCCTGHN	1e0	-9.936e-01	0.8840	678.0	15.33%	3183.0	15.14%
PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer	NGTGTTCAVTSAAGCGKAAA	1e0	-9.902e-01	0.8840	80.0	1.81%	365.7	1.74%
ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer	SMCAGTCWGAKGGAGGAGGC	1e0	-9.776e-01	0.8840	7.0	0.16%	28.9	0.14%
OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATWATTCATGA	1e0	-9.526e-01	0.8993	40.0	0.90%	180.3	0.86%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e0	-9.498e-01	0.8993	380.0	8.59%	1779.5	8.47%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-9.425e-01	0.8993	38.0	0.86%	171.9	0.82%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e0	-9.027e-01	0.9285	901.0	20.38%	4250.7	20.22%
DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer	YDGHTACAWTGTADC	1e0	-8.795e-01	0.9447	257.0	5.81%	1204.9	5.73%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-8.355e-01	0.9814	886.0	20.04%	4188.3	19.93%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e0	-8.174e-01	0.9936	110.0	2.49%	514.6	2.45%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e0	-8.152e-01	0.9936	497.0	11.24%	2346.4	11.16%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e0	-8.096e-01	0.9936	126.0	2.85%	590.5	2.81%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-7.684e-01	1.0000	561.0	12.69%	2655.0	12.63%
Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer	RAACAATGGN	1e0	-7.670e-01	1.0000	1503.0	33.99%	7128.5	33.92%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e0	-7.570e-01	1.0000	780.0	17.64%	3696.5	17.59%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e0	-7.448e-01	1.0000	17.0	0.38%	78.7	0.37%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e0	-7.326e-01	1.0000	1090.0	24.65%	5172.5	24.61%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-7.002e-01	1.0000	93.0	2.10%	440.9	2.10%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-6.983e-01	1.0000	210.0	4.75%	996.1	4.74%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e0	-6.655e-01	1.0000	72.0	1.63%	342.2	1.63%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	RGGTCADNNAGAGGTCAV	1e0	-6.636e-01	1.0000	3.0	0.07%	13.3	0.06%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-6.342e-01	1.0000	88.0	1.99%	420.2	2.00%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-6.063e-01	1.0000	647.0	14.63%	3086.0	14.68%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e0	-5.844e-01	1.0000	34.0	0.77%	165.0	0.78%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e0	-5.607e-01	1.0000	275.0	6.22%	1319.2	6.28%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e0	-5.208e-01	1.0000	120.0	2.71%	581.9	2.77%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e0	-4.754e-01	1.0000	124.0	2.80%	604.4	2.88%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e0	-4.752e-01	1.0000	1759.0	39.78%	8406.9	40.00%
ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer	AACATCTGGA	1e0	-4.394e-01	1.0000	223.0	5.04%	1084.9	5.16%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e0	-4.382e-01	1.0000	392.0	8.86%	1895.1	9.02%
Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATATTC	1e0	-4.370e-01	1.0000	193.0	4.36%	940.4	4.47%
ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer	YTKGATAHAGTATTCTWGGTNGGCA	1e0	-4.202e-01	1.0000	118.0	2.67%	580.6	2.76%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-4.143e-01	1.0000	51.0	1.15%	255.0	1.21%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e0	-4.003e-01	1.0000	228.0	5.16%	1113.3	5.30%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e0	-3.651e-01	1.0000	167.0	3.78%	823.0	3.92%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e0	-3.630e-01	1.0000	972.0	21.98%	4685.7	22.29%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e0	-3.188e-01	1.0000	62.0	1.40%	316.0	1.50%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-3.164e-01	1.0000	65.0	1.47%	331.3	1.58%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e0	-3.138e-01	1.0000	12.0	0.27%	66.5	0.32%
ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer	TGGAACAGMA	1e0	-3.123e-01	1.0000	611.0	13.82%	2970.2	14.13%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer	CCATATATGGNM	1e0	-3.109e-01	1.0000	428.0	9.68%	2091.8	9.95%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-2.976e-01	1.0000	22.0	0.50%	118.9	0.57%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e0	-2.546e-01	1.0000	1241.0	28.06%	6004.2	28.57%
PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	GGAAGTGAAAST	1e0	-2.472e-01	1.0000	181.0	4.09%	909.0	4.32%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-2.390e-01	1.0000	335.0	7.58%	1659.0	7.89%
RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer	TGCATGCA	1e0	-2.377e-01	1.0000	1640.0	37.09%	7915.2	37.66%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-2.245e-01	1.0000	9.0	0.20%	54.8	0.26%
ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer	AAGGKGRCGCAGGCA	1e0	-2.126e-01	1.0000	20.0	0.45%	113.8	0.54%
 Ik-1	NHTTGGGAATRCC	1e0	-2.104e-01	1.0000	4422.0	100.00%	21017.6	100.00%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e0	-1.929e-01	1.0000	1753.0	39.64%	8474.6	40.32%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e0	-1.899e-01	1.0000	536.0	12.12%	2644.7	12.58%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	-1.881e-01	1.0000	14.0	0.32%	83.2	0.40%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	GCTGTGGTTW	1e0	-1.834e-01	1.0000	458.0	10.36%	2269.8	10.80%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-1.776e-01	1.0000	320.0	7.24%	1601.8	7.62%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e0	-1.742e-01	1.0000	335.0	7.58%	1675.2	7.97%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e0	-1.739e-01	1.0000	771.0	17.44%	3783.8	18.00%
PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer	AAGAACATWHTGTTC	1e0	-1.730e-01	1.0000	199.0	4.50%	1011.4	4.81%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e0	-1.633e-01	1.0000	403.0	9.11%	2009.9	9.56%
ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer	GAGCCTGGTACTGWGCCTGR	1e0	-1.580e-01	1.0000	36.0	0.81%	201.1	0.96%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e0	-1.566e-01	1.0000	35.0	0.79%	196.9	0.94%
ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer	GARTGGTCATCGCCC	1e0	-1.431e-01	1.0000	43.0	0.97%	239.2	1.14%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-1.419e-01	1.0000	4421.0	99.98%	21014.2	99.98%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-1.383e-01	1.0000	357.0	8.07%	1794.9	8.54%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-1.380e-01	1.0000	2142.0	48.44%	10357.9	49.28%
Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer	AGGVNCCTTTGT	1e0	-1.379e-01	1.0000	780.0	17.64%	3843.3	18.29%
ZNF528(Zf)/HEK293-ZNF528.GFP-ChIP-Seq(GSE58341)/Homer	AGAAATGACTTCCCT	1e0	-1.368e-01	1.0000	2.0	0.05%	17.8	0.08%
Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer	SCTGTCAVTCAV	1e0	-1.279e-01	1.0000	110.0	2.49%	581.3	2.77%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-1.193e-01	1.0000	211.0	4.77%	1085.4	5.16%
Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	TATGCWAATBAV	1e0	-1.138e-01	1.0000	406.0	9.18%	2043.3	9.72%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-9.322e-02	1.0000	1040.0	23.52%	5123.1	24.38%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-8.783e-02	1.0000	76.0	1.72%	419.6	2.00%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-8.674e-02	1.0000	133.0	3.01%	708.6	3.37%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-8.321e-02	1.0000	294.0	6.65%	1509.2	7.18%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer	AGGTCANTGACCTB	1e0	-8.225e-02	1.0000	164.0	3.71%	865.0	4.12%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e0	-7.709e-02	1.0000	832.0	18.82%	4133.8	19.67%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-7.692e-02	1.0000	48.0	1.09%	277.9	1.32%
SeqBias: A/T bias	WWWWWWWWWW	1e0	-7.394e-02	1.0000	4414.0	99.82%	20994.0	99.89%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-7.341e-02	1.0000	433.0	9.79%	2197.7	10.46%
FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer	TRTTTACTTW	1e0	-7.322e-02	1.0000	1397.0	31.59%	6855.5	32.62%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-6.835e-02	1.0000	199.0	4.50%	1046.8	4.98%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-6.108e-02	1.0000	432.0	9.77%	2201.5	10.47%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e0	-6.089e-02	1.0000	793.0	17.93%	3959.2	18.84%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-5.655e-02	1.0000	166.0	3.75%	887.7	4.22%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e0	-5.633e-02	1.0000	65.0	1.47%	372.6	1.77%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-5.294e-02	1.0000	527.0	11.92%	2673.3	12.72%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-5.006e-02	1.0000	4.0	0.09%	37.0	0.18%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-4.864e-02	1.0000	698.0	15.78%	3511.9	16.71%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-4.857e-02	1.0000	152.0	3.44%	822.0	3.91%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e0	-4.442e-02	1.0000	668.0	15.11%	3370.4	16.04%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-4.054e-02	1.0000	149.0	3.37%	811.6	3.86%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer	CTGTTTAC	1e0	-3.291e-02	1.0000	1807.0	40.86%	8874.9	42.23%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e0	-3.031e-02	1.0000	709.0	16.03%	3590.2	17.08%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e0	-2.978e-02	1.0000	849.0	19.20%	4272.4	20.33%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e0	-2.815e-02	1.0000	785.0	17.75%	3964.2	18.86%
ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer	WDNCTGGGCA	1e0	-2.666e-02	1.0000	377.0	8.53%	1966.7	9.36%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e0	-2.659e-02	1.0000	30.0	0.68%	197.8	0.94%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-2.615e-02	1.0000	627.0	14.18%	3197.2	15.21%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-2.435e-02	1.0000	242.0	5.47%	1296.6	6.17%
SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer	TWCCAWWTWTGG	1e0	-2.205e-02	1.0000	719.0	16.26%	3655.7	17.39%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-2.186e-02	1.0000	209.0	4.73%	1133.1	5.39%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e0	-1.910e-02	1.0000	320.0	7.24%	1695.0	8.06%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-1.871e-02	1.0000	443.0	10.02%	2307.5	10.98%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-1.844e-02	1.0000	61.0	1.38%	372.3	1.77%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-1.472e-02	1.0000	310.0	7.01%	1654.4	7.87%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-1.407e-02	1.0000	67.0	1.52%	409.9	1.95%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-1.361e-02	1.0000	238.0	5.38%	1294.4	6.16%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-1.330e-02	1.0000	88.0	1.99%	522.6	2.49%
ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer	GRTGMTRGAGCC	1e0	-1.234e-02	1.0000	213.0	4.82%	1170.3	5.57%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-9.861e-03	1.0000	177.0	4.00%	992.2	4.72%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-9.248e-03	1.0000	760.0	17.19%	3897.8	18.55%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	ATTTTCCATT	1e0	-7.916e-03	1.0000	1282.0	28.99%	6441.7	30.65%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-7.854e-03	1.0000	380.0	8.59%	2026.5	9.64%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-7.166e-03	1.0000	613.0	13.86%	3186.9	15.16%
Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer	WATGCAAATGAG	1e0	-6.024e-03	1.0000	542.0	12.26%	2843.0	13.53%
Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer	GCTATTTTTGGM	1e0	-5.509e-03	1.0000	1334.0	30.17%	6711.5	31.93%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer	GYCATCMATCAT	1e0	-5.458e-03	1.0000	135.0	3.05%	788.2	3.75%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-5.286e-03	1.0000	87.0	1.97%	534.2	2.54%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e0	-2.994e-03	1.0000	674.0	15.24%	3522.9	16.76%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e0	-2.877e-03	1.0000	419.0	9.48%	2255.7	10.73%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e0	-2.285e-03	1.0000	231.0	5.22%	1307.7	6.22%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e0	-2.184e-03	1.0000	616.0	13.93%	3247.7	15.45%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e0	-2.158e-03	1.0000	967.0	21.87%	4974.1	23.67%
ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer	GNCTGTASTRNTGBCTCHTT	1e0	-2.123e-03	1.0000	13.0	0.29%	122.8	0.58%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e0	-1.728e-03	1.0000	565.0	12.78%	3002.8	14.29%
Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer	KBCTACCTGW	1e0	-1.655e-03	1.0000	297.0	6.72%	1654.5	7.87%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e0	-1.421e-03	1.0000	5.0	0.11%	68.6	0.33%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e0	-1.366e-03	1.0000	100.0	2.26%	628.4	2.99%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-1.183e-03	1.0000	68.0	1.54%	454.7	2.16%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e0	-1.070e-03	1.0000	1748.0	39.53%	8783.6	41.79%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e0	-9.000e-04	1.0000	1155.0	26.12%	5928.2	28.21%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-7.910e-04	1.0000	704.0	15.92%	3720.4	17.70%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e0	-6.320e-04	1.0000	449.0	10.15%	2453.6	11.67%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e0	-5.900e-04	1.0000	567.0	12.82%	3048.7	14.51%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e0	-4.910e-04	1.0000	376.0	8.50%	2090.7	9.95%
