| Matrix_93 | YAB5 | Not Available | | 78.11% |
| Matrix_430 | TOE2 | Not Available | | 72.08% |
| Matrix_351 | HAT9; ATHB-4; ATHB2; HAT22; HAT14 | Not Available | | 71.96% |
| Matrix_435 | ATHB51 | Not Available | | 71.17% |
| Matrix_302 | HAT1; HAT2 | Not Available | | 69.63% |
| Matrix_461 | ATHB12 | Not Available | | 68.87% |
| Matrix_479 | TOE1 | Not Available | | 68.37% |
| Matrix_182 | ATHB6 | Not Available | | 67.47% |
| Matrix_87 | AT1G19000 | Not Available | | 67.19% |
| Matrix_382 | AT3G04850 | Not Available | | 66.75% |
| Matrix_508 | APL; AT3G12730; AT3G24120; UNE16 | Not Available | | 66.39% |
| Matrix_54 | AHL20 | Not Available | | 65.95% |
| Matrix_71 | ATHB7 | Not Available | | 65.93% |
| Matrix_491 | AT1G68670; AT3G25790 | Not Available | | 65.92% |
| Matrix_308 | INO | Not Available | | 65.61% |
| Matrix_162 | AtPHR1 | Not Available | | 65.24% |
| Motif_285 | HDZIP2ATATHB2 | Binding site of the Arabidopsis homeobox gene (ATHB-2) found in its own promoter; Located between -72 and -80; Similar to the HD-ZIP-2 binding consensus sequence; ATHB-2 is regulated by light signals which function as a negative autoregulator of its own gene | | 64.78% |
| Matrix_441 | ATHB5 | Not Available | | 64.66% |
| Matrix_442 | AT5G62260 | Not Available | | 64.55% |
| Matrix_16 | AT3G04450; PHL1 | Not Available | | 64.45% |
| Matrix_212 | ATHB-12 | Not Available | | 64.33% |
| Matrix_131 | HDG12; EDT1; GL2; HDG8 | Not Available | | 63.81% |
| Matrix_69 | AT2G03500 | Not Available | | 63.49% |
| Matrix_284 | KAN2; KAN3; KAN; KAN4 | Not Available | | 63.42% |
| Matrix_259 | AT1G50680; AT1G51120 | Not Available | | 63.26% |
| Matrix_341 | HMGA | Not Available | | 63.25% |
| Matrix_495 | HD-GL2-1; ANL2 | Not Available | | 63.21% |
| Matrix_125 | AHL12 | Not Available | | 63.19% |
| Matrix_157 | LHY; RVE2 | Not Available | | 63.11% |
| Motif_138 | RAP2.2 | Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves | | 62.83% |
| Matrix_97 | APRR2 | Not Available | | 62.75% |
| Matrix_8 | KAN1 | Not Available | | 62.74% |
| Matrix_231 | HDG2; HDG3; ATML1; HB-7 | Not Available | | 62.63% |
| Matrix_500 | WRKY43 | Not Available | | 62.57% |
| Matrix_114 | EPR1; AT3G10113 | Not Available | | 62.49% |
| Matrix_88 | AHL12 | Not Available | | 62.17% |
| Matrix_483 | ICU4 | Not Available | | 62.12% |
| Matrix_354 | AHL12 | Not Available | | 62.01% |
| Matrix_32 | AHL25 | Not Available | | 61.99% |
| Matrix_103 | ATHB1 | The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities | | 61.99% |
| Matrix_322 | NST3; ANAC015; BRN2 | Not Available | | 61.90% |
| Matrix_249 | WRKY11 | Not Available | | 61.83% |
| Matrix_447 | RVE1 | Not Available | | 61.58% |
| Matrix_324 | AT2G01060 | Not Available | | 61.37% |
| Matrix_168 | AHL25 | Not Available | | 61.34% |
| Motif_624 | ATHB6 binding site motif | Consensus binding sequence for Arabidopsis homeodomain-leucine zipper protein, ATHB6; ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses; Homeodomain protein ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses in Arabidopsis | | 61.05% |
| Matrix_202 | WRKY71; WRKY28; WRKY8 | Not Available | | 60.85% |
| Matrix_204 | WOX13 | Not Available | | 60.66% |
| Motif_352 | ATHB5 binding site motif | Consensus binding sequence for Arabidopsis class I HDzip (Homeodomein-leucine zipper) protein, ATHB5; ATHB5 protein forms dimers in solution; ATHB5 and ATHB6 exhibit identical DNA binding specificities; ATHB5 forms heterodimers with other class I HDzip proteins; DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro | | 60.63% |
