Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/A/13:22NANA
1/A/31:39NANA
1/A/53:61NANA
1/C1/38:45
geometric
HL_4WF9_006
NA

HL_23481.5*
1/C1/69:74
homologous
HL_5TBW_114
NA
1/C1/90:96
homologous
HL_5TBW_115
NA
1/C1/132:136
homologous
HL_5TBW_116
NA
1/C1/194:201
homologous
HL_5TBW_117
NA
1/C1/208:212
homologous
HL_5TBW_118
NA
1/C1/216:224
homologous
HL_5TBW_119
NA
1/C1/278:287
homologous
HL_5TBW_120
NA
1/C1/303:312
homologous
HL_5TBW_121
NA
1/C1/357:362
homologous
HL_5TBW_122
NA
1/C1/382:387
homologous
HL_5TBW_123
NA
1/C1/543:548
geometric
HL_7RQB_011
NA

HL_98557.5*
1/C1/599:604
homologous
HL_5TBW_125
NA
1/C1/640:649
homologous
HL_5TBW_126
NA
1/C1/686:694
homologous
HL_5TBW_127
NA
1/C1/707:712
homologous
HL_5TBW_128
NA
1/C1/732:737
homologous
HL_5TBW_129
NA
1/C1/763:768
geometric
HL_5TBW_018
NA

HL_00996.1*
1/C1/844:849
homologous
HL_5TBW_131
NA
1/C1/876:885
homologous
HL_5TBW_132
NA
1/C1/910:918
homologous
HL_5TBW_133
NA
1/C1/958:963
homologous
HL_5TBW_134
NA
1/C1/1023:1029
homologous
HL_5TBW_135
NA
1/C1/1076:1083
homologous
HL_5TBW_136
NA
1/C1/1126:1132
homologous
HL_5TBW_137
NA
1/C1/1148:1155
homologous
HL_5TBW_138
NA
1/C1/1239:1249
homologous
HL_5TBW_139
NA
1/C1/1267:1274
homologous
HL_5TBW_140
NA
1/C1/1403:1408
homologous
HL_5TBW_142
NA
1/C1/1462:1470
homologous
HL_5TBW_143
NA
1/C1/1506:1512
homologous
HL_5TBW_144
NA
1/C1/1544:1549
homologous
HL_5TBW_145
NA
1/C1/1599:1608
homologous
HL_5TBW_147
NA
1/C1/1634:1639
homologous
HL_5TBW_148
NA
1/C1/1680:1688
homologous
HL_5TBW_149
NA
1/C1/1719:1725
homologous
HL_5TBW_150
NA
1/C1/1759:1766
homologous
HL_5TBW_151
NA
1/C1/1792:1796
homologous
HL_5TBW_152
NA
1/C1/1844:1851
homologous
HL_5TBW_153
NA
1/C1/1862:1868
homologous
HL_5TBW_154
NA
1/C1/1923:1928
homologous
HL_5TBW_155
NA
1/C1/2110:2114
homologous
HL_5TBW_157
NA
1/C1/2135:2145
homologous
HL_5TBW_158
NA
1/C1/2164:2170
homologous
HL_5TBW_159
NA
1/C1/2220:2225
homologous
HL_5TBW_160
NA
1/C1/2253:2263
homologous
HL_5TBW_161
NA
1/C1/2292:2300
homologous
HL_5TBW_162
NA
1/C1/2369:2378
homologous
HL_5TBW_163
NA
1/C1/2535:2544NANA
1/C1/2568:2573
geometric
HL_2Y8W_001
NA

HL_69459.1*
1/C1/2616:2624
homologous
HL_5TBW_167
NA
1/C1/2633:2645
homologous
HL_5TBW_168
NA
1/C1/2673:2681
homologous
HL_5TBW_169
NA
1/C1/2693:2700
homologous
HL_5TBW_170
NA
1/C1/2724:2732
homologous
HL_5TBW_171
NA
1/C1/2744:2749
homologous
HL_5TBW_172
NA
1/C1/2776:2784
homologous
HL_5TBW_173
NA
1/C1/2840:2848
homologous
HL_5TBW_174
NA
1/C1/2897:2904
homologous
HL_5TBW_175
NA
1/C1/2920:2926
homologous
HL_5TBW_176
NA
1/C1/2963:2968
homologous
HL_5TBW_177
NA
1/C1/3025:3030
homologous
HL_5TBW_178
NA
1/C1/3068:3073
homologous
HL_5TBW_179
NA
1/C1/3110:3124
homologous
HL_5TBW_180
NA
1/C1/3194:3197
geometric
HL_5TBW_068
NA

