Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/A1/38:45
geometric
HL_5TBW_001
NA

HL_23481.5*
1/A1/69:74
geometric
HL_5TBW_002
NA

HL_96776.3*
1/A1/90:96
geometric
HL_7RQB_008
NA

HL_67216.5*
1/A1/132:136
geometric
HL_5TBW_004
NA

HL_36982.3*
1/A1/194:201T-loop with 1 bulged base
geometric
HL_4V9F_010
NA

HL_68493.6*
1/A1/208:212
geometric
HL_5TBW_006
NA

HL_98557.5*
1/A1/216:224
geometric
HL_5TBW_007
NA

HL_08002.6*
1/A1/278:287
geometric
HL_5TBW_008
NA

HL_54035.7*
1/A1/303:312
geometric
HL_5TBW_009
NA

HL_46142.8*
1/A1/357:362GNRA
geometric
HL_5J7L_196
NA

HL_43074.18*
1/A1/382:387GNRA
geometric
HL_5J7L_010
NA

HL_43074.18*
1/A1/540:551NANA
1/A1/599:604GNRA
geometric
HL_5J7L_004
NA

HL_43074.18*
1/A1/638:651
geometric
HL_4V9F_011
NA

HL_98557.5*
1/A1/686:694
geometric
HL_5TBW_015
NA

HL_80105.3*
1/A1/707:712GNRA
geometric
HL_5TBW_016
NA

HL_43074.18*
1/A1/732:737GNRA
geometric
HL_5B2P_001
NA

HL_43074.18*
1/A1/763:768
geometric
HL_5TBW_018
NA

HL_00996.1*
1/A1/844:849
geometric
HL_6LAX_002
NA

HL_62604.1*
1/A1/875:886NANA
1/A1/910:918
geometric
HL_5TBW_021
NA

HL_05832.1*
1/A1/958:963
geometric
HL_2Y8W_001
NA

HL_69459.1*
1/A1/1013:1037NANA
1/A1/1076:1083
geometric
HL_5TBW_024
NA

HL_54035.7*
1/A1/1126:1132GNRA
geometric
HL_5TBW_025
NA

HL_43074.18*
1/A1/1148:1155
geometric
HL_5TBW_026
NA

HL_72451.5*
1/A1/1239:1249NANA
1/A1/1266:1275NANA
1/A1/1347:1357
geometric
HL_4OOG_001
NA

HL_68529.2*
1/A1/1403:1408
geometric
HL_7RQB_032
NA

HL_43074.18*
1/A1/1462:1470T-loop with 2 stacked bulged bases
geometric
HL_5TBW_031
NA

HL_33239.17*
1/A1/1506:1512
geometric
HL_5TBW_032
NA

HL_86880.5*
1/A1/1544:1549Other HL
geometric
HL_5TBW_033
NA

HL_43074.18*
1/A1/1566:1572NANA
1/A1/1599:1608
geometric
HL_5TBW_035
NA

HL_78457.4*
1/A1/1634:1639GNRA
geometric
HL_5TBW_036
NA

HL_43074.18*
1/A1/1680:1688
geometric
HL_5TBW_037
NA

HL_73793.2*
1/A1/1719:1725
geometric
HL_5TBW_038
NA

HL_00923.1*
1/A1/1759:1766NANA
1/A1/1792:1796
geometric
HL_5TBW_040
NA

HL_69353.7*
1/A1/1844:1851
geometric
HL_5TBW_041
NA

HL_66171.3*
1/A1/1862:1868GNRA with one bulged base
geometric
HL_5TBW_042
NA

HL_02361.6*
1/A1/1923:1928UNCG
geometric
HL_4V9F_044
NA

HL_79299.11*
1/A1/1953:2094NANA
1/A1/2110:2114
geometric
HL_5TBW_045
NA

HL_99223.1*
1/A1/2135:2145
geometric
HL_5J7L_178
NA

HL_43613.4*
1/A1/2164:2170GNRA
geometric
HL_5TBW_047
NA

HL_43074.18*
1/A1/2219:2226
geometric
HL_6CF2_001
NA

HL_80105.3*
1/A1/2251:2265NANA
1/A1/2292:2300
geometric
HL_5TBW_050
NA

HL_53760.4*
1/A1/2369:2378
geometric
HL_5TBW_051
NA

HL_90642.5*
1/A1/2439:2508
geometric
HL_2Y8W_001
NA

HL_69459.1*
1/A1/2534:2545NANA
1/A1/2568:2573
geometric
HL_6CZR_089
NA

HL_18722.3*
1/A1/2616:2624
geometric
HL_4WF9_049
NA

HL_46891.3*
1/A1/2633:2645
geometric
HL_5TBW_055
NA

HL_19870.5*
1/A1/2672:2682
geometric
HL_5J7L_188
NA

HL_11805.3*
1/A1/2693:2700
geometric
HL_5TBW_057
NA

HL_46142.8*
1/A1/2723:2733NANA
1/A1/2744:2749GNRA
geometric
HL_5TBW_059
NA

HL_43074.18*
1/A1/2776:2784
geometric
HL_5TBW_060
NA

HL_46142.8*
1/A1/2840:2848
geometric
HL_4V9F_062
NA

HL_36421.5*
1/A1/2897:2904
geometric
HL_5TBW_062
NA

HL_92681.5*
1/A1/2920:2926
geometric
HL_2ZNI_001
NA

HL_40469.1*
1/A1/2963:2968GNRA
geometric
HL_5J7L_196
NA

HL_43074.18*
1/A1/3025:3030
geometric
HL_7A0S_063
NA

HL_43074.18*
1/A1/3068:3073Ribsomal LSU H95
geometric
HL_5TBW_066
NA

HL_67719.1*
1/A1/3110:3124
geometric
HL_5TBW_067
NA

HL_56677.5*
1/A1/3194:3197
geometric
HL_4V88_192
NA

HL_69353.7*
1/A1/3240:3247
geometric
HL_2Y9H_003
NA

HL_98557.5*
1/A1/3303:3311
geometric
HL_5TBW_070
NA

HL_05018.6*
1/A1/3350:3353
geometric
HL_5F9R_002
NA

HL_69353.7*
1/A3/36:41
geometric
HL_5TBW_185
NA

HL_02733.5*
1/A3/88:93GNRA
geometric
HL_5J7L_010
NA

HL_43074.18*
1/A4/69:89NANA
1/A4/108:114
geometric
HL_5TBW_075
NA

HL_06569.2*
1/A4/124:129
geometric
HL_5TBW_076
NA

HL_60357.1*
1/B5/7:17
geometric
HL_4V88_186
NA

HL_67265.4*
1/B5/70:81
geometric
HL_4V9F_011
NA

HL_98557.5*
1/B5/154:160Other HL
geometric
HL_4V88_188
NA

HL_43074.18*
1/B5/186:199NANA
1/B5/228:237NANA
1/B5/243:250T-loop with 1 bulged base
geometric
HL_4V88_191
NA

HL_68493.6*
1/B5/276:279
geometric
HL_6U8D_003
NA

HL_18722.3*
1/B5/330:338
geometric
HL_4V88_193
NA

HL_93727.5*
1/B5/368:373
geometric
HL_4V88_194
NA

HL_18785.1*
1/B5/393:404
geometric
HL_4V88_195
NA

HL_22443.1*
1/B5/411:422NANA
1/B5/450:456
geometric
HL_5NFV_001
NA

HL_58912.1*
1/B5/490:497NANA
1/B5/520:532
geometric
HL_4V88_199
NA

HL_17086.2*
1/B5/569:574Other HL
geometric
HL_4V88_200
NA

HL_43074.18*
1/B5/717:723NANA
1/B5/764:772
geometric
HL_4V88_203
NA

HL_72066.1*
1/B5/777:783NANA
1/B5/827:845NANA
1/B5/900:909
geometric
HL_4V88_206
NA

HL_87219.4*
1/B5/937:942Other HL
geometric
HL_4V88_207
NA

HL_43074.18*
1/B5/995:1009
geometric
HL_2ZZM_002
NA

HL_18218.2*
1/B5/1055:1064NANA
1/B5/1084:1089Other HL
geometric
HL_4V88_210
NA

HL_43074.18*
1/B5/1120:1127
geometric
HL_7A0S_056
NA

HL_93727.5*
1/B5/1188:1197NANA
1/B5/1238:1247
geometric
HL_4V88_213
NA

HL_30819.1*
1/B5/1296:1301GNRA
geometric
HL_4V9F_065
NA

HL_43074.18*
1/B5/1309:1316
geometric
HL_4V88_215
NA

HL_54035.7*
1/B5/1360:1363NANA
1/B5/1396:1402GNRA
geometric
HL_6CZR_090
NA

HL_43074.18*
1/B5/1501:1506GNRA
geometric
HL_4V88_218
NA

HL_43074.18*
1/B5/1550:1561
geometric
HL_4V88_219
NA

HL_32458.3*
1/B5/1594:1602
geometric
HL_4V88_220
NA

HL_01181.4*
1/B5/1778:1783Other HL
geometric
HL_4V88_222
NA

HL_43074.18*

Problematic loops

#loop idProblemSequence
HL_7MPJ_112NA

Valid loops

#loop idlocationannotation
(mapped to, source)
motif group
(similar to)
1/A1/7:8,
1/A4/150:152
Single bulged C
geometric
IL_5TBW_002
NA

IL_61258.10*
1/A1/13:15,
1/A4/144:145
Single bulged U
geometric
IL_5TBW_003
NA

IL_83039.11*
1/A1/27:28,
1/A1/56:58
Single stack bend
geometric
IL_5TBW_004
NA

IL_04038.4*
1/A1/31:38,
1/A1/45:53
tSH-tHW-tHH-tHS
geometric
IL_5TBW_005
NA

IL_22863.1*
1/A1/82:89,
1/A1/97:103

geometric
IL_5TBW_006
NA

IL_29509.1*
1/A1/123:124,
1/A1/144:149

geometric
IL_5TBW_007
NA

IL_19724.1*
1/A1/125:127,
1/A1/141:143

geometric
IL_5TBW_008
NA

IL_01312.13*
1/A1/163:166,
1/A1/256:258
NANA
1/A1/168:171,
1/A1/246:254
NANA
1/A1/171:175,
1/A1/243:246
NANA
1/A1/176:179,
1/A1/237:242
NANA
1/A1/189:191,
1/A1/204:205
Single bulged U
geometric
IL_5TBW_012
NA

IL_83039.11*
1/A1/337:339,
1/A4/25:26
Single bulged A
geometric
IL_5TBW_013
NA

IL_80007.16*
1/A1/376:379,
1/A1/390:403

geometric
IL_5TBW_014
NA

IL_60992.5*
1/A1/404:410,
1/A4/13:19
Triple sheared with non-canonical cWW
geometric
IL_5TBW_015
NA

IL_66414.5*
1/A1/417:419,
1/A4/4:6

geometric
IL_3LA5_001
NA

IL_01312.13*
1/A1/429:431,
1/A1/628:630

geometric
IL_5TBW_016
NA

IL_01312.13*
1/A1/435:495,
1/A1/618:624
NANA
1/A1/512:513,
1/A1/577:579
Single bulged A
geometric
IL_5TBW_018
NA

IL_40508.4*
1/A1/517:525,
1/A1/567:573

geometric
IL_5TBW_019
NA

IL_41593.1*
1/A1/531:538,
1/A1/553:561

geometric
IL_5TBW_020
NA

IL_94501.1*
1/A1/668:670,
1/A1/792:794

geometric
IL_5TBW_021
NA

IL_01312.13*
1/A1/680:684,
1/A1/696:700

geometric
IL_5TBW_022
NA

IL_92343.1*
1/A1/725:728,
1/A1/741:745
UAA/GAN
geometric
IL_5TBW_023
NA

IL_53523.5*
1/A1/752:753,
1/A1/779:781
Single bulged A
geometric
IL_5TBW_024
NA

IL_80007.16*
1/A1/758:763,
1/A1/768:773

geometric
IL_5TBW_026
NA

IL_19954.1*
1/A1/803:809,
1/A1/931:940
NANA
1/A1/826:828,
1/A1/897:899

geometric
IL_5TBW_110
NA

IL_01312.13*
1/A1/828:829,
1/A1/895:897
Single bulged A
geometric
IL_4V9F_025
NA

IL_80007.16*
1/A1/833:834,
1/A1/859:861
Single bulged G
geometric
IL_5TBW_029
NA

IL_99645.1*
1/A1/834:838,
1/A1/855:859
Triple sheared
geometric
IL_5J7L_263
NA

IL_56467.6*
1/A1/869:872,
1/A1/888:890
Major groove platform with extra cWW
geometric
IL_5TBW_031
NA

IL_95485.6*
1/A1/873:875,
1/A1/886:887
Single bulged U
geometric
IL_5TBW_032
NA

IL_83039.11*
1/A1/907:909,
1/A1/919:923
Multiple bulged bases
geometric
IL_5TBW_033
NA

IL_90991.5*
1/A1/969:970,
1/A1/1111:1113
Single stack bend
geometric
IL_5TBW_035
NA

IL_04038.4*
1/A1/970:972,
1/A1/1109:1111
Stack and bulge
geometric
IL_2O3X_001
NA

IL_04038.4*
1/A1/977:982,
1/A1/1101:1104
NANA
1/A1/983:985,
1/A1/1099:1100
Single bulged G
geometric
IL_5TBW_037
NA

IL_59137.10*
1/A1/989:991,
1/A1/1058:1060

geometric
IL_1NBS_006
NA

IL_01312.13*
1/A1/991:998,
1/A1/1050:1058
NANA
1/A1/999:1005,
1/A1/1045:1049

geometric
IL_4V9F_035
NA

IL_21121.1*
1/A1/1006:1009,
1/A1/1041:1044
Tandem non-canonical cWW pairs
geometric
IL_6JDV_001
NA

IL_85877.10*
1/A1/1009:1011,
1/A1/1039:1041

geometric
IL_5TBW_042
NA

IL_01312.13*
1/A1/1069:1071,
1/A1/1087:1089

geometric
IL_5CCB_001
NA

IL_01312.13*
1/A1/1074:1076,
1/A1/1083:1084
Single bulged A
geometric
IL_5TBW_045
NA

IL_80007.16*
1/A1/1120:1122,
1/A1/1136:1138

geometric
IL_5TBW_046
NA

IL_01312.13*
1/A1/1167:1171,
1/A1/1328:1332
UAA/GAN
geometric
IL_5TBW_048
NA

IL_53523.5*
1/A1/1173:1180,
1/A1/1325:1326
SSU/LSU pseudoknot
geometric
IL_5TBW_049
NA

IL_15861.6*
1/A1/1180:1182,
1/A1/1324:1325
Single bulged U
geometric
IL_5TBW_050
NA

IL_83039.11*
1/A1/1187:1194,
1/A1/1314:1319

geometric
IL_5TBW_051
NA

IL_17971.1*
1/A1/1194:1205,
1/A1/1299:1314

geometric
IL_5TBW_052
NA

IL_94878.1*
1/A1/1207:1209,
1/A1/1296:1297
Single bulged U
geometric
IL_4V9F_107
NA

IL_83039.11*
1/A1/1218:1226,
1/A1/1283:1287
Kink-turn
geometric
IL_4V9F_042
NA

IL_90538.3*
1/A1/1262:1266,
1/A1/1275:1277
NANA
1/A1/1376:1378,
1/A1/1428:1431
Isolated cWS basepair
geometric
IL_5TBW_057
NA

IL_01312.13*
1/A1/1385:1387,
1/A1/1420:1421
Single bulged A
geometric
IL_5TBW_058
NA

IL_80007.16*
1/A1/1388:1395,
1/A1/1415:1419
Kink-turn
geometric
IL_5TBW_059
NA

IL_29549.9*
1/A1/1398:1400,
1/A1/1411:1412
Single bulged A
geometric
IL_5TBW_060
NA

IL_80007.16*
1/A1/1444:1451,
1/A1/2353:2359
8x7 Sarcin-Ricin with CC bifurcated pair; G-bulge
geometric
IL_4V9F_012
NA

IL_59724.1*
1/A1/1500:1505,
1/A1/1513:1516

geometric
IL_5TBW_062
NA

IL_47743.1*
1/A1/1532:1536,
1/A1/1585:1590
UAA/GAN
geometric
IL_5TBW_063
NA

IL_53523.5*
1/A1/1561:1562,
1/A1/1577:1579
Single stack bend
geometric
IL_7KGA_003
NA

IL_04038.4*
1/A1/1562:1566,
1/A1/1572:1577
NANA
1/A1/1618:1621,
1/A1/1824:1826
Other IL
geometric
IL_5TBW_064
NA

IL_87630.5*
1/A1/1623:1625,
1/A1/1818:1822
Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010
NA

IL_01312.13*
1/A1/1627:1631,
1/A1/1811:1816
NANA
1/A1/1645:1649,
1/A1/1806:1810
Triple sheared
geometric
IL_5TBW_067
NA

IL_56467.6*
1/A1/1661:1663,
1/A1/1786:1788

geometric
IL_5TBW_068
NA

IL_01312.13*
1/A1/1669:1670,
1/A1/1778:1780
Single bulged C
geometric
IL_5TBW_069
NA

IL_61258.10*
1/A1/1670:1671,
1/A1/1776:1778
Single stack bend
geometric
IL_5TBW_070
NA

IL_72766.2*
1/A1/1702:1707,
1/A1/1737:1743

geometric
IL_5TBW_072
NA

IL_98876.1*
1/A1/1711:1717,
1/A1/1727:1733
Kink-turn
geometric
IL_5TBW_073
NA

IL_76900.1*
1/A1/1880:1882,
1/A1/2350:2352
Not an internal loop
geometric
IL_5VCI_005
NA

IL_04038.4*
1/A1/1882:1889,
1/A1/2346:2350
NANA
1/A1/1894:1897,
1/A1/2338:2341
NANA
1/A1/1897:1901,
1/A1/2336:2338
Major groove platform with extra pair
geometric
IL_7RQB_093
NA

IL_87630.5*
1/A1/1901:1906,
1/A1/2333:2336
Intercalated tWH
geometric
IL_4V9F_062
NA

IL_01312.13*
1/A1/1918:1923,
1/A1/1928:1934
tSH-tSH-tHH-tHS
geometric
IL_4V9F_063
NA

IL_66584.5*
1/A1/1940:1942,
1/A1/2106:2108

geometric
IL_1U9S_007
NA

IL_01312.13*
1/A1/1947:1948,
1/A1/2098:2101

geometric
IL_5TBW_080
NA

IL_76195.1*
1/A1/1949:1953,
1/A1/2094:2097
NANA
1/A1/2128:2130,
1/A1/2322:2325
Intercalated cWW
geometric
IL_7A0S_044
NA

IL_04038.4*
1/A1/2156:2161,
1/A1/2173:2180
Kink-turn related
geometric
IL_5TBW_083
NA

IL_95993.1*
1/A1/2190:2192,
1/A1/2315:2317
Stack and bulge
geometric
IL_2ET8_001
NA

IL_04038.4*
1/A1/2196:2199,
1/A1/2245:2246
Major groove outside cWW, minor groove, intercalation pocket
geometric
IL_5J7L_314
NA

IL_06437.11*
1/A1/2200:2201,
1/A1/2241:2244
Major groove outside cWW, minor groove, intercalation pocket
geometric
IL_5J7L_315
NA

IL_13730.12*
1/A1/2204:2206,
1/A1/2237:2238
Single bulged U
geometric
IL_5TBW_025
NA

IL_83039.11*
1/A1/2206:2210,
1/A1/2235:2237
NANA
1/A1/2211:2217,
1/A1/2228:2234

geometric
IL_5TBW_088
NA

IL_36973.5*
1/A1/2249:2251,
1/A1/2265:2267
Stack and bulge
geometric
IL_2O3X_001
NA

IL_04038.4*
1/A1/2276:2277,
1/A1/2307:2310
Multiple bulged bases
geometric
IL_5TBW_089
NA

IL_69632.1*
1/A1/2277:2289,
1/A1/2303:2307
NANA
1/A1/2391:2394,
1/A1/2986:2988
Major groove platform with extra pair
geometric
IL_5TBW_091
NA

IL_87630.5*
1/A1/2396:2398,
1/A1/2981:2984
Minor groove platform with intercalation
geometric
IL_5TBW_092
NA

IL_86964.1*
1/A1/2409:2411,
1/A1/2811:2812
Single bulged U
geometric
IL_5TBW_093
NA

IL_83039.11*
1/A1/2412:2413,
1/A1/2807:2810
Minor groove platform
geometric
IL_5TBW_094
NA

IL_06437.11*
1/A1/2420:2422,
1/A1/2608:2610

geometric
IL_4WF9_042
NA

IL_01312.13*
1/A1/2423:2425,
1/A1/2604:2607
Isolated tHS basepair with bulges
geometric
IL_5TBW_095
NA

IL_38958.6*
1/A1/2520:2526,
1/A1/2584:2587

geometric
IL_5TBW_096
NA

IL_98353.1*
1/A1/2614:2615,
1/A1/2625:2627
Single bulged A
geometric
IL_4WF9_098
NA

IL_71960.4*
1/A1/2666:2668,
1/A1/2686:2690
Isolated tHS basepair with bulges
geometric
IL_5TBW_099
NA

IL_38958.6*
1/A1/2718:2722,
1/A1/2734:2738

geometric
IL_5TBW_121
NA

IL_05867.1*
1/A1/2766:2768,
1/A1/2790:2792
UU cWW
geometric
IL_3SZX_003
NA

IL_01312.13*
1/A1/2770:2773,
1/A1/2787:2788
Single stack bend with bulge
geometric
IL_5TBW_101
NA

IL_31836.1*
1/A1/2823:2828,
1/A1/2862:2867
NANA
1/A1/2828:2830,
1/A1/2858:2862

geometric
IL_5TBW_105
NA

IL_07931.5*
1/A1/2835:2839,
1/A1/2849:2853
Triple sheared
geometric
IL_5J7L_338
NA

IL_56467.6*
1/A1/2876:2877,
1/A1/2949:2951
Major groove platform
geometric
IL_5TBW_107
NA

IL_80663.10*
1/A1/2877:2879,
1/A1/2947:2949

geometric
IL_2ZNI_001
NA

IL_01312.13*
1/A1/2879:2881,
1/A1/2943:2947
NANA
1/A1/2881:2882,
1/A1/2940:2943
Multiple bulged bases
geometric
IL_5TBW_109
NA

IL_13730.12*
1/A1/2889:2891,
1/A1/2912:2914

geometric
IL_5TBW_110
NA

IL_01312.13*
1/A1/2891:2892,
1/A1/2909:2912
Minor groove platform with intercalation
geometric
IL_5TBW_111
NA

IL_95601.1*
1/A1/2918:2920,
1/A1/2926:2928

geometric
IL_5TBW_112
NA

IL_01312.13*
1/A1/2958:2960,
1/A1/2972:2974
Isolated cWH basepair
geometric
IL_4J50_003
NA

IL_01312.13*
1/A1/2960:2961,
1/A1/2970:2972
Single bulged A
geometric
IL_1U9S_001
NA

IL_80007.16*
1/A1/3004:3007,
1/A1/3139:3144
Double sheared
geometric
IL_5TBW_114
NA

IL_09705.7*
1/A1/3012:3014,
1/A1/3040:3042

geometric
IL_5TBW_115
NA

IL_01312.13*
1/A1/3016:3018,
1/A1/3036:3038
UG cWW
geometric
IL_4LFB_061
NA

IL_01312.13*
1/A1/3018:3025,
1/A1/3030:3036
8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA

IL_04346.5*
1/A1/3047:3051,
1/A1/3091:3094
Major groove minor groove platform with tHH
geometric
IL_5TBW_117
NA

IL_28060.3*
1/A1/3054:3059,
1/A1/3084:3088
UAA/GAN related
geometric
IL_5TBW_118
NA

IL_53523.5*
1/A1/3063:3064,
1/A1/3077:3080
Multiple bulged bases
geometric
IL_5TBW_119
NA

IL_13730.12*
1/A1/3103:3107,
1/A1/3127:3131
UAA/GAN
geometric
IL_5TBW_120
NA

IL_53523.5*
1/A1/3164:3166,
1/A1/3284:3286

geometric
IL_1YZ9_002
NA

IL_01312.13*
1/A1/3168:3170,
1/A1/3280:3282
CC cWW
geometric
IL_4KNQ_002
NA

IL_01312.13*
1/A1/3177:3179,
1/A1/3210:3211
Single bulged A
geometric
IL_5TBW_123
NA

IL_80007.16*
1/A1/3179:3188,
1/A1/3204:3210

geometric
IL_5TBW_124
NA

IL_56867.1*
1/A1/3193:3194,
1/A1/3197:3199
Single bulged U
geometric
IL_5J7L_298
NA

IL_83039.11*
1/A1/3225:3229,
1/A1/3258:3260

geometric
IL_5TBW_126
NA

IL_50789.1*
1/A1/3233:3235,
1/A1/3252:3254
AA cWW
geometric
IL_5ED1_002
NA

IL_01312.13*
1/A1/3235:3238,
1/A1/3249:3252
Tandem non-canonical cWW pairs
geometric
IL_4UYK_003
NA

IL_85877.10*
1/A1/3300:3303,
1/A1/3311:3314
Tandem non-canonical cWW pairs
geometric
IL_5TBW_129
NA

IL_85877.10*
1/A1/3318:3320,
1/A1/3387:3388
Single bulged U
geometric
IL_5J7L_279
NA

IL_83039.11*
1/A1/3324:3325,
1/A1/3381:3383
Single bulged U
geometric
IL_2A64_002
NA

IL_83039.11*
1/A1/3328:3330,
1/A1/3373:3378
Isolated non-canonical cWW with bulges
geometric
IL_5TBW_132
NA

IL_55456.1*
1/A1/3332:3337,
1/A1/3367:3371

geometric
IL_5TBW_133
NA

IL_47002.1*
1/A1/3340:3342,
1/A1/3363:3364
Single bulged U
geometric
IL_3WBM_001
NA

IL_83039.11*
1/A1/3342:3345,
1/A1/3360:3363
Double sheared
geometric
IL_4V9F_100
NA

IL_09705.7*
1/A1/3349:3350,
1/A1/3353:3356
Multiple bulged bases
geometric
IL_5TBW_136
NA

IL_13730.12*
1/A3/15:16,
1/A3/63:65
Single bulged A
geometric
IL_5TBW_372
NA

IL_80007.16*
1/A3/21:27,
1/A3/53:58

geometric
IL_5TBW_373
NA

IL_05523.1*
1/A3/28:29,
1/A3/49:52
Minor groove platform
geometric
IL_5TBW_374
NA

IL_94431.4*
1/A3/29:30,
1/A3/47:49
Single stack bend
geometric
IL_5TBW_375
NA

IL_04038.4*
1/A3/32:36,
1/A3/41:45
Symmetric double minor groove platform
geometric
IL_5TBW_376
NA

IL_58103.5*
1/A3/72:80,
1/A3/100:106
8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_377
NA

IL_04346.5*
1/A3/84:87,
1/A3/94:96

geometric
IL_5MSF_001
NA

IL_01312.13*
1/A4/44:64,
1/A4/96:100

geometric
IL_5TBW_144
NA

IL_23735.1*
1/A4/64:66,
1/A4/93:96
Isolated non-canonical cWW with bulges
geometric
IL_5TBW_145
NA

IL_55456.1*
1/A4/68:69,
1/A4/89:91
Single bulged U
geometric
IL_5TBW_146
NA

IL_83039.11*
1/B5/24:26,
1/B5/600:601
Single bulged C
geometric
IL_7KGA_004
NA

IL_61258.10*
1/B5/27:29,
1/B5/597:599
UU cWW
geometric
IL_3SZX_003
NA

IL_01312.13*
1/B5/35:37,
1/B5/471:473
UC cWW
geometric
IL_4V88_385
NA

IL_01312.13*
1/B5/42:48,
1/B5/431:433

geometric
IL_4V88_387
NA

IL_34626.4*
1/B5/50:52,
1/B5/428:429
Minor groove platform
geometric
IL_4V88_388
NA

IL_06437.11*
1/B5/58:63,
1/B5/87:89

geometric
IL_4V88_389
NA

IL_96451.1*
1/B5/64:69,
1/B5/82:86

geometric
IL_4V88_390
NA

IL_59423.1*
1/B5/109:113,
1/B5/301:305

geometric
IL_4V88_422
NA

IL_79670.1*
1/B5/113:116,
1/B5/300:301
Multiple bulged bases
geometric
IL_4V88_392
NA

IL_13730.12*
1/B5/117:122,
1/B5/295:299

geometric
IL_4V88_393
NA

IL_76386.1*
1/B5/143:149,
1/B5/165:172
tWH-tWH-tHW-tHW
geometric
IL_4V88_394
NA

IL_92440.5*
1/B5/150:152,
1/B5/162:164
Isolated cWH basepair
geometric
IL_3W3S_003
NA

IL_42589.6*
1/B5/204:206,
1/B5/259:263
Major groove platform with extra cWW
geometric
IL_4V88_397
NA

IL_95485.6*
1/B5/206:208,
1/B5/257:259

geometric
IL_4V88_398
NA

IL_01312.13*
1/B5/210:212,
1/B5/253:255
Not an internal loop
geometric
IL_5VCI_005
NA

IL_04038.4*
1/B5/265:267,
1/B5/288:289
Single bulged A
geometric
IL_4V88_399
NA

IL_80007.16*
1/B5/270:273,
1/B5/283:285

geometric
IL_4V88_400
NA

IL_05922.1*
1/B5/275:276,
1/B5/279:281
NANA
1/B5/311:316,
1/B5/348:355
Kink-turn with non-sequential stacking
geometric
IL_4V88_402
NA

IL_29549.9*
1/B5/318:323,
1/B5/345:346

geometric
IL_5Y58_001
NA

IL_98882.3*
1/B5/363:365,
1/B5/376:381

geometric
IL_4V88_404
NA

IL_46732.1*
1/B5/389:391,
1/B5/406:408
Isolated cWH basepair
geometric
IL_4V88_405
NA

IL_42589.6*
1/B5/439:441,
1/B5/463:464
Single bulged U
geometric
IL_4V88_407
NA

IL_83039.11*
1/B5/443:447,
1/B5/460:461
C-loop
geometric
IL_5J7L_018
NA

IL_08376.2*
1/B5/447:448,
1/B5/458:460
Single bulged G
geometric
IL_5J7L_019
NA

IL_59137.10*
1/B5/480:484,
1/B5/503:508
NANA
1/B5/516:518,
1/B5/533:536
Minor groove platform with extra cWW
geometric
IL_4V88_411
NA

IL_87332.1*
1/B5/518:520,
1/B5/532:533
Minor groove platform
geometric
IL_4V88_412
NA

IL_06437.11*
1/B5/550:557,
1/B5/587:588
SSU/LSU pseudoknot
geometric
IL_4V88_413
NA

IL_15861.6*
1/B5/557:559,
1/B5/586:587
Single bulged U
geometric
IL_4V88_414
NA

IL_83039.11*
1/B5/561:568,
1/B5/575:584
NANA
1/B5/616:622,
1/B5/1104:1105

geometric
IL_4V88_416
NA

IL_12418.1*
1/B5/624:626,
1/B5/973:975

geometric
IL_4V88_417
NA

IL_01312.13*
1/B5/627:631,
1/B5/968:972
tSH-tHW-tHS
geometric
IL_4V88_418
NA

IL_39521.5*
1/B5/631:633,
1/B5/966:968
Stack and bulge
geometric
IL_2O3X_001
NA

IL_04038.4*
1/B5/646:648,
1/B5/686:688
Isolated near basepair
geometric
IL_4V88_406
NA

IL_01312.13*
1/B5/651:658,
1/B5/676:683
NANA
1/B5/746:747,
1/B5/802:805
Major groove minor groove platform; mini C-loop
geometric
IL_4V88_423
NA

IL_09061.4*
1/B5/748:750,
1/B5/799:801

geometric
IL_4V88_424
NA

IL_01312.13*
1/B5/751:760,
1/B5/790:798
NANA
1/B5/817:824,
1/B5/848:854
NANA
1/B5/865:866,
1/B5/962:965
Major groove platform; stack outside cWW
geometric
IL_4V88_428
NA

IL_70995.6*
1/B5/868:869,
1/B5/958:960
Single bulged U
geometric
IL_6UFH_004
NA

IL_83039.11*
1/B5/871:874,
1/B5/953:956
Tandem non-canonical cWW pairs
geometric
IL_4V88_430
NA

IL_85877.10*
1/B5/874:878,
1/B5/950:953
Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA

IL_85877.10*
1/B5/885:888,
1/B5/924:927
Tandem non-canonical cWW pairs
geometric
IL_4V88_432
NA

IL_85877.10*
1/B5/893:899,
1/B5/910:919
NANA
1/B5/985:990,
1/B5/1014:1016
Other IL
geometric
IL_4V88_435
NA

IL_51590.1*
1/B5/990:994,
1/B5/1010:1014
tSH-tHW-tHS
geometric
IL_4V88_436
NA

IL_39521.5*
1/B5/1034:1036,
1/B5/1095:1101

geometric
IL_4V88_437
NA

IL_19557.1*
1/B5/1041:1044,
1/B5/1074:1077
Tandem non-canonical cWW pairs
geometric
IL_4V88_438
NA

IL_85877.10*
1/B5/1051:1053,
1/B5/1066:1067
Single bulged U
geometric
IL_5J7L_017
NA

IL_83039.11*
1/B5/1111:1118,
1/B5/1129:1134
8x6 Sarcin-Ricin with inserted Y; G-bulge
geometric
IL_4V88_440
NA

IL_24606.1*
1/B5/1146:1147,
1/B5/1630:1632
Single bulged A
geometric
IL_5J7L_039
NA

IL_80007.16*
1/B5/1149:1151,
1/B5/1627:1628
Single bulged G
geometric
IL_4V88_442
NA

IL_59137.10*
1/B5/1157:1160,
1/B5/1617:1621
C-loop
geometric
IL_4V88_443
NA

IL_63596.4*
1/B5/1173:1175,
1/B5/1464:1466

geometric
IL_4V88_444
NA

IL_01312.13*
1/B5/1178:1179,
1/B5/1459:1461
Minor groove platform
geometric
IL_4V88_445
NA

IL_06437.11*
1/B5/1213:1215,
1/B5/1448:1450

geometric
IL_4V88_446
NA

IL_01312.13*
1/B5/1224:1233,
1/B5/1252:1259
NANA
1/B5/1234:1236,
1/B5/1249:1251

geometric
IL_4V88_448
NA

IL_01312.13*
1/B5/1270:1272,
1/B5/1438:1440

geometric
IL_5Y7M_007
NA

IL_01312.13*
1/B5/1272:1276,
1/B5/1436:1438
Isolated cWS basepair