RNA 3D Hub //

9SRA Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9SRA_0011/1/12:20No text annotation
geometric
HL_4V9F_069
HL_37889.3
HL_9SRA_0041/1/173:182Pseudoknot with intercalation
homologous
HL_4V9F_001
HL_17803.3
HL_9SRA_0051/1/201:209Pseudoknot geometry
homologous
HL_4V9F_002
HL_52651.4
HL_9SRA_0061/1/236:241No text annotation
homologous
HL_4V9F_003
HL_75660.10
HL_9SRA_0091/1/298:305No text annotation
homologous
HL_4V9F_006
HL_02262.1
HL_9SRA_0101/1/329:334No text annotation
geometric
HL_4WF9_007
HL_23875.1
HL_9SRA_0131/1/460:467T-loop with 2 stacked bulged bases
homologous
HL_4V9F_010
HL_13999.5
HL_9SRA_0151/1/538:547No text annotation
homologous
HL_4V9F_013
HL_91228.1
HL_9SRA_0161/1/564:572Pseudoknot geometry
homologous
HL_4V9F_014
HL_52651.4
HL_9SRA_0171/1/616:621GNRA
homologous
HL_4V9F_015
HL_34789.6
HL_9SRA_0181/1/641:646GNRA
homologous
HL_4V9F_016
HL_34789.6
HL_9SRA_0201/1/772:781T-loop with 2 stacked bulged bases
homologous
HL_4V9F_018
HL_33597.6
HL_9SRA_0221/1/840:845GNRA
homologous
HL_4V9F_020
HL_34789.6
HL_9SRA_0251/1/962:967No text annotation
HL_9SRA_0261/1/995:1004No text annotation
homologous
HL_4V9F_024
HL_50204.3
HL_9SRA_0271/1/1030:1036No text annotation
homologous
HL_4V9F_025
HL_79773.1
HL_9SRA_0281/1/1077:1082No text annotation
homologous
HL_4V9F_026
HL_27530.3
HL_9SRA_0301/1/1208:1213GNRA
homologous
HL_4V9F_028
HL_34789.6
HL_9SRA_0311/1/1229:1236No text annotation
homologous
HL_4V9F_029
HL_47171.3
HL_9SRA_0351/1/1480:1485GNRA
homologous
HL_4V9F_033
HL_34789.6
HL_9SRA_0361/1/1540:1548T-loop with 2 stacked bulged bases
homologous
HL_4V9F_034
HL_33597.6
HL_9SRA_0371/1/1584:1590Pseudoknot geometry with 3' bulge
homologous
HL_4V9F_035
HL_49081.2
HL_9SRA_0381/1/1622:1628GNRA
homologous
HL_4V9F_036
HL_34789.6
HL_9SRA_0391/1/1651:1660No text annotation
homologous
HL_4V9F_037
HL_77449.3
HL_9SRA_0401/1/1682:1687GNRA
geometric
HL_2Z75_004
HL_34789.6
HL_9SRA_0421/1/1765:1771Other HL
homologous
HL_4V9F_039
HL_67772.3
HL_9SRA_0431/1/1804:1810No text annotation
HL_9SRA_0441/1/1835:1839Mini UNCG
homologous
HL_4V9F_041
HL_90436.5
HL_9SRA_0451/1/1885:1892No text annotation
homologous
HL_4V9F_042
HL_28592.4
HL_9SRA_0461/1/1904:1910No text annotation
geometric
HL_9AXU_039
HL_34789.6
HL_9SRA_0471/1/1967:1972UNCG
homologous
HL_4V9F_044
HL_61337.6
HL_9SRA_0481/1/1992:1998GNRA
homologous
HL_4V9F_045
HL_34789.6
HL_9SRA_0491/1/2008:2012No text annotation
homologous
HL_4V9F_046
HL_80709.5
HL_9SRA_0501/1/2033:2043No text annotation
homologous
HL_4V9F_047
HL_87681.3
HL_9SRA_0511/1/2062:2067GNRA
homologous
HL_4V9F_048
HL_34789.6
HL_9SRA_0521/1/2116:2123GNRA related
homologous
HL_4V9F_049
HL_28253.1
HL_9SRA_0531/1/2151:2161No text annotation
HL_9SRA_0541/1/2191:2197No text annotation
geometric
HL_9G4Q_002
HL_07380.1
HL_9SRA_0551/1/2267:2276No text annotation
homologous
HL_4V9F_052
HL_78372.3
HL_9SRA_0571/1/2444:2449GNRA
homologous
HL_4V9F_054
HL_34789.6
HL_9SRA_0581/1/2478:2486LSU P loop
homologous
HL_4V9F_055
HL_11974.4
HL_9SRA_0591/1/2495:2507No text annotation
homologous
HL_4V9F_056
HL_02042.3
HL_9SRA_0621/1/2587:2595No text annotation
HL_9SRA_0651/1/2703:2711No text annotation
homologous
HL_4V9F_062
HL_52011.3
HL_9SRA_0661/1/2760:2767GNRA variation
homologous
HL_4V9F_063
HL_02262.1
HL_9SRA_0671/1/2782:2790No text annotation
HL_9SRA_0681/1/2826:2831GNRA
homologous
HL_4V9F_065
HL_34789.6
HL_9SRA_0691/1/2891:2896GNRA
homologous
HL_4V9F_066
HL_34789.6
HL_9SRA_0701/1/2933:2938Ribsomal LSU H95
homologous
HL_4V9F_067
HL_12125.4
HL_9SRA_0711/1/2975:2989No text annotation
homologous
HL_4V9F_068
HL_53269.4
HL_9SRA_0721/2/19:29No text annotation
HL_9SRA_0741/2/155:160No text annotation
HL_9SRA_0751/2/190:197No text annotation
HL_9SRA_0771/2/268:276No text annotation
HL_9SRA_0781/2/305:310No text annotation
HL_9SRA_0791/2/329:342No text annotation
HL_9SRA_0801/2/351:356No text annotation
HL_9SRA_0811/2/388:393No text annotation
HL_9SRA_0821/2/422:426No text annotation
HL_9SRA_0831/2/444:452No text annotation
HL_9SRA_0841/2/488:493No text annotation
HL_9SRA_0851/2/583:589No text annotation
HL_9SRA_0861/2/656:665No text annotation
HL_9SRA_0871/2/693:698No text annotation
HL_9SRA_0881/2/753:763No text annotation
HL_9SRA_0891/2/809:815No text annotation
HL_9SRA_0901/2/833:838No text annotation
HL_9SRA_0911/2/868:873No text annotation
HL_9SRA_0921/2/935:944No text annotation
HL_9SRA_0931/2/985:991No text annotation
HL_9SRA_0941/2/1041:1046No text annotation
HL_9SRA_0951/2/1054:1061No text annotation
HL_9SRA_0961/2/1104:1109No text annotation
HL_9SRA_0971/2/1139:1145No text annotation
HL_9SRA_0981/2/1239:1244No text annotation
HL_9SRA_0991/2/1288:1297No text annotation
HL_9SRA_1001/2/1331:1339No text annotation
HL_9SRA_1011/2/1419:1424No text annotation
HL_9SRA_1021/2/1484:1489No text annotation
HL_9SRA_1051/3/90:95GNRA
homologous
HL_4V9F_072
HL_34789.6

Problematic loops

#loop idProblemSequence
HL_9SRA_002No text annotation
HL_9SRA_003No text annotation
HL_9SRA_007No text annotation
HL_9SRA_008No text annotation
HL_9SRA_011No text annotation
HL_9SRA_012GNRA
HL_9SRA_014T-loop with unstacked turn
HL_9SRA_019GNRA
HL_9SRA_021No text annotation
HL_9SRA_023No text annotation
HL_9SRA_024GNRA
HL_9SRA_029No text annotation
HL_9SRA_032No text annotation
HL_9SRA_033GNRA with tandem sheared
HL_9SRA_034No text annotation
HL_9SRA_041No text annotation
HL_9SRA_056No text annotation
HL_9SRA_060No text annotation
HL_9SRA_061Pseudoknot geometry
HL_9SRA_063tRNA anticodon loop
HL_9SRA_064Pseudoknot geometry
HL_9SRA_073No text annotation
HL_9SRA_076No text annotation
HL_9SRA_103No text annotation
HL_9SRA_104No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9SRA_0011/1/1:4,
1/1/91:94		Double sheared
geometric
IL_9E6Q_100
IL_58355.4
IL_9SRA_0021/1/31:32,
1/1/80:82		No text annotation
geometric