HL_46546.1*
1/C1/3240:3247
homologous
HL_5TBW_182
NA
1/C1/3303:3311
homologous
HL_5TBW_183
NA
1/C1/3350:3353
homologous
HL_5TBW_184
NA
1/C2/7:17
homologous
HL_4V88_186
NA

HL_67265.4*
1/C2/154:160Other HL
homologous
HL_4V88_188
NA

HL_43074.18*
1/C2/190:195NANA
1/C2/228:237NANA
1/C2/243:250T-loop with 1 bulged base
homologous
HL_4V88_191
NA

HL_68493.6*
1/C2/276:279NANA
1/C2/330:338
homologous
HL_4V88_193
NA

HL_93727.5*
1/C2/368:373
homologous
HL_4V88_194
NA

HL_18785.1*
1/C2/393:404
homologous
HL_4V88_195
NA

HL_22443.1*
1/C2/414:419UNCG
homologous
HL_4V88_196
NA

HL_79299.11*
1/C2/450:456
homologous
HL_4V88_197
NA

HL_50374.1*
1/C2/520:532
geometric
HL_4V88_199
NA

HL_17086.2*
1/C2/569:574Other HL
homologous
HL_4V88_200
NA

HL_43074.18*
1/C2/764:772
homologous
HL_4V88_203
NA

HL_72066.1*
1/C2/777:783NANA
1/C2/829:843
homologous
HL_4V88_205
NA

HL_03603.1*
1/C2/900:909
homologous
HL_4V88_206
NA

HL_87219.4*
1/C2/937:942Other HL
homologous
HL_4V88_207
NA

HL_43074.18*
1/C2/997:1007
homologous
HL_4V88_208
NA

HL_87219.4*
1/C2/1055:1064NANA
1/C2/1084:1089Other HL
homologous
HL_4V88_210
NA

HL_43074.18*
1/C2/1121:1126GNRA
homologous
HL_4V88_211
NA

HL_43074.18*
1/C2/1188:1197
homologous
HL_4V88_212
NA

HL_96854.1*
1/C2/1238:1247
homologous
HL_4V88_213
NA

HL_30819.1*
1/C2/1296:1301GNRA
homologous
HL_4V88_214
NA

HL_43074.18*
1/C2/1309:1316
homologous
HL_4V88_215
NA

HL_54035.7*
1/C2/1359:1364
homologous
HL_4V88_216
NA

HL_82678.2*
1/C2/1396:1402
homologous
HL_4V88_217
NA

HL_67216.5*
1/C2/1501:1506GNRA
homologous
HL_4V88_218
NA

HL_43074.18*
1/C2/1550:1561
homologous
HL_4V88_219
NA

HL_32458.3*
1/C2/1594:1602
homologous
HL_4V88_220
NA

HL_01181.4*
1/C2/1778:1783Other HL
homologous
HL_4V88_222
NA

HL_43074.18*
1/C3/69:89NANA
1/C3/108:114
homologous
HL_5TBW_075
NA

HL_06569.2*
1/C3/124:129
homologous
HL_5TBW_076
NA

HL_60357.1*
1/C4/36:41NANA
1/C4/88:93NANA
1/P/12:23NANA
1/P/31:39NANA
1/P/53:61NANA

Problematic loops

#loop idProblemSequence
HL_7RR5_032
homologous
HL_5TBW_141
HL_7RR5_037NA
HL_7RR5_047
geometric
HL_7RQB_011
HL_7RR5_055NA
HL_7RR5_077NA
HL_7RR5_088
geometric
HL_2Y8W_001
HL_7RR5_091NA
HL_7RR5_092NA
HL_7RR5_111NA

Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/C1/3:4,
1/C3/155:156
NANA
1/C1/7:8,
1/C3/150:152
Single bulged C
homologous
IL_5TBW_002
NA

