3JAI Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3JAI_001 | 1/2/12:23 | No text annotation | ||
| HL_3JAI_002 | 1/2/31:39 | tRNA anticodon loop | homologous HL_4TUE_034 HL_06059.6 | |
| HL_3JAI_003 | 1/2/53:61 | T-loop with 2 stacked bulged bases | homologous HL_3ZGZ_003 HL_28252.8 | |
| HL_3JAI_004 | 1/3/13:22 | No text annotation | homologous HL_4YYE_001 NA | |
| HL_3JAI_005 | 1/3/31:39 | tRNA anticodon loop | homologous HL_4TUE_034 HL_06059.6 | |
| HL_3JAI_006 | 1/3/53:61 | T-loop with 2 stacked bulged bases | homologous HL_6PMO_005 NA | |
| HL_3JAI_007 | 1/5/37:44 | No text annotation | geometric HL_4V9F_006 HL_30068.2 | |
| HL_3JAI_008 | 1/5/68:73 | No text annotation | homologous HL_8C3A_002 NA | |
| HL_3JAI_009 | 1/5/89:95 | No text annotation | homologous HL_8C3A_003 NA | |
| HL_3JAI_010 | 1/5/131:137 | No text annotation | homologous HL_8C3A_004 NA | |
| HL_3JAI_011 | 1/5/204:211 | T-loop with 2 stacked bulged bases | homologous HL_5TBW_005 NA | |
| HL_3JAI_012 | 1/5/222:226 | No text annotation | homologous HL_8C3A_006 NA | |
| HL_3JAI_013 | 1/5/230:238 | T-loop with unstacked turn | homologous HL_5TBW_007 NA | |
| HL_3JAI_014 | 1/5/289:298 | No text annotation | homologous HL_5TBW_008 NA | |
| HL_3JAI_015 | 1/5/314:323 | Pseudoknot geometry | geometric HL_4QLM_002 HL_77600.2 | |
| HL_3JAI_016 | 1/5/368:373 | GNRA | homologous HL_8C3A_010 NA | |
| HL_3JAI_017 | 1/5/393:398 | GNRA | homologous HL_8C3A_011 NA | |
| HL_3JAI_121 | 1/5/996:1047 | No text annotation | ||
| HL_3JAI_018 | 1/5/1178:1183 | GNRA | geometric HL_4FRG_002 HL_37824.7 | |
| HL_3JAI_019 | 1/5/1252:1258 | GNRA | geometric HL_4LFB_012 HL_37824.7 | |
| HL_3JAI_020 | 1/5/1317:1326 | T-loop with 2 stacked bulged bases | homologous HL_5TBW_014 NA | |
| HL_3JAI_021 | 1/5/1364:1373 | No text annotation | ||
| HL_3JAI_022 | 1/5/1389:1394 | GNRA | homologous HL_8C3A_016 NA | |
| HL_3JAI_023 | 1/5/1406:1411 | Mini UNCG | geometric HL_5T16_002 HL_56334.1 | |
| HL_3JAI_024 | 1/5/1436:1448 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 | |
| HL_3JAI_025 | 1/5/1479:1486 | Other HL | geometric HL_5J7L_200 HL_08100.1 | |
| HL_3JAI_026 | 1/5/1561:1566 | GNRA | homologous HL_8C3A_019 NA | |
| HL_3JAI_027 | 1/5/1593:1602 | No text annotation | homologous HL_5TBW_020 NA | |
| HL_3JAI_028 | 1/5/1627:1635 | No text annotation | homologous HL_5TBW_021 NA | |
| HL_3JAI_029 | 1/5/1675:1680 | Externally structured | homologous HL_8C3A_022 NA | |
| HL_3JAI_030 | 1/5/1763:1769 | GNRA | homologous HL_5TBW_023 NA | |
| HL_3JAI_031 | 1/5/1814:1823 | No text annotation | ||
| HL_3JAI_032 | 1/5/1864:1870 | GNRA | homologous HL_5TBW_025 NA | |
| HL_3JAI_033 | 1/5/1886:1893 | No text annotation | homologous HL_5TBW_026 NA | |
| HL_3JAI_122 | 1/5/1973:1993 | No text annotation | ||
| HL_3JAI_034 | 1/5/1978:1988 | No text annotation | homologous HL_5TBW_027 NA | |
| HL_3JAI_035 | 1/5/2006:2013 | GNRA wlth tandem sheared | homologous HL_8C3A_028 NA | |
| HL_3JAI_036 | 1/5/2130:2244 | No text annotation | ||
| HL_3JAI_037 | 1/5/2317:2322 | GNRA | homologous HL_5TBW_030 NA | |
| HL_3JAI_038 | 1/5/2376:2384 | T-loop with 2 stacked bulged bases | homologous HL_8C3A_031 NA | |
| HL_3JAI_039 | 1/5/2420:2426 | Pseudoknot geometry with 3' bulge | homologous HL_5TBW_032 NA | |
| HL_3JAI_040 | 1/5/2458:2463 | GNRA variation | homologous HL_5TBW_033 NA | |
| HL_3JAI_041 | 1/5/2487:2491 | No text annotation | ||
| HL_3JAI_042 | 1/5/2523:2532 | No text annotation | homologous HL_5TBW_035 NA | |
| HL_3JAI_043 | 1/5/2561:2566 | GNRA | geometric HL_4QK9_002 HL_37824.7 | |
| HL_3JAI_044 | 1/5/2578:2583 | GNRA | homologous HL_8C3A_036 NA | |
| HL_3JAI_045 | 1/5/2623:2632 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_3JAI_127 | 1/5/2623:2633 | No text annotation | ||
| HL_3JAI_046 | 1/5/2664:2670 | No text annotation | homologous HL_8C3A_038 NA | |
| HL_3JAI_047 | 1/5/2705:2710 | No text annotation | geometric HL_4WF9_003 HL_75660.5 | |
| HL_3JAI_048 | 1/5/2738:2742 | No text annotation | homologous HL_8C3A_040 NA | |
| HL_3JAI_049 | 1/5/2792:2799 | No text annotation | homologous HL_5TBW_041 NA | |
| HL_3JAI_050 | 1/5/2810:2816 | GNRA | homologous HL_5TBW_042 NA | |
| HL_3JAI_051 | 1/5/2872:2877 | UNCG | homologous HL_8C3A_043 NA | |
| HL_3JAI_124 | 1/5/2910:3584 | No text annotation | ||
| HL_3JAI_052 | 1/5/3614:3618 | No text annotation | homologous HL_8C3A_045 NA | |
| HL_3JAI_053 | 1/5/3639:3649 | No text annotation | homologous HL_5TBW_046 NA | |
| HL_3JAI_054 | 1/5/3668:3674 | GNRA | homologous HL_8C3A_047 NA | |
| HL_3JAI_055 | 1/5/3723:3729 | tRNA D-loop | geometric HL_4V9K_033 HL_48417.5 | |
| HL_3JAI_056 | 1/5/3757:3767 | No text annotation | homologous HL_8C3A_049 NA | |
| HL_3JAI_057 | 1/5/3796:3804 | No text annotation | homologous HL_8C3A_050 NA | |
| HL_3JAI_058 | 1/5/3873:3882 | No text annotation | homologous HL_8C3A_051 NA | |
| HL_3JAI_059 | 1/5/3948:4065 | No text annotation | geometric HL_5AMQ_001 HL_48417.5 | |
| HL_3JAI_060 | 1/5/4102:4107 | UNCG | geometric HL_5J7L_171 HL_34617.5 | |
| HL_3JAI_061 | 1/5/4139:4145 | No text annotation | geometric HL_8C3A_221 NA | |
| HL_3JAI_062 | 1/5/4193:4201 | No text annotation | homologous HL_8C3A_055 NA | |
| HL_3JAI_063 | 1/5/4210:4222 | No text annotation | homologous HL_5TBW_055 NA | |
| HL_3JAI_064 | 1/5/4250:4258 | No text annotation | homologous HL_8C3A_057 NA | |
| HL_3JAI_065 | 1/5/4270:4277 | Pseudoknot geometry | homologous HL_5TBW_057 NA | |
| HL_3JAI_066 | 1/5/4301:4309 | No text annotation | homologous HL_8C3A_059 NA | |
| HL_3JAI_067 | 1/5/4321:4326 | GNRA | homologous HL_5TBW_059 NA | |
| HL_3JAI_068 | 1/5/4352:4362 | No text annotation | geometric HL_4V83_139 NA | |
| HL_3JAI_069 | 1/5/4417:4425 | No text annotation | homologous HL_5TBW_061 NA | |
| HL_3JAI_070 | 1/5/4473:4481 | GNRA with extra cWW | geometric HL_4WF9_053 HL_04259.3 | |
| HL_3JAI_071 | 1/5/4497:4503 | No text annotation | geometric HL_5TBW_063 NA | |
| HL_3JAI_072 | 1/5/4540:4545 | GNRA | homologous HL_5TBW_064 NA | |
| HL_3JAI_073 | 1/5/4603:4608 | GNRA | geometric HL_4V9F_066 HL_37824.7 | |
| HL_3JAI_074 | 1/5/4646:4651 | Ribsomal LSU H95 | homologous HL_8C3A_067 NA | |
| HL_3JAI_075 | 1/5/4688:4702 | No text annotation | homologous HL_8C3A_068 NA | |
| HL_3JAI_076 | 1/5/4907:4914 | No text annotation | geometric HL_4WF9_003 HL_75660.5 | |
| HL_3JAI_077 | 1/5/4975:4983 | No text annotation | geometric HL_5TBW_070 NA | |
| HL_3JAI_078 | 1/5/5021:5028 | No text annotation | geometric HL_6VMY_004 HL_53890.2 | |
| HL_3JAI_125 | 1/7/32:45 | No text annotation | homologous HL_9DFE_067 HL_97756.2 | |
| HL_3JAI_079 | 1/7/36:41 | No text annotation | homologous HL_5TBW_185 NA | |
| HL_3JAI_080 | 1/7/86:91 | GNRA | homologous HL_5TBW_186 NA | |
| HL_3JAI_081 | 1/8/47:56 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 | |
| HL_3JAI_082 | 1/8/68:90 | No text annotation | homologous HL_8C3A_075 NA | |
| HL_3JAI_083 | 1/8/107:112 | No text annotation | ||
| HL_3JAI_084 | 1/8/121:129 | No text annotation | ||
| HL_3JAI_085 | 1/9/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_3JAI_086 | 1/9/69:80 | No text annotation | geometric HL_2ZZM_002 HL_13963.3 | |
| HL_3JAI_087 | 1/9/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_3JAI_088 | 1/9/197:202 | GNRA | geometric HL_6CZR_078 NA | |
| HL_3JAI_089 | 1/9/288:295 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_3JAI_090 | 1/9/322:329 | No text annotation | geometric HL_2ZZM_002 HL_13963.3 | |
| HL_3JAI_091 | 1/9/377:387 | No text annotation | geometric HL_6UFM_001 HL_04642.1 | |
| HL_3JAI_092 | 1/9/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_3JAI_093 | 1/9/441:452 | No text annotation | homologous HL_4V88_195 NA | |
| HL_3JAI_094 | 1/9/462:467 | UNCG | homologous HL_4V88_196 NA | |
| HL_3JAI_095 | 1/9/498:504 | No text annotation | homologous HL_4V88_197 NA | |
| HL_3JAI_096 | 1/9/539:544 | GNRA | geometric HL_5J7L_007 HL_37824.7 | |
| HL_3JAI_097 | 1/9/569:581 | No text annotation | geometric HL_4V88_199 NA | |
| HL_3JAI_098 | 1/9/618:623 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_3JAI_126 | 1/9/698:732 | No text annotation | ||
| HL_3JAI_101 | 1/9/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_3JAI_102 | 1/9/833:841 | No text annotation | homologous HL_8P9A_207 HL_48417.5 | |
| HL_3JAI_103 | 1/9/885:901 | Pseudoknot geometry | homologous HL_4V88_205 NA | |
| HL_3JAI_104 | 1/9/957:966 | No text annotation | homologous HL_4V88_206 NA | |
| HL_3JAI_105 | 1/9/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_3JAI_106 | 1/9/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_3JAI_107 | 1/9/1112:1121 | No text annotation | ||
| HL_3JAI_108 | 1/9/1141:1146 | GNRA | homologous HL_4V88_210 NA | |
| HL_3JAI_109 | 1/9/1178:1183 | GNRA | homologous HL_4V88_211 NA | |
| HL_3JAI_110 | 1/9/1245:1254 | No text annotation | homologous HL_4V88_212 NA | |
| HL_3JAI_111 | 1/9/1295:1304 | Anticodon loop related | homologous HL_4V88_213 NA | |
| HL_3JAI_112 | 1/9/1353:1358 | GNRA | homologous HL_4V88_214 NA | |
| HL_3JAI_113 | 1/9/1366:1373 | No text annotation | homologous HL_4V88_215 NA | |
| HL_3JAI_114 | 1/9/1421:1426 | GNRA | geometric HL_5FQ5_003 HL_37824.7 | |
| HL_3JAI_115 | 1/9/1460:1466 | GNRA | homologous HL_4V88_217 NA | |
| HL_3JAI_116 | 1/9/1565:1570 | GNRA | homologous HL_4V88_218 NA | |
| HL_3JAI_117 | 1/9/1614:1625 | No text annotation | homologous HL_4V88_219 NA | |
| HL_3JAI_118 | 1/9/1658:1666 | No text annotation | homologous HL_4V88_220 NA | |
| HL_3JAI_119 | 1/9/1760:1772 | No text annotation | geometric HL_8KAL_003 HL_75660.5 | |
| HL_3JAI_120 | 1/9/1847:1852 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3JAI_123 | No text annotation | ||
| HL_3JAI_099 | No text annotation | ||
| HL_3JAI_100 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3JAI_001 | 1/2/2:4, 1/2/69:71 | No text annotation | homologous IL_5EL4_357 NA | |
| IL_3JAI_002 | 1/5/6:7, 1/8/149:151 | Single bulged C | homologous IL_8C3A_002 NA | |
| IL_3JAI_003 | 1/5/12:14, 1/8/143:144 | Single bulged U | homologous IL_8C3A_003 NA | |
| IL_3JAI_004 | 1/5/16:18, 1/8/139:141 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_3JAI_005 | 1/5/26:27, 1/5/55:57 | Single stack bend | homologous IL_5TBW_004 NA | |
| IL_3JAI_006 | 1/5/30:37, 1/5/44:52 | 9x8 Sarcin-Ricin; G-bulge | geometric IL_4WF9_008 IL_84694.2 | |
| IL_3JAI_007 | 1/5/81:88, 1/5/96:102 | No text annotation | homologous IL_8C3A_006 NA | |
| IL_3JAI_008 | 1/5/118:121, 1/5/152:153 | Multiple bulged bases | geometric IL_5WTK_001 IL_82107.4 | |
| IL_3JAI_268 | 1/5/118:122, 1/5/147:153 | No text annotation | ||
| IL_3JAI_009 | 1/5/121:122, 1/5/147:152 | No text annotation | geometric IL_5TBW_007 NA | |
| IL_3JAI_010 | 1/5/125:126, 1/5/142:144 | No text annotation | ||
| IL_3JAI_011 | 1/5/168:173, 1/5/263:267 | No text annotation | ||
| IL_3JAI_012 | 1/5/180:182, 1/5/255:256 | Single stack bend | geometric IL_7KGA_003 IL_90729.1 | |
| IL_3JAI_013 | 1/5/184:189, 1/5/252:253 | Major groove intercalation | geometric IL_1NBS_009 IL_82107.4 | |
| IL_3JAI_014 | 1/5/195:196, 1/5/244:246 | Single bulged C | geometric IL_3D0U_001 IL_61258.15 | |