SeqBias: CG bias	SSSSSSSSSS	1e0	-3.390e-04	1.0000	3579.0	80.94%	17418.3	82.87%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e0	-2.570e-04	1.0000	179.0	4.05%	1083.9	5.16%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-1.490e-04	1.0000	1879.0	42.49%	9496.1	45.18%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	AGGTCAAGGTCA	1e0	-1.160e-04	1.0000	30.0	0.68%	258.9	1.23%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e0	-1.050e-04	1.0000	1421.0	32.13%	7306.2	34.76%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e0	-7.400e-05	1.0000	1143.0	25.85%	5966.1	28.39%
ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer	NGNTCTAGAACCNGV	1e0	-6.400e-05	1.0000	210.0	4.75%	1275.2	6.07%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-5.900e-05	1.0000	683.0	15.45%	3700.3	17.61%
Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer	BTBRAGTGSN	1e0	-5.300e-05	1.0000	1388.0	31.39%	7172.1	34.12%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-4.200e-05	1.0000	272.0	6.15%	1611.4	7.67%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-2.500e-05	1.0000	979.0	22.14%	5197.4	24.73%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e0	-2.400e-05	1.0000	864.0	19.54%	4630.3	22.03%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-1.500e-05	1.0000	43.0	0.97%	360.2	1.71%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-1.300e-05	1.0000	407.0	9.20%	2339.2	11.13%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e0	-1.200e-05	1.0000	2200.0	49.75%	11120.4	52.91%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e0	-8.000e-06	1.0000	927.0	20.96%	4975.7	23.67%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-4.000e-06	1.0000	1056.0	23.88%	5632.5	26.80%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e0	-3.000e-06	1.0000	1637.0	37.02%	8472.4	40.31%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-3.000e-06	1.0000	1536.0	34.74%	7984.3	37.99%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-3.000e-06	1.0000	182.0	4.12%	1176.5	5.60%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e0	-3.000e-06	1.0000	1001.0	22.64%	5373.4	25.57%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e0	-3.000e-06	1.0000	79.0	1.79%	597.3	2.84%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-2.000e-06	1.0000	1755.0	39.69%	9053.6	43.08%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e0	-1.000e-06	1.0000	153.0	3.46%	1030.1	4.90%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-1.000e-06	1.0000	2022.0	45.73%	10355.0	49.27%
Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer	TTRAGTGSYK	1e0	-1.000e-06	1.0000	1564.0	35.37%	8160.0	38.82%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e0	-1.000e-06	1.0000	78.0	1.76%	603.3	2.87%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-1.000e-06	1.0000	604.0	13.66%	3422.7	16.28%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e0	-0.000e+00	1.0000	857.0	19.38%	4705.1	22.39%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-0.000e+00	1.0000	155.0	3.51%	1055.4	5.02%
HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer	TTTTATKRGG	1e0	-0.000e+00	1.0000	1707.0	38.60%	8884.4	42.27%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e0	-0.000e+00	1.0000	1284.0	29.04%	6844.6	32.57%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e0	-0.000e+00	1.0000	699.0	15.81%	3933.4	18.71%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e0	-0.000e+00	1.0000	882.0	19.95%	4859.2	23.12%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-0.000e+00	1.0000	1022.0	23.11%	5572.6	26.51%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-0.000e+00	1.0000	973.0	22.00%	5339.5	25.41%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e0	-0.000e+00	1.0000	2034.0	46.00%	10501.4	49.96%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e0	-0.000e+00	1.0000	1745.0	39.46%	9120.5	43.39%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-0.000e+00	1.0000	303.0	6.85%	1906.2	9.07%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e0	-0.000e+00	1.0000	2074.0	46.90%	10703.1	50.92%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e0	-0.000e+00	1.0000	1961.0	44.35%	10183.3	48.45%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-0.000e+00	1.0000	464.0	10.49%	2774.1	13.20%
Tal1	CATCTG	1e0	-0.000e+00	1.0000	877.0	19.83%	4893.1	23.28%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e0	-0.000e+00	1.0000	2055.0	46.47%	10641.2	50.63%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e0	-0.000e+00	1.0000	1288.0	29.13%	6941.2	33.03%
Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer	NNYTAATTAR	1e0	-0.000e+00	1.0000	1787.0	40.41%	9367.8	44.57%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-0.000e+00	1.0000	522.0	11.80%	3090.2	14.70%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e0	-0.000e+00	1.0000	285.0	6.45%	1836.5	8.74%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e0	-0.000e+00	1.0000	1496.0	33.83%	7980.5	37.97%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e0	-0.000e+00	1.0000	1772.0	40.07%	9326.0	44.37%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e0	-0.000e+00	1.0000	2997.0	67.77%	15089.1	71.79%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-0.000e+00	1.0000	1165.0	26.35%	6387.2	30.39%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e0	-0.000e+00	1.0000	1479.0	33.45%	7985.7	38.00%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e0	-0.000e+00	1.0000	1428.0	32.29%	7765.4	36.95%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-0.000e+00	1.0000	1317.0	29.78%	7235.3	34.42%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e0	-0.000e+00	1.0000	1649.0	37.29%	8866.8	42.19%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-0.000e+00	1.0000	788.0	17.82%	4602.1	21.90%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e0	-0.000e+00	1.0000	1438.0	32.52%	7865.3	37.42%
LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer	ADAAATATCT	1e0	-0.000e+00	1.0000	1813.0	41.00%	9724.0	46.27%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e0	-0.000e+00	1.0000	1330.0	30.08%	7393.5	35.18%
SeqBias: GA-repeat	GAGAGAGAGA	1e0	-0.000e+00	1.0000	3751.0	84.83%	18592.2	88.46%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-0.000e+00	1.0000	694.0	15.69%	4191.1	19.94%
PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer	HAATAAAGNN	1e0	-0.000e+00	1.0000	2819.0	63.75%	14483.9	68.91%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	-0.000e+00	1.0000	513.0	11.60%	3261.8	15.52%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-0.000e+00	1.0000	1737.0	39.28%	9470.7	45.06%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-0.000e+00	1.0000	2227.0	50.36%	11812.3	56.20%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e0	-0.000e+00	1.0000	1418.0	32.07%	7924.9	37.71%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e0	-0.000e+00	1.0000	2296.0	51.92%	12143.0	57.78%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-0.000e+00	1.0000	252.0	5.70%	1896.4	9.02%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e0	0.000e+00	1.0000	910.0	20.58%	5899.3	28.07%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e0	0.000e+00	1.0000	2410.0	54.50%	12833.6	61.06%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	0.000e+00	1.0000	2102.0	47.54%	11459.9	54.53%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	0.000e+00	1.0000	1135.0	25.67%	7001.2	33.31%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e0	0.000e+00	1.0000	2394.0	54.14%	12959.8	61.66%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e0	0.000e+00	1.0000	3353.0	75.83%	18362.3	87.37%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	0.000e+00	1.0000	948.0	21.44%	5743.9	27.33%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e0	0.000e+00	1.0000	1964.0	44.41%	10694.1	50.88%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e0	0.000e+00	1.0000	3332.0	75.35%	17724.4	84.33%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e0	0.000e+00	1.0000	3231.0	73.07%	18099.9	86.12%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	1e0	0.000e+00	1.0000	0.0	0.00%	1.9	0.01%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e0	0.000e+00	1.0000	2075.0	46.92%	12163.5	57.87%
Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer	YTGWCADY	1e0	0.000e+00	1.0000	2346.0	53.05%	12590.4	59.90%
Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer	TGTCANYT	1e0	0.000e+00	1.0000	2457.0	55.56%	13047.4	62.08%
ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer	GGGTTTTGAAGGATGARTAGGAGTT	1e0	0.000e+00	1.0000	0.0	0.00%	1.0	0.00%
ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer	MACCTTCYATGGCTCCCTAKTGCCY	1e0	0.000e+00	1.0000	0.0	0.00%	1.2	0.01%
SeqBias: CA-repeat	CACACACACA	1e0	0.000e+00	1.0000	3212.0	72.64%	16943.9	80.62%
SeqBias: polyC-repeat	CCCCCCCCCC	1e0	0.000e+00	1.0000	4359.0	98.58%	20979.8	99.82%
KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer	ARGAATAWWN	1e0	0.000e+00	1.0000	2198.0	49.71%	11858.0	56.42%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	0.000e+00	1.0000	1032.0	23.34%	6105.7	29.05%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e0	0.000e+00	1.0000	2028.0	45.86%	11170.7	53.15%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e0	0.000e+00	1.0000	1946.0	44.01%	10592.1	50.40%