IL_61258.10*
1/C1/12:15,
1/C3/144:146

geometric
IL_4WF9_083
NA

IL_01312.13*
1/C1/27:28,
1/C1/56:58

homologous
IL_5TBW_240
NA
1/C1/31:38,
1/C1/45:53

homologous
IL_5TBW_241
NA
1/C1/82:89,
1/C1/97:103

homologous
IL_5TBW_242
NA
1/C1/123:124,
1/C1/144:149

geometric
IL_5TBW_007
NA

IL_19724.1*
1/C1/125:127,
1/C1/141:143

homologous
IL_5TBW_244
NA
1/C1/163:165,
1/C1/257:258

homologous
IL_5TBW_245
NA
1/C1/169:170,
1/C1/248:253

homologous
IL_5TBW_246
NA
1/C1/177:178,
1/C1/238:241
Major groove platform
geometric
IL_5J7L_320
NA

IL_80663.10*
1/C1/189:191,
1/C1/204:205

homologous
IL_5TBW_248
NA
1/C1/337:339,
1/C3/25:26
Single bulged A
homologous
IL_5TBW_013
NA

IL_80007.16*
1/C1/376:379,
1/C1/390:403

homologous
IL_5TBW_250
NA
1/C1/404:410,
1/C3/13:19
Triple sheared with non-canonical cWW
homologous
IL_5TBW_015
NA

IL_66414.5*
1/C1/429:431,
1/C1/628:630

homologous
IL_5TBW_252
NA
1/C1/512:513,
1/C1/577:579

homologous
IL_5TBW_254
NA
1/C1/517:525,
1/C1/567:573

homologous
IL_5TBW_255
NA
1/C1/531:538,
1/C1/553:561

homologous
IL_5TBW_256
NA
1/C1/668:670,
1/C1/792:794

homologous
IL_5TBW_257
NA
1/C1/680:684,
1/C1/696:700

homologous
IL_5TBW_258
NA
1/C1/725:728,
1/C1/741:745

homologous
IL_5TBW_259
NA
1/C1/752:753,
1/C1/779:781

homologous
IL_5TBW_260
NA
1/C1/755:756,
1/C1/775:777

homologous
IL_5TBW_261
NA
1/C1/758:763,
1/C1/768:773

homologous
IL_5TBW_262
NA
1/C1/803:805,
1/C1/938:940

homologous
IL_5TBW_263
NA
1/C1/805:809,
1/C1/931:938

geometric
IL_5TBW_028
NA

IL_17470.5*
1/C1/833:834,
1/C1/859:861

homologous
IL_5TBW_265
NA
1/C1/834:838,
1/C1/855:859
Triple sheared
geometric
IL_5J7L_263
NA

IL_56467.6*
1/C1/869:872,
1/C1/888:890

homologous
IL_5TBW_267
NA
1/C1/873:875,
1/C1/886:887

homologous
IL_5TBW_268
NA
1/C1/907:909,
1/C1/919:923
Multiple bulged bases
geometric
IL_5TBW_033
NA

IL_90991.5*
1/C1/954:956,
1/C1/965:967

homologous
IL_5TBW_270
NA
1/C1/969:970,
1/C1/1111:1113

homologous
IL_5TBW_271
NA
1/C1/977:982,
1/C1/1101:1104
NANA
1/C1/983:985,
1/C1/1099:1100

homologous
IL_5TBW_273
NA
1/C1/991:997,
1/C1/1052:1058

homologous
IL_5TBW_274
NA
1/C1/997:998,
1/C1/1050:1052
Minor groove platform
geometric
IL_6DLR_003
NA

IL_06437.11*
1/C1/999:1004,
1/C1/1046:1049

homologous
IL_5TBW_276
NA
1/C1/1006:1009,
1/C1/1041:1044
Tandem non-canonical cWW pairs
geometric
IL_5TBW_041
NA

IL_85877.10*
1/C1/1009:1011,
1/C1/1039:1041

homologous
IL_5TBW_278
NA
1/C1/1013:1018,
1/C1/1034:1037

homologous
IL_5TBW_279
NA
1/C1/1069:1071,
1/C1/1087:1089

homologous
IL_5TBW_280
NA
1/C1/1074:1076,
1/C1/1083:1084
Single bulged A
geometric
IL_5TBW_045
NA

IL_80007.16*
1/C1/1120:1122,
1/C1/1136:1138

homologous
IL_5TBW_282
NA
1/C1/1167:1171,
1/C1/1328:1332

homologous
IL_5TBW_284
NA
1/C1/1173:1180,
1/C1/1325:1326
Multiple bulged bases
geometric
IL_1R3E_001
NA

IL_13730.12*
1/C1/1180:1182,
1/C1/1324:1325

homologous
IL_5TBW_286
NA
1/C1/1187:1194,
1/C1/1314:1319

homologous
IL_5TBW_287
NA
1/C1/1194:1205,
1/C1/1299:1314

geometric
IL_5TBW_052
NA

IL_94878.1*
1/C1/1207:1209,
1/C1/1296:1297

homologous
IL_5TBW_289
NA
1/C1/1218:1226,
1/C1/1283:1287

homologous
IL_5TBW_290
NA
1/C1/1233:1238,
1/C1/1250:1255
NANA
1/C1/1262:1266,
1/C1/1275:1277
Major groove platform with extra cWW
geometric
IL_5D8H_003
NA

IL_95485.6*
1/C1/1376:1378,
1/C1/1428:1431

homologous
IL_5TBW_293
NA
1/C1/1385:1387,
1/C1/1420:1421

homologous
IL_5TBW_294
NA
1/C1/1388:1395,
1/C1/1415:1419

homologous
IL_5TBW_295
NA
1/C1/1398:1400,
1/C1/1411:1412

homologous
IL_5TBW_296
NA
1/C1/1444:1450,
1/C1/2354:2359

homologous
IL_5TBW_297
NA
1/C1/1500:1505,
1/C1/1513:1516

homologous
IL_5TBW_298
NA
1/C1/1532:1536,
1/C1/1585:1590

homologous
IL_5TBW_299
NA
1/C1/1618:1621,
1/C1/1824:1826

homologous
IL_5TBW_300
NA
1/C1/1623:1627,
1/C1/1816:1822
NANA
1/C1/1627:1631,
1/C1/1811:1816

geometric
IL_5TBW_066
NA

IL_74736.1*
1/C1/1645:1649,
1/C1/1806:1810
Triple sheared
geometric
IL_5TBW_067
NA

IL_56467.6*
1/C1/1661:1663,
1/C1/1786:1788

homologous
IL_5TBW_304
NA
1/C1/1669:1670,
1/C1/1778:1780

homologous
IL_5TBW_305
NA
1/C1/1670:1671,
1/C1/1776:1778
Single stack bend
geometric
IL_5TBW_070
NA

IL_72766.2*
1/C1/1694:1698,
1/C1/1747:1752

homologous
IL_5TBW_307
NA
1/C1/1702:1707,
1/C1/1737:1743

homologous
IL_5TBW_308
NA
1/C1/1711:1717,
1/C1/1727:1733

homologous
IL_5TBW_309
NA
1/C1/1883:1889,
1/C1/2346:2349

homologous
IL_5TBW_310
NA
1/C1/1895:1897,
1/C1/2338:2340

homologous
IL_5TBW_311
NA
1/C1/1898:1901,
1/C1/2336:2337

homologous
IL_5TBW_312
NA
1/C1/1901:1906,
1/C1/2333:2336
Intercalated tWH
geometric
IL_5TBW_077
NA

IL_98882.3*
1/C1/1918:1923,
1/C1/1928:1934
tSH-tSH-tHH-tHS
geometric
IL_7RQB_068
NA

IL_66584.5*
1/C1/1940:1942,
1/C1/2106:2108

homologous
IL_5TBW_315
NA
1/C1/1947:1948,
1/C1/2098:2101

homologous
IL_5TBW_316
NA
1/C1/2128:2129,
1/C1/2323:2325

homologous
IL_5TBW_318
NA
1/C1/2156:2161,
1/C1/2173:2180

homologous
IL_5TBW_319
NA
1/C1/2196:2199,
1/C1/2245:2246

homologous
IL_5TBW_320
NA
1/C1/2200:2201,
1/C1/2241:2244

homologous
IL_5TBW_321
NA
1/C1/2204:2206,
1/C1/2237:2238
Single stack bend
geometric
IL_7A0S_054
NA

IL_04038.4*
1/C1/2206:2210,
1/C1/2235:2237
NANA
1/C1/2211:2217,
1/C1/2228:2234

homologous
IL_5TBW_324
NA
1/C1/2276:2277,
1/C1/2307:2310
Multiple bulged bases
geometric
IL_5TBW_089
NA

IL_69632.1*
1/C1/2277:2288,
1/C1/2304:2307

homologous
IL_5TBW_326
NA
1/C1/2391:2394,
1/C1/2986:2988

homologous
IL_5TBW_327
NA
1/C1/2396:2398,
1/C1/2981:2984

homologous
IL_5TBW_328
NA
1/C1/2409:2411,
1/C1/2811:2812

homologous
IL_5TBW_329
NA
1/C1/2412:2413,
1/C1/2807:2810

homologous
IL_5TBW_330
NA
1/C1/2423:2425,
1/C1/2604:2607

homologous
IL_5TBW_331
NA
1/C1/2520:2526,
1/C1/2584:2587

homologous
IL_5TBW_332
NA
1/C1/2614:2615,
1/C1/2625:2627

homologous
IL_5TBW_333
NA
1/C1/2666:2668,
1/C1/2686:2690
Isolated tHS basepair with bulges
geometric
IL_5TBW_099
NA

IL_38958.6*
1/C1/2718:2721,
1/C1/2735:2738

homologous
IL_5TBW_335
NA
1/C1/2770:2773,
1/C1/2787:2788

homologous
IL_5TBW_336
NA
1/C1/2823:2824,
1/C1/2865:2867

homologous
IL_5TBW_337
NA
1/C1/2824:2826,
1/C1/2863:2865

geometric
IL_7RQB_017
NA

IL_01312.13*
1/C1/2826:2828,
1/C1/2862:2863
Major groove platform
geometric
IL_5TBW_104
NA

IL_80663.10*
1/C1/2828:2830,
1/C1/2858:2862

homologous
IL_5TBW_340
NA
1/C1/2835:2839,
1/C1/2849:2853

homologous
IL_5TBW_341
NA
1/C1/2876:2877,
1/C1/2949:2951

homologous
IL_5TBW_342
NA
1/C1/2879:2881,
1/C1/2943:2947
Isolated non-canonical cWW with bulges
geometric
IL_5TBW_108
NA

IL_01312.13*
1/C1/2881:2882,
1/C1/2940:2943

homologous
IL_5TBW_344
NA
1/C1/2889:2891,
1/C1/2912:2914

geometric
IL_4KR9_001
NA

IL_01312.13*
1/C1/2891:2892,
1/C1/2909:2912
Minor groove platform with intercalation
geometric
IL_5TBW_111
NA

IL_95601.1*
1/C1/2918:2920,
1/C1/2926:2928

geometric
IL_5TBW_112
NA

IL_01312.13*
1/C1/2960:2961,
1/C1/2970:2972
Single bulged A
geometric
IL_7RQB_101
NA

IL_80007.16*
1/C1/3004:3007,
1/C1/3139:3144

homologous
IL_5TBW_349
NA
1/C1/3012:3014,
1/C1/3040:3042

homologous
IL_5TBW_350
NA
1/C1/3018:3025,
1/C1/3030:3036
8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA

IL_04346.5*
1/C1/3047:3051,
1/C1/3091:3094

homologous
IL_5TBW_352
NA
1/C1/3054:3059,
1/C1/3084:3088

homologous
IL_5TBW_353
NA
1/C1/3063:3064,
1/C1/3077:3080

homologous
IL_5TBW_354
NA
1/C1/3103:3107,
1/C1/3127:3131

homologous
IL_5TBW_355
NA
1/C1/3164:3166,
1/C1/3284:3286
UG cWW
geometric
IL_4LFB_061
NA

IL_01312.13*
1/C1/3168:3170,
1/C1/3280:3282

homologous
IL_5TBW_357
NA
1/C1/3177:3179,
1/C1/3210:3211
Single bulged A
geometric
IL_5TBW_123
NA

IL_80007.16*
1/C1/3179:3188,
1/C1/3204:3210

homologous
IL_5TBW_359
NA
1/C1/3193:3194,
1/C1/3197:3199

homologous
IL_5TBW_360
NA
1/C1/3225:3229,
1/C1/3258:3260

homologous
IL_5TBW_361
NA
1/C1/3233:3235,
1/C1/3252:3254

geometric
IL_5TBW_042
NA

IL_01312.13*
1/C1/3235:3238,
1/C1/3249:3252

homologous
IL_5TBW_363
NA
1/C1/3300:3303,
1/C1/3311:3314
Tandem non-canonical cWW pairs
geometric
IL_5TBW_129
NA

