RNA 3D Hub //

4V6I Internal, Hairpin and 3-way Junction Loop Motifs

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Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/CA/7:17NANA
1/CA/154:160NANA
1/CA/226:232
geometric
HL_361D_002		NA

HL_18218.2*
1/CA/275:281NANA
1/CA/329:339
geometric
HL_4WSM_226		NA

HL_87219.4*
1/CA/368:373
homologous
HL_4V88_194		NA

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

HL_22443.1*
1/CA/414:419
geometric
HL_5U3G_001		NA

HL_40469.1*
1/CA/450:456NANA
1/CA/491:496
geometric
HL_5U3G_001		NA

HL_40469.1*
1/CA/568:575NANA
1/CA/663:669
geometric
HL_5NFV_001		NA

HL_58912.1*
1/CA/827:845NANA
1/CA/899:910NANA
1/CA/937:942Other HL
homologous
HL_4V88_207		NA

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

HL_87219.4*
1/CA/1057:1062NANA
1/CA/1084:1089Other HL
homologous
HL_4V88_210		NA

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

HL_43074.18*
1/CA/1233:1246NANA
1/CA/1296:1301GNRA
homologous
HL_4V88_214		NA

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

HL_54035.7*
1/CA/1395:1403NANA
1/CA/1501:1506GNRA
homologous
HL_4V88_218		NA

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

HL_32458.3*
1/CA/1592:1604NANA
1/CA/1698:1703
geometric
HL_5M3H_001		NA

HL_35894.3*
1/CA/1778:1783Other HL
homologous
HL_4V88_222		NA

HL_43074.18*
1/CB/13:22NANA
1/CB/31:39NANA
1/CB/52:60NANA
1/DA/38:45
homologous
HL_5TBW_001		NA

HL_23481.5*
1/DA/69:74NANA
1/DA/90:96
homologous
HL_5TBW_003		NA

HL_67216.5*
1/DA/132:136NANA
1/DA/194:201T-loop with 1 bulged base
homologous
HL_5TBW_005		NA

HL_68493.6*
1/DA/216:224NANA
1/DA/278:287
homologous
HL_5TBW_008		NA

HL_54035.7*
1/DA/303:312
homologous
HL_5TBW_009		NA

HL_46142.8*
1/DA/357:362Other HL
homologous
HL_5TBW_010		NA

HL_43074.18*
1/DA/382:387GNRA
homologous
HL_5TBW_011		NA

HL_43074.18*
1/DA/463:468
geometric
HL_4WF9_003		NA

HL_62869.3*
1/DA/543:548NANA
1/DA/599:604GNRA
homologous
HL_5TBW_013		NA

HL_43074.18*
1/DA/640:649T-loop with 2 stacked bulged bases
homologous
HL_5TBW_014		NA

HL_33239.17*
1/DA/687:693NANA
1/DA/707:712GNRA
homologous
HL_5TBW_016		NA

HL_43074.18*
1/DA/732:737
geometric
HL_361D_002		NA

HL_18218.2*
1/DA/763:768NANA
1/DA/844:849GNRA
homologous
HL_5TBW_019		NA

HL_43074.18*
1/DA/876:885
homologous
HL_5TBW_020		NA

HL_39334.5*
1/DA/910:918
geometric
HL_6CF2_001		NA

HL_80105.3*
1/DA/957:964
geometric
HL_361D_002		NA

HL_18218.2*
1/DA/1076:1083NANA
1/DA/1126:1132GNRA
homologous
HL_5TBW_025		NA

HL_43074.18*
1/DA/1148:1155
homologous
HL_5TBW_026		NA

HL_72451.5*
1/DA/1239:1249
homologous
HL_5TBW_139		NA
1/DA/1267:1274
homologous
HL_5TBW_140		NA
1/DA/1403:1408GNRA
geometric
HL_3W3S_003		NA

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

HL_33239.17*
1/DA/1506:1512
homologous
HL_5TBW_032		NA

HL_86880.5*
1/DA/1544:1549Other HL
homologous
HL_5TBW_033		NA

HL_43074.18*
1/DA/1565:1574NANA
1/DA/1599:1608
homologous
HL_5TBW_035		NA

HL_78457.4*
1/DA/1679:1689NANA
1/DA/1719:1725Other HL
geometric
HL_4V9F_039		NA

HL_68493.6*
1/DA/1760:1765Other HL
geometric
HL_4Y1M_004		NA

HL_43074.18*
1/DA/1792:1796
homologous
HL_5TBW_040		NA

HL_69353.7*
1/DA/1844:1851
homologous
HL_5TBW_041		NA

HL_66171.3*
1/DA/1862:1868NANA
1/DA/1923:1928UNCG
homologous
HL_5TBW_043		NA

HL_79299.11*
1/DA/2008:2013
geometric
HL_2Y9H_003		NA

HL_98557.5*
1/DA/2065:2071
geometric
HL_3IGI_004		NA

HL_91287.1*
1/DA/2110:2114
geometric
HL_4V9F_046		NA

HL_79272.3*
1/DA/2135:2145
homologous
HL_5TBW_046		NA

HL_43613.4*
1/DA/2220:2225Other HL
homologous
HL_5TBW_048		NA

HL_43074.18*
1/DA/2253:2263
homologous
HL_5TBW_049		NA

HL_98248.1*
1/DA/2292:2300
homologous
HL_5TBW_050		NA

HL_53760.4*
1/DA/2369:2378
homologous
HL_5TBW_051		NA

HL_90642.5*
1/DA/2470:2475NANA
1/DA/2536:2543
geometric
HL_7A0S_056		NA

HL_93727.5*
1/DA/2568:2573
geometric
HL_4YAZ_004		NA

HL_57052.3*
1/DA/2616:2624
homologous
HL_5TBW_054		NA

HL_46891.3*
1/DA/2633:2645NANA
1/DA/2673:2681NANA
1/DA/2693:2700
homologous
HL_5TBW_057		NA

HL_46142.8*
1/DA/2724:2732NANA
1/DA/2744:2749GNRA
homologous
HL_5TBW_059		NA

HL_43074.18*
1/DA/2776:2784
homologous
HL_5TBW_060		NA

HL_46142.8*
1/DA/2840:2848
homologous
HL_5TBW_061		NA

HL_36421.5*
1/DA/2897:2904
homologous
HL_5TBW_062		NA

HL_92681.5*
1/DA/2920:2926
geometric
HL_5TBW_063		NA

HL_26055.6*
1/DA/2963:2968GNRA
homologous
HL_5TBW_064		NA

HL_43074.18*
1/DA/3025:3030GNRA
geometric
HL_5J7L_197		NA

HL_43074.18*
1/DA/3068:3073Ribsomal LSU H95
homologous
HL_5TBW_066		NA

HL_67719.1*
1/DA/3110:3124
homologous
HL_5TBW_067		NA

HL_56677.5*
1/DA/3214:3219NANA
1/DA/3240:3247NANA
1/DA/3303:3311
homologous
HL_5TBW_070		NA

HL_05018.6*
1/DA/3349:3356
geometric
HL_4WF9_041		NA

HL_93727.5*
1/DB/47:56
geometric
HL_4V9F_001		NA

HL_55136.1*
1/DB/109:113
geometric
HL_5TBW_006		NA

HL_98557.5*
1/DB/123:130
geometric
HL_6CF2_001		NA

HL_80105.3*
1/DC/36:41NANA
1/DC/85:90NANA

Problematic loops

#loop idProblemSequence
HL_4V6I_003NA
HL_4V6I_021
homologous
HL_4V88_212
HL_4V6I_025NA
HL_4V6I_057NA
HL_4V6I_063NA
HL_4V6I_070NA
HL_4V6I_082GNRA
homologous
HL_5TBW_047

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/CA/24:27,
1/CA/599:601
geometric
IL_4V83_235		NA

IL_01312.13*
1/CA/37:41,
1/CA/466:471
homologous
IL_4V88_386		NA

IL_53318.1*
1/CA/50:52,
1/CA/428:429		Minor groove platform
homologous
IL_4V88_388		NA

IL_06437.11*
1/CA/58:62,
1/CA/88:89		Multiple bulged bases
geometric
IL_4YAZ_007		NA

IL_66450.1*
1/CA/63:69,
1/CA/82:87		NANA
1/CA/109:113,
1/CA/301:305
geometric
IL_5TBW_121		NA

IL_05867.1*
1/CA/113:116,
1/CA/300:301		Multiple bulged bases
geometric
IL_4V88_392		NA

IL_13730.12*
1/CA/149:152,
1/CA/162:165		NANA
1/CA/177:180,
1/CA/194:197		Tandem non-canonical cWW pairs
geometric
IL_6JDV_002		NA

IL_85877.10*
1/CA/270:272,
1/CA/284:285		Single stack bend
geometric
IL_7A0S_022		NA

IL_04038.4*
1/CA/311:317,
1/CA/347:355		NANA
1/CA/363:366,
1/CA/375:381		NANA
1/CA/389:391,
1/CA/406:408		Isolated cWH basepair
homologous
IL_4V88_405		NA

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

IL_01312.13*
1/CA/439:441,
1/CA/463:464		Single bulged U
geometric
IL_4LFB_014		NA

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

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

IL_59137.10*
1/CA/481:482,
1/CA/505:507		Single stack bend
geometric
IL_7KGA_003		NA

IL_04038.4*
1/CA/562:568,
1/CA/575:583
homologous
IL_4V88_415		NA

IL_04667.1*
1/CA/616:622,
1/CA/1104:1105
homologous
IL_4V88_416		NA

IL_12418.1*
1/CA/624:626,
1/CA/973:975
homologous
IL_4V88_417		NA

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

IL_39521.5*
1/CA/660:663,
1/CA/669:672		Tandem non-canonical cWW pairs
geometric
IL_4WF9_109		NA

IL_85877.10*
1/CA/868:869,
1/CA/958:960		Major groove platform
geometric
IL_7RQB_090		NA

IL_80663.10*
1/CA/871:874,
1/CA/953:956		tSH-tHW
geometric
IL_5UNE_005		NA

IL_08757.3*
1/CA/874:878,
1/CA/950:953		Tandem non-canonical cWW pairs
homologous
IL_4V88_431		NA

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

IL_85877.10*
1/CA/892:899,
1/CA/910:920		NANA
1/CA/985:990,
1/CA/1014:1016		Other IL
homologous
IL_4V88_435		NA

IL_51590.1*
1/CA/990:994,
1/CA/1010:1014		tSH-tHW-tHS
geometric
IL_4LFB_033		NA

IL_39521.5*
1/CA/1041:1045,
1/CA/1073:1077
geometric
IL_5TBW_121		NA

IL_05867.1*
1/CA/1051:1053,
1/CA/1066:1067		Single stack bend
geometric
IL_4C7O_002		NA

IL_72766.2*
1/CA/1053:1057,
1/CA/1062:1066		NANA
1/CA/1111:1118,
1/CA/1129:1134		NANA
1/CA/1146:1151,
1/CA/1627:1632		NANA
1/CA/1173:1175,
1/CA/1464:1466
homologous
IL_4V88_444		NA

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

IL_06437.11*
1/CA/1268:1270,
1/CA/1440:1441		Single bulged U
homologous
IL_4V88_449		NA

IL_83039.11*
1/CA/1271:1275,
1/CA/1437:1439		Isolated non-canonical cWW with bulges
geometric
IL_3KTW_002		NA

IL_01312.13*
1/CA/1280:1281,
1/CA/1426:1428		Single bulged A
homologous
IL_4V88_452		NA

IL_80007.16*
1/CA/1290:1293,
1/CA/1322:1325		Tandem non-canonical cWW pairs
geometric
IL_6JDV_002		NA

IL_85877.10*
1/CA/1333:1334,
1/CA/1417:1419		NANA
1/CA/1335:1337,
1/CA/1415:1416		Single stack bend
geometric
IL_5VSU_003		NA

IL_06437.11*
1/CA/1340:1342,
1/CA/1383:1384		NANA
1/CA/1345:1348,
1/CA/1377:1380		NANA
1/CA/1351:1355,
1/CA/1368:1374		NANA
1/CA/1540:1545,
1/CA/1566:1571
homologous
IL_4V88_462		NA

IL_19954.1*
1/CA/1636:1641,
1/CA/1760:1767		NANA
1/CA/1642:1644,
1/CA/1757:1759
homologous
IL_4V88_465		NA

IL_01312.13*
1/CA/1644:1647,
1/CA/1753:1757		NANA
1/CA/1649:1652,
1/CA/1748:1751		NANA
1/CA/1653:1656,
1/CA/1744:1747		Double sheared
geometric
IL_4WF9_016		NA

IL_09705.7*
1/CA/1656:1658,
1/CA/1743:1744		Single stack bend
geometric
IL_5J7L_032		NA

IL_04038.4*
1/CA/1664:1667,
1/CA/1734:1737		Tandem non-canonical cWW pairs
geometric
IL_4WF9_109		NA

IL_85877.10*
1/CA/1669:1672,
1/CA/1729:1732		Double sheared
homologous
IL_4V88_471		NA

IL_09705.7*
1/CA/1672:1674,
1/CA/1727:1729
geometric
IL_1YZ9_001		NA

IL_01312.13*
1/CA/1675:1678,
1/CA/1723:1726		Tandem non-canonical cWW pairs
geometric
IL_5TBW_129		NA

IL_85877.10*
1/CA/1678:1682,
1/CA/1719:1723		Triple sheared
homologous
IL_4V88_474		NA

IL_56467.6*
1/CA/1688:1690,
1/CA/1711:1713		Other IL
homologous
IL_4V88_476		NA

IL_67621.5*
1/CA/1693:1695,
1/CA/1706:1708
geometric
IL_5TBW_112		NA

IL_01312.13*
1/DA/7:8,
1/DB/150:152		Single stack bend
geometric
IL_7KGA_006		NA

IL_06437.11*
1/DA/13:15,
1/DB/144:145		Single stack bend
geometric
IL_7A0S_054		NA

IL_04038.4*
1/DA/27:28,
1/DA/56:58		Single stack bend
geometric
IL_4V9F_005		NA

IL_04038.4*
1/DA/32:38,
1/DA/45:52		8x7 Sarcin-Ricin; G-bulge
geometric
IL_4V9F_006		NA

IL_04346.5*
1/DA/82:89,
1/DA/97:103
homologous
IL_5TBW_006		NA

IL_29509.1*
1/DA/125:127,
1/DA/141:143
homologous
IL_5TBW_008		NA

IL_01312.13*
1/DA/159:160,
1/DA/260:262		NANA
1/DA/161:164,
1/DA/257:259
geometric
IL_4N0T_004		NA

IL_87332.1*
1/DA/169:170,
1/DA/248:253		NANA
1/DA/176:179,
1/DA/237:242		NANA
1/DA/185:186,
1/DA/229:231		NANA
1/DA/189:191,
1/DA/204:205		Single bulged U
geometric
IL_4V9F_013		NA

IL_83039.11*
1/DA/328:332,
1/DB/31:33		Major groove platform with extra cWW
geometric
IL_4V9F_003		NA

IL_95485.6*
1/DA/336:339,
1/DB/25:27		Isolated non-canonical cWW with bulges
geometric
IL_3TD0_005		NA

IL_01312.13*
1/DA/376:379,
1/DA/390:403
homologous
IL_5TBW_014		NA

IL_60992.5*
1/DA/404:410,
1/DB/13:19		Triple sheared with non-canonical cWW
homologous
IL_5TBW_015		NA

IL_66414.5*
1/DA/429:431,
1/DA/628:630
homologous
IL_5TBW_016		NA

IL_01312.13*
1/DA/460:462,
1/DA/469:470		Single stack bend
geometric
IL_4WF9_007		NA

IL_04038.4*
1/DA/511:512,
1/DA/578:580		NANA
1/DA/517:525,
1/DA/567:573		NANA
1/DA/531:534,
1/DA/559:561		NANA
1/DA/537:538,
1/DA/553:556		NANA
1/DA/594:597,
1/DA/606:608		NANA
1/DA/668:670,
1/DA/792:794
homologous
IL_5TBW_021		NA

IL_01312.13*
1/DA/679:683,
1/DA/697:701		NANA
1/DA/725:726,
1/DA/743:745		Single stack bend
geometric
IL_7KGA_006		NA

IL_06437.11*
1/DA/726:728,
1/DA/741:743
geometric
IL_5UNE_006		NA

IL_01312.13*
1/DA/755:757,
1/DA/774:777
geometric
IL_4N0T_004		NA

IL_87332.1*
1/DA/758:763,
1/DA/768:773
geometric
IL_5TBW_026		NA

IL_19954.1*
1/DA/803:805,
1/DA/938:940		CC cWW
geometric
IL_4E59_001		NA

IL_01312.13*
1/DA/805:809,
1/DA/931:938
homologous
IL_5TBW_028		NA

IL_17470.5*
1/DA/833:834,
1/DA/859:861		Single bulged G
geometric
IL_5J7L_262		NA

IL_59137.10*
1/DA/834:839,
1/DA/854:859		NANA
1/DA/869:872,
1/DA/888:890		NANA
1/DA/873:875,
1/DA/886:887		Single bulged U
homologous
IL_5TBW_032		NA

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

IL_90991.5*
1/DA/954:956,
1/DA/965:967
homologous
IL_5TBW_034		NA

IL_01312.13*
1/DA/969:970,
1/DA/1111:1113		Single stack bend
homologous
IL_5TBW_035		NA

IL_04038.4*
1/DA/982:984,
1/DA/1100:1104		NANA
1/DA/988:990,
1/DA/1061:1063		Stack and bulge
geometric
IL_2ET8_001		NA

IL_04038.4*
1/DA/991:998,
1/DA/1052:1060		NANA
1/DA/999:1001,
1/DA/1050:1051		Single stack bend
geometric
IL_5TBW_375		NA

IL_04038.4*
1/DA/1001:1010,
1/DA/1042:1050		NANA
1/DA/1010:1013,
1/DA/1039:1042		Double sheared
geometric
IL_4ZNP_002		NA

IL_09705.7*
1/DA/1013:1020,
1/DA/1034:1039		NANA
1/DA/1067:1071,
1/DA/1089:1093
geometric
IL_5TBW_121		NA

IL_05867.1*
1/DA/1072:1076,
1/DA/1083:1088		NANA
1/DA/1120:1122,
1/DA/1136:1138
homologous
IL_5TBW_046		NA

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

IL_53523.5*
1/DA/1173:1180,
1/DA/1325:1326		SSU/LSU pseudoknot
geometric
IL_4V9F_038		NA

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

IL_83039.11*
1/DA/1187:1206,
1/DA/1298:1319		NANA
1/DA/1207:1210,
1/DA/1295:1297		Isolated non-canonical cWW with bulges
geometric
IL_3TD0_002		NA

IL_01312.13*
1/DA/1218:1226,
1/DA/1283:1287		Kink-turn
homologous
IL_5TBW_054		NA

IL_90538.3*
1/DA/1234:1238,
1/DA/1250:1254		NANA
1/DA/1262:1266,
1/DA/1275:1277		Major groove platform with extra cWW
homologous
IL_5TBW_056		NA

IL_95485.6*
1/DA/1376:1378,
1/DA/1428:1431		Isolated cWS basepair
homologous
IL_5TBW_057		NA

IL_01312.13*
1/DA/1388:1394,
1/DA/1415:1419		NANA
1/DA/1394:1396,
1/DA/1413:1415
geometric
IL_1MFQ_003		NA

IL_01312.13*
1/DA/1444:1451,
1/DA/2353:2359		8x7 Sarcin-Ricin with CC bifurcated pair; G-bulge
geometric
IL_4V9F_012		NA

IL_59724.1*
1/DA/1492:1495,
1/DA/1835:1836		Major groove platform; stack outside cWW
geometric
IL_7RQB_050		NA

IL_70995.6*
1/DA/1501:1505,
1/DA/1513:1515		C-loop
geometric
IL_7RQB_104		NA

IL_63596.4*
1/DA/1532:1536,
1/DA/1585:1590		UAA/GAN
homologous
IL_5TBW_063		NA

IL_53523.5*
1/DA/1624:1630,
1/DA/1811:1820		NANA
1/DA/1645:1649,
1/DA/1806:1810		Triple sheared
homologous
IL_5TBW_067		NA

IL_56467.6*
1/DA/1661:1663,
1/DA/1786:1788
geometric
IL_5ZTM_001		NA

IL_01312.13*
1/DA/1665:1671,
1/DA/1776:1784		NANA
1/DA/1695:1698,
1/DA/1748:1752
geometric
IL_7RQB_046		NA

IL_68574.2*
1/DA/1698:1707,
1/DA/1739:1748		NANA
1/DA/1707:1711,
1/DA/1735:1739		Tandem non-canonical cWW pairs
geometric
IL_4EYA_010		NA

IL_85877.10*
1/DA/1711:1718,
1/DA/1726:1735		NANA
1/DA/1883:1889,
1/DA/2346:2349
homologous
IL_5TBW_074		NA

IL_79393.8*
1/DA/1895:1897,
1/DA/2338:2340		Isolated tWW turn
homologous
IL_5TBW_075		NA

IL_54997.5*
1/DA/1898:1901,
1/DA/2336:2337		Major groove platform; stack outside cWW
geometric
IL_4WF9_064		NA

IL_70995.6*
1/DA/1901:1906,
1/DA/2333:2336		Intercalated tWH
homologous
IL_5TBW_077		NA

IL_98882.3*
1/DA/1918:1923,
1/DA/1928:1934		tSH-tSH-tHH-tHS
geometric
IL_4V9F_063		NA

IL_66584.5*
1/DA/1940:1942,
1/DA/2106:2108
homologous
IL_5TBW_079		NA

IL_01312.13*
1/DA/1947:1948,
1/DA/2098:2101		NANA
1/DA/1965:1968,
1/DA/2054:2057		NANA
1/DA/1971:1976,
1/DA/2046:2051		NANA
1/DA/1981:1982,
1/DA/2039:2041		Single stack bend
geometric
IL_4WF9_007		NA

IL_04038.4*
1/DA/1988:1991,
1/DA/2030:2033		Tandem non-canonical cWW pairs
geometric
IL_5EW4_001		NA

IL_85877.10*
1/DA/1994:1996,
1/DA/2025:2027
geometric
IL_7A0S_107		NA

IL_01312.13*
1/DA/2128:2130,
1/DA/2322:2325		Self complementary
geometric
IL_5M0H_001		NA

IL_01312.13*
1/DA/2156:2162,
1/DA/2172:2180		Kink-turn related
geometric
IL_7RQB_070		NA

IL_17069.3*
1/DA/2196:2199,
1/DA/2245:2246		Major groove outside cWW, minor groove, intercalation pocket
homologous
IL_5TBW_084		NA

IL_72766.2*
1/DA/2200:2201,
1/DA/2241:2244		Major groove outside cWW, minor groove, intercalation pocket
homologous
IL_5TBW_085		NA

IL_13730.12*
1/DA/2204:2206,
1/DA/2237:2238		Single stack bend
geometric
IL_4V9F_081		NA

IL_04038.4*
1/DA/2206:2210,
1/DA/2235:2237		NANA
1/DA/2211:2217,
1/DA/2228:2234
homologous
IL_5TBW_088		NA

IL_36973.5*
1/DA/2276:2277,
1/DA/2307:2310
geometric
IL_4V9F_070		NA

IL_69632.1*
1/DA/2277:2288,
1/DA/2304:2307
homologous
IL_5TBW_090		NA

IL_45481.1*
1/DA/2391:2394,
1/DA/2986:2988		Major groove platform with extra pair
homologous
IL_5TBW_091		NA

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

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

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

IL_06437.11*
1/DA/2423:2425,
1/DA/2604:2607		Isolated tHS basepair with bulges
homologous
IL_5TBW_095		NA

IL_38958.6*
1/DA/2444:2445,
1/DA/2501:2503		NANA
1/DA/2451:2462,
1/DA/2493:2495		NANA
1/DA/2466:2469,
1/DA/2476:2489		NANA
1/DA/2666:2668,
1/DA/2686:2690		NANA
1/DA/2718:2721,
1/DA/2735:2738		NANA
1/DA/2823:2824,
1/DA/2865:2867		Major groove platform
geometric
IL_4V9F_082		NA

IL_80663.10*
1/DA/2824:2826,
1/DA/2863:2865
homologous
IL_5TBW_103		NA

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

IL_95601.1*
1/DA/2828:2831,
1/DA/2857:2862		NANA
1/DA/2835:2839,
1/DA/2849:2853		Triple sheared
homologous
IL_5TBW_106		NA

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

IL_80663.10*
1/DA/2879:2881,
1/DA/2943:2947		Isolated non-canonical cWW with bulges
geometric
IL_4V9F_087		NA

IL_55456.1*
1/DA/2881:2882,
1/DA/2940:2943		Multiple bulged bases
homologous
IL_5TBW_109		NA

IL_13730.12*
1/DA/2889:2891,
1/DA/2912:2914		Not an internal loop
geometric
IL_5VCI_005		NA

IL_04038.4*
1/DA/2891:2892,
1/DA/2909:2912		Minor groove platform with intercalation
homologous
IL_5TBW_111		NA

IL_95601.1*
1/DA/2918:2920,
1/DA/2926:2928
homologous
IL_5TBW_112		NA

IL_01312.13*
1/DA/2960:2961,
1/DA/2970:2972		Single bulged A
geometric
IL_5TBW_372		NA

IL_80007.16*
1/DA/3003:3007,
1/DA/3139:3145		NANA
1/DA/3012:3014,
1/DA/3040:3042
homologous
IL_5TBW_115		NA

IL_01312.13*
1/DA/3019:3025,
1/DA/3030:3035		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_4V9F_092		NA

IL_35110.5*
1/DA/3047:3051,
1/DA/3091:3094		Major groove minor groove platform with tHH
homologous
IL_5TBW_117		NA

IL_28060.3*
1/DA/3054:3059,
1/DA/3084:3088		NANA
1/DA/3103:3107,
1/DA/3127:3131		NANA
1/DA/3164:3166,
1/DA/3284:3286
geometric
IL_3RW6_004		NA

IL_01312.13*
1/DA/3211:3214,
1/DA/3219:3224		NANA
1/DA/3233:3235,
1/DA/3253:3254		NANA
1/DA/3236:3238,
1/DA/3249:3252
geometric
IL_4N0T_004		NA

IL_87332.1*
1/DA/3300:3303,
1/DA/3311:3314		Tandem non-canonical cWW pairs
geometric
IL_1D4R_003		NA

IL_85877.10*
1/DA/3324:3325,
1/DA/3381:3383		Single stack bend
geometric
IL_5TBW_035		NA

IL_04038.4*
1/DA/3332:3337,
1/DA/3367:3371
geometric
IL_4WF9_108		NA

IL_83162.3*
1/DA/3340:3345,
1/DA/3360:3364		NANA
1/DC/20:27,
1/DC/52:58		NANA
1/DC/28:31,
1/DC/46:51		NANA
1/DC/32:36,
1/DC/41:45		NANA
1/DC/70:78,
1/DC/97:103		NANA

Problematic loops

#loop idProblemSequence
IL_4V6I_003
geometric
IL_4LFB_003
IL_4V6I_009NA
IL_4V6I_014
geometric
IL_5Y58_001
IL_4V6I_022NA
IL_4V6I_040NA
IL_4V6I_045NA
IL_4V6I_070Not an internal loop
geometric
IL_5VCI_005
IL_4V6I_085NA
IL_4V6I_107NA
IL_4V6I_129
geometric
IL_4KNQ_003
IL_4V6I_130Isolated cWH basepair
geometric
IL_6F4H_001
IL_4V6I_174NA
IL_4V6I_192
geometric
IL_5VSU_002
IL_4V6I_200NA
IL_4V6I_203NA

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/CA/41:42,
1/CA/433:439,
1/CA/464:466		NANA
1/CA/881:884,
1/CA/928:937,
1/CA/942:947
homologous
J3_4V88_033		NA
1/CA/1036:1040,
1/CA/1078:1083,
1/CA/1090:1095		NANA
1/CA/1161:1164,
1/CA/1581:1587,
1/CA/1609:1616		NANA
1/CA/1168:1171,
1/CA/1468:1470,
1/CA/1574:1577		NANA
1/CA/1180:1187,
1/CA/1198:1209,
1/CA/1454:1458		NANA
1/CA/1283:1289,
1/CA/1326:1333,
1/CA/1419:1424		NANA
1/CA/1293:1294,
1/CA/1303:1308,
1/CA/1317:1322		NANA
1/CA/1337:1338,
1/CA/1386:1392,
1/CA/1406:1415		NANA
1/CA/1470:1474,
1/CA/1533:1540,
1/CA/1571:1574		NANA
1/DA/186:189,
1/DA/205:214,
1/DA/226:229		NANA
1/DA/369:376,
1/DA/403:404,
1/DB/19:20
homologous
J3_5TBW_002		NA
1/DA/814:820,
1/DA/905:907,
1/DA/923:926		NANA
1/DA/828:831,
1/DA/863:867,
1/DA/892:897
homologous
J3_5TBW_005		NA
1/DA/1230:1232,
1/DA/1256:1262,
1/DA/1277:1279		NANA
1/DA/1479:1485,
1/DA/1857:1860,
1/DA/1870:1874		NANA
1/DA/1488:1491,
1/DA/1837:1843,
1/DA/1852:1854		NANA
1/DA/1526:1531,
1/DA/1591:1595,
1/DA/1612:1613
homologous
J3_5TBW_010		NA
1/DA/2432:2435,
1/DA/2512:2517,
1/DA/2590:2597
homologous
J3_5TBW_012		NA
1/DA/2529:2532,
1/DA/2547:2563,
1/DA/2578:2581		NANA
1/DA/2651:2653,
1/DA/2754:2765,
1/DA/2793:2798		NANA
1/DA/2664:2666,
1/DA/2690:2692,
1/DA/2701:2706
homologous
J3_5TBW_013		NA
1/DA/2886:2889,
1/DA/2914:2916,
1/DA/2930:2936		NANA
1/DA/3299:3300,
1/DA/3314:3320,
1/DA/3387:3389		NANA
1/DC/9:14,
1/DC/64:66,
1/DC/107:109		NANA

Problematic loops

#loop idProblemSequence
J3_4V6I_015NA
J3_4V6I_020NA
J3_4V6I_021NA

Coloring options:
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