5U4I Internal, hairpin and 3-way junction loop motifs

182 Internal loops
109 Hairpin loops
27 Junction loops

Valid loops

#	loop id	location	motif
1	IL_5U4I_113 ➜	1/B/17:18,1/B/65:67	NA
2	IL_5U4I_114 ➜	1/B/23:28,1/B/56:60	NA
3	IL_5U4I_115 ➜	1/B/30:31,1/B/51:54	NA
4	IL_5U4I_116 ➜	1/B/34:38,1/B/44:48	NA
5	IL_5U4I_117 ➜	1/B/71:79,1/B/97:105	NA
6	IL_5U4I_118 ➜	1/a/30:33,1/a/551:553	NA
7	IL_5U4I_119 ➜	1/a/44:45,1/a/396:398	NA
8	IL_5U4I_120 ➜	1/a/47:52,1/a/359:361	NA
9	IL_5U4I_121 ➜	1/a/54:56,1/a/356:357	NA
10	IL_5U4I_122 ➜	1/a/63:66,1/a/103:104	NA
11	IL_5U4I_123 ➜	1/a/67:69,1/a/99:102	NA
12	IL_5U4I_124 ➜	1/a/70:73,1/a/97:98	NA
13	IL_5U4I_125 ➜	1/a/75:78,1/a/91:95	NA
14	IL_5U4I_126 ➜	1/a/128:131,1/a/231:233	NA
15	IL_5U4I_127 ➜	1/a/132:136,1/a/227:230	NA
16	IL_5U4I_128 ➜	1/a/144:146,1/a/176:178	NA
17	IL_5U4I_129 ➜	1/a/147:153,1/a/168:175	NA
18	IL_5U4I_130 ➜	1/a/242:247,1/a/277:284	NA
19	IL_5U4I_131 ➜	1/a/249:252,1/a/274:275	NA
20	IL_5U4I_132 ➜	1/a/291:293,1/a/304:309	NA
21	IL_5U4I_133 ➜	1/a/367:369,1/a/392:393	NA
22	IL_5U4I_134 ➜	1/a/370:375,1/a/389:391	NA
23	IL_5U4I_135 ➜	1/a/375:376,1/a/387:389	NA
24	IL_5U4I_136 ➜	1/a/409:416,1/a/427:433	NA
25	IL_5U4I_137 ➜	1/a/440:442,1/a/492:497	NA
26	IL_5U4I_138 ➜	1/a/446:450,1/a/483:488	NA
27	IL_5U4I_139 ➜	1/a/450:455,1/a/477:483	NA
28	IL_5U4I_140 ➜	1/a/504:511,1/a/540:541	NA
29	IL_5U4I_141 ➜	1/a/514:521,1/a/528:537	NA
30	IL_5U4I_142 ➜	1/a/569:575,1/a/880:881	NA
31	IL_5U4I_143 ➜	1/a/580:584,1/a/757:761	NA
32	IL_5U4I_144 ➜	1/a/594:596,1/a/644:645	NA
33	IL_5U4I_145 ➜	1/a/597:598,1/a/640:643	NA
34	IL_5U4I_146 ➜	1/a/604:613,1/a/627:634	NA
35	IL_5U4I_147 ➜	1/a/654:655,1/a/751:754	NA
36	IL_5U4I_148 ➜	1/a/658:659,1/a/746:748	NA
37	IL_5U4I_149 ➜	1/a/662:666,1/a/740:743	NA
38	IL_5U4I_150 ➜	1/a/673:678,1/a/712:717	NA
39	IL_5U4I_151 ➜	1/a/684:688,1/a/699:706	NA
40	IL_5U4I_152 ➜	1/a/774:778,1/a/804:805	NA
41	IL_5U4I_153 ➜	1/a/779:783,1/a/799:803	NA
42	IL_5U4I_154 ➜	1/a/887:894,1/a/905:910	NA
43	IL_5U4I_155 ➜	1/a/922:923,1/a/1393:1395	NA
44	IL_5U4I_156 ➜	1/a/925:927,1/a/1390:1391	NA
45	IL_5U4I_157 ➜	1/a/933:935,1/a/1380:1384	NA
46	IL_5U4I_158 ➜	1/a/953:954,1/a/1226:1228	NA
47	IL_5U4I_159 ➜	1/a/993:997,1/a/1044:1045	NA
48	IL_5U4I_160 ➜	1/a/998:1000,1/a/1040:1043	NA
49	IL_5U4I_161 ➜	1/a/1027:1029,1/a/1033:1034	NA
50	IL_5U4I_162 ➜	1/a/1048:1050,1/a/1208:1209	NA
51	IL_5U4I_163 ➜	1/a/1050:1052,1/a/1206:1208	NA
52	IL_5U4I_164 ➜	1/a/1052:1056,1/a/1204:1206	NA
53	IL_5U4I_165 ➜	1/a/1057:1058,1/a/1199:1203	NA
54	IL_5U4I_166 ➜	1/a/1060:1061,1/a/1195:1197	NA
55	IL_5U4I_167 ➜	1/a/1061:1063,1/a/1193:1195	NA
56	IL_5U4I_168 ➜	1/a/1124:1128,1/a/1144:1149	NA
57	IL_5U4I_169 ➜	1/a/1129:1132,1/a/1142:1143	NA
58	IL_5U4I_170 ➜	1/a/1158:1161,1/a/1175:1181	NA
59	IL_5U4I_171 ➜	1/a/1247:1253,1/a/1284:1290	NA
60	IL_5U4I_172 ➜	1/a/1255:1258,1/a/1277:1282	NA
61	IL_5U4I_173 ➜	1/a/1259:1263,1/a/1272:1276	NA
62	IL_5U4I_174 ➜	1/a/1303:1308,1/a/1329:1334	NA
63	IL_5U4I_175 ➜	1/a/1399:1401,1/a/1501:1504	NA
64	IL_5U4I_176 ➜	1/a/1401:1404,1/a/1497:1501	NA
65	IL_5U4I_177 ➜	1/a/1405:1409,1/a/1491:1496	NA
66	IL_5U4I_178 ➜	1/a/1412:1414,1/a/1486:1488	NA
67	IL_5U4I_179 ➜	1/a/1416:1419,1/a/1481:1484	NA
68	IL_5U4I_180 ➜	1/a/1430:1435,1/a/1466:1470	NA
69	IL_5U4I_181 ➜	1/a/1440:1442,1/a/1460:1461	NA
70	IL_5U4I_182 ➜	1/a/1445:1448,1/a/1455:1457	NA

Problematic loops

#	loop id	Problem	Sequence
1	IL_5U4I_001 ➜	missing nts	24, 25, 26, 27, 28, 29, 30, 510, 511, 512, 513, 514, 515, 516
2	IL_5U4I_002 ➜	missing nts	36, 37, 442, 443, 444
3	IL_5U4I_003 ➜	missing nts	43, 44, 434, 435, 436
4	IL_5U4I_004 ➜	missing nts	81, 82, 83, 84, 85, 97, 98, 99, 100, 101, 102, 103, 104, 105
5	IL_5U4I_005 ➜	missing nts	152, 153, 172, 173, 174
6	IL_5U4I_006 ➜	missing nts	153, 154, 155, 171, 172
7	IL_5U4I_007 ➜	missing nts	183, 184, 212, 213, 214
8	IL_5U4I_008 ➜	missing nts	188, 189, 190, 191, 192, 193, 194, 201, 202, 203, 204, 205, 206, 207, 208
9	IL_5U4I_009 ➜	missing nts	239, 240, 241, 242, 243, 244, 245, 253, 254, 255, 256, 257, 258
10	IL_5U4I_010 ➜	missing nts	269, 270, 271, 366, 367, 368, 369, 370
11	IL_5U4I_011 ➜	missing nts	274, 275, 276, 277, 278, 279, 280, 281, 359, 360, 361, 362, 363
12	IL_5U4I_012 ➜	missing nts	293, 294, 295, 343, 344, 345, 346, 347
13	IL_5U4I_013 ➜	missing nts	481, 482, 483, 484, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509
14	IL_5U4I_014 ➜	missing nts	536, 537, 538, 539, 554, 555, 556, 557
15	IL_5U4I_015 ➜	missing nts	564, 565, 566, 575, 576, 577
16	IL_5U4I_016 ➜	missing nts	606, 607, 608, 609, 610, 618, 619, 620, 621, 622
17	IL_5U4I_017 ➜	missing nts	672, 673, 674, 806, 807, 808
18	IL_5U4I_018 ➜	missing nts	674, 675, 676, 677, 678, 799, 800, 801, 802, 803, 804, 805, 806
19	IL_5U4I_019 ➜	missing nts	697, 698, 763, 764, 765
20	IL_5U4I_020 ➜	missing nts	702, 703, 728, 729, 730
21	IL_5U4I_021 ➜	missing nts	703, 704, 705, 706, 707, 724, 725, 726, 727, 728
22	IL_5U4I_022 ➜	missing nts	738, 739, 740, 757, 758
23	IL_5U4I_023 ➜	missing nts	775, 776, 777, 787, 788, 789, 790, 791
24	IL_5U4I_024 ➜	missing nts	844, 845, 846, 847, 933, 934
25	IL_5U4I_025 ➜	missing nts	847, 848, 930, 931, 932, 933
