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_022 ➜	1/A/844:848,1/A/930:934	NA
18	IL_3JCE_023 ➜	1/A/850:851,1/A/926:928	NA
19	IL_3JCE_024 ➜	1/A/856:862,1/A/915:921	NA
20	IL_3JCE_025 ➜	1/A/862:863,1/A/913:915	NA
21	IL_3JCE_029 ➜	1/A/994:996,1/A/1159:1160	NA
22	IL_3JCE_030 ➜	1/A/997:1002,1/A/1153:1158	NA
23	IL_3JCE_031 ➜	1/A/1004:1011,1/A/1150:1151	NA
24	IL_3JCE_032 ➜	1/A/1011:1013,1/A/1149:1150	NA
25	IL_3JCE_033 ➜	1/A/1018:1024,1/A/1140:1144	NA
26	IL_3JCE_034 ➜	1/A/1024:1030,1/A/1124:1140	NA
27	IL_3JCE_040 ➜	1/A/1196:1199,1/A/1246:1250	NA
28	IL_3JCE_041 ➜	1/A/1202:1207,1/A/1239:1243	NA
29	IL_3JCE_042 ➜	1/A/1208:1215,1/A/1234:1238	NA
30	IL_3JCE_043 ➜	1/A/1262:1269,1/A/2011:2017	NA
31	IL_3JCE_044 ➜	1/A/1310:1313,1/A/1603:1604	NA
32	IL_3JCE_045 ➜	1/A/1319:1323,1/A/1331:1333	NA
33	IL_3JCE_046 ➜	1/A/1351:1355,1/A/1376:1380	NA
34	IL_3JCE_047 ➜	1/A/1357:1361,1/A/1370:1374	NA
35	IL_3JCE_048 ➜	1/A/1415:1416,1/A/1582:1587	NA
36	IL_3JCE_049 ➜	1/A/1417:1421,1/A/1577:1581	NA
37	IL_3JCE_050 ➜	1/A/1432:1435,1/A/1557:1561	NA
38	IL_3JCE_051 ➜	1/A/1437:1440,1/A/1551:1555	NA
39	IL_3JCE_052 ➜	1/A/1450:1451,1/A/1459:1461	NA
40	IL_3JCE_053 ➜	1/A/1468:1471,1/A/1520:1524	NA
41	IL_3JCE_054 ➜	1/A/1474:1478,1/A/1513:1517	NA
42	IL_3JCE_055 ➜	1/A/1481:1482,1/A/1507:1510	NA
43	IL_3JCE_056 ➜	1/A/1489:1491,1/A/1499:1500	NA
44	IL_3JCE_057 ➜	1/A/1526:1529,1/A/1542:1546	NA
45	IL_3JCE_058 ➜	1/A/1651:1656,1/A/2004:2006	NA
46	IL_3JCE_059 ➜	1/A/1663:1665,1/A/1995:1997	NA
47	IL_3JCE_060 ➜	1/A/1666:1669,1/A/1993:1994	NA
48	IL_3JCE_061 ➜	1/A/1669:1674,1/A/1990:1993	NA
49	IL_3JCE_063 ➜	1/A/1712:1718,1/A/1742:1746	NA
50	IL_3JCE_064 ➜	1/A/1720:1724,1/A/1736:1740	NA
51	IL_3JCE_065 ➜	1/A/1727:1728,1/A/1731:1733	NA
52	IL_3JCE_074 ➜	1/A/2050:2052,1/A/2617:2618	NA
53	IL_3JCE_075 ➜	1/A/2054:2056,1/A/2612:2615	NA
54	IL_3JCE_096 ➜	1/A/2636:2640,1/A/2774:2782	NA
55	IL_3JCE_097 ➜	1/A/2652:2658,1/A/2663:2668	NA
56	IL_3JCE_098 ➜	1/A/2680:2684,1/A/2725:2727	NA
57	IL_3JCE_099 ➜	1/A/2687:2691,1/A/2718:2722	NA
58	IL_3JCE_100 ➜	1/A/2695:2696,1/A/2711:2714	NA
59	IL_3JCE_101 ➜	1/A/2737:2742,1/A/2762:2767	NA
60	IL_3JCE_102 ➜	1/A/2806:2811,1/A/2889:2892	NA
61	IL_3JCE_103 ➜	1/A/2838:2839,1/A/2878:2880	NA
62	IL_3JCE_104 ➜	1/A/2843:2846,1/A/2870:2874	NA
63	IL_3JCE_105 ➜	1/A/2847:2852,1/A/2865:2869	NA
64	IL_3JCE_106 ➜	1/B/17:19,1/B/64:67	NA
65	IL_3JCE_107 ➜	1/B/23:28,1/B/56:60	NA
66	IL_3JCE_108 ➜	1/B/29:31,1/B/51:55	NA
67	IL_3JCE_109 ➜	1/B/33:38,1/B/44:49	NA
68	IL_3JCE_110 ➜	1/B/71:79,1/B/97:105	NA
69	IL_3JCE_111 ➜	1/a/30:32,1/a/552:553	NA
70	IL_3JCE_133 ➜	1/a/504:511,1/a/540:541	NA
71	IL_3JCE_134 ➜	1/a/515:521,1/a/528:536	NA
72	IL_3JCE_135 ➜	1/a/569:575,1/a/880:881	NA
73	IL_3JCE_147 ➜	1/a/887:894,1/a/905:910	NA
74	IL_3JCE_148 ➜	1/a/922:923,1/a/1393:1395	NA
75	IL_3JCE_149 ➜	1/a/925:927,1/a/1390:1391	NA
76	IL_3JCE_156 ➜	1/a/1057:1058,1/a/1199:1203	NA
77	IL_3JCE_157 ➜	1/a/1060:1063,1/a/1193:1197	NA
78	IL_3JCE_165 ➜	1/a/1399:1401,1/a/1501:1504	NA
79	IL_3JCE_166 ➜	1/a/1401:1404,1/a/1497:1501	NA
80	IL_3JCE_167 ➜	1/a/1405:1407,1/a/1494:1496	NA
81	IL_3JCE_168 ➜	1/a/1407:1409,1/a/1491:1494	NA
82	IL_3JCE_169 ➜	1/a/1412:1414,1/a/1486:1488	NA
83	IL_3JCE_170 ➜	1/a/1416:1419,1/a/1481:1484	NA

Problematic loops

#	loop id	Problem	Sequence
1	IL_3JCE_017 ➜	missing nts	697, 698, 763, 764, 765
2	IL_3JCE_018 ➜	missing nts	702, 703, 728, 729, 730
3	IL_3JCE_019 ➜	missing nts	703, 704, 705, 706, 707, 724, 725, 726, 727, 728
4	IL_3JCE_020 ➜	missing nts	738, 739, 740, 757, 758
5	IL_3JCE_021 ➜	missing nts	775, 776, 777, 787, 788, 789, 790, 791
6	IL_3JCE_026 ➜	missing nts	864, 865, 866, 867, 868, 909, 910, 911, 912
7	IL_3JCE_027 ➜	missing nts	870, 871, 872, 905, 906, 907
8	IL_3JCE_028 ➜	missing nts	875, 876, 877, 878, 879, 898, 899, 900, 901, 902
9	IL_3JCE_035 ➜	missing nts	1031, 1032, 1033, 1034, 1121, 1122, 1123
10	IL_3JCE_036 ➜	missing nts	1038, 1039, 1040, 1041, 1114, 1115, 1116, 1117
11	IL_3JCE_037 ➜	missing nts	1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1052, 1107, 1108, 1109, 1110, 1111, 1112
12	IL_3JCE_038 ➜	missing nts	1059, 1060, 1061, 1062, 1076, 1077, 1078, 1079
13	IL_3JCE_039 ➜	missing nts	1087, 1088, 1089, 1090, 1101, 1102
14	IL_3JCE_062 ➜	missing nts	1686, 1687, 1688, 1689, 1690, 1691, 1696, 1697, 1698, 1699, 1700, 1701, 1702
15	IL_3JCE_066 ➜	missing nts	1770, 1771, 1980, 1981, 1982
16	IL_3JCE_067 ➜	missing nts	1798, 1799, 1800, 1801, 1802, 1803, 1804, 1813, 1814, 1815, 1816, 1817, 1818, 1819, 1820, 1821
17	IL_3JCE_068 ➜	missing nts	1837, 1838, 1839, 1840, 1902, 1903
18	IL_3JCE_069 ➜	missing nts	1841, 1842, 1898, 1899, 1900, 1901
19	IL_3JCE_070 ➜	missing nts	1846, 1847, 1848, 1849, 1893, 1894
20	IL_3JCE_071 ➜	missing nts	1864, 1865, 1866, 1867, 1874, 1875, 1876, 1877, 1878
21	IL_3JCE_072 ➜	missing nts	1933, 1934, 1964, 1965, 1966, 1967
22	IL_3JCE_073 ➜	missing nts	1934, 1935, 1936, 1937, 1938, 1939, 1940, 1941, 1942, 1943, 1944, 1945, 1961, 1962, 1963, 1964