| IL_3JAI_015 | 1/5/199:201, 1/5/214:215 | Single bulged U | homologous IL_8C3A_013 NA | |
| IL_3JAI_016 | 1/5/339:342, 1/8/32:33 | Minor groove platform, major groove intercalation | geometric IL_1U9S_005 IL_95583.2 | |
| IL_3JAI_017 | 1/5/348:350, 1/8/25:26 | Single bulged A | homologous IL_8C3A_014 NA | |
| IL_3JAI_018 | 1/5/387:390, 1/5/401:414 | No text annotation | homologous IL_5TBW_014 NA | |
| IL_3JAI_019 | 1/5/415:421, 1/8/13:19 | Triple sheared with non-canonical cWW | homologous IL_5TBW_015 NA | |
| IL_3JAI_020 | 1/5/443:446, 1/5/1300:1304 | No text annotation | geometric IL_7MLW_007 IL_99358.1 | |
| IL_3JAI_021 | 1/5/459:460, 1/5/695:697 | No text annotation | ||
| IL_3JAI_022 | 1/5/462:464, 1/5/691:693 | Isolated non-canonical cWW pair | geometric IL_5ED1_002 IL_87907.2 | |
| IL_3JAI_023 | 1/5/465:466, 1/5/688:690 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAI_024 | 1/5/466:472, 1/5/682:688 | No text annotation | ||
| IL_3JAI_025 | 1/5/482:486, 1/5/670:672 | No text annotation | geometric IL_4P3T_002 NA | |
| IL_3JAI_026 | 1/5/488:490, 1/5/664:668 | No text annotation | ||
| IL_3JAI_027 | 1/5/490:493, 1/5/661:664 | No text annotation | ||
| IL_3JAI_028 | 1/5/495:496, 1/5/657:659 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_3JAI_029 | 1/5/497:499, 1/5/655:656 | No text annotation | ||
| IL_3JAI_288 | 1/5/500:505, 1/5/653:654 | No text annotation | ||
| IL_3JAI_031 | 1/5/508:510, 1/5/649:650 | Single bulged A | geometric IL_6WPI_001 IL_31462.6 | |
| IL_3JAI_032 | 1/5/511:515, 1/5/646:648 | Isolated non-canonical cWW pair | geometric IL_1U6B_001 IL_57744.1 | |
| IL_3JAI_033 | 1/5/708:709, 1/5/1287:1289 | Single bulged G | geometric IL_4LFB_036 IL_00225.13 | |
| IL_3JAI_034 | 1/5/722:724, 1/5/942:946 | No text annotation | ||
| IL_3JAI_035 | 1/5/726:731, 1/5/938:940 | No text annotation | ||
| IL_3JAI_036 | 1/5/731:735, 1/5/928:938 | No text annotation | ||
| IL_3JAI_037 | 1/5/735:737, 1/5/927:928 | Single stack bend | geometric IL_7A0S_054 IL_26793.1 | |
| IL_3JAI_038 | 1/5/740:742, 1/5/922:924 | Isolated non-canonical cWW pair | geometric IL_4P43_004 NA | |
| IL_3JAI_269 | 1/5/745:752, 1/5/911:919 | No text annotation | ||
| IL_3JAI_040 | 1/5/989:992, 1/5/1051:1064 | No text annotation | ||
| IL_3JAI_041 | 1/5/1074:1076, 1/5/1235:1236 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_3JAI_270 | 1/5/1074:1079, 1/5/1221:1236 | No text annotation | ||
| IL_3JAI_042 | 1/5/1076:1077, 1/5/1233:1235 | Single stack bend with bulge | geometric IL_5TBW_101 NA | |
| IL_3JAI_043 | 1/5/1077:1079, 1/5/1221:1233 | No text annotation | ||
| IL_3JAI_044 | 1/5/1081:1082, 1/5/1217:1219 | Minor groove platform | geometric IL_6DLR_003 IL_51454.3 | |
| IL_3JAI_045 | 1/5/1082:1085, 1/5/1212:1217 | No text annotation | ||
| IL_3JAI_046 | 1/5/1086:1087, 1/5/1209:1211 | Single bulged C | geometric IL_3W3S_001 IL_61258.15 | |
| IL_3JAI_047 | 1/5/1097:1098, 1/5/1197:1199 | Single stack bend | geometric IL_5J7L_249 IL_90729.1 | |
| IL_3JAI_048 | 1/5/1173:1175, 1/5/1186:1188 | Isolated near basepair | geometric IL_4V88_406 NA | |
| IL_3JAI_049 | 1/5/1357:1360, 1/5/1378:1382 | No text annotation | ||
| IL_3JAI_050 | 1/5/1360:1361, 1/5/1376:1378 | No text annotation | ||
| IL_3JAI_051 | 1/5/1425:1429, 1/5/1455:1460 | Triple sheared related | geometric IL_4V9F_018 IL_97631.1 | |
| IL_3JAI_052 | 1/5/1431:1434, 1/5/1450:1453 | Double sheared | geometric IL_4WF9_087 IL_09705.15 | |
| IL_3JAI_053 | 1/5/1467:1468, 1/5/1496:1498 | Single bulged A | homologous IL_5TBW_024 NA | |
| IL_3JAI_054 | 1/5/1474:1476, 1/5/1489:1490 | Single stack bend | geometric IL_7A0S_005 IL_90729.1 | |
| IL_3JAI_055 | 1/5/1520:1522, 1/5/1655:1657 | Isolated non-canonical cWW pair | homologous IL_8C3A_029 NA | |
| IL_3JAI_056 | 1/5/1522:1526, 1/5/1648:1655 | tHW-tHW cross-strand stack | geometric IL_5TBW_028 NA | |
| IL_3JAI_057 | 1/5/1550:1551, 1/5/1576:1578 | Single bulged G | homologous IL_5TBW_029 NA | |
| IL_3JAI_058 | 1/5/1551:1555, 1/5/1572:1576 | Triple sheared | geometric IL_4V9F_027 IL_50730.2 | |
| IL_3JAI_059 | 1/5/1586:1589, 1/5/1605:1607 | Major groove platform with extra cWW | homologous IL_8C3A_034 NA | |
| IL_3JAI_060 | 1/5/1590:1592, 1/5/1603:1604 | Single bulged U | homologous IL_8C3A_035 NA | |
| IL_3JAI_061 | 1/5/1624:1626, 1/5/1636:1640 | Multiple bulged bases | homologous IL_5TBW_033 NA | |
| IL_3JAI_062 | 1/5/1671:1673, 1/5/1682:1684 | Isolated non-canonical cWW pair | homologous IL_5TBW_034 NA | |
| IL_3JAI_063 | 1/5/1686:1688, 1/5/1848:1851 | No text annotation | ||
| IL_3JAI_064 | 1/5/1694:1725, 1/5/1837:1842 | No text annotation | ||
| IL_3JAI_065 | 1/5/1732:1737, 1/5/1792:1797 | 5x5 Sarcin-Ricin with intercalated A; G-bulge | geometric IL_7A0S_027 NA | |
| IL_3JAI_066 | 1/5/1737:1738, 1/5/1790:1792 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_3JAI_067 | 1/5/1739:1744, 1/5/1786:1789 | C-loop with bulged stacked A's | homologous IL_5TBW_040 NA | |
| IL_3JAI_068 | 1/5/1746:1749, 1/5/1781:1784 | Tandem non-canonical cWW pairs | homologous IL_5TBW_041 NA | |
| IL_3JAI_069 | 1/5/1749:1751, 1/5/1779:1781 | Isolated non-canonical cWW pair | geometric IL_5TBW_042 NA | |
| IL_3JAI_070 | 1/5/1753:1756, 1/5/1775:1777 | Intercalated cWW | geometric IL_7A0S_044 IL_31737.3 | |
| IL_3JAI_071 | 1/5/1756:1758, 1/5/1774:1775 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_3JAI_072 | 1/5/1761:1763, 1/5/1769:1771 | Isolated non-canonical cWW pair | geometric IL_4WF9_083 IL_87907.2 | |
| IL_3JAI_073 | 1/5/1858:1860, 1/5/1874:1876 | Isolated non-canonical cWW pair | homologous IL_5TBW_046 NA | |
