3JCE Internal, hairpin and 3-way junction loop motifs

173 Internal loops
112 Hairpin loops
26 Junction loops

Valid loops

#	loop id	location	motif
1	IL_3JCE_001 ➜	1/6/26:27,1/6/43:45	NA
2	IL_3JCE_002 ➜	1/9/3:5,1/9/68:71	NA
3	IL_3JCE_003 ➜	1/A/24:30,1/A/510:516	NA
4	IL_3JCE_004 ➜	1/A/36:37,1/A/442:444	NA
5	IL_3JCE_005 ➜	1/A/43:45,1/A/433:436	NA
6	IL_3JCE_006 ➜	1/A/80:85,1/A/97:106	NA
7	IL_3JCE_007 ➜	1/A/188:194,1/A/201:208	NA
8	IL_3JCE_008 ➜	1/A/239:245,1/A/253:258	NA
9	IL_3JCE_009 ➜	1/A/269:271,1/A/366:370	NA
10	IL_3JCE_010 ➜	1/A/274:281,1/A/359:363	NA
11	IL_3JCE_011 ➜	1/A/293:295,1/A/343:347	NA
12	IL_3JCE_012 ➜	1/A/481:484,1/A/496:509	NA
13	IL_3JCE_013 ➜	1/A/536:539,1/A/554:557	NA
14	IL_3JCE_014 ➜	1/A/606:610,1/A/618:622	NA
15	IL_3JCE_015 ➜	1/A/672:674,1/A/806:808	NA
16	IL_3JCE_016 ➜	1/A/674:678,1/A/799:806	NA
17	IL_3JCE_017 ➜	1/A/697:698,1/A/763:765	NA
18	IL_3JCE_018 ➜	1/A/702:703,1/A/728:730	NA
19	IL_3JCE_019 ➜	1/A/703:707,1/A/724:728	NA
20	IL_3JCE_020 ➜	1/A/738:740,1/A/757:758	NA
21	IL_3JCE_021 ➜	1/A/775:777,1/A/787:791	NA
22	IL_3JCE_022 ➜	1/A/844:848,1/A/930:934	NA
23	IL_3JCE_023 ➜	1/A/850:851,1/A/926:928	NA
24	IL_3JCE_024 ➜	1/A/856:862,1/A/915:921	NA
25	IL_3JCE_025 ➜	1/A/862:863,1/A/913:915	NA
26	IL_3JCE_026 ➜	1/A/864:868,1/A/909:912	NA
27	IL_3JCE_027 ➜	1/A/870:872,1/A/905:907	NA
28	IL_3JCE_028 ➜	1/A/875:879,1/A/898:902	NA
29	IL_3JCE_029 ➜	1/A/994:996,1/A/1159:1160	NA
30	IL_3JCE_030 ➜	1/A/997:1002,1/A/1153:1158	NA
31	IL_3JCE_031 ➜	1/A/1004:1011,1/A/1150:1151	NA
32	IL_3JCE_032 ➜	1/A/1011:1013,1/A/1149:1150	NA
33	IL_3JCE_033 ➜	1/A/1018:1024,1/A/1140:1144	NA
34	IL_3JCE_034 ➜	1/A/1024:1030,1/A/1124:1140	NA
35	IL_3JCE_035 ➜	1/A/1031:1034,1/A/1121:1123	NA
36	IL_3JCE_036 ➜	1/A/1038:1041,1/A/1114:1117	NA
37	IL_3JCE_037 ➜	1/A/1043:1052,1/A/1107:1112	NA
38	IL_3JCE_038 ➜	1/A/1059:1062,1/A/1076:1079	NA
39	IL_3JCE_039 ➜	1/A/1087:1090,1/A/1101:1102	NA
40	IL_3JCE_040 ➜	1/A/1196:1199,1/A/1246:1250	NA
