| Position | Strand | Sequence | Score | Description | Distance upstream | Intergenic size |
| 4715608 | - | TTGGCACGGCTATTGCG | 95 | - mll5840 C COG1301 C4-dicarboxylate transport protein | 52 | 197 |
| 5976828 | - | CTGGCACAGCGCTTGCA | 95 | - mll7237 C COG1301 C4-dicarboxylate transport protein | 104 | 306 |
| 759960 | - | CTGGCACAACAATTGCT | 94 | - mll0941 - - unknown protein | 589 | 1188 |
| 4389083 | - | GTGGCACGGTTGTTGCG | 94 | - mll5475 - - unknown protein | 76 | 93 |
| 5823169 | + | CTGGCACAGCGATTGCA | 94 | - mlr7061 R COG1744 hypothetical protein | 59 | 300 |
| 236183 | + | GTGGCACACGAATTGCA | 92 | - mlr0339 E COG0174 glutamine synthetase II | 71 | 589 |
| 1094101 | - | GTGGCATGTGTCTTGCT | 92 | - mll1296 P COG0715 permease protein of ABC transporter | 77 | 266 |
| 1712488 | + | TTGGCACGGAGTTTGCC | 92 | - mlr2091 - - hypothetical protein | 68 | 260 |
| 2329374 | - | ATGGCATGAGGCTTGCT | 92 | - mll2890 E COG3842 ABC transporter, ATP-binding component | 136 | 140 |
| 4795109 | + | CTGGCATGACGTTTGCT | 92 | - msr5928 - - hypothetical protein | 994 | 1562 |
| 4832272 | + | TTGGCACGGTTCATGCT | 92 | - mlr5971 E COG1509 L-lysine 2,3-aminomutase | 153 | 425 |
| 5006089 | - | ATGGCATAGCGCTTGCT | 92 | - mll6183 G COG2814 hypothetical protein | 486 | 1144 |
| 5213640 | - | TTGGCACGTCGCTTGCG | 92 | - mll6389 - - porin | 270 | 1333 |
| 128255 | - | CTGGCACGCTTCCTGCT | 91 | - mll0186 S COG5388 unknown protein | 60 | 412 |
| 599933 | - | TTGGCATGGGGGTTGCA | 91 | - mll0762 E COG0683 urea/short-chain amide ABC transporter, periplasmic urea/short-chain amide-binding protein | 59 | 314 |
| 4694108 | + | TTGGTACGGAGCTTGCT | 91 | - mlr5819 - - hypothetical protein | 490 | 861 |
| 4735969 | - | TTGGCACGAATGATGCT | 91 | - mll5862 C COG2086 nitrogen fixation protein,fixA | 69 | 187 |
| 4797607 | + | TTGGCACGGTACATGCT | 91 | - mlr5932 E COG2515 1-aminocyclopropane-1-carboxylate deaminase | 681 | 1668 |
| 240176 | - | CTGGCACAGTTCGTGCT | 90 | - mll0345 E COG0347 nitrogen regulatory protein P-II | 77 | 357 |
| 1706236 | + | CTGGCAGGCTTATTGCA | 90 | - mlr2085 M COG0438 hypothetical protein | 44 | 344 |
| 2358499 | + | ATGGCACTTACATTGCT | 90 | - mlr2932 - - CHEMOTAXIS MOTC PROTEIN | 181 | 702 |
| 4682355 | + | TTGGCACGACTTTTGAT | 90 | - mlr5805 P COG1858 cytochrome c peroxidase | 146 | 693 |
| 4744417 | - | ATGGCATGGCGCTTGCG | 90 | - mll5873 O COG0678 peroxiredoxin 2 family protein | 284 | 1004 |
| 4831619 | - | TTGGCACGACACATGCA | 90 | - mll5970 E COG0006 putative peptidase | 758 | 956 |
| 5976815 | + | CTGGCAAGGAGTTTGCA | 90 | - mlr7238 T COG4191 two-component C4-dicarboxylate transport system, sensor protein | 198 | 306 |
| 6937726 | - | TTGGCACGCATGATGCA | 90 | - mll8445 E COG3842 ABC-transporter ATP-binding protein | 47 | 216 |
| 46875 | - | CTGGCACGTCTCTGGCA | 89 | - mll0061 - - hypothetical protein | 59 | 351 |
| 298779 | + | CTGGCACGAACGATGCT | 89 | - mlr0414 R COG0431 hypothetical protein | 136 | 534 |
| 3848034 | - | TTGGCACGATACTGGCT | 89 | - msl4838 - - unknown protein | 45 | 144 |
| 4206912 | + | CTGGCATGAAGCTTGCG | 89 | - mlr5276 D COG0489 exopolysaccharide polymerization protein, SUCCINOGLYCAN BIOSYNTHESIS TRANSPORT PROTEIN EXOP | 190 | 285 |
| 4634820 | + | CTGGCACGAAGCATGCA | 89 | - msr5754 - - unknown protein | 1356 | 1864 |
| 4745092 | + | TTGGCACGACTTTTGAA | 89 | - mlr5875 - - unknown protein | 28 | 1004 |
| 1718401 | + | TTGGCATGGCTTGTGCT | 88 | - mlr2098 S COG3237 hypothetical protein | 394 | 452 |
| 3389784 | - | TTGGCACGGAGCTTGAA | 88 | - mll4247 E COG0347 GlnK, nitrogen regulatory protein P-II | 98 | 322 |
| 4559038 | - | TTGACACGGATGTTGCA | 88 | - mll5669 I COG1835 O-antigen acetylase | 154 | 212 |
| 4686758 | - | CTGGCACAAGTTGTGCT | 88 | - mll5809 C COG1012 succinic semialdehyde dehydrogenase | 48 | 552 |
| 4738262 | + | TTGGCGCGGCTTTTGCG | 88 | - mlr5867 V COG1132 ABC transporter, ATP-binding protein exsA | 111 | 403 |
| 4751327 | + | TCGGCACGCGCCTTGCT | 88 | - mlr5882 G COG2513 Phosphoenolpyruvate Mutase | 118 | 508 |
| 4771652 | + | TTGGCACGAGTTTTGAA | 88 | - mlr5905 P COG1348 nitrogenase iron protein, nifH | 69 | 369 |
| 4806248 | - | CTGGCACGTCCTGTGCA | 88 | - mll5942 S COG0316 hypothetical protein | 53 | 1006 |
| 4813543 | - | CTGGCACGAATTTTGAA | 88 | - mll8752 K COG2771 unknown protein | 189 | 1238 |
| 5816251 | + | CTGGCAGCGCTATTGCA | 88 | - msr7053 - - unknown protein | 91 | 727 |
| 6308987 | - | TTGGCACGATTCCTGCG | 88 | - mll7617 - - unknown protein | 42 | 104 |
| 873578 | + | GTGGCGCGGCCTTTGCG | 87 | - mlr1038 K COG1802 probable transcriptional regulator | 4 | 51 |
| 2020619 | + | CTGCCACGCCGTTTGCT | 87 | - mlr2489 E COG0505 carbamoyl-phosphate synthetase small subunit | 42 | 281 |
| 3752607 | + | TTGGCATGACACCTGCT | 87 | - mlr4729 E COG0111 D-3-phosphoglycerate dehydrogenase, frame shift 110-119 (F1->F3) | 241 | 928 |
| 4730179 | - | TTGGCATATCTCTTGCG | 87 | - mll5855 R COG0535 nitrogen fixation protein nifB | 56 | 251 |
| 4788957 | + | GTGGCACGTTCGATGCA | 87 | - mlr5923 Q COG3486 lysine:N6-hydroxylase | 228 | 624 |
| 4960010 | - | TTGGCACGACACATGCG | 87 | - mll6127 M COG3047 outer membrane protein | 115 | 231 |
| 6200491 | - | ATGGCACGGCCATTTCA | 87 | - mll7513 T COG2202 hypothetical protein | 399 | 1228 |
| 135330 | + | GTGGCAAAACCCTTGCC | 86 | - mlr0198 C COG3761 hypothetical protein | 45 | 171 |
| 426122 | - | GTGGGACTATTTTTGCT | 86 | - mll0576 R COG3899 hypothetical protein | 291 | 1130 |
| 2728282 | - | TTGGCACATTTCTGGCT | 86 | - mll3393 E COG0006 putative peptidase | 112 | 370 |
| 3488780 | + | GTGGCGTGCATATTGCA | 86 | - mlr4395 S COG3152 hypothetical protein, putative cytochrome | 37 | 71 |
| 4634423 | - | TTGGAACGGCGATTGCG | 86 | - mll5753 - - unknown protein | 94 | 1864 |
| 4798266 | + | ATGGAACGAGTTTTGCG | 86 | - mlr5932 E COG2515 1-aminocyclopropane-1-carboxylate deaminase | 22 | 1668 |
| 298660 | - | GTAGCACAGACGTTGCT | 85 | - mll0412 E COG0010 probable agmatinase | 262 | 534 |
| 1706062 | - | CCGGCATGAACCTTGCT | 85 | - mll2084 M COG0438 unknown protein | 109 | 344 |
| 1802947 | - | TTGGCATGCAGGGTGCT | 85 | - msl2239 - - unknown protein | 4 | 489 |
| 1931481 | + | TTGGCCGGTCTCTTGCT | 85 | - msr2379 - - unknown protein | 26 | 778 |
| 2012713 | + | CAGGCACTGTAATTGCT | 85 | - mlr2476 K COG0789 probable transcriptional regulator | 16 | 113 |
| 3328396 | + | AGGGCATGAGCCTTGCT | 85 | - mlr4172 Q COG1028 short-chain dehydrogenase | 115 | 294 |
| 4240673 | - | CTGGCATTTGCTTTGCT | 85 | - mll5312 K COG0789 transcriptional regulator | 156 | 225 |
| 5187496 | + | TTGGCACGAGTTTTGAG | 85 | - mlr6364 Q COG2124 cytochrome P-450 | 404 | 624 |
| 5214416 | - | ATGGAACGCAGCTTGCC | 85 | - mll6389 - - porin | 1046 | 1333 |
| 6065817 | - | ATGGCTTGCACCTTGCA | 85 | - msl7333 - - unknown protein | 79 | 239 |