| Motif_377 | SURE2STPAT21 | Sucrose Responsive Element 2 (SURE2); A motif conserved among genes regulated by sucrose; See also SURE1ST; Found between -184 and -156 bp in the patatin (a major tuber protein) gene promoter of potato | | 60.51% |
| Matrix_415 | WRKY27 | Not Available | | 60.45% |
| Matrix_361 | AT1G25550 | Not Available | | 60.40% |
| Matrix_283 | GATA15; GATA17; AT4G16141; GATA22; GATA23; GATA16; GNC | Not Available | | 60.37% |
| Matrix_4 | ARR14 | Not Available | | 60.36% |
| Matrix_318 | ATHB16 | Not Available | | 60.35% |
| Matrix_273 | ANAC55 | Not Available | | 60.32% |
| Matrix_210 | ARR1 | Not Available | | 60.31% |
| Matrix_142 | ZFP8 | Not Available | | 60.29% |
| Matrix_336 | AT5G08520 | Not Available | | 60.25% |
| Matrix_143 | GATA14; GATA6; GATA5 | Not Available | | 60.20% |
| Matrix_258 | WOX13 | Not Available | | 60.09% |
| Matrix_423 | AT3G04030 | Not Available | | 59.85% |
| Matrix_391 | AHL20 | Not Available | | 59.77% |
| Matrix_197 | NAP | Not Available | | 59.71% |
| Matrix_116 | ANAC55 | Not Available | | 59.70% |
| Matrix_46 | AT4G21895 | Not Available | | 59.65% |
| Matrix_99 | DOF4.7 | Not Available | | 59.11% |
| Matrix_236 | CCA1 | Not Available | | 58.96% |
| Matrix_167 | ZAT6 | Not Available | | 58.93% |
| Motif_169 | ATHB2 binding site motif | Recognition sequence of Arabidopsis Athb-2 protein; Athb-2 protein has a HD-Zip motif (homeodomain (HD) with a closely linked leucine zipper motif (Zip)); The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities | | 58.76% |
| Matrix_141 | AT3G25990 | Not Available | | 58.26% |
| Matrix_12 | EIN3; EIL2 | Not Available | | 58.25% |
| Matrix_316 | WRKY15; WRKY39; WRKY7; WRKY74 | Not Available | | 58.24% |
| Matrix_20 | ANAC030; NST1; NAC066 | Not Available | | 58.24% |
| Matrix_328 | AT1G76580 | Not Available | | 58.19% |
| Matrix_151 | ASIL1 | Not Available | | 58.06% |
| Matrix_431 | ATHB21; HB-3 | Not Available | | 58.05% |
| Motif_277 | ATHB1 binding site motif | Recognition sequence of Arabidopsis Athb-1 protein; Athb-1 protein has a HD-Zip motif (homeodomain (HD) with a closely linked leucine zipper motif (Zip)); HD-Zip domain binds to DNA as a dimer; The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities | | 58.05% |
| Matrix_333 | GATA3 | Not Available | | 58.02% |
| Matrix_314 | WRKY65; WRKY14; WRKY35; WRKY69; WRKY16; ATWRKY52 | Not Available | | 57.98% |
| Matrix_185 | AHL25 | Not Available | | 57.87% |
| Matrix_62 | HAT5 | Not Available | | 57.81% |
| Matrix_383 | CCA1 | Not Available | | 57.78% |
| Motif_87 | AGL22; AGL20; AGL24 | Regulation of floral patterning by flowering time genes | | 57.77% |
| Motif_235 | C8GCARGAT | Binding site of plant MADS-domain protein AGL15; CArG motif with a longer A/T-rich core;A variant of CArG motif, with a longer A/T-rich core; Binding site for AGL15 (AGAMOUS-like 15) | | 57.76% |
| Matrix_9 | AT5G04760 | Not Available | | 57.70% |
| Matrix_72 | CDF2 | Not Available | | 57.64% |
| Matrix_160 | RVE1 | Not Available | | 57.50% |
| Matrix_207 | WRKY10; WRKY57; AT2G44745; ATWRKY13; WRKY49 | Not Available | | 57.48% |
| Matrix_521 | AHL20 | Not Available | | 57.46% |
| Matrix_241 | HB-1; AT5G44180 | Not Available | | 57.21% |
