| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 4271081 | - | CTGGCACGACGGTTGCA | 96 | - ECs4264 S COG1690 hypothetical protein | 54 | 188 |
| 405333 | + | GTGGCACACCCCTTGCT | 95 | - ECs0385 G COG2513 putative phosphonomutase 2 | 31 | 239 |
| 4320083 | - | CTGGCACAGTTGTTGCT | 95 | - ECs4310 K COG0568 RNA polymerase sigma32 factor | 56 | 245 |
| 538607 | + | CTGGCACACCGCTTGCA | 94 | - ECs0504 E COG0347 nitrogen regulatory protein P-II 2 | 37 | 181 |
| 3574299 | + | CTGGCACAATTATTGCT | 94 | - ECs3582 R COG0375 HypA protein | 15 | 212 |
| 769404 | - | TTGGCACATCTATTGCT | 93 | - ECs0694 E COG0834 putative periplasmic binding transport protein | 297 | 397 |
| 4153964 | + | CTGGCACTACTTTTGCT | 93 | - ECs4141 E COG0834 putative periplasmic binding transport protein | 173 | 539 |
| 2468408 | + | ATGGCATGAGAGTTGCT | 91 | - ECs2492 T COG2766 hypothetical protein | 88 | 436 |
| 2731475 | - | CTGGCAAGCATCTTGCA | 91 | - ECs2784 K COG0583 nitrogen assimilation control protein | 71 | 457 |
| 2431582 | - | CTGGCACGAACCCTGCA | 90 | - ECs2454 E COG4992 acetylornithine delta-aminotransferase | 88 | 446 |
| 3498638 | - | CTGGCAGAGCTTTTGCT | 90 | - ECs3512 L COG0582 putative site specific recombinase | 221 | 323 |
| 1753394 | - | AGGGCACGGTTTTTGCA | 89 | - ECs1750 P COG1226 putative potassium channel protein | 281 | 301 |
| 3556350 | + | CTGGCACGCAATCTGCA | 89 | - ECs3566 C COG0426 putative flavodoxin | 32 | 112 |
| 939083 | - | TTGGCAGGTTAATTGCT | 88 | - ECs0858 S COG0391 putative structural protein | 71 | 397 |
| 3411733 | - | TTGGCACAGTTACTGCA | 88 | - ECs3422 T COG0642 putative 2-component sensor protein | 206 | 513 |
| 4853932 | - | TTGGCACAGTTTTCGCT | 88 | - ECs4792 E COG0174 glutamine synthetase | 99 | 373 |
| 972380 | - | CTGGCACGATTTTTTCA | 87 | - ECs0889 E COG0834 permease of periplasmic glutamine-binding protein | 70 | 404 |
| 3574171 | - | TTGGCACAAAAAATGCT | 87 | - ECs3581 - - transcriptional repressor of hyc and hyp operons | 52 | 212 |
| 1304427 | + | ATGGCAGCGTATTTGCT | 86 | - ECs1243 - - hypothetical protein | 104 | 286 |
| 1314875 | - | CTGGCATCCGCTTTGCA | 86 | - ECs1258 C COG2141 hypothetical protein | 44 | 231 |
| 1875845 | + | TTGGCACGCAAATTGTA | 86 | - ECs1881 K COG1842 phage shock protein | 36 | 152 |
| 5010718 | + | ATGGCATGATTTCTGCT | 86 | - ECs4926 T COG0642 sensor kinase HydH | 16 | 97 |
| 5294822 | - | CTGGCATCACACTTGCG | 86 | - ECs5194 R COG3054 hypothetical protein | 97 | 286 |
| 1831552 | + | CTGGCAATAGATTTGCT | 85 | - ECs1846 L COG0551 DNA topoisomerase type I omega protein | 186 | 380 |
| 3744501 | + | CTGGCACACTTATTGTT | 85 | - ECs3743 E COG0078 putative carbamoyl transferase | 75 | 476 |
| 4163270 | + | CTGGCACGGAGTTAGCC | 85 | - ECs4145 R COG0663 putative transferase | 745 | 5833 |
| 4735771 | - | CTGGCACGGAGTTAGCC | 85 | - ECs4697 K COG2186 hypothetical protein | 1144 | 5945 |
| 5017472 | - | CTGGCACGGAGTTAGCC | 85 | - ECs4929 F COG0138 phosphoribosylaminoimidazolecarboxamideformyltra nsferase | 1136 | 5744 |
