5GAK Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
# | loop id | location | motif |
---|---|---|---|
1 | ➜ | 1/1/5:7,1/4/152:154 | NA |
2 | ➜ | 1/1/7:8,1/4/150:152 | NA |
3 | ➜ | 1/1/8:12,1/4/146:150 | NA |
4 | ➜ | 1/1/12:15,1/4/144:146 | NA |
5 | ➜ | 1/1/27:28,1/1/56:58 | NA |
6 | ➜ | 1/1/82:89,1/1/97:103 | NA |
7 | ➜ | 1/1/123:124,1/1/144:149 | NA |
8 | ➜ | 1/1/125:127,1/1/141:143 | NA |
9 | ➜ | 1/1/163:165,1/1/257:258 | NA |
10 | ➜ | 1/1/169:170,1/1/248:253 | NA |
11 | ➜ | 1/1/177:179,1/1/237:241 | NA |
12 | ➜ | 1/1/333:335,1/4/28:30 | NA |
13 | ➜ | 1/1/336:339,1/4/25:27 | NA |
14 | ➜ | 1/1/376:379,1/1/390:403 | NA |
15 | ➜ | 1/1/404:412,1/4/11:20 | NA |
16 | ➜ | 1/1/413:416,1/4/7:10 | NA |
17 | ➜ | 1/1/429:431,1/1/628:630 | NA |
18 | ➜ | 1/1/512:513,1/1/577:579 | NA |
19 | ➜ | 1/1/517:525,1/1/567:573 | NA |
20 | ➜ | 1/1/531:538,1/1/553:561 | NA |
21 | ➜ | 1/1/668:670,1/1/792:794 | NA |
22 | ➜ | 1/1/680:684,1/1/696:700 | NA |
23 | ➜ | 1/1/725:728,1/1/741:745 | NA |
24 | ➜ | 1/1/752:753,1/1/779:781 | NA |
25 | ➜ | 1/1/755:756,1/1/775:777 | NA |
26 | ➜ | 1/1/803:805,1/1/938:940 | NA |
27 | ➜ | 1/1/805:809,1/1/931:938 | NA |
28 | ➜ | 1/1/954:956,1/1/965:967 | NA |
29 | ➜ | 1/1/969:970,1/1/1111:1113 | NA |
30 | ➜ | 1/1/977:981,1/1/1102:1104 | NA |
31 | ➜ | 1/1/983:985,1/1/1099:1100 | NA |
32 | ➜ | 1/1/1120:1123,1/1/1135:1138 | NA |
33 | ➜ | 1/1/1167:1171,1/1/1328:1332 | NA |
34 | ➜ | 1/1/1173:1180,1/1/1325:1326 | NA |
35 | ➜ | 1/1/1180:1182,1/1/1324:1325 | NA |
36 | ➜ | 1/1/1187:1194,1/1/1314:1319 | NA |
37 | ➜ | 1/1/1194:1205,1/1/1299:1314 | NA |
38 | ➜ | 1/1/1207:1209,1/1/1296:1297 | NA |
39 | ➜ | 1/1/1217:1226,1/1/1283:1288 | NA |
40 | ➜ | 1/1/1376:1378,1/1/1428:1431 | NA |
41 | ➜ | 1/1/1385:1387,1/1/1420:1421 | NA |
42 | ➜ | 1/1/1388:1396,1/1/1414:1419 | NA |
43 | ➜ | 1/1/1398:1400,1/1/1411:1412 | NA |
44 | ➜ | 1/1/1444:1450,1/1/2354:2359 | NA |
45 | ➜ | 1/1/2391:2394,1/1/2986:2988 | NA |
46 | ➜ | 1/1/2824:2826,1/1/2863:2865 | NA |
47 | ➜ | 1/1/2826:2831,1/1/2857:2863 | NA |
48 | ➜ | 1/1/2835:2839,1/1/2849:2853 | NA |
49 | ➜ | 1/1/2876:2877,1/1/2949:2951 | NA |
50 | ➜ | 1/1/2879:2881,1/1/2943:2947 | NA |
51 | ➜ | 1/1/2881:2882,1/1/2940:2943 | NA |
52 | ➜ | 1/1/2889:2891,1/1/2912:2914 | NA |
53 | ➜ | 1/1/2891:2892,1/1/2909:2912 | NA |
54 | ➜ | 1/1/2918:2920,1/1/2926:2928 | NA |
55 | ➜ | 1/1/3004:3007,1/1/3139:3144 | NA |
56 | ➜ | 1/1/3012:3014,1/1/3040:3042 | NA |
57 | ➜ | 1/1/3018:3025,1/1/3030:3036 | NA |
