Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/5/38:45
homologous
HL_5TBW_113
NA
1/5/69:74
homologous
HL_5TBW_114
NA
1/5/90:96
homologous
HL_5TBW_115
NA
1/5/132:136
homologous
HL_5TBW_116
NA
1/5/194:201
homologous
HL_5TBW_117
NA
1/5/208:212
homologous
HL_5TBW_118
NA
1/5/216:224
homologous
HL_5TBW_119
NA
1/5/278:287
homologous
HL_5TBW_120
NA
1/5/303:312
homologous
HL_5TBW_121
NA
1/5/357:362
homologous
HL_5TBW_122
NA
1/5/382:387
homologous
HL_5TBW_123
NA
1/5/543:548
geometric
HL_1U1Y_001
NA

HL_16568.1*
1/5/599:604
homologous
HL_5TBW_125
NA
1/5/640:649
homologous
HL_5TBW_126
NA
1/5/686:694
homologous
HL_5TBW_127
NA
1/5/707:712
homologous
HL_5TBW_128
NA
1/5/732:737
homologous
HL_5TBW_129
NA
1/5/763:768
homologous
HL_5TBW_130
NA
1/5/844:849
homologous
HL_5TBW_131
NA
1/5/876:885
homologous
HL_5TBW_132
NA
1/5/910:918
homologous
HL_5TBW_133
NA
1/5/958:963
homologous
HL_5TBW_134
NA
1/5/1076:1083
geometric
HL_5TBW_024
NA

HL_54035.7*
1/5/1126:1132
homologous
HL_5TBW_137
NA
1/5/1148:1155
homologous
HL_5TBW_138
NA
1/5/1239:1249
homologous
HL_5TBW_139
NA
1/5/1267:1274
homologous
HL_5TBW_140
NA
1/5/1347:1357
homologous
HL_5TBW_141
NA
1/5/1403:1408
homologous
HL_5TBW_142
NA
1/5/1462:1470
homologous
HL_5TBW_143
NA
1/5/1506:1512
homologous
HL_5TBW_144
NA
1/5/1544:1549
homologous
HL_5TBW_145
NA
1/5/1567:1571
geometric
HL_4O26_001
NA

HL_61984.1*
1/5/1599:1608
homologous
HL_5TBW_147
NA
1/5/1634:1639
homologous
HL_5TBW_148
NA
1/5/1680:1688
homologous
HL_5TBW_149
NA
1/5/1719:1725
homologous
HL_5TBW_150
NA
1/5/1759:1766
geometric
HL_6D12_002
NA

HL_82678.2*
1/5/1792:1796
homologous
HL_5TBW_152
NA
1/5/1844:1851
homologous
HL_5TBW_153
NA
1/5/1862:1868
homologous
HL_5TBW_154
NA
1/5/1923:1928
homologous
HL_5TBW_155
NA
1/5/2110:2114
homologous
HL_5TBW_157
NA
1/5/2135:2145
homologous
HL_5TBW_158
NA
1/5/2164:2170
homologous
HL_5TBW_159
NA
1/5/2220:2225
homologous
HL_5TBW_160
NA
1/5/2292:2300
homologous
HL_5TBW_162
NA
1/5/2369:2378
homologous
HL_5TBW_163
NA
1/5/2535:2544NANA
1/5/2568:2573NANA
1/5/2616:2624
homologous
HL_5TBW_167
NA
1/5/2633:2645
homologous
HL_5TBW_168
NA
1/5/2673:2681
homologous
HL_5TBW_169
NA
1/5/2693:2700
homologous
HL_5TBW_170
NA
1/5/2724:2732
homologous
HL_5TBW_171
NA
1/5/2744:2749
homologous
HL_5TBW_172
NA
1/5/2776:2784
homologous
HL_5TBW_173
NA
1/5/2840:2848
homologous
HL_5TBW_174
NA
1/5/2897:2904
homologous
HL_5TBW_175
NA
1/5/2920:2926
geometric
HL_5TBW_063
NA

HL_26055.6*
1/5/2963:2968
homologous
HL_5TBW_177
NA
1/5/3025:3030
homologous
HL_5TBW_178
NA
1/5/3068:3073
homologous
HL_5TBW_179
NA
1/5/3110:3124
homologous
HL_5TBW_180
NA
1/5/3194:3197
homologous
HL_5TBW_181
NA
1/5/3240:3247
homologous
HL_5TBW_182
NA
1/5/3303:3311
homologous
HL_5TBW_183
NA
1/5/3350:3353
geometric
HL_5U30_001
NA

HL_69353.7*
1/7/36:41NANA
1/7/88:93NANA
1/8/69:89NANA
1/8/108:114
homologous
HL_5TBW_075
NA

HL_06569.2*
1/8/124:129
homologous
HL_5TBW_076
NA

HL_60357.1*

Problematic loops

#loop idProblemSequence
HL_5APO_023NA
HL_5APO_044NA
HL_5APO_051NA

Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/5/7:8,
1/8/150:152
Single bulged C
homologous
IL_5TBW_002
NA

IL_61258.10*
1/5/13:15,
1/8/144:145
Single bulged U
homologous
IL_5TBW_003
NA

IL_83039.11*
1/5/27:28,
1/5/56:58

homologous
IL_5TBW_240
NA
1/5/31:38,
1/5/45:53
tSH-tHW-tHH-tHS
geometric
IL_5TBW_005
NA

IL_22863.1*
1/5/82:89,
1/5/97:103

homologous
IL_5TBW_242
NA
1/5/123:124,
1/5/144:149

geometric
IL_5TBW_007
NA

IL_19724.1*
1/5/125:127,
1/5/141:143

homologous
IL_5TBW_244
NA
1/5/163:165,
1/5/257:258

homologous
IL_5TBW_245
NA
1/5/169:170,
1/5/248:253
NANA
1/5/177:178,
1/5/238:241
Major groove platform
geometric
IL_7A0S_073
NA

IL_80663.10*
1/5/189:191,
1/5/204:205

homologous
IL_5TBW_248
NA
1/5/337:339,
1/8/25:26
Single bulged A
homologous
IL_5TBW_013
NA

IL_80007.16*
1/5/376:379,
1/5/390:403

homologous
IL_5TBW_250
NA
1/5/404:410,
1/8/13:19
Triple sheared with non-canonical cWW
homologous
IL_5TBW_015
NA

IL_66414.5*
1/5/428:431,
1/5/628:631
Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
NA

IL_85877.10*
1/5/512:513,
1/5/577:579

homologous
IL_5TBW_254
NA
1/5/517:525,
1/5/567:573

homologous
IL_5TBW_255
NA
1/5/531:538,
1/5/553:561

homologous
IL_5TBW_256
NA
1/5/668:670,
1/5/792:794

homologous
IL_5TBW_257
NA
1/5/680:684,
1/5/696:700

homologous
IL_5TBW_258
NA
1/5/725:728,
1/5/741:745

homologous
IL_5TBW_259
NA
1/5/752:753,
1/5/779:781

homologous
IL_5TBW_260
NA
1/5/755:756,
1/5/775:777

homologous
IL_5TBW_261
NA
1/5/758:763,
1/5/768:773

geometric
IL_5TBW_026
NA

IL_19954.1*
1/5/803:805,
1/5/938:940

homologous
IL_5TBW_263
NA
1/5/805:809,
1/5/931:938

geometric
IL_5TBW_028
NA

IL_17470.5*
1/5/828:829,
1/5/895:897
Single bulged A
geometric
IL_4V9F_025
NA

IL_80007.16*
1/5/833:834,
1/5/859:861
Single bulged G
geometric
IL_5TBW_029
NA

IL_99645.1*
1/5/834:838,
1/5/855:859

homologous
IL_5TBW_266
NA
1/5/869:872,
1/5/888:890

homologous
IL_5TBW_267
NA
1/5/873:875,
1/5/886:887

homologous
IL_5TBW_268
NA
1/5/907:909,
1/5/919:923
Multiple bulged bases
geometric
IL_5TBW_033
NA

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

homologous
IL_5TBW_270
NA
1/5/969:970,
1/5/1111:1113

homologous
IL_5TBW_271
NA
1/5/977:982,
1/5/1101:1104
NANA
1/5/983:985,
1/5/1099:1100

homologous
IL_5TBW_273
NA
1/5/991:997,
1/5/1052:1058
7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_5TBW_038
NA

