Table 1. sRNA identification and characteristics.
| Flanking Genes | |||||||||||||
| ID | Start | End | Size (nt) | Strand | Up | Down | Orientation | ΔG | Conservation | Previously identified | Confirmation | Motif/Family | Virulence |
| R1 | 171483 | 171628 | 146 | − | SP0178 | SP0179 | < > > | −46.9 | α γ | SN4 (a), srn029 (d) | Northern | ||
| R2 | 1221797 | 1221902 | 106 | − | SP1286 | SP1287 | > < < | −23.1 | α | No Signal | Motif 2 | ||
| R3 | 1275652 | 1275704 | 53 | − | SP1355 | SP1356 | < < < | −5.4 | α β | No, BOX element | |||
| R4 | 1351009 | 1351076 | 68 | − | SP1431 | SP1432 | > < > | −6.6 | α | No Signal | Blood | ||
| R6 | 1731557 | 1731734 | 178 | − | SP1820 | SP1821 | < < < | −42.37 | α | srn400 (d) | Northern | T-box | |
| R7 | 1791010 | 1791080 | 71 | − | SP1886 | SP1887 | > < < | −13 | α | Northern | Motif 4 | ||
| R8 | 1892645 | 1892717 | 73 | − | SP1988 | SP1989 | < < < | −11 | α | Northern | Nasopharynx,Blood | ||
| R9 | 1903548 | 1903638 | 91 | − | SP1999 | SP2000 | < < < | −19.5 | α | trn0935 (d) | Northern | ||
| R10 | 1987487 | 1987533 | 47 | − | SP2076 | SP2077 | < < < | −7.1 | α β γ | Northern | |||
| R11 | 2002164 | 2002195 | 32 | − | SP2093 | SP2094 | > < < | −2.1 | α γ | Northern | |||
| R12 | 1731041 | 1731440 | 400 | − | SP1818 | SP1819 | > < < | −111.39 | α | trn0830 (d) | Northern | Motif 1 & 5 | Nasopharynx, Blood |
| R13 | 623327 | 623372 | 46 | − | SP0649 | SP0650 | < < > | −8.7 | α γ | No Signal | |||
| R14 | 1034021 | 1034100 | 80 | − | SP1100 | SP1101 | > < < | −9.8 | α | qRT-PCR | Lung | ||
| R15 | 1214248 | 1214371 | 124 | − | SP1278 | SP1279 | < < < | −38.9 | α | SN42 (a), srn299 (d) | Previous Study | Pyr | |
| R16 | 1227703 | 1227744 | 42 | − | SP1292 | SP1293 | > < < | −3.9 | α γ | No Signal | Nasopharynx | ||
| R17 | 1277341 | 1277388 | 48 | − | SP1356 | SP1357 | < < < | −3.7 | α β | No Signal | |||
| R18 | 1364575 | 1364706 | 132 | − | SP1444 | SP1445 | > < < | −25.5 | α | Northern | |||
| R19 | 1390953 | 1391074 | 122 | − | SP1477 | SP1478 | < < < | −23.1 | α β | trn0663 (d) | Northern | ||
| R20 | 1455141 | 1455185 | 45 | − | SP1547 | SP1548 | < < < | −12.2 | α γ | Northern | |||
| R21 | 1461116 | 1461178 | 63 | − | SP1551 | SP1552 | < < > | −11.3 | α | SN44 (a), srn351 (d) | Previous Study | ||
| F1 | 91593 | 91664 | 72 | + | SP0085 | SP0086 | > > > | −17.1 | α | Northern | Motif 2 | ||
| F2 | 106533 | 106577 | 45 | + | SP0103 | SP0104 | > > < | −5.9 | α γ | No, BOX element | Motif 2 | Blood | |
| F3 | 117143 | 117248 | 106 | + | SP0115 | SP0116 | > > > | −21.97 | α | qRT-PCR | |||
| F4 | 118118 | 118166 | 49 | + | SP0116 | SP0117 | > > > | −11 | α γ | No Signal | |||
| F5 | 120678 | 120848 | 171 | + | SP0117 | SP0118 | > > > | −51.6 | α | trn0052 (d) | No, BOX element | Blood | |
| F6 | 130439 | 130495 | 57 | + | SP0129 | SP0130 | > > < | −19.9 | α | Northern | |||
| F7 | 209812 | 209917 | 106 | + | SP0239 | SP0240 | > > > | −18.9 | α | csRNA5, (b), SN35 (a), srn061 (d) | Northern | Lung, IN Challenge | |
| F8 | 228667 | 228720 | 54 | + | SP0256 | SP0257 | > > > | −14.5 | α | csRNA1, (b), (c), SN5 (a) | Previous Study | Motif 3 | |
| F9 | 231310 | 231359 | 50 | + | SP0257 | SP0258 | > > < | −6.4 | α β γ | No, BOX element | |||
| F10 | 284261 | 284317 | 57 | + | SP0311 | SP0312 | > > > | −17.9 | α | trn0157 (d) | Northern | Motif 3 | |
| F11 | 286614 | 286708 | 95 | + | SP0312 | SP0313 | > > < | −17.9 | α | Northern | |||
| F12 | 444624 | 444663 | 40 | + | SP0464 | SP0465 | > > < | −4.7 | α γ | No, BOX element | |||
| F13 | 470344 | 470441 | 98 | + | SP0493 | SP0494 | > > > | −32.1 | α | srn145 (d) | No, BOX element | ||
| F14 | 499570 | 499689 | 120 | + | SP0518 | SP0519 | > > > | −12.87 | α | Northern | Nasopharynx | ||
| F15 | 501732 | 501844 | 113 | + | SP0519 | SP0520 | > > < | −10.53 | α | (c), srn151 (d) | Northern | ||
| F16 | 528096 | 528162 | 67 | + | SP0560 | SP0561 | < > > | −7.3 | α | No, BOX element | Motif 1,5 | ||
| F17 | 530769 | 530895 | 127 | + | SP0564 | SP0565 | > > > | −7.3 | α | (c) | Previous Study | T-box | |
| F18 | 538437 | 538492 | 56 | + | SP0571 | SP0572 | > > < | −14.16 | α | Northern | Motif 4 | ||
| F19 | 543052 | 543150 | 99 | + | SP0575 | SP0576 | > > > | −29.23 | α | Northern | |||
| F20 | 547541 | 547749 | 209 | + | SP0578 | SP0579 | > > > | −49.72 | α β | srn157 (d) | Northern | Nasopharynx, IN Challenge | |
| F21 | 557415 | 557447 | 33 | + | SP0586 | SP0587 | > > < | −1.3 | α | No, BOX element | |||
| F22 | 592573 | 592712 | 140 | + | SP0625 | SP0626 | > > > | −36.8 | α | qRT-PCR | IN Challenge | ||
| F23 | 603204 | 603346 | 143 | + | SP0640 | SP0641 | > > > | −28.34 | α | trn0329 (d) | No, BOX element | ||
| F24 | 610528 | 610660 | 133 | + | SP0641 | SP0642 | > > < | −32.25 | α β | Northern | Motif 4 | Nasopharynx | |
| F25 | 623244 | 623345 | 102 | + | SP0649 | SP0650 | < > < | −32.8 | α | SN11 (a), trn0332 (d) | Northern | Blood, IN Challenge | |
| F26 | 668007 | 668112 | 106 | + | SP0700 | SP0701 | < > > | −31.18 | α | SN12 (a) | Northern | Pyr | |
| F27 | 684656 | 684797 | 142 | + | SP0718 | SP0719 | > > > | −31.95 | α | trn0358 (d) | No, BOX element | TPP | Blood |
| F28 | 709064 | 709122 | 59 | + | SP0749 | SP0750 | > > > | −26.3 | α | No, BOX element | |||
| F29 | 743792 | 743828 | 37 | + | SP0788 | SP0789 | > > > | −9.2 | α | No, BOX element | Lung | ||
| F30 | 743886 | 743933 | 48 | + | SP0788 | SP0789 | > > > | −6.2 | α γ | No, BOX element | Motif 5 | ||
| F31 | 810811 | 810862 | 52 | + | SP0863 | SP0864 | < > > | −10.4 | α β | (c) | Previous Study | ||
| F32 | 821924 | 822271 | 348 | + | SP0873 | SP0874 | > > < | −81.41 | α β | SN16 (a), srn226 (d) | Previous Study | tmRNA | Lung, IN Challenge |
| F33 | 863736 | 863818 | 83 | + | SP0910 | SP0911 | > > < | −17.38 | α | (c) | Previous Study | Motif 2 | |
| F34 | 907218 | 907312 | 95 | + | SP0958 | SP0959 | > > > | −34.2 | α | (c), SN40 (a), srn239 (d) | Previous Study | ||
| F35 | 909029 | 909169 | 141 | + | SP0962 | SP0963 | > > > | −38.03 | α | srn241 (d) | Northern | ||
| F36 | 941435 | 941487 | 53 | + | SP1000 | SP1001 | > > > | −16.1 | α | Northern | |||
| F38 | 956782 | 956928 | 147 | + | SP1012 | SP1013 | > > > | −45.94 | α | ©, srn254 (d) | Previous Study | Nasopharynx | |
| F39 | 972498 | 972607 | 110 | + | SP1029 | SP1030 | > > > | −18.52 | α γ | qRT-PCR | |||
| F40 | 1063101 | 1063151 | 51 | + | SP1128 | SP1129 | > > < | −17.3 | Northern | Motif 2 | |||
| F41 | 1071112 | 1071214 | 103 | + | SP1142 | SP1143 | > > > | −33.08 | srn277 (d) | Northern | Nasopharynx, Blood, IN Challenge | ||
| F42 | 1093532 | 1093614 | 83 | + | SP1157 | SP1158 | > > < | −23.2 | α | No Signal | |||
| F43 | 1216148 | 1216246 | 99 | + | SP1281 | SP1282 | > > > | −27.8 | α | Northern | |||
| F44 | 1220366 | 1220460 | 95 | + | SP1285 | SP1286 | > > > | −20.74 | α | Northern | IN Challenge | ||
