| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 2140847 | + | GTGGCACGGCAGTTGCT | 97 | cspA BPP2001 - - cold shock-like protein | 149 | 265 |
| 1427410 | + | CTGGCACGGCGTTTGCA | 96 | acoD BPP1323 - - aldehyde dehydrogenase | 4 | 195 |
| 2414700 | + | CTGGCACGCCGTTTGCA | 95 | - BPP2268 - - putative membrane protein | 42 | 267 |
| 3001723 | - | CTGGCACGGCATTTGCG | 94 | hmgL BPP2803 - - hydroxymethylglutaryl-CoA lyase | 1258 | 1373 |
| 2795935 | - | ATGGCATGGAATTTGCA | 93 | - BPP2593 - - nitrogen regulatory protein P-II | 56 | 670 |
| 2532574 | - | CTGGCACGGTTTGTGCT | 91 | - BPP2368 - - putative membrane protein | 76 | 305 |
| 3092933 | + | CTGGCACCGATCTTGCG | 91 | rpoN BPP2887 - - RNA polymerase sigma-54 factor | 36 | 227 |
| 2868735 | - | CGGGCACGGCGCTTGCT | 90 | - BPP2671 - - conserved hypothetical protein | 49 | 54 |
| 3214757 | - | CTGGCGCGCATTTTGCT | 90 | glnA BPP2988 - - glutamine synthetase | 77 | 186 |
| 999356 | + | CCGGCACGGCGGTTGCT | 89 | - BPP0924 - - conserved hypothetical protein | 38 | 189 |
| 2903387 | - | CGGGCACGGGCCTTGCT | 89 | - BPP2704 - - Putative membrane protein | 1614 | 1647 |
| 3624368 | - | CTGGCGCGGCTCTTGCG | 89 | - BPP3363 - - AraC-family regulatory protein | 853 | 1468 |
| 2758622 | + | CTTGCACGGAATTTGCT | 88 | xseA BPP2566 - - exodeoxyribonuclease large subunit | 80 | 350 |
| 2863936 | - | CGGGCACGCCGTTTGCT | 88 | - BPP2665 - - putative membrane protein | 11 | 20 |
| 3883536 | + | GTGGCGCGAGAGTTGCA | 88 | - BPP3595 - - putative LysR-family transcriptional regulator | 52 | 126 |
| 278336 | + | CTGGCCCGGGTGTTGCG | 87 | - BPP0268 - - conserved hypothetical protein | 284 | 323 |
| 969123 | + | GTGGCAGCGGAATTGCT | 87 | - BPP0897 - - probable LysR-family transcriptional regulator | 70 | 110 |
| 1239929 | + | CTGGCGCATCTGTTGCT | 87 | maeB BPP1160 - - NADP-dependent malic enzyme | 198 | 930 |
| 1672867 | + | CTGGCGTGGCGCTTGCT | 87 | gdhA BPP1568 - - glutamate dehydrogenase | 136 | 1069 |
| 2871641 | - | CGGGCACGCGGTTTGCT | 87 | - BPP2674 - - conserved hypothetical protein | 47 | 94 |
| 3292599 | - | CTGGCATGGAATGTGCT | 87 | - BPP3052 - - putative exported protein | 114 | 289 |
| 3573265 | + | CTGGCAGCCCCCTTGCA | 87 | rne BPP3318 - - ribonuclease E | 296 | 508 |
| 817191 | + | GTGGCGCTGGCCTTGCT | 86 | gcvT BPP0769 - - glycine cleavage system T protein | 650 | 1290 |
| 1696217 | + | CTGGCGCGTCTATTGCG | 86 | - BPP1589 - - putative transmembrane regulator | 40 | 127 |
| 2176124 | - | TTGGCCCGATCCTTGCC | 86 | paaG BPP2036 - - probable enoyl-CoA hydratase | 219 | 270 |
| 2855014 | - | CGGGCACGGCGCTTGCC | 86 | - BPP2655 - - Putative exported protein | 72 | 188 |
| 3011316 | - | CTGGCGCCGGACTTGCT | 86 | gabD BPP2812 - - succinate-semialdehyde dehydrogenase [NADP+] | 225 | 1704 |
| 3095032 | + | CGGGCACGGCGCTTGCG | 86 | glgA BPP2889 - - glycogen synthase | 49 | 258 |
| 4443618 | + | GTGGCGCGACGCTTGCG | 86 | - BPP4111 - - putative cytochrome c | 226 | 488 |
| 425657 | + | CCGGCAGGGAACTTGCT | 85 | psiF BPP0406 - - phosphate starvation-inducible protein precursor | 88 | 240 |
| 797750 | + | GCGGCACCAATGTTGCA | 85 | - BPP0752 - - putative lipoprotein | 183 | 229 |
| 2704928 | - | CTGGCACCACCCTTGGT | 85 | - BPP2510 - - hypothetical protein | 241 | 570 |
| 2750812 | - | TTGGCGCTGGGCTTGCA | 85 | rpst BPP2556 - - 30s ribosomal protein s20 | 74 | 1316 |
| 2855054 | + | CCGGCACAGCACTTGCG | 85 | - BPP2656 - - Conserved hypothetical protein | 59 | 188 |
| 2866792 | - | CGGGCACGCCGCTTGCC | 85 | - BPP2669 - - hypothetical protein | 11 | 18 |
| 2871671 | + | CGGGCACGACGCTTGCG | 85 | - BPP2675 - - Hypothetical protein | 0 | 94 |
| 2927314 | - | ATGGCACTGCGTTGGCT | 85 | - BPP2730 - - putative exported protein | 73 | 147 |
| 4381025 | + | ATGGCGCCGCCGTTGCA | 85 | argB BPP4047 - - acetylglutamate kinase | 30 | 130 |
