Table 4.
Secondary structure prediction analysis of families.
| Species | Family | P | Conserved structure | Conserved SLS position | SLS folding aptitude | Type |
| B. anthracis | Bcr1 | 0.99 | s | + | + | I |
| B. halodurans | Bhal-1 | 0.98 | s | + | ++ | I |
| Bhal-2 | 0.99 | c | - | I | ||
| C. perfringens | Clop-1 | 0.96 | s | + | + | I |
| C. tetani | Clot-1 | 0.95 | s | + | ++ | I |
| E. faecalis | Efa-1 | 0.85 | s | + | +++ | I |
| Efa-2 | 1.00 | s | + | - | G | |
| L. johnsonii | Lac-1 | 0.97 | c | +° | - | G |
| S. aureus | Sta-1 | 0.84 | s | + | +++ | I |
| Sta-2 | 1.00 | s | + | ++ | S | |
| Sta-3 | 0.97 | s | + | + | I | |
| B. melithensis | Bru-RS | 0.98 | s | + | + | I |
| R. conorii | Rpe-4 | 0.73 | s | + | - | I |
| Rpe-5 | 1.00 | s | + | + | I | |
| Rpe-6 | 0.45 | - | +° | + | ||
| Rpe-7 | 0.99 | s | + | ++ | ||
| M. genitalium | Myg-1 | 0.06 | - | +° | - | I |
| M. pneumoniae | Myp-1 | 0.00 | - | +° | - | G |
| Myp-2 | 0.95 | s | + | ++ | G | |
| Myp-3 | 0.89 | s | + | - | G | |
| Myp-4 | 0.09 | - | +° | - | G | |
| Myp-5 | 0.74 | s | + | - | G | |
| Myp-6 | 0.55 | c | - | G | ||
| Myp-7 | 0.67 | s | + | - | G | |
| C. diphtheriae | Cod-1 | 0.97 | s | + | +++ | I |
| Cod-2 | 0.98 | s | - | G | ||
| Cod-3 | 0.99 | s | + | +++ | ||
| M. tuberculosis | Myt-1 | 0.74 | s | + | +++ | |
| Myt-8 | 0.90 | s | + | ++ | ||
| M. leprae | REPLEP | 1.00 | c | +° | - | I |
| RLEP | 1.00 | s | + | ++ | S | |
| Myl-1 | 0.61 | s | + | ++ | S | |
| Myl-2 | 0.97 | s | + | + | S | |
| B. bronchiseptica | Bor-1 | 0.86 | s | + | ++ | I |
| Bor-2 | 1.00 | s | + | - | I | |
| B. pertussis | Bor-1 | 0.93 | s | + | ++ | I |
| N. meningitides | ATR | 1.00 | s | + | - | I |
| Nem-2 | 0.93 | s | + | + | ||
| Nem-4 | 0.93 | s | + | +++ | I | |
| dRS3 | 0.98 | c | - | I | ||
| NEMIS | 1.00 | s | + | + | I | |
| Rep2 | 0.98 | s | + | + | I | |
| P. multocida | Pam-1 | 0.96 | s | + | +++ | S |
| E. coli | BoxC | 0.99 | c | +° | - | |
| Eco-1 | 0.18 | - | +° | - | G | |
| ERIC | 0.94 | s | + | ++ | S | |
| PU-BIME | 0.94 | s | + | + | ||
| H. influenzae | Hin-1 | 0.96 | s | + | + | I |
| P. aeruginosa | Pae-1 | 0.97 | s | + | ++ | I |
| Pae-3 | 0.26 | - | +° | - | G | |
| Pae-4 | 0.93 | s | + | ++ | ||
| P. putida | Ppu-1 | 0.97 | s | + | + | I |
| Ppu-2 | 1.00 | s | + | +++ | S | |
| Ppu-4 | 0.95 | s | + | - | I | |
| Ppu-9 | 0.54 | s | + | - | I | |
| S. typhi | PU-BIME | 0.97 | c | - | I | |
| PU*-BIME | 0.98 | s | + | - | ||
| S. typhimurium | PU-BIME | 0.98 | s | + | - | |
| Sal-1 | 0.94 | c | - | I | ||
| Sal-2 | 1.00 | c | - | G | ||
| Y. pestis | ERIC | 0.90 | s | + | - | I |
| YPAL | 1.00 | s | + | +++ | I | |
| YPAL* | 0.96 | c | - | I |
The ability to form a consensus secondary structure was evaluated by RNAz: the prediction scores are reported in column "P" for each family. The type of predicted structure is indicated in column "conserved structure", where "s" indicates a stem-loop based structure, while "c" indicates a more complex structure, where a stem-loop compatible with the original search is not present. For each family, the aligned localization of the original SLSs is indicated by '+' in column "conserved SLS position"; when SLS alignment is not in agreement with the RNAz prediction, a '°' is added to the '+' symbol. The column marked "SLS folding aptitude" reports the behavior of family elements in the RANDFOLD test: the number of '+' symbols describes the percent of positive elements ('+++' if 90% or above; '++' if 70–90%; '+' if 50–70%; '-' if less than 50%). The localization of family members, as already described in Table 3, is also reported in the last column.