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2.595 } ], "num_hairpins": 22, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 1 ], "summary": "[1] 9 [A.654 A.664] 4", "num_nts": 11, "nts_short": "UUUGGUCCUAG", "nts_long": "///A/654,///A/655,///A/656,///A/657,///A/658,///A/659,///A/660,///A/661,///A/662,///A/663,///A/664", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UUGGUCCUA", "nts_long": "///A/655,///A/656,///A/657,///A/658,///A/659,///A/660,///A/661,///A/662,///A/663" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ -3 ], "summary": "[1] 6 [A.701 A.708] 1", "num_nts": 8, "nts_short": "GCAUCCCC", "nts_long": "///A/701,///A/702,///A/703,///A/704,///A/705,///A/706,///A/707,///A/708", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CAUCCC", "nts_long": "///A/702,///A/703,///A/704,///A/705,///A/706,///A/707" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 11 ], 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{ "index": 6, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 16 ], "summary": "[1] 4 [A.804 A.809] 3", "num_nts": 6, "nts_short": "CCCACG", "nts_long": "///A/804,///A/805,///A/806,///A/807,///A/808,///A/809", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CCAC", "nts_long": "///A/805,///A/806,///A/807,///A/808" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 18 ], "summary": "[1] 4 [A.842 A.847] 4", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/842,///A/843,///A/844,///A/845,///A/846,///A/847", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/843,///A/844,///A/845,///A/846" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 16 ], "stem_indices": [ 20 ], "summary": "[1] 16 [A.879 A.896] 3", "num_nts": 18, "nts_short": "UCAAUUUCGUGCCAGCCA", "nts_long": "///A/879,///A/880,///A/881,///A/882,///A/883,///A/884,///A/885,///A/886,///A/887,///A/888,///A/889,///A/890,///A/891,///A/892,///A/893,///A/894,///A/895,///A/896", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 16, "nts_short": "CAAUUUCGUGCCAGCC", "nts_long": "///A/880,///A/881,///A/882,///A/883,///A/884,///A/885,///A/886,///A/887,///A/888,///A/889,///A/890,///A/891,///A/892,///A/893,///A/894,///A/895" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 22 ], "summary": "[1] 4 [A.894 A.899] 2", "num_nts": 6, "nts_short": "CCACCG", "nts_long": "///A/894,///A/895,///A/896,///A/897,///A/898,///A/899", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CACC", "nts_long": "///A/895,///A/896,///A/897,///A/898" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 30 ], "summary": "[1] 8 [A.989 A.998] 2", "num_nts": 10, "nts_short": "UUGUAAAAAA", "nts_long": "///A/989,///A/990,///A/991,///A/992,///A/993,///A/994,///A/995,///A/996,///A/997,///A/998", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UGUAAAAA", "nts_long": "///A/990,///A/991,///A/992,///A/993,///A/994,///A/995,///A/996,///A/997" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 31 ], "summary": "[1] 4 [A.1023 A.1028] 2", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/1023,///A/1024,///A/1025,///A/1026,///A/1027,///A/1028", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/1024,///A/1025,///A/1026,///A/1027" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 34 ], "summary": "[1] 9 [A.1074 A.1084] 4", "num_nts": 11, "nts_short": "GAtUAGAUACC", "nts_long": "///A/1074,///A/1075,///A/1076,///A/1077,///A/1078,///A/1079,///A/1080,///A/1081,///A/1082,///A/1083,///A/1084", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AtUAGAUAC", "nts_long": "///A/1075,///A/1076,///A/1077,///A/1078,///A/1079,///A/1080,///A/1081,///A/1082,///A/1083" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 35 ], "summary": "[1] 10 [A.1115 A.1126] 5", "num_nts": 12, "nts_short": "UAAAUCAACAAA", "nts_long": "///A/1115,///A/1116,///A/1117,///A/1118,///A/1119,///A/1120,///A/1121,///A/1122,///A/1123,///A/1124,///A/1125,///A/1126", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "AAAUCAACAA", "nts_long": "///A/1116,///A/1117,///A/1118,///A/1119,///A/1120,///A/1121,///A/1122,///A/1123,///A/1124,///A/1125" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 37 ], "summary": "[1] 4 [A.1150 A.1155] 4", "num_nts": 6, "nts_short": "CCACAG", "nts_long": "///A/1150,///A/1151,///A/1152,///A/1153,///A/1154,///A/1155", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CACA", "nts_long": "///A/1151,///A/1152,///A/1153,///A/1154" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 45 ], "summary": "[1] 8 [A.1217 A.1226] 2", "num_nts": 10, "nts_short": "GAUAAACCCC", "nts_long": "///A/1217,///A/1218,///A/1219,///A/1220,///A/1221,///A/1222,///A/1223,///A/1224,///A/1225,///A/1226", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "AUAAACCC", "nts_long": "///A/1218,///A/1219,///A/1220,///A/1221,///A/1222,///A/1223,///A/1224,///A/1225" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 53 ], "summary": "[1] 5 [A.1281 A.1287] 3", "num_nts": 7, "nts_short": "UGAUGAA", "nts_long": "///A/1281,///A/1282,///A/1283,///A/1284,///A/1285,///A/1286,///A/1287", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUGA", "nts_long": "///A/1282,///A/1283,///A/1284,///A/1285,///A/1286" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 54 ], "summary": "[1] 4 [A.1310 A.1315] 3", "num_nts": 6, "nts_short": "CCCACG", "nts_long": "///A/1310,///A/1311,///A/1312,///A/1313,///A/1314,///A/1315", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CCAC", "nts_long": "///A/1311,///A/1312,///A/1313,///A/1314" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 55 ], "summary": "[1] 5 [A.1373 A.1379] 4", "num_nts": 7, "nts_short": "UACCCCA", "nts_long": "///A/1373,///A/1374,///A/1375,///A/1376,///A/1377,///A/1378,///A/1379", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "ACCCC", "nts_long": "///A/1374,///A/1375,///A/1376,///A/1377,///A/1378" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 56 ], "summary": "[1] 7 [A.1399 A.1407] 7", "num_nts": 9, "nts_short": "AUGAAACUU", "nts_long": "///A/1399,///A/1400,///A/1401,///A/1402,///A/1403,///A/1404,///A/1405,///A/1406,///A/1407", "num_stems": 1, "bridges": [ { "index": 1, 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"num_nts": 5, "nts_short": "AAUAU", "nts_long": "///A/685,///A/686,///A/859,///A/860,///A/861", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/860" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -2, 7 ], "summary": "[2] 1 0 [A.690 A.823 A.692 A.822] 1 3", "num_nts": 5, "nts_short": "UACGA", "nts_long": "///A/690,///A/691,///A/692,///A/822,///A/823", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/691" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 7, 8 ], "summary": "[2] 1 0 [A.694 A.820 A.696 A.819] 3 3", "num_nts": 5, "nts_short": "CAUAG", "nts_long": "///A/694,///A/695,///A/696,///A/819,///A/820", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/695" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -5, 14 ], "summary": "[2] 0 1 [A.765 A.777 A.766 A.775] 1 3", "num_nts": 5, "nts_short": "CGCAG", "nts_long": "///A/765,///A/766,///A/775,///A/776,///A/777", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/776" } ] }, { "index": 6, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -6, 17 ], "summary": "[2] 1 0 [A.830 A.856 A.832 A.855] 1 3", "num_nts": 5, "nts_short": "UUUAA", "nts_long": "///A/830,///A/831,///A/832,///A/855,///A/856", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/831" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 7, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -7, 18 ], "summary": "[2] 0 1 [A.838 A.852 A.839 A.850] 1 4", "num_nts": 5, "nts_short": "UAUAA", "nts_long": "///A/838,///A/839,///A/850,///A/851,///A/852", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/851" } ] }, { "index": 8, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -10, 31 ], "summary": "[2] 1 0 [A.1020 A.1030 A.1022 A.1029] 1 2", "num_nts": 5, "nts_short": "CUAUG", "nts_long": "///A/1020,///A/1021,///A/1022,///A/1029,///A/1030", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1021" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 9, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 38, 39 ], "summary": "[2] 0 1 [A.1175 A.1479 A.1176 A.1477] 2 3", "num_nts": 5, "nts_short": "GGUAC", "nts_long": "///A/1175,///A/1176,///A/1477,///A/1478,///A/1479", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1478" } ] }, { "index": 10, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 39, 40 ], "summary": "[2] 1 0 [A.1178 A.1475 A.1180 A.1474] 3 6", "num_nts": 5, "nts_short": "GGUGC", "nts_long": "///A/1178,///A/1179,///A/1180,///A/1474,///A/1475", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1179" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 11, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 43, 44 ], "summary": "[2] 0 1 [A.1208 A.1357 A.1209 A.1355] 8 2", "num_nts": 5, "nts_short": "UCGAA", "nts_long": "///A/1208,///A/1209,///A/1355,///A/1356,///A/1357", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1356" } ] }, { "index": 12, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 47, 48 ], "summary": "[2] 1 0 [A.1253 A.1339 A.1255 A.1338] 2 3", "num_nts": 5, "nts_short": "CCUAG", "nts_long": "///A/1253,///A/1254,///A/1255,///A/1338,///A/1339", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1254" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 13, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 50, -13 ], "summary": "[2] 0 1 [A.1265 A.1327 A.1266 A.1325] 3 1", "num_nts": 5, "nts_short": "CAUAG", "nts_long": "///A/1265,///A/1266,///A/1325,///A/1326,///A/1327", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1326" } ] }, { "index": 14, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -20, -21 ], "summary": "[2] 0 1 [A.1510 A.1540 A.1511 A.1538] 1 1", "num_nts": 5, "nts_short": "UCGCA", "nts_long": "///A/1510,///A/1511,///A/1538,///A/1539,///A/1540", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1539" } ] }, { "index": 15, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 13, -5 ], "summary": "[2] 2 0 [A.762 A.778 A.765 A.777] 2 1", "num_nts": 6, "nts_short": "GCACGC", "nts_long": "///A/762,///A/763,///A/764,///A/765,///A/777,///A/778", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/763,///A/764" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 16, "type": "bulge", "bridging_nts": [ 3, 0 ], "stem_indices": [ 17, -7 ], "summary": "[2] 3 0 [A.834 A.853 A.838 A.852] 3 1", "num_nts": 7, "nts_short": "GCAAUAC", "nts_long": "///A/834,///A/835,///A/836,///A/837,///A/838,///A/852,///A/853", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAA", "nts_long": "///A/835,///A/836,///A/837" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 17, "type": "bulge", "bridging_nts": [ 3, 0 ], "stem_indices": [ 32, 33 ], "summary": "[2] 3 0 [A.1062 A.1093 A.1066 A.1092] 6 2", "num_nts": 7, "nts_short": "GACCCGC", "nts_long": "///A/1062,///A/1063,///A/1064,///A/1065,///A/1066,///A/1092,///A/1093", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACC", "nts_long": "///A/1063,///A/1064,///A/1065" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 18, "type": "bulge", "bridging_nts": [ 0, 3 ], "stem_indices": [ 49, 50 ], "summary": "[2] 0 3 [A.1262 A.1333 A.1263 A.1329] 2 3", "num_nts": 7, "nts_short": "CGUCAAG", "nts_long": "///A/1262,///A/1263,///A/1329,///A/1330,///A/1331,///A/1332,///A/1333", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 3, "nts_short": "CAA", "nts_long": "///A/1330,///A/1331,///A/1332" } ] }, { "index": 19, "type": "bulge", "bridging_nts": [ 0, 7 ], "stem_indices": [ 52, 53 ], "summary": "[2] 0 7 [A.1278 A.1297 A.1279 A.1289] 2 3", "num_nts": 11, "nts_short": "CCGCUACAAAG", "nts_long": "///A/1278,///A/1279,///A/1289,///A/1290,///A/1291,///A/1292,///A/1293,///A/1294,///A/1295,///A/1296,///A/1297", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 7, "nts_short": "CUACAAA", "nts_long": "///A/1290,///A/1291,///A/1292,///A/1293,///A/1294,///A/1295,///A/1296" } ] } ], "num_iloops": 27, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 3, 4 ], "summary": "[2] 1 1 [A.674 A.923 A.676 A.921] 6 2", "num_nts": 6, "nts_short": "UAGUCA", "nts_long": "///A/674,///A/675,///A/676,///A/921,///A/922,///A/923", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/675" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/922" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 28, 29 ], "summary": "[2] 1 1 [A.982 A.1006 A.984 A.1004] 3 3", "num_nts": 6, "nts_short": "ACCGUU", "nts_long": "///A/982,///A/983,///A/984,///A/1004,///A/1005,///A/1006", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/983" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1005" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -12, 35 ], "summary": "[2] 1 1 [A.1109 A.1132 A.1111 A.1130] 1 5", "num_nts": 6, "nts_short": "AACGCU", "nts_long": "///A/1109,///A/1110,///A/1111,///A/1130,///A/1131,///A/1132", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1110" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1131" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -13, -14 ], "summary": "[2] 1 1 [A.1266 A.1325 A.1268 A.1323] 1 1", "num_nts": 6, "nts_short": "AUCGUU", "nts_long": "///A/1266,///A/1267,///A/1268,///A/1323,///A/1324,///A/1325", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1267" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1324" } ] }, { "index": 5, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 58, -19 ], "summary": "[2] 1 1 [A.1489 A.1561 A.1491 A.1559] 2 1", "num_nts": 6, "nts_short": "GUCGUC", "nts_long": "///A/1489,///A/1490,///A/1491,///A/1559,///A/1560,///A/1561", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1490" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1560" } ] }, { "index": 6, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 10, -4 ], "summary": "[2] 1 2 [A.727 A.747 A.729 A.744] 4 1", "num_nts": 7, "nts_short": "UCUAAAA", "nts_long": "///A/727,///A/728,///A/729,///A/744,///A/745,///A/746,///A/747", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/728" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/745,///A/746" } ] }, { "index": 7, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ -4, 11 ], "summary": "[2] 2 1 [A.729 A.744 A.732 A.742] 1 3", "num_nts": 7, "nts_short": "UAAAUCA", "nts_long": "///A/729,///A/730,///A/731,///A/732,///A/742,///A/743,///A/744", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/730,///A/731" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/743" } ] }, { "index": 8, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 29, 30 ], "summary": "[2] 1 2 [A.986 A.1002 A.988 A.999] 3 2", "num_nts": 7, "nts_short": "GAGCUCC", "nts_long": "///A/986,///A/987,///A/988,///A/999,///A/1000,///A/1001,///A/1002", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/987" }, { "index": 2, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/1000,///A/1001" } ] }, { "index": 9, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -17, -18 ], "summary": "[2] 1 2 [A.1483 A.1569 A.1485 A.1566] 1 1", "num_nts": 7, "nts_short": "CCGCAUG", "nts_long": "///A/1483,///A/1484,///A/1485,///A/1566,///A/1567,///A/1568,///A/1569", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1484" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1567,///A/1568" } ] }, { "index": 10, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 59, 60 ], "summary": "[2] 2 1 [A.1500 A.1549 A.1503 A.1547] 6 5", "num_nts": 7, "nts_short": "CAAGUAG", "nts_long": "///A/1500,///A/1501,///A/1502,///A/1503,///A/1547,///A/1548,///A/1549", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1501,///A/1502" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1548" } ] }, { "index": 11, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 48, 49 ], "summary": "[2] 3 1 [A.1257 A.1336 A.1261 A.1334] 3 2", "num_nts": 8, "nts_short": "UAUACGUG", "nts_long": "///A/1257,///A/1258,///A/1259,///A/1260,///A/1261,///A/1334,///A/1335,///A/1336", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/1258,///A/1259,///A/1260" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1335" } ] }, { "index": 12, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 51, 52 ], "summary": "[2] 2 2 [A.1274 A.1301 A.1277 A.1298] 2 2", "num_nts": 8, "nts_short": "CAAAUAAG", "nts_long": "///A/1274,///A/1275,///A/1276,///A/1277,///A/1298,///A/1299,///A/1300,///A/1301", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1275,///A/1276" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1299,///A/1300" } ] }, { "index": 13, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 60, -20 ], "summary": "[2] 2 2 [A.1507 A.1543 A.1510 A.1540] 5 1", "num_nts": 8, "nts_short": "ACUUAUUU", "nts_long": "///A/1507,///A/1508,///A/1509,///A/1510,///A/1540,///A/1541,///A/1542,///A/1543", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/1508,///A/1509" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/1541,///A/1542" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ -21, 61 ], "summary": "[2] 2 2 [A.1511 A.1538 A.1514 A.1535] 1 3", "num_nts": 8, "nts_short": "CAAAUACG", "nts_long": "///A/1511,///A/1512,///A/1513,///A/1514,///A/1535,///A/1536,///A/1537,///A/1538", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1512,///A/1513" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/1536,///A/1537" } ] }, { "index": 15, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ -18, 58 ], "summary": "[2] 2 3 [A.1485 A.1566 A.1488 A.1562] 1 2", "num_nts": 9, "nts_short": "GcCcGUAAC", "nts_long": "///A/1485,///A/1486,///A/1487,///A/1488,///A/1562,///A/1563,///A/1564,///A/1565,///A/1566", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "cC", "nts_long": "///A/1486,///A/1487" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1563,///A/1564,///A/1565" } ] }, { "index": 16, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 33, 34 ], "summary": "[2] 3 3 [A.1067 A.1091 A.1071 A.1087] 2 4", "num_nts": 10, "nts_short": "AAACUACUAU", "nts_long": "///A/1067,///A/1068,///A/1069,///A/1070,///A/1071,///A/1087,///A/1088,///A/1089,///A/1090,///A/1091", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/1068,///A/1069,///A/1070" }, { "index": 2, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/1088,///A/1089,///A/1090" } ] }, { "index": 17, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ 25, 26 ], "summary": "[2] 3 4 [A.946 A.1049 A.950 A.1044] 4 3", "num_nts": 11, "nts_short": "UUUUAUGAACA", "nts_long": "///A/946,///A/947,///A/948,///A/949,///A/950,///A/1044,///A/1045,///A/1046,///A/1047,///A/1048,///A/1049", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUU", "nts_long": "///A/947,///A/948,///A/949" }, { "index": 2, "num_nts": 4, "nts_short": "GAAC", "nts_long": "///A/1045,///A/1046,///A/1047,///A/1048" } ] }, { "index": 18, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ -19, 59 ], "summary": "[2] 3 4 [A.1491 A.1559 A.1495 A.1554] 1 6", "num_nts": 11, "nts_short": "CACCCGACAAG", "nts_long": "///A/1491,///A/1492,///A/1493,///A/1494,///A/1495,///A/1554,///A/1555,///A/1556,///A/1557,///A/1558,///A/1559", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACC", "nts_long": "///A/1492,///A/1493,///A/1494" }, { "index": 2, "num_nts": 4, "nts_short": "ACAA", "nts_long": "///A/1555,///A/1556,///A/1557,///A/1558" } ] }, { "index": 19, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 61, 62 ], "summary": "[2] 4 3 [A.1516 A.1533 A.1521 A.1529] 3 2", "num_nts": 11, "nts_short": "GACAUUAACCC", "nts_long": "///A/1516,///A/1517,///A/1518,///A/1519,///A/1520,///A/1521,///A/1529,///A/1530,///A/1531,///A/1532,///A/1533", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "ACAU", "nts_long": "///A/1517,///A/1518,///A/1519,///A/1520" }, { "index": 2, "num_nts": 3, "nts_short": "ACC", "nts_long": "///A/1530,///A/1531,///A/1532" } ] }, { "index": 20, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 40, 41 ], "summary": "[2] 4 4 [A.1185 A.1469 A.1190 A.1464] 6 3", "num_nts": 12, "nts_short": "CAUAUCGCCCUG", "nts_long": "///A/1185,///A/1186,///A/1187,///A/1188,///A/1189,///A/1190,///A/1464,///A/1465,///A/1466,///A/1467,///A/1468,///A/1469", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUAU", "nts_long": "///A/1186,///A/1187,///A/1188,///A/1189" }, { "index": 2, "num_nts": 4, "nts_short": "CCCU", "nts_long": "///A/1465,///A/1466,///A/1467,///A/1468" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -16, 56 ], "summary": "[2] 4 4 [A.1388 A.1418 A.1393 A.1413] 1 7", "num_nts": 12, "nts_short": "CGAUAGUCGAAG", "nts_long": "///A/1388,///A/1389,///A/1390,///A/1391,///A/1392,///A/1393,///A/1413,///A/1414,///A/1415,///A/1416,///A/1417,///A/1418", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAUA", "nts_long": "///A/1389,///A/1390,///A/1391,///A/1392" }, { "index": 2, "num_nts": 4, "nts_short": "CGAA", "nts_long": "///A/1414,///A/1415,///A/1416,///A/1417" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 4, 6 ], "stem_indices": [ 12, 13 ], "summary": "[2] 4 6 [A.756 A.786 A.761 A.779] 4 2", "num_nts": 14, "nts_short": "CAUCAAUCAAAACG", "nts_long": "///A/756,///A/757,///A/758,///A/759,///A/760,///A/761,///A/779,///A/780,///A/781,///A/782,///A/783,///A/784,///A/785,///A/786", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUCA", "nts_long": "///A/757,///A/758,///A/759,///A/760" }, { "index": 2, "num_nts": 6, "nts_short": "CAAAAC", "nts_long": "///A/780,///A/781,///A/782,///A/783,///A/784,///A/785" } ] }, { "index": 23, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ -9, 28 ], "summary": "[2] 5 5 [A.974 A.1014 A.980 A.1008] 1 3", "num_nts": 14, "nts_short": "UAAAACUACACAAA", "nts_long": "///A/974,///A/975,///A/976,///A/977,///A/978,///A/979,///A/980,///A/1008,///A/1009,///A/1010,///A/1011,///A/1012,///A/1013,///A/1014", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AAAAC", "nts_long": "///A/975,///A/976,///A/977,///A/978,///A/979" }, { "index": 2, "num_nts": 5, "nts_short": "CACAA", "nts_long": "///A/1009,///A/1010,///A/1011,///A/1012,///A/1013" } ] }, { "index": 24, "type": "asymmetric internal loop", "bridging_nts": [ 7, 4 ], "stem_indices": [ 46, 47 ], "summary": "[2] 7 4 [A.1244 A.1345 A.1252 A.1340] 7 2", "num_nts": 15, "nts_short": "CUUGCUCAGCCCAUG", "nts_long": "///A/1244,///A/1245,///A/1246,///A/1247,///A/1248,///A/1249,///A/1250,///A/1251,///A/1252,///A/1340,///A/1341,///A/1342,///A/1343,///A/1344,///A/1345", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUGCUCA", "nts_long": "///A/1245,///A/1246,///A/1247,///A/1248,///A/1249,///A/1250,///A/1251" }, { "index": 2, "num_nts": 4, "nts_short": "CCAU", "nts_long": "///A/1341,///A/1342,///A/1343,///A/1344" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 21, 22 ], "summary": "[2] 5 7 [A.887 A.908 A.893 A.900] 3 2", "num_nts": 16, "nts_short": "GUGCCAGCGGUCACAC", "nts_long": "///A/887,///A/888,///A/889,///A/890,///A/891,///A/892,///A/893,///A/900,///A/901,///A/902,///A/903,///A/904,///A/905,///A/906,///A/907,///A/908", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGCCA", "nts_long": "///A/888,///A/889,///A/890,///A/891,///A/892" }, { "index": 2, "num_nts": 7, "nts_short": "GGUCACA", "nts_long": "///A/901,///A/902,///A/903,///A/904,///A/905,///A/906,///A/907" } ] }, { "index": 26, "type": "asymmetric internal loop", "bridging_nts": [ 7, 5 ], "stem_indices": [ 36, 37 ], "summary": "[2] 7 5 [A.1139 A.1164 A.1147 A.1158] 2 4", "num_nts": 16, "nts_short": "AACACUACGUAAAACU", "nts_long": "///A/1139,///A/1140,///A/1141,///A/1142,///A/1143,///A/1144,///A/1145,///A/1146,///A/1147,///A/1158,///A/1159,///A/1160,///A/1161,///A/1162,///A/1163,///A/1164", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "ACACUAC", "nts_long": "///A/1140,///A/1141,///A/1142,///A/1143,///A/1144,///A/1145,///A/1146" }, { "index": 2, "num_nts": 5, "nts_short": "AAAAC", "nts_long": "///A/1159,///A/1160,///A/1161,///A/1162,///A/1163" } ] }, { "index": 27, "type": "asymmetric internal loop", "bridging_nts": [ 15, 5 ], "stem_indices": [ 26, 27 ], "summary": "[2] 15 5 [A.952 A.1042 A.968 A.1036] 3 6", "num_nts": 24, "nts_short": "AUCACCCCCUCCCCAAUAACAUAU", "nts_long": "///A/952,///A/953,///A/954,///A/955,///A/956,///A/957,///A/958,///A/959,///A/960,///A/961,///A/962,///A/963,///A/964,///A/965,///A/966,///A/967,///A/968,///A/1036,///A/1037,///A/1038,///A/1039,///A/1040,///A/1041,///A/1042", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 15, "nts_short": "UCACCCCCUCCCCAA", "nts_long": "///A/953,///A/954,///A/955,///A/956,///A/957,///A/958,///A/959,///A/960,///A/961,///A/962,///A/963,///A/964,///A/965,///A/966,///A/967" }, { "index": 2, "num_nts": 5, "nts_short": "ACAUA", "nts_long": "///A/1037,///A/1038,///A/1039,///A/1040,///A/1041" } ] } ], "num_junctions": 13, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 0, 5, 0 ], "stem_indices": [ 27, -9, -10 ], "summary": "[3] 0 5 0 [A.973 A.1031 A.974 A.1014 A.1020 A.1030] 6 1 1", "num_nts": 11, "nts_short": "CUAAUAGACGG", "nts_long": "///A/973,///A/974,///A/1014,///A/1015,///A/1016,///A/1017,///A/1018,///A/1019,///A/1020,///A/1030,///A/1031", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "AUAGA", "nts_long": "///A/1015,///A/1016,///A/1017,///A/1018,///A/1019" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 2, 1, 2 ], "stem_indices": [ 42, 43, -15 ], "summary": "[3] 2 1 2 [A.1198 A.1424 A.1201 A.1364 A.1366 A.1421] 5 8 1", "num_nts": 11, "nts_short": "AGGAUACGGAU", "nts_long": "///A/1198,///A/1199,///A/1200,///A/1201,///A/1364,///A/1365,///A/1366,///A/1421,///A/1422,///A/1423,///A/1424", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/1199,///A/1200" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1365" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/1422,///A/1423" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 2, 5, 2 ], "stem_indices": [ 4, 5, 19 ], "summary": "[3] 2 5 2 [A.677 A.920 A.680 A.866 A.872 A.917] 2 6 5", "num_nts": 15, "nts_short": "CUCUACCCCAGCAAG", "nts_long": "///A/677,///A/678,///A/679,///A/680,///A/866,///A/867,///A/868,///A/869,///A/870,///A/871,///A/872,///A/917,///A/918,///A/919,///A/920", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/678,///A/679" }, { "index": 2, "num_nts": 5, "nts_short": "CCCCA", "nts_long": "///A/867,///A/868,///A/869,///A/870,///A/871" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/918,///A/919" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 2, 6, 1 ], "stem_indices": [ 6, -2, -6 ], "summary": "[3] 2 6 1 [A.687 A.858 A.690 A.823 A.830 A.856] 2 1 1", "num_nts": 15, "nts_short": "GAUUAUUAACCUAGC", "nts_long": "///A/687,///A/688,///A/689,///A/690,///A/823,///A/824,///A/825,///A/826,///A/827,///A/828,///A/829,///A/830,///A/856,///A/857,///A/858", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/688,///A/689" }, { "index": 2, "num_nts": 6, "nts_short": "UUAACC", "nts_long": "///A/824,///A/825,///A/826,///A/827,///A/828,///A/829" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///A/857" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 3, 5, 2 ], "stem_indices": [ -15, 55, -16 ], "summary": "[3] 3 5 2 [A.1366 A.1421 A.1370 A.1382 A.1388 A.1418] 1 4 1", "num_nts": 16, "nts_short": "CAUUUAAACUACGGUG", "nts_long": "///A/1366,///A/1367,///A/1368,///A/1369,///A/1370,///A/1382,///A/1383,///A/1384,///A/1385,///A/1386,///A/1387,///A/1388,///A/1418,///A/1419,///A/1420,///A/1421", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AUU", "nts_long": "///A/1367,///A/1368,///A/1369" }, { "index": 2, "num_nts": 5, "nts_short": "AACUA", "nts_long": "///A/1383,///A/1384,///A/1385,///A/1386,///A/1387" }, { "index": 3, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/1419,///A/1420" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 1, 5, 5 ], "stem_indices": [ 41, 42, 57 ], "summary": "[3] 1 5 5 [A.1192 A.1462 A.1194 A.1428 A.1434 A.1456] 3 5 7", "num_nts": 17, "nts_short": "CUCGCAGUAAUGAACAG", "nts_long": "///A/1192,///A/1193,///A/1194,///A/1428,///A/1429,///A/1430,///A/1431,///A/1432,///A/1433,///A/1434,///A/1456,///A/1457,///A/1458,///A/1459,///A/1460,///A/1461,///A/1462", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1193" }, { "index": 2, "num_nts": 5, "nts_short": "CAGUA", "nts_long": "///A/1429,///A/1430,///A/1431,///A/1432,///A/1433" }, { "index": 3, "num_nts": 5, "nts_short": "GAACA", "nts_long": "///A/1457,///A/1458,///A/1459,///A/1460,///A/1461" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 4, 5, 5 ], "stem_indices": [ -14, 51, 54 ], "summary": "[3] 4 5 5 [A.1268 A.1323 A.1273 A.1302 A.1308 A.1317] 1 2 3", "num_nts": 20, "nts_short": "CUUCAGCGCAAGUAAAGACG", "nts_long": "///A/1268,///A/1269,///A/1270,///A/1271,///A/1272,///A/1273,///A/1302,///A/1303,///A/1304,///A/1305,///A/1306,///A/1307,///A/1308,///A/1317,///A/1318,///A/1319,///A/1320,///A/1321,///A/1322,///A/1323", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCA", "nts_long": "///A/1269,///A/1270,///A/1271,///A/1272" }, { "index": 2, "num_nts": 5, "nts_short": "GCAAG", "nts_long": "///A/1303,///A/1304,///A/1305,///A/1306,///A/1307" }, { "index": 3, "num_nts": 5, "nts_short": "AAGAC", "nts_long": "///A/1318,///A/1319,///A/1320,///A/1321,///A/1322" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 5, 10, 2 ], "stem_indices": [ 44, 45, 46 ], "summary": "[3] 5 10 2 [A.1210 A.1354 A.1216 A.1227 A.1238 A.1351] 2 2 7", "num_nts": 23, "nts_short": "UGUAAUCGAUCAACCUCACGCAA", "nts_long": "///A/1210,///A/1211,///A/1212,///A/1213,///A/1214,///A/1215,///A/1216,///A/1227,///A/1228,///A/1229,///A/1230,///A/1231,///A/1232,///A/1233,///A/1234,///A/1235,///A/1236,///A/1237,///A/1238,///A/1351,///A/1352,///A/1353,///A/1354", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GUAAU", "nts_long": "///A/1211,///A/1212,///A/1213,///A/1214,///A/1215" }, { "index": 2, "num_nts": 10, "nts_short": "AUCAACCUCA", "nts_long": "///A/1228,///A/1229,///A/1230,///A/1231,///A/1232,///A/1233,///A/1234,///A/1235,///A/1236,///A/1237" }, { "index": 3, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/1352,///A/1353" } ] }, { "index": 9, "type": "4-way junction", "bridging_nts": [ 6, 2, 1, 0 ], "stem_indices": [ 9, 10, 12, 15 ], "summary": "[4] 6 2 1 0 [A.717 A.798 A.724 A.750 A.753 A.789 A.791 A.797] 3 4 4 2", "num_nts": 17, "nts_short": "GAGUUCACGACAUAGCC", "nts_long": "///A/717,///A/718,///A/719,///A/720,///A/721,///A/722,///A/723,///A/724,///A/750,///A/751,///A/752,///A/753,///A/789,///A/790,///A/791,///A/797,///A/798", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AGUUCA", "nts_long": "///A/718,///A/719,///A/720,///A/721,///A/722,///A/723" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/751,///A/752" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/790" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 10, "type": "4-way junction", "bridging_nts": [ 2, 6, 1, 5 ], "stem_indices": [ 8, -3, 9, 16 ], "summary": "[4] 2 6 1 5 [A.698 A.817 A.701 A.708 A.715 A.800 A.802 A.811] 3 1 3 3", "num_nts": 22, "nts_short": "CAAGCGUUCCAGCACGAAACAG", "nts_long": "///A/698,///A/699,///A/700,///A/701,///A/708,///A/709,///A/710,///A/711,///A/712,///A/713,///A/714,///A/715,///A/800,///A/801,///A/802,///A/811,///A/812,///A/813,///A/814,///A/815,///A/816,///A/817", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/699,///A/700" }, { "index": 2, "num_nts": 6, "nts_short": "GUUCCA", "nts_long": "///A/709,///A/710,///A/711,///A/712,///A/713,///A/714" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/801" }, { "index": 4, "num_nts": 5, "nts_short": "AAACA", "nts_long": "///A/812,///A/813,///A/814,///A/815,///A/816" } ] }, { "index": 11, "type": "4-way junction", "bridging_nts": [ 1, 4, 10, 0 ], "stem_indices": [ -8, 25, 32, -12 ], "summary": "[4] 1 4 10 0 [A.941 A.1133 A.943 A.1052 A.1057 A.1098 A.1109 A.1132] 1 4 6 1", "num_nts": 23, "nts_short": "GAGCAAUAGCCCUAAACCUCAUC", "nts_long": "///A/941,///A/942,///A/943,///A/1052,///A/1053,///A/1054,///A/1055,///A/1056,///A/1057,///A/1098,///A/1099,///A/1100,///A/1101,///A/1102,///A/1103,///A/1104,///A/1105,///A/1106,///A/1107,///A/1108,///A/1109,///A/1132,///A/1133", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/942" }, { "index": 2, "num_nts": 4, "nts_short": "AAUA", "nts_long": "///A/1053,///A/1054,///A/1055,///A/1056" }, { "index": 3, "num_nts": 10, "nts_short": "CCUAAACCUC", "nts_long": "///A/1099,///A/1100,///A/1101,///A/1102,///A/1103,///A/1104,///A/1105,///A/1106,///A/1107,///A/1108" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 12, "type": "5-way junction", "bridging_nts": [ 0, 0, 1, 5, 2 ], "stem_indices": [ 19, 20, 22, 20, 21 ], "summary": "[5] 0 0 1 5 2 [A.876 A.913 A.877 A.898 A.899 A.894 A.896 A.879 A.885 A.910] 5 3 2 3 3", "is_repeated": true, "num_nts": 18, "nts_short": "UGCGCCAUCAAUUUAUUA", "nts_long": "///A/876,///A/877,///A/898,///A/899,///A/894,///A/895,///A/896,///A/879,///A/880,///A/881,///A/882,///A/883,///A/884,///A/885,///A/910,///A/911,///A/912,///A/913", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 1, "nts_short": "C", "nts_long": "///A/895" }, { "index": 4, "num_nts": 5, "nts_short": "CAAUU", "nts_long": "///A/880,///A/881,///A/882,///A/883,///A/884" }, { "index": 5, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/911,///A/912" } ] }, { "index": 13, "type": "5-way junction", "bridging_nts": [ 0, 2, 6, 3, 0 ], "stem_indices": [ 23, 24, 35, 24, -8 ], "summary": "[5] 0 2 6 3 0 [A.935 A.1134 A.936 A.1123 A.1126 A.1115 A.1122 A.937 A.941 A.1133] 3 2 5 2 1", "is_repeated": true, "num_nts": 21, "nts_short": "CGCAAAUAAAUCAAUAAAGCG", "nts_long": "///A/935,///A/936,///A/1123,///A/1124,///A/1125,///A/1126,///A/1115,///A/1116,///A/1117,///A/1118,///A/1119,///A/1120,///A/1121,///A/1122,///A/937,///A/938,///A/939,///A/940,///A/941,///A/1133,///A/1134", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1124,///A/1125" }, { "index": 3, "num_nts": 6, "nts_short": "AAAUCA", "nts_long": "///A/1116,///A/1117,///A/1118,///A/1119,///A/1120,///A/1121" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/938,///A/939,///A/940" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] } ], "num_ssSegments": 8, "ssSegments": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/648" }, { "index": 2, "num_nts": 4, "nts_short": "AGCC", "nts_long": "///A/929,///A/930,///A/931,///A/932" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1137" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1166,///A/1167,///A/1168" }, { "index": 5, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/1481,///A/1482" }, { "index": 6, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/1570,///A/1571" }, { "index": 7, "num_nts": 8, "nts_short": "GACGAACC", "nts_long": "///A/1595,///A/1596,///A/1597,///A/1598,///A/1599,///A/1600,///A/1601,///A/1602" }, { "index": 8, "is_broken": true, "num_nts": 2, "nts_short": "ag", "nts_long": "///X/402,///X/403" } ], "num_Aminors": 41, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/691 vs ///A/715,///A/800", "A_nt1": { "desc": "///A/691 vs ///A/715", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/691 vs ///A/800", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.10],N1-O2'(hydroxyl)[3.19]" } }, { "index": 2, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/691 vs ///A/716,///A/799", "A_nt1": { "desc": "///A/691 vs ///A/716", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[2.62],N6(amino)-O2(carbonyl)[2.53]" }, "A_nt2": { "desc": "///A/691 vs ///A/799", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 3, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/695 vs ///A/694,///A/820", "A_nt1": { "desc": "///A/695 vs ///A/694", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/695 vs ///A/820", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[3.21],N6(amino)-N3[3.43]" } }, { "index": 4, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/718 vs ///A/716,///A/799", "A_nt1": { "desc": "///A/718 vs ///A/716", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/718 vs ///A/799", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.88],N1-O2'(hydroxyl)[3.27]" } }, { "index": 5, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/723 vs ///A/791,///A/797", "A_nt1": { "desc": "///A/723 vs ///A/791", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.59]" }, "A_nt2": { "desc": "///A/723 vs ///A/797", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.18]" } }, { "index": 6, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/730 vs ///A/729,///A/744", "A_nt1": { "desc": "///A/730 vs ///A/729", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O4'-O2'(hydroxyl)[3.34]" }, "A_nt2": { "desc": "///A/730 vs ///A/744", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.24]" } }, { "index": 7, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/745 vs ///A/729,///A/744", "A_nt1": { "desc": "///A/745 vs ///A/729", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.36]" }, "A_nt2": { "desc": "///A/745 vs ///A/744", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O4'-O2'(hydroxyl)[3.13]" } }, { "index": 8, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///A/784 vs ///A/761,///A/779", "A_nt1": { "desc": "///A/784 vs ///A/761", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.69]" }, "A_nt2": { "desc": "///A/784 vs ///A/779", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.25]" } }, { "index": 9, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/816 vs ///A/715,///A/800", "A_nt1": { "desc": "///A/816 vs ///A/715", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.00],O2'(hydroxyl)-N3[2.90],N3-N2(amino)[3.34]" }, "A_nt2": { "desc": "///A/816 vs ///A/800", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 10, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/836 vs ///A/833,///A/854", "A_nt1": { "desc": "///A/836 vs ///A/833", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/836 vs ///A/854", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.66],N1-O2'(hydroxyl)[3.08]" } }, { "index": 11, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/836 vs ///A/834,///A/853", "A_nt1": { "desc": "///A/836 vs ///A/834", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[3.29],N6(amino)-N3[3.29]" }, "A_nt2": { "desc": "///A/836 vs ///A/853", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 12, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/837 vs ///A/834,///A/853", "A_nt1": { "desc": "///A/837 vs ///A/834", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/837 vs ///A/853", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.86],N1-O2'(hydroxyl)[2.91]" } }, { "index": 13, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/881 vs ///A/874,///A/915", "A_nt1": { "desc": "///A/881 vs ///A/874", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/881 vs ///A/915", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.65],N3-O2'(hydroxyl)[2.86]" } }, { "index": 14, "type": "I", "desc_short": "A vs U-A (WC)", "desc_long": "///A/882 vs ///A/875,///A/914", "A_nt1": { "desc": "///A/882 vs ///A/875", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.08]" }, "A_nt2": { "desc": "///A/882 vs ///A/914", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.09],O2'(hydroxyl)-N3[3.36]" } }, { "index": 15, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/907 vs ///A/894,///A/899", "A_nt1": { "desc": "///A/907 vs ///A/894", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/907 vs ///A/899", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.32],N1-O2'(hydroxyl)[2.56]" } }, { "index": 16, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/938 vs ///A/661,///A/1169", "A_nt1": { "desc": "///A/938 vs ///A/661", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.97]" }, "A_nt2": { "desc": "///A/938 vs ///A/1169", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.06],N3-N2(amino)[3.46]" } }, { "index": 17, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/939 vs ///A/933,///A/1136", "A_nt1": { "desc": "///A/939 vs ///A/933", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/939 vs ///A/1136", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.99],N3-O2'(hydroxyl)[2.96]" } }, { "index": 18, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/940 vs ///A/934,///A/1135", "A_nt1": { "desc": "///A/940 vs ///A/934", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.61],N3-N2(amino)[3.34]" }, "A_nt2": { "desc": "///A/940 vs ///A/1135", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.52],O2'(hydroxyl)-O2(carbonyl)[2.86]" } }, { "index": 19, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/996 vs ///A/1073,///A/1085", "A_nt1": { "desc": "///A/996 vs ///A/1073", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/996 vs ///A/1085", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.07],N1*O2(carbonyl)[3.31]" } }, { "index": 20, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1025 vs ///A/944,///A/1051", "A_nt1": { "desc": "///A/1025 vs ///A/944", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.19],O2'(hydroxyl)-O2'(hydroxyl)[2.67],N3-O2'(hydroxyl)[3.15]" }, "A_nt2": { "desc": "///A/1025 vs ///A/1051", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 21, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1026 vs ///A/943,///A/1052", "A_nt1": { "desc": "///A/1026 vs ///A/943", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.50]" }, "A_nt2": { "desc": "///A/1026 vs ///A/1052", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.10]" } }, { "index": 22, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1054 vs ///A/1575,///A/1590", "A_nt1": { "desc": "///A/1054 vs ///A/1575", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1054 vs ///A/1590", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.49]" } }, { "index": 23, "type": "I", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1102 vs ///A/1575,///A/1590", "A_nt1": { "desc": "///A/1102 vs ///A/1575", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.99]" }, "A_nt2": { "desc": "///A/1102 vs ///A/1590", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 24, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1116 vs ///A/1114,///A/1127", "A_nt1": { "desc": "///A/1116 vs ///A/1114", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.93]" }, "A_nt2": { "desc": "///A/1116 vs ///A/1127", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 25, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1121 vs ///A/660,///A/1170", "A_nt1": { "desc": "///A/1121 vs ///A/660", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.15]" }, "A_nt2": { "desc": "///A/1121 vs ///A/1170", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.91]" } }, { "index": 26, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1162 vs ///A/1497,///A/1552", "A_nt1": { "desc": "///A/1162 vs ///A/1497", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.68]" }, "A_nt2": { "desc": "///A/1162 vs ///A/1552", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 27, "type": "I", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/1166 vs ///A/654,///A/664", "A_nt1": { "desc": "///A/1166 vs ///A/654", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1166 vs ///A/664", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.80],N3-N2(amino)[3.40]" } }, { "index": 28, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1213 vs ///A/1239,///A/1350", "A_nt1": { "desc": "///A/1213 vs ///A/1239", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.89],N3-O2'(hydroxyl)[2.72]" }, "A_nt2": { "desc": "///A/1213 vs ///A/1350", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 29, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1214 vs ///A/1238,///A/1351", "A_nt1": { "desc": "///A/1214 vs ///A/1238", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.00],O2'(hydroxyl)-O2(carbonyl)[3.01]" }, "A_nt2": { "desc": "///A/1214 vs ///A/1351", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.04],N3-N2(amino)[3.26]" } }, { "index": 30, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1286 vs ///A/658,///A/1172", "A_nt1": { "desc": "///A/1286 vs ///A/658", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.87]" }, "A_nt2": { "desc": "///A/1286 vs ///A/1172", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.15]" } }, { "index": 31, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1296 vs ///A/1279,///A/1289", "A_nt1": { "desc": "///A/1296 vs ///A/1279", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.85]" }, "A_nt2": { "desc": "///A/1296 vs ///A/1289", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O3'-O2'(hydroxyl)[3.51]" } }, { "index": 32, "type": "X", "desc_short": "A vs G-U (Wobble)", "desc_long": "///A/1332 vs ///A/1263,///A/1329", "A_nt1": { "desc": "///A/1332 vs ///A/1263", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[3.35],N6(amino)-N3[3.51]" }, "A_nt2": { "desc": "///A/1332 vs ///A/1329", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "OP1-O2'(hydroxyl)[3.12]" } }, { "index": 33, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1356 vs ///A/1209,///A/1355", "A_nt1": { "desc": "///A/1356 vs ///A/1209", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.24]" }, "A_nt2": { "desc": "///A/1356 vs ///A/1355", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N7-N2(amino)[3.24]" } }, { "index": 34, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1367 vs ///A/1370,///A/1382", "A_nt1": { "desc": "///A/1367 vs ///A/1370", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.61]" }, "A_nt2": { "desc": "///A/1367 vs ///A/1382", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 35, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1417 vs ///A/1201,///A/1364", "A_nt1": { "desc": "///A/1417 vs ///A/1201", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.15],N3-O2'(hydroxyl)[2.50]" }, "A_nt2": { "desc": "///A/1417 vs ///A/1364", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 36, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1459 vs ///A/1194,///A/1428", "A_nt1": { "desc": "///A/1459 vs ///A/1194", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.57],N3-O2'(hydroxyl)[3.12]" }, "A_nt2": { "desc": "///A/1459 vs ///A/1428", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 37, "type": "X", "desc_short": "A vs c-A (~Wobble)", "desc_long": "///A/1478 vs ///A/1486,///A/1565", "A_nt1": { "desc": "///A/1478 vs ///A/1486", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1478 vs ///A/1565", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.02],N1-O2'(hydroxyl)[2.87]" } }, { "index": 38, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1482 vs ///A/1175,///A/1479", "A_nt1": { "desc": "///A/1482 vs ///A/1175", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.10],N3-N2(amino)[3.20]" }, "A_nt2": { "desc": "///A/1482 vs ///A/1479", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.65],O2'(hydroxyl)-O2(carbonyl)[3.01]" } }, { "index": 39, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1567 vs ///A/1177,///A/1476", "A_nt1": { "desc": "///A/1567 vs ///A/1177", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///A/1567 vs ///A/1476", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O5'-O2'(hydroxyl)[3.11],N3-N2(amino)[3.60]" } }, { "index": 40, "type": "I", "desc_short": "a vs c-G (WC)", "desc_long": "///A/1583 vs ///A/1488,///A/1562", "A_nt1": { "desc": "///A/1583 vs ///A/1488", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1583 vs ///A/1562", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.92]" } }, { "index": 41, "type": "I", "desc_short": "a vs c-G (WC)", "desc_long": "///A/1584 vs ///A/1488,///A/1562", "A_nt1": { "desc": "///A/1584 vs ///A/1488", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.63],O2'(hydroxyl)-O2(carbonyl)[2.20]" }, "A_nt2": { "desc": "///A/1584 vs ///A/1562", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.06]" } } ], "num_riboseZippers": 9, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///A/658,///A/659,///A/1285,///A/1286" }, { "index": 2, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/714,///A/715,///A/816,///A/817" }, { "index": 3, "num_nts": 4, "nts_short": "AAAC", "nts_long": "///A/881,///A/882,///A/914,///A/915" }, { "index": 4, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/939,///A/940,///A/1135,///A/1136" }, { "index": 5, "num_nts": 4, "nts_short": 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"residue_pair": "aa:aa" }, { "index": 7063, "atom1_serNum": 68471, "atom2_serNum": 68510, "donAcc_type": "acceptable", "distance": 2.981, "atom1_id": "///8/258/O", "atom2_id": "///8/262/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 7064, "atom1_serNum": 68480, "atom2_serNum": 68510, "donAcc_type": "acceptable", "distance": 2.414, "atom1_id": "///8/259/O", "atom2_id": "///8/262/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 7065, "atom1_serNum": 68497, "atom2_serNum": 68503, "donAcc_type": "standard", "distance": 2.623, "atom1_id": "///8/261/N", "atom2_id": "///8/261/OD1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 7066, "atom1_serNum": 68508, "atom2_serNum": 68510, "donAcc_type": "acceptable", "distance": 2.920, "atom1_id": "///8/262/O", "atom2_id": "///8/262/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 7067, "atom1_serNum": 68514, "atom2_serNum": 68538, "donAcc_type": "acceptable", "distance": 2.974, "atom1_id": "///A/1701/O1A", "atom2_id": "///A/1701/O2N", "atom_pair": "O:O", "residue_pair": "ligand:ligand" }, { "index": 7068, "atom1_serNum": 68519, "atom2_serNum": 68553, "donAcc_type": "standard", "distance": 2.848, "atom1_id": "///A/1701/O4B", "atom2_id": "///A/1701/N7N", "atom_pair": "O:N", "residue_pair": "ligand:ligand" }, { "index": 7069, "atom1_serNum": 68579, "atom2_serNum": 68610, "donAcc_type": "acceptable", "distance": 2.927, "atom1_id": "///A/1703/N31", "atom2_id": "///A/1703/O63", "atom_pair": "N:O", "residue_pair": "ligand:ligand" }, { "index": 7070, "atom1_serNum": 68581, "atom2_serNum": 68608, "donAcc_type": "standard", "distance": 3.130, "atom1_id": "///A/1703/NE1", "atom2_id": "///A/1703/O53", "atom_pair": "N:O", "residue_pair": "ligand:ligand" }, { "index": 7071, "atom1_serNum": 68581, "atom2_serNum": 68610, "donAcc_type": "acceptable", "distance": 2.790, "atom1_id": "///A/1703/NE1", "atom2_id": "///A/1703/O63", "atom_pair": "N:O", "residue_pair": "ligand:ligand" }, { "index": 7072, "atom1_serNum": 68732, "atom2_serNum": 68743, "donAcc_type": "acceptable", "distance": 3.073, "atom1_id": "///X/403/O1B", "atom2_id": "///X/403/O3'", "atom_pair": "O:O", "residue_pair": "ligand:ligand" }, { "index": 7073, "atom1_serNum": 68733, "atom2_serNum": 68737, "donAcc_type": "acceptable", "distance": 2.660, "atom1_id": "///X/403/O2B", "atom2_id": "///X/403/O2A", "atom_pair": "O:O", "residue_pair": "ligand:ligand" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "8qrm", "num_aaChains": 31, "aaChains": "0=215,1=276,2=117,3=70,4=588,8=191,B=225,C=132,D=340,E=122,F=208,G=323,H=140,I=137,J=108,K=101,L=174,M=119,N=110,O=194,P=97,Q=86,R=295,S=135,T=168,U=176,V=362,W=100,X=354,Y=149,Z=100", "num_naChains": 1, "naChains": "A=955", "num_atoms": 68726, "num_waters": 0, "num_metals": 81, "metals_desc": "Mg=59,K=17,Fe=4,Zn=1", "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 20, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-bulges.pdb", "desc": "an ensemble of bulges" }, { "index": 7, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 8, "name": "dssr-junctions.pdb", "desc": "an ensemble of junctions (multi-branch)" }, { "index": 9, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 10, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 11, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 12, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 13, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 14, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 15, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 16, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 17, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 18, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 19, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 20, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }