Motif Name	Consensus	P-value	Log P-value	q-value (Benjamini)	# of Target Sequences with Motif(of 2450)	% of Target Sequences with Motif	# of Background Sequences with Motif(of 2590)	% of Background Sequences with Motif
CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer	GHCACGTG	1e-3	-8.996e+00	0.0479	49.0	2.00%	20.2	0.78%
PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer	KTGTTTGC	1e-3	-8.393e+00	0.0479	460.0	18.81%	389.8	15.09%
FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	AGTAAACAAAAAAGAACAND	1e-3	-8.362e+00	0.0479	17.0	0.70%	2.6	0.10%
FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer	WAAGTAAACA	1e-2	-6.586e+00	0.1334	171.0	6.99%	128.5	4.97%
USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer	SGTCACGTGR	1e-2	-5.748e+00	0.2467	32.0	1.31%	14.5	0.56%
FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WAAGTAAACA	1e-2	-5.737e+00	0.2467	201.0	8.22%	160.9	6.23%
FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer	WWTRTAAACAVG	1e-2	-5.504e+00	0.2467	154.0	6.30%	118.5	4.59%
MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer	GCTGASTCAGCA	1e-2	-5.141e+00	0.2832	17.0	0.70%	5.3	0.21%
Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer	NGRTGACGTCAY	1e-2	-4.789e+00	0.3577	50.0	2.04%	30.6	1.18%
E-box/Arabidopsis-Promoters/Homer	GCCACGTG	1e-2	-4.688e+00	0.3577	25.0	1.02%	11.5	0.45%
IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer	CACGTGCC	1e-2	-4.613e+00	0.3577	116.0	4.74%	88.3	3.42%
Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer	GTCACGTGGT	1e-1	-4.406e+00	0.3633	27.0	1.10%	13.3	0.51%
ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer	ATTTCCCAGVAKSCY	1e-1	-4.406e+00	0.3633	27.0	1.10%	13.4	0.52%
MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer	RTCATGTGAC	1e-1	-4.358e+00	0.3633	80.0	3.27%	57.2	2.21%
HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer	RTACGTGC	1e-1	-4.295e+00	0.3633	74.0	3.03%	52.4	2.03%
Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGCATAATTCA	1e-1	-4.274e+00	0.3633	67.0	2.74%	46.5	1.80%
c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer	VCCACGTG	1e-1	-4.228e+00	0.3633	21.0	0.86%	9.0	0.35%
SeqBias: GA-repeat	GAGAGAGAGA	1e-1	-4.190e+00	0.3633	844.0	34.51%	816.7	31.61%
Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer	AAGCACGTGBGD	1e-1	-4.186e+00	0.3633	10.0	0.41%	3.0	0.12%
Unknown6/Drosophila-Promoters/Homer	AATTTTAAAA	1e-1	-4.142e+00	0.3633	186.0	7.60%	156.9	6.07%
ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer	AACCGGAAGT	1e-1	-4.098e+00	0.3633	112.0	4.58%	87.1	3.37%
CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	DRTGTTGCAA	1e-1	-4.043e+00	0.3633	93.0	3.80%	70.4	2.73%
GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NNNNNBAGATAWYATCTVHN	1e-1	-3.838e+00	0.3633	20.0	0.82%	9.4	0.36%
Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	ATTGCATCAT	1e-1	-3.755e+00	0.3775	29.0	1.19%	16.4	0.63%
SeqBias: TA-repeat	TATATATATA	1e-1	-3.582e+00	0.4305	768.0	31.40%	746.6	28.90%
Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer	SAGATAAGRV	1e-1	-3.566e+00	0.4305	66.0	2.70%	49.0	1.90%
c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	VVCCACGTGG	1e-1	-3.527e+00	0.4305	32.0	1.31%	19.2	0.74%
Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer	CCATTGTTNY	1e-1	-3.455e+00	0.4366	188.0	7.69%	163.5	6.33%
bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer	NAGTTTCABTHTGACTNW	1e-1	-3.331e+00	0.4772	49.0	2.00%	34.9	1.35%
LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer	ATGATTRATG	1e-1	-3.315e+00	0.4772	192.0	7.85%	168.1	6.51%
PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GCAGCCAAGCRTGACH	1e-1	-3.291e+00	0.4772	25.0	1.02%	14.2	0.55%
Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATATTC	1e-1	-3.216e+00	0.4853	17.0	0.70%	8.7	0.34%
KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer	RGKGGGCGKGGC	1e-1	-3.118e+00	0.5188	107.0	4.37%	88.0	3.41%
RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	GGGRAARRGRMCAGMTG	1e-1	-3.095e+00	0.5188	18.0	0.74%	9.3	0.36%
E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer	CWGGCGGGAA	1e-1	-3.088e+00	0.5188	8.0	0.33%	2.3	0.09%
FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer	TRTTTACTTW	1e-1	-2.995e+00	0.5377	147.0	6.01%	127.4	4.93%
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	VTGACTCATC	1e-1	-2.976e+00	0.5377	63.0	2.58%	48.6	1.88%
IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	CTTTCANTATGACTV	1e-1	-2.967e+00	0.5377	15.0	0.61%	7.9	0.31%
caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer	GGYCATAAAW	1e-1	-2.955e+00	0.5377	129.0	5.27%	110.6	4.28%
n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer	VRCCACGTGG	1e-1	-2.952e+00	0.5377	37.0	1.51%	25.8	1.00%
SUT1?/SacCer-Promoters/Homer	CCCCGCGC	1e-1	-2.946e+00	0.5377	429.0	17.54%	408.3	15.80%
FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer	NYYTGTTTACHN	1e-1	-2.925e+00	0.5377	55.0	2.25%	41.2	1.59%
Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	DATGASTCATHN	1e-1	-2.904e+00	0.5377	56.0	2.29%	42.5	1.64%
Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer	AWWNTGCTGAGTCAT	1e-1	-2.884e+00	0.5377	4.0	0.16%	0.0	0.00%
Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer	HTGCTGAGTCAT	1e-1	-2.884e+00	0.5377	4.0	0.16%	0.8	0.03%
NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer	GATGACTCAGCA	1e-1	-2.884e+00	0.5377	4.0	0.16%	0.8	0.03%
ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer	GAGSCCGAGC	1e-1	-2.861e+00	0.5377	12.0	0.49%	5.6	0.22%
EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer	AVCAGGAAGT	1e-1	-2.818e+00	0.5377	106.0	4.33%	89.5	3.46%
Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer	CGGTCACSCCAC	1e-1	-2.805e+00	0.5377	9.0	0.37%	3.8	0.15%
Unknown4/Drosophila-Promoters/Homer	AAAAATACCRMA	1e-1	-2.798e+00	0.5377	27.0	1.10%	17.5	0.68%
Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer	NRRTGACGTCAT	1e-1	-2.747e+00	0.5377	28.0	1.14%	18.9	0.73%
HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer	GCACGTACCC	1e-1	-2.745e+00	0.5377	17.0	0.70%	9.9	0.38%
Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer	TGCGTGGGYG	1e-1	-2.681e+00	0.5377	37.0	1.51%	26.4	1.02%
NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer	CYTGGCABNSTGCCAR	1e-1	-2.657e+00	0.5377	18.0	0.74%	11.0	0.42%
Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer	GCCACRCCCACY	1e-1	-2.657e+00	0.5377	18.0	0.74%	10.8	0.42%
c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	ATGACGTCATCY	1e-1	-2.657e+00	0.5377	30.0	1.23%	20.3	0.79%
Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer	GGGGGGGG	1e-1	-2.582e+00	0.5377	63.0	2.58%	51.0	1.97%
GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer	RACCGGAAGT	1e-1	-2.582e+00	0.5377	63.0	2.58%	50.3	1.95%
Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer	TCACGTGAYH	1e-1	-2.580e+00	0.5377	19.0	0.78%	11.8	0.46%
E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer	DNRCAGCTGY	1e-1	-2.573e+00	0.5377	99.0	4.05%	84.0	3.25%
GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer	VAGRACAKWCTGTYC	1e-1	-2.494e+00	0.5377	15.0	0.61%	8.2	0.32%
KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer	DGGGYGKGGC	1e-1	-2.468e+00	0.5377	73.0	2.98%	60.9	2.36%
PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer	NGTGTTCAVTSAAGCGKAAA	1e-1	-2.453e+00	0.5377	11.0	0.45%	5.9	0.23%
HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer	VCAGCTGBNN	1e-1	-2.416e+00	0.5398	136.0	5.56%	121.4	4.70%
Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer	CCCACGTGCT	1e-1	-2.410e+00	0.5398	16.0	0.65%	9.9	0.38%
FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer	AGGTCANTGACCTB	1e-1	-2.409e+00	0.5398	29.0	1.19%	20.2	0.78%
LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer	ADAAATATCT	1e-1	-2.385e+00	0.5398	150.0	6.13%	135.8	5.26%
Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer	HTTTCCCASG	1e-1	-2.343e+00	0.5467	120.0	4.91%	106.7	4.13%
Unknown5/Drosophila-Promoters/Homer	GCTGATAASV	1e-1	-2.316e+00	0.5532	55.0	2.25%	44.2	1.71%
SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer	WNBCACGTGA	1e-1	-2.306e+00	0.5532	73.0	2.98%	61.6	2.38%
ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer	TGGGGAAGGGCM	1e-1	-2.304e+00	0.5532	56.0	2.29%	45.8	1.77%
Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer	BBCTTATCTS	1e0	-2.290e+00	0.5532	75.0	3.07%	63.6	2.46%
MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer	HWWGTCAGCAWWTTT	1e0	-2.288e+00	0.5532	33.0	1.35%	24.9	0.97%
E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer	GGCGGGAAAH	1e0	-2.275e+00	0.5532	18.0	0.74%	11.9	0.46%
Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer	CTGTTTAC	1e0	-2.244e+00	0.5532	188.0	7.69%	174.1	6.74%
SFP1/SacCer-Promoters/Homer	DDAAAAATTTTY	1e0	-2.234e+00	0.5532	26.0	1.06%	18.0	0.70%
Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer	SCTGTCAMTCAN	1e0	-2.221e+00	0.5532	19.0	0.78%	12.0	0.47%
EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer	VACAGGAAAT	1e0	-2.218e+00	0.5532	36.0	1.47%	27.4	1.06%
Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer	GCTATTTTTGGM	1e0	-2.183e+00	0.5532	140.0	5.72%	127.7	4.94%
PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer	AAGAACATWHTGTTC	1e0	-2.172e+00	0.5532	20.0	0.82%	13.2	0.51%
Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer	SCTGTCAVTCAV	1e0	-2.172e+00	0.5532	20.0	0.82%	13.2	0.51%
NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	SARTGGAAAAWRTGAGTCAB	1e0	-2.172e+00	0.5532	20.0	0.82%	13.2	0.51%
ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer	WDNCTGGGCA	1e0	-2.164e+00	0.5532	99.0	4.05%	87.0	3.37%
EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer	TGCAARYGCGCTCYA	1e0	-2.163e+00	0.5532	3.0	0.12%	0.0	0.00%
Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer	CCWTTGTYYB	1e0	-2.155e+00	0.5532	172.0	7.03%	159.8	6.19%
ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer	AWTGATAAGA	1e0	-2.111e+00	0.5532	80.0	3.27%	69.9	2.70%
EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer	ATTTCCTGTN	1e0	-2.053e+00	0.5711	65.0	2.66%	55.8	2.16%
Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer	GATGACGTCA	1e0	-2.046e+00	0.5711	66.0	2.70%	56.0	2.17%
Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer	MTGATGCAAT	1e0	-2.033e+00	0.5711	34.0	1.39%	26.3	1.02%
PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer	HAATAAAGNN	1e0	-2.016e+00	0.5725	364.0	14.88%	355.4	13.75%
Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)	NNAYTTCCTGHN	1e0	-2.016e+00	0.5725	71.0	2.90%	61.4	2.38%
RLR1?/SacCer-Promoters/Homer	WTTTTCYYTTTT	1e0	-1.986e+00	0.5775	128.0	5.23%	117.6	4.55%
Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer	NBWGATAAGR	1e0	-1.984e+00	0.5775	130.0	5.31%	119.1	4.61%
GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATGKDGAGATAAG	1e0	-1.973e+00	0.5775	11.0	0.45%	6.8	0.26%
Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer	NNVVCAGCTGBN	1e0	-1.956e+00	0.5775	85.0	3.48%	75.9	2.94%
Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAW	1e0	-1.902e+00	0.6014	65.0	2.66%	56.1	2.17%
Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer	ACTYKNATTCGTGNTACTTC	1e0	-1.901e+00	0.6014	12.0	0.49%	8.0	0.31%
ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer	ACAGGAAGTG	1e0	-1.859e+00	0.6153	75.0	3.07%	66.7	2.58%
Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer	CYAAAAATAG	1e0	-1.852e+00	0.6153	77.0	3.15%	68.7	2.66%
SeqBias: C/A-bias	MMMMMMMMMM	1e0	-1.821e+00	0.6261	2341.0	95.71%	2456.4	95.07%
Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer	CYTGTTTACWYW	1e0	-1.821e+00	0.6261	89.0	3.64%	80.7	3.12%
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer	RGGATTAR	1e0	-1.819e+00	0.6261	205.0	8.38%	196.5	7.61%
IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer	GAAAGTGAAAGT	1e0	-1.791e+00	0.6266	14.0	0.57%	9.1	0.35%
BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer	GNCACGTG	1e0	-1.782e+00	0.6266	142.0	5.81%	133.5	5.17%
ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer	ACAGGAAGTG	1e0	-1.782e+00	0.6266	132.0	5.40%	123.6	4.78%
PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer	ACTTTCACTTTC	1e0	-1.773e+00	0.6266	62.0	2.53%	54.8	2.12%
DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer	YDGHTACAWTGTADC	1e0	-1.769e+00	0.6266	24.0	0.98%	18.4	0.71%
PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer	GSCTGTCACTCA	1e0	-1.767e+00	0.6266	4.0	0.16%	1.4	0.06%
Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer	CTTCCGGGAA	1e0	-1.754e+00	0.6266	40.0	1.64%	33.2	1.29%
bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer	KCACGTGMCN	1e0	-1.749e+00	0.6266	15.0	0.61%	11.0	0.43%
SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer	ASWTCCTGBT	1e0	-1.711e+00	0.6297	84.0	3.43%	76.9	2.98%
Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer	NGCGTGGGCGGR	1e0	-1.699e+00	0.6320	9.0	0.37%	5.2	0.20%
Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer	YCATYAATCA	1e0	-1.687e+00	0.6340	126.0	5.15%	118.1	4.57%
BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer	DATGASTCAT	1e0	-1.673e+00	0.6371	52.0	2.13%	45.2	1.75%
SeqBias: polyC-repeat	CCCCCCCCCC	1e0	-1.644e+00	0.6499	1832.0	74.90%	1906.1	73.78%
DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer	TWGHWACAWTGTWDC	1e0	-1.638e+00	0.6499	33.0	1.35%	27.9	1.08%
Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer	CCATTGTATGCAAAT	1e0	-1.608e+00	0.6571	20.0	0.82%	15.2	0.59%
Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer	GTCATGCHTGRCTGS	1e0	-1.608e+00	0.6571	20.0	0.82%	15.9	0.62%
HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer	CARRGKBCAAAGTYCA	1e0	-1.603e+00	0.6571	37.0	1.51%	31.3	1.21%
AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer	ATGCCCTGAGGC	1e0	-1.576e+00	0.6669	41.0	1.68%	35.4	1.37%
PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer	ADGGYAGYAGCATCT	1e0	-1.541e+00	0.6848	24.0	0.98%	19.3	0.75%
BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer	NHAACBGYYV	1e0	-1.517e+00	0.6961	139.0	5.68%	133.0	5.15%
HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer	TACGTGCV	1e0	-1.510e+00	0.6961	13.0	0.53%	9.8	0.38%
PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	MGGAAGTGAAAC	1e0	-1.502e+00	0.6961	122.0	4.99%	116.8	4.52%
Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer	GGCCATAAATCA	1e0	-1.497e+00	0.6961	68.0	2.78%	62.8	2.43%
Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer	ATGMATATDC	1e0	-1.494e+00	0.6961	184.0	7.52%	179.0	6.93%
Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer	MAATCACTGC	1e0	-1.490e+00	0.6961	76.0	3.11%	71.0	2.75%
Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer	YCTTTGTTCC	1e0	-1.488e+00	0.6961	82.0	3.35%	76.2	2.95%
p53(p53)/Saos-p53-ChIP-Seq/Homer	RRCATGYCYRGRCATGYYYN	1e0	-1.480e+00	0.6961	6.0	0.25%	3.1	0.12%
JunD(bZIP)/K562-JunD-ChIP-Seq/Homer	ATGACGTCATCN	1e0	-1.480e+00	0.6961	6.0	0.25%	3.3	0.13%
p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer	RRCATGYCYRGRCATGYYYN	1e0	-1.480e+00	0.6961	6.0	0.25%	3.1	0.12%
Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer	BAACAGCTGT	1e0	-1.471e+00	0.6961	31.0	1.27%	26.8	1.04%
GFY-Staf(?,Zf)/Promoter/Homer	RACTACAATTCCCAGAAKGC	1e0	-1.442e+00	0.6961	2.0	0.08%	0.0	0.00%
ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer	YTKGATAHAGTATTCTWGGTNGGCA	1e0	-1.436e+00	0.6961	16.0	0.65%	12.6	0.49%
SeqBias: CA-repeat	CACACACACA	1e0	-1.417e+00	0.6961	581.0	23.75%	591.8	22.90%
Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer	GYMATAAAAH	1e0	-1.414e+00	0.6961	121.0	4.95%	116.7	4.52%
GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer	CGTGGGTGGTCC	1e0	-1.409e+00	0.6961	7.0	0.29%	4.8	0.18%
E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer	GGCGGGAARN	1e0	-1.388e+00	0.6999	19.0	0.78%	15.2	0.59%
KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer	ARGAATAWWN	1e0	-1.368e+00	0.7088	192.0	7.85%	189.3	7.33%
Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer	NATGASTCABNN	1e0	-1.365e+00	0.7088	21.0	0.86%	18.0	0.70%
THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer	GGTCANYTGAGGWCA	1e0	-1.300e+00	0.7479	31.0	1.27%	27.7	1.07%
Unknown1/Arabidopsis-Promoters/Homer	RGGGTAWWWTHGTAA	1e0	-1.291e+00	0.7493	10.0	0.41%	7.6	0.29%
MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer	GGCVGTTR	1e0	-1.287e+00	0.7493	143.0	5.85%	140.3	5.43%
Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer	NRYTTCCGGH	1e0	-1.274e+00	0.7520	70.0	2.86%	66.5	2.58%
PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer	ACTGATAAGA	1e0	-1.268e+00	0.7520	51.0	2.09%	47.2	1.83%
REB1/SacCer-Promoters/Homer	KCCGGGTAAYRR	1e0	-1.249e+00	0.7606	12.0	0.49%	9.9	0.38%
SeqBias: G/A bias	RRRRRRRRRR	1e0	-1.231e+00	0.7684	2393.0	97.83%	2520.8	97.57%
Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer	CAAAGGTCAG	1e0	-1.230e+00	0.7684	151.0	6.17%	149.3	5.78%
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer	GATGASTCATCN	1e0	-1.208e+00	0.7759	15.0	0.61%	12.4	0.48%
Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer	RTCACSCCAY	1e0	-1.199e+00	0.7781	16.0	0.65%	13.9	0.54%
Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer	DCYAAAAATAGM	1e0	-1.190e+00	0.7799	82.0	3.35%	79.7	3.09%
PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer	ACCRTGACTAATTNN	1e0	-1.177e+00	0.7843	19.0	0.78%	16.1	0.62%
PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer	VAGRACAKNCTGTBC	1e0	-1.154e+00	0.7979	179.0	7.32%	179.2	6.93%
Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer	ATATGCAAAT	1e0	-1.153e+00	0.7979	54.0	2.21%	51.3	1.98%
EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer	GTCCCCWGGGGA	1e0	-1.152e+00	0.7979	53.0	2.17%	50.3	1.95%
Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer	VCAGCTGYTG	1e0	-1.146e+00	0.7979	45.0	1.84%	42.1	1.63%
Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	TATGCWAATBAV	1e0	-1.144e+00	0.7979	43.0	1.76%	40.9	1.58%
ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer	GARTGGTCATCGCCC	1e0	-1.144e+00	0.7979	4.0	0.16%	2.7	0.10%
Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer	GTTGCCATGGCAACM	1e0	-1.144e+00	0.7979	4.0	0.16%	2.8	0.11%
ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer	RCAGGATGTGGT	1e0	-1.144e+00	0.7979	4.0	0.16%	2.8	0.11%
GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer	NRGVACABNVTGTYCY	1e0	-1.144e+00	0.7979	4.0	0.16%	2.6	0.10%
IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer	ACTGAAACCA	1e0	-1.144e+00	0.7979	33.0	1.35%	30.1	1.17%
ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer	GTGGGCCCCA	1e0	-1.097e+00	0.7979	5.0	0.20%	3.3	0.13%
PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer	GTCACGCTCSCTGM	1e0	-1.068e+00	0.8112	6.0	0.25%	4.9	0.19%
Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer	BCCATTGTTC	1e0	-1.035e+00	0.8328	90.0	3.68%	89.9	3.48%
BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer	CNNBRGCGCCCCCTGSTGGC	1e0	-1.034e+00	0.8328	8.0	0.33%	6.1	0.24%
Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer	NNATGASTCATH	1e0	-1.024e+00	0.8328	42.0	1.72%	40.1	1.55%
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	KGTTGCCATGGCAA	1e0	-1.015e+00	0.8345	10.0	0.41%	8.2	0.32%
Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer	TGCTGAGTCA	1e0	-1.005e+00	0.8382	12.0	0.49%	10.7	0.41%
p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer	NNDRCATGYCYNRRCATGYH	1e0	-9.951e-01	0.8416	17.0	0.70%	15.7	0.61%
RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer	AAACCACARM	1e0	-9.862e-01	0.8442	69.0	2.82%	68.2	2.64%
Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer	NNTGTGGATTSS	1e0	-9.762e-01	0.8476	65.0	2.66%	64.1	2.48%
CHR(?)/Hela-CellCycle-Expression/Homer	SRGTTTCAAA	1e0	-9.539e-01	0.8618	88.0	3.60%	88.0	3.41%
GAGA-repeat/SacCer-Promoters/Homer	CTYTCTYTCTCTCTC	1e0	-9.517e-01	0.8618	510.0	20.85%	529.0	20.48%
STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer	ABTTCYYRRGAA	1e0	-9.504e-01	0.8618	55.0	2.25%	54.6	2.11%
Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer	WATGCAAATGAG	1e0	-9.396e-01	0.8618	51.0	2.09%	50.4	1.95%
AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer	SCCTSAGGSCAW	1e0	-9.396e-01	0.8618	51.0	2.09%	50.4	1.95%
Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer	SSCMATWAAA	1e0	-8.923e-01	0.8908	92.0	3.76%	93.7	3.63%
Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer	TAATCCCN	1e0	-8.770e-01	0.8995	601.0	24.57%	627.5	24.29%
STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer	NATTTCCNGGAAAT	1e0	-8.730e-01	0.8995	29.0	1.19%	28.9	1.12%
Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer	AAGCACTTAA	1e0	-8.724e-01	0.8995	241.0	9.85%	249.7	9.66%
ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer	RGGGCACTAACY	1e0	-8.695e-01	0.8995	28.0	1.14%	27.7	1.07%
NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer	KCCACGTGAC	1e0	-8.368e-01	0.9159	73.0	2.98%	74.7	2.89%
Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer	TAATTAGN	1e0	-8.256e-01	0.9212	157.0	6.42%	162.3	6.28%
Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer	CCWTTGTY	1e0	-8.135e-01	0.9273	193.0	7.89%	200.9	7.78%
ETS(ETS)/Promoter/Homer	AACCGGAAGT	1e0	-8.044e-01	0.9308	12.0	0.49%	11.3	0.44%
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCHGATTAC	1e0	-7.885e-01	0.9407	9.0	0.37%	8.1	0.32%
Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer	GTRGGTCASTGGGTCA	1e0	-7.826e-01	0.9412	8.0	0.33%	7.8	0.30%
X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	GGTTGCCATGGCAA	1e0	-7.764e-01	0.9420	7.0	0.29%	6.1	0.23%
SeqBias: GCW-triplet	GCWGCWGCWGCW	1e0	-7.597e-01	0.9528	2277.0	93.09%	2402.8	93.00%
RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer	CGGTTGCCATGGCAAC	1e0	-7.456e-01	0.9563	3.0	0.12%	2.6	0.10%
OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer	ATGAATWATTCATGA	1e0	-7.456e-01	0.9563	3.0	0.12%	2.7	0.10%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	RGGTCADNNAGAGGTCAV	1e0	-7.349e-01	0.9616	2.0	0.08%	1.1	0.04%
Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	MACAGGAAGT	1e0	-7.246e-01	0.9666	23.0	0.94%	23.3	0.90%
Unknown3/Drosophila-Promoters/Homer	ACVAKCTGGCAGCGC	1e0	-7.208e-01	0.9666	1.0	0.04%	0.0	0.00%
CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	TGCAGTTCCMVNWRTGGCCA	1e0	-7.208e-01	0.9666	1.0	0.04%	0.9	0.03%
OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer	ATGAATATTCATGAG	1e0	-7.208e-01	0.9666	1.0	0.04%	0.0	0.00%
GFX(?)/Promoter/Homer	ATTCTCGCGAGA	1e0	-7.208e-01	0.9666	1.0	0.04%	0.0	0.00%
ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer	CCTCATGGTGYCYTWYTCCCTTGTG	1e0	-7.208e-01	0.9666	1.0	0.04%	0.0	0.00%
E2F(E2F)/Hela-CellCycle-Expression/Homer	TTSGCGCGAAAA	1e0	-7.208e-01	0.9666	1.0	0.04%	0.0	0.00%
SeqBias: CG bias	SSSSSSSSSS	1e0	-7.181e-01	0.9666	679.0	27.76%	715.0	27.68%
Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer	RAACAATGGN	1e0	-7.033e-01	0.9666	129.0	5.27%	135.0	5.23%
SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer	AAAGRGGAAGTG	1e0	-6.989e-01	0.9666	19.0	0.78%	19.3	0.75%
Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer	TBGCACGCAA	1e0	-6.929e-01	0.9666	36.0	1.47%	37.5	1.45%
PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer	NNBCACGTGN	1e0	-6.911e-01	0.9666	89.0	3.64%	93.0	3.60%
Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer	RCCACGTGGYYN	1e0	-6.599e-01	0.9666	30.0	1.23%	31.6	1.22%
MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer	RRCAGCTGYTSY	1e0	-6.599e-01	0.9666	30.0	1.23%	31.6	1.22%
Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer	CCTGCTGAGH	1e0	-6.484e-01	0.9728	44.0	1.80%	46.9	1.81%
Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer	ASATCAAAGGVA	1e0	-6.435e-01	0.9730	43.0	1.76%	45.3	1.75%
ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer	NGNTCTAGAACCNGV	1e0	-6.413e-01	0.9730	27.0	1.10%	28.8	1.11%
KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer	GGGGGTGTGTCC	1e0	-6.413e-01	0.9730	27.0	1.10%	29.0	1.12%
HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer	GYCATCMATCAT	1e0	-6.398e-01	0.9730	12.0	0.49%	12.3	0.47%
RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer	SAAACCACAG	1e0	-6.385e-01	0.9730	42.0	1.72%	44.8	1.73%
RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer	AAYTAGGTCA	1e0	-6.288e-01	0.9730	11.0	0.45%	11.3	0.44%
Unknown2/Drosophila-Promoters/Homer	CATCMCTA	1e0	-6.208e-01	0.9730	85.0	3.48%	90.3	3.49%
HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer	GGCCATAAATCA	1e0	-6.208e-01	0.9730	85.0	3.48%	90.6	3.51%
TATA-Box(TBP)/Promoter/Homer	CCTTTTAWAGSC	1e0	-6.169e-01	0.9730	148.0	6.05%	157.2	6.09%
Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer	NNNCTTTCCAGGAAA	1e0	-6.149e-01	0.9730	115.0	4.70%	122.4	4.74%
PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer	AGAGGAAGTG	1e0	-6.118e-01	0.9730	37.0	1.51%	39.3	1.52%
RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer	TGCATGCA	1e0	-6.105e-01	0.9730	178.0	7.28%	189.9	7.35%
Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer	NAACAGCTGG	1e0	-6.081e-01	0.9730	51.0	2.09%	55.0	2.13%
TATA-box/Drosophila-Promoters/Homer	CTATAAAAGCSV	1e0	-6.036e-01	0.9730	9.0	0.37%	10.0	0.39%
ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer	RGRACASNSTGTYCYB	1e0	-6.036e-01	0.9730	9.0	0.37%	9.0	0.35%
HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer	NTATYGATCH	1e0	-5.956e-01	0.9730	63.0	2.58%	67.9	2.63%
Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer	CTGGCAGSCTGCCA	1e0	-5.626e-01	0.9799	17.0	0.70%	18.9	0.73%
SeqBias: CG-repeat	CGCGCGCGCG	1e0	-5.623e-01	0.9799	29.0	1.19%	31.4	1.21%
PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer	BCACGTGVDN	1e0	-5.530e-01	0.9806	67.0	2.74%	72.5	2.80%
IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer	GAAASYGAAASY	1e0	-5.524e-01	0.9806	6.0	0.25%	6.1	0.24%
AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer	TGGCAGTTGG	1e0	-5.517e-01	0.9806	124.0	5.07%	133.9	5.18%
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer	GCTAATCC	1e0	-5.447e-01	0.9806	338.0	13.82%	361.1	13.98%
ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer	ACVAGGAAGT	1e0	-5.367e-01	0.9806	50.0	2.04%	54.5	2.11%
Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer	AGGVNCCTTTGT	1e0	-5.345e-01	0.9806	76.0	3.11%	82.6	3.20%
Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	TAATCAATTA	1e0	-5.305e-01	0.9806	14.0	0.57%	16.0	0.62%
PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer	GGAAGTGAAAST	1e0	-5.184e-01	0.9848	13.0	0.53%	14.4	0.56%
Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer	TGTCANYT	1e0	-5.038e-01	0.9950	329.0	13.45%	353.1	13.67%
ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer	SMCAGTCWGAKGGAGGAGGC	1e0	-4.998e-01	0.9950	4.0	0.16%	4.7	0.18%
Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer	ADBTAATTAR	1e0	-4.955e-01	0.9950	248.0	10.14%	267.8	10.37%
Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer	AGGTGTGAAM	1e0	-4.919e-01	0.9950	104.0	4.25%	113.2	4.38%
Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer	YTAATYNRATTA	1e0	-4.903e-01	0.9950	65.0	2.66%	71.6	2.77%
MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer	TGCTGACTCA	1e0	-4.889e-01	0.9950	41.0	1.68%	45.3	1.75%
SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer	TWCCAWWTWTGG	1e0	-4.771e-01	0.9965	39.0	1.59%	43.5	1.68%
Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer	TGACCTTTNCNT	1e0	-4.757e-01	0.9965	10.0	0.41%	11.1	0.43%
E-box(bHLH)/Promoter/Homer	SSGGTCACGTGA	1e0	-4.613e-01	0.9999	3.0	0.12%	3.7	0.14%
E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer	VDTTTCCCGCCA	1e0	-4.613e-01	0.9999	3.0	0.12%	3.0	0.12%
VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer	ARAGGTCANWGAGTTCANNN	1e0	-4.586e-01	0.9999	9.0	0.37%	10.6	0.41%
Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer	GGTGYTGACAGS	1e0	-4.586e-01	0.9999	9.0	0.37%	10.9	0.42%
ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer	AGGCCTRG	1e0	-4.533e-01	0.9999	80.0	3.27%	88.9	3.44%
HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer	RACAGCTGTTBH	1e0	-4.387e-01	1.0000	43.0	1.76%	48.6	1.88%
NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer	YTGCCAAG	1e0	-4.315e-01	1.0000	110.0	4.50%	121.6	4.71%
Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer	NNYTAATTAR	1e0	-4.286e-01	1.0000	173.0	7.07%	189.6	7.34%
RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer	AGGTCAAGGTCA	1e0	-4.183e-01	1.0000	7.0	0.29%	8.0	0.31%
STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer	RTTTCTNAGAAA	1e0	-4.177e-01	1.0000	30.0	1.23%	34.5	1.34%
NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer	GCCATCTGTT	1e0	-4.157e-01	1.0000	49.0	2.00%	55.1	2.13%
Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer	ASWTCAAAGG	1e0	-4.148e-01	1.0000	21.0	0.86%	24.7	0.96%
EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer	ATTTAATGGG	1e0	-4.116e-01	1.0000	232.0	9.48%	253.1	9.80%
HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer	TTTTATKRGG	1e0	-4.114e-01	1.0000	140.0	5.72%	154.3	5.97%
NRF(NRF)/Promoter/Homer	STGCGCATGCGC	1e0	-4.052e-01	1.0000	2.0	0.08%	2.2	0.08%
GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer	CCGACAYYTYACGGG	1e0	-4.052e-01	1.0000	2.0	0.08%	2.0	0.08%
p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer	ACATGCCCGGGCAT	1e0	-4.052e-01	1.0000	2.0	0.08%	2.0	0.08%
GFY(?)/Promoter/Homer	ACTACAATTCCC	1e0	-4.052e-01	1.0000	2.0	0.08%	2.2	0.09%
HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer	NCYAATAAAA	1e0	-4.039e-01	1.0000	175.0	7.15%	192.6	7.46%
NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer	WGGGGATTTCCC	1e0	-4.027e-01	1.0000	28.0	1.14%	32.7	1.27%
STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer	NYTTCCWGGAAR	1e0	-3.989e-01	1.0000	88.0	3.60%	98.7	3.82%
GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATAASR	1e0	-3.955e-01	1.0000	197.0	8.05%	216.1	8.36%
Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer	NTAATTDGCYAATTANNWWD	1e0	-3.937e-01	1.0000	6.0	0.25%	7.9	0.31%
Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer	NRYTTCCGGY	1e0	-3.842e-01	1.0000	18.0	0.74%	21.7	0.84%
Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer	GCCACACCCA	1e0	-3.731e-01	1.0000	17.0	0.70%	20.9	0.81%
GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer	CRGCTGBNGNSNNSAGATAA	1e0	-3.649e-01	1.0000	5.0	0.20%	6.8	0.26%
GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	AGATSTNDNNDSAGATAASN	1e0	-3.649e-01	1.0000	5.0	0.20%	6.8	0.26%
ABF1/SacCer-Promoters/Homer	CGTRNAAARTGA	1e0	-3.649e-01	1.0000	5.0	0.20%	6.3	0.24%
Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer	TTRAGTGSYK	1e0	-3.648e-01	1.0000	233.0	9.53%	256.1	9.91%
Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer	GGGAAAAMCCCG	1e0	-3.638e-01	1.0000	10.0	0.41%	12.9	0.50%
Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer	BTCAAGGTCA	1e0	-3.610e-01	1.0000	23.0	0.94%	27.0	1.05%
Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer	CVGTSCTCCC	1e0	-3.536e-01	1.0000	107.0	4.37%	120.2	4.65%
Tal1	CATCTG	1e0	-3.534e-01	1.0000	118.0	4.82%	132.5	5.13%
Initiator/Drosophila-Promoters/Homer	NTCAGTYG	1e0	-3.499e-01	1.0000	212.0	8.67%	234.4	9.07%
ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer	GAGCCTGGTACTGWGCCTGR	1e0	-3.455e-01	1.0000	9.0	0.37%	12.0	0.46%
ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer	AGGCCTAG	1e0	-3.368e-01	1.0000	112.0	4.58%	126.4	4.89%
MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer	AACAGCTG	1e0	-3.307e-01	1.0000	51.0	2.09%	59.5	2.30%
ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer	GTCWGCTGTYYCTCT	1e0	-3.302e-01	1.0000	4.0	0.16%	5.5	0.21%
Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer	VBSYGTCTGG	1e0	-3.241e-01	1.0000	87.0	3.56%	99.1	3.83%
ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer	GRTGMTRGAGCC	1e0	-3.163e-01	1.0000	25.0	1.02%	30.3	1.17%
SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer	CCAAAAAGGG	1e0	-3.098e-01	1.0000	145.0	5.93%	163.7	6.34%
CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer	NTNATGCAAYMNNHTGMAAY	1e0	-3.080e-01	1.0000	12.0	0.49%	15.2	0.59%
EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer	NWGGGTGTGGCY	1e0	-3.080e-01	1.0000	12.0	0.49%	15.6	0.60%
ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer	GGVTCTCGCGAGAAC	1e0	-3.062e-01	1.0000	1.0	0.04%	1.2	0.05%
NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer	GGAAATTCCC	1e0	-3.062e-01	1.0000	1.0	0.04%	2.0	0.08%
Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer	NRAACCRGTTYRAACCRGYT	1e0	-3.062e-01	1.0000	1.0	0.04%	1.3	0.05%