| IL_3JAI_074 | 1/5/1905:1909, 1/5/2067:2071 | UAA/GAN | homologous IL_5TBW_048 NA | |
| IL_3JAI_075 | 1/5/1911:1918, 1/5/2064:2065 | SSU/LSU pseudoknot | geometric IL_7RQB_037 NA | |
| IL_3JAI_076 | 1/5/1918:1920, 1/5/2063:2064 | Single bulged G | geometric IL_7D7V_002 IL_00225.13 | |
| IL_3JAI_077 | 1/5/1920:1922, 1/5/2062:2063 | No text annotation | ||
| IL_3JAI_078 | 1/5/1926:1933, 1/5/2053:2058 | No text annotation | geometric IL_5TBW_051 NA | |
| IL_3JAI_079 | 1/5/1933:1944, 1/5/2038:2053 | No text annotation | geometric IL_5TBW_052 NA | |
| IL_3JAI_080 | 1/5/1946:1948, 1/5/2035:2036 | Single bulged U | homologous IL_5TBW_053 NA | |
| IL_3JAI_081 | 1/5/1957:1965, 1/5/2022:2026 | Kink-turn | homologous IL_8C3A_057 NA | |
| IL_3JAI_082 | 1/5/1973:1977, 1/5/1989:1993 | No text annotation | homologous IL_8C3A_058 NA | |
| IL_3JAI_083 | 1/5/2001:2005, 1/5/2014:2016 | Major groove platform with extra cWW | homologous IL_8C3A_059 NA | |
| IL_3JAI_084 | 1/5/2083:2085, 1/5/2272:2273 | Single bulged C | geometric IL_3DIL_001 IL_61258.15 | |
| IL_3JAI_273 | 1/5/2087:2128, 1/5/2246:2270 | No text annotation | ||
| IL_3JAI_085 | 1/5/2290:2292, 1/5/2342:2345 | Isolated cWS basepair | homologous IL_5TBW_057 NA | |
| IL_3JAI_086 | 1/5/2299:2301, 1/5/2334:2335 | Single bulged A | homologous IL_8C3A_062 NA | |
| IL_3JAI_087 | 1/5/2302:2309, 1/5/2329:2333 | Kink-turn | homologous IL_5TBW_059 NA | |
| IL_3JAI_088 | 1/5/2312:2314, 1/5/2325:2326 | Single bulged A | homologous IL_5TBW_060 NA | |
| IL_3JAI_089 | 1/5/2358:2364, 1/5/3858:3863 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5TBW_061 NA | |
| IL_3JAI_090 | 1/5/2415:2419, 1/5/2427:2429 | C-loop | geometric IL_7A0S_047 IL_83150.2 | |
| IL_3JAI_091 | 1/5/2446:2450, 1/5/2509:2514 | UAA/GAN | homologous IL_8C3A_067 NA | |
| IL_3JAI_092 | 1/5/2477:2479, 1/5/2499:2500 | Not an internal loop | geometric IL_4UYK_002 NA | |
| IL_3JAI_093 | 1/5/2542:2547, 1/5/2772:2774 | Isolated non-canonical cWW pair | geometric IL_5TBW_145 NA | |
| IL_3JAI_094 | 1/5/2589:2593, 1/5/2752:2756 | Triple sheared | homologous IL_5TBW_067 NA | |
| IL_3JAI_095 | 1/5/2613:2614, 1/5/2724:2726 | Single bulged A | geometric IL_7A0S_012 IL_31462.6 | |
| IL_3JAI_096 | 1/5/2614:2615, 1/5/2722:2724 | Single stack bend | homologous IL_8C3A_076 NA | |
| IL_3JAI_097 | 1/5/2622:2623, 1/5/2632:2634 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAI_098 | 1/5/2646:2648, 1/5/2685:2688 | Isolated tHS basepair with bulges | geometric IL_4V9F_076 IL_85599.2 | |
| IL_3JAI_099 | 1/5/2651:2653, 1/5/2681:2682 | Single bulged G | geometric IL_3NDB_004 IL_00225.13 | |
| IL_3JAI_100 | 1/5/2656:2662, 1/5/2672:2678 | Kink-turn | homologous IL_5TBW_073 NA | |
| IL_3JAI_101 | 1/5/2704:2705, 1/5/2710:2712 | No text annotation | ||
| IL_3JAI_102 | 1/5/2832:2838, 1/5/3850:3853 | No text annotation | homologous IL_5TBW_074 NA | |
| IL_3JAI_103 | 1/5/2844:2846, 1/5/3842:3844 | Isolated tWW turn | homologous IL_5TBW_075 NA | |
| IL_3JAI_104 | 1/5/2847:2850, 1/5/3840:3841 | Major groove platform; stack outside cWW | geometric IL_5TBW_076 NA | |
| IL_3JAI_274 | 1/5/2847:2855, 1/5/3837:3841 | No text annotation | homologous IL_8C3A_484 NA | |
| IL_3JAI_105 | 1/5/2850:2855, 1/5/3837:3840 | Intercalated tWH | homologous IL_5TBW_077 NA | |
| IL_3JAI_106 | 1/5/2867:2872, 1/5/2877:2883 | tSH-tSH-tHH-tHS | geometric IL_4V9F_063 IL_47346.2 | |
| IL_3JAI_107 | 1/5/2889:2891, 1/5/3610:3612 | Isolated non-canonical cWW pair | homologous IL_8C3A_085 NA | |
| IL_3JAI_108 | 1/5/2896:2897, 1/5/3602:3605 | No text annotation | homologous IL_8C3A_086 NA | |
| IL_3JAI_109 | 1/5/2901:2905, 1/5/3589:3598 | No text annotation | ||
| IL_3JAI_110 | 1/5/3632:3633, 1/5/3827:3829 | Single bulged A | homologous IL_5TBW_082 NA | |
| IL_3JAI_111 | 1/5/3660:3665, 1/5/3677:3684 | Kink-turn related | homologous IL_5TBW_083 NA | |
| IL_3JAI_112 | 1/5/3700:3703, 1/5/3749:3750 | Major groove intercalation | homologous IL_5TBW_084 NA | |
| IL_3JAI_113 | 1/5/3704:3705, 1/5/3745:3748 | Multiple bulged bases | homologous IL_8C3A_090 NA | |
| IL_3JAI_114 | 1/5/3708:3710, 1/5/3741:3742 | Single stack bend | homologous IL_8C3A_091 NA | |
| IL_3JAI_115 | 1/5/3710:3714, 1/5/3739:3741 | No text annotation | homologous IL_8C3A_092 NA | |
| IL_3JAI_116 | 1/5/3715:3721, 1/5/3732:3738 | No text annotation | homologous IL_5TBW_088 NA | |
| IL_3JAI_117 | 1/5/3722:3723, 1/5/3729:3731 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAI_118 | 1/5/3780:3781, 1/5/3811:3814 | No text annotation | homologous IL_8C3A_094 NA | |
| IL_3JAI_119 | 1/5/3781:3792, 1/5/3808:3811 | No text annotation | geometric IL_5TBW_090 NA | |
| IL_3JAI_120 | 1/5/3895:3898, 1/5/4563:4565 | Major groove platform with extra pair | homologous IL_5TBW_091 NA | |
| IL_3JAI_121 | 1/5/3900:3902, 1/5/4558:4561 | Major groove platform with intercalation | homologous IL_5TBW_092 NA | |
| IL_3JAI_122 | 1/5/3913:3915, 1/5/4388:4389 | Single bulged U | homologous IL_5TBW_093 NA | |
| IL_3JAI_123 | 1/5/3916:3917, 1/5/4384:4387 | Minor groove platform | homologous IL_5TBW_094 NA | |
| IL_3JAI_124 | 1/5/3927:3929, 1/5/4181:4184 | No text annotation | homologous IL_8C3A_100 NA | |
| IL_3JAI_125 | 1/5/4082:4088, 1/5/4161:4164 | No text annotation | homologous IL_8C3A_106 NA | |
| IL_3JAI_126 | 1/5/4095:4097, 1/5/4112:4113 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_3JAI_127 | 1/5/4191:4192, 1/5/4202:4204 | Single bulged A | homologous IL_8C3A_107 NA | |
| IL_3JAI_128 | 1/5/4243:4245, 1/5/4263:4267 | Isolated tHS basepair with bulges | homologous IL_5TBW_099 NA | |
| IL_3JAI_129 | 1/5/4291:4293, 1/5/4317:4318 | Single bulged A | geometric IL_4V88_399 NA | |
| IL_3JAI_130 | 1/5/4295:4298, 1/5/4312:4315 | Tandem non-canonical cWW pairs | homologous IL_8C3A_109 NA | |
| IL_3JAI_131 | 1/5/4347:4350, 1/5/4364:4365 | Single stack bend | geometric IL_5J7L_032 IL_26793.1 | |
| IL_3JAI_132 | 1/5/4400:4401, 1/5/4442:4444 | Major groove platform | homologous IL_5TBW_102 NA | |
| IL_3JAI_133 | 1/5/4401:4403, 1/5/4440:4442 | Isolated non-canonical cWW pair | geometric IL_5TBW_103 NA | |
| IL_3JAI_134 | 1/5/4403:4405, 1/5/4439:4440 | Major groove platform | homologous IL_5TBW_104 NA | |
| IL_3JAI_135 | 1/5/4405:4407, 1/5/4435:4439 | Major groove minor groove platform with extra cWW | geometric IL_5TBW_105 NA | |
| IL_3JAI_136 | 1/5/4412:4416, 1/5/4426:4430 | No text annotation | homologous IL_8C3A_114 NA | |
| IL_3JAI_137 | 1/5/4453:4454, 1/5/4526:4528 | Major groove platform | homologous IL_8C3A_115 NA | |
| IL_3JAI_138 | 1/5/4456:4458, 1/5/4520:4524 | Isolated non-canonical cWW with bulges | geometric IL_5TBW_108 NA | |
| IL_3JAI_139 | 1/5/4458:4459, 1/5/4517:4520 | Multiple bulged bases | homologous IL_5TBW_109 NA | |
| IL_3JAI_140 | 1/5/4466:4468, 1/5/4489:4491 | Isolated non-canonical cWW pair | geometric IL_5TBW_110 NA | |
| IL_3JAI_276 | 1/5/4466:4470, 1/5/4485:4491 | No text annotation | ||
| IL_3JAI_141 | 1/5/4468:4470, 1/5/4485:4489 | No text annotation | geometric IL_3DD2_004 IL_55516.2 | |
| IL_3JAI_142 | 1/5/4472:4473, 1/5/4481:4483 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAI_143 | 1/5/4495:4497, 1/5/4503:4505 | Isolated non-canonical cWW pair | homologous IL_5TBW_112 NA | |
| IL_3JAI_144 | 1/5/4537:4538, 1/5/4547:4549 | Single bulged A | geometric IL_7RQB_101 NA | |
| IL_3JAI_277 | 1/5/4578:4582, 1/5/4721:4725 | No text annotation | ||
| IL_3JAI_145 | 1/5/4580:4582, 1/5/4721:4723 | Isolated cWH basepair | geometric IL_4E5C_001 IL_10167.6 | |
| IL_3JAI_146 | 1/5/4582:4585, 1/5/4717:4721 | Double sheared | homologous IL_8C3A_123 NA | |
| IL_3JAI_147 | 1/5/4590:4592, 1/5/4618:4620 | Isolated non-canonical cWW pair | homologous IL_8C3A_124 NA | |
| IL_3JAI_148 | 1/5/4596:4603, 1/5/4608:4614 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_8C3A_125 NA | |
| IL_3JAI_149 | 1/5/4624:4629, 1/5/4669:4673 | No text annotation | ||
| IL_3JAI_150 | 1/5/4632:4637, 1/5/4662:4666 | UAA/GAN related | homologous IL_5TBW_118 NA | |
| IL_3JAI_151 | 1/5/4638:4640, 1/5/4659:4661 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10167.6 | |
| IL_3JAI_152 | 1/5/4641:4642, 1/5/4655:4658 | Multiple bulged bases | homologous IL_5TBW_119 NA | |
| IL_3JAI_153 | 1/5/4681:4685, 1/5/4705:4709 | UAA/GAN | homologous IL_8C3A_129 NA | |
| IL_3JAI_154 | 1/5/4739:4743, 1/5/4957:4960 | No text annotation | geometric IL_4DB2_001 IL_68909.1 | |
| IL_3JAI_278 | 1/5/4739:4746, 1/5/4954:4960 | No text annotation | ||
| IL_3JAI_155 | 1/5/4743:4746, 1/5/4954:4957 | Tandem non-canonical cWW pairs | geometric IL_3WBM_002 IL_85033.2 | |
| IL_3JAI_156 | 1/5/4755:4766, 1/5/4868:4878 | No text annotation | ||
| IL_3JAI_279 | 1/5/4769:4772, 1/5/4863:4865 | No text annotation | geometric IL_8VTW_096 NA | |
| IL_3JAI_158 | 1/5/4885:4888, 1/5/4931:4934 | Tandem non-canonical cWW pairs | geometric IL_1MFQ_004 IL_85033.2 | |
| IL_3JAI_159 | 1/5/4891:4896, 1/5/4924:4928 | No text annotation | ||
| IL_3JAI_160 | 1/5/4899:4901, 1/5/4920:4921 | No text annotation | ||
| IL_3JAI_161 | 1/5/4966:4968, 1/5/5065:5066 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_3JAI_162 | 1/5/4972:4975, 1/5/4983:4986 | Tandem non-canonical cWW pairs | homologous IL_8C3A_135 NA | |
| IL_3JAI_163 | 1/5/4992:4994, 1/5/5057:5059 | Isolated non-canonical cWW pair | geometric IL_3HHN_004 IL_87907.2 | |
| IL_3JAI_164 | 1/5/4996:4997, 1/5/5053:5055 | Single bulged C | geometric IL_1KUQ_002 IL_61258.15 | |
| IL_3JAI_165 | 1/5/5000:5002, 1/5/5045:5050 | Isolated non-canonical cWW pair | homologous IL_5TBW_132 NA | |
| IL_3JAI_166 | 1/5/5003:5009, 1/5/5039:5044 | No text annotation | ||
| IL_3JAI_167 | 1/5/5012:5014, 1/5/5035:5036 | Single bulged U | homologous IL_8C3A_140 NA | |
| IL_3JAI_168 | 1/5/5014:5017, 1/5/5032:5035 | Double sheared | geometric IL_4V9F_100 IL_09705.15 | |
| IL_3JAI_169 | 1/7/15:16, 1/7/62:64 | Single bulged A | homologous IL_5TBW_372 NA | |
| IL_3JAI_170 | 1/7/21:27, 1/7/52:57 | Minor groove platform related | homologous IL_5TBW_373 NA | |
| IL_3JAI_171 | 1/7/28:29, 1/7/48:51 | Major groove minor groove platform; mini C-loop | homologous IL_7RQB_113 NA | |
| IL_3JAI_172 | 1/7/32:36, 1/7/41:45 | Symmetric double minor groove platform | geometric IL_7RQB_114 NA | |
| IL_3JAI_173 | 1/7/71:78, 1/7/98:104 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5TBW_377 NA | |
| IL_3JAI_174 | 1/7/79:81, 1/7/95:97 | Isolated non-canonical cWW pair | geometric IL_4Y1M_005 IL_07785.1 | |
| IL_3JAI_175 | 1/7/82:85, 1/7/92:94 | Isolated non-canonical cWW pair | homologous IL_5TBW_378 NA | |
| IL_3JAI_176 | 1/8/64:66, 1/8/92:95 | Isolated non-canonical cWW pair | geometric IL_5TBW_145 NA | |
| IL_3JAI_177 | 1/9/23:25, 1/9/649:651 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 IL_87907.2 | |
| IL_3JAI_178 | 1/9/34:36, 1/9/519:521 | Isolated non-canonical cWW pair | homologous IL_4V88_385 NA | |
| IL_3JAI_179 | 1/9/37:40, 1/9/514:518 | Double sheared | geometric IL_4WF9_016 IL_09705.15 | |
| IL_3JAI_180 | 1/9/41:47, 1/9/479:481 | No text annotation | homologous IL_4V88_387 NA | |
| IL_3JAI_181 | 1/9/49:51, 1/9/476:477 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_3JAI_182 | 1/9/57:62, 1/9/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_3JAI_183 | 1/9/63:68, 1/9/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_3JAI_184 | 1/9/108:110, 1/9/351:353 | Isolated non-canonical cWW pair | geometric IL_4TS2_004 IL_28037.2 | |
| IL_3JAI_185 | 1/9/110:112, 1/9/349:351 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_87907.2 | |
| IL_3JAI_186 | 1/9/112:115, 1/9/348:349 | Multiple bulged bases | homologous IL_4V88_392 NA | |
| IL_3JAI_187 | 1/9/116:121, 1/9/343:347 | No text annotation | homologous IL_4V88_393 NA | |
| IL_3JAI_188 | 1/9/145:151, 1/9/167:174 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_3JAI_189 | 1/9/152:154, 1/9/164:166 | Isolated cWH basepair | geometric IL_4KQ0_003 IL_10167.6 | |
| IL_3JAI_190 | 1/9/188:192, 1/9/207:211 | Triple sheared | geometric IL_4WFL_001 IL_17948.2 | |
| IL_3JAI_191 | 1/9/223:288, 1/9/295:298 | No text annotation | ||
| IL_3JAI_192 | 1/9/317:321, 1/9/330:333 | No text annotation | ||
| IL_3JAI_193 | 1/9/359:364, 1/9/396:403 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_3JAI_194 | 1/9/366:371, 1/9/393:394 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_3JAI_195 | 1/9/411:413, 1/9/424:429 | No text annotation | homologous IL_4V88_404 NA | |
| IL_3JAI_196 | 1/9/437:439, 1/9/454:456 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_3JAI_197 | 1/9/459:461, 1/9/468:470 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_3JAI_198 | 1/9/487:489, 1/9/511:512 | Single bulged U | geometric IL_4LFB_014 IL_89505.4 | |
| IL_3JAI_199 | 1/9/491:495, 1/9/508:509 | C-loop | geometric IL_5J7L_018 IL_03109.3 | |
| IL_3JAI_200 | 1/9/495:496, 1/9/506:508 | Single bulged G | geometric IL_5J7L_019 IL_00225.13 | |
| IL_3JAI_201 | 1/9/528:530, 1/9/554:557 | Isolated non-canonical cWW contact | geometric IL_5UNE_009 IL_44465.1 | |
| IL_3JAI_202 | 1/9/535:537, 1/9/546:549 | Isolated non-canonical cWW with bulges | geometric IL_4V9F_097 IL_07785.1 | |
| IL_3JAI_203 | 1/9/566:569, 1/9/581:584 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_77658.1 | |
| IL_3JAI_204 | 1/9/599:608, 1/9/635:637 | No text annotation | ||
| IL_3JAI_205 | 1/9/611:617, 1/9/624:632 | Kink-turn related | homologous IL_8C3A_425 NA | |
| IL_3JAI_206 | 1/9/663:665, 1/9/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_3JAI_207 | 1/9/665:671, 1/9/1161:1162 | No text annotation | geometric IL_4V88_416 NA | |
| IL_3JAI_208 | 1/9/673:675, 1/9/1030:1032 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_3JAI_209 | 1/9/676:680, 1/9/1025:1029 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_3JAI_210 | 1/9/692:694, 1/9/736:738 | Isolated non-canonical cWW pair | geometric IL_4M4O_001 IL_87907.2 | |
| IL_3JAI_211 | 1/9/694:696, 1/9/734:736 | Isolated non-canonical cWW pair | geometric IL_4E48_002 IL_87907.2 | |
| IL_3JAI_212 | 1/9/745:751, 1/9/791:796 | No text annotation | ||
| IL_3JAI_213 | 1/9/802:803, 1/9/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_3JAI_214 | 1/9/805:807, 1/9/856:858 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_3JAI_215 | 1/9/807:815, 1/9/849:856 | No text annotation | homologous IL_4V88_425 NA | |
| IL_3JAI_216 | 1/9/874:879, 1/9/907:911 | No text annotation | geometric IL_5TBW_121 NA | |
| IL_3JAI_217 | 1/9/922:923, 1/9/1019:1022 | Major groove platform; stack outside cWW | geometric IL_4V88_428 NA | |
| IL_3JAI_218 | 1/9/925:927, 1/9/1014:1017 | Isolated cWH basepair | geometric IL_3SJ2_002 IL_10167.6 | |
| IL_3JAI_219 | 1/9/928:931, 1/9/1010:1013 | Tandem non-canonical cWW pairs | geometric IL_4V88_430 NA | |
| IL_3JAI_220 | 1/9/931:935, 1/9/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_3JAI_221 | 1/9/942:945, 1/9/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_3JAI_289 | 1/9/942:946, 1/9/980:984 | Triple non-canonical cWW pairs | geometric IL_4LFB_065 IL_49751.4 | |
| IL_3JAI_222 | 1/9/952:956, 1/9/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_3JAI_223 | 1/9/1042:1047, 1/9/1071:1073 | Other IL | homologous IL_4V88_435 NA | |
| IL_3JAI_224 | 1/9/1047:1051, 1/9/1067:1071 | tSH-tHW-tHS | geometric IL_5J7L_037 IL_17136.7 | |
| IL_3JAI_225 | 1/9/1091:1093, 1/9/1152:1158 | No text annotation | homologous IL_4V88_437 NA | |
| IL_3JAI_226 | 1/9/1098:1101, 1/9/1131:1134 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_3JAI_227 | 1/9/1101:1103, 1/9/1129:1131 | Isolated non-canonical cWW pair | geometric IL_1YZ9_002 IL_87907.2 | |
| IL_3JAI_228 | 1/9/1108:1110, 1/9/1123:1124 | Minor groove platform | geometric IL_7RQB_032 NA | |
| IL_3JAI_229 | 1/9/1168:1175, 1/9/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_3JAI_230 | 1/9/1203:1204, 1/9/1694:1696 | Single bulged A | homologous IL_4V88_441 NA | |
| IL_3JAI_231 | 1/9/1206:1208, 1/9/1691:1692 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_3JAI_232 | 1/9/1214:1217, 1/9/1681:1685 | C-loop | homologous IL_4V88_443 NA | |
| IL_3JAI_233 | 1/9/1230:1232, 1/9/1526:1528 | Isolated non-canonical cWW pair | homologous IL_4V88_444 NA | |
| IL_3JAI_234 | 1/9/1235:1236, 1/9/1521:1523 | Minor groove platform | homologous IL_4V88_445 NA | |
| IL_3JAI_235 | 1/9/1270:1272, 1/9/1510:1512 | Isolated non-canonical cWW pair | homologous IL_4V88_446 NA | |
| IL_3JAI_236 | 1/9/1281:1291, 1/9/1307:1316 | No text annotation | ||
| IL_3JAI_237 | 1/9/1291:1294, 1/9/1305:1307 | No text annotation | ||
| IL_3JAI_238 | 1/9/1325:1327, 1/9/1502:1503 | Single bulged U | homologous IL_4V88_449 NA | |
| IL_3JAI_239 | 1/9/1329:1333, 1/9/1498:1500 | Isolated cWS basepair | geometric IL_4V88_450 NA | |
| IL_3JAI_283 | 1/9/1329:1335, 1/9/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_3JAI_240 | 1/9/1333:1335, 1/9/1492:1498 | Minor groove platform with extra cWW | homologous IL_4V88_451 NA | |
| IL_3JAI_241 | 1/9/1337:1338, 1/9/1488:1490 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_3JAI_242 | 1/9/1347:1349, 1/9/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_3JAI_243 | 1/9/1363:1365, 1/9/1374:1375 | Minor groove platform | geometric IL_5ML7_009 IL_51454.3 | |
| IL_3JAI_244 | 1/9/1395:1399, 1/9/1447:1450 | Tandem non-canonical cWW pairs | geometric IL_6JDV_002 IL_85033.2 | |
| IL_3JAI_245 | 1/9/1400:1401, 1/9/1444:1446 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_3JAI_284 | 1/9/1400:1405, 1/9/1441:1446 | No text annotation | ||
| IL_3JAI_246 | 1/9/1401:1405, 1/9/1441:1444 | No text annotation | ||
| IL_3JAI_290 | 1/9/1408:1413, 1/9/1433:1438 | No text annotation | ||
| IL_3JAI_285 | 1/9/1415:1419, 1/9/1428:1431 | Other IL | geometric IL_5TBW_064 NA | |
| IL_3JAI_249 | 1/9/1453:1456, 1/9/1470:1475 | No text annotation | ||
| IL_3JAI_250 | 1/9/1536:1537, 1/9/1595:1597 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAI_251 | 1/9/1537:1539, 1/9/1594:1595 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAI_286 | 1/9/1541:1550, 1/9/1582:1592 | No text annotation | ||
| IL_3JAI_252 | 1/9/1550:1558, 1/9/1577:1582 | No text annotation | ||
| IL_3JAI_253 | 1/9/1560:1562, 1/9/1573:1575 | Isolated non-canonical cWW pair | geometric IL_5TBW_016 NA | |
| IL_3JAI_254 | 1/9/1604:1610, 1/9/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_3JAI_255 | 1/9/1700:1702, 1/9/1833:1836 | No text annotation | geometric IL_4V88_463 NA | |
| IL_3JAI_256 | 1/9/1702:1705, 1/9/1829:1833 | No text annotation | homologous IL_4V88_464 NA | |
| IL_3JAI_257 | 1/9/1706:1708, 1/9/1826:1828 | Isolated non-canonical cWW pair | homologous IL_4V88_465 NA | |
| IL_3JAI_258 | 1/9/1708:1711, 1/9/1822:1826 | Tandem non-canonical cWW pairs | geometric IL_1JID_002 IL_85033.2 | |
| IL_3JAI_259 | 1/9/1714:1716, 1/9/1817:1819 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_3JAI_260 | 1/9/1717:1720, 1/9/1813:1816 | Double sheared | homologous IL_4V88_468 NA | |
| IL_3JAI_261 | 1/9/1720:1722, 1/9/1812:1813 | Single bulged U | geometric IL_4V88_469 NA | |
| IL_3JAI_262 | 1/9/1729:1731, 1/9/1803:1805 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_3JAI_263 | 1/9/1733:1736, 1/9/1798:1801 | Double sheared | homologous IL_4V88_471 NA | |
| IL_3JAI_264 | 1/9/1739:1741, 1/9/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_001 IL_87907.2 | |
| IL_3JAI_265 | 1/9/1742:1746, 1/9/1788:1792 | Triple sheared | homologous IL_4V88_474 NA | |
| IL_3JAI_266 | 1/9/1750:1751, 1/9/1782:1784 | No text annotation | ||
| IL_3JAI_287 | 1/9/1750:1752, 1/9/1780:1784 | Major groove platform with extra cWW | geometric IL_4V9F_028 IL_51387.2 | |
| IL_3JAI_267 | 1/9/1751:1752, 1/9/1780:1782 | Single stack bend | geometric IL_5J7L_249 IL_90729.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3JAI_030 | No text annotation | ||
| IL_3JAI_039 | No text annotation | ||
| IL_3JAI_271 | Tandem non-canonical cWW pairs | ||
| IL_3JAI_272 | Tandem non-canonical cWW pairs | ||
| IL_3JAI_275 | No text annotation | ||
| IL_3JAI_157 | Tandem non-canonical cWW pairs | ||
| IL_3JAI_280 | No text annotation | ||
| IL_3JAI_281 | No text annotation | ||
| IL_3JAI_282 | No text annotation | ||
| IL_3JAI_247 | No text annotation | ||
| IL_3JAI_248 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3JAI_001 | 1/5/112:116, 1/5/155:160, 1/5/275:278 | No text annotation | ||
| J3_3JAI_032 | 1/5/196:199, 1/5/215:228, 1/5/240:244 | No text annotation | ||
| J3_3JAI_033 | 1/5/351:367, 1/5/374:379, 1/8/21:24 | No text annotation | homologous J3_8P9A_045 J3_30040.2 | |
| J3_3JAI_002 | 1/5/380:387, 1/5/414:415, 1/8/19:20 | No text annotation | homologous J3_5TBW_002 NA | |
| J3_3JAI_034 | 1/5/380:390, 1/5/401:415, 1/8/19:20 | No text annotation | homologous J3_8C3A_049 NA | |
| J3_3JAI_003 | 1/5/448:455, 1/5/701:704, 1/5/1293:1298 | No text annotation | ||
| J3_3JAI_004 | 1/5/711:713, 1/5/955:976, 1/5/1278:1285 | No text annotation | ||
| J3_3JAI_005 | 1/5/1531:1537, 1/5/1622:1624, 1/5/1640:1643 | No text annotation | homologous J3_8C3A_003 NA | |
| J3_3JAI_006 | 1/5/1545:1548, 1/5/1580:1584, 1/5/1609:1614 | No text annotation | homologous J3_5TBW_005 NA | |
| J3_3JAI_035 | 1/5/1726:1727, 1/5/1802:1806, 1/5/1832:1836 | No text annotation | ||
| J3_3JAI_036 | 1/5/1965:1971, 1/5/1995:2001, 1/5/2016:2022 | No text annotation | ||
| J3_3JAI_007 | 1/5/2393:2399, 1/5/2805:2807, 1/5/2819:2822 | No text annotation | homologous J3_5TBW_008 NA | |
| J3_3JAI_008 | 1/5/2402:2405, 1/5/2785:2791, 1/5/2800:2802 | No text annotation | homologous J3_8C3A_007 NA | |
| J3_3JAI_009 | 1/5/2440:2445, 1/5/2515:2519, 1/5/2536:2537 | No text annotation | homologous J3_5TBW_010 NA | |
| J3_3JAI_037 | 1/5/2451:2456, 1/5/2465:2476, 1/5/2501:2508 | No text annotation | ||
| J3_3JAI_010 | 1/5/2549:2555, 1/5/2572:2575, 1/5/2757:2770 | No text annotation | ||
| J3_3JAI_011 | 1/5/2575:2576, 1/5/2585:2589, 1/5/2756:2757 | No text annotation | homologous J3_8C3A_054 NA | |
| J3_3JAI_038 | 1/5/2598:2602, 1/5/2737:2738, 1/5/2742:2747 | No text annotation | homologous J3_8C3A_055 NA | |
| J3_3JAI_012 | 1/5/3937:3939, 1/5/4074:4078, 1/5/4168:4173 | Kink-turn in J3 | geometric J3_5J7L_044 J3_89368.5 | |
| J3_3JAI_013 | 1/5/4091:4094, 1/5/4114:4129, 1/5/4155:4158 | No text annotation | homologous J3_8C3A_009 NA | |
| J3_3JAI_039 | 1/5/4228:4230, 1/5/4331:4342, 1/5/4370:4375 | No text annotation | homologous J3_8C3A_056 NA | |
| J3_3JAI_014 | 1/5/4241:4243, 1/5/4267:4269, 1/5/4278:4283 | No text annotation | homologous J3_5TBW_013 NA | |