IL_93830.2*
1/5/997:998,
1/5/1050:1052

homologous
IL_5TBW_275
NA
1/5/999:1004,
1/5/1046:1049

homologous
IL_5TBW_276
NA
1/5/1006:1009,
1/5/1041:1044

homologous
IL_5TBW_277
NA
1/5/1009:1011,
1/5/1039:1041

geometric
IL_4LFB_059
NA

IL_01312.13*
1/5/1069:1071,
1/5/1087:1089

homologous
IL_5TBW_280
NA
1/5/1074:1076,
1/5/1083:1084

homologous
IL_5TBW_281
NA
1/5/1120:1122,
1/5/1136:1138

homologous
IL_5TBW_282
NA
1/5/1123:1125,
1/5/1133:1135

homologous
IL_5TBW_283
NA
1/5/1167:1171,
1/5/1328:1332

homologous
IL_5TBW_284
NA
1/5/1173:1180,
1/5/1325:1326
SSU/LSU pseudoknot
geometric
IL_5TBW_049
NA

IL_15861.6*
1/5/1180:1182,
1/5/1324:1325

homologous
IL_5TBW_286
NA
1/5/1187:1194,
1/5/1314:1319

homologous
IL_5TBW_287
NA
1/5/1194:1205,
1/5/1299:1314

geometric
IL_5TBW_052
NA

IL_94878.1*
1/5/1207:1209,
1/5/1296:1297

homologous
IL_5TBW_289
NA
1/5/1218:1226,
1/5/1283:1287

homologous
IL_5TBW_290
NA
1/5/1234:1238,
1/5/1250:1254

homologous
IL_5TBW_291
NA
1/5/1262:1266,
1/5/1275:1277

homologous
IL_5TBW_292
NA
1/5/1376:1378,
1/5/1428:1431

homologous
IL_5TBW_293
NA
1/5/1385:1387,
1/5/1420:1421

homologous
IL_5TBW_294
NA
1/5/1388:1395,
1/5/1415:1419

homologous
IL_5TBW_295
NA
1/5/1398:1400,
1/5/1411:1412

homologous
IL_5TBW_296
NA
1/5/1444:1450,
1/5/2354:2359

homologous
IL_5TBW_297
NA
1/5/1492:1495,
1/5/1835:1836
Major groove platform; stack outside cWW
geometric
IL_4V9F_050
NA

IL_70995.6*
1/5/1501:1505,
1/5/1513:1515
C-loop
geometric
IL_7RQB_051
NA

IL_63596.4*
1/5/1532:1536,
1/5/1585:1590

homologous
IL_5TBW_299
NA
1/5/1565:1566,
1/5/1572:1574
Minor groove platform
geometric
IL_2QWY_009
NA

IL_06437.11*
1/5/1618:1621,
1/5/1824:1826

homologous
IL_5TBW_300
NA
1/5/1623:1625,
1/5/1818:1822
Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010
NA

IL_01312.13*
1/5/1627:1631,
1/5/1811:1816

homologous
IL_5TBW_302
NA
1/5/1645:1649,
1/5/1806:1810

homologous
IL_5TBW_303
NA
1/5/1661:1663,
1/5/1786:1788

homologous
IL_5TBW_304
NA
1/5/1669:1670,
1/5/1778:1780
Single bulged C
geometric
IL_5TBW_069
NA

IL_61258.10*
1/5/1670:1671,
1/5/1776:1778

homologous
IL_5TBW_306
NA
1/5/1694:1698,
1/5/1747:1752

homologous
IL_5TBW_307
NA
1/5/1702:1707,
1/5/1737:1743

homologous
IL_5TBW_308
NA
1/5/1711:1717,
1/5/1727:1733

homologous
IL_5TBW_309
NA
1/5/1883:1889,
1/5/2346:2349

homologous
IL_5TBW_310
NA
1/5/1895:1897,
1/5/2338:2340

homologous
IL_5TBW_311
NA
1/5/1898:1901,
1/5/2336:2337
Major groove platform; stack outside cWW
geometric
IL_5TBW_076
NA

IL_80663.10*
1/5/1901:1906,
1/5/2333:2336

homologous
IL_5TBW_313
NA
1/5/1918:1923,
1/5/1928:1934
tSH-tSH-tHH-tHS
geometric
IL_4V9F_063
NA

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

homologous
IL_5TBW_315
NA
1/5/1947:1948,
1/5/2098:2101

homologous
IL_5TBW_316
NA
1/5/2128:2129,
1/5/2323:2325

homologous
IL_5TBW_318
NA
1/5/2156:2161,
1/5/2173:2180

homologous
IL_5TBW_319
NA
1/5/2196:2199,
1/5/2245:2246

homologous
IL_5TBW_320
NA
1/5/2200:2201,
1/5/2241:2244

homologous
IL_5TBW_321
NA
1/5/2204:2206,
1/5/2237:2238
Single bulged U
geometric
IL_6UFG_004
NA

IL_83039.11*
1/5/2276:2278,
1/5/2307:2310
Intercalated cWW
geometric
IL_4WF9_047
NA

IL_04038.4*
1/5/2278:2288,
1/5/2304:2307
NANA
1/5/2391:2394,
1/5/2986:2988

homologous
IL_5TBW_327
NA
1/5/2396:2398,
1/5/2981:2984

homologous
IL_5TBW_328
NA
1/5/2409:2411,
1/5/2811:2812

homologous
IL_5TBW_329
NA
1/5/2411:2412,
1/5/2809:2811
NANA
1/5/2412:2413,
1/5/2807:2809
NANA
1/5/2423:2425,
1/5/2604:2607

homologous
IL_5TBW_331
NA
1/5/2435:2437,
1/5/2510:2512

geometric
IL_4P3U_012
NA

IL_01312.13*
1/5/2520:2526,
1/5/2584:2587

homologous
IL_5TBW_332
NA
1/5/2614:2615,
1/5/2625:2627

homologous
IL_5TBW_333
NA
1/5/2666:2668,
1/5/2686:2690
Isolated tHS basepair with bulges
geometric
IL_5TBW_099
NA

IL_38958.6*
1/5/2714:2717,
1/5/2739:2741

geometric
IL_4V88_455
NA

IL_01312.13*
1/5/2718:2721,
1/5/2735:2738

homologous
IL_5TBW_335
NA
1/5/2770:2773,
1/5/2787:2788

homologous
IL_5TBW_336
NA
1/5/2823:2824,
1/5/2865:2867

homologous
IL_5TBW_337
NA
1/5/2824:2826,
1/5/2863:2865

geometric
IL_5TBW_103
NA

IL_05265.1*
1/5/2826:2828,
1/5/2862:2863
Major groove platform
geometric
IL_4V9F_083
NA

IL_95601.1*
1/5/2828:2830,
1/5/2858:2862

homologous
IL_5TBW_340
NA
1/5/2835:2839,
1/5/2849:2853

homologous
IL_5TBW_341
NA
1/5/2876:2877,
1/5/2949:2951

homologous
IL_5TBW_342
NA
1/5/2879:2881,
1/5/2943:2947

homologous
IL_5TBW_343
NA
1/5/2881:2882,
1/5/2940:2943
Multiple bulged bases
geometric
IL_5TBW_109
NA

IL_13730.12*
1/5/2889:2891,
1/5/2912:2914

homologous
IL_5TBW_345
NA
1/5/2891:2892,
1/5/2909:2912
Minor groove platform with intercalation
geometric
IL_5TBW_111
NA

IL_95601.1*
1/5/2918:2920,
1/5/2926:2928

homologous
IL_5TBW_347
NA
1/5/2960:2961,
1/5/2970:2972

homologous
IL_5TBW_348
NA
1/5/3004:3007,
1/5/3139:3144

homologous
IL_5TBW_349
NA
1/5/3012:3014,
1/5/3040:3042

homologous
IL_5TBW_350
NA
1/5/3018:3025,
1/5/3030:3036
8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA

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

homologous
IL_5TBW_352
NA
1/5/3054:3059,
1/5/3084:3088

homologous
IL_5TBW_353
NA
1/5/3063:3064,
1/5/3077:3080

homologous
IL_5TBW_354
NA
1/5/3103:3107,
1/5/3127:3131

homologous
IL_5TBW_355
NA
1/5/3164:3166,
1/5/3284:3286
UG cWW
geometric
IL_4LFB_061
NA