IL_9E6Q_101
IL_77710.2
IL_9SRA_0031/1/36:37,
1/1/74:76		Single bulged G
geometric
IL_8TSV_002
IL_28408.4
IL_9SRA_0041/1/40:45,
1/1/67:71		No text annotation
geometric
IL_9PN5_129
IL_48489.3
IL_9SRA_0051/1/49:52,
1/1/60:63		Double sheared
geometric
IL_9E6Q_104
IL_58355.4
IL_9SRA_0071/1/138:144,
1/1/662:668		Triple sheared with non-canonical cWW
homologous
IL_4V9F_001
IL_22311.3
IL_9SRA_0101/1/157:158,
1/1/589:591		No text annotation
geometric
IL_12CJ_004
IL_98469.1
IL_9SRA_0111/1/195:199,
1/1/211:218		Kink-turn
homologous
IL_4V9F_004
IL_71972.2
IL_9SRA_0121/1/287:288,
1/1/316:318		Single stack bend
homologous
IL_4V9F_005
IL_15011.5
IL_9SRA_0131/1/292:298,
1/1/305:312		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4V9F_006
IL_62167.5
IL_9SRA_0141/1/343:349,
1/1/357:362		7x6 Sarcin-Ricin; G-bulge
homologous
IL_4V9F_007
IL_02666.3
IL_9SRA_0161/1/378:382,
1/1/404:410		Kink-turn with embedded cWW pair
geometric
IL_4V9F_108
IL_65996.1
IL_9SRA_0171/1/381:382,
1/1/404:409		No text annotation
homologous
IL_4V9F_009
IL_10396.3
IL_9SRA_0231/1/635:638,
1/1/649:661		No text annotation
geometric
IL_9AXU_014
IL_44923.3
IL_9SRA_0241/1/694:699,
1/1/755:757		No text annotation
geometric
IL_9E6Q_019
IL_93336.3
IL_9SRA_0251/1/700:707,
1/1/750:754		Kink-turn
geometric
IL_5G4T_002
IL_90775.3
IL_9SRA_0311/1/921:923,
1/1/1057:1059		Isolated non-canonical cWW pair
homologous
IL_4V9F_023
IL_01003.6
IL_9SRA_0321/1/923:927,
1/1/1050:1057		tHW-tHW cross-strand stack
homologous
IL_4V9F_024
IL_73855.3
IL_9SRA_0331/1/946:947,
1/1/1014:1016		Single bulged A
homologous
IL_4V9F_025
IL_14190.4
IL_9SRA_0341/1/951:952,
1/1/977:979		Single bulged G
homologous
IL_4V9F_026
IL_28408.4
IL_9SRA_0351/1/952:956,
1/1/973:977		Triple sheared
homologous
IL_4V9F_027
IL_15190.4
IL_9SRA_0361/1/988:991,
1/1/1007:1009		Major groove platform with extra cWW
homologous
IL_4V9F_028
IL_36931.4
IL_9SRA_0371/1/992:994,
1/1/1005:1006		Single bulged U
homologous
IL_4V9F_029
IL_97561.7
IL_9SRA_0381/1/1026:1028,
1/1/1038:1042		Multiple bulged bases
homologous
IL_4V9F_030
IL_57881.1
IL_9SRA_0391/1/1088:1089,
1/1/1194:1196		No text annotation
geometric
IL_9E6Q_033
IL_15011.5
IL_9SRA_0441/1/1116:1120,
1/1/1161:1164		C-loop
geometric
IL_7A0S_029
IL_16301.3
IL_9SRA_0451/1/1122:1125,
1/1/1156:1159		No text annotation
homologous
IL_4V9F_036
IL_02203.1
IL_9SRA_0491/1/1202:1203,
1/1/1218:1220		Stack outside cWW
geometric
IL_6JQ6_004
IL_77710.2
IL_9SRA_0531/1/1268:1274,
1/1/1394:1399		Kink-turn related
homologous
IL_4V9F_040
IL_57188.6
IL_9SRA_0541/1/1275:1285,
1/1/1379:1393		No text annotation
IL_9SRA_0551/1/1287:1289,
1/1/1376:1377		Single bulged G
homologous
IL_4V9F_041
IL_28408.4
IL_9SRA_0581/1/1455:1457,
1/1/1505:1508		Isolated cWS basepair
homologous
IL_4V9F_046
IL_84227.1
IL_9SRA_0591/1/1466:1473,
1/1/1492:1496		Kink-turn
homologous
IL_4V9F_048
IL_90775.3
IL_9SRA_0601/1/1521:1527,
1/1/2252:2257		7x6 Sarcin-Ricin; G-bulge