| J3_3JAI_015 | 1/5/4463:4466, 1/5/4491:4493, 1/5/4507:4513 | No text annotation | homologous J3_5TBW_014 NA | |
| J3_3JAI_040 | 1/5/4748:4754, 1/5/4879:4884, 1/5/4935:4952 | No text annotation | ||
| J3_3JAI_016 | 1/5/4970:4972, 1/5/4986:4991, 1/5/5060:5063 | No text annotation | ||
| J3_3JAI_017 | 1/7/9:14, 1/7/65:66, 1/7/109:110 | No text annotation | homologous J3_5TBW_045 NA | |
| J3_3JAI_018 | 1/8/44:45, 1/8/58:64, 1/8/95:99 | No text annotation | homologous J3_8P9A_067 J3_35667.2 | |
| J3_3JAI_019 | 1/9/40:41, 1/9/481:487, 1/9/512:514 | No text annotation | geometric J3_4V88_078 NA | |
| J3_3JAI_041 | 1/9/40:47, 1/9/479:487, 1/9/512:514 | No text annotation | homologous J3_8P9A_069 J3_46317.4 | |
| J3_3JAI_020 | 1/9/682:685, 1/9/917:922, 1/9/1022:1023 | No text annotation | ||
| J3_3JAI_042 | 1/9/682:685, 1/9/917:923, 1/9/1019:1023 | No text annotation | ||
| J3_3JAI_021 | 1/9/816:819, 1/9/829:831, 1/9/843:848 | No text annotation | homologous J3_8P9A_073 J3_97642.1 | |
| J3_3JAI_022 | 1/9/938:941, 1/9/985:993, 1/9/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_3JAI_023 | 1/9/1094:1096, 1/9/1136:1140, 1/9/1147:1151 | No text annotation | ||
| J3_3JAI_024 | 1/9/1218:1221, 1/9/1645:1651, 1/9/1673:1680 | No text annotation | homologous J3_4V88_035 NA | |
| J3_3JAI_025 | 1/9/1225:1228, 1/9/1530:1532, 1/9/1638:1641 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_3JAI_026 | 1/9/1237:1244, 1/9/1255:1266, 1/9/1516:1520 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_3JAI_027 | 1/9/1272:1277, 1/9/1320:1324, 1/9/1504:1510 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_3JAI_028 | 1/9/1340:1345, 1/9/1384:1389, 1/9/1481:1486 | No text annotation | homologous J3_4V88_039 NA | |
| J3_3JAI_029 | 1/9/1350:1351, 1/9/1360:1363, 1/9/1375:1379 | No text annotation | homologous J3_8P9A_081 J3_76043.3 | |
| J3_3JAI_030 | 1/9/1391:1395, 1/9/1450:1453, 1/9/1475:1479 | No text annotation | ||
| J3_3JAI_043 | 1/9/1391:1395, 1/9/1450:1456, 1/9/1470:1479 | No text annotation | ||
| J3_3JAI_031 | 1/9/1532:1536, 1/9/1597:1604, 1/9/1635:1638 | No text annotation | homologous J3_4V88_041 NA | |
| J4_3JAI_001 | 1/2/7:10, 1/2/25:27, 1/2/43:49, 1/2/65:66 | tRNA junction | homologous J4_4WJ4_001 J4_70449.28 | |
| J4_3JAI_002 | 1/3/7:10, 1/3/25:27, 1/3/43:49, 1/3/65:66 | No text annotation | homologous J4_8VU0_001 J4_70449.28 | |
| J4_3JAI_003 | 1/5/111:112, 1/5/278:283, 1/5/304:310, 1/5/327:330 | No text annotation | homologous J4_8P9A_012 J4_45801.6 | |
| J4_3JAI_004 | 1/5/196:199, 1/5/215:222, 1/5/226:228, 1/5/240:244 | No text annotation | ||
| J4_3JAI_005 | 1/5/980:983, 1/5/1070:1074, 1/5/1236:1245, 1/5/1265:1274 | No text annotation | ||
| J4_3JAI_006 | 1/5/2365:2371, 1/5/2389:2391, 1/5/2824:2829, 1/5/3856:3857 | No text annotation | ||
| J4_3JAI_007 | 1/5/2406:2410, 1/5/2434:2439, 1/5/2538:2539, 1/5/2777:2784 | No text annotation | homologous J4_8C3A_004 NA | |
| J4_3JAI_008 | 1/5/2618:2619, 1/5/2637:2642, 1/5/2692:2698, 1/5/2718:2719 | No text annotation | ||
| J4_3JAI_009 | 1/5/3634:3638, 1/5/3650:3654, 1/5/3690:3694, 1/5/3821:3826 | No text annotation | homologous J4_8P9A_017 J4_07509.2 | |
| J4_3JAI_010 | 1/5/3696:3698, 1/5/3752:3754, 1/5/3770:3780, 1/5/3814:3819 | No text annotation | ||
| J4_3JAI_011 | 1/5/4231:4235, 1/5/4289:4291, 1/5/4318:4319, 1/5/4328:4330 | No text annotation | ||
| J4_3JAI_012 | 1/5/4231:4235, 1/5/4289:4293, 1/5/4317:4319, 1/5/4328:4330 | No text annotation | homologous J4_8C3A_008 NA | |
| J4_3JAI_013 | 1/5/4587:4590, 1/5/4620:4621, 1/5/4676:4678, 1/5/4712:4715 | No text annotation | ||
| J4_3JAI_014 | 1/9/98:106, 1/9/355:357, 1/9/405:409, 1/9/431:432 | No text annotation | homologous J4_8P9A_021 J4_15241.1 | |
| J4_3JAI_015 | 1/9/671:673, 1/9/1032:1037, 1/9/1078:1089, 1/9/1160:1161 | No text annotation | homologous J4_8C3A_022 NA | |
| J5_3JAI_001 | 1/5/20:21, 1/8/35:42, 1/8/101:106, 1/8/113:114, 1/8/136:137 | No text annotation | ||
| J5_3JAI_002 | 1/5/1335:1340, 1/5/1516:1519, 1/5/1658:1661, 1/5/2288:2290, 1/5/2345:2351 | No text annotation | homologous J5_8P9A_011 J5_63811.1 | |
| J5_3JAI_003 | 1/5/2855:2863, 1/5/2887:2888, 1/5/3613:3614, 1/5/3618:3626, 1/5/3835:3837 | No text annotation | homologous J5_8C3A_004 NA | |
| J5_3JAI_004 | 1/5/3903:3910, 1/5/4392:4400, 1/5/4444:4453, 1/5/4528:4534, 1/5/4552:4557 | No text annotation | ||
| J5_3JAI_005 | 1/5/3920:3923, 1/5/4188:4191, 1/5/4204:4205, 1/5/4227:4228, 1/5/4375:4381 | No text annotation | homologous J5_8C3A_006 NA | |
| J5_3JAI_006 | 1/9/30:34, 1/9/521:527, 1/9/558:565, 1/9/585:595, 1/9/641:644 | No text annotation | ||
| J5_3JAI_007 | 1/9/53:56, 1/9/89:96, 1/9/434:436, 1/9/457:459, 1/9/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_3JAI_010 | 1/9/124:144, 1/9/175:185, 1/9/214:219, 1/9/302:314, 1/9/336:339 | No text annotation | ||
| J5_3JAI_011 | 1/9/685:691, 1/9/739:744, 1/9/797:800, 1/9/865:873, 1/9/912:917 | No text annotation | ||
| J6_3JAI_001 | 1/5/21:26, 1/5/57:67, 1/5/74:78, 1/5/105:109, 1/5/332:339, 1/8/33:35 | No text annotation | ||
| J6_3JAI_002 | 1/5/1352:1355, 1/5/1384:1388, 1/5/1395:1399, 1/5/1418:1421, 1/5/1464:1466, 1/5/1499:1504 | No text annotation | ||
| J6_3JAI_003 | 1/5/3920:3923, 1/5/4188:4191, 1/5/4204:4205, 1/5/4227:4230, 1/5/4331:4342, 1/5/4370:4381 | No text annotation | ||
| J7_3JAI_001 | 1/5/1666:1671, 1/5/1684:1685, 1/5/1852:1855, 1/5/1879:1884, 1/5/1895:1899, 1/5/2077:2078, 1/5/2278:2283 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J5_3JAI_008 | No text annotation | ||
| J5_3JAI_009 | No text annotation |
Coloring options: