Table 2.
Pattern discovery using ROMs (regions of overlapping matches) with maximal score to find binding sites in DNA
| Regulatory protein | Number of genes in the regulon* | Touched by max† | Percent touched by max‡ | Touched by other§ | Total percent touched¶ | Not touched** | Without dyads†† |
| ArgR | 6 | 2 | 33.33 | 4 | 100.00 | 0 | 0 |
| CRP | 54 | 42 | 77.78 | 8 | 92.59 | 4 | 0 |
| FNR | 17 | 10 | 58.82 | 0 | 58.82 | 2 | 5 |
| GlpR | 4 | 3 | 75.00 | 1 | 100.00 | 0 | 0 |
| IlvY | 2 | 2 | 100.00 | 0 | 100.00 | 0 | 0 |
| LexA | 8 | 8 | 100.00 | 0 | 100.00 | 0 | 0 |
| MalI | 2 | 2 | 100.00 | 0 | 100.00 | 0 | 0 |
| MalT | 4 | 4 | 100.00 | 0 | 100.00 | 0 | 0 |
| MelR | 2 | 2 | 100.00 | 0 | 100.00 | 0 | 0 |
| NR_I | 3 | 3 | 100.00 | 0 | 100.00 | 0 | 0 |
| NarL | 6 | 3 | 50.00 | 0 | 50.00 | 2 | 1 |
| PhoB | 4 | 4 | 100.00 | 0 | 100.00 | 0 | 0 |
| PurR | 12 | 11 | 91.67 | 0 | 91.67 | 1 | 0 |
| TorR | 1 | 1 | 100.00 | 0 | 100.00 | 0 | 0 |
| TrpR | 5 | 4 | 80.00 | 1 | 100.00 | 0 | 0 |
| TyrR | 8 | 7 | 87.50 | 0 | 87.50 | 1 | 0 |
*The total number of genes in the regulon with a known binding site (in the 400+50 upstream regions). †The number of regions where a ROM (region of overlapping matches) with the highest number of matches (max ROM) touches a known binding site. ‡This value expressed as a percentage. §Number of regions where either a ROM or dyad touches a known binding site, but the max ROM does not. ¶The percentage of all upstream regions in which any ROM touches a binding site. **Number of regions with dyads, but no match between known binding sites and ROMs. ††Number of regions with no dyads at all.