9BDN Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9BDN_001 | 1/A18S/7:17 | No text annotation | homologous HL_8C3A_192 NA | |
| HL_9BDN_002 | 1/A18S/69:80 | No text annotation | ||
| HL_9BDN_003 | 1/A18S/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_9BDN_004 | 1/A18S/197:202 | GNRA | geometric HL_4V88_218 NA | |
| HL_9BDN_005 | 1/A18S/288:295 | T-loop with 1 bulged base | geometric HL_4V88_191 NA | |
| HL_9BDN_007 | 1/A18S/377:387 | No text annotation | ||
| HL_9BDN_008 | 1/A18S/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_9BDN_009 | 1/A18S/441:452 | No text annotation | homologous HL_4V88_195 NA | |
| HL_9BDN_010 | 1/A18S/462:467 | UNCG | homologous HL_8C3A_202 NA | |
| HL_9BDN_011 | 1/A18S/498:504 | No text annotation | homologous HL_8C3A_203 NA | |
| HL_9BDN_012 | 1/A18S/539:544 | No text annotation | geometric HL_3SIU_002 HL_66103.1 | |
| HL_9BDN_013 | 1/A18S/569:581 | No text annotation | homologous HL_8C3A_205 NA | |
| HL_9BDN_014 | 1/A18S/618:623 | GNRA variation | homologous HL_8C3A_206 NA | |
| HL_9BDN_016 | 1/A18S/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_9BDN_132 | 1/A18S/885:901 | No text annotation | ||
| HL_9BDN_019 | 1/A18S/957:966 | No text annotation | homologous HL_4V88_206 NA | |
| HL_9BDN_020 | 1/A18S/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_9BDN_021 | 1/A18S/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_9BDN_022 | 1/A18S/1114:1119 | No text annotation | ||
| HL_9BDN_023 | 1/A18S/1141:1146 | GNRA | homologous HL_4V88_210 NA | |
| HL_9BDN_024 | 1/A18S/1178:1183 | GNRA | homologous HL_8C3A_216 NA | |
| HL_9BDN_025 | 1/A18S/1245:1254 | No text annotation | homologous HL_4V88_212 NA | |
| HL_9BDN_125 | 1/A18S/1294:1305 | No text annotation | ||
| HL_9BDN_026 | 1/A18S/1295:1304 | Anticodon loop related | homologous HL_4V88_213 NA | |
| HL_9BDN_027 | 1/A18S/1353:1358 | GNRA | homologous HL_4V88_214 NA | |
| HL_9BDN_028 | 1/A18S/1366:1373 | T-loop related | homologous HL_8C3A_220 NA | |
| HL_9BDN_030 | 1/A18S/1460:1466 | No text annotation | homologous HL_8C3A_222 NA | |
| HL_9BDN_031 | 1/A18S/1565:1570 | GNRA | geometric HL_5J7L_190 HL_37824.7 | |
| HL_9BDN_032 | 1/A18S/1614:1625 | No text annotation | homologous HL_4V88_219 NA | |
| HL_9BDN_033 | 1/A18S/1658:1666 | No text annotation | homologous HL_4V88_220 NA | |
| HL_9BDN_034 | 1/A18S/1847:1852 | GNRA variation | homologous HL_4V88_222 NA | |
| HL_9BDN_035 | 1/A28S/37:44 | No text annotation | geometric HL_5TBW_001 NA | |
| HL_9BDN_036 | 1/A28S/68:73 | No text annotation | homologous HL_8C3A_002 NA | |
| HL_9BDN_037 | 1/A28S/89:95 | No text annotation | homologous HL_5TBW_003 NA | |
| HL_9BDN_038 | 1/A28S/131:137 | No text annotation | geometric HL_2ZNI_001 HL_75660.5 | |
| HL_9BDN_039 | 1/A28S/204:211 | T-loop with 2 stacked bulged bases | homologous HL_8C3A_005 NA | |
| HL_9BDN_040 | 1/A28S/222:226 | No text annotation | homologous HL_5TBW_006 NA | |
| HL_9BDN_041 | 1/A28S/230:238 | T-loop with unstacked turn | homologous HL_5TBW_007 NA | |
| HL_9BDN_042 | 1/A28S/289:298 | No text annotation | homologous HL_8C3A_008 NA | |
| HL_9BDN_043 | 1/A28S/314:323 | Pseudoknot geometry | homologous HL_8C3A_009 NA | |
| HL_9BDN_044 | 1/A28S/368:373 | GNRA | homologous HL_8C3A_010 NA | |
| HL_9BDN_045 | 1/A28S/393:398 | GNRA | homologous HL_8C3A_011 NA | |
| HL_9BDN_047 | 1/A28S/758:905 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_9BDN_048 | 1/A28S/962:970 | No text annotation | geometric HL_2Y9H_003 HL_75660.5 | |
| HL_9BDN_133 | 1/A28S/1178:1183 | No text annotation | ||
| HL_9BDN_051 | 1/A28S/1317:1326 | T-loop with 2 stacked bulged bases | homologous HL_8C3A_014 NA | |
| HL_9BDN_126 | 1/A28S/1364:1373 | No text annotation | ||
| HL_9BDN_053 | 1/A28S/1389:1394 | GNRA | homologous HL_8C3A_016 NA | |
| HL_9BDN_054 | 1/A28S/1436:1448 | Pseudoknot geometry | geometric HL_4GXY_003 HL_65794.5 | |
| HL_9BDN_055 | 1/A28S/1479:1486 | No text annotation | geometric HL_8C3A_203 NA | |
| HL_9BDN_056 | 1/A28S/1561:1566 | GNRA | homologous HL_5TBW_019 NA | |
| HL_9BDN_057 | 1/A28S/1593:1602 | No text annotation | homologous HL_5TBW_020 NA | |
| HL_9BDN_058 | 1/A28S/1627:1635 | No text annotation | homologous HL_8C3A_021 NA | |
| HL_9BDN_059 | 1/A28S/1675:1680 | Externally structured | homologous HL_5TBW_022 NA | |
| HL_9BDN_060 | 1/A28S/1763:1769 | GNRA | geometric HL_5TBW_025 NA | |
| HL_9BDN_061 | 1/A28S/1816:1823 | No text annotation | geometric HL_5TBW_024 NA | |
| HL_9BDN_062 | 1/A28S/1864:1870 | GNRA | homologous HL_8C3A_025 NA | |
| HL_9BDN_063 | 1/A28S/1886:1893 | No text annotation | homologous HL_5TBW_026 NA | |
| HL_9BDN_064 | 1/A28S/1969:2018 | No text annotation | ||
| HL_9BDN_066 | 1/A28S/2317:2322 | GNRA | homologous HL_5TBW_030 NA | |
| HL_9BDN_127 | 1/A28S/2376:2384 | T-loop with 2 stacked bulged bases | homologous HL_8C3A_031 NA | |
| HL_9BDN_068 | 1/A28S/2420:2426 | Pseudoknot geometry with 3' bulge | homologous HL_5TBW_032 NA | |
| HL_9BDN_069 | 1/A28S/2458:2463 | GNRA variation | homologous HL_5TBW_033 NA | |
| HL_9BDN_070 | 1/A28S/2487:2491 | No text annotation | geometric HL_2Y8Y_001 HL_81100.2 | |
| HL_9BDN_071 | 1/A28S/2523:2532 | No text annotation | homologous HL_5TBW_035 NA | |
| HL_9BDN_072 | 1/A28S/2561:2566 | GNRA | geometric HL_3NKB_002 HL_37824.7 | |
| HL_9BDN_073 | 1/A28S/2578:2583 | GNRA | homologous HL_5TBW_036 NA | |
| HL_9BDN_074 | 1/A28S/2624:2632 | No text annotation | homologous HL_5TBW_037 NA | |
| HL_9BDN_075 | 1/A28S/2664:2670 | No text annotation | homologous HL_8C3A_038 NA | |
| HL_9BDN_076 | 1/A28S/2705:2710 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_9BDN_077 | 1/A28S/2738:2742 | No text annotation | homologous HL_8C3A_040 NA | |
| HL_9BDN_078 | 1/A28S/2792:2799 | No text annotation | homologous HL_5TBW_041 NA | |
| HL_9BDN_079 | 1/A28S/2810:2816 | GNRA | homologous HL_5TBW_042 NA | |
| HL_9BDN_080 | 1/A28S/2872:2877 | UNCG | homologous HL_8C3A_043 NA | |
