| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 1928404 | + | TTGGCACGGCTGTTGCT | 99 | nifH blr1769 P COG1348 dinitrogenase reductase protein | 146 | 182 |
| 2004000 | + | CTGGCACGGTTGTTGCT | 98 | - blr1850 - - blr1850 | 110 | 427 |
| 6241044 | - | CTGGCACGGCGCTTGCT | 98 | - bll5679 T COG5126 bll5679 | 70 | 255 |
| 7904159 | - | ATGGCACGGAAATTGCT | 97 | - bll7180 E COG0145 hydantoin utilization protein | 59 | 141 |
| 2227019 | - | ATGGCACGCCGATTGCT | 96 | nrgC bll2063 I COG1960 nrgC | 406 | 1222 |
| 2994937 | + | ATGGCACGGCGTTTGCA | 96 | - blr2725 Q COG1335 blr2725 | 25 | 332 |
| 3531701 | - | CTGGCACGGACATTGCT | 96 | - bll3193 T COG0664 bll3193 | 50 | 356 |
| 6156927 | + | ATGGCACGGGAATTGCT | 96 | - blr5598 E COG0601 ABC transporter permease protein | 93 | 255 |
| 6759402 | + | CTGGCACGGTAGTTGCT | 96 | dctA blr6145 C COG1301 C4-dicarboxylate transport protein | 26 | 87 |
| 1919031 | + | CTGGCACGTGACTTGCT | 95 | - blr1755 S COG0316 blr1755 | 17 | 131 |
| 4065705 | + | CTGGCACGCCCATTGCA | 95 | - blr3677 - - blr3677 | 273 | 485 |
| 8020309 | + | CTGGCACACCGCTTGCT | 95 | luxA2 blr7289 C COG2141 luxA2 | 34 | 202 |
| 9099484 | - | ATGGCACGTCGCTTGCT | 95 | - bll8310 - - bll8310 | 258 | 867 |
| 6132603 | + | TTGGCACGGACCTTGCG | 94 | - blr5573 E COG3842 ABC transporter ATP-binding protein | 21 | 270 |
| 1145832 | + | CTGGCACGAACCTTGCG | 93 | - blr1036 E COG0747 ABC transporter substrate-binding protein | 26 | 407 |
| 1156318 | - | ATGGCACATCGCTTGCT | 93 | - bll1044 J COG0154 glutamyl-tRNA(Gln) amidotransferase | 68 | 208 |
| 2149110 | + | TTGGCATGCCAGTTGCT | 93 | - blr1992 - - blr1992 | 312 | 488 |
| 5318470 | - | ATGGCACACGAATTGCT | 93 | - bll4798 E COG2066 bll4798 | 46 | 106 |
| 7373234 | - | CTGGCACATCGCTTGCT | 93 | - bll6702 O COG0625 glutathione S-transferase | 27 | 100 |
| 918291 | + | GTGGCACGGATCGTGCT | 92 | - blr0855 T COG0664 blr0855 | 32 | 88 |
| 1893572 | + | TTGGCATGCGCCTTGCT | 92 | - blr1726 - - blr1726 | 26 | 181 |
| 2816819 | - | CTGGCACTCTCCTTGCT | 92 | - bsl2575 - - bsl2575 | 73 | 204 |
| 3708978 | + | ATGGCATGATGCTTGCT | 92 | - blr3349 F COG0044 blr3349 | 18 | 293 |
| 5121454 | + | GTGGCACGCGATTTGCG | 92 | - blr4624 - - blr4624 | 22 | 252 |
| 7633606 | - | GTGGCACATGCCTTGCT | 92 | hupG bll6937 O COG0526 HupG protein | 60 | 273 |
| 212531 | + | CTGGCAGGCGTTTTGCT | 91 | ptsP blr0217 T COG3605 phosphoenolpyruvate-protein phosphotransferase | 202 | 289 |
| 593259 | - | GTGGCCCGGAGCTTGCT | 91 | guaA bll0553 F COG0518 GMP synthase | 109 | 130 |
| 1887422 | + | GTGGCACTCGAATTGCT | 91 | modB blr1719 P COG4149 molybdenum transport system permease protein | 220 | 1108 |
| 1907768 | + | CTGGCATGCCGGTTGCA | 91 | nifD blr1743 C COG2710 nitrogenase molybdenum-iron protein alpha chain | 40 | 545 |
| 2032449 | + | CTGGCATGTCGATTGCT | 91 | - blr1879 O COG2214 blr1879 | 115 | 1107 |
| 2108902 | - | TTGGCACATGCATTGCT | 91 | - bll1944 - - bll1944 | 362 | 760 |
| 4614600 | + | ATGGCAGGGCAGTTGCA | 91 | - bsr4179 - - bsr4179 | 132 | 388 |
| 5485199 | - | TTGGTACGGAATTTGCT | 91 | clpX bll4943 O COG1219 ATP-dependent Clp protease ATP-binding subunit | 96 | 449 |
| 6396331 | + | TTGGCACGGCTTTCGCT | 91 | flgF blr5827 N COG4786 flagellar basal-body rod protein | 97 | 386 |
| 6709478 | - | CTGGCAAGTTTCTTGCT | 91 | - bll6091 P COG1116 ABC transporter ATP-binding protein | 71 | 105 |
| 7062488 | - | ATGGCAAGAAAATTGCT | 91 | - bll6414 K COG2771 transcriptional regulatory protein | 43 | 221 |
| 966740 | - | CTGGCGCGGAGCTTGCT | 90 | - bll0889 G COG0477 bll0889 | 37 | 157 |
| 3694874 | + | CTGGCGCGCAACTTGCT | 90 | - blr3337 E COG0747 ABC transporter substrate-binding protein | 37 | 125 |
| 3700191 | + | CTGGCATACCATTTGCA | 90 | - blr3341 E COG0747 ABC transporter substrate-binding protein | 57 | 143 |
| 3727697 | - | TCGGCACGCGTCTTGCT | 90 | - bll3363 R COG2244 bll3363 | 20 | 122 |
| 5331857 | - | TTGGCACGTGATTTGCG | 90 | - bsl4812 U COG3847 bsl4812 | 6 | 247 |
| 5920712 | + | CTGGAACGATTATTGCT | 90 | - blr5374 S COG3181 blr5374 | 26 | 188 |
| 6763851 | + | CTGGCACAAAGCTTGCG | 90 | - blr6148 R COG1744 ABC transporter substrate-binding protein | 15 | 346 |
| 7704383 | + | CTGGCCCGCTCCTTGCT | 90 | - blr6996 N COG3144 blr6996 | 20 | 344 |
| 655278 | + | CTGGCACGGCATTTGAT | 89 | glnK blr0612 E COG0347 nitrogen regulatory protein PII | 28 | 385 |
| 1883094 | + | TTGGCAAAAATGTTGCA | 89 | - blr1716 L COG3335 blr1716 | 103 | 879 |
| 2114254 | + | GCGGCACGCAGCTTGCT | 89 | - blr1954 - - blr1954 | 294 | 451 |
| 2237541 | - | CTGGCACGCACGATGCT | 89 | - bsl2070 - - bsl2070 | 1476 | 2291 |
| 2275760 | + | ATGGCAGGCCTTTTGCG | 89 | ectC blr2106 G COG0662 L-ectoine synthase | 140 | 733 |
| 3645169 | - | CGGGCACGAGACTTGCT | 89 | - bll3287 E COG3842 ABC transporter ATP-binding protein | 46 | 89 |
| 4607099 | + | TTGGCACGCTAAATGCT | 89 | glnII blr4169 E COG0174 glutamine synthetase II | 71 | 179 |
| 4801573 | + | CTGGCATTGAATTTGCT | 89 | - blr4344 S COG0316 blr4344 | 8 | 64 |
| 5100123 | - | ATGGCAGGAAGGTTGCA | 89 | - bll4604 H COG1893 bll4604 | 132 | 236 |
| 5850660 | - | ATGGCTCGCTGCTTGCT | 89 | - bll5301 T COG4566 two-component response regulator | 48 | 600 |
| 6302055 | - | CTGGCACGCTCCATGCA | 89 | - bll5738 O COG1765 bll5738 | 72 | 248 |
| 28141 | + | CTGGCATCGACGTTGCA | 88 | - blr0028 Q COG4689 blr0028 | 315 | 515 |
| 774450 | + | TTGGCACCGGGATTGCG | 88 | ptsN blr0725 G COG1762 nitrogen regulatory IIA protein | 123 | 223 |
| 2026911 | - | CCGGCACGCGGCTTGCT | 88 | - bll1872 - - bll1872 | 48 | 383 |
| 2171896 | + | TTGGTATGGCACTTGCT | 88 | - bsr2010 - - bsr2010 | 14 | 487 |
| 2198487 | + | ATGGTACAAGACTTGCT | 88 | fixA blr2038 C COG2086 electron transfer flavoprotein beta chain | 23 | 518 |
| 2223072 | - | CTGGCCTGACTCTTGCT | 88 | groES3 bll2060 O COG0234 GroES3 chaperonin | 75 | 349 |
| 2232118 | - | CTGGCACGAAGAATGCA | 88 | nfeC bll2067 - - nodulate formation efficiency C protein | 211 | 1189 |
| 2256359 | - | TCGGCACGCGACTTGCT | 88 | - bll2085 - - bll2085 | 170 | 280 |
| 2317564 | + | TCGGCACGCGATTTGCT | 88 | - blr2143 Q COG2124 blr2143 | 19 | 94 |
| 2899171 | - | CTGGCCCGGGGGTTGCA | 88 | dxs bll2651 H COG1154 1-deoxy-D-xylulose-5-phosphate synthase | 297 | 529 |
| 3083669 | + | TTGGCACGGAAATTGAA | 88 | - blr2806 P COG2223 nitrite extrusion protein | 133 | 339 |
| 3169364 | - | TTGGCGCGTTCCTTGCT | 88 | - bll2877 E COG0747 ABC transporter substrate-binding protein | 117 | 400 |
| 5610396 | - | CGGGCACGAACATTGCT | 88 | - bll5056 E COG0747 bll5056 | 63 | 257 |
| 6069944 | - | CTGGCGCGTCATTTGCA | 88 | - bsl5509 - - bsl5509 | 150 | 253 |
| 6297299 | - | GTGGCATGCTCCTTGCG | 88 | nrtA bll5734 P COG0715 ABC transporter nitrate-binding protein | 49 | 157 |
| 6405375 | + | GTGGCACAGCACTCGCA | 88 | flgI blr5838 N COG1706 flagellar P-ring protein precursor | 9 | 219 |
| 6431120 | - | TTGGCATAGCCCTTGCG | 88 | - bll5854 N COG1749 bll5854 | 79 | 271 |
| 7453363 | + | TCGGCACGCAGCTTGCA | 88 | - blr6766 G COG0366 blr6766 | 171 | 204 |
| 7650576 | + | CCGGCACGCCGATTGCT | 88 | modA blr6951 P COG0725 molybdenum ABC transporter Molybdate-binding protein | 56 | 179 |
| 8447589 | - | GTGGCAGCGCGCTTGCT | 88 | - bll7701 - - bll7701 | 283 | 427 |
| 508391 | - | TTGGCTCGCGGATTGCT | 87 | acnA bll0466 C COG1048 aconitase | 177 | 243 |
| 1940448 | - | ACGGCACGCGGATTGCT | 87 | - bll1780 P COG4148 bll1780 | 538 | 692 |
| 2056563 | - | TTGGCATCATGGTTGCT | 87 | - bll1900 L COG4584 bll1900 | 495 | 1343 |
| 2138787 | - | TCGGCACGCCTCTTGCC | 87 | - bll1981 - - bll1981 | 98 | 363 |
| 3169349 | - | CTGGAATGGCGCTTGCA | 87 | - bll2877 E COG0747 ABC transporter substrate-binding protein | 102 | 400 |
| 5064208 | - | CTGGCACGCAACTTGTA | 87 | - bll4571 P COG0155 bll4571 | 92 | 239 |
| 6511253 | - | TTGGCGCCGATCTTGCA | 87 | lspL bll5920 M COG0451 UDP-glucuronic acid epimerase | 141 | 222 |
| 6733821 | - | TTGGCTTGGAACTTGCT | 87 | - bsl6119 - - bsl6119 | 85 | 115 |
| 7638461 | - | TTGGCCTGCTTCTTGCT | 87 | hupS bll6942 C COG1740 uptake hydrogenase precursor | 60 | 198 |
| 7649205 | - | CTGGCCCGAATGTTGCC | 87 | hupN bll6949 P COG3376 HupN protein | 8 | 287 |
| 8191630 | + | GTGGCACGCGGCTTGTT | 87 | proC blr7454 E COG0345 delta 1-pyrroline-5-carboxylate reductase | 14 | 146 |
| 1060020 | - | TTGGTACGGGATTTGCG | 86 | - bll0966 T COG0642 two-component hybrid sensor and regulator | 48 | 72 |
| 1904566 | + | CTGGCACAAGACTTGAT | 86 | - bsr1739 C COG1145 ferredoxin | 28 | 539 |
| 2584348 | + | ACGGCACGAATTTTGCC | 86 | - blr2374 M COG0438 blr2374 | 37 | 863 |
| 2611102 | - | TTGGCAGGGAACATGCT | 86 | - bll2394 T COG2199 bll2394 | 202 | 431 |
| 3674475 | + | TTGGTATGCAAATTGCT | 86 | - blr3320 I COG1028 hypothetical oxidoreductase | 23 | 69 |
| 5027592 | + | CTGGGATGCTTCTTGCA | 86 | - blr4538 S COG1944 blr4538 | 658 | 832 |
| 5193190 | - | CCGGCACGGCGTTTGCG | 86 | - bll4688 I COG1835 bll4688 | 275 | 330 |
| 6777949 | + | TTGGCTCTGGTCTTGCA | 86 | - blr6160 C COG1319 blr6160 | 32 | 136 |
| 7044356 | + | GTGGCACGATCATTCCT | 86 | - blr6398 E COG0765 blr6399 | 150 | 470 |
| 7384756 | - | TTGGCTCTCGTCTTGCT | 86 | - bll6708 - - bll6708 | 153 | 450 |
| 7906462 | + | GTGTCACGAGGGTTGCT | 86 | - bsr7184 - - conserved hypothetical protein | 705 | 731 |
| 8087674 | - | TTGGCACTACACCTGCA | 86 | sigA bll7349 K COG0568 primary sigma factor | 204 | 375 |
| 8783697 | - | ATGGCGCGCCATTTGCG | 86 | - bll7996 - - bll7996 | 16 | 578 |
| 1174735 | - | ATGGCTCGCCATTTGCC | 85 | - bll1060 K COG0583 transcriptional regulatory protein | 80 | 250 |
| 2066078 | + | TTGGCATGAATGTGGCA | 85 | - blr1911 L COG3335 blr1911 | 127 | 1530 |
| 2400184 | + | GTGGCCTGATAATTGCT | 85 | dadA blr2222 E COG0665 D-amino acid dehydrogenase, small subunit | 47 | 71 |
| 4847926 | - | CTGGCCCCAGAATTGCT | 85 | - bll4384 E COG0834 bll4384 | 52 | 169 |
| 4862222 | + | ATCGCATGGTTGTTGCT | 85 | - blr4400 - - blr4400 | 217 | 243 |
| 5360962 | - | TTGGCAGGGCCTATGCA | 85 | glnS bll4837 J COG0008 glutaminyl-tRNA synthetase | 151 | 155 |
| 5491376 | + | TTGGCATAGACCCTGCT | 85 | glnB blr4948 E COG0347 nitrogen regulatory protein PII | 156 | 345 |
| 6700057 | - | CTGGCGCCGTCGTTGCA | 85 | - bll6082 I COG1028 bll6082 | 75 | 197 |
| 6785272 | - | ATGGAATGCTCTTTGCT | 85 | - bll6165 - - bll6165 | 62 | 91 |
| 7594138 | - | CCGGCATGGAAATTGCT | 85 | - bll6899 E COG0683 ABC transporter substrate-binding protein | 49 | 60 |
| 8413483 | - | TTGGCACCGATATTGAT | 85 | - bsl7667 - - bsl7667 | 94 | 1088 |
