RNA 3D Hub //

6HCJ Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6HCJ_0011/33/13:21No text annotation
homologous
HL_3WFS_001
NA
HL_6HCJ_1191/33/29:39No text annotation
homologous
HL_4WZD_209
NA
HL_6HCJ_0021/33/30:38tRNA anticodon loop
homologous
HL_6UFG_007
HL_06059.7
HL_6HCJ_0031/33/52:60T-loop with 2 stacked bulged bases
homologous
HL_6CFJ_108
HL_28252.9
HL_6HCJ_0041/51/30:52No text annotation
HL_6HCJ_0051/51/68:73No text annotation
homologous
HL_8C3A_002
NA
HL_6HCJ_0061/51/89:95No text annotation
homologous
HL_8C3A_003
NA
HL_6HCJ_0071/51/131:137No text annotation
geometric
HL_8G9Z_001
HL_75660.5
HL_6HCJ_0081/51/204:211T-loop with 2 stacked bulged bases
homologous
HL_8C3A_005
NA
HL_6HCJ_0091/51/222:226No text annotation
homologous
HL_8C3A_006
NA
HL_6HCJ_0101/51/230:238T-loop with unstacked turn
homologous
HL_5TBW_007
NA
HL_6HCJ_1591/51/289:298T-loop related
homologous
HL_8CRE_008
HL_77436.5
HL_6HCJ_0121/51/314:323Pseudoknot geometry
homologous
HL_8C3A_009
NA
HL_6HCJ_0131/51/368:373GNRA
homologous
HL_8C3A_010
NA
HL_6HCJ_1601/51/393:398GNRA
homologous
HL_8CRE_011
HL_37824.8
HL_6HCJ_1251/51/518:643No text annotation
HL_6HCJ_1611/51/755:908No text annotation
HL_6HCJ_0161/51/757:906No text annotation
HL_6HCJ_0171/51/962:970No text annotation
HL_6HCJ_1621/51/989:1065No text annotation
HL_6HCJ_0191/51/1178:1183No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_6HCJ_1631/51/1317:1326T-loop with 2 stacked bulged bases
homologous
HL_8CRE_013
HL_28252.9
HL_6HCJ_1271/51/1357:1382No text annotation
HL_6HCJ_0211/51/1361:1376No text annotation
HL_6HCJ_1641/51/1406B:1411ANo text annotation
HL_6HCJ_0231/51/1431:1453No text annotation
HL_6HCJ_1651/51/1479:1486No text annotation
homologous
HL_8CRE_017
HL_86870.2
HL_6HCJ_0251/51/1559:1568No text annotation
HL_6HCJ_1661/51/1593:1602No text annotation
homologous
HL_8CRE_019
HL_88205.2
HL_6HCJ_0271/51/1627:1635No text annotation
homologous
HL_8C3A_021
NA
HL_6HCJ_0281/51/1675:1680Externally structured
homologous
HL_5TBW_022
NA
HL_6HCJ_0291/51/1760:1772tRNA D-loop
geometric
HL_7UQ6_001
HL_20811.4
HL_6HCJ_0301/51/1814:1824No text annotation
HL_6HCJ_1671/51/1858:1876No text annotation
HL_6HCJ_0311/51/1864:1870GNRA
homologous
HL_8C3A_025
NA
HL_6HCJ_0321/51/1886:1893No text annotation
homologous
HL_5TBW_026
NA
HL_6HCJ_0331/51/2006:2013GNRA wlth tandem sheared
homologous
HL_8C3A_028
NA
HL_6HCJ_0341/51/2087:2270No text annotation
HL_6HCJ_0351/51/2317:2322GNRA
homologous
HL_5TBW_030
NA
HL_6HCJ_1681/51/2376:2384T-loop with 2 stacked bulged bases
homologous
HL_8CRE_030
HL_28252.9
HL_6HCJ_0371/51/2420:2426Pseudoknot geometry with 3' bulge
homologous
HL_8C3A_032
NA
HL_6HCJ_0381/51/2458:2463GNRA variation
homologous
HL_8C3A_033
NA
HL_6HCJ_0391/51/2487:2491No text annotation
HL_6HCJ_0401/51/2521:2534No text annotation
HL_6HCJ_0411/51/2559:2568No text annotation
geometric
HL_7KI3_001
HL_75660.5
HL_6HCJ_0421/51/2578:2583GNRA
homologous
HL_5TBW_036
NA
HL_6HCJ_0431/51/2624:2632No text annotation
homologous
HL_5TBW_037
NA
HL_6HCJ_0441/51/2664:2670No text annotation
homologous
HL_8C3A_038
NA
HL_6HCJ_0451/51/2704:2712No text annotation
HL_6HCJ_0461/51/2792:2799No text annotation
homologous
HL_5TBW_041
NA
HL_6HCJ_0471/51/2810:2816GNRA
homologous
HL_5TBW_042
NA
HL_6HCJ_1691/51/2867:2883No text annotation
HL_6HCJ_0481/51/2872:2877UNCG
homologous
HL_5TBW_043
NA
HL_6HCJ_1701/51/2901:3598No text annotation
HL_6HCJ_0501/51/3614:3618No text annotation
homologous
HL_8C3A_045
NA
HL_6HCJ_0511/51/3668:3674GNRA
homologous
HL_8C3A_047
NA
HL_6HCJ_1711/51/3724:3729GNRA
homologous
HL_8P9A_159
HL_37824.8
HL_6HCJ_0531/51/3795:3805No text annotation
geometric
HL_7VTI_001
HL_48417.6
HL_6HCJ_0541/51/3839:3843No text annotation
HL_6HCJ_1361/51/3869:3886No text annotation
HL_6HCJ_0551/51/3873:3882No text annotation
homologous
HL_5TBW_051
NA
HL_6HCJ_0561/51/3976:4035No text annotation
geometric
HL_1KH6_003
HL_27483.1
HL_6HCJ_0571/51/4137:4147No text annotation
homologous
HL_8C3A_054
NA
HL_6HCJ_1371/51/4191:4204No text annotation
HL_6HCJ_0581/51/4192:4202No text annotation
HL_6HCJ_0591/51/4208:4224No text annotation
HL_6HCJ_0601/51/4250:4258No text annotation
homologous
HL_5TBW_056
NA
HL_6HCJ_0611/51/4270:4277Pseudoknot geometry
homologous
HL_5TBW_057
NA
HL_6HCJ_0621/51/4301:4309No text annotation
homologous
HL_5TBW_058
NA
HL_6HCJ_0631/51/4319:4328No text annotation
HL_6HCJ_1721/51/4347:4365No text annotation
HL_6HCJ_0641/51/4352:4362No text annotation
geometric
HL_2ZZM_002
HL_13963.3
HL_6HCJ_1391/51/4412:4430No text annotation
HL_6HCJ_0651/51/4417:4425No text annotation
homologous
HL_5TBW_061
NA
HL_6HCJ_0661/51/4474:4481No text annotation
homologous
HL_5TBW_062
NA
HL_6HCJ_0671/51/4497:4503No text annotation
geometric
HL_5TBW_063
NA
HL_6HCJ_0681/51/4540:4545GNRA
homologous
HL_5TBW_064
NA
HL_6HCJ_0691/51/4603:4608GNRA
geometric
HL_5J7L_004
HL_37824.8
HL_6HCJ_0701/51/4646:4651Ribsomal LSU H95
homologous
HL_5TBW_066
NA