26	IL_5U4I_026 ➜	missing nts	849, 850, 927, 928, 929
27	IL_5U4I_027 ➜	missing nts	856, 857, 858, 859, 860, 861, 862, 915, 916, 917, 918, 919, 920, 921
28	IL_5U4I_028 ➜	missing nts	862, 863, 913, 914, 915
29	IL_5U4I_029 ➜	missing nts	864, 865, 866, 867, 868, 909, 910, 911, 912
30	IL_5U4I_030 ➜	missing nts	869, 870, 871, 872, 905, 906, 907, 908
31	IL_5U4I_031 ➜	missing nts	875, 876, 877, 878, 879, 898, 899, 900, 901, 902
32	IL_5U4I_032 ➜	missing nts	880, 881, 895, 896, 897
33	IL_5U4I_033 ➜	missing nts	994, 995, 996, 1159, 1160
34	IL_5U4I_034 ➜	missing nts	998, 999, 1000, 1001, 1002, 1153, 1154, 1155, 1156, 1157
35	IL_5U4I_035 ➜	missing nts	1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1150, 1151
36	IL_5U4I_036 ➜	missing nts	1011, 1012, 1013, 1149, 1150
37	IL_5U4I_037 ➜	missing nts	1018, 1019, 1020, 1021, 1022, 1023, 1024, 1140, 1141, 1142, 1143, 1144
38	IL_5U4I_038 ➜	missing nts	1024, 1025, 1026, 1027, 1028, 1029, 1030, 1124, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140
39	IL_5U4I_039 ➜	missing nts	1031, 1032, 1033, 1034, 1121, 1122, 1123
40	IL_5U4I_040 ➜	missing nts	1038, 1039, 1040, 1041, 1114, 1115, 1116, 1117
41	IL_5U4I_041 ➜	missing nts	1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1108, 1109, 1110, 1111, 1112
42	IL_5U4I_042 ➜	missing nts	1059, 1060, 1061, 1062, 1076, 1077, 1078, 1079
43	IL_5U4I_043 ➜	missing nts	1087, 1088, 1089, 1090, 1101, 1102
44	IL_5U4I_044 ➜	missing nts	1197, 1198, 1247, 1248, 1249
45	IL_5U4I_045 ➜	missing nts	1202, 1203, 1204, 1205, 1206, 1240, 1241, 1242, 1243
46	IL_5U4I_046 ➜	missing nts	1208, 1209, 1210, 1211, 1212, 1213, 1214, 1215, 1234, 1235, 1236, 1237, 1238
47	IL_5U4I_047 ➜	missing nts	1262, 1263, 1264, 1265, 1266, 1267, 1268, 1269, 2011, 2012, 2013, 2014, 2015, 2016, 2017
48	IL_5U4I_048 ➜	missing nts	1310, 1311, 1312, 1313, 1603, 1604
49	IL_5U4I_049 ➜	missing nts	1319, 1320, 1321, 1322, 1323, 1331, 1332, 1333
50	IL_5U4I_050 ➜	missing nts	1351, 1352, 1353, 1354, 1355, 1376, 1377, 1378, 1379, 1380
51	IL_5U4I_051 ➜	missing nts	1357, 1358, 1359, 1360, 1361, 1370, 1371, 1372, 1373, 1374
52	IL_5U4I_052 ➜	missing nts	1405, 1406, 1407, 1595, 1596
53	IL_5U4I_053 ➜	missing nts	1415, 1416, 1582, 1583, 1584, 1585, 1586, 1587
54	IL_5U4I_054 ➜	missing nts	1417, 1418, 1419, 1420, 1421, 1577, 1578, 1579, 1580, 1581
55	IL_5U4I_055 ➜	missing nts	1432, 1433, 1434, 1435, 1557, 1558, 1559, 1560, 1561
56	IL_5U4I_056 ➜	missing nts	1437, 1438, 1439, 1440, 1551, 1552, 1553, 1554, 1555
57	IL_5U4I_057 ➜	missing nts	1450, 1451, 1459, 1460, 1461
58	IL_5U4I_058 ➜	missing nts	1468, 1469, 1470, 1471, 1472, 1519, 1520, 1521, 1522, 1523, 1524
59	IL_5U4I_059 ➜	missing nts	1474, 1475, 1476, 1477, 1478, 1513, 1514, 1515, 1516, 1517
60	IL_5U4I_060 ➜	missing nts	1481, 1482, 1507, 1508, 1509, 1510
61	IL_5U4I_061 ➜	missing nts	1489, 1490, 1491, 1499, 1500
62	IL_5U4I_062 ➜	missing nts	1526, 1527, 1528, 1529, 1542, 1543, 1544, 1545, 1546
63	IL_5U4I_063 ➜	missing nts	1651, 1652, 1653, 1654, 1655, 1656, 2004, 2005, 2006
64	IL_5U4I_064 ➜	missing nts	1663, 1664, 1665, 1995, 1996, 1997
65	IL_5U4I_065 ➜	missing nts	1666, 1667, 1668, 1669, 1993, 1994
66	IL_5U4I_066 ➜	missing nts	1669, 1670, 1671, 1672, 1673, 1674, 1990, 1991, 1992, 1993
67	IL_5U4I_067 ➜	missing nts	1686, 1687, 1688, 1689, 1690, 1691, 1696, 1697, 1698, 1699, 1700, 1701, 1702
68	IL_5U4I_068 ➜	missing nts	1712, 1713, 1714, 1715, 1716, 1717, 1718, 1719, 1741, 1742, 1743, 1744, 1745, 1746
69	IL_5U4I_069 ➜	missing nts	1719, 1720, 1721, 1722, 1723, 1724, 1725, 1735, 1736, 1737, 1738, 1739, 1740, 1741
70	IL_5U4I_070 ➜	missing nts	1770, 1771, 1980, 1981, 1982
71	IL_5U4I_071 ➜	missing nts	1798, 1799, 1800, 1801, 1802, 1803, 1804, 1813, 1814, 1815, 1816, 1817, 1818, 1819, 1820, 1821
72	IL_5U4I_072 ➜	missing nts	1837, 1838, 1839, 1840, 1902, 1903
73	IL_5U4I_073 ➜	missing nts	1841, 1842, 1898, 1899, 1900, 1901
74	IL_5U4I_074 ➜	missing nts	1846, 1847, 1848, 1849, 1893, 1894
75	IL_5U4I_075 ➜	missing nts	1863, 1864, 1865, 1866, 1867, 1874, 1875, 1876, 1877, 1878, 1879
76	IL_5U4I_076 ➜	missing nts	1933, 1934, 1964, 1965, 1966, 1967
77	IL_5U4I_077 ➜	missing nts	5MU, 5MC
78	IL_5U4I_078 ➜	missing nts	2050, 2051, 2052, 2617, 2618
79	IL_5U4I_079 ➜	missing nts	2054, 2055, 2056, 2612, 2613, 2614, 2615
80	IL_5U4I_080 ➜	missing nts	2MG
81	IL_5U4I_081 ➜	missing nts	2067, 2068, 2069, 2070, 2441, 2442, 2443
82	IL_5U4I_082 ➜	missing nts	2070, 2071, 2438, 2439, 2440, 2441
83	IL_5U4I_083 ➜	missing nts	2081, 2082, 2083, 2236, 2237, 2238, 2239
84	IL_5U4I_084 ➜	missing nts	2085, 2086, 2087, 2232, 2233, 2234
85	IL_5U4I_085 ➜	missing nts	2103, 2104, 2105, 2184, 2185, 2186
86	IL_5U4I_086 ➜	missing nts	2106, 2107, 2108, 2109, 2110, 2179, 2180, 2181, 2182, 2183
87	IL_5U4I_087 ➜	missing nts	2110, 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2177, 2178, 2179
88	IL_5U4I_088 ➜	missing nts	2123, 2124, 2125, 2126, 2127, 2128, 2129, 2159, 2160, 2161, 2162, 2163, 2164, 2165, 2166, 2167, 2168, 2169, 2170, 2171, 2172, 2173, 2174, 2175
89	IL_5U4I_089 ➜	missing nts	2129, 2130, 2131, 2132, 2133, 2134, 2135, 2136, 2155, 2156, 2157, 2158, 2159
90	IL_5U4I_090 ➜	missing nts	2201, 2202, 2203, 2204, 2205, 2219, 2220, 2221, 2222
91	IL_5U4I_091 ➜	missing nts	2350, 2351, 2352, 2353, 2364, 2365, 2366, 2367
92	IL_5U4I_092 ➜	missing nts	2401, 2402, 2403, 2414, 2415
93	IL_5U4I_093 ➜	missing nts	OMC
94	IL_5U4I_094 ➜	missing nts	PSU
95	IL_5U4I_095 ➜	missing nts	2459, 2460, 2461, 2489, 2490, 2491, 2492, 2493
96	IL_5U4I_096 ➜	missing nts	2466, 2467, 2468, 2469, 2470, 2480, 2481, 2482, 2483, 2484
97	IL_5U4I_097 ➜	missing nts	PSU
98	IL_5U4I_098 ➜	missing nts	2510, 2511, 2512, 2574, 2575, 2576, 2577, 2578
99	IL_5U4I_099 ➜	missing nts	2512, 2513, 2571, 2572, 2573, 2574
100	IL_5U4I_100 ➜	missing nts	2522, 2523, 2540, 2541, 2542, 2543
101	IL_5U4I_101 ➜	missing nts	PSU
102	IL_5U4I_102 ➜	missing nts	2591, 2592, 2601, 2602, 2603
103	IL_5U4I_103 ➜	missing nts	2636, 2637, 2638, 2639, 2640, 2774, 2775, 2776, 2777, 2778, 2779, 2780, 2781, 2782
104	IL_5U4I_104 ➜	missing nts	2652, 2653, 2654, 2655, 2656, 2657, 2658, 2663, 2664, 2665, 2666, 2667, 2668
105	IL_5U4I_105 ➜	missing nts	2680, 2681, 2682, 2683, 2684, 2725, 2726, 2727
106	IL_5U4I_106 ➜	missing nts	2687, 2688, 2689, 2690, 2691, 2718, 2719, 2720, 2721, 2722
107	IL_5U4I_107 ➜	missing nts	2695, 2696, 2711, 2712, 2713, 2714
108	IL_5U4I_108 ➜	missing nts	2737, 2738, 2739, 2740, 2741, 2742, 2762, 2763, 2764, 2765, 2766, 2767
109	IL_5U4I_109 ➜	missing nts	2806, 2807, 2808, 2809, 2810, 2811, 2889, 2890, 2891, 2892
110	IL_5U4I_110 ➜	missing nts	2838, 2839, 2840, 2877, 2878, 2879, 2880
111	IL_5U4I_111 ➜	missing nts	2843, 2844, 2845, 2846, 2870, 2871, 2872, 2873, 2874
112	IL_5U4I_112 ➜	missing nts	2846, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2864, 2865, 2866, 2867, 2868, 2869, 2870

Valid loops

#	loop id	location	motif
1	HL_5U4I_048 ➜	1/A/1910:1920	NA
2	HL_5U4I_070 ➜	1/B/38:44	NA
3	HL_5U4I_071 ➜	1/B/86:90	NA
4	HL_5U4I_072 ➜	1/a/12:22	NA
5	HL_5U4I_073 ➜	1/a/80:89	NA
6	HL_5U4I_074 ➜	1/a/158:163	NA
7	HL_5U4I_075 ➜	1/a/186:191	NA
8	HL_5U4I_076 ➜	1/a/202:215	NA
9	HL_5U4I_077 ➜	1/a/259:267	NA
10	HL_5U4I_078 ➜	1/a/296:301	NA
11	HL_5U4I_079 ➜	1/a/320:333	NA
12	HL_5U4I_080 ➜	1/a/342:347	NA
13	HL_5U4I_081 ➜	1/a/379:384	NA
14	HL_5U4I_082 ➜	1/a/419:424	NA
15	HL_5U4I_083 ➜	1/a/462:470	NA
16	HL_5U4I_084 ➜	1/a/521:528	NA
17	HL_5U4I_085 ➜	1/a/617:623	NA
18	HL_5U4I_086 ➜	1/a/689:698	NA
19	HL_5U4I_087 ➜	1/a/726:731	NA
20	HL_5U4I_088 ➜	1/a/786:796	NA
21	HL_5U4I_089 ➜	1/a/839:847	NA
22	HL_5U4I_090 ➜	1/a/862:867	NA
23	HL_5U4I_091 ➜	1/a/897:902	NA
24	HL_5U4I_092 ➜	1/a/963:972	NA
25	HL_5U4I_093 ➜	1/a/1012:1017	NA
26	HL_5U4I_094 ➜	1/a/1029:1033	NA
27	HL_5U4I_095 ➜	1/a/1076:1081	NA
28	HL_5U4I_096 ➜	1/a/1089:1096	NA
29	HL_5U4I_097 ➜	1/a/1133:1141	NA
30	HL_5U4I_098 ➜	1/a/1165:1171	NA
31	HL_5U4I_099 ➜	1/a/1265:1270	NA
32	HL_5U4I_100 ➜	1/a/1314:1323	NA
33	HL_5U4I_101 ➜	1/a/1356:1366	NA
34	HL_5U4I_102 ➜	1/a/1449:1454	NA
35	HL_5U4I_103 ➜	1/a/1515:1520	NA
36	HL_5U4I_104 ➜	1/x/12:22	NA
37	HL_5U4I_105 ➜	1/x/31:39	NA
38	HL_5U4I_106 ➜	1/x/53:61	NA
39	HL_5U4I_107 ➜	1/y/12:22	NA
40	HL_5U4I_108 ➜	1/y/31:39	NA
41	HL_5U4I_109 ➜	1/y/53:61	NA

Problematic loops

#	loop id	Problem	Sequence
1	HL_5U4I_001 ➜	missing nts	59, 60, 61, 62, 63, 64, 65, 66, 67, 68
2	HL_5U4I_002 ➜	missing nts	87, 88, 89, 90, 91, 92, 93, 94, 95
3	HL_5U4I_003 ➜	missing nts	123, 124, 125, 126, 127, 128
4	HL_5U4I_004 ➜	missing nts	136, 137, 138, 139, 140, 141, 142, 143
5	HL_5U4I_005 ➜	missing nts	158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168
6	HL_5U4I_006 ➜	missing nts	194, 195, 196, 197, 198, 199, 200, 201
7	HL_5U4I_007 ➜	missing nts	225, 226, 227, 228, 229, 230
8	HL_5U4I_008 ➜	missing nts	246, 247, 248, 249, 250, 251, 252
9	HL_5U4I_009 ➜	missing nts	305, 306, 307, 308, 309, 310, 311, 312
10	HL_5U4I_010 ➜	missing nts	319, 320, 321, 322, 323
11	HL_5U4I_011 ➜	missing nts	327, 328, 329, 330, 331, 332, 333, 334, 335
12	HL_5U4I_012 ➜	missing nts	382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392
13	HL_5U4I_013 ➜	missing nts	410, 411, 412, 413, 414, 415, 416, 417
14	HL_5U4I_014 ➜	missing nts	462, 463, 464, 465, 466, 467
15	HL_5U4I_015 ➜	missing nts	487, 488, 489, 490, 491, 492, 493
16	HL_5U4I_016 ➜	missing nts	544, 545, 546, 547, 548, 549
17	HL_5U4I_017 ➜	missing nts	566, 567, 568, 569, 570, 571, 572, 573, 574, 575
18	HL_5U4I_018 ➜	missing nts	611, 612, 613, 614, 615, 616, 617
19	HL_5U4I_019 ➜	missing nts	629, 630, 631, 632, 633, 634
20	HL_5U4I_020 ➜	missing nts	640, 641, 642, 643, 644, 645, 646, 647, 648
21	HL_5U4I_021 ➜	missing nts	712, 713, 714, 715, 716, 717, 718, 719
22	HL_5U4I_022 ➜	missing nts	1MG, PSU, 5MU
23	HL_5U4I_023 ➜	missing nts	779, 780, 781, 782, 783, 784, 785
24	HL_5U4I_024 ➜	missing nts	826, 827, 828, 829, 830, 831
25	HL_5U4I_025 ➜	missing nts	885, 886, 887, 888, 889, 890, 891
26	HL_5U4I_026 ➜	missing nts	PSU
27	HL_5U4I_027 ➜	missing nts	978, 979, 980, 981, 982, 983, 984, 985
28	HL_5U4I_028 ➜	missing nts	1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074
29	HL_5U4I_029 ➜	missing nts	1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099
30	HL_5U4I_030 ➜	missing nts	1172, 1173, 1174, 1175, 1176, 1177
31	HL_5U4I_031 ➜	missing nts	1222, 1223, 1224, 1225, 1226, 1227
32	HL_5U4I_032 ➜	missing nts	1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289
33	HL_5U4I_033 ➜	missing nts	1324, 1325, 1326, 1327, 1328, 1329, 1330
34	HL_5U4I_034 ➜	missing nts	1363, 1364, 1365, 1366, 1367, 1368
35	HL_5U4I_035 ➜	missing nts	1389, 1390, 1391, 1392, 1393, 1394, 1395, 1396, 1397, 1398
36	HL_5U4I_036 ➜	missing nts	1451, 1452, 1453, 1454, 1455, 1456, 1457, 1458, 1459
37	HL_5U4I_037 ➜	missing nts	1492, 1493, 1494, 1495, 1496, 1497, 1498
38	HL_5U4I_038 ➜	missing nts	1533, 1534, 1535, 1536, 1537, 1538
39	HL_5U4I_039 ➜	missing nts	1565, 1566, 1567, 1568
40	HL_5U4I_040 ➜	missing nts	1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619
41	HL_5U4I_041 ➜	missing nts	1630, 1631, 1632, 1633, 1634, 1635, 1636
42	HL_5U4I_042 ➜	missing nts	1691, 1692, 1693, 1694, 1695, 1696
43	HL_5U4I_043 ➜	missing nts	1727, 1728, 1729, 1730, 1731, 1732, 1733
44	HL_5U4I_044 ➜	missing nts	1752, 1753, 1754, 1755, 1756
45	HL_5U4I_045 ➜	missing nts	1777, 1778, 1779, 1780, 1781, 1782, 1783, 1784, 1785, 1786, 1787
46	HL_5U4I_046 ➜	missing nts	1806, 1807, 1808, 1809, 1810, 1811
47	HL_5U4I_047 ➜	missing nts	1868, 1869, 1870, 1871, 1872, 1873
48	HL_5U4I_049 ➜	missing nts	1949, 1950, 1951, 1952, 1953, 1954, 1955, 1956, 1957
49	HL_5U4I_050 ➜	missing nts	2027, 2028, 2029, 2030, 2031, 2032, 2033, 2034, 2035, 2036
50	HL_5U4I_051 ➜	missing nts	2143, 2144, 2145, 2146, 2147, 2148
51	HL_5U4I_052 ➜	missing nts	2209, 2210, 2211, 2212, 2213, 2214, 2215
52	HL_5U4I_053 ➜	missing nts	OMG
53	HL_5U4I_054 ➜	missing nts	2264, 2265, 2266, 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, 2276
54	HL_5U4I_055 ➜	missing nts	2303, 2304, 2305, 2306, 2307, 2308, 2309, 2310, 2311, 2312, 2313
55	HL_5U4I_056 ➜	missing nts	2324, 2325, 2326, 2327, 2328, 2329, 2330, 2331
56	HL_5U4I_057 ➜	missing nts	2356, 2357, 2358, 2359, 2360, 2361
57	HL_5U4I_058 ➜	missing nts	2374, 2375, 2376, 2377, 2378, 2379
58	HL_5U4I_059 ➜	missing nts	2404, 2405, 2406, 2407, 2408, 2409, 2410, 2411, 2412, 2413
59	HL_5U4I_060 ➜	missing nts	2471, 2472, 2473, 2474, 2475, 2476, 2477, 2478, 2479
60	HL_5U4I_061 ➜	missing nts	2528, 2529, 2530, 2531, 2532, 2533, 2534, 2535
61	HL_5U4I_062 ➜	missing nts	OMU
62	HL_5U4I_063 ➜	missing nts	2594, 2595, 2596, 2597, 2598, 2599
63	HL_5U4I_064 ➜	missing nts	2658, 2659, 2660, 2661, 2662, 2663
64	HL_5U4I_065 ➜	missing nts	2701, 2702, 2703, 2704, 2705, 2706
65	HL_5U4I_066 ➜	missing nts	2745, 2746, 2747, 2748, 2749, 2750, 2751, 2752, 2753, 2754, 2755, 2756, 2757, 2758, 2759
66	HL_5U4I_067 ➜	missing nts	2795, 2796, 2797, 2798, 2799, 2800, 2801