41	IL_3JCE_041 ➜	1/A/1202:1207,1/A/1239:1243	NA
42	IL_3JCE_042 ➜	1/A/1208:1215,1/A/1234:1238	NA
43	IL_3JCE_043 ➜	1/A/1262:1269,1/A/2011:2017	NA
44	IL_3JCE_044 ➜	1/A/1310:1313,1/A/1603:1604	NA
45	IL_3JCE_045 ➜	1/A/1319:1323,1/A/1331:1333	NA
46	IL_3JCE_046 ➜	1/A/1351:1355,1/A/1376:1380	NA
47	IL_3JCE_047 ➜	1/A/1357:1361,1/A/1370:1374	NA
48	IL_3JCE_048 ➜	1/A/1415:1416,1/A/1582:1587	NA
49	IL_3JCE_049 ➜	1/A/1417:1421,1/A/1577:1581	NA
50	IL_3JCE_050 ➜	1/A/1432:1435,1/A/1557:1561	NA
51	IL_3JCE_051 ➜	1/A/1437:1440,1/A/1551:1555	NA
52	IL_3JCE_052 ➜	1/A/1450:1451,1/A/1459:1461	NA
53	IL_3JCE_053 ➜	1/A/1468:1471,1/A/1520:1524	NA
54	IL_3JCE_054 ➜	1/A/1474:1478,1/A/1513:1517	NA
55	IL_3JCE_055 ➜	1/A/1481:1482,1/A/1507:1510	NA
56	IL_3JCE_056 ➜	1/A/1489:1491,1/A/1499:1500	NA
57	IL_3JCE_057 ➜	1/A/1526:1529,1/A/1542:1546	NA
58	IL_3JCE_058 ➜	1/A/1651:1656,1/A/2004:2006	NA
59	IL_3JCE_059 ➜	1/A/1663:1665,1/A/1995:1997	NA
60	IL_3JCE_060 ➜	1/A/1666:1669,1/A/1993:1994	NA
61	IL_3JCE_061 ➜	1/A/1669:1674,1/A/1990:1993	NA
62	IL_3JCE_062 ➜	1/A/1686:1691,1/A/1696:1702	NA
63	IL_3JCE_063 ➜	1/A/1712:1718,1/A/1742:1746	NA
64	IL_3JCE_064 ➜	1/A/1720:1724,1/A/1736:1740	NA
65	IL_3JCE_065 ➜	1/A/1727:1728,1/A/1731:1733	NA
66	IL_3JCE_066 ➜	1/A/1770:1771,1/A/1980:1982	NA
67	IL_3JCE_067 ➜	1/A/1798:1804,1/A/1813:1821	NA
68	IL_3JCE_068 ➜	1/A/1837:1840,1/A/1902:1903	NA
69	IL_3JCE_069 ➜	1/A/1841:1842,1/A/1898:1901	NA
70	IL_3JCE_070 ➜	1/A/1846:1849,1/A/1893:1894	NA
71	IL_3JCE_071 ➜	1/A/1864:1867,1/A/1874:1878	NA
72	IL_3JCE_072 ➜	1/A/1933:1934,1/A/1964:1967	NA
73	IL_3JCE_073 ➜	1/A/1934:1945,1/A/1961:1964	NA
74	IL_3JCE_074 ➜	1/A/2050:2052,1/A/2617:2618	NA
75	IL_3JCE_075 ➜	1/A/2054:2056,1/A/2612:2615	NA
76	IL_3JCE_076 ➜	1/A/2067:2069,1/A/2442:2443	NA
77	IL_3JCE_077 ➜	1/A/2070:2071,1/A/2438:2441	NA
78	IL_3JCE_078 ➜	1/A/2081:2083,1/A/2236:2239	NA
79	IL_3JCE_079 ➜	1/A/2085:2087,1/A/2232:2234	NA
80	IL_3JCE_080 ➜	1/A/2103:2105,1/A/2184:2186	NA
81	IL_3JCE_081 ➜	1/A/2105:2110,1/A/2179:2184	NA
82	IL_3JCE_083 ➜	1/A/2138:2142,1/A/2149:2153	NA
83	IL_3JCE_084 ➜	1/A/2202:2204,1/A/2220:2221	NA
84	IL_3JCE_085 ➜	1/A/2350:2353,1/A/2364:2367	NA
85	IL_3JCE_086 ➜	1/A/2401:2403,1/A/2414:2415	NA
86	IL_3JCE_087 ➜	1/A/2454:2455,1/A/2496:2498	NA
87	IL_3JCE_088 ➜	1/A/2457:2459,1/A/2493:2494	NA
88	IL_3JCE_089 ➜	1/A/2459:2461,1/A/2489:2493	NA
89	IL_3JCE_090 ➜	1/A/2466:2470,1/A/2480:2484	NA
90	IL_3JCE_091 ➜	1/A/2507:2508,1/A/2580:2582	NA
91	IL_3JCE_092 ➜	1/A/2510:2512,1/A/2574:2578	NA
92	IL_3JCE_093 ➜	1/A/2512:2513,1/A/2571:2574	NA
93	IL_3JCE_094 ➜	1/A/2522:2523,1/A/2540:2543	NA
94	IL_3JCE_095 ➜	1/A/2591:2592,1/A/2601:2603	NA
95	IL_3JCE_096 ➜	1/A/2636:2640,1/A/2774:2782	NA
96	IL_3JCE_097 ➜	1/A/2652:2658,1/A/2663:2668	NA
97	IL_3JCE_098 ➜	1/A/2680:2684,1/A/2725:2727	NA
98	IL_3JCE_099 ➜	1/A/2687:2691,1/A/2718:2722	NA
99	IL_3JCE_100 ➜	1/A/2695:2696,1/A/2711:2714	NA
100	IL_3JCE_101 ➜	1/A/2737:2742,1/A/2762:2767	NA
101	IL_3JCE_102 ➜	1/A/2806:2811,1/A/2889:2892	NA
102	IL_3JCE_103 ➜	1/A/2838:2839,1/A/2878:2880	NA
103	IL_3JCE_104 ➜	1/A/2843:2846,1/A/2870:2874	NA
104	IL_3JCE_105 ➜	1/A/2847:2852,1/A/2865:2869	NA
105	IL_3JCE_106 ➜	1/B/17:19,1/B/64:67	NA
106	IL_3JCE_107 ➜	1/B/23:28,1/B/56:60	NA
107	IL_3JCE_108 ➜	1/B/29:31,1/B/51:55	NA
108	IL_3JCE_109 ➜	1/B/33:38,1/B/44:49	NA
109	IL_3JCE_110 ➜	1/B/71:79,1/B/97:105	NA
110	IL_3JCE_111 ➜	1/a/30:32,1/a/552:553	NA
111	IL_3JCE_133 ➜	1/a/504:511,1/a/540:541	NA
112	IL_3JCE_135 ➜	1/a/569:575,1/a/880:881	NA
113	IL_3JCE_147 ➜	1/a/887:894,1/a/905:910	NA
114	IL_3JCE_148 ➜	1/a/922:923,1/a/1393:1395	NA
115	IL_3JCE_149 ➜	1/a/925:927,1/a/1390:1391	NA
116	IL_3JCE_156 ➜	1/a/1057:1058,1/a/1199:1203	NA
117	IL_3JCE_157 ➜	1/a/1060:1063,1/a/1193:1197	NA
118	IL_3JCE_165 ➜	1/a/1399:1401,1/a/1501:1504	NA
119	IL_3JCE_169 ➜	1/a/1412:1414,1/a/1486:1488	NA
120	IL_3JCE_170 ➜	1/a/1416:1419,1/a/1481:1484	NA

Disqualified loops

#	loop id	Reason for disqualification	Sequence
1	IL_3JCE_082 ➜	missing	2110, 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2122, 2123, 2124, 2174, 2175, 2176, 2177, 2178, 2179
2	IL_3JCE_112 ➜	missing	44, 45, 396, 397, 398
3	IL_3JCE_113 ➜	missing	47, 48, 49, 50, 51, 52, 359, 360, 361
4	IL_3JCE_114 ➜	missing	54, 55, 56, 356, 357
5	IL_3JCE_115 ➜	missing	63, 64, 65, 66, 103, 104
6	IL_3JCE_116 ➜	missing	67, 68, 69, 99, 100, 101, 102
7	IL_3JCE_117 ➜	missing	69, 70, 71, 72, 73, 97, 98, 99
8	IL_3JCE_118 ➜	missing	128, 129, 130, 131, 231, 232, 233
9	IL_3JCE_119 ➜	missing	132, 133, 134, 135, 136, 227, 228, 229, 230
10	IL_3JCE_120 ➜	missing	144, 145, 146, 176, 177, 178
11	IL_3JCE_121 ➜	missing	147, 148, 149, 150, 151, 152, 153, 168, 169, 170, 171, 172, 173, 174, 175
12	IL_3JCE_122 ➜	missing	203, 204, 205, 206, 207, 212, 213, 214
13	IL_3JCE_123 ➜	missing	242, 243, 244, 245, 246, 247, 277, 278, 279, 280, 281, 282, 283, 284
14	IL_3JCE_124 ➜	missing	249, 250, 251, 252, 274, 275
15	IL_3JCE_125 ➜	missing	292, 293, 304, 305, 306, 307, 308
16	IL_3JCE_126 ➜	missing	367, 368, 369, 392, 393
17	IL_3JCE_127 ➜	missing	371, 372, 373, 374, 375, 389, 390
18	IL_3JCE_128 ➜	missing	375, 376, 387, 388, 389
19	IL_3JCE_129 ➜	missing	409, 410, 411, 412, 413, 414, 415, 416, 427, 428, 429, 430, 431, 432, 433
20	IL_3JCE_130 ➜	missing	440, 441, 442, 492, 493, 494, 495, 496, 497
21	IL_3JCE_131 ➜	missing	446, 447, 448, 449, 450, 483, 484, 485, 486, 487, 488
22	IL_3JCE_132 ➜	missing	450, 451, 452, 453, 454, 455, 477, 478, 479, 480, 481, 482, 483
23	IL_3JCE_134 ➜	modified	PSU
24	IL_3JCE_136 ➜	missing	580, 581, 582, 583, 584, 757, 758, 759, 760, 761
25	IL_3JCE_137 ➜	missing	594, 595, 596, 644, 645
26	IL_3JCE_138 ➜	missing	597, 598, 640, 641, 642, 643
27	IL_3JCE_139 ➜	missing	605, 606, 607, 608, 609, 610, 611, 612, 628, 629, 630, 631, 632, 633
28	IL_3JCE_140 ➜	missing	654, 655, 751, 752, 753, 754
29	IL_3JCE_141 ➜	missing	659, 660, 745, 746, 747
30	IL_3JCE_142 ➜	missing	661, 662, 663, 664, 665, 666, 740, 741, 742, 743, 744
31	IL_3JCE_143 ➜	missing	673, 674, 675, 676, 677, 678, 712, 713, 714, 715, 716, 717
32	IL_3JCE_144 ➜	missing	684, 685, 686, 687, 688, 699, 700, 701, 702, 703, 704, 705, 706
33	IL_3JCE_145 ➜	missing	774, 775, 776, 777, 778, 804, 805
34	IL_3JCE_146 ➜	missing	779, 780, 781, 782, 783, 799, 800, 801, 802, 803
35	IL_3JCE_150 ➜	missing	933, 934, 935, 1380, 1381, 1382, 1383, 1384
36	IL_3JCE_151 ➜	missing	953, 954, 1226, 1227, 1228
37	IL_3JCE_152 ➜	missing	993, 994, 995, 996, 997, 1044, 1045
38	IL_3JCE_153 ➜	missing	998, 999, 1000, 1040, 1041, 1042, 1043
39	IL_3JCE_154 ➜	missing	1048, 1049, 1050, 1208, 1209
40	IL_3JCE_155 ➜	missing	1052, 1053, 1054, 1055, 1056, 1204, 1205, 1206
41	IL_3JCE_158 ➜	missing	1124, 1125, 1126, 1127, 1128, 1144, 1145, 1146, 1147, 1148, 1149
42	IL_3JCE_159 ➜	missing	1129, 1130, 1131, 1132, 1133, 1141, 1142, 1143
43	IL_3JCE_160 ➜	missing	1158, 1159, 1160, 1161, 1175, 1176, 1177, 1178, 1179, 1180, 1181
44	IL_3JCE_161 ➜	missing	1247, 1248, 1249, 1250, 1251, 1252, 1253, 1284, 1285, 1286, 1287, 1288, 1289, 1290
45	IL_3JCE_162 ➜	missing	1255, 1256, 1257, 1258, 1277, 1278, 1279, 1280, 1281, 1282
46	IL_3JCE_163 ➜	missing	1259, 1260, 1261, 1262, 1263, 1272, 1273, 1274, 1275, 1276
47	IL_3JCE_164 ➜	missing	1303, 1304, 1305, 1306, 1307, 1308, 1329, 1330, 1331, 1332, 1333, 1334
48	IL_3JCE_166 ➜	modified	4OC, UR3
49	IL_3JCE_167 ➜	modified	5MC
50	IL_3JCE_168 ➜	modified	5MC
51	IL_3JCE_171 ➜	missing	1430, 1431, 1432, 1433, 1434, 1435, 1466, 1467, 1468, 1469, 1470
52	IL_3JCE_172 ➜	missing	1440, 1441, 1442, 1460, 1461
53	IL_3JCE_173 ➜	missing	1445, 1446, 1447, 1448, 1455, 1456, 1457

Valid loops

#	loop id	location	motif
1	HL_3JCE_001 ➜	1/6/13:22	NA
2	HL_3JCE_002 ➜	1/6/31:39	NA
3	HL_3JCE_003 ➜	1/6/53:61	NA
4	HL_3JCE_004 ➜	1/8/13:22	NA
5	HL_3JCE_005 ➜	1/8/31:39	NA
6	HL_3JCE_006 ➜	1/8/53:61	NA
7	HL_3JCE_007 ➜	1/9/13:22	NA
8	HL_3JCE_008 ➜	1/9/30:40	NA
9	HL_3JCE_009 ➜	1/9/53:61	NA
10	HL_3JCE_010 ➜	1/A/59:68	NA
11	HL_3JCE_011 ➜	1/A/87:95	NA
12	HL_3JCE_012 ➜	1/A/123:128	NA
13	HL_3JCE_013 ➜	1/A/137:142	NA
14	HL_3JCE_014 ➜	1/A/158:168	NA
15	HL_3JCE_015 ➜	1/A/194:201	NA
16	HL_3JCE_016 ➜	1/A/225:230	NA
17	HL_3JCE_017 ➜	1/A/246:252	NA
18	HL_3JCE_018 ➜	1/A/304:313	NA
19	HL_3JCE_019 ➜	1/A/319:323	NA
20	HL_3JCE_020 ➜	1/A/327:335	NA
21	HL_3JCE_021 ➜	1/A/382:392	NA
22	HL_3JCE_022 ➜	1/A/410:417	NA
23	HL_3JCE_023 ➜	1/A/462:467	NA
24	HL_3JCE_024 ➜	1/A/487:493	NA
25	HL_3JCE_025 ➜	1/A/543:550	NA
26	HL_3JCE_026 ➜	1/A/564:577	NA
27	HL_3JCE_027 ➜	1/A/611:617	NA
28	HL_3JCE_028 ➜	1/A/629:634	NA
29	HL_3JCE_029 ➜	1/A/641:647	NA
30	HL_3JCE_030 ➜	1/A/712:719	NA
31	HL_3JCE_031 ➜	1/A/744:753	NA
32	HL_3JCE_032 ➜	1/A/779:785	NA
33	HL_3JCE_033 ➜	1/A/826:831	NA
34	HL_3JCE_035 ➜	1/A/955:962	NA
35	HL_3JCE_036 ➜	1/A/978:985	NA
36	HL_3JCE_037 ➜	1/A/1064:1074	NA
37	HL_3JCE_038 ➜	1/A/1092:1099	NA
38	HL_3JCE_039 ➜	1/A/1171:1178	NA
39	HL_3JCE_040 ➜	1/A/1222:1227	NA
40	HL_3JCE_041 ➜	1/A/1281:1289	NA
41	HL_3JCE_042 ➜	1/A/1324:1330	NA
42	HL_3JCE_043 ➜	1/A/1363:1368	NA
43	HL_3JCE_044 ➜	1/A/1389:1398	NA
44	HL_3JCE_045 ➜	1/A/1451:1459	NA
45	HL_3JCE_046 ➜	1/A/1492:1498	NA
46	HL_3JCE_047 ➜	1/A/1531:1540	NA
47	HL_3JCE_048 ➜	1/A/1565:1568	NA
48	HL_3JCE_049 ➜	1/A/1612:1619	NA
49	HL_3JCE_050 ➜	1/A/1630:1636	NA
50	HL_3JCE_051 ➜	1/A/1691:1696	NA
51	HL_3JCE_052 ➜	1/A/1728:1731	NA
52	HL_3JCE_053 ➜	1/A/1752:1756	NA
53	HL_3JCE_054 ➜	1/A/1777:1787	NA
54	HL_3JCE_055 ➜	1/A/1806:1811	NA
55	HL_3JCE_056 ➜	1/A/1868:1873	NA
56	HL_3JCE_057 ➜	1/A/1910:1920	NA
57	HL_3JCE_058 ➜	1/A/1949:1957	NA
58	HL_3JCE_059 ➜	1/A/2027:2036	NA
59	HL_3JCE_060 ➜	1/A/2143:2148	NA
60	HL_3JCE_061 ➜	1/A/2209:2215	NA
61	HL_3JCE_062 ➜	1/A/2248:2256	NA
62	HL_3JCE_063 ➜	1/A/2264:2276	NA
63	HL_3JCE_064 ➜	1/A/2303:2313	NA
64	HL_3JCE_065 ➜	1/A/2324:2331	NA
65	HL_3JCE_066 ➜	1/A/2356:2361	NA
66	HL_3JCE_067 ➜	1/A/2374:2379	NA
67	HL_3JCE_068 ➜	1/A/2404:2413	NA
68	HL_3JCE_069 ➜	1/A/2471:2479	NA
69	HL_3JCE_070 ➜	1/A/2528:2535	NA
70	HL_3JCE_071 ➜	1/A/2551:2557	NA
71	HL_3JCE_072 ➜	1/A/2594:2599	NA
72	HL_3JCE_073 ➜	1/A/2658:2663	NA
73	HL_3JCE_074 ➜	1/A/2701:2706	NA
74	HL_3JCE_075 ➜	1/A/2745:2759	NA
75	HL_3JCE_076 ➜	1/A/2795:2801	NA
76	HL_3JCE_077 ➜	1/A/2819:2827	NA
77	HL_3JCE_078 ➜	1/A/2856:2861	NA
78	HL_3JCE_079 ➜	1/B/38:44	NA
79	HL_3JCE_080 ➜	1/B/86:90	NA
80	HL_3JCE_081 ➜	1/a/12:22	NA
81	HL_3JCE_100 ➜	1/a/897:902	NA
82	HL_3JCE_104 ➜	1/a/1076:1081	NA

Disqualified loops

#	loop id	Reason for disqualification	Sequence
1	HL_3JCE_034 ➜	missing	880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897
2	HL_3JCE_082 ➜	missing	74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96
3	HL_3JCE_083 ➜	missing	158, 159, 160, 161, 162, 163
4	HL_3JCE_084 ➜	missing	186, 187, 188, 189, 190, 191
5	HL_3JCE_085 ➜	missing	207, 208, 209, 210, 211, 212
6	HL_3JCE_086 ➜	missing	259, 260, 261, 262, 263, 264, 265, 266, 267
7	HL_3JCE_087 ➜	missing	296, 297, 298, 299, 300, 301
8	HL_3JCE_088 ➜	missing	319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334
9	HL_3JCE_089 ➜	missing	342, 343, 344, 345, 346, 347
10	HL_3JCE_090 ➜	missing	379, 380, 381, 382, 383, 384
11	HL_3JCE_091 ➜	missing	419, 420, 421, 422, 423, 424
12	HL_3JCE_092 ➜	missing	462, 463, 464, 465, 466, 467, 468, 469, 470
13	HL_3JCE_093 ➜	modified	G7M
14	HL_3JCE_094 ➜	missing	617, 618, 619, 620, 621, 622, 623
15	HL_3JCE_095 ➜	missing	689, 690, 691, 692, 693, 694, 695, 696, 697, 698
16	HL_3JCE_096 ➜	missing	726, 727, 728, 729, 730, 731
17	HL_3JCE_097 ➜	missing	786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796
18	HL_3JCE_098 ➜	missing	840, 841, 842, 843, 844, 845, 846
19	HL_3JCE_099 ➜	missing	862, 863, 864, 865, 866, 867
20	HL_3JCE_101 ➜	missing	963, 964, 965, 966, 967, 968, 969, 970, 971, 972
21	HL_3JCE_102 ➜	missing	1012, 1013, 1014, 1015, 1016, 1017
22	HL_3JCE_103 ➜	missing	1027, 1028, 1029, 1030, 1031, 1032, 1033, 1034
23	HL_3JCE_105 ➜	missing	1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096
24	HL_3JCE_106 ➜	missing	1134, 1135, 1136, 1137, 1138, 1139, 1140
25	HL_3JCE_107 ➜	missing	1165, 1166, 1167, 1168, 1169, 1170, 1171
26	HL_3JCE_108 ➜	missing	1265, 1266, 1267, 1268, 1269, 1270
27	HL_3JCE_109 ➜	missing	1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 1322, 1323
28	HL_3JCE_110 ➜	missing	1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366
29	HL_3JCE_111 ➜	missing	1449, 1450, 1451, 1452, 1453, 1454
30	HL_3JCE_112 ➜	modified	2MG, MA6, MA6

Valid loops

#	loop id	location	motif
1	J3_3JCE_001 ➜	1/A/30:31,1/A/474:481,1/A/509:510	NA
2	J3_3JCE_002 ➜	1/A/55:59,1/A/68:76,1/A/110:115	NA
3	J3_3JCE_003 ➜	1/A/682:689,1/A/773:775,1/A/791:795	NA
4	J3_3JCE_004 ➜	1/A/698:700,1/A/732:736,1/A/760:763	NA
5	J3_3JCE_005 ➜	1/A/1055:1058,1/A/1080:1087,1/A/1102:1104	NA
6	J3_3JCE_006 ➜	1/A/1298:1303,1/A/1625:1627,1/A/1639:1642	NA
7	J3_3JCE_007 ➜	1/A/1306:1309,1/A/1605:1611,1/A/1620:1622	NA
8	J3_3JCE_008 ➜	1/A/1343:1349,1/A/1382:1385,1/A/1402:1404	NA
9	J3_3JCE_009 ➜	1/A/2091:2093,1/A/2196:2200,1/A/2223:2228	NA
10	J3_3JCE_010 ➜	1/A/2295:2299,1/A/2317:2323,1/A/2332:2337	NA
11	J3_3JCE_011 ➜	1/A/2517:2520,1/A/2545:2547,1/A/2561:2567	NA
12	J3_3JCE_012 ➜	1/A/2789:2791,1/A/2805:2806,1/A/2892:2894	NA
13	J3_3JCE_013 ➜	1/A/2812:2815,1/A/2831:2836,1/A/2882:2888	NA
14	J3_3JCE_014 ➜	1/B/10:16,1/B/68:70,1/B/106:110	NA
15	J3_3JCE_023 ➜	1/a/1063:1068,1/a/1107:1113,1/a/1187:1193	NA
16	J3_3JCE_024 ➜	1/a/1073:1074,1/a/1083:1087,1/a/1098:1102	NA

Disqualified loops

#	loop id	Reason for disqualification	Sequence
1	J3_3JCE_015 ➜	missing	46, 47, 361, 362, 363, 364, 365, 366, 367, 393, 394, 395
2	J3_3JCE_016 ➜	missing	586, 587, 588, 651, 652, 653, 654, 754, 755
3	J3_3JCE_017 ➜	missing	672, 673, 717, 718, 719, 720, 721, 722, 723, 724, 725, 732, 733, 734
4	J3_3JCE_018 ➜	missing	826, 827, 828, 829, 857, 858, 859, 860, 861, 868, 869, 870, 871, 872, 873, 874
5	J3_3JCE_019 ➜	missing	943, 944, 945, 946, 1235, 1236, 1237, 1337, 1338, 1339, 1340
6	J3_3JCE_020 ➜	missing	955, 956, 957, 958, 959, 960, 961, 962, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 1221, 1222, 1223, 1224, 1225
7	J3_3JCE_021 ➜	missing	990, 991, 992, 993, 1045, 1046, 1047, 1210, 1211, 1212, 1213, 1214, 1215
8	J3_3JCE_022 ➜	missing	1003, 1004, 1005, 1006, 1007, 1022, 1023, 1024, 1025, 1026, 1027, 1034, 1035, 1036, 1037
9	J3_3JCE_025 ➜	missing	1116, 1117, 1118, 1119, 1154, 1155, 1156, 1157, 1158, 1181, 1182, 1183, 1184
10	J3_3JCE_026 ➜	missing	1237, 1238, 1239, 1240, 1241, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1334, 1335, 1336, 1337

Coloring options: Nucleotide numbers