HL_6HCJ_0711/51/4688:4702No text annotation
homologous
HL_8C3A_068
NA
HL_6HCJ_0731/51/4906:4915No text annotation
HL_6HCJ_0741/51/4975:4983No text annotation
homologous
HL_8C3A_071
NA
HL_6HCJ_0751/51/5020:5029No text annotation
geometric
HL_5TBW_012
NA
HL_6HCJ_0761/71/32:45No text annotation
HL_6HCJ_1731/71/71:104No text annotation
HL_6HCJ_0771/71/85:92GNRA with extra cWW
geometric
HL_7A0S_056
HL_04259.3
HL_6HCJ_0781/81/47:56Pseudoknot with intercalation
geometric
HL_7A0S_001
HL_93438.2
HL_6HCJ_1421/81/50:75No text annotation
HL_6HCJ_0801/81/106:113No text annotation
geometric
HL_2Y9H_005
HL_86870.2
HL_6HCJ_0811/81/121:129No text annotation
geometric
HL_4V88_194
NA
HL_6HCJ_1741/A2/7:17No text annotation
homologous
HL_8CRE_191
HL_89881.5
HL_6HCJ_1751/A2/63:85No text annotation
HL_6HCJ_0831/A2/68:81No text annotation
HL_6HCJ_1451/A2/152:166No text annotation
HL_6HCJ_0841/A2/156:162No text annotation
geometric
HL_4V9F_011
HL_75660.5
HL_6HCJ_1461/A2/193:206No text annotation
HL_6HCJ_0851/A2/196:203No text annotation
geometric
HL_4WF9_009
HL_81100.2
HL_6HCJ_0871/A2/288:295T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_6HCJ_1761/A2/377:387No text annotation
HL_6HCJ_0901/A2/416:421No text annotation
homologous
HL_4V88_194
NA
HL_6HCJ_1471/A2/437:456No text annotation
HL_6HCJ_0911/A2/441:452No text annotation
homologous
HL_4V88_195
NA
HL_6HCJ_0921/A2/462:467UNCG
homologous
HL_4V88_196
NA
HL_6HCJ_0931/A2/498:504No text annotation
homologous
HL_4V88_197
NA
HL_6HCJ_1771/A2/539:544No text annotation
HL_6HCJ_1491/A2/563:592No text annotation
HL_6HCJ_0951/A2/565:585No text annotation
HL_6HCJ_0961/A2/618:623GNRA variation
homologous
HL_4V88_200
NA
HL_6HCJ_0981/A2/883:903No text annotation
geometric
HL_5D5L_002
HL_88364.2
HL_6HCJ_0991/A2/957:966No text annotation
homologous
HL_4V88_206
NA
HL_6HCJ_1001/A2/994:999GNRA
geometric
HL_1G1X_005
HL_37824.8
HL_6HCJ_1521/A2/1047:1071No text annotation
HL_6HCJ_1011/A2/1054:1064No text annotation
homologous
HL_4V88_208
NA
HL_6HCJ_1781/A2/1114:1119No text annotation
HL_6HCJ_1031/A2/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_6HCJ_1041/A2/1178:1183GNRA
homologous
HL_4V88_211
NA
HL_6HCJ_1051/A2/1245:1254No text annotation
geometric
HL_5J7L_143
HL_75660.5
HL_6HCJ_1541/A2/1290:1309No text annotation
HL_6HCJ_1061/A2/1294:1306No text annotation
HL_6HCJ_1791/A2/1353:1358GNRA
homologous
HL_8P9A_217
HL_37824.8
HL_6HCJ_1551/A2/1363:1375No text annotation
HL_6HCJ_1081/A2/1366:1373No text annotation
homologous
HL_4V88_215
NA
HL_6HCJ_1101/A2/1460:1466GNRA
homologous
HL_4V88_217
NA
HL_6HCJ_1561/A2/1563:1572No text annotation
HL_6HCJ_1111/A2/1565:1570GNRA
homologous
HL_4V88_218
NA
HL_6HCJ_1121/A2/1614:1625No text annotation
homologous
HL_4V88_219
NA
HL_6HCJ_1131/A2/1656:1668No text annotation
HL_6HCJ_1151/A2/1847:1852GNRA variation
homologous
HL_4V88_222
NA
HL_6HCJ_1571/q3/11:24No text annotation
homologous
HL_4WT8_218
NA
HL_6HCJ_1801/q3/31:39tRNA anticodon loop
homologous
HL_5IBB_210
HL_06059.7
HL_6HCJ_1181/q3/53:61T-loop with 2 stacked bulged bases
homologous
HL_3AMU_003
HL_28252.9

Problematic loops

#loop idProblemSequence
HL_6HCJ_120No text annotation
HL_6HCJ_121No text annotation
HL_6HCJ_122No text annotation
HL_6HCJ_123No text annotation
HL_6HCJ_011No text annotation
HL_6HCJ_124No text annotation
HL_6HCJ_014No text annotation
HL_6HCJ_015No text annotation
HL_6HCJ_126No text annotation
HL_6HCJ_018No text annotation
HL_6HCJ_020No text annotation
HL_6HCJ_022No text annotation
HL_6HCJ_128No text annotation
HL_6HCJ_024No text annotation
HL_6HCJ_129No text annotation
HL_6HCJ_026No text annotation
HL_6HCJ_130No text annotation
HL_6HCJ_131No text annotation
HL_6HCJ_036No text annotation
HL_6HCJ_132tRNA D-loop
HL_6HCJ_133No text annotation
HL_6HCJ_134No text annotation
HL_6HCJ_049No text annotation
HL_6HCJ_052GNRA with extra cWW
HL_6HCJ_135tRNA D-loop
HL_6HCJ_138No text annotation
HL_6HCJ_072No text annotation
HL_6HCJ_140No text annotation
HL_6HCJ_141No text annotation
HL_6HCJ_079No text annotation
HL_6HCJ_143No text annotation
HL_6HCJ_082No text annotation
HL_6HCJ_144No text annotation
HL_6HCJ_086No text annotation
HL_6HCJ_088No text annotation
HL_6HCJ_089No text annotation
HL_6HCJ_148No text annotation
HL_6HCJ_094GNRA with extra cWW
HL_6HCJ_150No text annotation
HL_6HCJ_097No text annotation
HL_6HCJ_151No text annotation
HL_6HCJ_102No text annotation
HL_6HCJ_153No text annotation
HL_6HCJ_107T-loop with 1 bulged base
HL_6HCJ_109No text annotation
HL_6HCJ_114No text annotation
HL_6HCJ_116No text annotation
HL_6HCJ_117No text annotation
HL_6HCJ_158No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6HCJ_0011/51/11:14,
1/81/143:145		Isolated cWH basepair
geometric
IL_2H1M_003
IL_10167.6
IL_6HCJ_0021/51/16:18,
1/81/139:141		Isolated cWH basepair
geometric
IL_4J50_001
IL_10167.6
IL_6HCJ_0031/51/81:88,
1/51/96:102		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5TBW_006
NA
IL_6HCJ_0041/51/118:121,
1/51/152:153		Stack outside cWW
geometric
IL_5J7L_268
IL_56987.1
IL_6HCJ_2971/51/118:126,
1/51/142:153		No text annotation
IL_6HCJ_0051/51/121:122,
1/51/147:152		No text annotation
geometric
IL_5TBW_007
NA
IL_6HCJ_2981/51/121:126,
1/51/142:152		No text annotation
IL_6HCJ_0061/51/125:127,
1/51/141:144		Isolated non-canonical cWW pair
homologous
IL_8C3A_008
NA
IL_6HCJ_0071/51/168:174,
1/51/262:267		No text annotation
IL_6HCJ_0081/51/174:177,
1/51/260:262		No text annotation
geometric
IL_4V9F_053
IL_09990.4
IL_6HCJ_0091/51/177:179,
1/51/257:260		Other IL
geometric
IL_5TBW_064
NA
IL_6HCJ_0101/51/180:182,
1/51/255:256		No text annotation
geometric
IL_8C3A_038
NA
IL_6HCJ_2111/51/180:189,
1/51/252:256		No text annotation
IL_6HCJ_0111/51/182:189,
1/51/252:255		No text annotation
IL_6HCJ_0121/51/195:196,
1/51/244:246		Single bulged C
geometric
IL_1DQF_001
IL_61258.15
IL_6HCJ_0131/51/199:202,
1/51/213:215		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_87907.2
IL_6HCJ_0141/51/339:342,
1/81/32:33		Minor groove platform
geometric
IL_7RQB_073
NA
IL_6HCJ_2991/51/345:379,
1/81/21:29		No text annotation
IL_6HCJ_0151/51/348:350,
1/81/25:26		Single bulged A
homologous
IL_8C3A_014
NA
IL_6HCJ_0161/51/387:390,
1/51/401:414		No text annotation
homologous
IL_5TBW_014
NA
IL_6HCJ_3001/51/423:427,
1/81/8:11		No text annotation
IL_6HCJ_0171/51/425:427,
1/81/8:9		Single stack bend
geometric
IL_5J7L_044
IL_26793.1
IL_6HCJ_0181/51/427:428,
1/81/6:8		Single stack bend
geometric
IL_5TBW_070
NA
IL_6HCJ_0191/51/443:446,
1/51/1300:1304		No text annotation
IL_6HCJ_3011/51/448:450,
1/51/1297:1298		No text annotation
IL_6HCJ_0211/51/458:460,
1/51/695:698		Isolated non-canonical cWW pair
geometric
IL_3TD0_002
IL_57744.1
IL_6HCJ_2171/51/462:472,
1/51/682:693		No text annotation
IL_6HCJ_2181/51/472:474,
1/51/681:682		Single stack bend
geometric
IL_5J7L_391
IL_26793.1
IL_6HCJ_3021/51/474:475,
1/51/679:681		Single stack bend
geometric
IL_5J7L_032
IL_26793.1
IL_6HCJ_0221/51/481:487,
1/51/669:673		Other IL
geometric
IL_4WF9_084
NA
IL_6HCJ_2201/51/481:491,
1/51/662:673		No text annotation
IL_6HCJ_0231/51/487:488,
1/51/665:669		Multiple bulged bases
geometric
IL_5XWP_001
IL_82107.5
IL_6HCJ_0241/51/491:493,
1/51/661:662		Single bulged U
geometric
IL_8TQX_002
IL_89505.4
IL_6HCJ_0251/51/494:500,
1/51/655:660		No text annotation
IL_6HCJ_3031/51/494:515,
1/51/646:660		No text annotation
IL_6HCJ_0261/51/508:510,
1/51/649:650		Single bulged A
geometric
IL_4V88_409
NA
IL_6HCJ_0271/51/709:710,
1/51/1286:1288		Single bulged G
geometric
IL_4LFB_036
IL_00225.14
IL_6HCJ_0281/51/723:725,
1/51/941:945		No text annotation
IL_6HCJ_3041/51/726:731,
1/51/938:940		No text annotation
IL_6HCJ_3051/51/726:739,
1/51/923:940		No text annotation
IL_6HCJ_0291/51/727:731,
1/51/938:939		No text annotation
IL_6HCJ_0301/51/731:737,
1/51/927:938		No text annotation
IL_6HCJ_3061/51/731:739,
1/51/923:938		No text annotation
IL_6HCJ_0311/51/737:739,
1/51/923:927		No text annotation
IL_6HCJ_3071/51/744:752,
1/51/911:920		No text annotation
IL_6HCJ_0331/51/1074:1077,
1/51/1233:1236		Tandem non-canonical cWW pairs
geometric
IL_6CZR_168
NA
IL_6HCJ_3081/51/1074:1084,
1/51/1213:1236		No text annotation
IL_6HCJ_0351/51/1086:1088,
1/51/1208:1211		Isolated non-canonical cWW pair
geometric
IL_5MSF_001
IL_87907.2
IL_6HCJ_3091/51/1086:1094,
1/51/1202:1211		No text annotation
IL_6HCJ_0361/51/1097:1098,
1/51/1197:1199		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_6HCJ_0371/51/1173:1177,
1/51/1184:1188		No text annotation
IL_6HCJ_2271/51/1173:1178,
1/51/1183:1188		No text annotation
IL_6HCJ_0381/51/1357:1360,
1/51/1379:1382		No text annotation
IL_6HCJ_0391/51/1360:1361,
1/51/1376:1379		Major groove intercalation
geometric
IL_1U9S_003
IL_82107.5
IL_6HCJ_0401/51/1425:1431,
1/51/1453:1460		No text annotation
IL_6HCJ_0411/51/1467:1468,
1/51/1496:1498		Single bulged A
homologous
IL_5TBW_024
NA
IL_6HCJ_0421/51/1469:1472,
1/51/1493:1495		No text annotation
geometric
IL_4N0T_004
IL_99358.1
IL_6HCJ_0431/51/1472:1474,
1/51/1490:1493		No text annotation
geometric
IL_4N0T_004
IL_99358.1
IL_6HCJ_2291/51/1472:1476,
1/51/1489:1493		No text annotation
IL_6HCJ_0441/51/1474:1476,
1/51/1489:1490		Single stack bend
geometric
IL_7A0S_005
IL_90729.1
IL_6HCJ_0451/51/1520:1522,
1/51/1655:1657		Isolated non-canonical cWW pair
homologous
IL_8C3A_029
NA
IL_6HCJ_0461/51/1522:1526,
1/51/1648:1655		No text annotation
homologous
IL_8C3A_030
NA
IL_6HCJ_3111/51/1541:1592,
1/51/1603:1618		No text annotation
IL_6HCJ_0471/51/1550:1551,
1/51/1576:1578		Single bulged G
homologous
IL_8C3A_032
NA
IL_6HCJ_0481/51/1551:1558,
1/51/1569:1576		No text annotation
IL_6HCJ_0491/51/1585:1590,
1/51/1605:1608		No text annotation
IL_6HCJ_0501/51/1624:1626,
1/51/1636:1640		Multiple bulged bases
geometric
IL_5J7L_265
IL_06549.2
IL_6HCJ_0511/51/1686:1688,
1/51/1848:1851		No text annotation
IL_6HCJ_0521/51/1694:1721,
1/51/1841:1842		No text annotation
IL_6HCJ_3121/51/1723:1725,
1/51/1838:1839		No text annotation
homologous
IL_8CRE_040
IL_00225.14
IL_6HCJ_0541/51/1732:1739,
1/51/1789:1797		No text annotation
IL_6HCJ_0551/51/1739:1745,
1/51/1785:1789		No text annotation
geometric
IL_4V9F_035
IL_06691.1
IL_6HCJ_0561/51/1745:1751,
1/51/1779:1785		No text annotation
IL_6HCJ_3131/51/1753:1756,
1/51/1776:1777		No text annotation
IL_6HCJ_0581/51/1857:1861,
1/51/1873:1877		No text annotation
IL_6HCJ_0601/51/1904:1909,
1/51/2067:2072		UAA/GAN with extra cWW
geometric
IL_4WF9_104
IL_49767.8
IL_6HCJ_3141/51/1905:1912,
1/51/2051:2071		No text annotation
IL_6HCJ_0611/51/1909:1918,
1/51/2064:2067		Tandem non-canonical cWW pairs
geometric
IL_7R9G_002
IL_85033.2
IL_6HCJ_2331/51/1914:1944,
1/51/2038:2049		No text annotation
IL_6HCJ_0621/51/1918:1920,
1/51/2063:2064		No text annotation
IL_6HCJ_0631/51/1920:1922,
1/51/2062:2063		No text annotation
IL_6HCJ_0641/51/1926:1944,
1/51/2038:2058		No text annotation
IL_6HCJ_3151/51/1946:1948,
1/51/2035:2036		Single bulged U
homologous
IL_8P9A_281
IL_89505.4
IL_6HCJ_3161/51/1955:2005,
1/51/2014:2028		No text annotation
IL_6HCJ_0661/51/2001:2005,
1/51/2014:2016		Major groove platform with extra cWW
homologous
IL_8C3A_059
NA
IL_6HCJ_0671/51/2083:2085,
1/51/2272:2273		No text annotation
IL_6HCJ_2361/51/2294:2301,
1/51/2334:2340		No text annotation
IL_6HCJ_0681/51/2299:2301,
1/51/2334:2335		Single bulged A
homologous
IL_8C3A_062
NA
IL_6HCJ_3171/51/2301:2314,
1/51/2325:2334		No text annotation
IL_6HCJ_0691/51/2302:2309,
1/51/2329:2333		Kink-turn
homologous
IL_5TBW_059
NA
IL_6HCJ_0701/51/2311:2314,
1/51/2325:2327		Isolated non-canonical cWW pair
homologous
IL_8C3A_064
NA
IL_6HCJ_0711/51/2357:2364,
1/51/3858:3864		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_6HCJ_3181/51/2415:2419,
1/51/2427:2429		C-loop
geometric
IL_7A0S_047
IL_83150.2
IL_6HCJ_0731/51/2446:2450,
1/51/2509:2514		UAA/GAN
homologous
IL_5TBW_063
NA
IL_6HCJ_3191/51/2542:2547,
1/51/2772:2774		No text annotation
IL_6HCJ_2411/51/2595:2602,
1/51/2737:2750		No text annotation
IL_6HCJ_0751/51/2613:2614,
1/51/2724:2726		Single bulged A
geometric
IL_7A0S_012
IL_31462.7
IL_6HCJ_3201/51/2613:2615,
1/51/2722:2726		No text annotation
geometric
IL_6ZDU_001
IL_99358.1
IL_6HCJ_0761/51/2614:2616,
1/51/2721:2724		Other IL
geometric
IL_5TBW_064
NA
IL_6HCJ_0771/51/2645:2648,
1/51/2685:2689		tSH-tHW
geometric
IL_7RQB_011
NA
IL_6HCJ_2431/51/2650:2662,
1/51/2672:2683		No text annotation
IL_6HCJ_0781/51/2651:2653,
1/51/2681:2682		Single bulged G
geometric
IL_3NDB_004
IL_00225.14
IL_6HCJ_0791/51/2654:2662,
1/51/2672:2680		No text annotation
IL_6HCJ_0801/51/2831:2838,
1/51/3850:3854		No text annotation
IL_6HCJ_3211/51/2832:2846,
1/51/3842:3853		No text annotation
IL_6HCJ_2451/51/2846:2855,
1/51/3837:3842		No text annotation
IL_6HCJ_0811/51/2867:2872,
1/51/2877:2883		tSH-tSH-tHH-tHS
geometric
IL_5TBW_078
NA
IL_6HCJ_0821/51/2889:2891,
1/51/3610:3612		Isolated non-canonical cWW pair
homologous
IL_5TBW_079
NA
IL_6HCJ_0831/51/2896:2897,
1/51/3602:3605		No text annotation
homologous
IL_8C3A_086
NA
IL_6HCJ_0841/51/3632:3633,
1/51/3827:3829		Single bulged A
homologous
IL_8C3A_087
NA
IL_6HCJ_0851/51/3660:3665,
1/51/3677:3684		Kink-turn related
homologous
IL_5TBW_083
NA
IL_6HCJ_0861/51/3699:3708,
1/51/3742:3751		No text annotation
IL_6HCJ_0871/51/3708:3710,
1/51/3741:3742		Single stack bend
geometric
IL_5J7L_044
IL_26793.1
IL_6HCJ_0881/51/3710:3714,
1/51/3739:3741		No text annotation
homologous
IL_8C3A_092
NA
IL_6HCJ_2471/51/3710:3721,
1/51/3733:3741		No text annotation
IL_6HCJ_2481/51/3721:3722,
1/51/3731:3733		Single stack bend
geometric
IL_8C3A_012
NA
IL_6HCJ_3221/51/3894:3898,
1/51/4563:4566		No text annotation
IL_6HCJ_0901/51/3895:3898,
1/51/4563:4565		Major groove platform with extra pair
homologous
IL_5TBW_091
NA
IL_6HCJ_0911/51/3900:3902,
1/51/4558:4561		No text annotation
homologous
IL_8C3A_097
NA
IL_6HCJ_0921/51/3916:3918,
1/51/4383:4387		No text annotation
IL_6HCJ_0931/51/3927:3929,
1/51/4181:4184		No text annotation
homologous
IL_8C3A_100
NA
IL_6HCJ_3231/51/3927:3932,
1/51/4178:4184		No text annotation
IL_6HCJ_3241/51/3941:3943,
1/51/4071:4072		Single stack bend
geometric
IL_5J7L_032
IL_26793.1
IL_6HCJ_2511/51/3943:3952,
1/51/4060:4071		No text annotation
IL_6HCJ_0951/51/3955:3970,
1/51/4051:4057		No text annotation
IL_6HCJ_2521/51/3955:3976,
1/51/4035:4057		No text annotation
IL_6HCJ_0961/51/3970:3974,
1/51/4037:4051		No text annotation
IL_6HCJ_0971/51/4082:4088,
1/51/4161:4164		No text annotation
homologous
IL_5TBW_096
NA
IL_6HCJ_3251/51/4091:4130,
1/51/4154:4158		No text annotation
IL_6HCJ_0991/51/4191:4192,
1/51/4202:4204		Single bulged A
geometric
IL_4V9F_079
IL_31462.7
IL_6HCJ_1001/51/4291:4294,
1/51/4316:4318		Isolated non-canonical cWW pair
geometric
IL_4V88_455
NA
IL_6HCJ_2541/51/4291:4297,
1/51/4314:4318		No text annotation
IL_6HCJ_1011/51/4295:4297,
1/51/4314:4315		Single stack bend
geometric
IL_5J7L_044
IL_26793.1
IL_6HCJ_1021/51/4297:4298,
1/51/4312:4314		Single stack bend
geometric
IL_5J7L_032
IL_26793.1
IL_6HCJ_1031/51/4347:4351,
1/51/4363:4365		No text annotation
geometric
IL_8C3A_419
NA
IL_6HCJ_1041/51/4400:4408,
1/51/4434:4444		No text annotation
IL_6HCJ_1051/51/4412:4416,
1/51/4426:4430		No text annotation
homologous
IL_8C3A_114
NA
IL_6HCJ_1061/51/4453:4455,
1/51/4525:4528		Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010
IL_07785.1
IL_6HCJ_1071/51/4456:4458,
1/51/4520:4524		Isolated non-canonical cWW with bulges
geometric
IL_5TBW_108
NA
IL_6HCJ_1081/51/4458:4459,
1/51/4517:4520		Multiple bulged bases
homologous
IL_5TBW_109
NA
IL_6HCJ_3261/51/4462:4466,
1/51/4491:4514		No text annotation
IL_6HCJ_1091/51/4466:4470,
1/51/4485:4491		No text annotation
IL_6HCJ_1101/51/4495:4497,
1/51/4503:4505		Isolated non-canonical cWW pair
homologous
IL_5TBW_112
NA
IL_6HCJ_3271/51/4536:4538,
1/51/4547:4550		Isolated non-canonical cWW pair
geometric
IL_7A0S_014
IL_87907.2
IL_6HCJ_1111/51/4537:4538,
1/51/4547:4549		Single bulged A
geometric
IL_7RQB_101
NA
IL_6HCJ_1121/51/4580:4582,
1/51/4721:4723		Isolated cWH basepair
geometric
IL_4E5C_001
IL_10167.6
IL_6HCJ_1131/51/4582:4585,
1/51/4717:4721		Double sheared
geometric
IL_4XWF_001
IL_09705.15
IL_6HCJ_1141/51/4590:4592,
1/51/4618:4620		Isolated non-canonical cWW pair
homologous
IL_5TBW_115
NA
IL_6HCJ_3281/51/4594:4603,
1/51/4608:4616		No text annotation
IL_6HCJ_1151/51/4596:4603,
1/51/4608:4614		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5TBW_116
NA
IL_6HCJ_3291/51/4624:4629,
1/51/4669:4673		No text annotation
IL_6HCJ_1171/51/4632:4637,
1/51/4662:4666		UAA/GAN related
geometric
IL_5TBW_118
NA
IL_6HCJ_3301/51/4632:4640,
1/51/4659:4666		No text annotation
IL_6HCJ_1181/51/4637:4641,
1/51/4658:4662		No text annotation
geometric
IL_5TBW_121
NA
IL_6HCJ_3311/51/4641:4642,
1/51/4655:4658		No text annotation
homologous
IL_8CRE_128
IL_42626.2
IL_6HCJ_1201/51/4679:4685,
1/51/4705:4711		No text annotation
IL_6HCJ_3321/51/4738:4746,
1/51/4954:4961		No text annotation
IL_6HCJ_1221/51/4756:4766,
1/51/4868:4877		No text annotation
IL_6HCJ_1231/51/4769:4773,
1/51/4862:4865		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_6HCJ_3331/51/4769:4775,
1/51/4860:4865		No text annotation
IL_6HCJ_2651/51/4885:4888,
1/51/4931:4934		Tandem non-canonical cWW pairs
geometric
IL_4K27_003
IL_77658.1
IL_6HCJ_1251/51/4890:4896,
1/51/4924:4929		No text annotation
IL_6HCJ_3341/51/4896:4902,
1/51/4919:4924		No text annotation
IL_6HCJ_1261/51/4898:4903,
1/51/4918:4922		No text annotation
IL_6HCJ_3351/51/4970:4994,
1/51/5057:5063		No text annotation
IL_6HCJ_1271/51/4992:4996,
1/51/5055:5059		No text annotation
geometric
IL_5TBW_121
NA
IL_6HCJ_1281/51/4996:4998,
1/51/5052:5055		Single bulged G, near cWW
geometric
IL_6CZR_128
NA
IL_6HCJ_2691/51/4999:5009,
1/51/5039:5051		No text annotation
IL_6HCJ_1291/51/5012:5017,
1/51/5032:5036		No text annotation
IL_6HCJ_3361/51/5012:5020,
1/51/5029:5036		No text annotation
IL_6HCJ_1301/71/15:17,
1/71/61:64		Isolated non-canonical cWW pair
geometric
IL_7A0S_026
IL_87907.2
IL_6HCJ_1311/71/19:27,
1/71/52:59		No text annotation
IL_6HCJ_3371/71/20:30,
1/71/47:58		No text annotation
IL_6HCJ_1321/71/27:30,
1/71/47:52		No text annotation
IL_6HCJ_1331/71/71:78,
1/71/98:104		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5TBW_377
NA
IL_6HCJ_1341/71/78:82,
1/71/94:98		Other IL
geometric
IL_4WF9_084
NA
IL_6HCJ_1351/71/82:85,
1/71/92:94		Isolated non-canonical cWW pair
geometric
IL_5TBW_378
NA
IL_6HCJ_1361/A2/23:25,
1/A2/649:651		Isolated non-canonical cWW pair
geometric
IL_4M4O_001
IL_87907.2
IL_6HCJ_1371/A2/34:36,
1/A2/519:521		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_6HCJ_1381/A2/37:40,
1/A2/514:518		Double sheared
geometric
IL_4WF9_016
IL_09705.15
IL_6HCJ_1391/A2/41:47,
1/A2/479:481		No text annotation
homologous
IL_4V88_387
NA
IL_6HCJ_1401/A2/49:52,
1/A2/475:477		No text annotation
geometric
IL_4P3T_002
NA
IL_6HCJ_1411/A2/62:68,
1/A2/81:86		No text annotation
IL_6HCJ_1421/A2/108:115,
1/A2/348:353		No text annotation
geometric
IL_5TBW_476
NA
IL_6HCJ_1431/A2/116:121,
1/A2/343:347		No text annotation
homologous
IL_4V88_393
NA
IL_6HCJ_2741/A2/144:146,
1/A2/174:175		Single stack bend
geometric
IL_5J7L_269
IL_26793.1
IL_6HCJ_2751/A2/146:151,
1/A2/167:174		No text annotation
IL_6HCJ_1451/A2/151:156,
1/A2/162:167		No text annotation
IL_6HCJ_1461/A2/188:192,
1/A2/207:211		No text annotation
IL_6HCJ_3381/A2/216:221,
1/A2/300:309		No text annotation
IL_6HCJ_1481/A2/316:320,
1/A2/331:334		No text annotation
IL_6HCJ_1491/A2/358:364,
1/A2/396:404		No text annotation
IL_6HCJ_3391/A2/366:371,
1/A2/393:394		No text annotation
homologous
IL_8P9A_392
IL_47074.2
IL_6HCJ_1511/A2/411:413,
1/A2/424:429		No text annotation
homologous
IL_4V88_404
NA
IL_6HCJ_1521/A2/437:439,
1/A2/454:456		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_6HCJ_1531/A2/459:461,
1/A2/468:470		Isolated near basepair
homologous
IL_4V88_406
NA
IL_6HCJ_3401/A2/487:489,
1/A2/511:512		Single bulged U
geometric
IL_8P9A_396
IL_89505.4
IL_6HCJ_1541/A2/491:496,
1/A2/506:509		C-loop with extra cWW pair
homologous
IL_4V88_408
NA
IL_6HCJ_2781/A2/491:498,
1/A2/504:509		No text annotation
IL_6HCJ_3411/A2/528:537,
1/A2/546:557		No text annotation
IL_6HCJ_1551/A2/563:565,
1/A2/585:592		No text annotation
homologous
IL_8C3A_420
NA
IL_6HCJ_1561/A2/599:608,
1/A2/635:637		Isolated non-canonical cWW pair
geometric
IL_4V88_470
NA
IL_6HCJ_3421/A2/611:617,
1/A2/624:632		No text annotation
homologous
IL_8CRE_423
IL_54177.4
IL_6HCJ_1581/A2/663:665,
1/A2/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_87907.2
IL_6HCJ_1591/A2/673:675,
1/A2/1030:1032		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_6HCJ_3431/A2/673:680,
1/A2/1025:1032		No text annotation
IL_6HCJ_1601/A2/676:681,
1/A2/1024:1029		No text annotation
geometric
IL_8ZA4_001
IL_76308.6
IL_6HCJ_1611/A2/692:696,
1/A2/730:734		No text annotation
geometric
IL_5TBW_121
NA
IL_6HCJ_1621/A2/802:803,
1/A2/860:863		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_6HCJ_1631/A2/805:807,
1/A2/856:858		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_6HCJ_1641/A2/877:879,
1/A2/907:909		Isolated non-canonical cWW pair
geometric
IL_4LFB_006
IL_87907.2
IL_6HCJ_1661/A2/922:923,
1/A2/1019:1022		Major groove platform; stack outside cWW
geometric
IL_4V88_428
NA
IL_6HCJ_1671/A2/924:927,
1/A2/1014:1018		Tandem non-canonical cWW pairs
geometric
IL_4V88_429
NA
IL_6HCJ_3441/A2/924:935,
1/A2/1007:1018		No text annotation
IL_6HCJ_1681/A2/927:931,
1/A2/1010:1014		No text annotation
geometric
IL_5TBW_121
NA
IL_6HCJ_1691/A2/931:935,
1/A2/1007:1010		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_6HCJ_3451/A2/938:945,
1/A2/981:1004		No text annotation
IL_6HCJ_1701/A2/941:947,
1/A2/979:985		No text annotation
IL_6HCJ_3461/A2/950:956,
1/A2/967:976		No text annotation
homologous
IL_8P9A_422
IL_57741.1
IL_6HCJ_1711/A2/952:956,
1/A2/967:974		Kink-turn
homologous
IL_4V88_434
NA
IL_6HCJ_1721/A2/1041:1047,
1/A2/1071:1074		No text annotation
IL_6HCJ_1731/A2/1047:1051,
1/A2/1067:1071		tSH-tHW-tHS
geometric
IL_6CZR_145
NA
IL_6HCJ_3471/A2/1091:1096,
1/A2/1136:1158		No text annotation
IL_6HCJ_1741/A2/1098:1103,
1/A2/1129:1134		No text annotation
geometric
IL_5TBW_476
NA
IL_6HCJ_3481/A2/1108:1110,
1/A2/1123:1124		Minor groove platform
geometric
IL_8P9A_401
IL_51454.3
IL_6HCJ_3491/A2/1168:1175,
1/A2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_8CRE_442
IL_41756.4
IL_6HCJ_1771/A2/1203:1206,
1/A2/1692:1696		No text annotation
IL_6HCJ_1781/A2/1206:1212,
1/A2/1687:1692		No text annotation
geometric
IL_6O5F_001
NA
IL_6HCJ_1791/A2/1214:1217,
1/A2/1681:1685		C-loop
homologous
IL_4V88_443
NA
IL_6HCJ_1801/A2/1230:1235,
1/A2/1523:1528		No text annotation
geometric
IL_6O5F_001
NA
IL_6HCJ_2881/A2/1230:1236,
1/A2/1521:1528		No text annotation
IL_6HCJ_1811/A2/1235:1236,
1/A2/1521:1523		Minor groove platform
homologous
IL_4V88_445
NA
IL_6HCJ_1821/A2/1279:1290,
1/A2/1309:1318		No text annotation
homologous
IL_8P9A_435
NA
IL_6HCJ_1831/A2/1290:1294,
1/A2/1306:1309		No text annotation
IL_6HCJ_1841/A2/1325:1327,
1/A2/1502:1503		Single bulged U
homologous
IL_4V88_449
NA
IL_6HCJ_1851/A2/1328:1335,
1/A2/1492:1501		No text annotation
IL_6HCJ_1861/A2/1335:1339,
1/A2/1487:1492		No text annotation
geometric
IL_5TBW_121
NA
IL_6HCJ_1871/A2/1345:1349,
1/A2/1380:1384		No text annotation
IL_6HCJ_1881/A2/1363:1365,
1/A2/1374:1375		Minor groove platform
homologous
IL_8C3A_460
NA
IL_6HCJ_1891/A2/1395:1399,
1/A2/1447:1450		Tandem non-canonical cWW pairs
geometric
IL_3WBM_003
IL_85033.2
IL_6HCJ_1901/A2/1399:1405,
1/A2/1441:1447		No text annotation
IL_6HCJ_1911/A2/1412:1414,
1/A2/1426:1429		No text annotation
IL_6HCJ_1921/A2/1536:1539,
1/A2/1594:1597		No text annotation
IL_6HCJ_2891/A2/1540:1558,
1/A2/1577:1593		No text annotation
IL_6HCJ_1931/A2/1550:1558,
1/A2/1577:1582		180 degree turn
geometric
IL_5J7L_055
IL_11344.2
IL_6HCJ_1941/A2/1560:1562,
1/A2/1573:1575		Isolated non-canonical cWW pair
geometric
IL_5TBW_016
NA
IL_6HCJ_1951/A2/1700:1702,
1/A2/1833:1836		No text annotation
homologous
IL_4V88_463
NA
IL_6HCJ_1961/A2/1702:1705,
1/A2/1829:1833		No text annotation
homologous
IL_8P9A_453
IL_65718.4
IL_6HCJ_3501/A2/1706:1711,
1/A2/1822:1828		No text annotation
IL_6HCJ_1981/A2/1713:1717,
1/A2/1817:1820		No text annotation
IL_6HCJ_2921/A2/1714:1722,
1/A2/1812:1819		No text annotation
IL_6HCJ_1991/A2/1717:1722,
1/A2/1812:1817		No text annotation
IL_6HCJ_3511/A2/1729:1733,
1/A2/1801:1805		No text annotation
IL_6HCJ_2011/A2/1733:1736,
1/A2/1798:1801		Double sheared
geometric
IL_3D0U_002
IL_09705.15
IL_6HCJ_3521/A2/1737:1741,
1/A2/1793:1797		Partly complementary
geometric
IL_7VYX_004
IL_49751.4
IL_6HCJ_2031/A2/1742:1746,
1/A2/1788:1792		Triple sheared
homologous
IL_4V88_474
NA
IL_6HCJ_2041/A2/1749:1751,
1/A2/1782:1785		No text annotation
homologous
