| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 226011 | - | TTGGCACACCTTTTGCT | 94 | Cj0243c Cj0243c - - hypothetical protein Cj0243c | 51 | 156 |
| 510067 | + | TTGGCACAGTTTTTGCT | 94 | flaG Cj0547 R COG1334 possible flagellar protein | 100 | 158 |
| 957621 | - | TTGGAACGCTTATTGCT | 88 | Cj1026c Cj1026c S COG3018 putative lipoprotein | 54 | 64 |
| 59111 | + | TTGGAACACTTCTTGCT | 87 | Cj0040 Cj0040 - - hypothetical protein Cj0040 | 26 | 135 |
| 1640798 | - | TTGGAACAGAACTTGCT | 87 | flgE2 Cj1729c N COG1749 flagellar hook subunit protein | 97 | 203 |
| 825957 | - | TTGGAACAGTTATTGCT | 86 | flaD Cj0887c N COG1344 putative flagellin | 72 | 383 |
| 61306 | + | TTGGAACACTTATTGCT | 85 | flgD Cj0042 N COG1843 putative flagellar hook assembly protein | 20 | 54 |
| 490442 | - | TTGGAACAGTATTTGCT | 85 | flgB Cj0528c N COG1815 putative flagellar basal-body rod protein | 49 | 81 |
| 1269139 | - | TTGGAACACTTTTTGCT | 85 | flaB Cj1338c N COG1344 flagellin | 53 | 146 |
| 1398430 | + | TTGGAACACTTTTTGCT | 85 | flgI Cj1462 N COG1706 flagellar P-ring protein | 21 | 59 |