| HL_9BDN_082 | 1/A28S/3614:3618 | No text annotation | homologous HL_8C3A_045 NA | |
| HL_9BDN_083 | 1/A28S/3639:3649 | No text annotation | homologous HL_5TBW_046 NA | |
| HL_9BDN_084 | 1/A28S/3668:3674 | GNRA | homologous HL_8C3A_047 NA | |
| HL_9BDN_085 | 1/A28S/3724:3729 | GNRA | homologous HL_5TBW_048 NA | |
| HL_9BDN_086 | 1/A28S/3757:3767 | No text annotation | homologous HL_5TBW_049 NA | |
| HL_9BDN_087 | 1/A28S/3796:3804 | No text annotation | homologous HL_8C3A_050 NA | |
| HL_9BDN_088 | 1/A28S/3873:3882 | No text annotation | homologous HL_5TBW_051 NA | |
| HL_9BDN_089 | 1/A28S/3975:4036 | No text annotation | geometric HL_8C3A_054 NA | |
| HL_9BDN_092 | 1/A28S/4193:4201 | No text annotation | homologous HL_5TBW_054 NA | |
| HL_9BDN_093 | 1/A28S/4210:4222 | No text annotation | homologous HL_5TBW_055 NA | |
| HL_9BDN_094 | 1/A28S/4250:4258 | No text annotation | homologous HL_8C3A_057 NA | |
| HL_9BDN_095 | 1/A28S/4270:4277 | Pseudoknot geometry | homologous HL_5TBW_057 NA | |
| HL_9BDN_096 | 1/A28S/4301:4309 | No text annotation | homologous HL_8C3A_059 NA | |
| HL_9BDN_097 | 1/A28S/4321:4326 | GNRA | homologous HL_8C3A_060 NA | |
| HL_9BDN_098 | 1/A28S/4352:4362 | No text annotation | geometric HL_4V83_139 NA | |
| HL_9BDN_099 | 1/A28S/4417:4425 | No text annotation | homologous HL_5TBW_061 NA | |
| HL_9BDN_100 | 1/A28S/4474:4481 | No text annotation | homologous HL_5TBW_062 NA | |
| HL_9BDN_101 | 1/A28S/4497:4503 | No text annotation | geometric HL_5TBW_063 NA | |
| HL_9BDN_102 | 1/A28S/4540:4545 | GNRA | homologous HL_5TBW_064 NA | |
| HL_9BDN_103 | 1/A28S/4603:4608 | GNRA | geometric HL_5J7L_197 HL_37824.7 | |
| HL_9BDN_104 | 1/A28S/4646:4651 | Ribsomal LSU H95 | homologous HL_8C3A_067 NA | |
| HL_9BDN_105 | 1/A28S/4688:4702 | No text annotation | homologous HL_8C3A_068 NA | |
| HL_9BDN_134 | 1/A28S/4906:4915 | No text annotation | ||
| HL_9BDN_108 | 1/A28S/4975:4983 | No text annotation | geometric HL_5J7L_201 HL_64690.6 | |
| HL_9BDN_110 | 1/A58S/47:56 | Pseudoknot with intercalation | geometric HL_4V9F_001 HL_93438.2 | |
| HL_9BDN_112 | 1/A58S/107:112 | No text annotation | homologous HL_5TBW_075 NA | |
| HL_9BDN_113 | 1/A58S/121:129 | No text annotation | geometric HL_5J7L_151 HL_80922.2 | |
| HL_9BDN_129 | 1/A5S/32:45 | No text annotation | homologous HL_8C3A_228 NA | |
| HL_9BDN_114 | 1/A5S/36:41 | No text annotation | homologous HL_8C3A_073 NA | |
| HL_9BDN_115 | 1/A5S/86:91 | GNRA | homologous HL_8C3A_074 NA | |
| HL_9BDN_116 | 1/ETRN/13:22 | tRNA D-loop | homologous HL_4V9K_033 HL_48417.5 | |
| HL_9BDN_117 | 1/ETRN/31:39 | tRNA anticodon loop | homologous HL_5UD5_002 HL_77082.1 | |
| HL_9BDN_118 | 1/ETRN/53:61 | T-loop with 2 stacked bulged bases | homologous HL_5UD5_003 HL_28252.8 | |
| HL_9BDN_119 | 1/PTRN/13:22 | No text annotation | homologous HL_6PMO_003 NA | |
| HL_9BDN_120 | 1/PTRN/31:39 | tRNA anticodon loop | homologous HL_5E81_212 HL_06059.6 | |
| HL_9BDN_121 | 1/PTRN/53:61 | T-loop with 2 stacked bulged bases | homologous HL_2BTE_004 HL_28252.8 | |
| HL_9BDN_131 | 1/TIRN/13:22 | No text annotation | homologous HL_7YSE_001 NA | |
| HL_9BDN_124 | 1/TIRN/53:61 | T-loop with 2 stacked bulged bases | homologous HL_4WT8_217 HL_28252.8 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9BDN_006 | No text annotation | ||
| HL_9BDN_015 | No text annotation | ||
| HL_9BDN_017 | No text annotation | ||
| HL_9BDN_018 | No text annotation | ||
| HL_9BDN_029 | No text annotation | ||
| HL_9BDN_046 | No text annotation | ||
| HL_9BDN_049 | No text annotation | ||
| HL_9BDN_050 | No text annotation | ||
| HL_9BDN_052 | No text annotation | ||
| HL_9BDN_065 | No text annotation | ||
| HL_9BDN_067 | No text annotation | ||
| HL_9BDN_081 | No text annotation | ||
| HL_9BDN_128 | No text annotation | ||
| HL_9BDN_090 | No text annotation | ||
| HL_9BDN_091 | No text annotation | ||
| HL_9BDN_106 | No text annotation | ||
| HL_9BDN_107 | No text annotation | ||
| HL_9BDN_109 | No text annotation | ||
| HL_9BDN_111 | No text annotation | ||
| HL_9BDN_130 | No text annotation | ||
| HL_9BDN_122 | No text annotation | ||
| HL_9BDN_123 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9BDN_001 | 1/A18S/23:25, 1/A18S/649:651 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 IL_87907.2 | |
| IL_9BDN_002 | 1/A18S/34:36, 1/A18S/519:521 | Isolated non-canonical cWW pair | homologous IL_8C3A_393 NA | |
| IL_9BDN_003 | 1/A18S/37:40, 1/A18S/514:518 | Double sheared | geometric IL_4WF9_016 IL_09705.15 | |
| IL_9BDN_004 | 1/A18S/41:47, 1/A18S/479:481 | No text annotation | homologous IL_8C3A_395 NA | |
| IL_9BDN_005 | 1/A18S/49:51, 1/A18S/476:477 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_9BDN_006 | 1/A18S/57:62, 1/A18S/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_9BDN_007 | 1/A18S/63:68, 1/A18S/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_9BDN_008 | 1/A18S/108:110, 1/A18S/351:353 | Isolated non-canonical cWW pair | geometric IL_1ZX7_004 NA | |
| IL_9BDN_009 | 1/A18S/110:112, 1/A18S/349:351 | Isolated non-canonical cWW pair | geometric IL_5TBW_110 NA | |
| IL_9BDN_010 | 1/A18S/112:115, 1/A18S/348:349 | Multiple bulged bases | homologous IL_4V88_392 NA | |
| IL_9BDN_011 | 1/A18S/116:121, 1/A18S/343:347 | No text annotation | homologous IL_4V88_393 NA | |
| IL_9BDN_012 | 1/A18S/145:151, 1/A18S/167:174 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_9BDN_013 | 1/A18S/152:154, 1/A18S/164:166 | Isolated cWH basepair | geometric IL_3CZW_001 IL_10167.6 | |
| IL_9BDN_014 | 1/A18S/188:192, 1/A18S/207:211 | Triple sheared | geometric IL_4WFL_001 IL_17948.2 | |
| IL_9BDN_015 | 1/A18S/216:219, 1/A18S/302:309 | No text annotation | ||
| IL_9BDN_017 | 1/A18S/312:314, 1/A18S/336:337 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_9BDN_018 | 1/A18S/317:319, 1/A18S/332:333 | No text annotation | ||
| IL_9BDN_272 | 1/A18S/317:320, 1/A18S/331:333 | No text annotation | homologous IL_8P9A_389 IL_15698.3 | |
| IL_9BDN_019 | 1/A18S/359:364, 1/A18S/396:403 | Kink-turn with non-sequential stacking | homologous IL_8C3A_410 NA | |
| IL_9BDN_020 | 1/A18S/366:371, 1/A18S/393:394 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_9BDN_021 | 1/A18S/411:413, 1/A18S/424:429 | No text annotation | homologous IL_4V88_404 NA | |
| IL_9BDN_022 | 1/A18S/437:439, 1/A18S/454:456 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_9BDN_023 | 1/A18S/459:461, 1/A18S/468:470 | Isolated non-canonical cWW pair | homologous IL_8C3A_414 NA | |
| IL_9BDN_024 | 1/A18S/487:489, 1/A18S/511:512 | Single bulged U | homologous IL_4V88_407 NA | |
| IL_9BDN_294 | 1/A18S/491:495, 1/A18S/508:509 | No text annotation | homologous IL_8P9A_397 IL_03109.3 | |
| IL_9BDN_295 | 1/A18S/495:496, 1/A18S/506:508 | Single bulged G | homologous IL_8P9A_398 IL_00225.13 | |
| IL_9BDN_026 | 1/A18S/529:530, 1/A18S/554:556 | Single bulged A | homologous IL_4V88_409 NA | |
| IL_9BDN_029 | 1/A18S/535:538, 1/A18S/545:549 | No text annotation | ||
| IL_9BDN_030 | 1/A18S/563:565, 1/A18S/585:592 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_9BDN_031 | 1/A18S/566:569, 1/A18S/581:584 | Tandem non-canonical cWW pairs | geometric IL_5C5W_001 IL_77658.1 | |
| IL_9BDN_032 | 1/A18S/599:608, 1/A18S/635:637 | No text annotation | ||
| IL_9BDN_033 | 1/A18S/611:617, 1/A18S/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_9BDN_034 | 1/A18S/663:665, 1/A18S/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_9BDN_296 | 1/A18S/665:671, 1/A18S/1161:1162 | No text annotation | homologous IL_8CRE_424 IL_38186.6 | |
| IL_9BDN_035 | 1/A18S/673:675, 1/A18S/1030:1032 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_9BDN_036 | 1/A18S/676:680, 1/A18S/1025:1029 | tSH-tHW-tHS | homologous IL_8C3A_428 NA | |
| IL_9BDN_037 | 1/A18S/690:692, 1/A18S/735:736 | Single stack bend | geometric IL_4V9F_081 IL_26793.1 | |
| IL_9BDN_297 | 1/A18S/691:694, 1/A18S/732:735 | No text annotation | geometric IL_8BH9_001 IL_51479.1 | |
| IL_9BDN_038 | 1/A18S/692:694, 1/A18S/732:735 | No text annotation | ||
| IL_9BDN_040 | 1/A18S/752:754, 1/A18S/790:791 | No text annotation | ||
| IL_9BDN_041 | 1/A18S/802:803, 1/A18S/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_9BDN_042 | 1/A18S/805:807, 1/A18S/856:858 | Isolated non-canonical cWW pair | homologous IL_8C3A_431 NA | |
| IL_9BDN_298 | 1/A18S/805:815, 1/A18S/849:858 | No text annotation | ||
| IL_9BDN_043 | 1/A18S/807:816, 1/A18S/848:856 | No text annotation | ||
| IL_9BDN_044 | 1/A18S/874:876, 1/A18S/910:912 | Isolated non-canonical cWW pair | geometric IL_4V88_417 NA | |
| IL_9BDN_045 | 1/A18S/877:879, 1/A18S/907:909 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 IL_87907.2 | |
| IL_9BDN_046 | 1/A18S/922:923, 1/A18S/1019:1022 | Major groove platform; stack outside cWW | homologous IL_4V88_428 NA | |
| IL_9BDN_275 | 1/A18S/925:926, 1/A18S/1015:1017 | Single bulged U | geometric IL_2PJP_001 IL_89505.4 | |
| IL_9BDN_048 | 1/A18S/928:931, 1/A18S/1010:1013 | Tandem non-canonical cWW pairs | homologous IL_4V88_430 NA | |
| IL_9BDN_049 | 1/A18S/931:935, 1/A18S/1007:1010 | Tandem non-canonical cWW pairs | geometric IL_4V88_431 NA | |
| IL_9BDN_050 | 1/A18S/942:945, 1/A18S/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_9BDN_051 | 1/A18S/952:956, 1/A18S/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_9BDN_052 | 1/A18S/1042:1047, 1/A18S/1071:1073 | Other IL | geometric IL_4V88_435 NA | |
| IL_9BDN_053 | 1/A18S/1047:1051, 1/A18S/1067:1071 | tSH-tHW-tHS | homologous IL_8C3A_442 NA | |
| IL_9BDN_054 | 1/A18S/1091:1093, 1/A18S/1152:1158 | No text annotation | homologous IL_8C3A_443 NA | |
| IL_9BDN_055 | 1/A18S/1098:1101, 1/A18S/1131:1134 | Tandem non-canonical cWW pairs | geometric IL_4V88_438 NA | |
| IL_9BDN_276 | 1/A18S/1098:1103, 1/A18S/1129:1134 | No text annotation | geometric IL_5TBW_476 NA | |
| IL_9BDN_056 | 1/A18S/1101:1103, 1/A18S/1129:1131 | Isolated non-canonical cWW pair | geometric IL_1YZ9_002 IL_87907.2 | |
| IL_9BDN_057 | 1/A18S/1108:1110, 1/A18S/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_9BDN_058 | 1/A18S/1168:1175, 1/A18S/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_9BDN_059 | 1/A18S/1203:1204, 1/A18S/1694:1696 | Single bulged A | homologous IL_4V88_441 NA | |
| IL_9BDN_060 | 1/A18S/1206:1208, 1/A18S/1691:1692 | Single bulged G | homologous IL_8C3A_448 NA | |
| IL_9BDN_061 | 1/A18S/1214:1217, 1/A18S/1681:1685 | C-loop | homologous IL_4V88_443 NA | |
| IL_9BDN_062 | 1/A18S/1230:1232, 1/A18S/1526:1528 | Isolated non-canonical cWW pair | homologous IL_4V88_444 NA | |
| IL_9BDN_063 | 1/A18S/1235:1236, 1/A18S/1521:1523 | Minor groove platform | homologous IL_4V88_445 NA | |
| IL_9BDN_064 | 1/A18S/1270:1272, 1/A18S/1510:1512 | Isolated non-canonical cWW pair | geometric IL_1Z7F_002 NA | |
| IL_9BDN_299 | 1/A18S/1281:1287, 1/A18S/1314:1316 | No text annotation | ||
| IL_9BDN_300 | 1/A18S/1281:1290, 1/A18S/1309:1316 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_9BDN_066 | 1/A18S/1287:1290, 1/A18S/1309:1314 | No text annotation | ||
| IL_9BDN_067 | 1/A18S/1291:1294, 1/A18S/1305:1308 | No text annotation | ||
| IL_9BDN_068 | 1/A18S/1325:1327, 1/A18S/1502:1503 | Single bulged U | homologous IL_4V88_449 NA | |
| IL_9BDN_069 | 1/A18S/1329:1333, 1/A18S/1498:1500 | No text annotation | homologous IL_8C3A_456 NA | |
| IL_9BDN_278 | 1/A18S/1329:1335, 1/A18S/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_9BDN_070 | 1/A18S/1333:1335, 1/A18S/1492:1498 | Minor groove platform with extra cWW | geometric IL_4V88_451 NA | |
| IL_9BDN_071 | 1/A18S/1337:1338, 1/A18S/1488:1490 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_9BDN_072 | 1/A18S/1347:1349, 1/A18S/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_9BDN_073 | 1/A18S/1363:1365, 1/A18S/1374:1375 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_9BDN_074 | 1/A18S/1395:1399, 1/A18S/1447:1450 | Tandem non-canonical cWW pairs | geometric IL_3WBM_003 IL_85033.2 | |
| IL_9BDN_076 | 1/A18S/1402:1405, 1/A18S/1441:1444 | Minor groove platform | geometric IL_4V88_456 NA | |
| IL_9BDN_078 | 1/A18S/1412:1413, 1/A18S/1427:1429 | Single bulged G | geometric IL_5J7L_019 IL_00225.13 | |
| IL_9BDN_079 | 1/A18S/1537:1539, 1/A18S/1594:1596 | Isolated non-canonical cWW pair | geometric IL_4NGF_002 IL_87907.2 | |
| IL_9BDN_301 | 1/A18S/1541:1550, 1/A18S/1582:1592 | No text annotation | ||
| IL_9BDN_080 | 1/A18S/1550:1558, 1/A18S/1577:1582 | 180 degree turn | geometric IL_5J7L_055 IL_11344.2 | |
| IL_9BDN_081 | 1/A18S/1560:1562, 1/A18S/1573:1575 | Isolated non-canonical cWW pair | homologous IL_8C3A_468 NA | |
| IL_9BDN_083 | 1/A18S/1604:1610, 1/A18S/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_9BDN_084 | 1/A18S/1700:1702, 1/A18S/1833:1836 | No text annotation | homologous IL_4V88_463 NA | |
| IL_9BDN_085 | 1/A18S/1702:1705, 1/A18S/1829:1833 | No text annotation | geometric IL_4V88_464 NA | |
| IL_9BDN_086 | 1/A18S/1706:1708, 1/A18S/1826:1828 | Isolated non-canonical cWW pair | homologous IL_4V88_465 NA | |
| IL_9BDN_087 | 1/A18S/1708:1711, 1/A18S/1822:1826 | No text annotation | geometric IL_6AZ4_001 NA | |
| IL_9BDN_088 | 1/A18S/1714:1716, 1/A18S/1817:1819 | Isolated non-canonical cWW pair | homologous IL_8C3A_474 NA | |
| IL_9BDN_089 | 1/A18S/1717:1720, 1/A18S/1813:1816 | Double sheared | geometric IL_4V88_468 NA | |
| IL_9BDN_090 | 1/A18S/1720:1722, 1/A18S/1812:1813 | Single bulged U | homologous IL_8C3A_476 NA | |
| IL_9BDN_091 | 1/A18S/1729:1731, 1/A18S/1803:1805 | Isolated non-canonical cWW pair | homologous IL_8C3A_477 NA | |
| IL_9BDN_092 | 1/A18S/1733:1736, 1/A18S/1798:1801 | Double sheared | homologous IL_8C3A_478 NA | |
| IL_9BDN_093 | 1/A18S/1739:1741, 1/A18S/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4Y1M_005 IL_07785.1 | |
| IL_9BDN_094 | 1/A18S/1742:1746, 1/A18S/1788:1792 | Triple sheared | homologous IL_8C3A_480 NA | |
| IL_9BDN_302 | 1/A18S/1750:1752, 1/A18S/1780:1784 | No text annotation | geometric IL_4V9F_053 IL_09990.4 | |
| IL_9BDN_097 | 1/A28S/6:7, 1/A58S/149:151 | Single bulged C | homologous IL_8C3A_002 NA | |
| IL_9BDN_098 | 1/A28S/12:14, 1/A58S/143:144 | Single bulged U | homologous IL_5TBW_003 NA | |
| IL_9BDN_099 | 1/A28S/16:18, 1/A58S/139:141 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_9BDN_100 | 1/A28S/26:27, 1/A28S/55:57 | No text annotation | homologous IL_8C3A_004 NA | |
| IL_9BDN_101 | 1/A28S/30:37, 1/A28S/44:52 | 9x8 Sarcin-Ricin; G-bulge | geometric IL_4WF9_008 IL_84694.2 | |
| IL_9BDN_102 | 1/A28S/81:88, 1/A28S/96:102 | No text annotation | homologous IL_8C3A_006 NA | |
| IL_9BDN_104 | 1/A28S/118:121, 1/A28S/152:153 | Stack outside cWW | geometric IL_5J7L_268 IL_56987.1 | |
| IL_9BDN_280 | 1/A28S/118:122, 1/A28S/147:153 | No text annotation | ||
| IL_9BDN_105 | 1/A28S/121:122, 1/A28S/147:152 | No text annotation | homologous IL_5TBW_007 NA | |
| IL_9BDN_106 | 1/A28S/125:126, 1/A28S/142:144 | Single bulged C | geometric IL_1S03_006 IL_61258.15 | |
| IL_9BDN_107 | 1/A28S/168:173, 1/A28S/263:267 | No text annotation | ||
| IL_9BDN_109 | 1/A28S/195:196, 1/A28S/244:246 | Single bulged C | geometric IL_1DQF_001 IL_61258.15 | |
| IL_9BDN_110 | 1/A28S/199:201, 1/A28S/214:215 | Single bulged U | homologous IL_8C3A_013 NA | |
| IL_9BDN_111 | 1/A28S/339:342, 1/A58S/32:33 | Minor groove platform | geometric IL_7RQB_073 NA | |
| IL_9BDN_112 | 1/A28S/348:350, 1/A58S/25:26 | Single bulged A | homologous IL_8C3A_014 NA | |
| IL_9BDN_113 | 1/A28S/387:390, 1/A28S/401:414 | No text annotation | homologous IL_5TBW_014 NA | |
| IL_9BDN_114 | 1/A28S/415:421, 1/A58S/13:19 | Triple sheared with non-canonical cWW | homologous IL_5TBW_015 NA | |
| IL_9BDN_115 | 1/A28S/443:446, 1/A28S/1300:1304 | No text annotation | geometric IL_7MLW_007 IL_99358.1 | |
| IL_9BDN_281 | 1/A28S/448:450, 1/A28S/1297:1298 | No text annotation | ||
| IL_9BDN_117 | 1/A28S/459:460, 1/A28S/695:697 | Single bulged C | geometric IL_1S03_002 IL_61258.15 | |
| IL_9BDN_118 | 1/A28S/462:464, 1/A28S/691:693 | Isolated non-canonical cWW pair | geometric IL_4J50_002 IL_87907.2 | |
| IL_9BDN_119 | 1/A28S/466:472, 1/A28S/682:689 | No text annotation | ||
| IL_9BDN_120 | 1/A28S/481:482, 1/A28S/672:673 | Single bulged C | geometric IL_4WF9_035 IL_61258.15 | |
| IL_9BDN_121 | 1/A28S/482:485, 1/A28S/671:672 | Multiple bulged bases | geometric IL_7V9E_001 NA | |
| IL_9BDN_122 | 1/A28S/487:488, 1/A28S/665:669 | Multiple bulged bases | geometric IL_1R3E_001 IL_84476.1 | |
| IL_9BDN_303 | 1/A28S/491:493, 1/A28S/661:662 | No text annotation | ||
| IL_9BDN_124 | 1/A28S/497:499, 1/A28S/656:657 | No text annotation | ||
| IL_9BDN_126 | 1/A28S/508:510, 1/A28S/649:650 | Single bulged A | geometric IL_6WPI_001 IL_31462.6 | |
| IL_9BDN_128 | 1/A28S/519:521, 1/A28S/641:642 | Single stack bend | geometric IL_5TBW_081 NA | |
| IL_9BDN_129 | 1/A28S/709:710, 1/A28S/1286:1288 | Single bulged G | geometric IL_4LFB_036 IL_00225.13 | |
| IL_9BDN_130 | 1/A28S/723:724, 1/A28S/942:945 | Multiple bulged bases | geometric IL_1R3E_001 IL_84476.1 | |
| IL_9BDN_131 | 1/A28S/727:731, 1/A28S/938:939 | No text annotation | ||
| IL_9BDN_132 | 1/A28S/732:735, 1/A28S/928:937 | No text annotation | ||
| IL_9BDN_133 | 1/A28S/737:739, 1/A28S/923:926 | No text annotation | geometric IL_5J7L_341 IL_42626.2 | |
| IL_9BDN_134 | 1/A28S/745:752, 1/A28S/911:919 | No text annotation | geometric IL_5TBW_020 NA | |
| IL_9BDN_135 | 1/A28S/1074:1076, 1/A28S/1234:1236 | Isolated non-canonical cWW pair | geometric IL_4LFB_061 NA | |
| IL_9BDN_304 | 1/A28S/1074:1080, 1/A28S/1219:1236 | No text annotation | ||
| IL_9BDN_136 | 1/A28S/1077:1081, 1/A28S/1218:1233 | No text annotation | ||
| IL_9BDN_137 | 1/A28S/1082:1084, 1/A28S/1213:1217 | Isolated cWS basepair | geometric IL_4TS2_003 NA | |
| IL_9BDN_138 | 1/A28S/1086:1087, 1/A28S/1209:1211 | Single bulged C | geometric IL_3W3S_001 IL_61258.15 | |
| IL_9BDN_139 | 1/A28S/1097:1098, 1/A28S/1197:1199 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_9BDN_285 | 1/A28S/1100:1168, 1/A28S/1193:1195 | No text annotation | ||
| IL_9BDN_141 | 1/A28S/1173:1175, 1/A28S/1186:1188 | Isolated cWH basepair | geometric IL_3W3S_003 IL_10167.6 | |
| IL_9BDN_142 | 1/A28S/1357:1360, 1/A28S/1379:1382 | No text annotation | ||
| IL_9BDN_286 | 1/A28S/1357:1361, 1/A28S/1376:1382 | No text annotation | ||
| IL_9BDN_143 | 1/A28S/1360:1361, 1/A28S/1376:1379 | Multiple bulged bases | geometric IL_1R3E_001 IL_84476.1 | |
| IL_9BDN_144 | 1/A28S/1425:1429, 1/A28S/1455:1460 | Triple sheared related | geometric IL_4V9F_018 IL_97631.1 | |
| IL_9BDN_145 | 1/A28S/1431:1434, 1/A28S/1450:1453 | Double sheared | geometric IL_4KZD_002 IL_09705.15 | |
| IL_9BDN_146 | 1/A28S/1467:1468, 1/A28S/1496:1498 | Single bulged A | homologous IL_8C3A_026 NA | |
| IL_9BDN_147 | 1/A28S/1474:1476, 1/A28S/1489:1490 | Single stack bend | geometric IL_7A0S_005 IL_90729.1 | |
| IL_9BDN_148 | 1/A28S/1520:1522, 1/A28S/1655:1657 | Isolated non-canonical cWW pair | geometric IL_5TBW_027 NA | |
| IL_9BDN_149 | 1/A28S/1522:1526, 1/A28S/1648:1655 | tHW-tHW cross-strand stack | homologous IL_5TBW_028 NA | |
| IL_9BDN_150 | 1/A28S/1550:1551, 1/A28S/1576:1578 | Single bulged G | homologous IL_8C3A_032 NA | |
| IL_9BDN_151 | 1/A28S/1551:1555, 1/A28S/1572:1576 | Triple sheared | geometric IL_4V9F_027 IL_50730.2 | |
| IL_9BDN_152 | 1/A28S/1586:1589, 1/A28S/1605:1607 | Major groove platform with extra cWW | homologous IL_8C3A_034 NA | |
| IL_9BDN_153 | 1/A28S/1590:1592, 1/A28S/1603:1604 | Single bulged U | homologous IL_8C3A_035 NA | |
| IL_9BDN_154 | 1/A28S/1624:1626, 1/A28S/1636:1640 | No text annotation | homologous IL_8C3A_036 NA | |
| IL_9BDN_155 | 1/A28S/1671:1673, 1/A28S/1682:1684 | Isolated non-canonical cWW pair | homologous IL_8C3A_037 NA | |
| IL_9BDN_156 | 1/A28S/1686:1688, 1/A28S/1848:1851 | No text annotation | ||
| IL_9BDN_157 | 1/A28S/1694:1721, 1/A28S/1841:1842 | No text annotation | ||
| IL_9BDN_158 | 1/A28S/1723:1725, 1/A28S/1838:1839 | Single bulged G | homologous IL_8C3A_040 NA | |
| IL_9BDN_159 | 1/A28S/1732:1737, 1/A28S/1792:1797 | 5x5 Sarcin-Ricin with intercalated A; G-bulge | geometric IL_7A0S_027 NA | |
| IL_9BDN_160 | 1/A28S/1737:1738, 1/A28S/1790:1792 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_9BDN_161 | 1/A28S/1739:1744, 1/A28S/1786:1789 | C-loop with bulged stacked A's | homologous IL_5TBW_040 NA | |
| IL_9BDN_162 | 1/A28S/1746:1749, 1/A28S/1781:1784 | Tandem non-canonical cWW pairs | geometric IL_5TBW_041 NA | |
| IL_9BDN_287 | 1/A28S/1746:1751, 1/A28S/1779:1784 | No text annotation | geometric IL_5TBW_476 NA | |
| IL_9BDN_163 | 1/A28S/1749:1751, 1/A28S/1779:1781 | Isolated non-canonical cWW pair | homologous IL_5TBW_042 NA | |
| IL_9BDN_305 | 1/A28S/1753:1756, 1/A28S/1776:1777 | Major groove platform | geometric IL_8DP3_001 IL_02555.1 | |
| IL_9BDN_306 | 1/A28S/1759:1761, 1/A28S/1772:1773 | No text annotation | ||
| IL_9BDN_166 | 1/A28S/1761:1763, 1/A28S/1769:1772 | No text annotation | ||
| IL_9BDN_167 | 1/A28S/1814:1816, 1/A28S/1823:1824 | Single bulged A | homologous IL_5TBW_045 NA | |
| IL_9BDN_168 | 1/A28S/1858:1860, 1/A28S/1874:1876 | Isolated non-canonical cWW pair | homologous IL_5TBW_046 NA | |
| IL_9BDN_170 | 1/A28S/1905:1909, 1/A28S/2067:2071 | UAA/GAN | homologous IL_5TBW_048 NA | |
| IL_9BDN_171 | 1/A28S/1911:1918, 1/A28S/2064:2065 | SSU/LSU pseudoknot | homologous IL_8C3A_052 NA | |
| IL_9BDN_172 | 1/A28S/1918:1920, 1/A28S/2063:2064 | No text annotation | ||
| IL_9BDN_173 | 1/A28S/1920:1922, 1/A28S/2062:2063 | No text annotation | ||
| IL_9BDN_174 | 1/A28S/1926:1933, 1/A28S/2053:2058 | No text annotation | homologous IL_5TBW_051 NA | |
| IL_9BDN_175 | 1/A28S/1933:1944, 1/A28S/2038:2053 | No text annotation | geometric IL_5TBW_052 NA | |
| IL_9BDN_176 | 1/A28S/1946:1948, 1/A28S/2035:2036 | Single bulged U | homologous IL_8C3A_056 NA | |
| IL_9BDN_307 | 1/A28S/1957:1965, 1/A28S/2022:2026 | Kink-turn | homologous IL_8CRE_057 IL_99692.2 | |
| IL_9BDN_179 | 1/A28S/2083:2085, 1/A28S/2272:2273 | Single bulged U | geometric IL_6CZR_156 NA | |
| IL_9BDN_180 | 1/A28S/2290:2292, 1/A28S/2342:2345 | Isolated cWS basepair | homologous IL_5TBW_057 NA | |
| IL_9BDN_181 | 1/A28S/2299:2301, 1/A28S/2334:2335 | Single bulged A | homologous IL_8C3A_062 NA | |
| IL_9BDN_182 | 1/A28S/2302:2309, 1/A28S/2329:2333 | Kink-turn | homologous IL_5TBW_059 NA | |
| IL_9BDN_183 | 1/A28S/2312:2314, 1/A28S/2325:2326 | Single bulged A | geometric IL_7RQB_033 NA | |
| IL_9BDN_184 | 1/A28S/2358:2364, 1/A28S/3858:3863 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5TBW_061 NA | |
| IL_9BDN_185 | 1/A28S/2415:2419, 1/A28S/2427:2429 | C-loop | geometric IL_7A0S_047 IL_83150.2 | |
| IL_9BDN_186 | 1/A28S/2446:2450, 1/A28S/2509:2514 | UAA/GAN | homologous IL_8C3A_067 NA | |
| IL_9BDN_308 | 1/A28S/2477:2479, 1/A28S/2499:2500 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_9BDN_188 | 1/A28S/2542:2547, 1/A28S/2772:2774 | Isolated non-canonical cWW pair | geometric IL_4RUM_001 IL_57744.1 | |
| IL_9BDN_189 | 1/A28S/2549:2550, 1/A28S/2768:2770 | Single bulged U | geometric IL_2A64_002 IL_89505.4 | |
| IL_9BDN_192 | 1/A28S/2589:2593, 1/A28S/2752:2756 | Triple sheared | homologous IL_5TBW_067 NA | |
| IL_9BDN_193 | 1/A28S/2613:2614, 1/A28S/2724:2726 | Single bulged C | homologous IL_5TBW_069 NA | |
| IL_9BDN_194 | 1/A28S/2614:2615, 1/A28S/2722:2724 | Single stack bend | geometric IL_5TBW_070 NA | |
| IL_9BDN_195 | 1/A28S/2646:2648, 1/A28S/2685:2688 | Isolated tHS basepair with bulges | geometric IL_4V9F_076 IL_85599.2 | |
| IL_9BDN_196 | 1/A28S/2651:2653, 1/A28S/2681:2682 | Single bulged G | geometric IL_7D7W_002 IL_00225.13 | |
| IL_9BDN_197 | 1/A28S/2656:2662, 1/A28S/2672:2678 | Kink-turn | homologous IL_5TBW_073 NA | |
| IL_9BDN_198 | 1/A28S/2704:2705, 1/A28S/2710:2712 | No text annotation | ||
| IL_9BDN_309 | 1/A28S/2832:2838, 1/A28S/3850:3853 | No text annotation | homologous IL_8P9A_302 IL_22829.2 | |
| IL_9BDN_200 | 1/A28S/2844:2846, 1/A28S/3842:3844 | No text annotation | homologous IL_8C3A_081 NA | |
| IL_9BDN_201 | 1/A28S/2847:2850, 1/A28S/3840:3841 | Major groove platform; stack outside cWW | geometric IL_5TBW_076 NA | |
| IL_9BDN_288 | 1/A28S/2847:2855, 1/A28S/3837:3841 | No text annotation | homologous IL_8C3A_484 NA | |
| IL_9BDN_202 | 1/A28S/2850:2855, 1/A28S/3837:3840 | No text annotation | homologous IL_8C3A_083 NA | |
| IL_9BDN_203 | 1/A28S/2867:2872, 1/A28S/2877:2883 | tSH-tSH-tHH-tHS | geometric IL_4V9F_063 IL_47346.2 | |
| IL_9BDN_204 | 1/A28S/2889:2891, 1/A28S/3610:3612 | Isolated non-canonical cWW pair | homologous IL_8C3A_085 NA | |
| IL_9BDN_205 | 1/A28S/2896:2897, 1/A28S/3602:3605 | No text annotation | homologous IL_8C3A_086 NA | |
| IL_9BDN_206 | 1/A28S/3632:3633, 1/A28S/3827:3829 | Single bulged A | homologous IL_5TBW_082 NA | |
| IL_9BDN_207 | 1/A28S/3660:3665, 1/A28S/3677:3684 | Kink-turn related | homologous IL_5TBW_083 NA | |
| IL_9BDN_208 | 1/A28S/3700:3703, 1/A28S/3749:3750 | No text annotation | homologous IL_8C3A_089 NA | |
| IL_9BDN_209 | 1/A28S/3704:3705, 1/A28S/3745:3748 | Multiple bulged bases | homologous IL_8C3A_090 NA | |
| IL_9BDN_210 | 1/A28S/3708:3710, 1/A28S/3741:3742 | Single stack bend | geometric IL_7A0S_054 IL_26793.1 | |
| IL_9BDN_289 | 1/A28S/3708:3714, 1/A28S/3739:3742 | No text annotation | ||
| IL_9BDN_211 | 1/A28S/3710:3714, 1/A28S/3739:3741 | No text annotation | homologous IL_8C3A_092 NA | |
| IL_9BDN_212 | 1/A28S/3715:3721, 1/A28S/3732:3738 | No text annotation | homologous IL_8C3A_093 NA | |
| IL_9BDN_213 | 1/A28S/3780:3781, 1/A28S/3811:3814 | Bulged stacked bases | homologous IL_5TBW_089 NA | |
| IL_9BDN_214 | 1/A28S/3781:3792, 1/A28S/3808:3811 | No text annotation | geometric IL_5TBW_090 NA | |
| IL_9BDN_215 | 1/A28S/3895:3898, 1/A28S/4563:4565 | Major groove platform with extra pair | homologous IL_5TBW_091 NA | |
| IL_9BDN_216 | 1/A28S/3900:3902, 1/A28S/4558:4561 | Major groove platform with intercalation | homologous IL_5TBW_092 NA | |
| IL_9BDN_217 | 1/A28S/3913:3915, 1/A28S/4388:4389 | Single bulged U | homologous IL_8C3A_098 NA | |
| IL_9BDN_218 | 1/A28S/3916:3917, 1/A28S/4384:4387 | Minor groove platform | homologous IL_5TBW_094 NA | |
| IL_9BDN_219 | 1/A28S/3927:3929, 1/A28S/4181:4184 | No text annotation | homologous IL_8C3A_100 NA | |
| IL_9BDN_220 | 1/A28S/3946:3952, 1/A28S/4060:4067 | No text annotation | ||
| IL_9BDN_310 | 1/A28S/3946:3973, 1/A28S/4038:4067 | No text annotation | ||
| IL_9BDN_221 | 1/A28S/3953:3969, 1/A28S/4052:4059 | No text annotation | ||
| IL_9BDN_222 | 1/A28S/3969:3974, 1/A28S/4037:4052 | No text annotation | ||
| IL_9BDN_223 | 1/A28S/4082:4088, 1/A28S/4161:4164 | No text annotation | homologous IL_8C3A_106 NA | |
| IL_9BDN_224 | 1/A28S/4191:4192, 1/A28S/4202:4204 | Single bulged A | homologous IL_5TBW_098 NA | |
| IL_9BDN_225 | 1/A28S/4243:4245, 1/A28S/4263:4267 | Isolated tHS basepair with bulges | homologous IL_5TBW_099 NA | |
| IL_9BDN_226 | 1/A28S/4291:4293, 1/A28S/4317:4318 | Single bulged A | geometric IL_5WWT_001 IL_31462.6 | |
| IL_9BDN_227 | 1/A28S/4295:4298, 1/A28S/4312:4315 | Tandem non-canonical cWW pairs | homologous IL_5TBW_100 NA | |
| IL_9BDN_228 | 1/A28S/4347:4350, 1/A28S/4364:4365 | Single stack bend | geometric IL_5J7L_032 IL_26793.1 | |
| IL_9BDN_229 | 1/A28S/4400:4401, 1/A28S/4442:4444 | Major groove platform | homologous IL_5TBW_102 NA | |
| IL_9BDN_230 | 1/A28S/4401:4403, 1/A28S/4440:4442 | Isolated non-canonical cWW pair | geometric IL_5TBW_103 NA | |
| IL_9BDN_231 | 1/A28S/4403:4405, 1/A28S/4439:4440 | Major groove platform | geometric IL_5TBW_104 NA | |
| IL_9BDN_232 | 1/A28S/4405:4407, 1/A28S/4435:4439 | Major groove minor groove platform with extra cWW | homologous IL_5TBW_105 NA | |
| IL_9BDN_233 | 1/A28S/4412:4416, 1/A28S/4426:4430 | No text annotation | homologous IL_8C3A_114 NA | |
| IL_9BDN_234 | 1/A28S/4453:4454, 1/A28S/4526:4528 | Major groove platform | homologous IL_5TBW_107 NA | |
| IL_9BDN_235 | 1/A28S/4456:4458, 1/A28S/4520:4524 | Isolated non-canonical cWW with bulges | homologous IL_5TBW_108 NA | |
| IL_9BDN_236 | 1/A28S/4458:4459, 1/A28S/4517:4520 | Multiple bulged bases | geometric IL_5TBW_109 NA | |
| IL_9BDN_237 | 1/A28S/4466:4468, 1/A28S/4489:4491 | Isolated non-canonical cWW pair | homologous IL_5TBW_110 NA | |
| IL_9BDN_291 | 1/A28S/4466:4470, 1/A28S/4485:4491 | No text annotation | ||
| IL_9BDN_238 | 1/A28S/4468:4470, 1/A28S/4485:4489 | No text annotation | geometric IL_3DD2_004 IL_55516.2 | |
| IL_9BDN_239 | 1/A28S/4495:4497, 1/A28S/4503:4505 | Isolated non-canonical cWW pair | homologous IL_5TBW_112 NA | |
| IL_9BDN_240 | 1/A28S/4537:4538, 1/A28S/4547:4549 | Single bulged A | geometric IL_7RQB_101 NA | |
| IL_9BDN_241 | 1/A28S/4580:4582, 1/A28S/4721:4723 | No text annotation | geometric IL_3ICQ_003 NA | |
| IL_9BDN_242 | 1/A28S/4582:4585, 1/A28S/4717:4721 | Double sheared | geometric IL_5TBW_114 NA | |
| IL_9BDN_243 | 1/A28S/4590:4592, 1/A28S/4618:4620 | Isolated non-canonical cWW pair | homologous IL_8C3A_124 NA | |
| IL_9BDN_244 | 1/A28S/4596:4603, 1/A28S/4608:4614 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_8C3A_125 NA | |
| IL_9BDN_245 | 1/A28S/4624:4629, 1/A28S/4669:4673 | No text annotation | ||
| IL_9BDN_246 | 1/A28S/4632:4637, 1/A28S/4662:4666 | UAA/GAN related | homologous IL_5TBW_118 NA | |
| IL_9BDN_247 | 1/A28S/4638:4640, 1/A28S/4659:4661 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10167.6 | |
| IL_9BDN_248 | 1/A28S/4641:4642, 1/A28S/4655:4658 | Multiple bulged bases | homologous IL_5TBW_119 NA | |
| IL_9BDN_249 | 1/A28S/4680:4685, 1/A28S/4705:4710 | UAA/GAN with extra cWW | geometric IL_5J7L_350 IL_49767.8 | |
| IL_9BDN_250 | 1/A28S/4740:4746, 1/A28S/4954:4959 | No text annotation | ||
| IL_9BDN_251 | 1/A28S/4756:4766, 1/A28S/4868:4877 | No text annotation | homologous IL_8P9A_352 IL_42231.1 | |
| IL_9BDN_252 | 1/A28S/4769:4773, 1/A28S/4862:4865 | Tandem non-canonical cWW pairs | geometric IL_3WBM_002 IL_85033.2 | |
| IL_9BDN_253 | 1/A28S/4885:4888, 1/A28S/4931:4934 | Tandem non-canonical cWW pairs | geometric IL_3TZR_003 IL_77658.1 | |
| IL_9BDN_292 | 1/A28S/4890:4902, 1/A28S/4919:4929 | No text annotation | ||
| IL_9BDN_254 | 1/A28S/4972:4975, 1/A28S/4983:4986 | Tandem non-canonical cWW pairs | homologous IL_8C3A_135 NA | |
| IL_9BDN_255 | 1/A28S/4992:4994, 1/A28S/5057:5059 | Isolated non-canonical cWW pair | geometric IL_3IVK_002 IL_87907.2 | |
| IL_9BDN_256 | 1/A28S/4996:4997, 1/A28S/5053:5055 | No text annotation | ||
| IL_9BDN_257 | 1/A28S/5000:5002, 1/A28S/5045:5050 | Isolated non-canonical cWW pair | homologous IL_5TBW_132 NA | |
| IL_9BDN_258 | 1/A28S/5003:5009, 1/A28S/5039:5044 | No text annotation | ||
| IL_9BDN_259 | 1/A28S/5012:5014, 1/A28S/5035:5036 | Single bulged C | geometric IL_6ZDP_001 IL_61258.15 | |
| IL_9BDN_260 | 1/A28S/5014:5017, 1/A28S/5032:5035 | Double sheared; A in syn | homologous IL_8C3A_141 NA | |
| IL_9BDN_293 | 1/A58S/64:66, 1/A58S/92:95 | No text annotation | homologous IL_8P9A_371 IL_07785.1 | |
| IL_9BDN_262 | 1/A5S/15:16, 1/A5S/62:64 | Single bulged A | homologous IL_8C3A_143 NA | |
| IL_9BDN_263 | 1/A5S/21:27, 1/A5S/52:57 | Minor groove platform related | homologous IL_5TBW_373 NA | |
| IL_9BDN_264 | 1/A5S/28:29, 1/A5S/48:51 | Major groove minor groove platform; mini C-loop | homologous IL_7RQB_113 NA | |
| IL_9BDN_265 | 1/A5S/32:36, 1/A5S/41:45 | Symmetric double minor groove platform | geometric IL_7RQB_114 NA | |
| IL_9BDN_266 | 1/A5S/71:78, 1/A5S/98:104 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_8C3A_148 NA | |
| IL_9BDN_267 | 1/A5S/79:81, 1/A5S/95:97 | Isolated non-canonical cWW pair | geometric IL_5TBW_034 NA | |
| IL_9BDN_268 | 1/A5S/82:85, 1/A5S/92:94 | Isolated non-canonical cWW pair | homologous IL_5TBW_378 NA | |
| IL_9BDN_271 | 1/TIRN/5:7, 1/TIRN/66:68 | No text annotation | homologous IL_5EL4_358 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9BDN_016 | No text annotation | ||
| IL_9BDN_025 | C-loop with extra cWW pair | ||
| IL_9BDN_027 | No text annotation | ||
| IL_9BDN_028 | Isolated non-canonical cWW pair | ||
| IL_9BDN_273 | No text annotation | ||
| IL_9BDN_039 | No text annotation | ||
| IL_9BDN_274 | No text annotation | ||
| IL_9BDN_047 | No text annotation | ||
| IL_9BDN_065 | No text annotation | ||
| IL_9BDN_277 | No text annotation | ||
| IL_9BDN_075 | No text annotation | ||
| IL_9BDN_077 | No text annotation | ||
| IL_9BDN_279 | No text annotation | ||
| IL_9BDN_082 | Isolated cWH basepair | ||
| IL_9BDN_095 | No text annotation | ||
| IL_9BDN_096 | Isolated non-canonical cWW pair | ||
| IL_9BDN_103 | Isolated non-canonical cWW pair | ||
| IL_9BDN_108 | No text annotation | ||
| IL_9BDN_116 | Isolated non-canonical cWW pair | ||
| IL_9BDN_123 | Isolated non-canonical cWW pair | ||
| IL_9BDN_282 | Tandem non-canonical cWW pairs | ||
| IL_9BDN_125 | Isolated non-canonical cWW pair | ||
| IL_9BDN_127 | Decoding loop related | ||
| IL_9BDN_283 | No text annotation | ||
| IL_9BDN_284 | Isolated non-canonical cWW pair | ||
| IL_9BDN_140 | No text annotation | ||
| IL_9BDN_164 | Major groove platform with extra cWW | ||
| IL_9BDN_165 | No text annotation | ||
| IL_9BDN_169 | No text annotation | ||
| IL_9BDN_177 | No text annotation | ||
| IL_9BDN_178 | No text annotation | ||
| IL_9BDN_187 | No text annotation | ||
| IL_9BDN_190 | No text annotation | ||
| IL_9BDN_191 | Isolated non-canonical cWW pair | ||
| IL_9BDN_199 | No text annotation | ||
| IL_9BDN_290 | No text annotation | ||
| IL_9BDN_261 | Other IL | ||
| IL_9BDN_269 | Isolated non-canonical cWW pair | ||
| IL_9BDN_270 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9BDN_023 | 1/A18S/40:41, 1/A18S/481:487, 1/A18S/512:514 | No text annotation | homologous J3_8C3A_082 NA | |
| J3_9BDN_024 | 1/A18S/682:685, 1/A18S/917:922, 1/A18S/1022:1023 | No text annotation | ||
| J3_9BDN_025 | 1/A18S/682:685, 1/A18S/917:923, 1/A18S/1019:1023 | No text annotation | ||
| J3_9BDN_001 | 1/A18S/816:819, 1/A18S/829:831, 1/A18S/843:848 | No text annotation | homologous J3_8P9A_073 J3_97642.1 | |
| J3_9BDN_002 | 1/A18S/938:941, 1/A18S/985:993, 1/A18S/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_9BDN_003 | 1/A18S/1094:1096, 1/A18S/1136:1140, 1/A18S/1147:1151 | No text annotation | ||
| J3_9BDN_004 | 1/A18S/1218:1221, 1/A18S/1645:1651, 1/A18S/1673:1680 | No text annotation | homologous J3_4V88_035 NA | |
| J3_9BDN_005 | 1/A18S/1225:1228, 1/A18S/1530:1532, 1/A18S/1638:1641 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_9BDN_006 | 1/A18S/1237:1244, 1/A18S/1255:1266, 1/A18S/1516:1520 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_9BDN_007 | 1/A18S/1272:1277, 1/A18S/1320:1324, 1/A18S/1504:1510 | No text annotation | homologous J3_4V88_038 NA | |
| J3_9BDN_008 | 1/A18S/1340:1345, 1/A18S/1384:1389, 1/A18S/1481:1486 | No text annotation | homologous J3_8P9A_080 J3_99563.1 | |
| J3_9BDN_026 | 1/A18S/1350:1351, 1/A18S/1360:1363, 1/A18S/1375:1379 | No text annotation | homologous J3_8P9A_081 J3_76043.3 | |
| J3_9BDN_009 | 1/A18S/1391:1395, 1/A18S/1450:1456, 1/A18S/1470:1479 | No text annotation | ||
| J3_9BDN_010 | 1/A18S/1532:1536, 1/A18S/1597:1604, 1/A18S/1635:1638 | No text annotation | homologous J3_8P9A_084 J3_37047.6 | |
| J3_9BDN_011 | 1/A28S/112:116, 1/A28S/155:160, 1/A28S/275:278 | No text annotation | ||
| J3_9BDN_027 | 1/A28S/351:367, 1/A28S/374:379, 1/A58S/21:24 | No text annotation | homologous J3_8P9A_045 J3_30040.2 | |
| J3_9BDN_028 | 1/A28S/380:387, 1/A28S/414:415, 1/A58S/19:20 | No text annotation | geometric J3_4WF9_010 J3_60031.2 | |
| J3_9BDN_029 | 1/A28S/380:390, 1/A28S/401:415, 1/A58S/19:20 | No text annotation | homologous J3_8C3A_049 NA | |
| J3_9BDN_030 | 1/A28S/451:455, 1/A28S/701:705, 1/A28S/1292:1296 | No text annotation | ||
| J3_9BDN_012 | 1/A28S/1531:1537, 1/A28S/1622:1624, 1/A28S/1640:1643 | No text annotation | homologous J3_8C3A_003 NA | |
| J3_9BDN_013 | 1/A28S/1545:1548, 1/A28S/1580:1584, 1/A28S/1609:1614 | No text annotation | homologous J3_5TBW_005 NA | |
| J3_9BDN_031 | 1/A28S/1726:1727, 1/A28S/1802:1806, 1/A28S/1832:1837 | No text annotation | homologous J3_8P9A_051 J3_09667.1 | |
| J3_9BDN_014 | 1/A28S/2393:2399, 1/A28S/2805:2807, 1/A28S/2819:2822 | No text annotation | homologous J3_5TBW_008 NA | |
| J3_9BDN_015 | 1/A28S/2402:2405, 1/A28S/2785:2791, 1/A28S/2800:2802 | No text annotation | homologous J3_8C3A_007 NA | |
| J3_9BDN_032 | 1/A28S/2440:2445, 1/A28S/2515:2519, 1/A28S/2536:2537 | No text annotation | homologous J3_8P9A_055 J3_31965.2 | |
| J3_9BDN_033 | 1/A28S/2451:2456, 1/A28S/2465:2476, 1/A28S/2501:2508 | No text annotation | ||
| J3_9BDN_016 | 1/A28S/2551:2555, 1/A28S/2572:2575, 1/A28S/2757:2767 | No text annotation | ||
| J3_9BDN_034 | 1/A28S/2598:2602, 1/A28S/2737:2738, 1/A28S/2742:2747 | No text annotation | homologous J3_8C3A_055 NA | |
| J3_9BDN_017 | 1/A28S/3937:3939, 1/A28S/4074:4078, 1/A28S/4168:4173 | No text annotation | geometric J3_7A0S_009 J3_89368.5 | |
| J3_9BDN_018 | 1/A28S/4091:4094, 1/A28S/4114:4129, 1/A28S/4155:4158 | No text annotation | homologous J3_8P9A_060 J3_28639.1 | |
| J3_9BDN_035 | 1/A28S/4228:4230, 1/A28S/4331:4342, 1/A28S/4370:4375 | No text annotation | homologous J3_8C3A_056 NA | |
| J3_9BDN_019 | 1/A28S/4241:4243, 1/A28S/4267:4269, 1/A28S/4278:4283 | No text annotation | homologous J3_8P9A_062 J3_61124.2 | |
| J3_9BDN_020 | 1/A28S/4463:4466, 1/A28S/4491:4493, 1/A28S/4507:4513 | No text annotation | homologous J3_8P9A_063 J3_62630.1 | |
| J3_9BDN_036 | 1/A28S/4749:4754, 1/A28S/4879:4883, 1/A28S/4936:4951 | No text annotation | ||
| J3_9BDN_021 | 1/A28S/4970:4972, 1/A28S/4986:4991, 1/A28S/5060:5063 | No text annotation | ||
| J3_9BDN_037 | 1/A58S/44:45, 1/A58S/58:64, 1/A58S/95:99 | No text annotation | homologous J3_8C3A_060 NA | |
| J3_9BDN_038 | 1/A5S/9:14, 1/A5S/65:66, 1/A5S/109:110 | No text annotation | homologous J3_8P9A_066 J3_12003.2 | |
| J4_9BDN_001 | 1/A18S/98:106, 1/A18S/355:357, 1/A18S/405:409, 1/A18S/431:432 | No text annotation | homologous J4_8C3A_021 NA | |
| J4_9BDN_016 | 1/A18S/671:673, 1/A18S/1032:1037, 1/A18S/1078:1089, 1/A18S/1160:1161 | No text annotation | homologous J4_8P9A_022 J4_61885.6 | |
| J4_9BDN_003 | 1/A28S/111:112, 1/A28S/278:283, 1/A28S/304:310, 1/A28S/327:330 | No text annotation | homologous J4_8P9A_012 J4_45801.6 | |
| J4_9BDN_004 | 1/A28S/196:199, 1/A28S/215:222, 1/A28S/226:228, 1/A28S/240:244 | No text annotation | ||
| J4_9BDN_005 | 1/A28S/2365:2371, 1/A28S/2389:2391, 1/A28S/2824:2829, 1/A28S/3856:3857 | No text annotation | ||
| J4_9BDN_006 | 1/A28S/2406:2410, 1/A28S/2434:2439, 1/A28S/2538:2539, 1/A28S/2777:2784 | No text annotation | homologous J4_8C3A_004 NA | |
| J4_9BDN_007 | 1/A28S/2551:2555, 1/A28S/2572:2576, 1/A28S/2585:2589, 1/A28S/2756:2767 | No text annotation | ||
| J4_9BDN_008 | 1/A28S/2618:2619, 1/A28S/2637:2642, 1/A28S/2692:2698, 1/A28S/2718:2719 | No text annotation | ||
| J4_9BDN_009 | 1/A28S/3634:3638, 1/A28S/3650:3654, 1/A28S/3690:3694, 1/A28S/3821:3826 | No text annotation | homologous J4_8P9A_017 J4_07509.2 | |
| J4_9BDN_010 | 1/A28S/3696:3698, 1/A28S/3752:3753, 1/A28S/3771:3780, 1/A28S/3814:3819 | No text annotation | homologous J4_8C3A_007 NA | |
| J4_9BDN_017 | 1/A28S/4231:4235, 1/A28S/4289:4291, 1/A28S/4318:4319, 1/A28S/4328:4330 | No text annotation | ||
| J4_9BDN_012 | 1/A28S/4587:4590, 1/A28S/4620:4621, 1/A28S/4676:4678, 1/A28S/4712:4715 | No text annotation | ||
| J4_9BDN_018 | 1/ETRN/7:10, 1/ETRN/25:27, 1/ETRN/43:49, 1/ETRN/65:66 | No text annotation | homologous J4_6JXM_001 J4_70449.28 | |
| J4_9BDN_014 | 1/PTRN/7:10, 1/PTRN/25:27, 1/PTRN/43:49, 1/PTRN/65:66 | tRNA junction | homologous J4_1IL2_001 J4_70449.28 | |
| J4_9BDN_015 | 1/TIRN/7:10, 1/TIRN/25:27, 1/TIRN/43:49, 1/TIRN/65:66 | No text annotation | homologous J4_7EQJ_002 J4_70449.28 | |
| J5_9BDN_001 | 1/A18S/30:34, 1/A18S/521:527, 1/A18S/558:563, 1/A18S/592:595, 1/A18S/641:644 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_9BDN_002 | 1/A18S/30:34, 1/A18S/521:527, 1/A18S/558:565, 1/A18S/585:595, 1/A18S/641:644 | No text annotation | ||
| J5_9BDN_003 | 1/A18S/53:56, 1/A18S/89:96, 1/A18S/434:436, 1/A18S/457:461, 1/A18S/468:474 | No text annotation | ||
| J5_9BDN_004 | 1/A28S/19:21, 1/A58S/35:42, 1/A58S/101:106, 1/A58S/113:114, 1/A58S/136:138 | No text annotation | homologous J5_8P9A_010 J5_01737.2 | |
| J5_9BDN_005 | 1/A28S/1335:1340, 1/A28S/1516:1519, 1/A28S/1658:1661, 1/A28S/2288:2290, 1/A28S/2345:2351 | No text annotation | homologous J5_8P9A_011 J5_63811.1 | |
| J5_9BDN_006 | 1/A28S/2855:2863, 1/A28S/2887:2888, 1/A28S/3613:3614, 1/A28S/3618:3626, 1/A28S/3835:3837 | No text annotation | homologous J5_8C3A_004 NA | |
| J5_9BDN_007 | 1/A28S/3903:3910, 1/A28S/4392:4400, 1/A28S/4444:4453, 1/A28S/4528:4534, 1/A28S/4552:4557 | No text annotation | ||
| J5_9BDN_008 | 1/A28S/3920:3923, 1/A28S/4188:4191, 1/A28S/4204:4205, 1/A28S/4227:4228, 1/A28S/4375:4381 | No text annotation | homologous J5_8P9A_015 J5_08912.1 | |
| J6_9BDN_001 | 1/A28S/21:26, 1/A28S/57:67, 1/A28S/74:78, 1/A28S/105:109, 1/A28S/332:339, 1/A58S/33:35 | No text annotation | ||
| J6_9BDN_002 | 1/A28S/1352:1355, 1/A28S/1384:1388, 1/A28S/1395:1399, 1/A28S/1418:1421, 1/A28S/1464:1466, 1/A28S/1499:1504 | No text annotation | ||
| J6_9BDN_003 | 1/A28S/3920:3923, 1/A28S/4188:4191, 1/A28S/4204:4205, 1/A28S/4227:4230, 1/A28S/4331:4342, 1/A28S/4370:4381 | No text annotation | ||
| J7_9BDN_001 | 1/A28S/1666:1671, 1/A28S/1684:1685, 1/A28S/1852:1855, 1/A28S/1879:1884, 1/A28S/1895:1899, 1/A28S/2077:2078, 1/A28S/2278:2283 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9BDN_022 | No text annotation | ||
| J4_9BDN_002 | No text annotation | ||
| J4_9BDN_011 | No text annotation | ||
| J4_9BDN_013 | No text annotation |
Coloring options: