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

121 Internal loops
70 Hairpin loops
10 Junction loops

Valid loops

#	loop id	location	motif
1	IL_5GAF_001 ➜	1/1/38:43,1/1/66:68	NA
2	IL_5GAF_002 ➜	1/1/45:50,1/1/59:64	NA
3	IL_5GAF_003 ➜	1/A/24:30,1/A/510:516	NA
4	IL_5GAF_004 ➜	1/A/36:37,1/A/442:444	NA
5	IL_5GAF_005 ➜	1/A/43:44,1/A/434:436	NA
6	IL_5GAF_006 ➜	1/A/81:85,1/A/97:105	NA
7	IL_5GAF_007 ➜	1/A/136:138,1/A/141:143	NA
8	IL_5GAF_008 ➜	1/A/183:184,1/A/212:214	NA
9	IL_5GAF_009 ➜	1/A/188:194,1/A/201:208	NA
10	IL_5GAF_010 ➜	1/A/239:245,1/A/253:258	NA
11	IL_5GAF_011 ➜	1/A/269:271,1/A/366:370	NA
12	IL_5GAF_012 ➜	1/A/274:281,1/A/359:363	NA
13	IL_5GAF_013 ➜	1/A/285:287,1/A/353:355	NA
14	IL_5GAF_014 ➜	1/A/293:295,1/A/343:347	NA
15	IL_5GAF_015 ➜	1/A/481:484,1/A/496:509	NA
16	IL_5GAF_016 ➜	1/A/536:539,1/A/554:557	NA
17	IL_5GAF_017 ➜	1/A/564:566,1/A/575:577	NA
18	IL_5GAF_018 ➜	1/A/606:610,1/A/618:622	NA
19	IL_5GAF_019 ➜	1/A/672:674,1/A/806:808	NA
20	IL_5GAF_020 ➜	1/A/674:678,1/A/799:806	NA
21	IL_5GAF_021 ➜	1/A/697:698,1/A/763:765	NA
22	IL_5GAF_022 ➜	1/A/702:703,1/A/728:730	NA
23	IL_5GAF_023 ➜	1/A/703:707,1/A/724:728	NA
24	IL_5GAF_024 ➜	1/A/738:740,1/A/757:758	NA
25	IL_5GAF_025 ➜	1/A/775:777,1/A/787:791	NA
26	IL_5GAF_026 ➜	1/A/837:838,1/A/940:942	NA
27	IL_5GAF_027 ➜	1/A/844:847,1/A/933:934	NA
28	IL_5GAF_028 ➜	1/A/847:848,1/A/930:933	NA
29	IL_5GAF_029 ➜	1/A/850:851,1/A/926:928	NA
30	IL_5GAF_030 ➜	1/A/856:862,1/A/915:921	NA
31	IL_5GAF_031 ➜	1/A/862:863,1/A/913:915	NA
32	IL_5GAF_032 ➜	1/A/864:868,1/A/909:912	NA
33	IL_5GAF_033 ➜	1/A/870:872,1/A/905:907	NA
34	IL_5GAF_034 ➜	1/A/875:879,1/A/898:902	NA
35	IL_5GAF_035 ➜	1/A/879:882,1/A/894:898	NA
36	IL_5GAF_036 ➜	1/A/994:996,1/A/1159:1160	NA
37	IL_5GAF_037 ➜	1/A/998:1002,1/A/1153:1157	NA
38	IL_5GAF_038 ➜	1/A/1004:1011,1/A/1150:1151	NA
39	IL_5GAF_039 ➜	1/A/1011:1013,1/A/1149:1150	NA
40	IL_5GAF_040 ➜	1/A/1018:1024,1/A/1140:1144	NA
