| Matrix_120 | BEE2 | Not available | Upstream | -270 |
| Matrix_331 | GBF1 | Not available | Upstream | -269 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -270 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -603 |
| | | Upstream | -954 |
| | | Upstream | -960 |
| Matrix_480 | BES1 | Not available | Upstream | -244 |
| Matrix_491 | AT1G68670;AT3G25790 | Not available | Upstream | -1029 |
| Motif_125 | BOXIINTPATPB | Box II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoter | Upstream | -7 |
| | | Upstream | -723 |
| Motif_139 | RHERPATEXPA7 | Right part of RHEs (Root Hair-specific cis-Elements) conserved among the Arabidopsis thaliana A7 (AtEXPA7) orthologous (and paralogous) genes from diverse angiosperm species with different hair distribution patterns | Upstream | -272 |
| | | Upstream | -533 |
| | | Upstream | -832 |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Upstream | -370 |
| Motif_69 | CTRMCAMV35S | CT-rich motif (inverted GAGA) found in a 60-nucleotide region (S1) downstream of the transcription start site of the CaMV 35S RNA; Can enhance gene expression; Inverted GAGA | Upstream | -629 |
| | | Upstream | -631 |
| | | Upstream | -633 |
| Motif_79 | UPRMOTIFIIAT | Motif II in the conserved UPR (unfolded protein response) cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90, SBR-like, Ca-ATPase 4, CNX1, PDI, etc | Upstream | -125 |
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