| Matrix_384 | ATWRKY17 | Not Available | | 57.18% |
| Matrix_494 | OBP4 | Not Available | | 56.98% |
| Matrix_262 | ATGRP2B; CSDP2 | Not Available | | 56.93% |
| Matrix_17 | WRKY22 | Not Available | | 56.86% |
| Motif_298 | GMHDLGMVSPB | Binding site of the soybean homeodomein leucine zipper proteins (GmHdl56, GmHdl57); Found in the phosphate response domain of the soybean VspB promoter; Located between -536 and -527; VspB encodes vacuolar glycoprotein acid phosphatase that serve as vegetative storage protein | | 56.80% |
| Matrix_193 | RAV1 | Not Available | | 56.74% |
| Matrix_265 | NGA3 | Not Available | | 56.74% |
| Matrix_420 | ANAC58 | Not Available | | 56.73% |
| Motif_642 | SEF1MOTIF | SEF1 (soybean embryo factor 1) binding motif; sequence found in 5'-upstream region (-640; -765) of soybean beta-conglicinin (7S globulin) gene | | 56.72% |
| Motif_34 | LECPLEACS2 | Core element in LeCp (tomato Cys protease) binding cis-element (from -715 to -675) in LeAcs2 gene | | 56.55% |
| Matrix_248 | ZFP5 | Not Available | | 56.50% |
| Matrix_59 | AT4G00238; AT4G00250 | Not Available | | 56.41% |
| Matrix_370 | WRKY50; WRKY51 | Not Available | | 56.40% |
| Motif_195 | TATABOX4 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | | 56.33% |
| Motif_142 | HDZIPIIIAT | Ath b-9 HD-Zip (HD-Zip-9), a member of a small family of HD-Zip proteins (HD-ZIP III), in Arabidopsis recognize this sequence | | 56.24% |
| Matrix_227 | AT1G64620 | Not Available | | 56.23% |
| Motif_166 | RAP2.2 | Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves | | 56.20% |
| Matrix_512 | HAT3 | Not Available | | 56.14% |
| Matrix_23 | ANAC46 | Not Available | | 55.89% |
| Matrix_255 | cdf3 | Not Available | | 55.89% |
| Matrix_268 | EMB2749; VND5; SMB; VND1; ANAC076; NAC101; ANAC105 | Not Available | | 55.86% |
| Matrix_163 | AT2G20110 | Not Available | | 55.86% |
| Matrix_335 | HSFB2A | Not Available | | 55.84% |
| Matrix_75 | WRKY29 | Not Available | | 55.73% |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | | 55.61% |
| Matrix_70 | GATA26 | Not Available | | 55.51% |
| Matrix_286 | GATA7 | Not Available | | 55.51% |
| Matrix_51 | LFY | Not Available | | 55.36% |
| Matrix_444 | AT1G19485; AT4G17950 | Not Available | | 55.26% |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 55.12% |
| Matrix_504 | WRKY40 | Not Available | | 55.11% |
| Matrix_271 | AT3G16350 | Not Available | | 55.09% |
| Matrix_416 | ASL5 | Not Available | | 55.01% |
| Matrix_102 | WRKY21 | Not Available | | 54.88% |
| Matrix_434 | ARR11 | Not Available | | 54.86% |
| Matrix_44 | CUC3; anac046; NAC3; ANAC087; ATNAC6; CUC2 | Not Available | | 54.75% |
| Matrix_152 | EIL1; AT5G65100 | Not Available | | 54.71% |
| Matrix_106 | AT5G47390 | Not Available | | 54.58% |
| Matrix_471 | KAN4 | Not Available | | 54.49% |
| Matrix_206 | CUC1; ANAC100 | Not Available | | 54.43% |
| Matrix_226 | GATA1 | Not Available | | 54.39% |
| Matrix_411 | DOF5.6 | Not Available | | 54.34% |
| Motif_131 | P1BS | PHR1-binding sequence found in the upstream regions of phosphate starvation responsive genes from several plant species; phr1 (phosphate starvation response 1) gene codes for PHR1 protein related to PSR1 gene in C. reinhardtii | | 54.15% |
| Matrix_523 | FUSCA3 | Not Available | | 54.11% |
| Matrix_463 | HAT3.1 | Not Available | | 54.10% |
| Matrix_263 | WRKY33; WRKY19; WRKY32 | Not Available | | 54.04% |
