| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | | 68.18% |
| Motif_49 | TATAPVTRNALEU | TATA-like motif; A TATA-like sequence found in Phaseolus vulgaris tRNALeu gene promoter; Frequently observed upstream of plant tRNA genes; Found in maize glycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter; Binding site of TATA binding protein (TBP) | | 63.64% |
| Matrix_205 | AGL15 | Not Available | | 63.06% |
| Matrix_523 | FUSCA3 | Not Available | | 62.93% |
| Matrix_51 | LFY | Not Available | | 62.46% |
| Matrix_391 | AHL20 | Not Available | | 61.23% |
| Motif_41 | ARR2 | Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators | | 59.09% |
| Motif_229 | D2GMAUX28 | D2; DNase I protected sequence found in the soybean auxin responsive gene, Aux28, promoter; Located between -703 and -716; A/T-rich sequence | | 59.09% |
| Motif_489 | SORLREP3AT | one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and also all SORLIPs;Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | | 59.09% |
| Matrix_225 | MYB52 | Not Available | | 57.17% |
| Matrix_483 | ICU4 | Not Available | | 56.56% |
| Matrix_444 | AT1G19485; AT4G17950 | Not Available | | 56.14% |
| Matrix_185 | AHL25 | Not Available | | 55.86% |
| Matrix_276 | AT1G01520; AT3G09600; AT4G01280; LCL1; AT5G52660 | Not Available | | 55.81% |
| Motif_55 | MRNASTA1CRPSBD | mRNA stability determinant found in 5'-UTR of psbD mRNA of Chlamydomonas reinhardtii; Required for the stable accumulation; Located within the first 12 nucleotides of the leader region | | 55.76% |
| Motif_147 | HDMOTIFPCPR2 | HD (homeodomain) protein target site in parsley pathogenesis-related protein 2 (PR2); A potential in vivo target site | | 55.76% |
| 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 | | 55.76% |
| Motif_62 | AtMYB44 | Two novel MYB homologues with changed expression in late embryogenesis-defective Arabidopsis mutants | | 55.76% |
| Motif_216 | PYRIMIDINEBOXHVEPB1 | Pyrimidine box found in the barley EPB-1 (cysteine proteinase) gene promoter; Located between -120 to -113; Required for GA induction | | 55.76% |
| Matrix_474 | ANAC014; ANAC062; NTL9; TIP | Not Available | | 55.76% |
| Matrix_424 | MYB59 | Not Available | | 55.59% |
| Matrix_29 | AP1 | Not Available | | 54.92% |
| Matrix_269 | FHY3/FAR1 | Not Available | | 54.62% |
| 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 | | 54.55% |
| Motif_136 | SEF4MOTIFGM7S | SEF4 binding site; Soybean consensus sequence found in 5'upstream region (-199) of beta-conglycinin (7S globulin) gene (Gmg17.1); Binding with SEF4 (soybean embryo factor 4) | | 54.55% |
| Motif_27 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | | 54.55% |
| Motif_321 | TATABOX5 | TATA box; TATA box found in the 5'upstream region of pea (Pisum sativum) glutamine synthetase gene; a functional TATA element by in vivo analysis | | 54.55% |
| Motif_533 | Bellringer/replumless/pennywise BS3 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 54.55% |
| Matrix_521 | AHL20 | Not Available | | 54.27% |
| Matrix_125 | AHL12 | Not Available | | 53.94% |
| Matrix_240 | AT4G29000 | Not Available | | 53.66% |
| Matrix_383 | CCA1 | Not Available | | 53.64% |
| Matrix_182 | ATHB6 | Not Available | | 53.26% |
| Matrix_382 | AT3G04850 | Not Available | | 53.09% |
| Matrix_88 | AHL12 | Not Available | | 53.00% |
| Matrix_204 | WOX13 | Not Available | | 52.93% |
| Matrix_32 | AHL25 | Not Available | | 52.91% |
| Matrix_318 | ATHB16 | Not Available | | 52.89% |
| Matrix_434 | ARR11 | Not Available | | 52.86% |
| Matrix_160 | RVE1 | Not Available | | 52.56% |
| 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 | | 52.44% |
| Motif_654 | DR5GMGH3 | DR5; A highly active synthetic auxin response element; Created by site-directed mutations in a natural composite AuxRE found in the soybean GH3 promoter; The DR5 showed greater auxin responsiveness; Binding site of ARF1 | | 52.44% |
| Motif_487 | ACIIIPVPAL2 | ACIII element found at -246 to -238 of bean PAL2 promoter; ACIII element is required for vascular-specific gene expression; See also ACIPVPAL2 and ACIIPVPAL2; Three AC-elements, which are possible Myb protein binding sites, together with a G-box, interact to direct the complex patterns of tissu-specific expression of pAL2 gene | | 52.44% |
| Motif_424 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 52.44% |
| Matrix_106 | AT5G47390 | Not Available | | 52.42% |
| Matrix_392 | ARR2 | Not Available | | 52.33% |
| Matrix_469 | NAC041; NAC083 | Not Available | | 52.13% |
| Matrix_6 | AT1G70000 | Not Available | | 52.10% |
| Matrix_431 | ATHB21; HB-3 | Not Available | | 51.85% |
| Matrix_89 | SOC1 | Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis | | 51.85% |
| Matrix_354 | AHL12 | Not Available | | 51.81% |
| Matrix_284 | KAN2; KAN3; KAN; KAN4 | Not Available | | 51.37% |
| Matrix_404 | OBP4 | Not Available | | 51.29% |
| Matrix_271 | AT3G16350 | Not Available | | 51.28% |
| Motif_231 | EIN3 | Ethylene signaling in Arabidopsis involves feedback regulation via the elaborate control of EBF2 expression by EIN3 | | 51.22% |
| 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 | | 51.22% |
| Motif_671 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 51.22% |
| Motif_323 | MYB1LEPR | Tomato Pti4(ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1(GTTAGTT), G box (CACGTG)) | | 51.22% |
| Motif_499 | AtMYC2 | A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth | | 51.22% |
| Motif_376 | WRKY63 | ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis | | 51.22% |
| Motif_668 | TCA1MOTIF | TCA-1 (tobacco nuclear protein 1) binding site; Related to salicylic acid-inducible expression of many genes; Found in barley beta-1,3-glucanase and over 30 different plant genes which are known to be induced by one or more forms of stress; A similar sequence (TCATTTCTT) was found in tobacco Tnt1 retrotransposon promoter | | 51.22% |
| Motif_73 | AtWER | Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis | | 51.22% |
| Motif_662 | MYB26PS | Myb26 binding site; Myb26 recognizes the c-Myb and P-box-like binding sites representing cis-elements in the promoter regions of several phenylpropanoid biosynthetic genes; Identical to P-box in maize, and to Myb305 binding site in snapdragon | | 51.22% |
| Motif_29 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 51.22% |
| Matrix_211 | MYB3 | Not Available | | 51.07% |
| Matrix_168 | AHL25 | Not Available | | 51.06% |
| Matrix_273 | ANAC55 | Not Available | | 51.04% |
| Matrix_435 | ATHB51 | Not Available | | 51.03% |
| Matrix_495 | HD-GL2-1; ANL2 | Not Available | | 50.60% |
| Matrix_203 | GATA9; GATA12 | Not Available | | 50.26% |
| Matrix_9 | AT5G04760 | Not Available | | 50.11% |
| Matrix_347 | WOX14; WOX10 | Not Available | | 50.10% |
| Matrix_337 | MYB46 | Not Available | | 50.09% |
| Motif_338 | HY5 | Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression | | 50.00% |
| Motif_295 | HY5 | Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression | | 50.00% |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | | 50.00% |
| Motif_601 | D3GMAUX28 | D3; DNase I protected sequence found in the soybean auxin responsive gene, Aux28, promoter; Located between -750 and -760; A/T-rich sequence | | 50.00% |
| 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 | | 50.00% |
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