IL_4V88_475
NA
IL_6HCJ_2951/A2/1749:1753,
1/A2/1779:1785		No text annotation
IL_6HCJ_2051/A2/1751:1753,
1/A2/1779:1782		Other IL
geometric
IL_5TBW_064
NA
IL_6HCJ_2061/A2/1840:1841,
1/A2/1858:1860		Single stack bend
geometric
IL_5TBW_070
NA
IL_6HCJ_3531/q3/3:6,
1/q3/68:70		No text annotation

Problematic loops

#loop idProblemSequence
IL_6HCJ_208No text annotation
IL_6HCJ_209No text annotation
IL_6HCJ_210No text annotation
IL_6HCJ_212Tandem non-canonical cWW pairs
IL_6HCJ_213No text annotation
IL_6HCJ_214No text annotation
IL_6HCJ_215Partly complementary
IL_6HCJ_020Isolated non-canonical cWW pair
IL_6HCJ_216Tandem non-canonical cWW pairs
IL_6HCJ_219No text annotation
IL_6HCJ_221No text annotation
IL_6HCJ_222No text annotation
IL_6HCJ_223No text annotation
IL_6HCJ_224No text annotation
IL_6HCJ_032No text annotation
IL_6HCJ_225No text annotation
IL_6HCJ_034No text annotation
IL_6HCJ_226No text annotation
IL_6HCJ_228No text annotation
IL_6HCJ_310No text annotation
IL_6HCJ_053Tandem non-canonical cWW pairs
IL_6HCJ_230Partly complementary
IL_6HCJ_231No text annotation
IL_6HCJ_057No text annotation
IL_6HCJ_059Isolated cWS basepair
IL_6HCJ_232No text annotation
IL_6HCJ_065Isolated non-canonical cWW with bulges
IL_6HCJ_234Tandem non-canonical cWW pairs
IL_6HCJ_235No text annotation
IL_6HCJ_237No text annotation
IL_6HCJ_072No text annotation
IL_6HCJ_238No text annotation
IL_6HCJ_239No text annotation
IL_6HCJ_074No text annotation
IL_6HCJ_240Tandem non-canonical cWW pairs
IL_6HCJ_242No text annotation
IL_6HCJ_244No text annotation
IL_6HCJ_246No text annotation
IL_6HCJ_089No text annotation
IL_6HCJ_249No text annotation
IL_6HCJ_250No text annotation
IL_6HCJ_094No text annotation
IL_6HCJ_253No text annotation
IL_6HCJ_098No text annotation
IL_6HCJ_255No text annotation
IL_6HCJ_256No text annotation
IL_6HCJ_257No text annotation
IL_6HCJ_258Partly complementary
IL_6HCJ_259No text annotation
IL_6HCJ_116No text annotation
IL_6HCJ_260No text annotation
IL_6HCJ_119Isolated non-canonical cWW pair
IL_6HCJ_261No text annotation
IL_6HCJ_262No text annotation
IL_6HCJ_121No text annotation
IL_6HCJ_263No text annotation
IL_6HCJ_264No text annotation
IL_6HCJ_124No text annotation
IL_6HCJ_266No text annotation
IL_6HCJ_267No text annotation
IL_6HCJ_268Tandem non-canonical cWW pairs
IL_6HCJ_270No text annotation
IL_6HCJ_271No text annotation
IL_6HCJ_272Partly complementary
IL_6HCJ_273No text annotation
IL_6HCJ_144No text annotation
IL_6HCJ_276No text annotation
IL_6HCJ_147No text annotation
IL_6HCJ_150No text annotation
IL_6HCJ_277No text annotation
IL_6HCJ_279No text annotation
IL_6HCJ_280No text annotation
IL_6HCJ_157No text annotation
IL_6HCJ_281No text annotation
IL_6HCJ_165No text annotation
IL_6HCJ_282No text annotation
IL_6HCJ_283No text annotation
IL_6HCJ_284No text annotation
IL_6HCJ_285No text annotation
IL_6HCJ_286No text annotation
IL_6HCJ_175No text annotation
IL_6HCJ_176No text annotation
IL_6HCJ_287No text annotation
IL_6HCJ_290Tandem non-canonical cWW pairs
IL_6HCJ_197No text annotation
IL_6HCJ_291No text annotation
IL_6HCJ_293No text annotation
IL_6HCJ_200No text annotation
IL_6HCJ_202No text annotation
IL_6HCJ_294No text annotation
IL_6HCJ_296No text annotation
IL_6HCJ_207No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6HCJ_0011/51/112:116,
1/51/155:160,
1/51/275:278		No text annotation
J3_6HCJ_0421/51/196:201,
1/51/214:228,
1/51/240:244		No text annotation
J3_6HCJ_0261/51/380:390,
1/51/401:421,
1/81/13:20		No text annotation
J3_6HCJ_0021/51/982:984,
1/51/1070:1074,
1/51/1236:1273		No text annotation
J3_6HCJ_0431/51/1100:1108,
1/51/1162:1167,
1/51/1194:1195		No text annotation
J3_6HCJ_0031/51/1530:1537,
1/51/1622:1624,
1/51/1640:1644		No text annotation
J3_6HCJ_0441/51/1531:1537,
1/51/1622:1626,
1/51/1636:1643		No text annotation
J3_6HCJ_0041/51/1545:1548,
1/51/1580:1585,
1/51/1608:1614		No text annotation
J3_6HCJ_0291/51/1726:1751,
1/51/1779:1806,
1/51/1832:1837		No text annotation
J3_6HCJ_0051/51/2393:2399,
1/51/2805:2809,
1/51/2817:2822		No text annotation
J3_6HCJ_0061/51/2402:2405,
1/51/2785:2791,
1/51/2800:2802		No text annotation
homologous
J3_5TBW_009
NA
J3_6HCJ_0451/51/2406:2412,
1/51/2432:2441,
1/51/2781:2784		No text annotation
J3_6HCJ_0311/51/2443:2445,
1/51/2515:2539,
1/51/2777:2779		No text annotation
J3_6HCJ_0461/51/2446:2456,
1/51/2465:2479,
1/51/2499:2514		No text annotation
J3_6HCJ_0071/51/2844:2855,
1/51/3837:3839,
1/51/3843:3844		No text annotation
J3_6HCJ_0081/51/3634:3655,
1/51/3689:3695,
1/51/3820:3826		No text annotation
J3_6HCJ_0091/51/3937:3939,
1/51/4074:4078,
1/51/4168:4173		Kink-turn 3-way junction
geometric
J3_5J7L_044
J3_89368.5
J3_6HCJ_0331/51/3937:3939,
1/51/4074:4088,
1/51/4161:4173		No text annotation
J3_6HCJ_0341/51/4231:4238,
1/51/4286:4291,
1/51/4318:4330		No text annotation
J3_6HCJ_0471/51/4239:4248,
1/51/4260:4269,
1/51/4278:4285		No text annotation
J3_6HCJ_0101/51/4241:4245,
1/51/4263:4269,
1/51/4278:4283		No text annotation
J3_6HCJ_0111/51/4462:4466,
1/51/4491:4493,
1/51/4507:4514		No text annotation
J3_6HCJ_0481/51/4587:4592,
1/51/4618:4621,
1/51/4676:4715		No text annotation
J3_6HCJ_0491/51/4749:4754,
1/51/4879:4883,
1/51/4936:4951		No text annotation
J3_6HCJ_0121/51/4970:4975,
1/51/4983:4992,
1/51/5059:5063		No text annotation
J3_6HCJ_0131/71/8:14,
1/71/65:67,
1/71/108:111		No text annotation
J3_6HCJ_0141/A2/40:41,
1/A2/481:489,
1/A2/511:514		No text annotation
J3_6HCJ_0151/A2/682:685,
1/A2/917:922,
1/A2/1022:1023		No text annotation
J3_6HCJ_0501/A2/682:685,
1/A2/917:923,
1/A2/1019:1023		No text annotation
J3_6HCJ_0161/A2/938:941,
1/A2/985:994,
1/A2/999:1004		No text annotation
homologous
J3_8P9A_074
J3_76375.1
J3_6HCJ_0171/A2/1091:1096,
1/A2/1136:1140,
1/A2/1147:1158		No text annotation
J3_6HCJ_0511/A2/1209:1221,
1/A2/1645:1651,
1/A2/1673:1690		No text annotation
J3_6HCJ_0181/A2/1218:1221,
1/A2/1645:1651,
1/A2/1673:1680		No text annotation
homologous
J3_4V88_035
NA
J3_6HCJ_0191/A2/1225:1228,
1/A2/1530:1532,
1/A2/1638:1641		No text annotation
homologous
J3_4V88_036
NA
J3_6HCJ_0521/A2/1225:1230,
1/A2/1528:1536,
1/A2/1597:1641		No text annotation
J3_6HCJ_0531/A2/1236:1244,
1/A2/1255:1269,
1/A2/1513:1521		No text annotation
J3_6HCJ_0201/A2/1237:1245,
1/A2/1254:1266,
1/A2/1516:1520		No text annotation
J3_6HCJ_0211/A2/1270:1277,
1/A2/1320:1324,
1/A2/1504:1512		No text annotation
J3_6HCJ_0411/A2/1270:1290,
1/A2/1309:1324,
1/A2/1504:1512		No text annotation
J3_6HCJ_0221/A2/1339:1345,
1/A2/1384:1390,
1/A2/1480:1487		No text annotation
J3_6HCJ_0231/A2/1350:1351,
1/A2/1360:1363,
1/A2/1375:1379		No text annotation
homologous
J3_8C3A_085
NA
J3_6HCJ_0241/A2/1391:1395,
1/A2/1450:1456,
1/A2/1470:1479		No text annotation
J4_6HCJ_0011/33/7:10,
1/33/24:26,
1/33/42:48,
1/33/64:65		tRNA junction
homologous
J4_8VU0_001
J4_70449.29
J4_6HCJ_0121/51/111:116,
1/51/155:160,
1/51/275:283,
1/51/304:330		No text annotation
J4_6HCJ_0131/51/1347:1355,
1/51/1384:1399,
1/51/1418:1472,
1/51/1493:1509		No text annotation
J4_6HCJ_0141/51/2365:2371,
1/51/2389:2391,
1/51/2824:2829,
1/51/3856:3857		No text annotation
J4_6HCJ_0151/51/2393:2405,
1/51/2785:2791,
1/51/2800:2807,
1/51/2819:2822		No text annotation
J4_6HCJ_0161/51/2549:2555,
1/51/2572:2576,
1/51/2585:2593,
1/51/2752:2770		No text annotation
J4_6HCJ_0171/51/2618:2620,
1/51/2636:2648,
1/51/2685:2702,
1/51/2714:2719		No text annotation
J4_6HCJ_0181/51/2855:2863,
1/51/2887:2888,
1/51/3613:3626,
1/51/3835:3837		No text annotation
J4_6HCJ_0191/51/3632:3655,
1/51/3689:3710,
1/51/3741:3792,
1/51/3808:3829		No text annotation
J4_6HCJ_0201/A2/30:36,
1/A2/519:527,
1/A2/558:595,
1/A2/641:644		No text annotation
J4_6HCJ_0101/A2/30:36,
1/A2/519:527,
1/A2/558:598,
1/A2/638:644		No text annotation
J4_6HCJ_0111/q3/6:10,
1/q3/25:28,
1/q3/42:49,
1/q3/65:68		No text annotation
J5_6HCJ_0031/51/1335:1340,
1/51/1516:1522,
1/51/1655:1662,
1/51/2287:2292,
1/51/2342:2351		No text annotation
J5_6HCJ_0041/A2/30:36,
1/A2/519:527,
1/A2/558:563,
1/A2/592:595,
1/A2/641:644		No text annotation
J6_6HCJ_0021/51/451:455,
1/51/701:713,
1/51/955:962,
1/51/970:984,
1/51/1070:1074,
1/51/1236:1296		No text annotation
J6_6HCJ_0031/A2/1085:1089,
1/A2/1160:1166,
1/A2/1193:1208,
1/A2/1691:1702,
1/A2/1833:1840,
1/A2/1860:1861		No text annotation
J7_6HCJ_0031/51/1666:1673,
1/51/1682:1686,
1/51/1851:1855,
1/51/1879:1884,
1/51/1895:1900,
1/51/2076:2085,
1/51/2272:2283		No text annotation
J7_6HCJ_0021/A2/1085:1089,
1/A2/1160:1166,
1/A2/1193:1221,
1/A2/1645:1651,
1/A2/1673:1702,
1/A2/1833:1840,
1/A2/1860:1861		No text annotation
J8_6HCJ_0031/51/3900:3923,
1/51/4188:4191,
1/51/4204:4230,
1/51/4331:4342,
1/51/4370:4400,
1/51/4444:4455,
1/51/4525:4534,
1/51/4552:4561		No text annotation
J8_6HCJ_0041/A2/40:62,
1/A2/86:106,
1/A2/355:365,
1/A2/395:413,
1/A2/424:436,
1/A2/457:461,
1/A2/468:487,
1/A2/512:514		No text annotation
J9_6HCJ_0021/51/19:27,
1/51/55:67,
1/51/74:78,
1/51/105:109,
1/51/332:342,
1/81/32:42,
1/81/101:106,
1/81/113:114,
1/81/136:138		No text annotation

Problematic loops

#loop idProblemSequence
J3_6HCJ_025No text annotation
J3_6HCJ_027No text annotation
J3_6HCJ_028No text annotation
J3_6HCJ_030No text annotation
J3_6HCJ_032No text annotation
J3_6HCJ_035No text annotation
J3_6HCJ_036No text annotation
J3_6HCJ_037No text annotation
J3_6HCJ_038No text annotation
J3_6HCJ_039No text annotation
J3_6HCJ_040No text annotation
J4_6HCJ_002No text annotation
J4_6HCJ_003No text annotation
J4_6HCJ_004No text annotation
J4_6HCJ_005No text annotation
J4_6HCJ_006No text annotation
J4_6HCJ_007No text annotation
J4_6HCJ_008No text annotation
J4_6HCJ_009No text annotation
J5_6HCJ_001No text annotation
J5_6HCJ_002No text annotation
J6_6HCJ_001No text annotation
J7_6HCJ_001No text annotation
J8_6HCJ_001No text annotation
J8_6HCJ_002No text annotation
J9_6HCJ_001No text annotation

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