23	IL_3JCE_076 ➜	missing nts	2067, 2068, 2069, 2442, 2443
24	IL_3JCE_077 ➜	missing nts	2070, 2071, 2438, 2439, 2440, 2441
25	IL_3JCE_078 ➜	missing nts	2081, 2082, 2083, 2236, 2237, 2238, 2239
26	IL_3JCE_079 ➜	missing nts	2085, 2086, 2087, 2232, 2233, 2234
27	IL_3JCE_080 ➜	missing nts	2103, 2104, 2105, 2184, 2185, 2186
28	IL_3JCE_081 ➜	missing nts	2105, 2106, 2107, 2108, 2109, 2110, 2179, 2180, 2181, 2182, 2183, 2184
29	IL_3JCE_082 ➜	missing nts	2110, 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2122, 2123, 2124, 2174, 2175, 2176, 2177, 2178, 2179
30	IL_3JCE_083 ➜	missing nts	2138, 2139, 2140, 2141, 2142, 2149, 2150, 2151, 2152, 2153
31	IL_3JCE_084 ➜	missing nts	2202, 2203, 2204, 2220, 2221
32	IL_3JCE_085 ➜	missing nts	2350, 2351, 2352, 2353, 2364, 2365, 2366, 2367
33	IL_3JCE_086 ➜	missing nts	2401, 2402, 2403, 2414, 2415
34	IL_3JCE_087 ➜	missing nts	2454, 2455, 2496, 2497, 2498
35	IL_3JCE_088 ➜	missing nts	2457, 2458, 2459, 2493, 2494
36	IL_3JCE_089 ➜	missing nts	2459, 2460, 2461, 2489, 2490, 2491, 2492, 2493
37	IL_3JCE_090 ➜	missing nts	2466, 2467, 2468, 2469, 2470, 2480, 2481, 2482, 2483, 2484
38	IL_3JCE_091 ➜	missing nts	2507, 2508, 2580, 2581, 2582
39	IL_3JCE_092 ➜	missing nts	2510, 2511, 2512, 2574, 2575, 2576, 2577, 2578
40	IL_3JCE_093 ➜	missing nts	2512, 2513, 2571, 2572, 2573, 2574
41	IL_3JCE_094 ➜	missing nts	2522, 2523, 2540, 2541, 2542, 2543
42	IL_3JCE_095 ➜	missing nts	2591, 2592, 2601, 2602, 2603
43	IL_3JCE_112 ➜	missing nts	44, 45, 396, 397, 398
44	IL_3JCE_113 ➜	missing nts	47, 48, 49, 50, 51, 52, 359, 360, 361
45	IL_3JCE_114 ➜	missing nts	54, 55, 56, 356, 357
46	IL_3JCE_115 ➜	missing nts	63, 64, 65, 66, 103, 104
47	IL_3JCE_116 ➜	missing nts	67, 68, 69, 99, 100, 101, 102
48	IL_3JCE_117 ➜	missing nts	69, 70, 71, 72, 73, 97, 98, 99
49	IL_3JCE_118 ➜	missing nts	128, 129, 130, 131, 231, 232, 233
50	IL_3JCE_119 ➜	missing nts	132, 133, 134, 135, 136, 227, 228, 229, 230
51	IL_3JCE_120 ➜	missing nts	144, 145, 146, 176, 177, 178
52	IL_3JCE_121 ➜	missing nts	147, 148, 149, 150, 151, 152, 153, 168, 169, 170, 171, 172, 173, 174, 175
53	IL_3JCE_122 ➜	missing nts	203, 204, 205, 206, 207, 212, 213, 214
54	IL_3JCE_123 ➜	missing nts	242, 243, 244, 245, 246, 247, 277, 278, 279, 280, 281, 282, 283, 284
55	IL_3JCE_124 ➜	missing nts	249, 250, 251, 252, 274, 275
56	IL_3JCE_125 ➜	missing nts	292, 293, 304, 305, 306, 307, 308
57	IL_3JCE_126 ➜	missing nts	367, 368, 369, 392, 393
58	IL_3JCE_127 ➜	missing nts	371, 372, 373, 374, 375, 389, 390
59	IL_3JCE_128 ➜	missing nts	375, 376, 387, 388, 389
60	IL_3JCE_129 ➜	missing nts	409, 410, 411, 412, 413, 414, 415, 416, 427, 428, 429, 430, 431, 432, 433
61	IL_3JCE_130 ➜	missing nts	440, 441, 442, 492, 493, 494, 495, 496, 497
62	IL_3JCE_131 ➜	missing nts	446, 447, 448, 449, 450, 483, 484, 485, 486, 487, 488
63	IL_3JCE_132 ➜	missing nts	450, 451, 452, 453, 454, 455, 477, 478, 479, 480, 481, 482, 483
64	IL_3JCE_136 ➜	missing nts	580, 581, 582, 583, 584, 757, 758, 759, 760, 761
65	IL_3JCE_137 ➜	missing nts	594, 595, 596, 644, 645
66	IL_3JCE_138 ➜	missing nts	597, 598, 640, 641, 642, 643
67	IL_3JCE_139 ➜	missing nts	605, 606, 607, 608, 609, 610, 611, 612, 628, 629, 630, 631, 632, 633
68	IL_3JCE_140 ➜	missing nts	654, 655, 751, 752, 753, 754
69	IL_3JCE_141 ➜	missing nts	659, 660, 745, 746, 747
70	IL_3JCE_142 ➜	missing nts	661, 662, 663, 664, 665, 666, 740, 741, 742, 743, 744
71	IL_3JCE_143 ➜	missing nts	673, 674, 675, 676, 677, 678, 712, 713, 714, 715, 716, 717
72	IL_3JCE_144 ➜	missing nts	684, 685, 686, 687, 688, 699, 700, 701, 702, 703, 704, 705, 706
73	IL_3JCE_145 ➜	missing nts	774, 775, 776, 777, 778, 804, 805
74	IL_3JCE_146 ➜	missing nts	779, 780, 781, 782, 783, 799, 800, 801, 802, 803
75	IL_3JCE_150 ➜	missing nts	933, 934, 935, 1380, 1381, 1382, 1383, 1384
76	IL_3JCE_151 ➜	missing nts	953, 954, 1226, 1227, 1228
77	IL_3JCE_152 ➜	missing nts	993, 994, 995, 996, 997, 1044, 1045
78	IL_3JCE_153 ➜	missing nts	998, 999, 1000, 1040, 1041, 1042, 1043
79	IL_3JCE_154 ➜	missing nts	1048, 1049, 1050, 1208, 1209
80	IL_3JCE_155 ➜	missing nts	1052, 1053, 1054, 1055, 1056, 1204, 1205, 1206
81	IL_3JCE_158 ➜	missing nts	1124, 1125, 1126, 1127, 1128, 1144, 1145, 1146, 1147, 1148, 1149
82	IL_3JCE_159 ➜	missing nts	1129, 1130, 1131, 1132, 1133, 1141, 1142, 1143
83	IL_3JCE_160 ➜	missing nts	1158, 1159, 1160, 1161, 1175, 1176, 1177, 1178, 1179, 1180, 1181
84	IL_3JCE_161 ➜	missing nts	1247, 1248, 1249, 1250, 1251, 1252, 1253, 1284, 1285, 1286, 1287, 1288, 1289, 1290
85	IL_3JCE_162 ➜	missing nts	1255, 1256, 1257, 1258, 1277, 1278, 1279, 1280, 1281, 1282
86	IL_3JCE_163 ➜	missing nts	1259, 1260, 1261, 1262, 1263, 1272, 1273, 1274, 1275, 1276
87	IL_3JCE_164 ➜	missing nts	1303, 1304, 1305, 1306, 1307, 1308, 1329, 1330, 1331, 1332, 1333, 1334
88	IL_3JCE_171 ➜	missing nts	1430, 1431, 1432, 1433, 1434, 1435, 1466, 1467, 1468, 1469, 1470
89	IL_3JCE_172 ➜	missing nts	1440, 1441, 1442, 1460, 1461
90	IL_3JCE_173 ➜	missing nts	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_032 ➜	1/A/779:785	NA
31	HL_3JCE_033 ➜	1/A/826:831	NA
32	HL_3JCE_035 ➜	1/A/955:962	NA
33	HL_3JCE_036 ➜	1/A/978:985	NA
34	HL_3JCE_039 ➜	1/A/1171:1178	NA
35	HL_3JCE_040 ➜	1/A/1222:1227	NA
36	HL_3JCE_041 ➜	1/A/1281:1289	NA
37	HL_3JCE_042 ➜	1/A/1324:1330	NA
38	HL_3JCE_043 ➜	1/A/1363:1368	NA
39	HL_3JCE_044 ➜	1/A/1389:1398	NA
40	HL_3JCE_045 ➜	1/A/1451:1459	NA
41	HL_3JCE_046 ➜	1/A/1492:1498	NA
42	HL_3JCE_047 ➜	1/A/1531:1540	NA
43	HL_3JCE_048 ➜	1/A/1565:1568	NA
44	HL_3JCE_049 ➜	1/A/1612:1619	NA
45	HL_3JCE_050 ➜	1/A/1630:1636	NA
46	HL_3JCE_052 ➜	1/A/1728:1731	NA
47	HL_3JCE_053 ➜	1/A/1752:1756	NA
48	HL_3JCE_059 ➜	1/A/2027:2036	NA
49	HL_3JCE_073 ➜	1/A/2658:2663	NA
50	HL_3JCE_074 ➜	1/A/2701:2706	NA
51	HL_3JCE_075 ➜	1/A/2745:2759	NA
52	HL_3JCE_076 ➜	1/A/2795:2801	NA
53	HL_3JCE_077 ➜	1/A/2819:2827	NA
54	HL_3JCE_078 ➜	1/A/2856:2861	NA
55	HL_3JCE_079 ➜	1/B/38:44	NA
56	HL_3JCE_080 ➜	1/B/86:90	NA
57	HL_3JCE_081 ➜	1/a/12:22	NA
58	HL_3JCE_093 ➜	1/a/522:527	NA
59	HL_3JCE_100 ➜	1/a/897:902	NA
60	HL_3JCE_104 ➜	1/a/1076:1081	NA
61	HL_3JCE_112 ➜	1/a/1515:1520	NA

Problematic loops

#	loop id	Problem	Sequence
1	HL_3JCE_030 ➜	missing nts	712, 713, 714, 715, 716, 717, 718, 719
2	HL_3JCE_031 ➜	missing nts	744, 745, 746, 747, 748, 749, 750, 751, 752, 753
3	HL_3JCE_034 ➜	missing nts	880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897
4	HL_3JCE_037 ➜	missing nts	1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074
5	HL_3JCE_038 ➜	missing nts	1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099
6	HL_3JCE_051 ➜	missing nts	1691, 1692, 1693, 1694, 1695, 1696
7	HL_3JCE_054 ➜	missing nts	1777, 1778, 1779, 1780, 1781, 1782, 1783, 1784, 1785, 1786, 1787
8	HL_3JCE_055 ➜	missing nts	1806, 1807, 1808, 1809, 1810, 1811
9	HL_3JCE_056 ➜	missing nts	1868, 1869, 1870, 1871, 1872, 1873
10	HL_3JCE_057 ➜	missing nts	1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 1920
11	HL_3JCE_058 ➜	missing nts	1949, 1950, 1951, 1952, 1953, 1954, 1955, 1956, 1957
12	HL_3JCE_060 ➜	missing nts	2143, 2144, 2145, 2146, 2147, 2148
13	HL_3JCE_061 ➜	missing nts	2209, 2210, 2211, 2212, 2213, 2214, 2215
14	HL_3JCE_062 ➜	missing nts	2248, 2249, 2250, 2251, 2252, 2253, 2254, 2255, 2256
15	HL_3JCE_063 ➜	missing nts	2264, 2265, 2266, 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, 2276
16	HL_3JCE_064 ➜	missing nts	2303, 2304, 2305, 2306, 2307, 2308, 2309, 2310, 2311, 2312, 2313
17	HL_3JCE_065 ➜	missing nts	2324, 2325, 2326, 2327, 2328, 2329, 2330, 2331
18	HL_3JCE_066 ➜	missing nts	2356, 2357, 2358, 2359, 2360, 2361
19	HL_3JCE_067 ➜	missing nts	2374, 2375, 2376, 2377, 2378, 2379
20	HL_3JCE_068 ➜	missing nts	2404, 2405, 2406, 2407, 2408, 2409, 2410, 2411, 2412, 2413
21	HL_3JCE_069 ➜	missing nts	2471, 2472, 2473, 2474, 2475, 2476, 2477, 2478, 2479
22	HL_3JCE_070 ➜	missing nts	2528, 2529, 2530, 2531, 2532, 2533, 2534, 2535
23	HL_3JCE_071 ➜	missing nts	2551, 2552, 2553, 2554, 2555, 2556, 2557
24	HL_3JCE_072 ➜	missing nts	2594, 2595, 2596, 2597, 2598, 2599
25	HL_3JCE_082 ➜	missing nts	74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96
26	HL_3JCE_083 ➜	missing nts	158, 159, 160, 161, 162, 163
27	HL_3JCE_084 ➜	missing nts	186, 187, 188, 189, 190, 191
28	HL_3JCE_085 ➜	missing nts	207, 208, 209, 210, 211, 212
29	HL_3JCE_086 ➜	missing nts	259, 260, 261, 262, 263, 264, 265, 266, 267
30	HL_3JCE_087 ➜	missing nts	296, 297, 298, 299, 300, 301
31	HL_3JCE_088 ➜	missing nts	319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334
32	HL_3JCE_089 ➜	missing nts	342, 343, 344, 345, 346, 347
33	HL_3JCE_090 ➜	missing nts	379, 380, 381, 382, 383, 384
34	HL_3JCE_091 ➜	missing nts	419, 420, 421, 422, 423, 424
35	HL_3JCE_092 ➜	missing nts	462, 463, 464, 465, 466, 467, 468, 469, 470
36	HL_3JCE_094 ➜	missing nts	617, 618, 619, 620, 621, 622, 623
37	HL_3JCE_095 ➜	missing nts	689, 690, 691, 692, 693, 694, 695, 696, 697, 698
38	HL_3JCE_096 ➜	missing nts	726, 727, 728, 729, 730, 731
39	HL_3JCE_097 ➜	missing nts	786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796
40	HL_3JCE_098 ➜	missing nts	840, 841, 842, 843, 844, 845, 846
41	HL_3JCE_099 ➜	missing nts	862, 863, 864, 865, 866, 867
42	HL_3JCE_101 ➜	missing nts	963, 964, 965, 966, 967, 968, 969, 970, 971, 972
43	HL_3JCE_102 ➜	missing nts	1012, 1013, 1014, 1015, 1016, 1017
44	HL_3JCE_103 ➜	missing nts	1027, 1028, 1029, 1030, 1031, 1032, 1033, 1034
45	HL_3JCE_105 ➜	missing nts	1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096
46	HL_3JCE_106 ➜	missing nts	1134, 1135, 1136, 1137, 1138, 1139, 1140
47	HL_3JCE_107 ➜	missing nts	1165, 1166, 1167, 1168, 1169, 1170, 1171
48	HL_3JCE_108 ➜	missing nts	1265, 1266, 1267, 1268, 1269, 1270
49	HL_3JCE_109 ➜	missing nts	1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 1322, 1323
50	HL_3JCE_110 ➜	missing nts	1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366
51	HL_3JCE_111 ➜	missing nts	1449, 1450, 1451, 1452, 1453, 1454

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_006 ➜	1/A/1298:1303,1/A/1625:1627,1/A/1639:1642	NA
4	J3_3JCE_007 ➜	1/A/1306:1309,1/A/1605:1611,1/A/1620:1622	NA
5	J3_3JCE_008 ➜	1/A/1343:1349,1/A/1382:1385,1/A/1402:1404	NA
6	J3_3JCE_012 ➜	1/A/2789:2791,1/A/2805:2806,1/A/2892:2894	NA
7	J3_3JCE_013 ➜	1/A/2812:2815,1/A/2831:2836,1/A/2882:2888	NA
8	J3_3JCE_014 ➜	1/B/10:16,1/B/68:70,1/B/106:110	NA
9	J3_3JCE_023 ➜	1/a/1063:1068,1/a/1107:1113,1/a/1187:1193	NA
10	J3_3JCE_024 ➜	1/a/1073:1074,1/a/1083:1087,1/a/1098:1102	NA

Problematic loops

#	loop id	Problem	Sequence
1	J3_3JCE_003 ➜	missing nts	682, 683, 684, 685, 686, 687, 688, 689, 773, 774, 775, 791, 792, 793, 794, 795
2	J3_3JCE_004 ➜	missing nts	698, 699, 700, 732, 733, 734, 735, 736, 760, 761, 762, 763
3	J3_3JCE_005 ➜	missing nts	1055, 1056, 1057, 1058, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1102, 1103, 1104
4	J3_3JCE_009 ➜	missing nts	2091, 2092, 2093, 2196, 2197, 2198, 2199, 2200, 2223, 2224, 2225, 2226, 2227, 2228
5	J3_3JCE_010 ➜	missing nts	2295, 2296, 2297, 2298, 2299, 2317, 2318, 2319, 2320, 2321, 2322, 2323, 2332, 2333, 2334, 2335, 2336, 2337
6	J3_3JCE_011 ➜	missing nts	2517, 2518, 2519, 2520, 2545, 2546, 2547, 2561, 2562, 2563, 2564, 2565, 2566, 2567
7	J3_3JCE_015 ➜	missing nts	46, 47, 361, 362, 363, 364, 365, 366, 367, 393, 394, 395
8	J3_3JCE_016 ➜	missing nts	586, 587, 588, 651, 652, 653, 654, 754, 755
9	J3_3JCE_017 ➜	missing nts	672, 673, 717, 718, 719, 720, 721, 722, 723, 724, 725, 732, 733, 734
10	J3_3JCE_018 ➜	missing nts	826, 827, 828, 829, 857, 858, 859, 860, 861, 868, 869, 870, 871, 872, 873, 874
11	J3_3JCE_019 ➜	missing nts	943, 944, 945, 946, 1235, 1236, 1237, 1337, 1338, 1339, 1340
12	J3_3JCE_020 ➜	missing nts	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
13	J3_3JCE_021 ➜	missing nts	990, 991, 992, 993, 1045, 1046, 1047, 1210, 1211, 1212, 1213, 1214, 1215
14	J3_3JCE_022 ➜	missing nts	1003, 1004, 1005, 1006, 1007, 1022, 1023, 1024, 1025, 1026, 1027, 1034, 1035, 1036, 1037
15	J3_3JCE_025 ➜	missing nts	1116, 1117, 1118, 1119, 1154, 1155, 1156, 1157, 1158, 1181, 1182, 1183, 1184
16	J3_3JCE_026 ➜	missing nts	1237, 1238, 1239, 1240, 1241, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1334, 1335, 1336, 1337

Coloring options: Nucleotide numbers