7NRD Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/LA/38:45 | homologous HL_5TBW_113 | NA | ||
| 1/LA/69:74 | homologous HL_5TBW_114 | NA | ||
| 1/LA/90:96 | homologous HL_5TBW_115 | NA | ||
| 1/LA/132:136 | homologous HL_5TBW_116 | NA | ||
| 1/LA/194:201 | homologous HL_5TBW_117 | NA | ||
| 1/LA/208:212 | homologous HL_5TBW_118 | NA | ||
| 1/LA/216:224 | homologous HL_5TBW_119 | NA | ||
| 1/LA/278:287 | homologous HL_5TBW_120 | NA | ||
| 1/LA/303:312 | homologous HL_5TBW_121 | NA | ||
| 1/LA/357:362 | homologous HL_5TBW_122 | NA | ||
| 1/LA/382:387 | homologous HL_5TBW_123 | NA | ||
| 1/LA/544:547 | NA | NA | ||
| 1/LA/599:604 | homologous HL_5TBW_125 | NA | ||
| 1/LA/640:649 | homologous HL_5TBW_126 | NA | ||
| 1/LA/686:694 | homologous HL_5TBW_127 | NA | ||
| 1/LA/707:712 | homologous HL_5TBW_128 | NA | ||
| 1/LA/732:737 | homologous HL_5TBW_129 | NA | ||
| 1/LA/763:768 | geometric HL_5TBW_018 | NA HL_00996.1* | ||
| 1/LA/844:849 | homologous HL_5TBW_131 | NA | ||
| 1/LA/876:885 | homologous HL_5TBW_132 | NA | ||
| 1/LA/910:918 | homologous HL_5TBW_133 | NA | ||
| 1/LA/958:963 | homologous HL_5TBW_134 | NA | ||
| 1/LA/1023:1029 | homologous HL_5TBW_135 | NA | ||
| 1/LA/1076:1083 | geometric HL_5TBW_024 | NA HL_54035.7* | ||
| 1/LA/1126:1132 | homologous HL_5TBW_137 | NA | ||
| 1/LA/1148:1155 | homologous HL_5TBW_138 | NA | ||
| 1/LA/1239:1249 | Other HL geometric HL_1P6V_001 | NA HL_79299.11* | ||
| 1/LA/1266:1275 | geometric HL_5TBW_028 | NA HL_87219.4* | ||
| 1/LA/1347:1357 | homologous HL_5TBW_141 | NA | ||
| 1/LA/1403:1408 | homologous HL_5TBW_142 | NA | ||
| 1/LA/1462:1470 | homologous HL_5TBW_143 | NA | ||
| 1/LA/1506:1512 | homologous HL_5TBW_144 | NA | ||
| 1/LA/1544:1549 | homologous HL_5TBW_145 | NA | ||
| 1/LA/1565:1574 | NA | NA | ||
| 1/LA/1599:1608 | homologous HL_5TBW_147 | NA | ||
| 1/LA/1634:1639 | homologous HL_5TBW_148 | NA | ||
| 1/LA/1680:1688 | homologous HL_5TBW_149 | NA | ||
| 1/LA/1719:1725 | homologous HL_5TBW_150 | NA | ||
| 1/LA/1759:1766 | homologous HL_5TBW_151 | NA | ||
| 1/LA/1792:1796 | homologous HL_5TBW_152 | NA | ||
| 1/LA/1844:1851 | homologous HL_5TBW_153 | NA | ||
| 1/LA/1861:1869 | geometric HL_4V9F_032 | NA HL_82851.1* | ||
| 1/LA/1923:1928 | geometric HL_7RQB_042 | NA HL_79299.11* | ||
| 1/LA/2110:2114 | homologous HL_5TBW_157 | NA | ||
| 1/LA/2135:2145 | homologous HL_5TBW_158 | NA | ||
| 1/LA/2164:2170 | homologous HL_5TBW_159 | NA | ||
| 1/LA/2220:2225 | homologous HL_5TBW_160 | NA | ||
| 1/LA/2253:2263 | homologous HL_5TBW_161 | NA | ||
| 1/LA/2292:2300 | homologous HL_5TBW_162 | NA | ||
| 1/LA/2369:2378 | homologous HL_5TBW_163 | NA | ||
| 1/LA/2535:2544 | NA | NA | ||
| 1/LA/2568:2573 | NA | NA | ||
| 1/LA/2616:2624 | homologous HL_5TBW_167 | NA | ||
| 1/LA/2633:2645 | homologous HL_5TBW_168 | NA | ||
| 1/LA/2673:2681 | homologous HL_5TBW_169 | NA | ||
| 1/LA/2693:2700 | homologous HL_5TBW_170 | NA | ||
| 1/LA/2724:2732 | homologous HL_5TBW_171 | NA | ||
| 1/LA/2744:2749 | homologous HL_5TBW_172 | NA | ||
| 1/LA/2776:2784 | homologous HL_5TBW_173 | NA | ||
| 1/LA/2840:2848 | homologous HL_5TBW_174 | NA | ||
| 1/LA/2897:2904 | homologous HL_5TBW_175 | NA | ||
| 1/LA/2920:2926 | homologous HL_5TBW_176 | NA | ||
| 1/LA/2963:2968 | homologous HL_5TBW_177 | NA | ||
| 1/LA/3025:3030 | homologous HL_5TBW_178 | NA | ||
| 1/LA/3068:3073 | homologous HL_5TBW_179 | NA | ||
| 1/LA/3110:3124 | homologous HL_5TBW_180 | NA | ||
| 1/LA/3194:3197 | homologous HL_5TBW_181 | NA | ||
| 1/LA/3240:3247 | NA | NA | ||
| 1/LA/3303:3311 | homologous HL_5TBW_183 | NA | ||
| 1/LA/3350:3353 | geometric HL_4V88_192 | NA HL_69353.7* | ||
| 1/LB/36:41 | NA | NA | ||
| 1/LB/88:93 | NA | NA | ||
| 1/LC/47:56 | geometric HL_7A0S_001 | NA HL_29414.1* | ||
| 1/LC/69:89 | NA | NA | ||
| 1/LC/108:114 | homologous HL_5TBW_075 | NA HL_06569.2* | ||
| 1/LC/124:129 | homologous HL_5TBW_076 | NA HL_60357.1* | ||
| 1/S2/7:17 | NA | NA | ||
| 1/S2/70:81 | homologous HL_4V88_187 | NA HL_07268.1* | ||
| 1/S2/154:160 | Other HL homologous HL_4V88_188 | NA HL_43074.18* | ||
| 1/S2/190:195 | homologous HL_4V88_189 | NA HL_39228.1* | ||
| 1/S2/228:237 | NA | NA | ||
| 1/S2/243:250 | T-loop with 1 bulged base homologous HL_4V88_191 | NA HL_68493.6* | ||
| 1/S2/276:279 | geometric HL_6U8D_003 | NA HL_18722.3* | ||
| 1/S2/330:338 | homologous HL_4V88_193 | NA HL_93727.5* | ||
| 1/S2/368:373 | homologous HL_4V88_194 | NA HL_18785.1* | ||
| 1/S2/393:404 | homologous HL_4V88_195 | NA HL_22443.1* | ||
| 1/S2/414:419 | UNCG geometric HL_4U7U_001 | NA HL_79299.11* | ||
| 1/S2/450:456 | homologous HL_4V88_197 | NA HL_50374.1* | ||
| 1/S2/491:496 | geometric HL_2Y8W_001 | NA HL_69459.1* | ||
| 1/S2/520:532 | geometric HL_4V88_199 | NA HL_17086.2* | ||
| 1/S2/569:574 | Other HL homologous HL_4V88_200 | NA HL_43074.18* | ||
| 1/S2/716:722 | geometric HL_5J7L_143 | NA HL_98557.5* | ||
| 1/S2/764:772 | homologous HL_4V88_203 | NA HL_72066.1* | ||
| 1/S2/777:783 | NA | NA | ||
| 1/S2/827:845 | NA | NA | ||
| 1/S2/900:909 | homologous HL_4V88_206 | NA HL_87219.4* | ||
| 1/S2/937:942 | Other HL homologous HL_4V88_207 | NA HL_43074.18* | ||
| 1/S2/997:1007 | homologous HL_4V88_208 | NA HL_87219.4* | ||
| 1/S2/1055:1064 | homologous HL_5TBW_212 | NA | ||
| 1/S2/1084:1089 | Other HL homologous HL_4V88_210 | NA HL_43074.18* | ||
| 1/S2/1121:1126 | GNRA homologous HL_4V88_211 | NA HL_43074.18* | ||
| 1/S2/1188:1197 | homologous HL_4V88_212 | NA HL_96854.1* | ||
| 1/S2/1238:1247 | homologous HL_4V88_213 | NA HL_30819.1* | ||
| 1/S2/1296:1301 | GNRA homologous HL_4V88_214 | NA HL_43074.18* | ||
| 1/S2/1309:1316 | homologous HL_4V88_215 | NA HL_54035.7* | ||
| 1/S2/1359:1364 | homologous HL_4V88_216 | NA HL_82678.2* | ||
| 1/S2/1396:1402 | homologous HL_4V88_217 | NA HL_67216.5* | ||
| 1/S2/1501:1506 | GNRA homologous HL_4V88_218 | NA HL_43074.18* | ||
| 1/S2/1550:1561 | homologous HL_4V88_219 | NA HL_32458.3* | ||
| 1/S2/1594:1602 | homologous HL_4V88_220 | NA HL_01181.4* | ||
| 1/S2/1698:1703 | NA | NA | ||
| 1/S2/1778:1783 | Other HL homologous HL_4V88_222 | NA HL_43074.18* | ||
| 1/Sm/13:23 | NA | NA | ||
| 1/Sm/32:40 | NA | NA | ||
| 1/Sm/54:62 | NA | NA | ||
| 1/Sn/13:22 | NA | NA | ||
| 1/Sn/31:39 | NA | NA | ||
| 1/Sn/53:61 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7NRD_044 | geometric HL_5TBW_044 | ||
| HL_7NRD_052 | NA |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/LA/3:4, 1/LC/155:156 | NA | NA | ||
| 1/LA/7:8, 1/LC/150:152 | Single bulged C homologous IL_5TBW_002 | NA IL_61258.10* | ||
| 1/LA/13:15, 1/LC/144:145 | Single bulged U homologous IL_5TBW_003 | NA IL_83039.11* | ||
| 1/LA/27:28, 1/LA/56:58 | homologous IL_5TBW_240 | NA | ||
| 1/LA/31:38, 1/LA/45:53 | tSH-tHW-tHH-tHS geometric IL_5TBW_005 | NA IL_22863.1* | ||
| 1/LA/82:89, 1/LA/97:103 | homologous IL_5TBW_242 | NA | ||
| 1/LA/123:124, 1/LA/144:149 | geometric IL_5TBW_007 | NA IL_19724.1* | ||
| 1/LA/125:127, 1/LA/141:143 | homologous IL_5TBW_244 | NA | ||
| 1/LA/163:167, 1/LA/255:258 | NA | NA | ||
| 1/LA/169:171, 1/LA/247:253 | NA | NA | ||
| 1/LA/171:173, 1/LA/245:247 | geometric IL_1Y27_001 | NA IL_01312.13* | ||
| 1/LA/177:178, 1/LA/238:241 | NA | NA | ||
| 1/LA/189:191, 1/LA/204:205 | homologous IL_5TBW_248 | NA | ||
| 1/LA/337:339, 1/LC/25:26 | Single bulged A homologous IL_5TBW_013 | NA IL_80007.16* | ||
| 1/LA/376:379, 1/LA/390:403 | geometric IL_5TBW_014 | NA IL_60992.5* | ||
| 1/LA/404:410, 1/LC/13:19 | Triple sheared with non-canonical cWW geometric IL_4V9F_001 | NA IL_66414.5* | ||
| 1/LA/429:431, 1/LA/628:630 | homologous IL_5TBW_252 | NA | ||
| 1/LA/512:513, 1/LA/577:579 | homologous IL_5TBW_254 | NA | ||
| 1/LA/517:525, 1/LA/567:573 | homologous IL_5TBW_255 | NA | ||
| 1/LA/531:538, 1/LA/553:561 | homologous IL_5TBW_256 | NA | ||
| 1/LA/668:670, 1/LA/792:794 | homologous IL_5TBW_257 | NA | ||
| 1/LA/680:684, 1/LA/696:700 | homologous IL_5TBW_258 | NA | ||
| 1/LA/725:728, 1/LA/741:745 | homologous IL_5TBW_259 | NA | ||
| 1/LA/752:753, 1/LA/779:781 | homologous IL_5TBW_260 | NA | ||
| 1/LA/755:756, 1/LA/775:777 | homologous IL_5TBW_261 | NA | ||
| 1/LA/758:763, 1/LA/768:773 | homologous IL_5TBW_262 | NA | ||
| 1/LA/803:805, 1/LA/938:940 | homologous IL_5TBW_263 | NA | ||
| 1/LA/805:809, 1/LA/931:938 | geometric IL_5TBW_028 | NA IL_17470.5* | ||
| 1/LA/833:838, 1/LA/855:861 | geometric IL_4V88_462 | NA IL_19954.1* | ||
| 1/LA/869:873, 1/LA/887:890 | NA | NA | ||
| 1/LA/873:875, 1/LA/886:887 | homologous IL_5TBW_268 | NA | ||
| 1/LA/907:909, 1/LA/919:923 | Multiple bulged bases geometric IL_5TBW_033 | NA IL_90991.5* | ||
| 1/LA/954:956, 1/LA/965:967 | homologous IL_5TBW_270 | NA | ||
| 1/LA/969:970, 1/LA/1111:1113 | homologous IL_5TBW_271 | NA | ||
| 1/LA/977:982, 1/LA/1101:1104 | NA | NA | ||
| 1/LA/983:985, 1/LA/1099:1100 | homologous IL_5TBW_273 | NA | ||
| 1/LA/991:997, 1/LA/1052:1058 | 7x7 Sarcin-Ricin with intercalated A; G-bulge geometric IL_5TBW_038 | NA IL_93830.2* | ||
| 1/LA/997:998, 1/LA/1050:1052 | homologous IL_5TBW_275 | NA | ||
| 1/LA/999:1004, 1/LA/1046:1049 | homologous IL_5TBW_276 | NA | ||
| 1/LA/1006:1009, 1/LA/1041:1044 | Tandem non-canonical cWW pairs geometric IL_5TBW_041 | NA IL_85877.10* | ||
| 1/LA/1009:1011, 1/LA/1039:1041 | homologous IL_5TBW_278 | NA | ||
| 1/LA/1014:1018, 1/LA/1034:1036 | NA | NA | ||
| 1/LA/1069:1071, 1/LA/1087:1089 | homologous IL_5TBW_280 | NA | ||
| 1/LA/1074:1076, 1/LA/1083:1084 | homologous IL_5TBW_281 | NA | ||
| 1/LA/1120:1122, 1/LA/1136:1138 | homologous IL_5TBW_282 | NA | ||
| 1/LA/1167:1171, 1/LA/1328:1332 | homologous IL_5TBW_284 | NA | ||
| 1/LA/1173:1180, 1/LA/1325:1326 | homologous IL_5TBW_285 | NA | ||
| 1/LA/1180:1182, 1/LA/1324:1325 | Single bulged U geometric IL_7A0S_035 | NA IL_83039.11* | ||
| 1/LA/1187:1194, 1/LA/1314:1319 | geometric IL_5TBW_051 | NA IL_17971.1* | ||
| 1/LA/1194:1205, 1/LA/1299:1314 | homologous IL_5TBW_288 | NA | ||
| 1/LA/1207:1209, 1/LA/1296:1297 | homologous IL_5TBW_289 | NA | ||
| 1/LA/1218:1226, 1/LA/1283:1287 | homologous IL_5TBW_290 | NA | ||
| 1/LA/1234:1239, 1/LA/1249:1254 | NA | NA | ||
| 1/LA/1262:1266, 1/LA/1275:1277 | Major groove platform with extra cWW geometric IL_1MMS_002 | NA IL_95485.6* | ||
| 1/LA/1376:1378, 1/LA/1428:1431 | homologous IL_5TBW_293 | NA | ||
| 1/LA/1385:1387, 1/LA/1420:1421 | homologous IL_5TBW_294 | NA | ||
| 1/LA/1388:1395, 1/LA/1415:1419 | homologous IL_5TBW_295 | NA | ||
| 1/LA/1398:1400, 1/LA/1411:1412 | homologous IL_5TBW_296 | NA | ||
| 1/LA/1444:1450, 1/LA/2354:2359 | homologous IL_5TBW_297 | NA | ||
| 1/LA/1500:1505, 1/LA/1513:1516 | homologous IL_5TBW_298 | NA | ||
| 1/LA/1532:1536, 1/LA/1585:1590 | homologous IL_5TBW_299 | NA | ||
| 1/LA/1561:1562, 1/LA/1577:1579 | Single stack bend geometric IL_7A0S_054 | NA IL_04038.4* | ||
| 1/LA/1618:1621, 1/LA/1824:1826 | homologous IL_5TBW_300 | NA | ||
| 1/LA/1623:1624, 1/LA/1819:1822 | Multiple bulged bases geometric IL_4V9F_021 | NA IL_13730.12* | ||
| 1/LA/1627:1631, 1/LA/1811:1816 | homologous IL_5TBW_302 | NA | ||
| 1/LA/1645:1649, 1/LA/1806:1810 | Triple sheared geometric IL_5TBW_067 | NA IL_56467.6* | ||
| 1/LA/1661:1663, 1/LA/1786:1788 | homologous IL_5TBW_304 | NA | ||
| 1/LA/1669:1670, 1/LA/1778:1780 | Single bulged C geometric IL_5TBW_069 | NA IL_61258.10* | ||
| 1/LA/1670:1671, 1/LA/1776:1778 | homologous IL_5TBW_306 | NA | ||
| 1/LA/1694:1698, 1/LA/1747:1752 | homologous IL_5TBW_307 | NA | ||
| 1/LA/1702:1707, 1/LA/1737:1743 | homologous IL_5TBW_308 | NA | ||
| 1/LA/1711:1717, 1/LA/1727:1733 | homologous IL_5TBW_309 | NA | ||
| 1/LA/1883:1889, 1/LA/2346:2349 | homologous IL_5TBW_310 | NA | ||
| 1/LA/1895:1897, 1/LA/2338:2340 | homologous IL_5TBW_311 | NA | ||
| 1/LA/1898:1901, 1/LA/2336:2337 | Major groove platform; stack outside cWW geometric IL_4V9F_008 | NA IL_70995.6* | ||
| 1/LA/1901:1906, 1/LA/2333:2336 | homologous IL_5TBW_313 | NA | ||
| 1/LA/1918:1923, 1/LA/1928:1934 | homologous IL_5TBW_314 | NA | ||
| 1/LA/1940:1942, 1/LA/2106:2108 | homologous IL_5TBW_315 | NA | ||
| 1/LA/1947:1948, 1/LA/2098:2101 | homologous IL_5TBW_316 | NA | ||
| 1/LA/1951:1953, 1/LA/2094:2095 | Single stack bend geometric IL_7RQB_005 | NA IL_04038.4* | ||
| 1/LA/2128:2129, 1/LA/2323:2325 | homologous IL_5TBW_318 | NA | ||
| 1/LA/2156:2161, 1/LA/2173:2180 | homologous IL_5TBW_319 | NA | ||
| 1/LA/2196:2199, 1/LA/2245:2246 | homologous IL_5TBW_320 | NA | ||
| 1/LA/2200:2201, 1/LA/2241:2244 | homologous IL_5TBW_321 | NA | ||
| 1/LA/2204:2206, 1/LA/2237:2238 | Single stack bend geometric IL_4WF9_089 | NA IL_04038.4* | ||
| 1/LA/2206:2210, 1/LA/2235:2237 | Decoding loop related geometric IL_3C3Z_002 | NA IL_04038.4* | ||
| 1/LA/2211:2217, 1/LA/2228:2234 | homologous IL_5TBW_324 | NA | ||
| 1/LA/2276:2277, 1/LA/2307:2310 | Multiple bulged bases geometric IL_5TBW_089 | NA IL_69632.1* | ||
| 1/LA/2277:2288, 1/LA/2304:2307 | homologous IL_5TBW_326 | NA | ||
| 1/LA/2391:2394, 1/LA/2986:2988 | homologous IL_5TBW_327 | NA | ||
| 1/LA/2396:2398, 1/LA/2981:2984 | homologous IL_5TBW_328 | NA | ||
| 1/LA/2409:2411, 1/LA/2811:2812 | homologous IL_5TBW_329 | NA | ||
| 1/LA/2412:2413, 1/LA/2807:2810 | homologous IL_5TBW_330 | NA | ||
| 1/LA/2423:2425, 1/LA/2604:2607 | homologous IL_5TBW_331 | NA | ||
| 1/LA/2444:2446, 1/LA/2500:2503 | NA | NA | ||
| 1/LA/2520:2526, 1/LA/2584:2587 | homologous IL_5TBW_332 | NA | ||
| 1/LA/2614:2615, 1/LA/2625:2627 | homologous IL_5TBW_333 | NA | ||
| 1/LA/2666:2668, 1/LA/2686:2690 | Isolated tHS basepair with bulges geometric IL_4V9F_080 | NA IL_38958.6* | ||
| 1/LA/2718:2721, 1/LA/2735:2738 | homologous IL_5TBW_335 | NA | ||
| 1/LA/2770:2773, 1/LA/2787:2788 | homologous IL_5TBW_336 | NA | ||
| 1/LA/2823:2824, 1/LA/2865:2867 | Major groove platform geometric IL_5TBW_102 | NA IL_80663.10* | ||
| 1/LA/2824:2828, 1/LA/2862:2865 | NA | NA | ||
| 1/LA/2828:2830, 1/LA/2858:2862 | Major groove minor groove platform with extra cWW geometric IL_4V9F_084 | NA IL_96042.4* | ||
| 1/LA/2835:2839, 1/LA/2849:2853 | homologous IL_5TBW_341 | NA | ||
| 1/LA/2876:2877, 1/LA/2949:2951 | homologous IL_5TBW_342 | NA | ||
| 1/LA/2879:2881, 1/LA/2943:2947 | Isolated non-canonical cWW with bulges geometric IL_5TBW_108 | NA IL_01312.13* | ||
| 1/LA/2881:2882, 1/LA/2940:2943 | homologous IL_5TBW_344 | NA | ||
| 1/LA/2889:2891, 1/LA/2912:2914 | geometric IL_5TBW_110 | NA IL_01312.13* | ||
| 1/LA/2891:2892, 1/LA/2909:2912 | Minor groove platform with intercalation geometric IL_5TBW_111 | NA IL_95601.1* | ||
| 1/LA/2918:2920, 1/LA/2926:2928 | geometric IL_5Y7M_007 | NA IL_01312.13* | ||
| 1/LA/2960:2961, 1/LA/2970:2972 | Single bulged A geometric IL_7RQB_101 | NA IL_80007.16* | ||
| 1/LA/3004:3007, 1/LA/3139:3144 | homologous IL_5TBW_349 | NA | ||
| 1/LA/3012:3014, 1/LA/3040:3042 | homologous IL_5TBW_350 | NA | ||
| 1/LA/3018:3025, 1/LA/3030:3036 | 8x7 Sarcin-Ricin; G-bulge geometric IL_5TBW_116 | NA IL_04346.5* | ||
| 1/LA/3047:3051, 1/LA/3091:3094 | homologous IL_5TBW_352 | NA | ||
| 1/LA/3054:3059, 1/LA/3084:3088 | homologous IL_5TBW_353 | NA | ||
| 1/LA/3063:3064, 1/LA/3077:3080 | homologous IL_5TBW_354 | NA | ||
| 1/LA/3103:3107, 1/LA/3127:3131 | homologous IL_5TBW_355 | NA | ||
| 1/LA/3158:3159, 1/LA/3291:3293 | Single stack bend geometric IL_7A0S_054 | NA IL_04038.4* | ||
| 1/LA/3164:3166, 1/LA/3284:3286 | geometric IL_4V9F_105 | NA IL_01312.13* | ||
| 1/LA/3168:3170, 1/LA/3280:3282 | homologous IL_5TBW_357 | NA | ||
| 1/LA/3177:3179, 1/LA/3210:3211 | homologous IL_5TBW_358 | NA | ||
| 1/LA/3179:3188, 1/LA/3204:3210 | geometric IL_5TBW_124 | NA IL_56867.1* | ||
| 1/LA/3193:3194, 1/LA/3197:3199 | Single bulged U geometric IL_5TBW_125 | NA IL_83039.11* | ||
| 1/LA/3225:3229, 1/LA/3258:3260 | homologous IL_5TBW_361 | NA | ||
| 1/LA/3233:3235, 1/LA/3252:3254 | geometric IL_4M4O_002 | NA IL_01312.13* | ||
| 1/LA/3235:3238, 1/LA/3249:3252 | homologous IL_5TBW_363 | NA | ||
| 1/LA/3300:3303, 1/LA/3311:3314 | Tandem non-canonical cWW pairs geometric IL_5TBW_129 | NA IL_85877.10* | ||
| 1/LA/3318:3320, 1/LA/3387:3388 | homologous IL_5TBW_365 | NA | ||
| 1/LA/3324:3325, 1/LA/3381:3383 | homologous IL_5TBW_366 | NA | ||
| 1/LA/3328:3330, 1/LA/3373:3378 | homologous IL_5TBW_367 | NA | ||
| 1/LA/3332:3337, 1/LA/3367:3371 | homologous IL_5TBW_368 | NA | ||
| 1/LA/3340:3342, 1/LA/3363:3364 | homologous IL_5TBW_369 | NA | ||
| 1/LA/3342:3345, 1/LA/3360:3363 | tWS-tSW geometric IL_5TBW_135 | NA IL_09705.7* | ||
| 1/LA/3349:3350, 1/LA/3353:3356 | homologous IL_5TBW_371 | NA | ||
| 1/LB/15:16, 1/LB/63:65 | NA | NA | ||
| 1/LB/21:27, 1/LB/53:58 | NA | NA | ||
| 1/LB/28:29, 1/LB/49:52 | NA | NA | ||
| 1/LB/29:30, 1/LB/47:49 | NA | NA | ||
| 1/LB/32:36, 1/LB/41:45 | NA | NA | ||
| 1/LB/72:80, 1/LB/100:106 | NA | NA | ||
| 1/LB/84:87, 1/LB/94:96 | NA | NA | ||
| 1/LC/64:66, 1/LC/93:96 | Isolated non-canonical cWW with bulges homologous IL_5TBW_145 | NA IL_55456.1* | ||
| 1/LC/68:69, 1/LC/89:91 | Single bulged U geometric IL_5TBW_146 | NA IL_83039.11* | ||
| 1/S2/24:26, 1/S2/600:601 | Single bulged C homologous IL_4V88_384 | NA IL_61258.10* | ||
| 1/S2/35:37, 1/S2/471:473 | UU cWW geometric IL_4ZC7_004 | NA IL_01312.13* | ||
| 1/S2/42:48, 1/S2/431:433 | homologous IL_4V88_387 | NA IL_34626.4* | ||
| 1/S2/50:52, 1/S2/428:429 | Minor groove platform homologous IL_4V88_388 | NA IL_06437.11* | ||
| 1/S2/58:63, 1/S2/87:89 | homologous IL_4V88_389 | NA IL_96451.1* | ||
| 1/S2/64:69, 1/S2/82:86 | homologous IL_4V88_390 | NA IL_59423.1* | ||
| 1/S2/109:112, 1/S2/302:305 | Tandem non-canonical cWW pairs homologous IL_4V88_391 | NA IL_85877.10* | ||
| 1/S2/113:116, 1/S2/300:301 | Multiple bulged bases homologous IL_4V88_392 | NA IL_13730.12* | ||
| 1/S2/117:122, 1/S2/295:299 | homologous IL_4V88_393 | NA IL_76386.1* | ||
| 1/S2/143:149, 1/S2/165:172 | tWH-tWH-tHW-tHW homologous IL_4V88_394 | NA IL_92440.5* | ||
| 1/S2/150:152, 1/S2/162:164 | Isolated cWH basepair geometric IL_6RA4_002 | NA IL_42589.6* | ||
| 1/S2/186:189, 1/S2/196:199 | Double sheared homologous IL_4V88_396 | NA IL_09705.7* | ||
| 1/S2/204:206, 1/S2/259:263 | Major groove platform with extra cWW homologous IL_4V88_397 | NA IL_95485.6* | ||
| 1/S2/206:208, 1/S2/257:259 | geometric IL_3TD0_001 | NA IL_01312.13* | ||
| 1/S2/270:273, 1/S2/283:285 | homologous IL_4V88_400 | NA IL_05922.1* | ||
| 1/S2/275:276, 1/S2/279:281 | Single bulged U homologous IL_4V88_401 | NA IL_83039.11* | ||
| 1/S2/311:316, 1/S2/348:355 | Kink-turn with non-sequential stacking homologous IL_4V88_402 | NA IL_29549.9* | ||
| 1/S2/318:323, 1/S2/345:346 | homologous IL_4V88_403 | NA IL_55658.1* | ||