58 | ➜ | 1/1/3046:3051,1/1/3091:3095 | NA |
59 | ➜ | 1/1/3054:3059,1/1/3084:3088 | NA |
60 | ➜ | 1/1/3063:3064,1/1/3077:3080 | NA |
61 | ➜ | 1/1/3103:3107,1/1/3127:3131 | NA |
62 | ➜ | 1/1/3164:3166,1/1/3284:3286 | NA |
63 | ➜ | 1/1/3177:3179,1/1/3210:3211 | NA |
64 | ➜ | 1/1/3179:3188,1/1/3204:3210 | NA |
65 | ➜ | 1/1/3193:3194,1/1/3197:3199 | NA |
66 | ➜ | 1/1/3225:3229,1/1/3258:3260 | NA |
67 | ➜ | 1/1/3233:3235,1/1/3252:3254 | NA |
68 | ➜ | 1/1/3235:3238,1/1/3249:3252 | NA |
69 | ➜ | 1/1/3300:3303,1/1/3311:3314 | NA |
70 | ➜ | 1/1/3324:3325,1/1/3381:3383 | NA |
71 | ➜ | 1/1/3328:3330,1/1/3373:3378 | NA |
72 | ➜ | 1/1/3332:3337,1/1/3367:3371 | NA |
73 | ➜ | 1/1/3340:3342,1/1/3363:3364 | NA |
74 | ➜ | 1/1/3342:3345,1/1/3360:3363 | NA |
75 | ➜ | 1/1/3349:3350,1/1/3353:3356 | NA |
76 | ➜ | 1/3/15:16,1/3/63:65 | NA |
77 | ➜ | 1/3/21:27,1/3/53:58 | NA |
78 | ➜ | 1/3/28:29,1/3/49:52 | NA |
79 | ➜ | 1/3/29:30,1/3/47:49 | NA |
80 | ➜ | 1/3/32:36,1/3/41:45 | NA |
81 | ➜ | 1/3/72:80,1/3/100:106 | NA |
82 | ➜ | 1/3/84:87,1/3/94:96 | NA |
83 | ➜ | 1/4/63:64,1/4/96:98 | NA |
84 | ➜ | 1/4/64:66,1/4/93:96 | NA |
85 | ➜ | 1/B/3:5,1/B/68:70 | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
1 | ➜ | 435, 436, 437, 438, 439, 440, 494, 495, 618, 619, 620, 621, 622, 623, 624 | |
2 | ➜ | GAC,GUC | |
3 | ➜ | 758, 759, 760, 761, 762, 763, 768, 769, 770, 771, 772, 773 | |
4 | ➜ | 833, 834, 859, 860, 861 | |
5 | ➜ | 834, 835, 836, 837, 838, 855, 856, 857, 858, 859 | |
6 | ➜ | 869, 870, 871, 872, 888, 889, 890 | |
7 | ➜ | 873, 874, 875, 886, 887 | |
8 | ➜ | 907, 908, 909, 919, 920, 921, 922, 923 | |
9 | ➜ | 991, 992, 993, 994, 995, 996, 997, 1052, 1053, 1054, 1055, 1056, 1057, 1058 | |
10 | ➜ | 997, 998, 1050, 1051, 1052 | |
11 | ➜ | 999, 1000, 1001, 1002, 1003, 1004, 1046, 1047, 1048, 1049 | |
12 | ➜ | 1006, 1007, 1008, 1009, 1041, 1042, 1043, 1044 | |
13 | ➜ | 1009, 1010, 1011, 1039, 1040, 1041 | |
14 | ➜ | 1013, 1014, 1015, 1016, 1017, 1018, 1034, 1035, 1036, 1037 | |
15 | ➜ | 1018, 1019, 1020, 1032, 1033, 1034 | |
16 | ➜ | 1069, 1070, 1071, 1087, 1088, 1089 | |
17 | ➜ | 1074, 1075, 1076, 1083, 1084 | |
18 | ➜ | 1234, 1235, 1236, 1237, 1238, 1250, 1251, 1252, 1253, 1254 | |
19 | ➜ | 1262, 1263, 1264, 1265, 1266, 1275, 1276, 1277 | |
20 | ➜ | 1500, 1501, 1502, 1503, 1504, 1505, 1513, 1514, 1515, 1516 | |
21 | ➜ | 1532, 1533, 1534, 1535, 1536, 1585, 1586, 1587, 1588, 1589, 1590 | |
22 | ➜ | 1560, 1561, 1562, 1563, 1577, 1578, 1579 | |
23 | ➜ | 1563, 1564, 1565, 1574, 1575, 1576, 1577 | |
24 | ➜ | 1618, 1619, 1620, 1621, 1824, 1825, 1826 | |
25 | ➜ | 1623, 1624, 1625, 1626, 1627, 1816, 1817, 1818, 1819, 1820, 1821, 1822 | |
26 | ➜ | 1627, 1628, 1629, 1630, 1631, 1811, 1812, 1813, 1814, 1815, 1816 | |
27 | ➜ | 1645, 1646, 1647, 1648, 1649, 1806, 1807, 1808, 1809, 1810 | |
28 | ➜ | 1661, 1662, 1663, 1786, 1787, 1788 | |
29 | ➜ | 1669, 1670, 1778, 1779, 1780 | |
30 | ➜ | 1670, 1671, 1776, 1777, 1778 | |
31 | ➜ | 1694, 1695, 1696, 1697, 1698, 1747, 1748, 1749, 1750, 1751, 1752 | |
32 | ➜ | 1702, 1703, 1704, 1705, 1706, 1707, 1737, 1738, 1739, 1740, 1741, 1742, 1743 | |
33 | ➜ | 1711, 1712, 1713, 1714, 1715, 1716, 1717, 1727, 1728, 1729, 1730, 1731, 1732, 1733 | |
34 | ➜ | AGA,UCU | |
35 | ➜ | 1883, 1884, 1885, 1886, 1887, 1888, 1889, 2346, 2347, 2348, 2349 | |
36 | ➜ | 1895, 1896, 1897, 2338, 2339, 2340 | |
37 | ➜ | 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 2333, 2334, 2335, 2336, 2337 | |
38 | ➜ | 1918, 1919, 1920, 1921, 1922, 1923, 1928, 1929, 1930, 1931, 1932, 1933, 1934 | |
39 | ➜ | 1940, 1941, 1942, 2106, 2107, 2108 | |
40 | ➜ | 1947, 1948, 2098, 2099, 2100, 2101 | |
41 | ➜ | AUC,GAU | |
42 | ➜ | 2128, 2129, 2323, 2324, 2325 | |
43 | ➜ | 2156, 2157, 2158, 2159, 2160, 2161, 2173, 2174, 2175, 2176, 2177, 2178, 2179, 2180 | |
44 | ➜ | 2196, 2197, 2198, 2199, 2245, 2246 | |
45 | ➜ | 2200, 2201, 2241, 2242, 2243, 2244 | |
46 | ➜ | 2202, 2203, 2204, 2238, 2239, 2240 | |
47 | ➜ | 2204, 2205, 2206, 2207, 2208, 2209, 2210, 2235, 2236, 2237, 2238 | |
48 | ➜ | 2211, 2212, 2213, 2214, 2215, 2216, 2217, 2218, 2227, 2228, 2229, 2230, 2231, 2232, 2233, 2234 | |
49 | ➜ | 2276, 2277, 2307, 2308, 2309, 2310 | |
50 | ➜ | 2277, 2278, 2279, 2280, 2281, 2282, 2283, 2284, 2285, 2286, 2287, 2288, 2304, 2305, 2306, 2307 | |
51 | ➜ | 2396, 2397, 2398, 2981, 2982, 2983, 2984 | |
52 | ➜ | 2409, 2410, 2411, 2811, 2812 | |
53 | ➜ | 2412, 2413, 2807, 2808, 2809, 2810 | |
54 | ➜ | 2422, 2423, 2424, 2425, 2604, 2605, 2606, 2607, 2608 | |
55 | ➜ | 2444, 2445, 2501, 2502, 2503 | |
56 | ➜ | 2520, 2521, 2522, 2523, 2524, 2525, 2526, 2584, 2585, 2586, 2587 | |
57 | ➜ | 2614, 2615, 2625, 2626, 2627 | |
58 | ➜ | 2666, 2667, 2668, 2686, 2687, 2688, 2689, 2690 | |
59 | ➜ | 2718, 2719, 2720, 2721, 2735, 2736, 2737, 2738 | |
60 | ➜ | 2770, 2771, 2772, 2773, 2787, 2788 | |
61 | ➜ | 2823, 2824, 2865, 2866, 2867 | |
62 | ➜ | 2957, 2958, 2959, 2973, 2974, 2975 | |
63 | ➜ | 2960, 2961, 2970, 2971, 2972 | |
64 | ➜ | GUC,GAC | |
65 | ➜ | 3168, 3169, 3170, 3280, 3281, 3282 | |
66 | ➜ | GUC,GAC | |
67 | ➜ | CAGG,CCUG |
Valid loops
# | loop id | location | motif |
---|---|---|---|
1 | ➜ | 1/1/31:53 | NA |
2 | ➜ | 1/1/69:74 | NA |
3 | ➜ | 1/1/90:96 | NA |
4 | ➜ | 1/1/132:136 | NA |
5 | ➜ | 1/1/194:201 | NA |
6 | ➜ | 1/1/208:212 | NA |
7 | ➜ | 1/1/216:224 | NA |
8 | ➜ | 1/1/278:287 | NA |
9 | ➜ | 1/1/357:362 | NA |
10 | ➜ | 1/1/382:387 | NA |
11 | ➜ | 1/1/543:548 | NA |
12 | ➜ | 1/1/599:604 | NA |
13 | ➜ | 1/1/640:649 | NA |
14 | ➜ | 1/1/686:694 | NA |
15 | ➜ | 1/1/707:712 | NA |
16 | ➜ | 1/1/732:737 | NA |
17 | ➜ | 1/1/958:963 | NA |
18 | ➜ | 1/1/1126:1132 | NA |
19 | ➜ | 1/1/1148:1155 | NA |
20 | ➜ | 1/1/1403:1408 | NA |
21 | ➜ | 1/1/2840:2848 | NA |
22 | ➜ | 1/1/2897:2904 | NA |
23 | ➜ | 1/1/2920:2926 | NA |
24 | ➜ | 1/1/3025:3030 | NA |
25 | ➜ | 1/1/3068:3073 | NA |
26 | ➜ | 1/1/3110:3124 | NA |
27 | ➜ | 1/1/3194:3197 | NA |
28 | ➜ | 1/1/3240:3247 | NA |
29 | ➜ | 1/1/3303:3311 | NA |
30 | ➜ | 1/1/3350:3353 | NA |
31 | ➜ | 1/3/36:41 | NA |
32 | ➜ | 1/3/88:93 | NA |
33 | ➜ | 1/4/47:56 | NA |
34 | ➜ | 1/4/108:114 | NA |
35 | ➜ | 1/4/124:129 | NA |
36 | ➜ | 1/A/12:23 | NA |
37 | ➜ | 1/A/31:39 | NA |
38 | ➜ | 1/A/53:61 | NA |
39 | ➜ | 1/B/13:22 | NA |
40 | ➜ | 1/B/31:39 | NA |
41 | ➜ | 1/B/53:61 | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
1 | ➜ | 303, 304, 305, 306, 307, 308, 309, 310, 311, 312 | |
2 | ➜ | 763, 764, 765, 766, 767, 768 | |
3 | ➜ | 844, 845, 846, 847, 848, 849 | |
4 | ➜ | 876, 877, 878, 879, 880, 881, 882, 883, 884, 885 | |
5 | ➜ | 910, 911, 912, 913, 914, 915, 916, 917, 918 | |
6 | ➜ | 1023, 1024, 1025, 1026, 1027, 1028, 1029 | |
7 | ➜ | 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083 | |
8 | ➜ | 1239, 1240, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249 | |
9 | ➜ | 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275 | |
10 | ➜ | 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357 | |
11 | ➜ | 1462, 1463, 1464, 1465, 1466, 1467, 1468, 1469, 1470 | |
12 | ➜ | 1506, 1507, 1508, 1509, 1510, 1511, 1512 | |
13 | ➜ | 1544, 1545, 1546, 1547, 1548, 1549 | |
14 | ➜ | 1565, 1566, 1567, 1568, 1569, 1570, 1571, 1572, 1573, 1574 | |
15 | ➜ | 1599, 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608 | |
16 | ➜ | 1634, 1635, 1636, 1637, 1638, 1639 | |
17 | ➜ | 1680, 1681, 1682, 1683, 1684, 1685, 1686, 1687, 1688 | |
18 | ➜ | 1719, 1720, 1721, 1722, 1723, 1724, 1725 | |
19 | ➜ | 1759, 1760, 1761, 1762, 1763, 1764, 1765, 1766 | |
20 | ➜ | 1792, 1793, 1794, 1795, 1796 | |
21 | ➜ | 1844, 1845, 1846, 1847, 1848, 1849, 1850, 1851 | |
22 | ➜ | 1862, 1863, 1864, 1865, 1866, 1867, 1868 | |
23 | ➜ | 1923, 1924, 1925, 1926, 1927, 1928 | |
24 | ➜ | 1952, 1953, 1954, 1955, 2093, 2094 | |
25 | ➜ | 2110, 2111, 2112, 2113, 2114 | |
26 | ➜ | 2135, 2136, 2137, 2138, 2139, 2140, 2141, 2142, 2143, 2144, 2145 | |
27 | ➜ | 2164, 2165, 2166, 2167, 2168, 2169, 2170 | |
28 | ➜ | 2220, 2221, 2222, 2223, 2224, 2225 | |
29 | ➜ | 2253, 2254, 2255, 2256, 2257, 2258, 2259, 2260, 2261, 2262, 2263 | |
30 | ➜ | 2292, 2293, 2294, 2295, 2296, 2297, 2298, 2299, 2300 | |
31 | ➜ | 2369, 2370, 2371, 2372, 2373, 2374, 2375, 2376, 2377, 2378 | |
32 | ➜ | 2450, 2451, 2452, 2492, 2493, 2494, 2495, 2496 | |
33 | ➜ | 2535, 2536, 2537, 2538, 2539, 2540, 2541, 2542, 2543, 2544 | |
34 | ➜ | 2567, 2568, 2569, 2570, 2571, 2572, 2573, 2574 | |
35 | ➜ | 2616, 2617, 2618, 2619, 2620, 2621, 2622, 2623, 2624 | |
36 | ➜ | 2633, 2634, 2635, 2636, 2637, 2638, 2639, 2640, 2641, 2642, 2643, 2644, 2645 | |
37 | ➜ | 2673, 2674, 2675, 2676, 2677, 2678, 2679, 2680, 2681 | |
38 | ➜ | 2693, 2694, 2695, 2696, 2697, 2698, 2699, 2700 | |
39 | ➜ | 2724, 2725, 2726, 2727, 2728, 2729, 2730, 2731, 2732 | |
40 | ➜ | 2744, 2745, 2746, 2747, 2748, 2749 | |
41 | ➜ | 2776, 2777, 2778, 2779, 2780, 2781, 2782, 2783, 2784 | |
42 | ➜ | 2963, 2964, 2965, 2966, 2967, 2968 | |
43 | ➜ | 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 |
Valid loops
# | loop id | location | motif |
---|---|---|---|
1 | ➜ | 1/1/113:123,1/1/149:158,1/1/263:267 | NA |
2 | ➜ | 1/1/2886:2889,1/1/2914:2916,1/1/2930:2936 | NA |
3 | ➜ | 1/1/3298:3300,1/1/3314:3320,1/1/3387:3390 | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
1 | ➜ | 814, 815, 816, 817, 818, 819, 820, 905, 906, 907, 923, 924, 925, 926 | |
2 | ➜ | 828, 829, 830, 831, 863, 864, 865, 866, 867, 892, 893, 894, 895, 896, 897 | |
3 | ➜ | 1230, 1231, 1232, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1277, 1278, 1279 | |
4 | ➜ | 1479, 1480, 1481, 1482, 1483, 1484, 1485, 1857, 1858, 1859, 1871, 1872, 1873, 1874 | |
5 | ➜ | 1488, 1489, 1490, 1491, 1837, 1838, 1839, 1840, 1841, 1842, 1843, 1852, 1853, 1854 | |
6 | ➜ | 2432, 2433, 2434, 2435, 2512, 2513, 2514, 2515, 2516, 2517, 2590, 2591, 2592, 2593, 2594, 2595, 2596, 2597 | |
7 | ➜ | 2664, 2665, 2666, 2690, 2691, 2692, 2701, 2702, 2703, 2704, 2705, 2706 |
Coloring options: