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| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 1142933 | + | ATGGCACAGTTATTGCT | 95 | - CT1219 - - conserved hypothetical protein | 38 | 220 |
| 1435838 | + | CTGGCACAAAAATTGCT | 93 | nifH CT1533 - - nitrogenase iron protein | 76 | 125 |
| 505440 | + | GCGGCACTGATATTGCT | 86 | - CT0492 - - hypothetical protein | 8 | 276 |
| 1648047 | - | TTGTCACGGATTTTGCG | 85 | - CT1733 - - hypothetical protein | 291 | 375 |