Table 2.
Predicted sRNAs
| Peaka (nt) | Start | End | cDNA # | Prev gene | Next gene | Gene direction | Name | Distributionb | |
|---|---|---|---|---|---|---|---|---|---|
| ncr1160 | 70 | 2697037 | 2697106 | 920 | yqaJ | yqaI | /−/+/−/ | – | (–) |
| ncr1159 | 50 | 2692882 | 2692931 | 352 | yqaO | yqaN | /−/+/−/ | – | (–) |
| ncr982 | 80 | 1917501 | 1917580 | 324 | yndN | lexA | /+/+/−/ | – | 8 |
| ncr1058 | 297 | 2273533 | 2273829 | 260 | yolA | yokL | /−/+/−/ | ncr46/bsrG | 2,7 |
| ncr1562 | 60 | 532583 | 532642 | 197 | ydcO | ydcP | /+/−/+/ | – | 8 |
| ncr1932 | 184 | 2273701 | 2273884 | 112 | yolA | yokL | /−/−/−/ | – | 2 |
| ncr1175 | 107 | 2773780 | 2773886 | 90 | yrhK | cypB | /+/+/−/ | – | 2 |
| ncr1937 | 69 | 2283685 | 2283753 | 89 | yokC | yokB | /−/−/−/ | – | (–) |
| ncr2768 | 56 | 3852061 | 3852116 | 54 | pbpG | ywhD | /+/−/−/ | – | 2,6,8 |
| ncr724 | 56 | 1451260 | 1451315 | 46 | stoA | zosA | /+/+/+/ | – | (–) |
| ncr1857 | 260 | 2069869 | 2070128 | 44 | yobI | yobJ | /−/−/−/ | bsrE | 2,3,4,7,8 |
| ncr1019 | 171 | 2069821 | 2069991 | 35 | yobI | yobJ | /−/+/−/ | ncr39 | 2,7,8 |
| ncr1575 | 199 | 606407 | 606605 | 34 | vmlR | ydgF | /−/−/−/ | ncr10 | 2,3,4,9,10,13 |
| ncr2184 | 232 | 2779137 | 2779368 | 32 | yrzI | yrhG | /−/−/−/ | ncr60 | 2,7,8 |
| ncr471 | 173 | 820666 | 820838 | 24 | yfmI | yfmG | /−/+/+/ | – | (–) |
| ncr264 | 248 | 376678 | 376925 | 23 | hxlR | srfAA | /+/+/+/ | – | (–) |
| ncr952 | 151 | 1780404 | 1780554 | 20 | mutL | ymzD | /+/+/−/ | – | 2 |
| ncr2424 | 58 | 3146126 | 3146183 | 20 | mntA | menC | /−/−/−/ | – | 7 |
| ncr1915 | 59 | 2208755 | 2208813 | 18 | yopM | yopL | /−/−/−/ | – | (–) |
| ncr629 | 117 | 1233429 | 1233545 | 16 | yizD | yjbH | /−/+/−/ | ncr22/rsaE | Diverse |
| ncr1015 | 120 | 2053989 | 2054108 | 14 | pps | xynA | /−/+/−/ | – | 2,7,11,14 |
| ncr1155 | 233 | 2678729 | 2678961 | 13 | yqdB | yqbM | /+/+/−/ | ncr58/bsrH | 2,5,7,8,11 |
| ncr1241 | 128 | 3225697 | 3225824 | 13 | yugI | alaT | /−/+/−/ | – | 2,7 |
| ncr2299 | 99 | 2913485 | 2913583 | 13 | trxA | xsa | /−/−/−/ | – | (–) |
| ncr738 | 58 | 1467704 | 1467761 | 13 | ykwD | pbpH | /−/+/+/ | – | 2 |
| ncr969 | 58 | 1868404 | 1868461 | 12 | ymzA | ymaA | /+/+/+/ | – | 2 |
| ncr2637 | 74 | 3573045 | 3573118 | 11 | yvcI | trxB | /−/−/−/ | – | 1,2,7,8 |
| ncr178 | 124 | 199857 | 199980 | 11 | glmM | glmS | /+/+/+/ | – | 2 |
| ncr560 | 230 | 1056390 | 1056619 | 11 | yhaZ | yhaX | /−/+/+/ | ncr18 | 2 |
| ncr992 | 72 | 1925548 | 1925619 | 7 | yneK | cotM | /−/+/−/ | – | 2 |
| ncr620 | 100 | 1219702 | 1219801 | 7 | trpS | oppA | /−/+/+/ | – | 2,7 |
| ncr585 | 201 | 1150478 | 1150678 | 7 | gerPA | yisI | /−/+/−/ | ncr20 | (–) |
| ncr1957 | 60 | 2316348 | 2316407 | 6 | ypbR | ypbQ | /−/−/−/ | – | 2 |
aCandidates for small RNA are selected based on cDNA signals from the intergenic regions (of the enriched sample), which do not correspond to a known gene, with at least 25 nt distance from both the upstream and downstream genes. The length is measured from the start to the end of the cDNA signals.
bOrganisms to which blast hits could be detected are denoted as: (–) B. subtilis only (1) Anoxybacillus flavithermus, (2) B. amyloliquefaciens, (3) B. anthracis, (4) B. cereus, (5) B. clausii, (6) B. intermedius, (7) B. licheniformis, (8) B. pumilus, (9) B. thuringiensis, (10) B. weihenstephanensis, (11) Brevibacillus brevis, (12) Geobacillus species, (13) Lysinibacillus sphaericus, (14) Paenibacillus species, (diverse) all of the above Bacillales families with the addition of Staphylococcus species.