| Motif_345 | GT-1 | Molecular dissection of GT-1 from Arabidopsis | | 53.94% |
| Matrix_254 | MYB52 | Not Available | | 53.93% |
| Matrix_6 | AT1G70000 | Not Available | | 53.91% |
| Motif_475 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 53.82% |
| Matrix_129 | ABF1 | Not Available | | 53.78% |
| Motif_370 | TATABOX2 | TATA box; TATA box found in the 5'upstream region of pea legA gene; sporamin A of sweet potato; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | | 53.75% |
| Matrix_13 | HAT5 | Not Available | | 53.73% |
| Matrix_56 | BZIP17; BZIP28; BZIP49 | Not Available | | 53.66% |
| Matrix_519 | ATDOF2.4 | Not Available | | 53.56% |
| Matrix_3 | WRKY48 | Not Available | | 53.55% |
| Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | | 53.52% |
| Matrix_195 | GATA2; GATA4 | Not Available | | 53.49% |
| Matrix_120 | BEE2 | Not Available | | 53.45% |
| Matrix_408 | GATA12 | Not Available | | 53.42% |
| Matrix_396 | AP3 | Not Available | | 53.41% |
| Matrix_1 | TOE2 | Not Available | | 53.32% |
| Matrix_177 | ADOF2 | Not Available | | 53.28% |
| Motif_373 | TATABOX1 | TATA box; TATA box found in the 5'upstream region of rice alpha-amylase; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | | 53.21% |
| Matrix_205 | AGL15 | Not Available | | 53.16% |
| Matrix_513 | SOL1; TSO1; TCX2 | Not Available | | 53.09% |
| Matrix_240 | AT4G29000 | Not Available | | 52.97% |
| Matrix_327 | ARR11 | Not Available | | 52.87% |
| Matrix_429 | KAN4 | Not Available | | 52.79% |
| Matrix_325 | WRKY4; WRKY3; WRKY58; ATWRKY34; WRKY20; ATWRKY2 | Not Available | | 52.78% |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | | 52.78% |
| Motif_590 | MYB3 binding site motif | Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses | | 52.75% |
| Matrix_225 | MYB52 | Not Available | | 52.71% |
| Matrix_100 | AT1G48610 | Not Available | | 52.71% |
| Matrix_85 | SPL5 | Not Available | | 52.68% |
| Matrix_171 | LBD3; LBD4 | Not Available | | 52.61% |
| Matrix_289 | WRKY25 | Not Available | | 52.57% |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | | 52.55% |
| Matrix_220 | WRKY18 | Not Available | | 52.42% |
| Matrix_101 | ERF5 | Not Available | | 52.41% |
| Matrix_357 | WRKY61; WRKY6; WRKY9; WRKY36; WRKY47; WRKY42; WRKY31; WRKY72 | Not Available | | 52.33% |
| Matrix_326 | AT5G07310; Rap2.6L; AT5G61890 | Not Available | | 52.31% |
| Matrix_422 | TOE1 | Not Available | | 52.30% |
| Matrix_317 | AT1G06070; AT2G31370; AT2G40620 | Not Available | | 52.28% |
| Matrix_112 | TBP2; TFIID-1 | Not Available | | 52.21% |
| Matrix_96 | TMO6 | Not Available | | 52.20% |
| Matrix_465 | MYC4 | Not Available | | 52.17% |
| Matrix_53 | MYC3 | Not Available | | 52.16% |
| Matrix_368 | ATWRKY56; WRKY45; WRKY75; WRKY24 | Not Available | | 52.16% |
| Matrix_161 | MYBC1; AT3G10760; LUX; AT5G05090; AT5G59570 | Not Available | | 52.15% |
| Matrix_355 | ERF10; ERF11 | Not Available | | 52.15% |
| Matrix_492 | ETT | Not Available | | 52.14% |
| Matrix_181 | Dof5.7 | Not Available | | 52.13% |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | | 52.10% |
| Matrix_78 | AT3G45610 | Not Available | | 52.07% |
| Matrix_427 | ZAT14 | Not Available | | 52.06% |
| Matrix_178 | HSFB2A | Not Available | | 52.04% |
| Matrix_340 | HSFC1 | Not Available | | 52.03% |
| Motif_5 | SORLREP1 | Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | | 51.90% |
| Motif_673 | Bellringer/replumless/pennywise BS2 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 51.77% |
| Matrix_311 | TGA1 | Not Available | | 51.76% |
| Motif_669 | FUS3; ABI3 | Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product | | 51.74% |
| Matrix_347 | WOX14; WOX10 | Not Available | | 51.51% |
| Matrix_487 | AT1G29160 | Not Available | | 51.49% |
| Matrix_166 | TGA4 | Not Available | | 51.45% |
| Motif_523 | GATA-2; GATA-4; GATA-3; GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 51.40% |
| Matrix_84 | AtGRF6 | Not Available | | 51.39% |
| Matrix_380 | ATMYR1 | Not Available | | 51.35% |
| Matrix_312 | ARF11; MP; ARF6; IAA21; ARF8; ARF4 | Not Available | | 51.22% |
| Matrix_63 | ARR10 | Not Available | | 51.18% |
| Motif_375 | ERELEE4 | ERE (ethylene responsive element) of tomato E4 and carnation GST1 genes; GST1 is related to senescence; Found in the 5'-LTR region of TLC1.1 retrotransposon family in Lycopersicon chilense; ERE motifs mediate ethylene-induced activation of the U3 promoter region | | 51.18% |
| Matrix_37 | GATA27 | Not Available | | 51.16% |
| Matrix_282 | bZIP60 | Not Available | | 51.15% |
| Matrix_389 | ILR3 | Not Available | | 51.13% |
| Matrix_330 | MYC2; TT8 | Not Available | | 51.12% |
| Matrix_515 | ddf2; ATCBF3; CBF1; CBF4 | Not Available | | 51.11% |
| Matrix_505 | GATA8 | Not Available | | 51.09% |
| Matrix_188 | SPL4 | Not Available | | 50.96% |
| Matrix_139 | OBF5 | Not Available | | 50.93% |
| Matrix_502 | AT3G13040 | Not Available | | 50.89% |
| Matrix_501 | DAG2 | Not Available | | 50.86% |
| Matrix_128 | TGA2 | Not Available | | 50.81% |
| Matrix_274 | EDF3 | Not Available | | 50.80% |
| Matrix_235 | WRKY67; WRKY64; WRKY63; WRKY66 | Not Available | | 50.73% |
| Matrix_425 | TIFY2A | Not Available | | 50.73% |
| Motif_356 | S2FSORPL21 | S2F binding site (S2 site) in spinach RPL21 gene encoding the plastid ribosomal protein L21; S2 site (CATACAWW) is conserved in promoter region of many nuclear genes encoding plastid proteins; Leaf-specific, light-independent regulatory element; S2 site is related to but different from the light-responsive GT-1 binding site | | 50.67% |
| Matrix_410 | TOE2 | Not Available | | 50.58% |
| Matrix_277 | RAP2.6 | Not Available | | 50.45% |
| Matrix_154 | AT1G22190; AT1G36060; AT1G64380; RAP2.4; AT2G20880; AT2G22200; AT4G13620; AT4G28140; AT4G39780; AT5G65130 | Not Available | | 50.41% |
| Matrix_199 | AT1G69170; SPL9; SPL15; SPL13A; SPL13B | Not Available | | 50.38% |
| Matrix_421 | GLK1 | Not Available | | 50.32% |
| Matrix_456 | bZIP60 | Not Available | | 50.11% |
| Motif_614 | MYBGAHV | Central element of gibberellin (GA) response complex (GARC) in high-pI alpha-amylase gene in barley; Similar to c-myb and v-myb consensus binding site; GAmyb binds specifically to the TAACAAA box in vitro; GAmyb is the sole GA-regulated transcriptional factor required for transcriptional activation of the high-pI alpha-amylase; GARC consist of the pyrimidine, TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE and pyrimidine box in RAmy1A are partially involved in sugar repression | | 50.09% |
| Motif_667 | TATABOXOSPAL | Binding site for OsTBP2, found in the promoter of rice pal gene encoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNA binding and bending activities of OsTBP2 and synergistically enhanced OsTBP2-mediated transcription from the pal promoter | | 50.01% |
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