| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 3131160 | + | CTGGCACAATTATTGCT | 94 | hypA c3286 - - HypA protein | 150 | 200 |
| 2610122 | + | CTGGCACTCCCCTTGCT | 93 | atoD c2764 - - Acetate CoA-transferase alpha subunit | 161 | 196 |
| 3850570 | + | CTGGCACTACTTTTGCT | 93 | yhdW c4034 - - Putative amino-acid ABC transporter binding protein yhdW precursor | 223 | 431 |
| 438253 | + | GTGGCACACTCATTGCT | 92 | prpB c0451 - - Probable methylisocitrate lyase | 64 | 239 |
| 2023924 | + | ATGGCATGAGAGTTGCT | 91 | yeaG c2188 - - Hypothetical protein yeaG | 200 | 436 |
| 2258738 | + | CTGGCAAGCATCTTGCA | 91 | nac c2446 - - Nitrogen assimilation Regulatory protein nac | 133 | 826 |
| 5103227 | - | CTGGCACAGTTCCTGCT | 90 | holC c5359 - - DNA polymerase III, chi subunit | 111 | 258 |
| 1554386 | - | AGGGCACGGTTTTTGCA | 89 | kch c1715 - - Putative potassium channel protein | 172 | 282 |
| 1019621 | + | CTGGCGCGCCTGTTGCG | 88 | ycaQ c1057 - - Hypothetical protein ycaQ | 711 | 1021 |
| 2954080 | - | TTGGCACAGTTACTGCA | 88 | yfhK c3079 - - Putative sensor-like histidine kinase yfhK | 70 | 513 |
| 3116125 | - | TTGGCTCGCCTTTTGCC | 87 | - c3264 - - Hypothetical protein | 166 | 424 |
| 3354528 | - | GTGGCGCGGACGTTGCG | 87 | serA c3494 - - D-3-phosphoglycerate dehydrogenase | 165 | 256 |
| 1610608 | + | TTGGCACGCAAATTGTA | 86 | pspA c1774 - - Phage shock protein A | 133 | 151 |
| 3303908 | + | CTGGCACGCCAGTTCCA | 86 | ygeX c3449 - - Putative diaminopropionate ammonia-lyase | 26 | 58 |
| 2181229 | + | TTGGCGCGCTGTTTGCG | 85 | yedA c2378 - - Hypothetical transport protein yedA | 62 | 173 |
| 2993212 | + | CTGGCACGGAGTTAGCC | 85 | - c3113 - - Hypothetical protein | 898 | 5596 |
| 3302463 | + | CTGGCACACTTATTGTT | 85 | ygeW c3448 - - Hypothetical protein ygeW | 223 | 476 |
| 3859466 | + | CTGGCACGGAGTTAGCC | 85 | yrdA c4040 - - Protein yrdA | 826 | 5346 |
| 4113450 | + | TTGGCACGGCCATTGAG | 85 | yhjE c4334 - - Hypothetical metabolite transport protein yhjE | 46 | 393 |
| 4443186 | - | CTGGCACGGAGTTAGCC | 85 | yieP c4683 - - Hypothetical transcriptional regulator yieP | 826 | 5805 |