67	HL_5U4I_068 ➜	missing nts	2819, 2820, 2821, 2822, 2823, 2824, 2825, 2826, 2827
68	HL_5U4I_069 ➜	missing nts	2856, 2857, 2858, 2859, 2860, 2861

Valid loops

#	loop id	location	motif
1	J3_5U4I_015 ➜	1/B/10:16,1/B/68:70,1/B/106:110	NA
2	J3_5U4I_016 ➜	1/a/46:47,1/a/361:367,1/a/393:395	NA
3	J3_5U4I_017 ➜	1/a/586:588,1/a/651:654,1/a/754:755	NA
4	J3_5U4I_018 ➜	1/a/672:673,1/a/717:725,1/a/732:734	NA
5	J3_5U4I_019 ➜	1/a/826:829,1/a/857:861,1/a/868:874	NA
6	J3_5U4I_020 ➜	1/a/936:939,1/a/1344:1350,1/a/1372:1379	NA
7	J3_5U4I_021 ➜	1/a/943:946,1/a/1235:1237,1/a/1337:1340	NA
8	J3_5U4I_022 ➜	1/a/955:962,1/a/973:984,1/a/1221:1225	NA
9	J3_5U4I_023 ➜	1/a/990:993,1/a/1045:1047,1/a/1210:1215	NA
10	J3_5U4I_024 ➜	1/a/1063:1068,1/a/1107:1113,1/a/1187:1193	NA
11	J3_5U4I_025 ➜	1/a/1073:1074,1/a/1083:1087,1/a/1098:1102	NA
12	J3_5U4I_026 ➜	1/a/1116:1118,1/a/1155:1158,1/a/1181:1184	NA
13	J3_5U4I_027 ➜	1/a/1237:1241,1/a/1296:1303,1/a/1334:1337	NA

Problematic loops

#	loop id	Problem	Sequence
1	J3_5U4I_001 ➜	missing nts	30, 31, 474, 475, 476, 477, 478, 479, 480, 481, 509, 510
2	J3_5U4I_002 ➜	missing nts	56, 57, 70, 71, 72, 73, 74, 75, 76, 110, 111, 112, 113, 114
3	J3_5U4I_003 ➜	missing nts	683, 684, 685, 686, 687, 688, 689, 773, 774, 775, 791, 792, 793, 794
4	J3_5U4I_004 ➜	missing nts	698, 699, 700, 732, 733, 734, 735, 736, 760, 761, 762, 763
5	J3_5U4I_005 ➜	missing nts	1055, 1056, 1057, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1102, 1103, 1104
6	J3_5U4I_006 ➜	missing nts	1298, 1299, 1300, 1301, 1302, 1303, 1625, 1626, 1627, 1639, 1640, 1641, 1642
7	J3_5U4I_007 ➜	missing nts	1306, 1307, 1308, 1309, 1605, 1606, 1607, 1608, 1609, 1610, 1611, 1620, 1621, 1622
8	J3_5U4I_008 ➜	missing nts	1344, 1345, 1346, 1347, 1348, 1349, 1350, 1381, 1382, 1383, 1384, 1385, 1402, 1403
9	J3_5U4I_009 ➜	missing nts	2091, 2092, 2093, 2196, 2197, 2198, 2199, 2200, 2223, 2224, 2225, 2226, 2227, 2228
10	J3_5U4I_010 ➜	missing nts	2282, 2283, 2284, 2384, 2385, 2386, 2387, 2388, 2389, 2390, 2391, 2392, 2393, 2394, 2395, 2421, 2422, 2423, 2424, 2425, 2426, 2427
11	J3_5U4I_011 ➜	missing nts	2295, 2296, 2297, 2298, 2299, 2317, 2318, 2319, 2320, 2321, 2322, 2323, 2332, 2333, 2334, 2335, 2336, 2337
12	J3_5U4I_012 ➜	missing nts	2517, 2518, 2519, 2520, 2545, 2546, 2547, 2561, 2562, 2563, 2564, 2565, 2566, 2567
13	J3_5U4I_013 ➜	missing nts	2789, 2790, 2791, 2805, 2806, 2892, 2893, 2894
14	J3_5U4I_014 ➜	missing nts	2812, 2813, 2814, 2815, 2831, 2832, 2833, 2834, 2835, 2836, 2882, 2883, 2884, 2885, 2886, 2887, 2888

Coloring options: Nucleotide numbers