41	IL_5GAF_041 ➜	1/A/1024:1030,1/A/1124:1140	NA
42	IL_5GAF_042 ➜	1/A/1031:1034,1/A/1121:1123	NA
43	IL_5GAF_043 ➜	1/A/1038:1041,1/A/1114:1117	NA
44	IL_5GAF_044 ➜	1/A/1043:1051,1/A/1108:1112	NA
45	IL_5GAF_045 ➜	1/A/1059:1062,1/A/1076:1079	NA
46	IL_5GAF_046 ➜	1/A/1087:1090,1/A/1101:1102	NA
47	IL_5GAF_047 ➜	1/A/1196:1198,1/A/1247:1250	NA
48	IL_5GAF_048 ➜	1/A/1202:1206,1/A/1240:1243	NA
49	IL_5GAF_049 ➜	1/A/1208:1215,1/A/1234:1238	NA
50	IL_5GAF_050 ➜	1/A/1262:1269,1/A/2011:2017	NA
51	IL_5GAF_051 ➜	1/A/1310:1313,1/A/1603:1604	NA
52	IL_5GAF_052 ➜	1/A/1319:1323,1/A/1331:1333	NA
53	IL_5GAF_053 ➜	1/A/1351:1355,1/A/1376:1380	NA
54	IL_5GAF_054 ➜	1/A/1357:1361,1/A/1370:1374	NA
55	IL_5GAF_055 ➜	1/A/1415:1416,1/A/1582:1587	NA
56	IL_5GAF_056 ➜	1/A/1417:1421,1/A/1577:1581	NA
57	IL_5GAF_057 ➜	1/A/1432:1435,1/A/1557:1561	NA
58	IL_5GAF_058 ➜	1/A/1437:1440,1/A/1551:1555	NA
59	IL_5GAF_059 ➜	1/A/1450:1451,1/A/1459:1461	NA
60	IL_5GAF_060 ➜	1/A/1468:1471,1/A/1520:1524	NA
61	IL_5GAF_061 ➜	1/A/1474:1478,1/A/1513:1517	NA
62	IL_5GAF_062 ➜	1/A/1481:1482,1/A/1507:1510	NA
63	IL_5GAF_063 ➜	1/A/1489:1491,1/A/1499:1500	NA
64	IL_5GAF_064 ➜	1/A/1526:1529,1/A/1542:1546	NA
65	IL_5GAF_065 ➜	1/A/1651:1656,1/A/2004:2006	NA
66	IL_5GAF_066 ➜	1/A/1663:1665,1/A/1995:1997	NA
67	IL_5GAF_067 ➜	1/A/1666:1669,1/A/1993:1994	NA
68	IL_5GAF_068 ➜	1/A/1669:1674,1/A/1990:1993	NA
69	IL_5GAF_069 ➜	1/A/1686:1691,1/A/1696:1702	NA
70	IL_5GAF_070 ➜	1/A/1712:1718,1/A/1742:1746	NA
71	IL_5GAF_071 ➜	1/A/1720:1724,1/A/1736:1740	NA
72	IL_5GAF_072 ➜	1/A/1770:1771,1/A/1980:1982	NA
73	IL_5GAF_073 ➜	1/A/1798:1804,1/A/1813:1821	NA
74	IL_5GAF_074 ➜	1/A/1837:1840,1/A/1902:1903	NA
75	IL_5GAF_075 ➜	1/A/1841:1842,1/A/1898:1901	NA
76	IL_5GAF_076 ➜	1/A/1846:1849,1/A/1893:1894	NA
77	IL_5GAF_077 ➜	1/A/1864:1867,1/A/1874:1878	NA
78	IL_5GAF_078 ➜	1/A/1933:1934,1/A/1964:1967	NA
79	IL_5GAF_079 ➜	1/A/1934:1945,1/A/1961:1964	NA
80	IL_5GAF_080 ➜	1/A/2050:2052,1/A/2617:2618	NA
81	IL_5GAF_081 ➜	1/A/2054:2056,1/A/2612:2615	NA
82	IL_5GAF_082 ➜	1/A/2067:2069,1/A/2442:2443	NA
83	IL_5GAF_083 ➜	1/A/2070:2071,1/A/2438:2441	NA
84	IL_5GAF_084 ➜	1/A/2081:2083,1/A/2236:2239	NA
85	IL_5GAF_085 ➜	1/A/2085:2087,1/A/2232:2234	NA
86	IL_5GAF_086 ➜	1/A/2102:2106,1/A/2183:2187	NA
87	IL_5GAF_087 ➜	1/A/2106:2123,1/A/2175:2183	NA
88	IL_5GAF_088 ➜	1/A/2124:2128,1/A/2160:2174	NA
89	IL_5GAF_089 ➜	1/A/2129:2136,1/A/2155:2159	NA
90	IL_5GAF_091 ➜	1/A/2202:2204,1/A/2220:2221	NA
91	IL_5GAF_093 ➜	1/A/2297:2299,1/A/2317:2321	NA
92	IL_5GAF_094 ➜	1/A/2350:2353,1/A/2364:2367	NA
93	IL_5GAF_095 ➜	1/A/2401:2403,1/A/2414:2415	NA
94	IL_5GAF_096 ➜	1/A/2453:2454,1/A/2498:2500	NA
95	IL_5GAF_097 ➜	1/A/2454:2455,1/A/2496:2498	NA
96	IL_5GAF_098 ➜	1/A/2457:2459,1/A/2493:2494	NA
97	IL_5GAF_099 ➜	1/A/2459:2462,1/A/2488:2493	NA
98	IL_5GAF_100 ➜	1/A/2466:2470,1/A/2480:2484	NA
99	IL_5GAF_101 ➜	1/A/2507:2508,1/A/2580:2582	NA
100	IL_5GAF_102 ➜	1/A/2510:2512,1/A/2574:2578	NA
101	IL_5GAF_103 ➜	1/A/2512:2513,1/A/2571:2574	NA
102	IL_5GAF_104 ➜	1/A/2522:2523,1/A/2540:2543	NA
103	IL_5GAF_105 ➜	1/A/2591:2592,1/A/2601:2603	NA
104	IL_5GAF_106 ➜	1/A/2636:2640,1/A/2774:2782	NA
105	IL_5GAF_107 ➜	1/A/2652:2658,1/A/2663:2668	NA
106	IL_5GAF_108 ➜	1/A/2680:2684,1/A/2725:2727	NA
107	IL_5GAF_109 ➜	1/A/2687:2691,1/A/2718:2722	NA
108	IL_5GAF_110 ➜	1/A/2695:2696,1/A/2711:2714	NA
109	IL_5GAF_111 ➜	1/A/2737:2742,1/A/2762:2767	NA
110	IL_5GAF_112 ➜	1/A/2795:2796,1/A/2799:2801	NA
111	IL_5GAF_113 ➜	1/A/2806:2811,1/A/2889:2892	NA
112	IL_5GAF_114 ➜	1/A/2838:2839,1/A/2878:2880	NA
113	IL_5GAF_115 ➜	1/A/2843:2846,1/A/2870:2874	NA
114	IL_5GAF_116 ➜	1/A/2847:2852,1/A/2865:2869	NA
115	IL_5GAF_117 ➜	1/B/17:18,1/B/65:67	NA
116	IL_5GAF_118 ➜	1/B/23:28,1/B/56:60	NA
117	IL_5GAF_119 ➜	1/B/30:31,1/B/51:54	NA
118	IL_5GAF_120 ➜	1/B/34:38,1/B/44:48	NA
119	IL_5GAF_121 ➜	1/B/71:79,1/B/97:105	NA

Problematic loops

#	loop id	Problem	Sequence
1	IL_5GAF_090 ➜	complementary	GAC,GUC
2	IL_5GAF_092 ➜	complementary	GAC,GUC

Valid loops

#	loop id	location	motif
1	HL_5GAF_001 ➜	1/1/52:57	NA
2	HL_5GAF_002 ➜	1/A/59:68	NA
3	HL_5GAF_003 ➜	1/A/87:95	NA
4	HL_5GAF_004 ➜	1/A/123:128	NA
5	HL_5GAF_005 ➜	1/A/138:141	NA
6	HL_5GAF_006 ➜	1/A/158:168	NA
7	HL_5GAF_007 ➜	1/A/194:201	NA
8	HL_5GAF_008 ➜	1/A/225:230	NA
9	HL_5GAF_009 ➜	1/A/246:252	NA
10	HL_5GAF_010 ➜	1/A/305:312	NA
11	HL_5GAF_011 ➜	1/A/319:323	NA
12	HL_5GAF_012 ➜	1/A/327:335	NA
13	HL_5GAF_013 ➜	1/A/381:393	NA
14	HL_5GAF_014 ➜	1/A/410:417	NA
15	HL_5GAF_015 ➜	1/A/462:467	NA
16	HL_5GAF_016 ➜	1/A/487:493	NA
17	HL_5GAF_017 ➜	1/A/566:575	NA
18	HL_5GAF_018 ➜	1/A/611:617	NA
19	HL_5GAF_019 ➜	1/A/629:634	NA
20	HL_5GAF_020 ➜	1/A/641:647	NA
21	HL_5GAF_021 ➜	1/A/712:719	NA
22	HL_5GAF_022 ➜	1/A/744:753	NA
23	HL_5GAF_023 ➜	1/A/779:785	NA
24	HL_5GAF_024 ➜	1/A/826:831	NA
25	HL_5GAF_025 ➜	1/A/955:962	NA
26	HL_5GAF_026 ➜	1/A/978:985	NA
27	HL_5GAF_027 ➜	1/A/1064:1074	NA
28	HL_5GAF_028 ➜	1/A/1092:1099	NA
29	HL_5GAF_029 ➜	1/A/1172:1177	NA
30	HL_5GAF_030 ➜	1/A/1222:1227	NA
31	HL_5GAF_031 ➜	1/A/1281:1289	NA
32	HL_5GAF_032 ➜	1/A/1324:1330	NA
33	HL_5GAF_033 ➜	1/A/1363:1368	NA
34	HL_5GAF_034 ➜	1/A/1389:1398	NA
35	HL_5GAF_035 ➜	1/A/1451:1459	NA
36	HL_5GAF_036 ➜	1/A/1492:1498	NA
37	HL_5GAF_037 ➜	1/A/1533:1538	NA
38	HL_5GAF_038 ➜	1/A/1565:1568	NA
39	HL_5GAF_039 ➜	1/A/1612:1619	NA
40	HL_5GAF_040 ➜	1/A/1630:1636	NA
41	HL_5GAF_041 ➜	1/A/1691:1696	NA
42	HL_5GAF_042 ➜	1/A/1727:1733	NA
43	HL_5GAF_043 ➜	1/A/1752:1756	NA
44	HL_5GAF_044 ➜	1/A/1777:1787	NA
45	HL_5GAF_045 ➜	1/A/1806:1811	NA
46	HL_5GAF_046 ➜	1/A/1868:1873	NA
47	HL_5GAF_047 ➜	1/A/1910:1920	NA
48	HL_5GAF_048 ➜	1/A/1949:1957	NA
49	HL_5GAF_049 ➜	1/A/2027:2036	NA
50	HL_5GAF_050 ➜	1/A/2143:2148	NA
51	HL_5GAF_051 ➜	1/A/2209:2215	NA
52	HL_5GAF_052 ➜	1/A/2248:2256	NA
53	HL_5GAF_053 ➜	1/A/2264:2276	NA
54	HL_5GAF_054 ➜	1/A/2303:2313	NA
55	HL_5GAF_055 ➜	1/A/2324:2331	NA
56	HL_5GAF_056 ➜	1/A/2356:2361	NA
57	HL_5GAF_057 ➜	1/A/2374:2379	NA
58	HL_5GAF_058 ➜	1/A/2404:2413	NA
59	HL_5GAF_059 ➜	1/A/2471:2479	NA
60	HL_5GAF_060 ➜	1/A/2528:2535	NA
61	HL_5GAF_061 ➜	1/A/2551:2557	NA
62	HL_5GAF_062 ➜	1/A/2594:2599	NA
63	HL_5GAF_063 ➜	1/A/2658:2663	NA
64	HL_5GAF_064 ➜	1/A/2701:2706	NA
65	HL_5GAF_065 ➜	1/A/2745:2759	NA
66	HL_5GAF_066 ➜	1/A/2796:2799	NA
67	HL_5GAF_067 ➜	1/A/2819:2827	NA
68	HL_5GAF_068 ➜	1/A/2856:2861	NA
69	HL_5GAF_069 ➜	1/B/38:44	NA
70	HL_5GAF_070 ➜	1/B/86:90	NA

Problematic loops

No problematic loops

Valid loops

#	loop id	location	motif
1	J3_5GAF_001 ➜	1/A/683:689,1/A/773:775,1/A/791:794	NA
2	J3_5GAF_002 ➜	1/A/698:700,1/A/732:736,1/A/760:763	NA
3	J3_5GAF_003 ➜	1/A/1055:1057,1/A/1081:1087,1/A/1102:1104	NA
4	J3_5GAF_004 ➜	1/A/1298:1303,1/A/1625:1627,1/A/1639:1642	NA
5	J3_5GAF_005 ➜	1/A/1306:1309,1/A/1605:1611,1/A/1620:1622	NA
6	J3_5GAF_006 ➜	1/A/2091:2093,1/A/2196:2200,1/A/2223:2228	NA
7	J3_5GAF_007 ➜	1/A/2295:2297,1/A/2321:2323,1/A/2332:2337	NA
8	J3_5GAF_008 ➜	1/A/2517:2520,1/A/2545:2547,1/A/2561:2567	NA
9	J3_5GAF_009 ➜	1/A/2812:2815,1/A/2831:2836,1/A/2882:2888	NA
10	J3_5GAF_010 ➜	1/B/10:16,1/B/68:70,1/B/106:110	NA

Problematic loops

No problematic loops

Coloring options: Nucleotide numbers