IL_01312.13*
1/5/3168:3170,
1/5/3280:3282

homologous
IL_5TBW_357
NA
1/5/3177:3179,
1/5/3210:3211

homologous
IL_5TBW_358
NA
1/5/3179:3188,
1/5/3204:3210

geometric
IL_5TBW_124
NA

IL_56867.1*
1/5/3193:3194,
1/5/3197:3199
Single bulged U
geometric
IL_5TBW_125
NA

IL_83039.11*
1/5/3225:3229,
1/5/3258:3260

homologous
IL_5TBW_361
NA
1/5/3233:3235,
1/5/3252:3254

homologous
IL_5TBW_362
NA
1/5/3235:3238,
1/5/3249:3252
Tandem non-canonical cWW pairs
geometric
IL_6MWN_005
NA

IL_85877.10*
1/5/3300:3303,
1/5/3311:3314
Tandem non-canonical cWW pairs
geometric
IL_5TBW_129
NA

IL_85877.10*
1/5/3318:3320,
1/5/3387:3388

homologous
IL_5TBW_365
NA
1/5/3324:3325,
1/5/3381:3383

homologous
IL_5TBW_366
NA
1/5/3328:3330,
1/5/3373:3378

homologous
IL_5TBW_367
NA
1/5/3332:3337,
1/5/3367:3371

homologous
IL_5TBW_368
NA
1/5/3340:3342,
1/5/3363:3364
Single bulged U
geometric
IL_6UFH_004
NA

IL_83039.11*
1/5/3342:3345,
1/5/3360:3363

homologous
IL_5TBW_370
NA
1/5/3349:3350,
1/5/3353:3356

homologous
IL_5TBW_371
NA
1/7/15:16,
1/7/63:65
NANA
1/7/21:27,
1/7/53:58
NANA
1/7/28:29,
1/7/49:52
NANA
1/7/29:30,
1/7/47:49
NANA
1/7/32:36,
1/7/41:45
NANA
1/7/72:80,
1/7/100:106
NANA
1/7/84:87,
1/7/94:96
NANA
1/8/44:64,
1/8/96:100

geometric
IL_5TBW_144
NA

IL_23735.1*
1/8/64:66,
1/8/93:96
Isolated non-canonical cWW with bulges
homologous
IL_5TBW_145
NA

IL_55456.1*
1/8/68:69,
1/8/89:91
Single bulged U
homologous
IL_5TBW_146
NA

IL_83039.11*

Problematic loops

#loop idProblemSequence
IL_5APO_001
geometric
IL_3ICQ_003
IL_5APO_017NA
IL_5APO_092
geometric
IL_4V9F_017
IL_5APO_096
geometric
IL_4V88_419
IL_5APO_100
geometric
IL_4WF9_042
IL_5APO_125
geometric
IL_4YHW_001

Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/5/113:123,
1/5/149:158,
1/5/263:267

homologous
J3_5TBW_030
NA
1/5/814:820,
1/5/905:907,
1/5/923:926

homologous
J3_5TBW_033
NA
1/5/829:831,
1/5/863:867,
1/5/892:895
NANA
1/5/1230:1232,
1/5/1256:1262,
1/5/1277:1279
NANA
1/5/1479:1485,
1/5/1857:1859,
1/5/1871:1874

homologous
J3_5TBW_037
NA
1/5/1488:1491,
1/5/1837:1843,
1/5/1852:1854

homologous
J3_5TBW_038
NA
1/5/2432:2435,
1/5/2512:2517,
1/5/2590:2597

homologous
J3_5TBW_041
NA
1/5/2529:2532,
1/5/2547:2563,
1/5/2578:2581
NANA
1/5/2664:2666,
1/5/2690:2692,
1/5/2701:2706

homologous
J3_5TBW_042
NA
1/5/2886:2889,
1/5/2914:2916,
1/5/2930:2936
NANA
1/5/3298:3300,
1/5/3314:3318,
1/5/3388:3390
NANA

Problematic loops

No problematic loops


Coloring options:
Copyright 2023 BGSU RNA group. Page generated in 0.0754 s