1N34 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
# | loop id | location | motif |
---|---|---|---|
1 | ➜ | 1/A/30:32,1/A/552:553 | NA |
2 | ➜ | 1/A/44:45,1/A/396:398 | NA |
3 | ➜ | 1/A/47:52,1/A/359:361 | NA |
4 | ➜ | 1/A/54:57,1/A/355:357 | NA |
5 | ➜ | 1/A/63:66,1/A/103:104 | NA |
6 | ➜ | 1/A/67:69,1/A/99:102 | NA |
7 | ➜ | 1/A/128:131,1/A/231:233 | NA |
8 | ➜ | 1/A/132:136,1/A/227:230 | NA |
9 | ➜ | 1/A/186:188,1/A/190K:191 | NA |
10 | ➜ | 1/A/242:247,1/A/277:284 | NA |
11 | ➜ | 1/A/248:252,1/A/274:276 | NA |
12 | ➜ | 1/A/292:293,1/A/304:308 | NA |
13 | ➜ | 1/A/370:375,1/A/389:391 | NA |
14 | ➜ | 1/A/375:377,1/A/386:389 | NA |
15 | ➜ | 1/A/409:417,1/A/426:433 | NA |
16 | ➜ | 1/A/446:450,1/A/483:488 | NA |
17 | ➜ | 1/A/450:456,1/A/476:483 | NA |
18 | ➜ | 1/A/504:511,1/A/540:541 | NA |
19 | ➜ | 1/A/515:521,1/A/528:536 | NA |
20 | ➜ | 1/A/605:612,1/A/628:633 | NA |
21 | ➜ | 1/A/662:666,1/A/740:743 | NA |
22 | ➜ | 1/A/673:679,1/A/711:717 | NA |
23 | ➜ | 1/A/683:688,1/A/699:707 | NA |
24 | ➜ | 1/A/922:923,1/A/1393:1395 | NA |
25 | ➜ | 1/A/925:927,1/A/1390:1391 | NA |
26 | ➜ | 1/A/933:935,1/A/1380:1384 | NA |
27 | ➜ | 1/A/953:954,1/A/1226:1228 | NA |
28 | ➜ | 1/A/1047:1051,1/A/1207:1210 | NA |
29 | ➜ | 1/A/1051:1056,1/A/1204:1207 | NA |
30 | ➜ | 1/A/1056:1059,1/A/1198:1204 | NA |
31 | ➜ | 1/A/1059:1061,1/A/1195:1198 | NA |
32 | ➜ | 1/A/1061:1063,1/A/1193:1195 | NA |
33 | ➜ | 1/A/1121:1128,1/A/1143:1152 | NA |
34 | ➜ | 1/A/1247:1253,1/A/1284:1290 | NA |
35 | ➜ | 1/A/1253:1258,1/A/1277:1284 | NA |
36 | ➜ | 1/A/1303:1308,1/A/1329:1334 | NA |
37 | ➜ | 1/A/1401:1404,1/A/1497:1501 | NA |
38 | ➜ | 1/A/1404:1407,1/A/1494:1497 | NA |
39 | ➜ | 1/A/1407:1409,1/A/1491:1494 | NA |
40 | ➜ | 1/A/1412:1414,1/A/1486:1488 | NA |
41 | ➜ | 1/A/1414:1416,1/A/1484:1486 | NA |
42 | ➜ | 1/A/1435:1438,1/A/1463:1466 | NA |
43 | ➜ | 1/A/1440:1447,1/A/1459:1461 | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
1 | ➜ | 69, 70, 73, 74, 75, 76, 77, 92, 93, 95, 96, 97, 98, 99 | |
2 | ➜ | 148, 149, 150, 151, 152, 153, 168, 169, 170, 171, 172, 173, 174 | |
3 | ➜ | CUCC,GGAG | |
4 | ➜ | GGA,UCC | |
5 | ➜ | CUCC,GGAG | |
6 | ➜ | 569, 570, 571, 572, 573, 574, 575, 880, 881 | |
7 | ➜ | 580, 581, 582, 583, 584, 757, 758, 759, 760, 761 | |
8 | ➜ | 594, 595, 596, 644, 645 | |
9 | ➜ | 597, 598, 640, 641, 642, 643 | |
10 | ➜ | 654, 655, 751, 752, 753, 754 | |
11 | ➜ | 657, 658, 747, 748, 749 | |
12 | ➜ | 774, 775, 776, 777, 778, 804, 805 | |
13 | ➜ | 779, 780, 781, 782, 783, 784, 798, 799, 800, 801, 802, 803 | |
14 | ➜ | 887, 888, 889, 890, 891, 892, 893, 894, 905, 906, 907, 908, 909, 910 | |
15 | ➜ | 948, 949, 950, 1231, 1232, 1233 | |
16 | ➜ | 1028, 1029, 1030, 1031, 1032, 1033 | |
17 | ➜ | CCCG,CGGG | |
18 | ➜ | 1258, 1259, 1260, 1261, 1262, 1273, 1274, 1275, 1276, 1277 | |
19 | ➜ | CCG,CGG | |
20 | ➜ | GUC,GAC | |
21 | ➜ | CGCC,GGCG | |
22 | ➜ | 1416, 1417, 1418, 1419, 1481, 1482, 1483, 1484 | |
23 | ➜ | CGGGC,GCCCG | |
24 | ➜ | 1431, 1432, 1433, 1434, 1435, 1466, 1467, 1468, 1469 |
Valid loops
# | loop id | location | motif |
---|---|---|---|
1 | ➜ | 1/A/12:22 | NA |
2 | ➜ | 1/A/158:163 | NA |
3 | ➜ | 1/A/190B:190G | NA |
4 | ➜ | 1/A/199:218 | NA |
5 | ➜ | 1/A/259:267 | NA |
6 | ➜ | 1/A/296:301 | NA |
7 | ➜ | 1/A/320:333 | NA |
8 | ➜ | 1/A/377:386 | NA |
9 | ➜ | 1/A/419:424 | NA |
10 | ➜ | 1/A/457:475 | NA |
11 | ➜ | 1/A/522:527 | NA |
12 | ➜ | 1/A/617:623 | NA |
13 | ➜ | 1/A/689:698 | NA |
14 | ➜ | 1/A/786:796 | NA |
15 | ➜ | 1/A/838:848 | NA |
16 | ➜ | 1/A/963:972 | NA |
17 | ➜ | 1/A/1076:1081 | NA |
18 | ➜ | 1/A/1089:1096 | NA |
19 | ➜ | 1/A/1164:1172 | NA |
20 | ➜ | 1/A/1449:1454 | NA |
21 | ➜ | 1/A/1515:1520 | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
1 | ➜ | 79, 80, 81, 82, 83, 84, 88, 89, 90 | |
2 | ➜ | 342, 343, 344, 345, 346, 347 | |
3 | ➜ | 726, 727, 728, 729, 730, 731 | |
4 | ➜ | 862, 863, 864, 865, 866, 867 | |
5 | ➜ | 897, 898, 899, 900, 901, 902 | |
6 | ➜ | 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022 | |
7 | ➜ | 1030, 1030, 1030, 1030, 1030, 1031 | |
8 | ➜ | 1128, 1129, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143 | |
9 | ➜ | 1265, 1266, 1267, 1268, 1269, 1270 | |
10 | ➜ | 1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 1322, 1323 | |
11 | ➜ | 1356, 1357, 1358, 1359, 1360, 1361, 1361, 1362, 1363, 1364, 1365, 1366 |
Valid loops
# | loop id | location | motif |
---|---|---|---|
1 | ➜ | 1/A/826:829,1/A/857:861,1/A/868:874 | NA |
2 | ➜ | 1/A/936:939,1/A/1344:1350,1/A/1372:1379 | NA |
3 | ➜ | 1/A/941:946,1/A/1235:1237,1/A/1337:1342 | NA |
4 | ➜ | 1/A/955:962,1/A/973:985,1/A/1220:1225 | NA |
5 | ➜ | 1/A/1063:1068,1/A/1107:1113,1/A/1187:1193 | NA |
6 | ➜ | 1/A/1116:1118,1/A/1155:1161,1/A/1175:1184 | NA |
7 | ➜ | 1/A/1237:1241,1/A/1296:1303,1/A/1334:1337 | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
1 | ➜ | 989, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999, 1000, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1210, 1211, 1212, 1213, 1214, 1215, 1216 | |
2 | ➜ | 1001, 1002, 1003, 1003, 1004, 1005, 1006, 1007, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040 |
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