| F45 | 1408204 | 1408275 | 72 | + | SP1499 | SP1500 | > > < | −22.1 | α | qRT-PCR | Motif 2 & 3 | Blood | |
| F46 | 1454220 | 1454277 | 58 | + | SP1546 | SP1547 | > > < | −20.6 | α | No, BOX element | |||
| F47 | 1530016 | 1530100 | 85 | + | SP1629 | SP1630 | > > > | −12.55 | α β | SN24 (a) | Northern | ||
| F48 | 1778293 | 1778427 | 135 | + | SP1872 | SP1873 | > > < | −38.3 | α | Northern | Motif 1 & 2 & 3 | IN Challenge | |
| F49 | 2026337 | 2026403 | 67 | + | SP2112 | SP2113 | > > < | −21.9 | α | No, BOX element | Motif 2 | ||
| F50 | 2085887 | 2085994 | 108 | + | SP2168 | SP2169 | > > < | −27.1 | α | No, BOX element | Motif 2 & 3 | ||
| F51 | 2133001 | 2133045 | 45 | + | SP2213 | SP2214 | < > < | −9.9 | α γ | Northern | Motif 3 | Nasopharynx | |
| F52 | 40336 | 40380 | 45 | + | SP0041 | SP0042 | > > > | −16.8 | α γ | No, BOX element | Nasopharynx | ||
| F53 | 588512 | 588590 | 79 | + | SP0619 | SP0620 | > > < | −12.62 | α | Northern | |||
| F54 | 1424517 | 1424756 | 240 | + | SP1516 | SP1517 | < > < | −64.4 | α | No, BOX element | Motif 1,5 | ||
| F55 | 1696066 | 1696162 | 97 | + | SP1777 | SP1778 | > > < | −11.97 | α | Northern | Motif 1 | ||
| F56 | 158993 | 159090 | 98 | + | SP0162 | SP0163 | > > > | −7.7 | Northern | ||||
| F57 | 553923 | 553982 | 60 | + | SP0584 | SP0585 | > > > | −10.6 | α | No Signal | |||
| F58 | 716443 | 716473 | 31 | + | SP0757 | SP0758 | > > > | −11.2 | α β γ | No Signal | |||
| F59 | 869510 | 869591 | 82 | + | SP0915 | SP0916 | < > > | −24.7 | α | SN20 (a), srn235 (d) | Previous Study | ||
| F60 | 950115 | 950165 | 51 | + | SP1004 | SP1005 | > > > | −2.8 | α | trn0485 (d) | No Signal | Lung | |
| F61 | 972327 | 972384 | 58 | + | SP1029 | SP1030 | > > > | −8.6 | α | Northern | |||
| F62 | 995726 | 995787 | 62 | + | SP1059 | SP1060 | > > > | −24.5 | Northern | Lung | |||
| F63 | 1090060 | 1090100 | 41 | + | SP1154 | SP1155 | > > > | −1.5 | α γ | No Signal | Nasopharynx | ||
| F64 | 1118416 | 1118462 | 47 | + | SP1179 | SP1180 | > > > | −1.7 | α γ | No Signal | Nasopharynx | ||
| F65 | 1350946 | 1351012 | 67 | + | SP1431 | SP1432 | > > > | −19.2 | α | No Signal | Motif 2 | Nasopharynx | |
| F66 | 2086087 | 2086325 | 239 | + | SP2168 | SP2169 | > > < | −73.9 | α | srn502 (d) | Northern | ||
| F67 | 2086466 | 2086584 | 119 | + | SP2168 | SP2169 | > > < | −25.5 | α | srn503 (d) | Northern | ||
| F68 | 2132994 | 2133050 | 57 | + | SP2213 | SP2214 | > > < | −11.3 | α | No Signal | Motif 3 |
Columns from left to right represent the identification of the sRNA (ID), the coordinates on the TIGR4 genome to which the sRNA mapped (Start, End), the predicted size, the strand that encodes the sRNA, the genes immediately flanking the sRNA, the orientation of the sRNA and flanking genes (> = forward, < = reverse, sRNA is in center), the predicted free energy of the sRNA (delta G), the conservation of the sRNA with α = homologs in Streptococcus pneumoniae, β = conserved amongst streptococci, γ = conserved in other gram-positive bacteria, whether sRNA was previously identified by (a) Kumar et al., 2010, (b) Halfman et al, 2007, (c) Livny et al., 2006 or (d) Acebo et al 2012, and the method of confirmation. Conserved motifs or Rfam assignments are indicated in the Motif/Family column. If deletion of the sRNA had an effect on virulence identified by Tn-seq, the host site is indicated in the final column. If the sRNA was attenuated by IN challenge, this is also indicated in the final column.