| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 1674862 | + | CTGGCACGCATTTTGCT | 97 | glnA BP1596 - - glutamine synthetase | 46 | 186 |
| 1860832 | + | GTGGCACGGCAGTTGCT | 97 | cspA BP1770 - - cold shock-like protein | 191 | 307 |
| 2279039 | - | CTGGCACGGCGTTTGCA | 96 | acoD BP2157 - - aldehyde dehydrogenase | 98 | 258 |
| 1641488 | - | CTGGCACGCCGTTTGCA | 95 | - BP1562 - - putative membrane protein | 73 | 268 |
| 2903582 | + | ATGGCATGGAATTTGCA | 93 | - BP2736 - - nitrogen regulatory protein P-II | 25 | 708 |
| 2100865 | - | CTGGCACGGTTTGTGCT | 91 | - BP1987 - - probable MarR-family transcriptional regulator | 1631 | 1860 |
| 1409033 | - | CGGGCACGGCGCTTGCT | 90 | - BP1335 - - conserved hypothetical protein | 49 | 908 |
| 531259 | + | CGGGCACGCCGCTTGCT | 89 | - BP0526 - - hypothetical protein | 27 | 109 |
| 2949517 | + | TTGGCGCGGGGCTTGCA | 89 | rpst BP2773 - - 30s ribosomal protein s20 | 43 | 101 |
| 2940671 | - | CTTGCACGGAATTTGCT | 88 | xseA BP2762 - - exodeoxyribonuclease large subunit | 111 | 168 |
| 3348122 | - | GCGGCACGAAAATTGCA | 88 | - BP3140 - - hypothetical protein | 111 | 318 |
| 3451787 | + | GTGGCGCGAGAGTTGCA | 88 | - BP3239 - - putative LysR-family transcriptional regulator | 52 | 126 |
| 488811 | - | CTGGCAGCCCCCTTGCA | 87 | rne BP0475 - - ribonuclease E | 327 | 523 |
| 1413034 | - | CGGGCACGCGGTTTGCT | 87 | - BP1340 - - conserved hypothetical protein | 47 | 394 |
| 1807976 | + | CTGGCATGGAATGTGCT | 87 | - BP1724 - - putative exported protein | 83 | 289 |
| 1945834 | + | CTGGCGTGGCGCTTGCT | 87 | gdhA BP1857 - - glutamate dehydrogenase | 196 | 1138 |
| 1288926 | + | CTGGCAAAGACCTTGCG | 86 | radA BP1227 - - DNA repair protein | 1238 | 1919 |
| 1828665 | - | CTGGCGCGTCTGTTGCG | 86 | cphA BP1740 - - cyanophycin synthetase | 2481 | 2527 |
| 176168 | + | GCGGCACCAATGTTGCA | 85 | - BP0177 - - putative lipoprotein | 182 | 1116 |
| 386084 | - | ATGGCGCCGCCGTTGCA | 85 | argB BP0383 - - acetylglutamate kinase | 193 | 262 |
| 1407090 | - | CGGGCACGCCGCTTGCC | 85 | - BP1333 - - hypothetical protein | 110 | 117 |
| 1413064 | + | CGGGCACGACGCTTGCG | 85 | - BP1342 - - conserved hypothetical protein | 300 | 394 |
| 3063598 | + | CTGGCACCACCCTTGGT | 85 | - BP2887 - - hypothetical protein | 162 | 515 |