YY1(Zf)/Promoter/Homer	CAAGATGGCGGC	1e0	-3.062e-01	1.0000	1.0	0.04%	1.1	0.04%
GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer	AAACYKGTTWDACMRGTTTB	1e0	-2.992e-01	1.0000	23.0	0.94%	28.6	1.11%
TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer	GAGGTCAAAGGTCA	1e0	-2.868e-01	1.0000	3.0	0.12%	4.3	0.17%
RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer	GCTGTGGTTW	1e0	-2.842e-01	1.0000	42.0	1.72%	50.5	1.96%
TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer	ACWTCAAAGG	1e0	-2.782e-01	1.0000	6.0	0.25%	8.7	0.34%
CRE(bZIP)/Promoter/Homer	CSGTGACGTCAC	1e0	-2.782e-01	1.0000	6.0	0.25%	8.5	0.33%
Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer	SCCTAGCAACAG	1e0	-2.772e-01	1.0000	15.0	0.61%	19.2	0.74%
LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer	RGGTTACTANAGGTCA	1e0	-2.758e-01	1.0000	10.0	0.41%	13.3	0.51%
E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer	NVCACCTGBN	1e0	-2.725e-01	1.0000	90.0	3.68%	104.8	4.06%
SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer	AVCAGCTG	1e0	-2.526e-01	1.0000	360.0	14.72%	399.5	15.46%
ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer	AVCCGGAAGT	1e0	-2.513e-01	1.0000	18.0	0.74%	23.9	0.93%
NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer	GGGGGAATCCCC	1e0	-2.497e-01	1.0000	5.0	0.20%	7.7	0.30%
Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer	KBCTACCTGW	1e0	-2.466e-01	1.0000	29.0	1.19%	36.7	1.42%
Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer	AGGTGTCA	1e0	-2.351e-01	1.0000	284.0	11.61%	318.8	12.34%
AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer	CCAGGAACAG	1e0	-2.312e-01	1.0000	281.0	11.49%	315.7	12.22%
RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer	AGGTCAAGGTCA	1e0	-2.292e-01	1.0000	2.0	0.08%	3.7	0.14%
Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer	BTCAAGGTCA	1e0	-2.180e-01	1.0000	37.0	1.51%	47.0	1.82%
GAGA-repeat/Arabidopsis-Promoters/Homer	CTCTCTCTCY	1e0	-2.147e-01	1.0000	88.0	3.60%	104.1	4.03%
Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer	VNRVCAGCTGGY	1e0	-2.069e-01	1.0000	62.0	2.53%	75.0	2.90%
Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer	ACAGCTGTTN	1e0	-1.989e-01	1.0000	182.0	7.44%	209.6	8.11%
Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer	RSCACTYRAG	1e0	-1.980e-01	1.0000	266.0	10.87%	301.4	11.66%
Unknown4/Arabidopsis-Promoters/Homer	CKTCKTCTTY	1e0	-1.968e-01	1.0000	74.0	3.03%	89.7	3.47%
Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer	TGATTRATGGCY	1e0	-1.943e-01	1.0000	13.0	0.53%	18.3	0.71%
PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer	TGACCTTTGCCCCA	1e0	-1.939e-01	1.0000	45.0	1.84%	56.4	2.18%
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer	NYTAATCCYB	1e0	-1.894e-01	1.0000	87.0	3.56%	104.7	4.05%
Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer	CTAATKGV	1e0	-1.721e-01	1.0000	224.0	9.16%	257.9	9.98%
ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer	TGGAACAGMA	1e0	-1.694e-01	1.0000	52.0	2.13%	66.0	2.55%
FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer	HHCACGCGCBTN	1e0	-1.692e-01	1.0000	5.0	0.20%	8.0	0.31%
ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer	AACATCTGGA	1e0	-1.649e-01	1.0000	28.0	1.14%	38.0	1.47%
Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer	VGCTGWCAVB	1e0	-1.608e-01	1.0000	107.0	4.37%	128.6	4.98%
Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer	GGTTAAWCATTAA	1e0	-1.600e-01	1.0000	14.0	0.57%	20.1	0.78%
SeqBias: polyA-repeat	AAAAAAAAAA	1e0	-1.598e-01	1.0000	2345.0	95.87%	2490.7	96.40%
Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer	HACTTCCGGY	1e0	-1.598e-01	1.0000	18.0	0.74%	25.8	1.00%
Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer	GKVTCADRTTWC	1e0	-1.598e-01	1.0000	18.0	0.74%	25.5	0.99%
PCF/Arabidopsis-Promoters/Homer	NNWWWTGGGCYTDDN	1e0	-1.567e-01	1.0000	22.0	0.90%	30.8	1.19%
TATA-box/SacCer-Promoters/Homer	BBHWTATATA	1e0	-1.565e-01	1.0000	105.0	4.29%	126.2	4.89%
Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer	GGGGCTYGKCTGGGA	1e0	-1.546e-01	1.0000	7.0	0.29%	11.6	0.45%
ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer	ARGAGGMCAAAATGW	1e0	-1.546e-01	1.0000	7.0	0.29%	11.2	0.43%
HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer	BSTTCTRGAABVTTCYAGAA	1e0	-1.546e-01	1.0000	7.0	0.29%	12.0	0.46%
CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer	CCATATATGGNM	1e0	-1.522e-01	1.0000	26.0	1.06%	35.3	1.37%
RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer	TAGGGCAAAGGTCA	1e0	-1.499e-01	1.0000	47.0	1.92%	60.9	2.36%
Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer	NAHCAGCTGD	1e0	-1.488e-01	1.0000	59.0	2.41%	74.8	2.90%
ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer	MACCTTCYATGGCTCCCTAKTGCCY	1e0	-1.455e-01	1.0000	1.0	0.04%	2.7	0.10%
Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer	CTGTCTGG	1e0	-1.356e-01	1.0000	88.0	3.60%	108.1	4.19%
RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer	NWAACCACADNN	1e0	-1.340e-01	1.0000	43.0	1.76%	56.3	2.18%
CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer	AYAGTGCCMYCTRGTGGCCA	1e0	-1.307e-01	1.0000	2.0	0.08%	5.0	0.19%
NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer	WNTGTTTRYTTTGGCA	1e0	-1.307e-01	1.0000	2.0	0.08%	4.0	0.15%
EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer	DGTCCCYRGGGA	1e0	-1.245e-01	1.0000	8.0	0.33%	13.1	0.51%
Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	CACAGCAGGGGG	1e0	-1.212e-01	1.0000	30.0	1.23%	41.9	1.62%
Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer	GKTAATGR	1e0	-1.209e-01	1.0000	407.0	16.64%	462.2	17.89%
CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer	ATTGCGCAAC	1e0	-1.137e-01	1.0000	85.0	3.48%	106.9	4.14%
E-box/Drosophila-Promoters/Homer	AACAGCTGTTHN	1e0	-1.136e-01	1.0000	10.0	0.41%	17.0	0.66%
ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer	AAGGKGRCGCAGGCA	1e0	-1.096e-01	1.0000	3.0	0.12%	6.2	0.24%
TOD6?/SacCer-Promoters/Homer	GCGATGAGMT	1e0	-1.087e-01	1.0000	7.0	0.29%	12.1	0.47%
Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer	YTGWCADY	1e0	-1.072e-01	1.0000	302.0	12.35%	349.1	13.51%
Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer	RCCATMTGTT	1e0	-1.053e-01	1.0000	162.0	6.62%	194.6	7.53%
ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer	VAGGTCACNSTGACC	1e0	-1.012e-01	1.0000	9.0	0.37%	15.4	0.60%
PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer	RGGTCTCTAACY	1e0	-1.006e-01	1.0000	22.0	0.90%	32.8	1.27%
Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer	RGAGAGAG	1e0	-1.004e-01	1.0000	200.0	8.18%	237.9	9.21%
Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer	NNNVCTGWGYAAACASN	1e0	-9.883e-02	1.0000	78.0	3.19%	99.8	3.86%
GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer	NAGATWNBNATCTNN	1e0	-9.083e-02	1.0000	4.0	0.16%	8.3	0.32%
Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer	RGCCATTAAC	1e0	-8.408e-02	1.0000	480.0	19.62%	547.7	21.20%
NFY(CCAAT)/Promoter/Homer	RGCCAATSRG	1e0	-8.239e-02	1.0000	59.0	2.41%	78.7	3.05%
Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer	GCTATTTTTAGC	1e0	-7.977e-02	1.0000	22.0	0.90%	33.2	1.28%
STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer	TTCCKNAGAA	1e0	-7.717e-02	1.0000	42.0	1.72%	58.4	2.26%
TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer	CCWGGAATGY	1e0	-7.234e-02	1.0000	36.0	1.47%	51.9	2.01%
Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer	TWGTCTGV	1e0	-6.703e-02	1.0000	213.0	8.71%	256.1	9.91%
Sp1(Zf)/Promoter/Homer	GGCCCCGCCCCC	1e0	-6.694e-02	1.0000	3.0	0.12%	7.7	0.30%
Unknown3/Arabidopsis-Promoters/Homer	AYTAAACCGG	1e0	-6.243e-02	1.0000	6.0	0.25%	12.6	0.49%
NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer	ATTTTCCATT	1e0	-6.116e-02	1.0000	81.0	3.31%	107.0	4.14%
Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer	SVYTTCCNGGAARB	1e0	-5.894e-02	1.0000	40.0	1.64%	57.8	2.24%
Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer	ANTTMRCASBNNNGTGYKAAN	1e0	-5.865e-02	1.0000	15.0	0.61%	25.7	0.99%
Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer	BTBRAGTGSN	1e0	-5.469e-02	1.0000	166.0	6.79%	205.9	7.97%
TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer	YCWGGAATGY	1e0	-5.424e-02	1.0000	56.0	2.29%	77.6	3.00%
SeqBias: A/T bias	WWWWWWWWWW	1e0	-4.448e-02	1.0000	1986.0	81.19%	2144.5	83.00%
DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer	TAGCGCGC	1e0	-4.281e-02	1.0000	10.0	0.41%	19.0	0.74%
AARE(HLH)/mES-cMyc-ChIP-Seq/Homer	GATTGCATCA	1e0	-4.051e-02	1.0000	3.0	0.12%	8.7	0.34%
TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer	CCWGGAATGY	1e0	-3.847e-02	1.0000	56.0	2.29%	79.9	3.09%
Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer	AGGTGHCAGACA	1e0	-3.532e-02	1.0000	7.0	0.29%	15.8	0.61%
OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer	ATTTGCATAACAATG	1e0	-3.428e-02	1.0000	18.0	0.74%	31.3	1.21%
Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer	ATTAACACCT	1e0	-3.144e-02	1.0000	230.0	9.40%	283.1	10.96%
Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer	KTGACCTTGA	1e0	-1.878e-02	1.0000	38.0	1.55%	60.1	2.33%
ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer	AGTTTCASTTTC	1e0	-1.848e-02	1.0000	1.0	0.04%	5.4	0.21%
CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer	AAATTSAATTTN	1e0	-6.942e-03	1.0000	79.0	3.23%	117.8	4.56%
ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer	AGGAARCAGCTG	1e0	-4.829e-03	1.0000	1.0	0.04%	7.4	0.29%
HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer	TTCTAGAABNTTCTA	1e0	-3.155e-03	1.0000	10.0	0.41%	26.9	1.04%
Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer	RRSCACTYAA	1e0	-2.096e-03	1.0000	190.0	7.77%	259.5	10.05%
Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer	MYGGTCACACTG	1e0	-6.860e-04	1.0000	8.0	0.33%	26.6	1.03%
NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer	CTGCGCATGCGC	1e0	0.000e+00	1.0000	0.0	0.00%	1.0	0.04%
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%
REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer	GGMGCTGTCCATGGTGCTGA	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%
Unknown2/Arabidopsis-Promoters/Homer	AAACGACGTCGTTTT	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
 Ik-1	NHTTGGGAATRCC	1e0	0.000e+00	1.0000	2446.0	100.00%	2583.7	100.00%
ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer	GGGTTTTGAAGGATGARTAGGAGTT	1e0	0.000e+00	1.0000	0.0	0.00%	0.0	0.00%
ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer	GNCTGTASTRNTGBCTCHTT	1e0	0.000e+00	1.0000	0.0	0.00%	1.2	0.04%
EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer	GGYAGCAYDTGCTDCCCNNN	1e0	0.000e+00	1.0000	0.0	0.00%	1.3	0.05%
DREF/Drosophila-Promoters/Homer	AVYTATCGATAD	1e0	0.000e+00	1.0000	0.0	0.00%	1.9	0.07%
T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer	ACTTTCGTTTCT	1e0	0.000e+00	1.0000	0.0	0.00%	1.7	0.07%