Table 3.
Families of SLS containing repeated sequences.
| Species | Family | This work | Literature | Type | Notes | |||
| size | copies | size | copies | ref. | ||||
| B. anthracis | Bant-1 | 72 | 104(29) | I | ||||
| Bcr1 | 167 | 31(21) | 147 | 12 | [24] | I | ||
| B. halodurans | Bhal-1 | 74 | 36(32) | I | ||||
| Bhal-2 | 76 | 50(41) | I | contains CRISPR repeats | ||||
| C. perfringens | Clop-1 | 93 | 44(28) | I | ||||
| C. tetani | Clot-1 | 74 | 19(16) | I | ||||
| Clot-2 | 31 | 34(32) | contains CRISPR repeats | |||||
| Clot-3 | 90 | 24(17) | I | contains CRISPR repeats | ||||
| E. faecalis | Efa-1 | 163 | 65 (18) | I | ||||
| Efa-2 | 292 | 11(9) | G | |||||
| L. johnsonii | Lac-1 | 231 | 34(6) | G | ||||
| S. aureus | Sta-1 | 105 | 25(25) | I | ||||
| Sta-2 | 460 | 9(8) | S | |||||
| Sta-3 | 136 | 24(15) | I | |||||
| Sta-4 | 99 | 46(27) | I | |||||
| S. pneumoniae | BOX | 84 | 205(105) | 100–200 | 127 | [25] | I | |
| RUP | 63 | 110(99) | 108 | 54 | [26] | I | ||
| Stre-1 | 45 | 241(225) | G | |||||
| B. melithensis | Bru-RS | 118 | 222(69) | 103–105 | 35–40 | [27] | I | |
| R. conorii | Rpe-4 | 100 | 97(74) | 95 | 94 | [28] | I | |
| Rpe-5 | 115 | 45(35) | 115 | 55 | [28] | I | ||
| Rpe-6 | 108 | 123(74) | 136 | 168 | [28] | |||
| Rpe-7 | 123 | 186 144) | 99 | 223 | [28] | |||
| M. genitalium | Myg-1 | 259 | 10(7) | I | ||||
| M. pneumoniae | Myp-1 | 143 | 25(18) | G | part of REPMP1 repeat | |||
| Myp-2 | 158 | 42(16) | G | part of REPMP4 repeat | ||||
| Myp-3 | 558 | 11(8) | G | part of REPMP5 repeat | ||||
| Myp-4 | 364 | 8(7) | G | part of REPMP5 repeat | ||||
| Myp-5 | 426 | 8 (8) | G | part of REPMP5 repeat | ||||
| Myp-6 | 468 | 11(11) | G | part of REPMP2/3 repeat | ||||
| Myp-8 | 674 | 9(9) | G | part of REPMP2/3 repeat | ||||
| Myp-9 | 226 | 9(9) | G | part of REPMP2/3 repeat | ||||
| Myp-10 | 330 | 12 (12) | G | part of REPMP2/3 repeat | ||||
| Myp-7 | 131 | 42(22) | G | |||||
| C. diphtheriae | Cod-1 | 140 | 17(16) | I | ||||
| Cod-2 | 32 | 43(39) | G | |||||
| Cod-3 | 170 | 23(20) | ||||||
| Cod-5 | 74 | 35(29) | I | |||||
| M. tuberculosis | Myt-1 | 72 | 75(70) | |||||
| Myt-2 | 115 | 769(223) | G | located within PE genes | ||||
| Myt-3 | 81 | 81(77) | G | located within PE genes | ||||
| Myt-4 | 83 | 196(68) | G | located within PE genes | ||||
| Myt-5 | 71 | 41(2) | G | contains CRISPR repeats | ||||
| Myt-7 | 136 | 278(68) | G | located within PE genes | ||||
| Myt-8 | 92 | 33(25) | ||||||
| Myt-9 | 67 | 53(15) | ||||||
| Myt-10 | 154 | 62(59) | G | located within PE genes | ||||
| Myt-11 | 65 | 56(21) | contains MIRU repeats | |||||
| M. leprae | REPLEP | 740 | 29(9) | 400–880 | 15 | [29] | I | |
| RLEP | 641 | 38(30) | 601–1075 | 37 | [29] | S | ||
| Myl-1 | 371 | 7(4) | S | part of LEPREP repeat | ||||
| Myl-2 | 1979 | 9(7) | S | part of LEPREP repeat | ||||
| B. bronchiseptica | Bor-1 | 117 | 196(92) | I | ||||
| Bor-2 | 167 | 17(6) | I | |||||
| Bor-3 | 134 | 34(32) | G | |||||
| Bor-4 | 81 | 164(114) | G | |||||
| Bor-5 | 112 | 135(101) | G | |||||
| Bor-6 | 147 | 37(31) | G | |||||
| B. pertussis | Bor-1 | 93 | 128(78) | I | ||||
| N. meningitidis | ATR | 206 | 14(9) | 183 | 13 | [30] | I | |
| Nem-2 | 341 | 11(7) | ||||||
| Nem-3 | 127 | 10(9) | G | |||||
| Nem-4 | 36 | 412(362) | I | contains DUS repeats | ||||
| dRS3 | 33 | 755(708) | 20 | 770 | [30] | I | ||
| NEMIS | 46 | 262(81) | 106–158 | 250 | [13] | I | ||
| Rep2 | 65 | 22(18) | 59–154 | 26 | [30] | I | ||
| P. multocida | Pam-1 | 155 | 12(12) | S | contains DUS repeats | |||
| E. coli | BoxC | 50 | 22(20) | 56 | 32 | [31] | ||
| Eco-1 | 734 | 9(7) | G | |||||
| ERIC | 140 | 19(19) | 127 | 21 | [32] | S | ||
| PU-BIME | 108 | 301(199) | 40 | 485 | [31] | |||
| H. influenzae | Hin-1 | 31 | 53(51) | I | contains DUS repeats | |||
| P. aeruginosa | Pae-1 | 84 | 133(61) | I | ||||
| Pae-2 | 287 | 65(24) | G | |||||
| Pae-3 | 220 | 16(13) | G | |||||
| Pae-4 | 52 | 41(35) | ||||||
| P. putida | Ppu-1 | 617 | 39(28) | I | ||||
| Ppu-2 | 2056 | 10(8) | S | |||||
| Ppu-3 | 251 | 27(23) | G | |||||
| Ppu-4 | 81 | 41(24) | I | |||||
| Ppu-9 | 124 | 57(31) | I | |||||
| REP | 39 | 588(496) | 30 | 804 | [33] | I | ||
| S. typhi | PU-BIME | 43 | 146(126) | 40 | 100 | [31] | I | |
| PU-BIME* | 80 | 59(37) | 40 | >100 | [31] | |||
| S. typhimurium | PU-BIME | 78 | 142(94) | 40 | 82 | [31] | ||
| Sal-1 | 115 | 27(17) | I | |||||
| Sal-2 | 120 | 33(3) | G | contains CRISPR repeats | ||||
| V. cholerae | ERIC | 103 | 97(66) | 127 | 80 | [31] | I | |
| Vic-1 | 184 | 14(1) | I | |||||
| Y. pestis | ERIC | 115 | 241(128) | 69–127 | 167 | [16] | I | |
| YPAL | 168 | 101(68) | 169 | 30 | [17] | I | ||
| YPAL* | 136 | 26(13) | 130 | 10 | [17] | I | ||
The final set of 92 families of repeated sequences is reported, grouped by species. For each family, the length of the model and the number of sequences fitting the model are given. The number of complete sequences, i.e. covering the model from end to end, is reported in parenthesis. Previously described sequence families have been named in column "Family", according to the current literature; for each of them, the number and typical size of its members are also provided, together with references. For novel families, a systematic name was built by fusing a shortened species name to a progressive number. In the column "type", I, G and S indicate the prevalent genomic location of the members of each families within intergenic, genic or border-spanning sequences. For some families, small previously described sequence motifs contribute to the formation of a substantially larger model; for others, their members are frequently located within larger previously described sequences. In both cases, a note is reported in the rightmost column.