| Matrix_236 | CCA1 | Not Available | | 77.37% |
| Matrix_327 | ARR11 | Not Available | | 73.34% |
| Matrix_199 | AT1G69170; SPL9; SPL15; SPL13A; SPL13B | Not Available | | 68.93% |
| Matrix_85 | SPL5 | Not Available | | 66.97% |
| Matrix_505 | GATA8 | Not Available | | 65.56% |
| Matrix_67 | GLK1 | Not Available | | 65.45% |
| Matrix_416 | ASL5 | Not Available | | 64.33% |
| Matrix_143 | GATA14; GATA6; GATA5 | Not Available | | 63.50% |
| Matrix_137 | SPL1; SPL12 | Not Available | | 63.42% |
| Matrix_70 | GATA26 | Not Available | | 62.94% |
| Matrix_333 | GATA3 | Not Available | | 62.70% |
| Matrix_276 | AT1G01520; AT3G09600; AT4G01280; LCL1; AT5G52660 | Not Available | | 62.38% |
| Matrix_522 | GATA11; GATA13 | Not Available | | 61.87% |
| Matrix_37 | GATA27 | Not Available | | 60.83% |
| Matrix_453 | EIL3 | Not Available | | 60.68% |
| Matrix_421 | GLK1 | Not Available | | 60.55% |
| Matrix_76 | GATA10 | Not Available | | 60.34% |
| Matrix_494 | OBP4 | Not Available | | 59.59% |
| Matrix_328 | AT1G76580 | Not Available | | 59.48% |
| Matrix_203 | GATA9; GATA12 | Not Available | | 59.23% |
| Matrix_284 | KAN2; KAN3; KAN; KAN4 | Not Available | | 58.67% |
| Matrix_218 | TIFY2B; TIFY1 | Not Available | | 58.24% |
| Motif_556 | INTRONUPPER | 5' exon-intron splice junctions of plant introns; Plant intron upper sequence; Consensus sequence for plant introns | | 58.14% |
| Matrix_383 | CCA1 | Not Available | | 57.61% |
| Matrix_254 | MYB52 | Not Available | | 57.11% |
| Matrix_38 | SPL14 | Not Available | | 57.09% |
| Matrix_444 | AT1G19485; AT4G17950 | Not Available | | 56.75% |
| Matrix_512 | HAT3 | Not Available | | 56.55% |
| Matrix_425 | TIFY2A | Not Available | | 56.48% |
| Motif_222 | AGMOTIFNTMYB2 | AG-motif found at -114 of the promoter of NtMyb2 gene; NtMyb2 is a regulator of the tobacco retrotransposon Tto1 and the defence-related gene phenylalanine ammonia lyase (PAL), which are induced by various stress such as wounding or elicitor treatment; AGP1 (GATA-type zinc finger protein) binding site | | 56.42% |
| Matrix_195 | GATA2; GATA4 | Not Available | | 56.22% |
| Matrix_160 | RVE1 | Not Available | | 56.21% |
| Motif_673 | Bellringer/replumless/pennywise BS2 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 56.10% |
| Motif_293 | NONAMERATH4 | Nonamer motif of Arabidopsis thaliana histone H4 promoter;Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene | | 55.91% |
| Matrix_125 | AHL12 | Not Available | | 55.80% |
| Matrix_180 | SPL1 | Not Available | | 55.76% |
| Matrix_408 | GATA12 | Not Available | | 55.72% |
| Matrix_415 | WRKY27 | Not Available | | 55.71% |
| Matrix_366 | ARR14 | Not Available | | 55.67% |
| Motif_282 | D4GMAUX28 | D4; DNase I protected sequence found in the soybean auxin responsive gene, Aux28, promoter; D1 and D4 share a very similar core sequence TAGTXXCTGT and TAGTXCTGT, respectively; D1/D4-like sequence were identified in several other auxin-responsive genes | | 55.61% |
| Matrix_434 | ARR11 | Not Available | | 55.26% |
| Motif_632 | EREGCC | GCC box in ERE (ethylene responsive element); Ethylene-responsive region of tobacco (N.t.) chitinase gene contains two copies of the GCC-box; ERF2 and ERF4 enhanced the GCC box-mediated transcription; ERF3 reduced the transcription of the reporter gene in tobacco protoplasts; Binding site of AtEBP; Pti4/5/6 proteins from tomato which belong to the ERF family activate the expression of GCC box-containing PR genes; ERF3 was found to interact with NtUBC2, a ubiquitin-conjugating enzyme; Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene | | 54.94% |
| Matrix_504 | WRKY40 | Not Available | | 54.81% |
| Motif_582 | ARR1; ARR2 | Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators | | 54.58% |
| Motif_443 | KN1; BP | The knotted1-like homeobox gene BREVIPEDICELLUS regulates cell differentiation by modulating metabolic pathways. Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity | | 54.31% |
| Matrix_502 | AT3G13040 | Not Available | | 54.08% |
| Matrix_450 | SPL7 | Not Available | | 53.87% |
| Matrix_471 | KAN4 | Not Available | | 53.79% |
| Matrix_243 | RAP2.12; RAP2.2 | Not Available | | 53.78% |
| Matrix_197 | NAP | Not Available | | 53.73% |
| Matrix_17 | WRKY22 | Not Available | | 53.73% |
| Motif_408 | EVENINGAT | Evening element found 46 times in the promoters of 31 cycling genes in Arabidopsis thaliana; Required for circadian control of gene expression; EE (evening element) motif; Also found in the promoter of the Solanum melongena gene encoding cysteine protease, and identified as cis-element for its circadian regulation;Orchestrated transcription of key pathways in Arabidopsis by the circadian clock | | 53.69% |
| Matrix_231 | HDG2; HDG3; ATML1; HB-7 | Not Available | | 53.65% |
| Matrix_350 | ARR14 | Not Available | | 53.55% |
| Matrix_412 | GL1 | Not Available | | 53.53% |
| Matrix_141 | AT3G25990 | Not Available | | 53.53% |
| Matrix_487 | AT1G29160 | Not Available | | 53.48% |
| Matrix_181 | Dof5.7 | Not Available | | 53.33% |
| Matrix_275 | ZAP1 | Characterization of a zinc-dependent transcriptional activator from Arabidopsis | | 53.26% |
| Matrix_8 | KAN1 | Not Available | | 53.23% |
| Matrix_75 | WRKY29 | Not Available | | 53.21% |
| Matrix_114 | EPR1; AT3G10113 | Not Available | | 53.15% |
| Matrix_202 | WRKY71; WRKY28; WRKY8 | Not Available | | 53.11% |
| Motif_464 | ARR1; ARR2 | Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators | | 53.08% |
| Motif_331 | AtWER | Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis | | 53.01% |
| Matrix_352 | LEC2 | Not Available | | 52.95% |
| Motif_485 | NRRBNEXTA | NRR (negative regulatory region) in promoter region of Brassica napus extA extensin gene; Removal of this region leads to expression in all tissues within the stem internode, petiole and root | | 52.94% |
| Matrix_152 | EIL1; AT5G65100 | Not Available | | 52.94% |
| Motif_52 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 52.85% |
| Matrix_129 | ABF1 | Not Available | | 52.74% |
| Matrix_230 | ARR11 | Not Available | | 52.74% |
| Matrix_334 | AT3G23230 | Not Available | | 52.70% |
| Motif_523 | GATA-2; GATA-4; GATA-3; GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 52.67% |
| Matrix_53 | MYC3 | Not Available | | 52.58% |
| Matrix_347 | WOX14; WOX10 | Not Available | | 52.55% |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | | 52.52% |
| Matrix_52 | ZAT18 | Not Available | | 52.46% |
| Matrix_79 | FUS3 | Not Available | | 52.42% |
| Matrix_66 | AtLEC2 | Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis | | 52.41% |
| Matrix_283 | GATA15; GATA17; AT4G16141; GATA22; GATA23; GATA16; GNC | Not Available | | 52.37% |
| Matrix_142 | ZFP8 | Not Available | | 52.35% |
| Matrix_221 | SPL7 | Not Available | | 52.35% |
| Matrix_226 | GATA1 | Not Available | | 52.34% |
| Matrix_88 | AHL12 | Not Available | | 52.33% |
| Matrix_411 | DOF5.6 | Not Available | | 52.23% |
| Matrix_165 | KNAT1 | Not Available | | 52.18% |
| Matrix_177 | ADOF2 | Not Available | | 52.11% |
| Motif_188 | CDA1ATCAB2 | CDA-1 (CAB2 DET1-associated factor 1) binding site in DtRE (dark response element) f of chlorophyll a/b-binding protein2 (CAB2) gene in Arabidopsis | | 52.09% |
| Matrix_256 | IXR11; KNAT5; KNAT4; KNAT3 | Not Available | | 52.04% |
| Matrix_279 | HRS1 | Not Available | | 52.00% |
| Motif_239 | MYB2 | Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen | | 51.99% |
| Matrix_286 | GATA7 | Not Available | | 51.92% |
| Matrix_303 | ATWOX13 | Not Available | | 51.92% |
| Motif_20 | HSELIKENTGLN2 | HSE-like sequence in 5' upstream region of beta-1,3-glucanase gene (GLN2) of tobacco | | 51.91% |
| Motif_183 | TRANSINITDICOTS | Context sequence of translational initiation codon in dicots | | 51.89% |
| Matrix_442 | AT5G62260 | Not Available | | 51.85% |
| Matrix_268 | EMB2749; VND5; SMB; VND1; ANAC076; NAC101; ANAC105 | Not Available | | 51.85% |
| Matrix_227 | AT1G64620 | Not Available | | 51.84% |
| Matrix_307 | RGL2; RGL3 | Not Available | | 51.81% |
| Motif_429 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | | 51.71% |
| Matrix_263 | WRKY33; WRKY19; WRKY32 | Not Available | | 51.69% |
| Matrix_507 | TCP3 | Not Available | | 51.67% |
| Matrix_259 | AT1G50680; AT1G51120 | Not Available | | 51.63% |
| Matrix_465 | MYC4 | Not Available | | 51.60% |
| Matrix_157 | LHY; RVE2 | Not Available | | 51.55% |
| Matrix_40 | TCP2 | Not Available | | 51.52% |
| Matrix_31 | SPL1 | Not Available | | 51.43% |
| Matrix_481 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | | 51.39% |
| Matrix_506 | DRNL; ATERF-4 | Not Available | | 51.33% |
| Matrix_3 | WRKY48 | Not Available | | 51.29% |
| Motif_191 | AtERF-4; AtERF-3 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression | | 51.29% |
| Matrix_330 | MYC2; TT8 | Not Available | | 51.12% |
| Matrix_120 | BEE2 | Not Available | | 51.11% |
| Matrix_469 | NAC041; NAC083 | Not Available | | 51.03% |
| Matrix_168 | AHL25 | Not Available | | 50.97% |
| Motif_580 | L1BOXATPDF1 | L1 box found in promoter of Arabidopsis thaliana PROTODERMAL FACTOR1 (PDF1) gene; Located between -134 and -127; Involved in L1 layer-specific expression; L1-specific homeodomain protein ATML can bind to the L1 box; Y=C/T; A cotton fiber gene, RD22-like 1 (RDL1), contains a homeodomain binding L1 box and a MYB binding motif ; HDZip IV; Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein | | 50.95% |
| Motif_512 | GLMHVCHORD | GLM (GCN4-like motif) found in the promoter of barley B1- and c-hordein gene; Involved in the nitrogen response of c-hordein promoter; SPA, a seed-specific basic leucine zipper protein from wheat, can activate transcription from the GCN4-like motif (GLM) of -326 LMWG-1D1 promoter | | 50.78% |
| Matrix_447 | RVE1 | Not Available | | 50.78% |
| Matrix_500 | WRKY43 | Not Available | | 50.76% |
| Motif_248 | L1-box | Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element | | 50.69% |
| Matrix_285 | DDF1 | Not Available | | 50.67% |
| Matrix_384 | ATWRKY17 | Not Available | | 50.66% |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | | 50.63% |
| Matrix_392 | ARR2 | Not Available | | 50.62% |
| Motif_637 | SARD1; CBP60g | Control of salicylic acid synthesis and systemic acquired resistance by two members of a plant-specific family of transcription factors | | 50.57% |
| Matrix_389 | ILR3 | Not Available | | 50.44% |
| Matrix_99 | DOF4.7 | Not Available | | 50.41% |
| Motif_574 | MYB2 binding site motif | MYB transcription factors in plants | | 50.35% |
| Matrix_410 | TOE2 | Not Available | | 50.33% |
| Matrix_306 | TGA1 | TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | | 50.26% |
| Matrix_72 | CDF2 | Not Available | | 50.18% |
| Matrix_368 | ATWRKY56; WRKY45; WRKY75; WRKY24 | Not Available | | 50.18% |
| Motif_106 | PR2GCNT | GC element conserved in the 5' upstream regions of group 2 PR protein genes (beta-1,3-glucanase (GLN2), chitinase (CHN17, CHN50)) of tobacco | | 50.17% |
| Matrix_427 | ZAT14 | Not Available | | 50.17% |
| Matrix_200 | PIL5; AT4G28790; AT4G28800; AT4G28811; AT4G28815 | Not Available | | 50.07% |
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