homologous
IL_4V9F_049
IL_02666.3
IL_9SRA_0611/1/1569:1572,
1/1/1876:1877		No text annotation
geometric
IL_9E6Q_052
IL_74641.4
IL_9SRA_0631/1/1579:1583,
1/1/1591:1593		C-loop
homologous
IL_4V9F_051
IL_63596.14
IL_9SRA_0641/1/1610:1614,
1/1/1637:1642		No text annotation
geometric
IL_9AXU_060
IL_08938.3
IL_9SRA_0651/1/1619:1620,
1/1/1630:1632		No text annotation
geometric
IL_8GLP_141
IL_57267.1
IL_9SRA_0661/1/1674:1677,
1/1/1859:1863		tSH-tHW
geometric
IL_2ZY6_001
IL_74317.1
IL_9SRA_0671/1/1714:1717,
1/1/1822:1826		No text annotation
geometric
IL_9E6Q_057
IL_74317.1
IL_9SRA_0681/1/1740:1744,
1/1/1792:1797		No text annotation
IL_9SRA_0691/1/1747:1752,
1/1/1784:1789		No text annotation
geometric
IL_9E6Q_072
IL_74322.2
IL_9SRA_0701/1/1757:1763,
1/1/1773:1779		Kink-turn
homologous
IL_4V9F_058
IL_32016.1
IL_9SRA_0711/1/1926:1932,
1/1/2245:2247		No text annotation
IL_9SRA_0721/1/1939:1941,
1/1/2236:2238		Isolated tWW turn
homologous
IL_4V9F_060
IL_10432.3
IL_9SRA_0731/1/1942:1945,
1/1/2234:2235		No text annotation
geometric
IL_8OI5_078
IL_74641.4
IL_9SRA_0741/1/1942:1950,
1/1/2231:2235		No text annotation
geometric
IL_9E6Q_064
IL_80252.3
IL_9SRA_0751/1/1945:1950,
1/1/2231:2234		Intercalated tWH
homologous
IL_4V9F_062
IL_28217.3
IL_9SRA_0761/1/1962:1967,
1/1/1972:1978		tSH-tSH-tHH-tHS
homologous
IL_4V9F_063
IL_20700.3
IL_9SRA_0771/1/2026:2027,
1/1/2221:2223		Single bulged A
homologous
IL_4V9F_064
IL_14190.4
IL_9SRA_0781/1/2054:2059,
1/1/2070:2077		No text annotation
IL_9SRA_0791/1/2093:2096,
1/1/2143:2144		Minor groove platform, major groove intercalation
homologous
IL_4V9F_066
IL_55206.3
IL_9SRA_0801/1/2097:2098,
1/1/2139:2142		Major groove intercalation
homologous
IL_4V9F_067
IL_71421.5
IL_9SRA_0811/1/2102:2106,
1/1/2133:2135		Major groove minor groove platform with extra cWW
geometric
IL_4WF9_012
IL_24466.1
IL_9SRA_0821/1/2107:2111,
1/1/2128:2132		UAA/GAN with extra stack
geometric
IL_9DFE_074
IL_89021.4
IL_9SRA_0831/1/2174:2175,
1/1/2205:2208		Bulged stacked bases
geometric
IL_4V9F_070
IL_24886.4
IL_9SRA_0841/1/2175:2186,
1/1/2202:2205		No text annotation
geometric
IL_9DFE_077
IL_84014.3
IL_9SRA_0851/1/2290:2292,
1/1/2849:2850		Major groove platform
geometric
IL_9DFE_078
IL_48076.10
IL_9SRA_0861/1/2294:2296,
1/1/2844:2847		No text annotation
homologous
IL_4V9F_073
IL_80025.3
IL_9SRA_0871/1/2307:2309,
1/1/2674:2675		Single bulged U
homologous
IL_4V9F_074
IL_97561.7
IL_9SRA_0881/1/2310:2311,
1/1/2670:2673		Minor groove platform
homologous
IL_4V9F_075
IL_98469.1
IL_9SRA_0891/1/2321:2323,
1/1/2466:2469		Isolated tHS basepair with bulges
homologous
IL_4V9F_076
IL_87316.4
IL_9SRA_0941/1/2476:2477,
1/1/2487:2489		Single bulged A
homologous
IL_4V9F_079
IL_14190.4
IL_9SRA_0971/1/2686:2687,
1/1/2728:2730		Major groove platform
homologous
IL_4V9F_082
IL_48076.10
IL_9SRA_0981/1/2689:2691,
1/1/2725:2726		Major groove platform
homologous
IL_4V9F_083
IL_46637.4
IL_9SRA_0991/1/2691:2693,
1/1/2721:2725		Major groove minor groove platform with extra cWW
homologous
IL_4V9F_084
IL_36931.4
IL_9SRA_1001/1/2698:2702,
1/1/2712:2716		Double sheared with non-canonical cWW
homologous
IL_4V9F_085
IL_87767.4
IL_9SRA_1011/1/2739:2740,
1/1/2812:2814		Major groove platform
homologous
IL_4V9F_086
IL_46637.4
IL_9SRA_1021/1/2742:2744,
1/1/2806:2810		Isolated non-canonical cWW with bulges
homologous
IL_4V9F_087
IL_30722.1
IL_9SRA_1031/1/2744:2745,
1/1/2803:2806		Multiple bulged bases
homologous
IL_4V9F_088
IL_44609.4
IL_9SRA_1041/1/2754:2755,
1/1/2772:2775		Major groove platform with intercalation
homologous
IL_4V9F_089
IL_94991.3
IL_9SRA_1051/1/2823:2824,
1/1/2833:2835		No text annotation
geometric
IL_8GLP_154
IL_14190.4
IL_9SRA_1061/1/2868:2872,
1/1/3004:3012		No text annotation
homologous
IL_4V9F_091
IL_04638.4
IL_9SRA_1071/1/2884:2891,
1/1/2896:2902		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_8GLP_159
IL_34443.1
IL_9SRA_1081/1/2913:2917,
1/1/2956:2958		C-loop
homologous
IL_4V9F_093
IL_63596.14
IL_9SRA_1091/1/2920:2924,
1/1/2949:2953		UAA/GAN variation
homologous
IL_4V9F_094
IL_45790.3
IL_9SRA_1101/1/2928:2929,
1/1/2942:2945		No text annotation
geometric
IL_9E6Q_098
IL_44609.4
IL_9SRA_1111/1/2967:2972,
1/1/2992:2997		UAA/GAN with extra cWW
homologous
IL_4V9F_096
IL_91079.1
IL_9SRA_1121/2/54:60,
1/2/368:370		No text annotation
IL_9SRA_1131/2/62:64,
1/2/365:366		No text annotation
IL_9SRA_1141/2/71:74,
1/2/99:100		No text annotation
IL_9SRA_1151/2/75:77,
1/2/96:98		No text annotation
IL_9SRA_1161/2/125:128,
1/2/240:241		No text annotation
IL_9SRA_1171/2/129:133,
1/2/236:239		No text annotation
IL_9SRA_1181/2/145:150,
1/2/165:171		No text annotation
IL_9SRA_1191/2/187:189,
1/2/198:199		No text annotation
IL_9SRA_1201/2/251:256,
1/2/286:293		No text annotation
IL_9SRA_1211/2/258:261,
1/2/283:284		No text annotation
IL_9SRA_1221/2/301:302,
1/2/313:317		No text annotation
IL_9SRA_1231/2/376:378,
1/2/401:402		No text annotation
IL_9SRA_1241/2/380:384,
1/2/398:399		No text annotation
IL_9SRA_1251/2/384:385,
1/2/396:398		No text annotation
IL_9SRA_1261/2/469:476,
1/2/506:507		No text annotation
IL_9SRA_1271/2/476:478,
1/2/505:506		No text annotation
IL_9SRA_1281/2/481:487,
1/2/494:502		No text annotation
IL_9SRA_1291/2/535:541,
1/2/851:852		No text annotation
IL_9SRA_1301/2/546:550,
1/2/724:728		No text annotation
IL_9SRA_1311/2/560:562,
1/2/611:612		No text annotation
IL_9SRA_1321/2/563:564,
1/2/607:610		No text annotation
IL_9SRA_1331/2/571:576,
1/2/596:600		No text annotation
IL_9SRA_1341/2/621:622,
1/2/718:721		No text annotation
IL_9SRA_1351/2/624:625,
1/2/714:716		No text annotation
IL_9SRA_1361/2/627:633,
1/2/707:712		No text annotation
IL_9SRA_1371/2/641:644,
1/2/680:683		No text annotation
IL_9SRA_1381/2/651:655,
1/2/666:673		No text annotation
IL_9SRA_1391/2/741:745,
1/2/771:772		No text annotation
IL_9SRA_1401/2/746:750,
1/2/766:770		No text annotation
IL_9SRA_1411/2/858:865,
1/2/876:881		No text annotation
IL_9SRA_1421/2/893:894,
1/2/1367:1369		No text annotation
IL_9SRA_1431/2/896:898,
1/2/1364:1365		No text annotation
IL_9SRA_1441/2/904:907,
1/2/1354:1358		No text annotation
IL_9SRA_1451/2/925:926,
1/2/1200:1202		No text annotation
IL_9SRA_1461/2/969:971,
1/2/1002:1005		No text annotation
IL_9SRA_1491/2/1013:1015,
1/2/1182:1183		No text annotation
IL_9SRA_1501/2/1017:1021,
1/2/1178:1180		No text annotation
IL_9SRA_1511/2/1022:1023,
1/2/1173:1177		No text annotation
IL_9SRA_1521/2/1025:1026,
1/2/1169:1171		No text annotation
IL_9SRA_1531/2/1089:1092,
1/2/1119:1123		No text annotation
IL_9SRA_1541/2/1094:1097,
1/2/1116:1117		No text annotation
IL_9SRA_1551/2/1132:1135,
1/2/1149:1155		No text annotation
IL_9SRA_1561/2/1221:1227,
1/2/1258:1264		No text annotation
IL_9SRA_1571/2/1229:1232,
1/2/1251:1256		No text annotation
IL_9SRA_1581/2/1233:1236,
1/2/1247:1250		No text annotation
IL_9SRA_1591/2/1277:1282,
1/2/1303:1308		No text annotation
IL_9SRA_1601/2/1373:1375,
1/2/1470:1473		No text annotation
IL_9SRA_1611/2/1375:1378,
1/2/1466:1470		No text annotation
IL_9SRA_1621/2/1379:1381,
1/2/1463:1465		No text annotation
IL_9SRA_1631/2/1381:1383,
1/2/1460:1463		No text annotation
IL_9SRA_1641/2/1386:1388,
1/2/1455:1457		No text annotation
IL_9SRA_1651/2/1390:1393,
1/2/1450:1453		No text annotation
IL_9SRA_1661/2/1405:1408,
1/2/1435:1438		No text annotation
IL_9SRA_1741/3/87:89,
1/3/96:97		Single bulged U
homologous
IL_4V9F_107
IL_97561.7

Problematic loops

#loop idProblemSequence
IL_9SRA_006Stack and bulge
IL_9SRA_008Single bulged A
IL_9SRA_009No text annotation
IL_9SRA_015No text annotation
IL_9SRA_018No text annotation
IL_9SRA_019No text annotation
IL_9SRA_020Minor groove platform related
IL_9SRA_021No text annotation
IL_9SRA_022Single bulged U
IL_9SRA_026No text annotation
IL_9SRA_0277x6 Sarcin-Ricin; G-bulge
IL_9SRA_028AAA cross-strand stack
IL_9SRA_029Major groove intercalation
IL_9SRA_030tSH-tWH-tHS
IL_9SRA_040Kink-turn
IL_9SRA_041Single bulged A
IL_9SRA_0425x5 Sarcin-Ricin with intercalated A; G-bulge
IL_9SRA_043Minor groove platform
IL_9SRA_046Stack outside cWW
IL_9SRA_047No text annotation
IL_9SRA_048No text annotation
IL_9SRA_050UAA/GAN
IL_9SRA_051SSU/LSU pseudoknot
IL_9SRA_052Single bulged U
IL_9SRA_056No text annotation
IL_9SRA_057Bulged stacked bases
IL_9SRA_062No text annotation
IL_9SRA_090No text annotation
IL_9SRA_091No text annotation
IL_9SRA_092Kink-turn
IL_9SRA_093No text annotation
IL_9SRA_095Isolated tHS basepair with bulges
IL_9SRA_096Single stack bend
IL_9SRA_147No text annotation
IL_9SRA_148No text annotation
IL_9SRA_167No text annotation
IL_9SRA_168Single bulged A
IL_9SRA_169Major groove intercalation
IL_9SRA_170No text annotation
IL_9SRA_171Major groove minor groove platform; mini C-loop
IL_9SRA_172Symmetric double minor groove platform
IL_9SRA_1736x5 Sarcin-Ricin; G-bulge

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9SRA_0011/1/7:9,
1/1/23:29,
1/1/84:88		No text annotation
J3_9SRA_0021/1/144:145,
1/1/628:635,
1/1/661:662		No text annotation
geometric
J3_9E6Q_001
J3_68715.3
J3_9SRA_0031/1/144:145,
1/1/628:638,
1/1/649:662		No text annotation
geometric
J3_9E6Q_002
J3_17917.3
J3_9SRA_0041/1/146:149,
1/1/599:615,
1/1/622:627		No text annotation
homologous
J3_4V9F_013
J3_07616.3
J3_9SRA_0051/1/170:171,
1/1/184:190,
1/1/223:227		No text annotation
homologous
J3_4V9F_014
J3_01004.3
J3_9SRA_0061/1/416:418,
1/1/526:532,
1/1/553:558		No text annotation
J3_9SRA_0081/1/932:938,
1/1/1024:1026,
1/1/1042:1045		No text annotation
homologous
J3_4V9F_002
J3_46658.3
J3_9SRA_0091/1/947:949,
1/1/981:986,
1/1/1011:1014		No text annotation
homologous
J3_4V9F_003
J3_69816.3
J3_9SRA_0111/1/1557:1562,
1/1/1899:1901,
1/1/1913:1916		No text annotation
geometric
J3_9PN5_013
J3_76012.3
J3_9SRA_0121/1/1564:1568,
1/1/1878:1884,
1/1/1893:1897		No text annotation
J3_9SRA_0131/1/1604:1609,
1/1/1643:1647,
1/1/1664:1665		No text annotation
homologous
J3_4V9F_016
J3_94309.3
J3_9SRA_0141/1/1677:1680,
1/1/1689:1693,
1/1/1853:1859		No text annotation
J3_9SRA_0151/1/1702:1706,
1/1/1834:1835,
1/1/1839:1844		No text annotation
homologous
J3_4V9F_017
J3_08594.3
J3_9SRA_0161/1/2331:2333,
1/1/2436:2440,
1/1/2453:2458		No text annotation
geometric
J3_9DFE_014
J3_17460.1
J3_9SRA_0171/1/2513:2515,
1/1/2618:2629,
1/1/2656:2661		No text annotation
geometric
J3_8GLP_034
J3_04772.3
J3_9SRA_0191/1/2749:2752,
1/1/2777:2780,
1/1/2792:2799		No text annotation
homologous
J3_4V9F_009
J3_68010.1
J3_9SRA_0201/2/53:54,
1/2/370:376,
1/2/402:404		No text annotation
J3_9SRA_0211/2/53:60,
1/2/368:376,
1/2/402:404		No text annotation
J3_9SRA_0221/2/552:554,
1/2/618:621,
1/2/721:722		No text annotation
J3_9SRA_0231/2/552:554,
1/2/618:622,
1/2/718:722		No text annotation
J3_9SRA_0241/2/639:640,
1/2/684:692,
1/2/699:701		No text annotation
J3_9SRA_0251/2/793:796,
1/2/828:832,
1/2/839:845		No text annotation
J3_9SRA_0261/2/908:911,
1/2/1318:1325,
1/2/1345:1353		No text annotation
J3_9SRA_0271/2/915:918,
1/2/1209:1211,
1/2/1311:1314		No text annotation
J3_9SRA_0281/2/927:934,
1/2/945:956,
1/2/1195:1199		No text annotation
J3_9SRA_0291/2/962:966,
1/2/1008:1012,
1/2/1184:1189		No text annotation
J3_9SRA_0301/2/1028:1033,
1/2/1072:1077,
1/2/1162:1167		No text annotation
J3_9SRA_0311/2/1038:1040,
1/2/1047:1051,
1/2/1064:1067		No text annotation
J3_9SRA_0321/2/1081:1083,
1/2/1129:1132,
1/2/1155:1158		No text annotation
J3_9SRA_0331/2/1081:1083,
1/2/1129:1135,
1/2/1149:1158		No text annotation
J3_9SRA_0341/2/1211:1215,
1/2/1270:1277,
1/2/1308:1311		No text annotation
J4_9SRA_0011/1/372:377,
1/1/411:416,
1/1/558:560,
1/1/576:579		No text annotation
J4_9SRA_0021/1/1528:1535,
1/1/1553:1554,
1/1/1919:1923,
1/1/2250:2251		No text annotation
homologous
J4_4V9F_003
J4_75426.1
J4_9SRA_0031/1/1569:1573,
1/1/1598:1603,
1/1/1666:1667,
1/1/1870:1877		No text annotation
J4_9SRA_0041/1/1572:1573,
1/1/1598:1603,
1/1/1666:1667,
1/1/1870:1876		No text annotation
homologous
J4_4V9F_005
J4_48150.2
J4_9SRA_0051/1/1722:1723,
1/1/1739:1740,
1/1/1797:1798,
1/1/1816:1817		No text annotation
homologous
J4_4V9F_006
J4_75575.3
J4_9SRA_0061/1/2028:2032,
1/1/2044:2048,
1/1/2083:2086,
1/1/2216:2220		No text annotation
J4_9SRA_0071/1/2089:2091,
1/1/2146:2147,
1/1/2165:2174,
1/1/2208:2213		No text annotation
homologous
J4_4V9F_008
J4_42306.3
J4_9SRA_0081/1/2516:2520,
1/1/2574:2578,
1/1/2604:2606,
1/1/2615:2617		No text annotation
homologous
J4_4V9F_009
J4_98139.1
J4_9SRA_0091/1/2875:2878,
1/1/2908:2909,
1/1/2962:2964,
1/1/3000:3001		No text annotation
J4_9SRA_0101/2/111:119,
1/2/247:249,
1/2/295:298,
1/2/320:321		No text annotation
J4_9SRA_0111/2/139:141,
1/2/175:179,
1/2/207:213,
1/2/228:230		No text annotation
J4_9SRA_0121/2/541:543,
1/2/731:735,
1/2/778:788,
1/2/850:851		No text annotation
J5_9SRA_0011/1/161:168,
1/1/229:234,
1/1/243:244,
1/1/257:259,
1/1/280:282		No text annotation
J5_9SRA_0021/1/372:377,
1/1/411:418,
1/1/526:532,
1/1/553:560,
1/1/576:579		No text annotation
J5_9SRA_0031/1/683:685,
1/1/766:769,
1/1/784:785,
1/1/1519:1520,
1/1/2258:2259		No text annotation
J5_9SRA_0041/1/790:795,
1/1/917:920,
1/1/1060:1063,
1/1/1454:1455,
1/1/1508:1514		No text annotation
homologous
J5_4V9F_003
J5_15067.1
J5_9SRA_0051/1/807:810,
1/1/835:839,
1/1/846:849,
1/1/885:886,
1/1/901:905		No text annotation
J5_9SRA_0061/1/807:810,
1/1/835:839,
1/1/846:852,
1/1/884:886,
1/1/901:905		No text annotation
homologous
J5_4V9F_005
J5_63867.1
J5_9SRA_0071/1/1950:1958,
1/1/1982:1983,
1/1/2007:2008,
1/1/2012:2020,
1/1/2229:2231		No text annotation
homologous
J5_4V9F_006
J5_99177.3
J5_9SRA_0081/1/2297:2304,
1/1/2678:2686,
1/1/2730:2738,
1/1/2815:2820,
1/1/2838:2843		No text annotation
J5_9SRA_0091/1/2314:2317,
1/1/2473:2476,
1/1/2489:2490,
1/1/2512:2513,
1/1/2661:2667		No text annotation
homologous
J5_4V9F_008
J5_96125.3
J5_9SRA_0101/2/42:45,
1/2/412:415,
1/2/433:438,
1/2/458:465,
1/2/511:514		No text annotation
J5_9SRA_0111/2/66:69,
1/2/102:109,
1/2/323:325,
1/2/346:348,
1/2/359:363		No text annotation
J6_9SRA_0011/1/159:160,
1/1/283:287,
1/1/318:328,
1/1/335:339,
1/1/366:370,
1/1/581:588		No text annotation
J6_9SRA_0021/1/2314:2317,
1/1/2473:2476,
1/1/2489:2490,
1/1/2512:2515,
1/1/2618:2629,
1/1/2656:2667		No text annotation
J7_9SRA_0011/1/1068:1073,
1/1/1086:1087,
1/1/1197:1200,
1/1/1222:1227,
1/1/1238:1242,
1/1/1418:1419,
1/1/1444:1449		No text annotation

Problematic loops

#loop idProblemSequence
J3_9SRA_007No text annotation
J3_9SRA_010No text annotation
J3_9SRA_018No text annotation
J3_9SRA_0355S rRNA junction

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