| 1/S2/363:365, 1/S2/376:381 | homologous IL_4V88_404 | NA IL_46732.1* | ||
| 1/S2/389:391, 1/S2/406:408 | Isolated cWH basepair homologous IL_4V88_405 | NA IL_42589.6* | ||
| 1/S2/411:414, 1/S2/419:422 | Tandem non-canonical cWW pairs geometric IL_5J7L_283 | NA IL_85877.10* | ||
| 1/S2/439:441, 1/S2/463:464 | Single bulged U homologous IL_4V88_407 | NA IL_83039.11* | ||
| 1/S2/443:447, 1/S2/460:461 | C-loop geometric IL_4LFB_015 | NA IL_63596.4* | ||
| 1/S2/447:448, 1/S2/458:460 | Single bulged G geometric IL_5J7L_019 | NA IL_59137.10* | ||
| 1/S2/480:483, 1/S2/504:508 | NA | NA | ||
| 1/S2/517:518, 1/S2/533:535 | Minor groove platform geometric IL_4LFB_004 | NA IL_06437.11* | ||
| 1/S2/518:520, 1/S2/532:533 | Minor groove platform homologous IL_4V88_412 | NA IL_06437.11* | ||
| 1/S2/550:557, 1/S2/587:588 | SSU/LSU pseudoknot geometric IL_4V88_413 | NA IL_15861.6* | ||
| 1/S2/557:559, 1/S2/586:587 | Single bulged U homologous IL_4V88_414 | NA IL_83039.11* | ||
| 1/S2/562:568, 1/S2/575:583 | homologous IL_4V88_415 | NA IL_04667.1* | ||
| 1/S2/616:622, 1/S2/1104:1105 | homologous IL_4V88_416 | NA IL_12418.1* | ||
| 1/S2/624:626, 1/S2/973:975 | homologous IL_4V88_417 | NA IL_01312.13* | ||
| 1/S2/627:631, 1/S2/968:972 | tSH-tHW-tHS homologous IL_4V88_418 | NA IL_39521.5* | ||
| 1/S2/646:648, 1/S2/686:688 | geometric IL_3DIL_006 | NA IL_01312.13* | ||
| 1/S2/648:650, 1/S2/685:686 | Single stack bend geometric IL_4V9F_005 | NA IL_04038.4* | ||
| 1/S2/650:651, 1/S2/683:685 | Single stack bend geometric IL_7RQB_091 | NA IL_04038.4* | ||
| 1/S2/651:658, 1/S2/676:683 | NA | NA | ||
| 1/S2/746:747, 1/S2/802:805 | Major groove minor groove platform; mini C-loop homologous IL_4V88_423 | NA IL_09061.4* | ||
| 1/S2/748:750, 1/S2/799:801 | homologous IL_4V88_424 | NA IL_01312.13* | ||
| 1/S2/751:759, 1/S2/791:798 | homologous IL_4V88_425 | NA IL_69091.1* | ||
| 1/S2/816:822, 1/S2/850:857 | NA | NA | ||
| 1/S2/865:866, 1/S2/962:965 | Major groove platform; stack outside cWW geometric IL_4V88_428 | NA IL_70995.6* | ||
| 1/S2/868:870, 1/S2/957:960 | geometric IL_1NBS_006 | NA IL_01312.13* | ||
| 1/S2/871:874, 1/S2/953:956 | Tandem non-canonical cWW pairs homologous IL_4V88_430 | NA IL_85877.10* | ||
| 1/S2/874:878, 1/S2/950:953 | Tandem non-canonical cWW pairs geometric IL_4V88_431 | NA IL_85877.10* | ||
| 1/S2/885:888, 1/S2/924:927 | Tandem non-canonical cWW pairs homologous IL_4V88_432 | NA IL_85877.10* | ||
| 1/S2/893:899, 1/S2/910:919 | homologous IL_5TBW_430 | NA | ||
| 1/S2/985:990, 1/S2/1014:1016 | Other IL geometric IL_4V88_435 | NA IL_51590.1* | ||
| 1/S2/990:994, 1/S2/1010:1014 | tSH-tHW-tHS homologous IL_4V88_436 | NA IL_39521.5* | ||
| 1/S2/1034:1036, 1/S2/1095:1101 | homologous IL_4V88_437 | NA IL_19557.1* | ||
| 1/S2/1041:1044, 1/S2/1074:1077 | Tandem non-canonical cWW pairs homologous IL_4V88_438 | NA IL_85877.10* | ||
| 1/S2/1051:1053, 1/S2/1066:1067 | Single bulged U geometric IL_3WBM_001 | NA IL_83039.11* | ||
| 1/S2/1111:1118, 1/S2/1129:1134 | 8x6 Sarcin-Ricin with inserted Y; G-bulge homologous IL_4V88_440 | NA IL_24606.1* | ||
| 1/S2/1146:1147, 1/S2/1630:1632 | Single bulged A homologous IL_4V88_441 | NA IL_80007.16* | ||
| 1/S2/1149:1151, 1/S2/1627:1628 | Single bulged G homologous IL_4V88_442 | NA IL_59137.10* | ||
| 1/S2/1157:1160, 1/S2/1617:1621 | C-loop homologous IL_4V88_443 | NA IL_63596.4* | ||
| 1/S2/1173:1175, 1/S2/1464:1466 | homologous IL_4V88_444 | NA IL_01312.13* | ||
| 1/S2/1178:1179, 1/S2/1459:1461 | Minor groove platform homologous IL_4V88_445 | NA IL_06437.11* | ||
| 1/S2/1213:1215, 1/S2/1448:1450 | homologous IL_4V88_446 | NA IL_01312.13* | ||
| 1/S2/1224:1233, 1/S2/1252:1259 | NA | NA | ||
| 1/S2/1234:1236, 1/S2/1249:1251 | homologous IL_4V88_448 | NA IL_01312.13* | ||
| 1/S2/1268:1270, 1/S2/1440:1441 | Single bulged U homologous IL_4V88_449 | NA IL_83039.11* | ||
| 1/S2/1271:1276, 1/S2/1436:1439 | Tandem non-canonical cWW pairs geometric IL_4V88_473 | NA IL_85877.10* | ||
| 1/S2/1276:1278, 1/S2/1430:1436 | Minor groove platform with extra cWW geometric IL_4V88_451 | NA IL_09768.1* | ||
| 1/S2/1280:1281, 1/S2/1426:1428 | Single bulged A homologous IL_4V88_452 | NA IL_80007.16* | ||
| 1/S2/1290:1292, 1/S2/1323:1325 | Isolated cWH basepair homologous IL_4V88_453 | NA IL_42589.6* | ||
| 1/S2/1306:1308, 1/S2/1317:1318 | Minor groove platform homologous IL_4V88_454 | NA IL_06437.11* | ||
| 1/S2/1339:1342, 1/S2/1383:1385 | homologous IL_4V88_455 | NA IL_01312.13* | ||
| 1/S2/1345:1348, 1/S2/1377:1380 | Minor groove platform homologous IL_4V88_456 | NA IL_69507.1* | ||
| 1/S2/1352:1354, 1/S2/1369:1373 | homologous IL_4V88_457 | NA IL_01312.13* | ||
| 1/S2/1389:1391, 1/S2/1407:1412 | Major groove platform; stack outside cWW homologous IL_4V88_458 | NA IL_60171.1* | ||
| 1/S2/1480:1487, 1/S2/1519:1527 | homologous IL_4V88_459 | NA IL_69573.1* | ||
| 1/S2/1488:1494, 1/S2/1513:1518 | homologous IL_4V88_460 | NA IL_75461.2* | ||
| 1/S2/1495:1498, 1/S2/1509:1512 | Tandem non-canonical cWW pairs homologous IL_4V88_461 | NA IL_85877.10* | ||
| 1/S2/1540:1545, 1/S2/1566:1571 | homologous IL_4V88_462 | NA IL_19954.1* | ||
| 1/S2/1636:1638, 1/S2/1764:1767 | geometric IL_4V88_463 | NA IL_36143.2* | ||
| 1/S2/1638:1641, 1/S2/1760:1764 | NA | NA | ||
| 1/S2/1642:1644, 1/S2/1757:1759 | homologous IL_4V88_465 | NA IL_01312.13* | ||
| 1/S2/1644:1647, 1/S2/1753:1757 | NA | NA | ||
| 1/S2/1650:1652, 1/S2/1748:1750 | AA cWW homologous IL_4V88_467 | NA IL_01312.13* | ||
| 1/S2/1653:1656, 1/S2/1744:1747 | Double sheared homologous IL_4V88_468 | NA IL_09705.7* | ||
| 1/S2/1656:1658, 1/S2/1743:1744 | Single bulged U geometric IL_4V88_469 | NA IL_21340.1* | ||
| 1/S2/1665:1667, 1/S2/1734:1736 | homologous IL_4V88_470 | NA IL_01312.13* | ||
| 1/S2/1669:1672, 1/S2/1729:1732 | Double sheared geometric IL_4V88_471 | NA IL_09705.7* | ||
| 1/S2/1672:1674, 1/S2/1727:1729 | homologous IL_4V88_472 | NA IL_01312.13* | ||
| 1/S2/1675:1678, 1/S2/1723:1726 | Tandem non-canonical cWW pairs homologous IL_4V88_473 | NA IL_85877.10* | ||
| 1/S2/1678:1682, 1/S2/1719:1723 | Triple sheared geometric IL_4V88_474 | NA IL_56467.6* | ||
| 1/S2/1688:1690, 1/S2/1711:1713 | geometric IL_ |