IL_85877.10*
1/C1/3318:3320,
1/C1/3387:3388
Single bulged U
geometric
IL_5TBW_130
NA

IL_83039.11*
1/C1/3324:3325,
1/C1/3381:3383

homologous
IL_5TBW_366
NA
1/C1/3328:3330,
1/C1/3373:3378

homologous
IL_5TBW_367
NA
1/C1/3332:3337,
1/C1/3367:3371

homologous
IL_5TBW_368
NA
1/C1/3340:3342,
1/C1/3363:3364
Single bulged U
geometric
IL_5TBW_134
NA

IL_83039.11*
1/C1/3342:3345,
1/C1/3360:3363

homologous
IL_5TBW_370
NA
1/C1/3349:3350,
1/C1/3353:3356
Multiple bulged bases
geometric
IL_5TBW_136
NA

IL_13730.12*
1/C2/24:26,
1/C2/600:601
Single bulged C
homologous
IL_4V88_384
NA

IL_61258.10*
1/C2/35:37,
1/C2/471:473
UC cWW
geometric
IL_4V88_385
NA

IL_01312.13*
1/C2/37:41,
1/C2/466:471

homologous
IL_4V88_386
NA

IL_53318.1*
1/C2/42:48,
1/C2/431:433

homologous
IL_4V88_387
NA

IL_34626.4*
1/C2/50:52,
1/C2/428:429
Minor groove platform
homologous
IL_4V88_388
NA

IL_06437.11*
1/C2/58:63,
1/C2/87:89

homologous
IL_4V88_389
NA

IL_96451.1*
1/C2/64:69,
1/C2/82:86

homologous
IL_4V88_390
NA

IL_59423.1*
1/C2/109:112,
1/C2/302:305
Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA

IL_85877.10*
1/C2/113:116,
1/C2/300:301
Multiple bulged bases
homologous
IL_4V88_392
NA

IL_13730.12*
1/C2/117:122,
1/C2/295:299

homologous
IL_4V88_393
NA

IL_76386.1*
1/C2/144:149,
1/C2/165:171
tWH-tWH-tHW-tHW
geometric
IL_4LFB_009
NA

IL_87677.1*
1/C2/150:152,
1/C2/162:164
Isolated cWH basepair
geometric
IL_6RA4_002
NA

IL_42589.6*
1/C2/186:189,
1/C2/196:199
Double sheared
homologous
IL_4V88_396
NA

IL_09705.7*
1/C2/204:206,
1/C2/259:263
Major groove platform with extra cWW
homologous
IL_4V88_397
NA

IL_95485.6*
1/C2/206:208,
1/C2/257:259

geometric
IL_2O3V_004
NA

IL_01312.13*
1/C2/265:267,
1/C2/288:289
Single bulged A
homologous
IL_4V88_399
NA

IL_80007.16*
1/C2/270:273,
1/C2/283:285

homologous
IL_4V88_400
NA

IL_05922.1*
1/C2/275:276,
1/C2/279:281
NANA
1/C2/311:316,
1/C2/348:355
Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA

IL_29549.9*
1/C2/318:323,
1/C2/345:346

homologous
IL_4V88_403
NA

IL_55658.1*
1/C2/363:365,
1/C2/376:381

homologous
IL_4V88_404
NA

IL_46732.1*
1/C2/389:391,
1/C2/406:408
Isolated cWH basepair
homologous
IL_4V88_405
NA

IL_42589.6*
1/C2/411:413,
1/C2/420:422
Isolated near basepair
homologous
IL_4V88_406
NA

IL_01312.13*
1/C2/439:441,
1/C2/463:464
Single bulged U
geometric
IL_4V88_407
NA

IL_83039.11*
1/C2/443:447,
1/C2/460:461
C-loop
geometric
IL_5J7L_018
NA

IL_08376.2*
1/C2/447:448,
1/C2/458:460
Single bulged G
geometric
IL_5J7L_019
NA

IL_59137.10*
1/C2/481:482,
1/C2/505:507
Single bulged A
homologous
IL_4V88_409
NA

IL_80007.16*
1/C2/517:518,
1/C2/533:535
Minor groove platform
geometric
IL_4V88_388
NA

IL_06437.11*
1/C2/518:520,
1/C2/532:533
Minor groove platform
geometric
IL_4V88_412
NA

IL_06437.11*
1/C2/550:557,
1/C2/587:588
SSU/LSU pseudoknot
homologous
IL_4V88_413
NA

IL_15861.6*
1/C2/557:559,
1/C2/586:587
Single bulged U
geometric
IL_4V88_414
NA

IL_83039.11*
1/C2/562:568,
1/C2/575:583

homologous
IL_4V88_415
NA

IL_04667.1*
1/C2/616:622,
1/C2/1104:1105

homologous
IL_4V88_416
NA

IL_12418.1*
1/C2/624:626,
1/C2/973:975

homologous
IL_4V88_417
NA

IL_01312.13*
1/C2/627:631,
1/C2/968:972
tSH-tHW-tHS
homologous
IL_4V88_418
NA

IL_39521.5*
1/C2/646:648,
1/C2/686:688

homologous
IL_4V88_419
NA

IL_01312.13*
1/C2/746:747,
1/C2/802:805
Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA

IL_09061.4*
1/C2/748:750,
1/C2/799:801

homologous
IL_4V88_424
NA

IL_01312.13*
1/C2/751:760,
1/C2/790:798
NANA
1/C2/817:824,
1/C2/848:854
NANA
1/C2/865:866,
1/C2/962:965
Major groove platform; stack outside cWW
geometric
IL_6N5P_003
NA

IL_70995.6*
1/C2/867:870,
1/C2/957:961
Tandem non-canonical cWW pairs
homologous
IL_4V88_429
NA

IL_85877.10*
1/C2/871:874,
1/C2/953:956
Tandem non-canonical cWW pairs
homologous
IL_4V88_430
NA

IL_85877.10*
1/C2/874:878,
1/C2/950:953
Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA

IL_85877.10*
1/C2/885:888,
1/C2/924:927
Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA

IL_85877.10*
1/C2/893:895,
1/C2/917:919

homologous
IL_4V88_433
NA

IL_01312.13*
1/C2/895:899,
1/C2/910:917
Kink-turn
geometric
IL_4V88_434
NA

IL_29549.9*
1/C2/985:990,
1/C2/1014:1016
Other IL
geometric
IL_4V88_435
NA

IL_51590.1*
1/C2/990:994,
1/C2/1010:1014
tSH-tHW-tHS
homologous
IL_4V88_436
NA

IL_39521.5*
1/C2/1034:1036,
1/C2/1095:1101

homologous
IL_4V88_437
NA

IL_19557.1*
1/C2/1041:1044,
1/C2/1074:1077
Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA

IL_85877.10*
1/C2/1051:1053,
1/C2/1066:1067
Single bulged U
homologous
IL_4V88_439
NA

IL_83039.11*
1/C2/1111:1118,
1/C2/1129:1134
8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA

IL_24606.1*
1/C2/1146:1147,
1/C2/1630:1632
Single bulged A
homologous
IL_4V88_441
NA

IL_80007.16*
1/C2/1149:1151,
1/C2/1627:1628
Single bulged G
homologous
IL_4V88_442
NA

IL_59137.10*
1/C2/1157:1160,
1/C2/1617:1621
C-loop
homologous
IL_4V88_443
NA

IL_63596.4*
1/C2/1173:1175,
1/C2/1464:1466

homologous
IL_4V88_444
NA

IL_01312.13*
1/C2/1178:1179,
1/C2/1459:1461
Minor groove platform
homologous
IL_4V88_445
NA

IL_06437.11*
1/C2/1213:1215,
1/C2/1448:1450
UU cWW
geometric
IL_3SZX_003
NA

IL_01312.13*
1/C2/1224:1230,
1/C2/1257:1259
NANA
1/C2/1230:1233,
1/C2/1252:1257
NANA
1/C2/1234:1236,
1/C2/1249:1251

homologous
IL_4V88_448
NA

IL_01312.13*
1/C2/1268:1270,
1/C2/1440:1441
Single bulged U
homologous
IL_4V88_449
NA

IL_83039.11*
1/C2/1272:1278,
1/C2/1430:1438
NANA
1/C2/1280:1281,
1/C2/1426:1428
Single bulged A
homologous
IL_4V88_452
NA

IL_80007.16*
1/C2/1290:1292,
1/C2/1323:1325
Isolated cWH basepair
homologous
IL_4V88_453
NA

IL_42589.6*
1/C2/1306:1308,
1/C2/1317:1318
Minor groove platform
homologous
IL_4V88_454
NA

IL_06437.11*
1/C2/1339:1342,
1/C2/1383:1385

homologous
IL_4V88_455
NA

IL_01312.13*
1/C2/1345:1348,
1/C2/1377:1380
Minor groove platform
homologous
IL_4V88_456
NA

IL_69507.1*
1/C2/1352:1354,
1/C2/1369:1373

homologous
IL_4V88_457
NA

IL_01312.13*
1/C2/1389:1391,
1/C2/1407:1412
Major groove platform; stack outside cWW
homologous
IL_4V88_458
NA

IL_60171.1*
1/C2/1480:1487,
1/C2/1519:1527

homologous
IL_4V88_459
NA

IL_69573.1*
1/C2/1488:1494,
1/C2/1513:1518

homologous
IL_4V88_460
NA

IL_75461.2*
1/C2/1495:1498,
1/C2/1509:1512
Tandem non-canonical cWW pairs
homologous
IL_4V88_461
NA

IL_85877.10*
1/C2/1540:1545,
1/C2/1566:1571

geometric
IL_4V88_462
NA

IL_19954.1*
1/C2/1636:1638,
1/C2/1764:1767

homologous
IL_4V88_463
NA

IL_36143.2*
1/C2/1638:1641,
1/C2/1760:1764

geometric
IL_4V88_464
NA

IL_59281.1*
1/C2/1642:1644,
1/C2/1757:1759
CC cWW
geometric
IL_4E59_001
NA

IL_01312.13*
1/C2/1644:1647,
1/C2/1753:1757
NANA
1/C2/1650:1652,
1/C2/1748:1750
AA cWW
homologous
IL_4V88_467
NA

IL_01312.13*
1/C2/1653:1656,
1/C2/1744:1747
Double sheared
homologous
IL_4V88_468
NA

IL_09705.7*
1/C2/1656:1658,
1/C2/1743:1744
Single bulged U
geometric
IL_4V88_469
NA

IL_21340.1*
1/C2/1665:1667,
1/C2/1734:1736

homologous
IL_4V88_470
NA

IL_01312.13*
1/C2/1669:1672,
1/C2/1729:1732
Double sheared
homologous
IL_4V88_471
NA

IL_09705.7*
1/C2/1672:1674,
1/C2/1727:1729

geometric
IL_3D0U_006
NA

IL_01312.13*
1/C2/1675:1678,
1/C2/1723:1726
Tandem non-canonical cWW pairs
homologous
IL_4V88_473
NA

IL_85877.10*
1/C2/1678:1682,
1/C2/1719:1723
Triple sheared
geometric
IL_7RQB_075
NA

IL_56467.6*
1/C3/44:64,
1/C3/96:100

geometric
IL_5TBW_144
NA

IL_23735.1*
1/C3/64:66,
1/C3/93:96
Isolated non-canonical cWW with bulges
homologous
IL_5TBW_145
NA

IL_55456.1*
1/C3/68:69,
1/C3/89:91
Single bulged U
homologous
IL_5TBW_146
NA

IL_83039.11*
1/C4/15:16,
1/C4/63:65
NANA
1/C4/21:27,
1/C4/53:58
NANA
1/C4/28:29,
1/C4/49:52
NANA
1/C4/29:30,
1/C4/47:49
NANA
1/C4/32:36,
1/C4/41:45
NANA
1/C4/72:80,
1/C4/100:106
NANA
1/C4/84:87,
1/C4/94:96
NANA

Problematic loops

#loop idProblemSequence
IL_7RR5_017NA
IL_7RR5_063NA
IL_7RR5_095Single stack bend
geometric
IL_7RQB_058
IL_7RR5_096NA
IL_7RR5_097NA
IL_7RR5_225Tandem non-canonical cWW pairs
geometric
IL_1D4R_003

Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)