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{ "index": 64, "type": "sugar", "atom": "///g/867/O4'", "nt": "///g/866", "vert_dist": 3.393 }, { "index": 65, "type": "sugar", "atom": "///g/868/O4'", "nt": "///g/873", "vert_dist": 2.993 }, { "index": 66, "type": "sugar", "atom": "///g/868/O2'", "nt": "///g/873", "vert_dist": 3.292 }, { "index": 67, "type": "sugar", "atom": "///g/888/O4'", "nt": "///g/887", "vert_dist": 3.481 }, { "index": 68, "type": "sugar", "atom": "///g/889/O4'", "nt": "///g/891", "vert_dist": 3.083 }, { "index": 69, "type": "sugar", "atom": "///g/916/O4'", "nt": "///g/915", "vert_dist": 3.454 }, { "index": 70, "type": "phosphate", "atom": "///g/959/OP2", "nt": "///g/957", "vert_dist": 3.471 }, { "index": 71, "type": "sugar", "atom": "///g/1062/O2'", "nt": "///g/968", "vert_dist": 3.038 }, { "index": 72, "type": "sugar", "atom": "///g/1365/O4'", "nt": "///g/971", "vert_dist": 3.165 }, { "index": 73, "type": "sugar", "atom": "///g/982/O4'", "nt": "///g/983", "vert_dist": 3.102 }, { "index": 74, "type": "sugar", 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"///g/1127/O4'", "nt": "///g/1280", "vert_dist": 3.338 }, { "index": 95, "type": "sugar", "atom": "///g/1127/O2'", "nt": "///g/1280", "vert_dist": 3.355 }, { "index": 96, "type": "sugar", "atom": "///g/1290/O4'", "nt": "///g/1289", "vert_dist": 3.241 }, { "index": 97, "type": "sugar", "atom": "///g/1298/O4'", "nt": "///g/1299", "vert_dist": 2.952 }, { "index": 98, "type": "sugar", "atom": "///g/1336/O4'", "nt": "///g/1337", "vert_dist": 2.927 }, { "index": 99, "type": "sugar", "atom": "///g/1350/O4'", "nt": "///g/1349", "vert_dist": 3.401 }, { "index": 100, "type": "other", "atom": "///w/58/OG", "nt": "///g/1360", "vert_dist": 3.318 }, { "index": 101, "type": "sugar", "atom": "///g/1419/O4'", "nt": "///g/1418", "vert_dist": 3.249 }, { "index": 102, "type": "sugar", "atom": "///g/149/O2'", "nt": "///g/1446", "vert_dist": 3.192 }, { "index": 103, "type": "sugar", "atom": "///g/1492/O2'", "nt": "///g/1493", "vert_dist": 3.483 }, { "index": 104, "type": "sugar", "atom": "///g/925/O4'", "nt": "///g/1502", "vert_dist": 3.137 }, { "index": 105, "type": "sugar", "atom": "///g/1504/O4'", "nt": "///g/1505", "vert_dist": 3.243 }, { "index": 106, "type": "sugar", "atom": "///g/795/O4'", "nt": "///g/1506", "vert_dist": 3.400 }, { "index": 107, "type": "phosphate", "atom": "///g/1518/OP2", "nt": "///g/1516", "vert_dist": 3.014 }, { "index": 108, "type": "phosphate", "atom": "///v/17/OP2", "nt": "///v/18", "vert_dist": 2.878 }, { "index": 109, "type": "phosphate", "atom": "///v/36/OP2", "nt": "///v/34", "vert_dist": 3.114 }, { "index": 110, "type": "phosphate", "atom": "///v/51/OP1", "nt": "///v/48", "vert_dist": 2.933 }, { "index": 111, "type": "sugar", "atom": "///v/55/O4'", "nt": "///v/54", "vert_dist": 3.048 }, { "index": 112, "type": "sugar", "atom": "///v/74/O4'", "nt": "///v/73", "vert_dist": 3.237 }, { "index": 113, "type": "sugar", "atom": "///N/14/O4'", "nt": "///N/13", "vert_dist": 3.363 }, { "index": 114, "type": "sugar", "atom": "///g/1400/O4'", "nt": "///N/18", "vert_dist": 3.084 } ], "num_hairpins": 36, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 1 ], "summary": "[1] 9 [g.12 g.22] 4", "num_nts": 11, "nts_short": "UUUGAUCAUGG", "nts_long": "///g/12,///g/13,///g/14,///g/15,///g/16,///g/17,///g/18,///g/19,///g/20,///g/21,///g/22", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UUGAUCAUG", "nts_long": "///g/13,///g/14,///g/15,///g/16,///g/17,///g/18,///g/19,///g/20,///g/21" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 13 ], "summary": "[1] 4 [g.82 g.87] 7", "num_nts": 6, "nts_short": "GCUUGC", "nts_long": "///g/82,///g/83,///g/84,///g/85,///g/86,///g/87", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUUG", "nts_long": "///g/83,///g/84,///g/85,///g/86" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 19 ], "summary": "[1] 4 [g.158 g.163] 6", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///g/158,///g/159,///g/160,///g/161,///g/162,///g/163", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///g/159,///g/160,///g/161,///g/162" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 20 ], "summary": "[1] 4 [g.186 g.191] 3", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///g/186,///g/187,///g/188,///g/189,///g/190,///g/191", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///g/187,///g/188,///g/189,///g/190" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 22 ], "summary": "[1] 4 [g.207 g.212] 2", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///g/207,///g/208,///g/209,///g/210,///g/211,///g/212", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///g/208,///g/209,///g/210,///g/211" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 25 ], "summary": "[1] 7 [g.259 g.267] 8", "num_nts": 9, "nts_short": "GGUAACGGC", "nts_long": "///g/259,///g/260,///g/261,///g/262,///g/263,///g/264,///g/265,///g/266,///g/267", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUAACGG", "nts_long": "///g/260,///g/261,///g/262,///g/263,///g/264,///g/265,///g/266" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 27 ], "summary": "[1] 4 [g.296 g.301] 4", "num_nts": 6, "nts_short": "UGAGAG", "nts_long": "///g/296,///g/297,///g/298,///g/299,///g/300,///g/301", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///g/297,///g/298,///g/299,///g/300" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 12 ], "stem_indices": [ 28 ], "summary": "[1] 12 [g.320 g.333] 5", "num_nts": 14, "nts_short": "AACUGAGACACGGU", "nts_long": "///g/320,///g/321,///g/322,///g/323,///g/324,///g/325,///g/326,///g/327,///g/328,///g/329,///g/330,///g/331,///g/332,///g/333", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 12, "nts_short": "ACUGAGACACGG", "nts_long": "///g/321,///g/322,///g/323,///g/324,///g/325,///g/326,///g/327,///g/328,///g/329,///g/330,///g/331,///g/332" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 29 ], "summary": "[1] 4 [g.342 g.347] 4", "num_nts": 6, "nts_short": "CUACGG", "nts_long": "///g/342,///g/343,///g/344,///g/345,///g/346,///g/347", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UACG", "nts_long": "///g/343,///g/344,///g/345,///g/346" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 31 ], "summary": "[1] 4 [g.379 g.384] 4", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///g/379,///g/380,///g/381,///g/382,///g/383,///g/384", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///g/380,///g/381,///g/382,///g/383" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 33 ], "summary": "[1] 4 [g.419 g.424] 4", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///g/419,///g/420,///g/421,///g/422,///g/423,///g/424", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///g/420,///g/421,///g/422,///g/423" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 35 ], "summary": "[1] 7 [g.462 g.470] 8", "num_nts": 9, "nts_short": "GUUAAUACC", "nts_long": "///g/462,///g/463,///g/464,///g/465,///g/466,///g/467,///g/468,///g/469,///g/470", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUAAUAC", "nts_long": "///g/463,///g/464,///g/465,///g/466,///g/467,///g/468,///g/469" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 16 ], "stem_indices": [ 37 ], "summary": "[1] 16 [g.507 g.524] 3", "num_nts": 18, "nts_short": "CUAACUCCGUGCCAGCAG", "nts_long": "///g/507,///g/508,///g/509,///g/510,///g/511,///g/512,///g/513,///g/514,///g/515,///g/516,///g/517,///g/518,///g/519,///g/520,///g/521,///g/522,///g/523,///g/524", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 16, "nts_short": "UAACUCCGUGCCAGCA", "nts_long": "///g/508,///g/509,///g/510,///g/511,///g/512,///g/513,///g/514,///g/515,///g/516,///g/517,///g/518,///g/519,///g/520,///g/521,///g/522,///g/523" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 39 ], "summary": "[1] 4 [g.522 g.527] 2", "num_nts": 6, "nts_short": "CAGCCG", "nts_long": "///g/522,///g/523,///g/524,///g/525,///g/526,///g/527", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGCC", "nts_long": "///g/523,///g/524,///g/525,///g/526" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 47 ], "summary": "[1] 5 [g.617 g.623] 6", "num_nts": 7, "nts_short": "GCUCAAC", "nts_long": "///g/617,///g/618,///g/619,///g/620,///g/621,///g/622,///g/623", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CUCAA", "nts_long": "///g/618,///g/619,///g/620,///g/621,///g/622" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 52 ], "summary": "[1] 8 [g.689 g.698] 2", "num_nts": 10, "nts_short": "CGGUGAAAUG", "nts_long": "///g/689,///g/690,///g/691,///g/692,///g/693,///g/694,///g/695,///g/696,///g/697,///g/698", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GGUGAAAU", "nts_long": "///g/690,///g/691,///g/692,///g/693,///g/694,///g/695,///g/696,///g/697" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 53 ], "summary": "[1] 4 [g.726 g.731] 2", "num_nts": 6, "nts_short": "CGAAGG", "nts_long": "///g/726,///g/727,///g/728,///g/729,///g/730,///g/731", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAG", "nts_long": "///g/727,///g/728,///g/729,///g/730" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 56 ], "summary": "[1] 9 [g.786 g.796] 4", "num_nts": 11, "nts_short": "GAUUAGAUACC", "nts_long": "///g/786,///g/787,///g/788,///g/789,///g/790,///g/791,///g/792,///g/793,///g/794,///g/795,///g/796", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AUUAGAUAC", "nts_long": "///g/787,///g/788,///g/789,///g/790,///g/791,///g/792,///g/793,///g/794,///g/795" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 58 ], "summary": "[1] 5 [g.840 g.846] 12", "num_nts": 7, "nts_short": "CCUUGAG", "nts_long": "///g/840,///g/841,///g/842,///g/843,///g/844,///g/845,///g/846", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CUUGA", "nts_long": "///g/841,///g/842,///g/843,///g/844,///g/845" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 59 ], "summary": "[1] 4 [g.862 g.867] 2", "num_nts": 6, "nts_short": "CUAACG", "nts_long": "///g/862,///g/863,///g/864,///g/865,///g/866,///g/867", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UAAC", "nts_long": "///g/863,///g/864,///g/865,///g/866" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 61 ], "summary": "[1] 4 [g.897 g.902] 4", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///g/897,///g/898,///g/899,///g/900,///g/901,///g/902", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///g/898,///g/899,///g/900,///g/901" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 69 ], "summary": "[1] 8 [g.963 g.972] 2", "num_nts": 10, "nts_short": "GAUGCAACGC", "nts_long": "///g/963,///g/964,///g/965,///g/966,///g/967,///g/968,///g/969,///g/970,///g/971,///g/972", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "AUGCAACG", "nts_long": "///g/964,///g/965,///g/966,///g/967,///g/968,///g/969,///g/970,///g/971" } ] }, { "index": 23, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 73 ], "summary": "[1] 4 [g.1012 g.1017] 5", "num_nts": 6, "nts_short": "AGAGAU", "nts_long": "///g/1012,///g/1013,///g/1014,///g/1015,///g/1016,///g/1017", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///g/1013,///g/1014,///g/1015,///g/1016" } ] }, { "index": 24, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 74 ], "summary": "[1] 4 [g.1028 g.1033] 2", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///g/1028,///g/1029,///g/1030,///g/1031,///g/1032,///g/1033", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///g/1029,///g/1030,///g/1031,///g/1032" } ] }, { "index": 25, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 80 ], "summary": "[1] 4 [g.1076 g.1081] 3", "num_nts": 6, "nts_short": "UGUGAA", "nts_long": "///g/1076,///g/1077,///g/1078,///g/1079,///g/1080,///g/1081", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///g/1077,///g/1078,///g/1079,///g/1080" } ] }, { "index": 26, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 81 ], "summary": "[1] 6 [g.1089 g.1096] 3", "num_nts": 8, "nts_short": "GUUAAGUC", "nts_long": "///g/1089,///g/1090,///g/1091,///g/1092,///g/1093,///g/1094,///g/1095,///g/1096", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUAAGU", "nts_long": "///g/1090,///g/1091,///g/1092,///g/1093,///g/1094,///g/1095" } ] }, { "index": 27, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 84 ], "summary": "[1] 5 [g.1134 g.1140] 3", "num_nts": 7, "nts_short": "GUCCGGC", "nts_long": "///g/1134,///g/1135,///g/1136,///g/1137,///g/1138,///g/1139,///g/1140", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UCCGG", "nts_long": "///g/1135,///g/1136,///g/1137,///g/1138,///g/1139" } ] }, { "index": 28, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 85 ], "summary": "[1] 5 [g.1165 g.1171] 5", "num_nts": 7, "nts_short": "UGAUAAA", "nts_long": "///g/1165,///g/1166,///g/1167,///g/1168,///g/1169,///g/1170,///g/1171", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUAA", "nts_long": "///g/1166,///g/1167,///g/1168,///g/1169,///g/1170" } ] }, { "index": 29, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 89 ], "summary": "[1] 4 [g.1265 g.1270] 3", "num_nts": 6, "nts_short": "CGCGAG", "nts_long": "///g/1265,///g/1266,///g/1267,///g/1268,///g/1269,///g/1270", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCGA", "nts_long": "///g/1266,///g/1267,///g/1268,///g/1269" } ] }, { "index": 30, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 90 ], "summary": "[1] 8 [g.1314 g.1323] 7", "num_nts": 10, "nts_short": "CUGCAACUCG", "nts_long": "///g/1314,///g/1315,///g/1316,///g/1317,///g/1318,///g/1319,///g/1320,///g/1321,///g/1322,///g/1323", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UGCAACUC", "nts_long": "///g/1315,///g/1316,///g/1317,///g/1318,///g/1319,///g/1320,///g/1321,///g/1322" } ] }, { "index": 31, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 91 ], "summary": "[1] 9 [g.1356 g.1366] 7", "num_nts": 11, "nts_short": "GAUCAGAAUGC", "nts_long": "///g/1356,///g/1357,///g/1358,///g/1359,///g/1360,///g/1361,///g/1362,///g/1363,///g/1364,///g/1365,///g/1366", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AUCAGAAUG", "nts_long": "///g/1357,///g/1358,///g/1359,///g/1360,///g/1361,///g/1362,///g/1363,///g/1364,///g/1365" } ] }, { "index": 32, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 98 ], "summary": "[1] 4 [g.1449 g.1454] 2", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///g/1449,///g/1450,///g/1451,///g/1452,///g/1453,///g/1454", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///g/1450,///g/1451,///g/1452,///g/1453" } ] }, { "index": 33, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 99 ], "summary": "[1] 4 [g.1515 g.1520] 9", "num_nts": 6, "nts_short": "GGGAAC", "nts_long": "///g/1515,///g/1516,///g/1517,///g/1518,///g/1519,///g/1520", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///g/1516,///g/1517,///g/1518,///g/1519" } ] }, { "index": 34, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 101 ], "summary": "[1] 9 [v.13 v.23] 4", "num_nts": 11, "nts_short": "CAGCCUGGUAG", "nts_long": "///v/13,///v/14,///v/15,///v/16,///v/17,///v/18,///v/19,///v/20,///v/21,///v/22,///v/23", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AGCCUGGUA", "nts_long": "///v/14,///v/15,///v/16,///v/17,///v/18,///v/19,///v/20,///v/21,///v/22" } ] }, { "index": 35, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 102 ], "summary": "[1] 7 [v.32 v.40] 5", "num_nts": 9, "nts_short": "GCUCAUAAC", "nts_long": "///v/32,///v/33,///v/34,///v/35,///v/36,///v/37,///v/38,///v/39,///v/40", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CUCAUAA", "nts_long": "///v/33,///v/34,///v/35,///v/36,///v/37,///v/38,///v/39" } ] }, { "index": 36, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 104 ], "summary": "[1] 7 [v.54 v.62] 5", "num_nts": 9, "nts_short": "GUUCAAAUC", "nts_long": "///v/54,///v/55,///v/56,///v/57,///v/58,///v/59,///v/60,///v/61,///v/62", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUCAAAU", "nts_long": "///v/55,///v/56,///v/57,///v/58,///v/59,///v/60,///v/61" } ] } ], "num_bulges": 27, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 3, 4 ], "summary": "[2] 1 0 [g.30 g.553 g.32 g.552] 4 5", "num_nts": 5, "nts_short": "UGAUA", "nts_long": "///g/30,///g/31,///g/32,///g/552,///g/553", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///g/31" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 5, 6 ], "summary": "[2] 0 1 [g.44 g.398 g.45 g.396] 6 2", "num_nts": 5, "nts_short": "AGCAU", "nts_long": "///g/44,///g/45,///g/396,///g/397,///g/398", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/397" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 7, 8 ], "summary": "[2] 1 0 [g.54 g.357 g.56 g.356] 3 3", "num_nts": 5, "nts_short": "CAUAG", "nts_long": "///g/54,///g/55,///g/56,///g/356,///g/357", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/55" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 12, 13 ], "summary": "[2] 0 1 [g.75 g.95 g.76 g.93] 3 7", "num_nts": 5, "nts_short": "GGUGC", "nts_long": "///g/75,///g/76,///g/93,///g/94,///g/95", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///g/94" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -4, 30 ], "summary": "[2] 1 0 [g.367 g.393 g.369 g.392] 1 3", "num_nts": 5, "nts_short": "UUGCA", "nts_long": "///g/367,///g/368,///g/369,///g/392,///g/393", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///g/368" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 6, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -5, 31 ], "summary": "[2] 0 1 [g.375 g.389 g.376 g.387] 1 4", "num_nts": 5, "nts_short": "UGUGA", "nts_long": "///g/375,///g/376,///g/387,///g/388,///g/389", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///g/388" } ] }, { "index": 7, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 44, 45 ], "summary": "[2] 1 0 [g.594 g.645 g.596 g.644] 7 2", "num_nts": 5, "nts_short": "UAAUG", "nts_long": "///g/594,///g/595,///g/596,///g/644,///g/645", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/595" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 8, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 48, 49 ], "summary": "[2] 0 1 [g.658 g.748 g.659 g.746] 4 4", "num_nts": 5, "nts_short": "CUAAG", "nts_long": "///g/658,///g/659,///g/746,///g/747,///g/748", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/747" } ] }, { "index": 9, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 62, 63 ], "summary": "[2] 0 1 [g.922 g.1395 g.923 g.1393] 2 3", "num_nts": 5, "nts_short": "GAUAC", "nts_long": "///g/922,///g/923,///g/1393,///g/1394,///g/1395", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1394" } ] }, { "index": 10, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 63, 64 ], "summary": "[2] 1 0 [g.925 g.1391 g.927 g.1390] 3 7", "num_nts": 5, "nts_short": "GGGUU", "nts_long": "///g/925,///g/926,///g/927,///g/1390,///g/1391", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///g/926" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 11, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 67, 68 ], "summary": "[2] 0 1 [g.953 g.1228 g.954 g.1226] 8 2", "num_nts": 5, "nts_short": "GGCAC", "nts_long": "///g/953,///g/954,///g/1226,///g/1227,///g/1228", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1227" } ] }, { "index": 12, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 71, 72 ], "summary": "[2] 0 1 [g.998 g.1043 g.999 g.1041] 2 5", "num_nts": 5, "nts_short": "CCGAG", "nts_long": "///g/998,///g/999,///g/1041,///g/1042,///g/1043", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1042" } ] }, { "index": 13, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 75, 76 ], "summary": "[2] 1 0 [g.1048 g.1209 g.1050 g.1208] 2 3", "num_nts": 5, "nts_short": "GUGCC", "nts_long": "///g/1048,///g/1049,///g/1050,///g/1208,///g/1209", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1049" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 14, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 78, -14 ], "summary": "[2] 0 1 [g.1060 g.1197 g.1061 g.1195] 3 1", "num_nts": 5, "nts_short": "UGCAA", "nts_long": "///g/1060,///g/1061,///g/1195,///g/1196,///g/1197", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1196" } ] }, { "index": 15, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 96, 97 ], "summary": "[2] 1 0 [g.1440 g.1461 g.1442 g.1460] 6 4", "num_nts": 5, "nts_short": "UAGCG", "nts_long": "///g/1440,///g/1441,///g/1442,///g/1460,///g/1461", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1441" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 16, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 9, 10 ], "summary": "[2] 2 0 [g.63 g.104 g.66 g.103] 3 2", "num_nts": 6, "nts_short": "CGAAUG", "nts_long": "///g/63,///g/64,///g/65,///g/66,///g/103,///g/104", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/64,///g/65" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 17, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 11, 12 ], "summary": "[2] 2 0 [g.70 g.98 g.73 g.97] 2 3", "num_nts": 6, "nts_short": "UAACGA", "nts_long": "///g/70,///g/71,///g/72,///g/73,///g/97,///g/98", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/71,///g/72" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 18, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 21, 22 ], "summary": "[2] 2 0 [g.203 g.214 g.206 g.213] 6 2", "num_nts": 6, "nts_short": "GGACGC", "nts_long": "///g/203,///g/204,///g/205,///g/206,///g/213,///g/214", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/204,///g/205" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 19, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 24, 25 ], "summary": "[2] 2 0 [g.249 g.275 g.252 g.274] 3 8", "num_nts": 6, "nts_short": "UAGUAG", "nts_long": "///g/249,///g/250,///g/251,///g/252,///g/274,///g/275", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AG", "nts_long": "///g/250,///g/251" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 20, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 45, 46 ], "summary": "[2] 0 2 [g.597 g.643 g.598 g.640] 2 8", "num_nts": 6, "nts_short": "GUAUAC", "nts_long": "///g/597,///g/598,///g/640,///g/641,///g/642,///g/643", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "UA", "nts_long": "///g/641,///g/642" } ] }, { "index": 21, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ -9, 48 ], "summary": "[2] 0 2 [g.654 g.754 g.655 g.751] 1 4", "num_nts": 6, "nts_short": "GAUGAC", "nts_long": "///g/654,///g/655,///g/751,///g/752,///g/753,///g/754", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/752,///g/753" } ] }, { "index": 22, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ -16, 84 ], "summary": "[2] 2 0 [g.1129 g.1143 g.1132 g.1142] 1 3", "num_nts": 6, "nts_short": "CAGCGG", "nts_long": "///g/1129,///g/1130,///g/1131,///g/1132,///g/1142,///g/1143", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AG", "nts_long": "///g/1130,///g/1131" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 23, "type": "bulge", "bridging_nts": [ 0, 3 ], "stem_indices": [ 26, 27 ], "summary": "[2] 0 3 [g.292 g.308 g.293 g.304] 4 4", "num_nts": 7, "nts_short": "GGUGACC", "nts_long": "///g/292,///g/293,///g/304,///g/305,///g/306,///g/307,///g/308", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 3, "nts_short": "GAC", "nts_long": "///g/305,///g/306,///g/307" } ] }, { "index": 24, "type": "bulge", "bridging_nts": [ 3, 0 ], "stem_indices": [ 30, -5 ], "summary": "[2] 3 0 [g.371 g.390 g.375 g.389] 3 1", "num_nts": 7, "nts_short": "ACAAUAU", "nts_long": "///g/371,///g/372,///g/373,///g/374,///g/375,///g/389,///g/390", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAA", "nts_long": "///g/372,///g/373,///g/374" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 25, "type": "bulge", "bridging_nts": [ 3, 0 ], "stem_indices": [ 54, 55 ], "summary": "[2] 3 0 [g.774 g.805 g.778 g.804] 6 2", "num_nts": 7, "nts_short": "GGGAGUC", "nts_long": "///g/774,///g/775,///g/776,///g/777,///g/778,///g/804,///g/805", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGA", "nts_long": "///g/775,///g/776,///g/777" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 26, "type": "bulge", "bridging_nts": [ 3, 0 ], "stem_indices": [ -12, 71 ], "summary": "[2] 3 0 [g.993 g.1045 g.997 g.1044] 1 2", "num_nts": 7, "nts_short": "GACAUAC", "nts_long": "///g/993,///g/994,///g/995,///g/996,///g/997,///g/1044,///g/1045", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACA", "nts_long": "///g/994,///g/995,///g/996" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 27, "type": "bulge", "bridging_nts": [ 0, 3 ], "stem_indices": [ 77, 78 ], "summary": "[2] 0 3 [g.1057 g.1203 g.1058 g.1199] 2 3", "num_nts": 7, "nts_short": "GGUCAUC", "nts_long": "///g/1057,///g/1058,///g/1199,///g/1200,///g/1201,///g/1202,///g/1203", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 3, "nts_short": "CAU", "nts_long": "///g/1200,///g/1201,///g/1202" } ] } ], "num_iloops": 38, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -1, 2 ], "summary": "[2] 1 1 [g.15 g.920 g.17 g.918] 1 3", "num_nts": 6, "nts_short": "GAUAAU", "nts_long": "///g/15,///g/16,///g/17,///g/918,///g/919,///g/920", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/16" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/919" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -3, 18 ], "summary": "[2] 1 1 [g.144 g.178 g.146 g.176] 1 2", "num_nts": 6, "nts_short": "GGGCGC", "nts_long": "///g/144,///g/145,///g/146,///g/176,///g/177,///g/178", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///g/145" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///g/177" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -13, 73 ], "summary": "[2] 1 1 [g.1006 g.1023 g.1008 g.1021] 1 5", "num_nts": 6, "nts_short": "GUUAAU", "nts_long": "///g/1006,///g/1007,///g/1008,///g/1021,///g/1022,///g/1023", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1007" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1022" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -14, -15 ], "summary": "[2] 1 1 [g.1061 g.1195 g.1063 g.1193] 1 1", "num_nts": 6, "nts_short": "GUCGUC", "nts_long": "///g/1061,///g/1062,///g/1063,///g/1193,///g/1194,///g/1195", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1062" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1194" } ] }, { "index": 5, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 92, -22 ], "summary": "[2] 1 1 [g.1405 g.1496 g.1407 g.1494] 2 1", "num_nts": 6, "nts_short": "GUCGUC", "nts_long": "///g/1405,///g/1406,///g/1407,///g/1494,///g/1495,///g/1496", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1406" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1495" } ] }, { "index": 6, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 93, 94 ], "summary": "[2] 1 1 [g.1412 g.1488 g.1414 g.1486] 4 3", "num_nts": 6, "nts_short": "CAUGGG", "nts_long": "///g/1412,///g/1413,///g/1414,///g/1486,///g/1487,///g/1488", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1413" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///g/1487" } ] }, { "index": 7, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 10, 11 ], "summary": "[2] 1 2 [g.67 g.102 g.69 g.99] 2 2", "num_nts": 7, "nts_short": "CGGCGAG", "nts_long": "///g/67,///g/68,///g/69,///g/99,///g/100,///g/101,///g/102", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///g/68" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/100,///g/101" } ] }, { "index": 8, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 15, 16 ], "summary": "[2] 2 1 [g.128 g.233 g.131 g.231] 7 2", "num_nts": 7, "nts_short": "GAAAUGC", "nts_long": "///g/128,///g/129,///g/130,///g/131,///g/231,///g/232,///g/233", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/129,///g/130" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///g/232" } ] }, { "index": 9, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -20, -21 ], "summary": "[2] 1 2 [g.1399 g.1504 g.1401 g.1501] 1 1", "num_nts": 7, "nts_short": "CCGCAAG", "nts_long": "///g/1399,///g/1400,///g/1401,///g/1501,///g/1502,///g/1503,///g/1504", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///g/1400" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/1502,///g/1503" } ] }, { "index": 10, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -22, 93 ], "summary": "[2] 1 2 [g.1407 g.1494 g.1409 g.1491] 1 4", "num_nts": 7, "nts_short": "CACGAAG", "nts_long": "///g/1407,///g/1408,///g/1409,///g/1491,///g/1492,///g/1493,///g/1494", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1408" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/1492,///g/1493" } ] }, { "index": 11, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 97, 98 ], "summary": "[2] 2 1 [g.1445 g.1457 g.1448 g.1455] 4 2", "num_nts": 7, "nts_short": "UAACGAG", "nts_long": "///g/1445,///g/1446,///g/1447,///g/1448,///g/1455,///g/1456,///g/1457", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/1446,///g/1447" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1456" } ] }, { "index": 12, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 64, 65 ], "summary": "[2] 1 3 [g.933 g.1384 g.935 g.1380] 7 2", "num_nts": 8, "nts_short": "GCAUUCCC", "nts_long": "///g/933,///g/934,///g/935,///g/1380,///g/1381,///g/1382,///g/1383,///g/1384", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///g/934" }, { "index": 2, "num_nts": 3, "nts_short": "UCC", "nts_long": "///g/1381,///g/1382,///g/1383" } ] }, { "index": 13, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 76, 77 ], "summary": "[2] 3 1 [g.1052 g.1206 g.1056 g.1204] 3 2", "num_nts": 8, "nts_short": "UGCAUAUG", "nts_long": "///g/1052,///g/1053,///g/1054,///g/1055,///g/1056,///g/1204,///g/1205,///g/1206", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GCA", "nts_long": "///g/1053,///g/1054,///g/1055" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///g/1205" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 94, 95 ], "summary": "[2] 2 2 [g.1416 g.1484 g.1419 g.1481] 3 12", "num_nts": 8, "nts_short": "GGAGUGAC", "nts_long": "///g/1416,///g/1417,///g/1418,///g/1419,///g/1481,///g/1482,///g/1483,///g/1484", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/1417,///g/1418" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/1482,///g/1483" } ] }, { "index": 15, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ -2, 7 ], "summary": "[2] 4 1 [g.47 g.361 g.52 g.359] 1 3", "num_nts": 9, "nts_short": "CCUAACGGG", "nts_long": "///g/47,///g/48,///g/49,///g/50,///g/51,///g/52,///g/359,///g/360,///g/361", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///g/48,///g/49,///g/50,///g/51" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///g/360" } ] }, { "index": 16, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 16, 17 ], "summary": "[2] 3 2 [g.132 g.230 g.136 g.227] 2 7", "num_nts": 9, "nts_short": "CUGCCGAUG", "nts_long": "///g/132,///g/133,///g/134,///g/135,///g/136,///g/227,///g/228,///g/229,///g/230", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGC", "nts_long": "///g/133,///g/134,///g/135" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///g/228,///g/229" } ] }, { "index": 17, "type": "asymmetric internal loop", "bridging_nts": [ 1, 4 ], "stem_indices": [ -6, 34 ], "summary": "[2] 1 4 [g.440 g.497 g.442 g.492] 1 5", "num_nts": 9, "nts_short": "CAGCAGAAG", "nts_long": "///g/440,///g/441,///g/442,///g/492,///g/493,///g/494,///g/495,///g/496,///g/497", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/441" }, { "index": 2, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///g/493,///g/494,///g/495,///g/496" } ] }, { "index": 18, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 49, 50 ], "summary": "[2] 3 2 [g.662 g.743 g.666 g.740] 4 7", "num_nts": 9, "nts_short": "UAGAGUGGA", "nts_long": "///g/662,///g/663,///g/664,///g/665,///g/666,///g/740,///g/741,///g/742,///g/743", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AGA", "nts_long": "///g/663,///g/664,///g/665" }, { "index": 2, "num_nts": 2, "nts_short": "GG", "nts_long": "///g/741,///g/742" } ] }, { "index": 19, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ -21, 92 ], "summary": "[2] 2 3 [g.1401 g.1501 g.1404 g.1497] 1 2", "num_nts": 9, "nts_short": "GCCCGUAAC", "nts_long": "///g/1401,///g/1402,///g/1403,///g/1404,///g/1497,///g/1498,///g/1499,///g/1500,///g/1501", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///g/1402,///g/1403" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///g/1498,///g/1499,///g/1500" } ] }, { "index": 20, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 42, 43 ], "summary": "[2] 3 3 [g.580 g.761 g.584 g.757] 4 3", "num_nts": 10, "nts_short": "CGCAGUCAGG", "nts_long": "///g/580,///g/581,///g/582,///g/583,///g/584,///g/757,///g/758,///g/759,///g/760,///g/761", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GCA", "nts_long": "///g/581,///g/582,///g/583" }, { "index": 2, "num_nts": 3, "nts_short": "CAG", "nts_long": "///g/758,///g/759,///g/760" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 55, 56 ], "summary": "[2] 3 3 [g.779 g.803 g.783 g.799] 2 4", "num_nts": 10, "nts_short": "CAAACGGUAG", "nts_long": "///g/779,///g/780,///g/781,///g/782,///g/783,///g/799,///g/800,///g/801,///g/802,///g/803", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAA", "nts_long": "///g/780,///g/781,///g/782" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///g/800,///g/801,///g/802" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 2, 4 ], "stem_indices": [ 87, 88 ], "summary": "[2] 2 4 [g.1255 g.1282 g.1258 g.1277] 3 2", "num_nts": 10, "nts_short": "GAAGCGGACC", "nts_long": "///g/1255,///g/1256,///g/1257,///g/1258,///g/1277,///g/1278,///g/1279,///g/1280,///g/1281,///g/1282", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/1256,///g/1257" }, { "index": 2, "num_nts": 4, "nts_short": "GGAC", "nts_long": "///g/1278,///g/1279,///g/1280,///g/1281" } ] }, { "index": 23, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 88, 89 ], "summary": "[2] 3 3 [g.1259 g.1276 g.1263 g.1272] 2 3", "num_nts": 10, "nts_short": "CGACCGCAAG", "nts_long": "///g/1259,///g/1260,///g/1261,///g/1262,///g/1263,///g/1272,///g/1273,///g/1274,///g/1275,///g/1276", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAC", "nts_long": "///g/1260,///g/1261,///g/1262" }, { "index": 2, "num_nts": 3, "nts_short": "CAA", "nts_long": "///g/1273,///g/1274,///g/1275" } ] }, { "index": 24, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ 34, -7 ], "summary": "[2] 3 4 [g.446 g.488 g.450 g.483] 5 1", "num_nts": 11, "nts_short": "GGAGGCGUUAC", "nts_long": "///g/446,///g/447,///g/448,///g/449,///g/450,///g/483,///g/484,///g/485,///g/486,///g/487,///g/488", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///g/447,///g/448,///g/449" }, { "index": 2, "num_nts": 4, "nts_short": "GUUA", "nts_long": "///g/484,///g/485,///g/486,///g/487" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 2, 5 ], "stem_indices": [ -17, 85 ], "summary": "[2] 2 5 [g.1158 g.1181 g.1161 g.1175] 1 5", "num_nts": 11, "nts_short": "CUGCGAGGAAG", "nts_long": "///g/1158,///g/1159,///g/1160,///g/1161,///g/1175,///g/1176,///g/1177,///g/1178,///g/1179,///g/1180,///g/1181", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UG", "nts_long": "///g/1159,///g/1160" }, { "index": 2, "num_nts": 5, "nts_short": "AGGAA", "nts_long": "///g/1176,///g/1177,///g/1178,///g/1179,///g/1180" } ] }, { "index": 26, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 95, 96 ], "summary": "[2] 4 3 [g.1430 g.1470 g.1435 g.1466] 12 6", "num_nts": 11, "nts_short": "AAGAAGCCACU", "nts_long": "///g/1430,///g/1431,///g/1432,///g/1433,///g/1434,///g/1435,///g/1466,///g/1467,///g/1468,///g/1469,///g/1470", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///g/1431,///g/1432,///g/1433,///g/1434" }, { "index": 2, "num_nts": 3, "nts_short": "CAC", "nts_long": "///g/1467,///g/1468,///g/1469" } ] }, { "index": 27, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -10, 51 ], "summary": "[2] 4 4 [g.673 g.717 g.678 g.712] 1 7", "num_nts": 12, "nts_short": "AGAAUUAGGAAU", "nts_long": "///g/673,///g/674,///g/675,///g/676,///g/677,///g/678,///g/712,///g/713,///g/714,///g/715,///g/716,///g/717", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///g/674,///g/675,///g/676,///g/677" }, { "index": 2, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///g/713,///g/714,///g/715,///g/716" } ] }, { "index": 28, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -19, 90 ], "summary": "[2] 4 4 [g.1303 g.1334 g.1308 g.1329] 1 7", "num_nts": 12, "nts_short": "CGGAUUAUGAAG", "nts_long": "///g/1303,///g/1304,///g/1305,///g/1306,///g/1307,///g/1308,///g/1329,///g/1330,///g/1331,///g/1332,///g/1333,///g/1334", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAU", "nts_long": "///g/1304,///g/1305,///g/1306,///g/1307" }, { "index": 2, "num_nts": 4, "nts_short": "UGAA", "nts_long": "///g/1330,///g/1331,///g/1332,///g/1333" } ] }, { "index": 29, "type": "asymmetric internal loop", "bridging_nts": [ 4, 5 ], "stem_indices": [ -7, 35 ], "summary": "[2] 4 5 [g.450 g.483 g.455 g.477] 1 8", "num_nts": 13, "nts_short": "GAAGGGCAUUGAC", "nts_long": "///g/450,///g/451,///g/452,///g/453,///g/454,///g/455,///g/477,///g/478,///g/479,///g/480,///g/481,///g/482,///g/483", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AAGG", "nts_long": "///g/451,///g/452,///g/453,///g/454" }, { "index": 2, "num_nts": 5, "nts_short": "AUUGA", "nts_long": "///g/478,///g/479,///g/480,///g/481,///g/482" } ] }, { "index": 30, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ 51, 52 ], "summary": "[2] 3 6 [g.684 g.706 g.688 g.699] 7 2 k-turn:normal", "num_nts": 13, "nts_short": "UGUAGCGUAGAGA", "nts_long": "///g/684,///g/685,///g/686,///g/687,///g/688,///g/699,///g/700,///g/701,///g/702,///g/703,///g/704,///g/705,///g/706", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUA", "nts_long": "///g/685,///g/686,///g/687" }, { "index": 2, "num_nts": 6, "nts_short": "GUAGAG", "nts_long": "///g/700,///g/701,///g/702,///g/703,///g/704,///g/705" } ] }, { "index": 31, "type": "asymmetric internal loop", "bridging_nts": [ 4, 5 ], "stem_indices": [ 83, -16 ], "summary": "[2] 4 5 [g.1124 g.1149 g.1129 g.1143] 7 1", "num_nts": 13, "nts_short": "GUUGCCGGAACUC", "nts_long": "///g/1124,///g/1125,///g/1126,///g/1127,///g/1128,///g/1129,///g/1143,///g/1144,///g/1145,///g/1146,///g/1147,///g/1148,///g/1149", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUGC", "nts_long": "///g/1125,///g/1126,///g/1127,///g/1128" }, { "index": 2, "num_nts": 5, "nts_short": "GAACU", "nts_long": "///g/1144,///g/1145,///g/1146,///g/1147,///g/1148" } ] }, { "index": 32, "type": "asymmetric internal loop", "bridging_nts": [ 4, 6 ], "stem_indices": [ 23, 24 ], "summary": "[2] 4 6 [g.242 g.284 g.247 g.277] 3 3 k-turn:normal", "num_nts": 14, "nts_short": "GAUUAGCGACGAUC", "nts_long": "///g/242,///g/243,///g/244,///g/245,///g/246,///g/247,///g/277,///g/278,///g/279,///g/280,///g/281,///g/282,///g/283,///g/284", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUUA", "nts_long": "///g/243,///g/244,///g/245,///g/246" }, { "index": 2, "num_nts": 6, "nts_short": "GACGAU", "nts_long": "///g/278,///g/279,///g/280,///g/281,///g/282,///g/283" } ] }, { "index": 33, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 46, 47 ], "summary": "[2] 6 4 [g.605 g.633 g.612 g.628] 8 6", "num_nts": 14, "nts_short": "UGAAAUCCGAACUG", "nts_long": "///g/605,///g/606,///g/607,///g/608,///g/609,///g/610,///g/611,///g/612,///g/628,///g/629,///g/630,///g/631,///g/632,///g/633", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAAAUC", "nts_long": "///g/606,///g/607,///g/608,///g/609,///g/610,///g/611" }, { "index": 2, "num_nts": 4, "nts_short": "AACU", "nts_long": "///g/629,///g/630,///g/631,///g/632" } ] }, { "index": 34, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 60, 61 ], "summary": "[2] 6 4 [g.887 g.910 g.894 g.905] 3 4", "num_nts": 14, "nts_short": "GGAGUACGUAAAAC", "nts_long": "///g/887,///g/888,///g/889,///g/890,///g/891,///g/892,///g/893,///g/894,///g/905,///g/906,///g/907,///g/908,///g/909,///g/910", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAGUAC", "nts_long": "///g/888,///g/889,///g/890,///g/891,///g/892,///g/893" }, { "index": 2, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///g/906,///g/907,///g/908,///g/909" } ] }, { "index": 35, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ 86, 87 ], "summary": "[2] 5 5 [g.1247 g.1290 g.1253 g.1284] 7 3", "num_nts": 14, "nts_short": "UACAAAGCAUAAAG", "nts_long": "///g/1247,///g/1248,///g/1249,///g/1250,///g/1251,///g/1252,///g/1253,///g/1284,///g/1285,///g/1286,///g/1287,///g/1288,///g/1289,///g/1290", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "ACAAA", "nts_long": "///g/1248,///g/1249,///g/1250,///g/1251,///g/1252" }, { "index": 2, "num_nts": 5, "nts_short": "AUAAA", "nts_long": "///g/1285,///g/1286,///g/1287,///g/1288,///g/1289" } ] }, { "index": 36, "type": "asymmetric internal loop", "bridging_nts": [ 5, 6 ], "stem_indices": [ 18, 19 ], "summary": "[2] 5 6 [g.147 g.175 g.153 g.168] 2 6", "num_nts": 15, "nts_short": "GGAUAACGCUAAUAC", "nts_long": "///g/147,///g/148,///g/149,///g/150,///g/151,///g/152,///g/153,///g/168,///g/169,///g/170,///g/171,///g/172,///g/173,///g/174,///g/175", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUAA", "nts_long": "///g/148,///g/149,///g/150,///g/151,///g/152" }, { "index": 2, "num_nts": 6, "nts_short": "CUAAUA", "nts_long": "///g/169,///g/170,///g/171,///g/172,///g/173,///g/174" } ] }, { "index": 37, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 32, 33 ], "summary": "[2] 6 5 [g.409 g.433 g.416 g.427] 4 4 k-turn:undecided", "num_nts": 15, "nts_short": "UGAAGAAGUGUAAAG", "nts_long": "///g/409,///g/410,///g/411,///g/412,///g/413,///g/414,///g/415,///g/416,///g/427,///g/428,///g/429,///g/430,///g/431,///g/432,///g/433", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAAGAA", "nts_long": "///g/410,///g/411,///g/412,///g/413,///g/414,///g/415" }, { "index": 2, "num_nts": 5, "nts_short": "GUAAA", "nts_long": "///g/428,///g/429,///g/430,///g/431,///g/432" } ] }, { "index": 38, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 38, 39 ], "summary": "[2] 5 7 [g.515 g.536 g.521 g.528] 5 2", "num_nts": 16, "nts_short": "GUGCCAGCGGUAAUAC", "nts_long": "///g/515,///g/516,///g/517,///g/518,///g/519,///g/520,///g/521,///g/528,///g/529,///g/530,///g/531,///g/532,///g/533,///g/534,///g/535,///g/536", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGCCA", "nts_long": "///g/516,///g/517,///g/518,///g/519,///g/520" }, { "index": 2, "num_nts": 7, "nts_short": "GGUAAUA", "nts_long": "///g/529,///g/530,///g/531,///g/532,///g/533,///g/534,///g/535" } ] } ], "num_junctions": 21, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 2, 0 ], "stem_indices": [ 43, 44, -9 ], "summary": "[3] 1 2 0 [g.586 g.755 g.588 g.651 g.654 g.754] 3 7 1", "num_nts": 9, "nts_short": "CGGCUUGCG", "nts_long": "///g/586,///g/587,///g/588,///g/651,///g/652,///g/653,///g/654,///g/754,///g/755", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///g/587" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///g/652,///g/653" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 2, 1, 2 ], "stem_indices": [ 66, 67, -18 ], "summary": "[3] 2 1 2 [g.943 g.1340 g.946 g.1235 g.1237 g.1337] 5 8 1", "num_nts": 11, "nts_short": "UGGAUACGGAA", "nts_long": "///g/943,///g/944,///g/945,///g/946,///g/1235,///g/1236,///g/1237,///g/1337,///g/1338,///g/1339,///g/1340", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GG", "nts_long": "///g/944,///g/945" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1236" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/1338,///g/1339" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 1, 2, 2 ], "stem_indices": [ 82, 83, -17 ], "summary": "[3] 1 2 2 [g.1116 g.1184 g.1118 g.1155 g.1158 g.1181] 4 7 1", "num_nts": 11, "nts_short": "UAUAGACGGUG", "nts_long": "///g/1116,///g/1117,///g/1118,///g/1155,///g/1156,///g/1157,///g/1158,///g/1181,///g/1182,///g/1183,///g/1184", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1117" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///g/1156,///g/1157" }, { "index": 3, "num_nts": 2, "nts_short": "GU", "nts_long": "///g/1182,///g/1183" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 0, 5, 1 ], "stem_indices": [ 6, -2, -4 ], "summary": "[3] 0 5 1 [g.46 g.395 g.47 g.361 g.367 g.393] 2 1 1", "num_nts": 12, "nts_short": "GCGGAAUAUAGC", "nts_long": "///g/46,///g/47,///g/361,///g/362,///g/363,///g/364,///g/365,///g/366,///g/367,///g/393,///g/394,///g/395", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "GAAUA", "nts_long": "///g/362,///g/363,///g/364,///g/365,///g/366" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///g/394" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 0, 3, 3 ], "stem_indices": [ 79, 80, 81 ], "summary": "[3] 0 3 3 [g.1073 g.1102 g.1074 g.1083 g.1087 g.1098] 6 3 3", "num_nts": 12, "nts_short": "UGUGUUGCGCAA", "nts_long": "///g/1073,///g/1074,///g/1083,///g/1084,///g/1085,///g/1086,///g/1087,///g/1098,///g/1099,///g/1100,///g/1101,///g/1102", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 3, "nts_short": "GUU", "nts_long": "///g/1084,///g/1085,///g/1086" }, { "index": 3, "num_nts": 3, "nts_short": "GCA", "nts_long": "///g/1099,///g/1100,///g/1101" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 2, 1, 4 ], "stem_indices": [ 70, -12, 75 ], "summary": "[3] 2 1 4 [g.990 g.1215 g.993 g.1045 g.1047 g.1210] 7 1 2", "num_nts": 13, "nts_short": "CUUGCAGCUUACG", "nts_long": "///g/990,///g/991,///g/992,///g/993,///g/1045,///g/1046,///g/1047,///g/1210,///g/1211,///g/1212,///g/1213,///g/1214,///g/1215", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///g/991,///g/992" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/1046" }, { "index": 3, "num_nts": 4, "nts_short": "UUAC", "nts_long": "///g/1211,///g/1212,///g/1213,///g/1214" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 2, 3, 2 ], "stem_indices": [ 72, -13, 74 ], "summary": "[3] 2 3 2 [g.1003 g.1037 g.1006 g.1023 g.1027 g.1034] 5 1 2", "num_nts": 13, "nts_short": "GAAGUGUGCGAAC", "nts_long": "///g/1003,///g/1004,///g/1005,///g/1006,///g/1023,///g/1024,///g/1025,///g/1026,///g/1027,///g/1034,///g/1035,///g/1036,///g/1037", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/1004,///g/1005" }, { "index": 2, "num_nts": 3, "nts_short": "GUG", "nts_long": "///g/1024,///g/1025,///g/1026" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/1035,///g/1036" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 0, 7, 1 ], "stem_indices": [ 50, -10, 53 ], "summary": "[3] 0 7 1 [g.672 g.734 g.673 g.717 g.725 g.732] 7 1 2", "num_nts": 14, "nts_short": "UAUACCGGUGGCGG", "nts_long": "///g/672,///g/673,///g/717,///g/718,///g/719,///g/720,///g/721,///g/722,///g/723,///g/724,///g/725,///g/732,///g/733,///g/734", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 7, "nts_short": "ACCGGUG", "nts_long": "///g/718,///g/719,///g/720,///g/721,///g/722,///g/723,///g/724" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///g/733" } ] }, { "index": 9, "type": "3-way junction", "bridging_nts": [ 2, 3, 5 ], "stem_indices": [ 57, 58, 59 ], "summary": "[3] 2 3 5 [g.826 g.874 g.829 g.857 g.861 g.868] 6 12 2", "num_nts": 16, "nts_short": "CUUGCGGAGCGUUAAG", "nts_long": "///g/826,///g/827,///g/828,///g/829,///g/857,///g/858,///g/859,///g/860,///g/861,///g/868,///g/869,///g/870,///g/871,///g/872,///g/873,///g/874", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///g/827,///g/828" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///g/858,///g/859,///g/860" }, { "index": 3, "num_nts": 5, "nts_short": "GUUAA", "nts_long": "///g/869,///g/870,///g/871,///g/872,///g/873" } ] }, { "index": 10, "type": "3-way junction", "bridging_nts": [ 3, 6, 2 ], "stem_indices": [ -18, 86, -19 ], "summary": "[3] 3 6 2 [g.1237 g.1337 g.1241 g.1296 g.1303 g.1334] 1 7 1", "num_nts": 17, "nts_short": "CAAUGCGUAGUCCGUCG", "nts_long": "///g/1237,///g/1238,///g/1239,///g/1240,///g/1241,///g/1296,///g/1297,///g/1298,///g/1299,///g/1300,///g/1301,///g/1302,///g/1303,///g/1334,///g/1335,///g/1336,///g/1337", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAU", "nts_long": "///g/1238,///g/1239,///g/1240" }, { "index": 2, "num_nts": 6, "nts_short": "GUAGUC", "nts_long": "///g/1297,///g/1298,///g/1299,///g/1300,///g/1301,///g/1302" }, { "index": 3, "num_nts": 2, "nts_short": "UC", "nts_long": "///g/1335,///g/1336" } ] }, { "index": 11, "type": "3-way junction", "bridging_nts": [ 2, 5, 6 ], "stem_indices": [ 65, 66, 91 ], "summary": "[3] 2 5 6 [g.936 g.1379 g.939 g.1344 g.1350 g.1372] 2 5 7", "num_nts": 19, "nts_short": "CAAGCUAGUAAUGAAUACG", "nts_long": "///g/936,///g/937,///g/938,///g/939,///g/1344,///g/1345,///g/1346,///g/1347,///g/1348,///g/1349,///g/1350,///g/1372,///g/1373,///g/1374,///g/1375,///g/1376,///g/1377,///g/1378,///g/1379", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/937,///g/938" }, { "index": 2, "num_nts": 5, "nts_short": "UAGUA", "nts_long": "///g/1345,///g/1346,///g/1347,///g/1348,///g/1349" }, { "index": 3, "num_nts": 6, "nts_short": "GAAUAC", "nts_long": "///g/1373,///g/1374,///g/1375,///g/1376,///g/1377,///g/1378" } ] }, { "index": 12, "type": "3-way junction", "bridging_nts": [ 4, 5, 5 ], "stem_indices": [ -15, 79, 82 ], "summary": "[3] 4 5 5 [g.1063 g.1193 g.1068 g.1107 g.1113 g.1187] 1 6 4", "num_nts": 20, "nts_short": "CGUCAGCGCAACCGAUGACG", "nts_long": "///g/1063,///g/1064,///g/1065,///g/1066,///g/1067,///g/1068,///g/1107,///g/1108,///g/1109,///g/1110,///g/1111,///g/1112,///g/1113,///g/1187,///g/1188,///g/1189,///g/1190,///g/1191,///g/1192,///g/1193", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUCA", "nts_long": "///g/1064,///g/1065,///g/1066,///g/1067" }, { "index": 2, "num_nts": 5, "nts_short": "GCAAC", "nts_long": "///g/1108,///g/1109,///g/1110,///g/1111,///g/1112" }, { "index": 3, "num_nts": 5, "nts_short": "AUGAC", "nts_long": "///g/1188,///g/1189,///g/1190,///g/1191,///g/1192" } ] }, { "index": 13, "type": "3-way junction", "bridging_nts": [ 6, 10, 3 ], "stem_indices": [ 68, 69, 70 ], "summary": "[3] 6 10 3 [g.955 g.1225 g.962 g.973 g.984 g.1221] 2 2 7", "num_nts": 25, "nts_short": "UUUAAUUCGAAGAACCUUACGGCUA", "nts_long": "///g/955,///g/956,///g/957,///g/958,///g/959,///g/960,///g/961,///g/962,///g/973,///g/974,///g/975,///g/976,///g/977,///g/978,///g/979,///g/980,///g/981,///g/982,///g/983,///g/984,///g/1221,///g/1222,///g/1223,///g/1224,///g/1225", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUAAUU", "nts_long": "///g/956,///g/957,///g/958,///g/959,///g/960,///g/961" }, { "index": 2, "num_nts": 10, "nts_short": "AAGAACCUUA", "nts_long": "///g/974,///g/975,///g/976,///g/977,///g/978,///g/979,///g/980,///g/981,///g/982,///g/983" }, { "index": 3, "num_nts": 3, "nts_short": "GCU", "nts_long": "///g/1222,///g/1223,///g/1224" } ] }, { "index": 14, "type": "4-way junction", "bridging_nts": [ 6, 0, 2, 0 ], "stem_indices": [ 14, 15, 23, 26 ], "summary": "[4] 6 0 2 0 [g.115 g.312 g.122 g.239 g.240 g.286 g.289 g.311] 3 7 3 4", "num_nts": 16, "nts_short": "GAGUAAUGUGCUAGCC", "nts_long": "///g/115,///g/116,///g/117,///g/118,///g/119,///g/120,///g/121,///g/122,///g/239,///g/240,///g/286,///g/287,///g/288,///g/289,///g/311,///g/312", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AGUAAU", "nts_long": "///g/116,///g/117,///g/118,///g/119,///g/120,///g/121" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "UA", "nts_long": "///g/287,///g/288" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 15, "type": "4-way junction", "bridging_nts": [ 2, 1, 5, 0 ], "stem_indices": [ 100, 101, 102, 104 ], "summary": "[4] 2 1 5 0 [v.7 v.67 v.10 v.26 v.28 v.44 v.50 v.66] 4 4 5 5", "num_nts": 16, "nts_short": "GUGGCGUAAGAUCGCC", "nts_long": "///v/7,///v/8,///v/9,///v/10,///v/26,///v/27,///v/28,///v/44,///v/45,///v/46,///v/47,///v/48,///v/49,///v/50,///v/66,///v/67", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UG", "nts_long": "///v/8,///v/9" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///v/27" }, { "index": 3, "num_nts": 5, "nts_short": "AGAUC", "nts_long": "///v/45,///v/46,///v/47,///v/48,///v/49" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 16, "type": "4-way junction", "bridging_nts": [ 1, 5, 4, 1 ], "stem_indices": [ 17, -3, 20, 21 ], "summary": "[4] 1 5 4 1 [g.142 g.221 g.144 g.178 g.184 g.193 g.198 g.219] 7 1 3 6", "num_nts": 19, "nts_short": "GAGCAUAACGCCAAAGUGC", "nts_long": "///g/142,///g/143,///g/144,///g/178,///g/179,///g/180,///g/181,///g/182,///g/183,///g/184,///g/193,///g/194,///g/195,///g/196,///g/197,///g/198,///g/219,///g/220,///g/221", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///g/143" }, { "index": 2, "num_nts": 5, "nts_short": "AUAAC", "nts_long": "///g/179,///g/180,///g/181,///g/182,///g/183" }, { "index": 3, "num_nts": 4, "nts_short": "CAAA", "nts_long": "///g/194,///g/195,///g/196,///g/197" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///g/220" } ] }, { "index": 17, "type": "4-way junction", "bridging_nts": [ 1, 4, 10, 0 ], "stem_indices": [ -8, 42, 54, 57 ], "summary": "[4] 1 4 10 0 [g.575 g.880 g.577 g.764 g.769 g.810 g.821 g.879] 1 4 6 6", "num_nts": 23, "nts_short": "GCGCGAAAGCCGUAAACGAUGCC", "nts_long": "///g/575,///g/576,///g/577,///g/764,///g/765,///g/766,///g/767,///g/768,///g/769,///g/810,///g/811,///g/812,///g/813,///g/814,///g/815,///g/816,///g/817,///g/818,///g/819,///g/820,///g/821,///g/879,///g/880", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///g/576" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///g/765,///g/766,///g/767,///g/768" }, { "index": 3, "num_nts": 10, "nts_short": "CGUAAACGAU", "nts_long": "///g/811,///g/812,///g/813,///g/814,///g/815,///g/816,///g/817,///g/818,///g/819,///g/820" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 18, "type": "5-way junction", "bridging_nts": [ 0, 0, 1, 3, 0 ], "stem_indices": [ 36, 37, 39, 37, 38 ], "summary": "[5] 0 0 1 3 0 [g.504 g.541 g.505 g.526 g.527 g.522 g.524 g.507 g.511 g.540] 5 3 2 3 5", "is_repeated": true, "num_nts": 14, "nts_short": "CGCGCAGCUAACGG", "nts_long": "///g/504,///g/505,///g/526,///g/527,///g/522,///g/523,///g/524,///g/507,///g/508,///g/509,///g/510,///g/511,///g/540,///g/541", "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": "A", "nts_long": "///g/523" }, { "index": 4, "num_nts": 3, "nts_short": "UAA", "nts_long": "///g/508,///g/509,///g/510" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 19, "type": "5-way junction", "bridging_nts": [ 0, 0, 2, 3, 0 ], "stem_indices": [ 40, 41, 59, 41, -8 ], "summary": "[5] 0 0 2 3 0 [g.569 g.881 g.570 g.866 g.867 g.862 g.865 g.571 g.575 g.880] 3 2 2 2 1", "is_repeated": true, "num_nts": 15, "nts_short": "CGCGCUAAUAAAGCG", "nts_long": "///g/569,///g/570,///g/866,///g/867,///g/862,///g/863,///g/864,///g/865,///g/571,///g/572,///g/573,///g/574,///g/575,///g/880,///g/881", "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": 2, "nts_short": "UA", "nts_long": "///g/863,///g/864" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///g/572,///g/573,///g/574" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 20, "type": "5-way junction", "bridging_nts": [ 2, 2, 3, 2, 2 ], "stem_indices": [ 4, 5, 32, -6, 36 ], "summary": "[5] 2 2 3 2 2 [g.36 g.548 g.39 g.403 g.406 g.436 g.440 g.497 g.500 g.545] 5 6 4 1 5", "num_nts": 21, "nts_short": "CUGGCGUGCUUUCGAAGCAAG", "nts_long": "///g/36,///g/37,///g/38,///g/39,///g/403,///g/404,///g/405,///g/406,///g/436,///g/437,///g/438,///g/439,///g/440,///g/497,///g/498,///g/499,///g/500,///g/545,///g/546,///g/547,///g/548", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UG", "nts_long": "///g/37,///g/38" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///g/404,///g/405" }, { "index": 3, "num_nts": 3, "nts_short": "UUU", "nts_long": "///g/437,///g/438,///g/439" }, { "index": 4, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/498,///g/499" }, { "index": 5, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/546,///g/547" } ] }, { "index": 21, "type": "5-way junction", "bridging_nts": [ 2, 6, 1, 1, 3 ], "stem_indices": [ 8, 9, 14, 28, 29 ], "summary": "[5] 2 6 1 1 3 [g.58 g.354 g.61 g.106 g.113 g.314 g.316 g.337 g.339 g.350] 3 3 3 5 4", "num_nts": 23, "nts_short": "CAAGCGGACGGGCACGACGGCAG", "nts_long": "///g/58,///g/59,///g/60,///g/61,///g/106,///g/107,///g/108,///g/109,///g/110,///g/111,///g/112,///g/113,///g/314,///g/315,///g/316,///g/337,///g/338,///g/339,///g/350,///g/351,///g/352,///g/353,///g/354", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///g/59,///g/60" }, { "index": 2, "num_nts": 6, "nts_short": "GGACGG", "nts_long": "///g/107,///g/108,///g/109,///g/110,///g/111,///g/112" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///g/315" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///g/338" }, { "index": 5, "num_nts": 3, "nts_short": "GCA", "nts_long": "///g/351,///g/352,///g/353" } ] } ], "num_ssSegments": 11, "ssSegments": [ { "index": 1, "num_nts": 7, "nts_short": "AAUUGAA", "nts_long": "///g/2,///g/3,///g/4,///g/5,///g/6,///g/7,///g/8" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///g/26" }, { "index": 3, "num_nts": 10, "nts_short": "GGAAUUACUG", "nts_long": "///g/557,///g/558,///g/559,///g/560,///g/561,///g/562,///g/563,///g/564,///g/565,///g/566" }, { "index": 4, "num_nts": 1, "nts_short": "U", "nts_long": "///g/884" }, { "index": 5, "num_nts": 3, "nts_short": "AAA", "nts_long": "///g/913,///g/914,///g/915" }, { "index": 6, "num_nts": 2, "nts_short": "CA", "nts_long": "///g/1397,///g/1398" }, { "index": 7, "num_nts": 2, "nts_short": "GU", "nts_long": "///g/1505,///g/1506" }, { "index": 8, "num_nts": 11, "nts_short": "GAUCACCUCCU", "nts_long": "///g/1530,///g/1531,///g/1532,///g/1533,///g/1534,///g/1535,///g/1536,///g/1537,///g/1538,///g/1539,///g/1540" }, { "index": 9, "num_nts": 3, "nts_short": "CGC", "nts_long": "///v/1,///v/2,///v/3" }, { "index": 10, "num_nts": 7, "nts_short": "GCAACCA", "nts_long": "///v/71,///v/72,///v/73,///v/74,///v/75,///v/76,///v/77" }, { "index": 11, "num_nts": 3, "nts_short": "AAU", "nts_long": "///N/13,///N/14,///N/15" } ], "num_Aminors": 67, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/51 vs ///g/113,///g/314", "A_nt1": { "desc": "///g/51 vs ///g/113", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/51 vs ///g/314", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.48]" } }, { "index": 2, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///g/51 vs ///g/114,///g/313", "A_nt1": { "desc": "///g/51 vs ///g/114", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N7-O2'(hydroxyl)[3.03],N6(amino)-O2'(hydroxyl)[3.05],N6(amino)-O2(carbonyl)[3.16]" }, "A_nt2": { "desc": "///g/51 vs ///g/313", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 3, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/55 vs ///g/54,///g/357", "A_nt1": { "desc": "///g/55 vs ///g/54", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O5'-O2'(hydroxyl)[3.04]" }, "A_nt2": { "desc": "///g/55 vs ///g/357", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[3.00],N6(amino)-N3[3.16]" } }, { "index": 4, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/71 vs ///g/69,///g/99", "A_nt1": { "desc": "///g/71 vs ///g/69", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/71 vs ///g/99", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.91],N1-O2'(hydroxyl)[3.19]" } }, { "index": 5, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///g/72 vs ///g/70,///g/98", "A_nt1": { "desc": "///g/72 vs ///g/70", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/72 vs ///g/98", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.89],N6(amino)-N3[2.93]" } }, { "index": 6, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///g/116 vs ///g/114,///g/313", "A_nt1": { "desc": "///g/116 vs ///g/114", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/116 vs ///g/313", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.08],N6(amino)-N3[3.39]" } }, { "index": 7, "type": "X", "desc_short": "A vs G-U (Wobble)", "desc_long": "///g/120 vs ///g/122,///g/239", "A_nt1": { "desc": "///g/120 vs ///g/122", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N7[3.51]" }, "A_nt2": { "desc": "///g/120 vs ///g/239", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 8, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/151 vs ///g/67,///g/102", "A_nt1": { "desc": "///g/151 vs ///g/67", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/151 vs ///g/102", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.31]" } }, { "index": 9, "type": "X", "desc_short": "A vs G-A (Imino)", "desc_long": "///g/152 vs ///g/68,///g/101", "A_nt1": { "desc": "///g/152 vs ///g/68", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-N2(amino)[3.29],N3-N2(amino)[2.92]" }, "A_nt2": { "desc": "///g/152 vs ///g/101", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 10, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/160 vs ///g/342,///g/347", "A_nt1": { "desc": "///g/160 vs ///g/342", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/160 vs ///g/347", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.07],N1-N2(amino)[2.90]" } }, { "index": 11, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/161 vs ///g/342,///g/347", "A_nt1": { "desc": "///g/161 vs ///g/342", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/161 vs ///g/347", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.59]" } }, { "index": 12, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///g/171 vs ///g/66,///g/103", "A_nt1": { "desc": "///g/171 vs ///g/66", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/171 vs ///g/103", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.56]" } }, { "index": 13, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///g/172 vs ///g/66,///g/103", "A_nt1": { "desc": "///g/172 vs ///g/66", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.47]" }, "A_nt2": { "desc": "///g/172 vs ///g/103", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 14, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/196 vs ///g/142,///g/221", "A_nt1": { "desc": "///g/196 vs ///g/142", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.27],N3-N2(amino)[3.34]" }, "A_nt2": { "desc": "///g/196 vs ///g/221", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 15, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/205 vs ///g/203,///g/214", "A_nt1": { "desc": "///g/205 vs ///g/203", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/205 vs ///g/214", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.86]" } }, { "index": 16, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/282 vs ///g/247,///g/277", "A_nt1": { "desc": "///g/282 vs ///g/247", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.39],N3-N2(amino)[3.12]" }, "A_nt2": { "desc": "///g/282 vs ///g/277", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.32]" } }, { "index": 17, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/353 vs ///g/113,///g/314", "A_nt1": { "desc": "///g/353 vs ///g/113", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O3'-O2'(hydroxyl)[3.53],O2'(hydroxyl)-N2(amino)[2.84]" }, "A_nt2": { "desc": "///g/353 vs ///g/314", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.33]" } }, { "index": 18, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/373 vs ///g/370,///g/391", "A_nt1": { "desc": "///g/373 vs ///g/370", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/373 vs ///g/391", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.85],N1-O2'(hydroxyl)[3.27]" } }, { "index": 19, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///g/374 vs ///g/371,///g/390", "A_nt1": { "desc": "///g/374 vs ///g/371", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/374 vs ///g/390", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.77]" } }, { "index": 20, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/465 vs ///g/202,///g/215", "A_nt1": { "desc": "///g/465 vs ///g/202", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/465 vs ///g/215", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.82]" } }, { "index": 21, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/465 vs ///g/203,///g/214", "A_nt1": { "desc": "///g/465 vs ///g/203", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.89],N1-O2'(hydroxyl)[2.78]" }, "A_nt2": { "desc": "///g/465 vs ///g/214", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 22, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/466 vs ///g/202,///g/215", "A_nt1": { "desc": "///g/466 vs ///g/202", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)*N2(amino)[3.21],N1-N2(amino)[3.34]" }, "A_nt2": { "desc": "///g/466 vs ///g/215", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 23, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/482 vs ///g/370,///g/391", "A_nt1": { "desc": "///g/482 vs ///g/370", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.21]" }, "A_nt2": { "desc": "///g/482 vs ///g/391", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.06]" } }, { "index": 24, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///g/509 vs ///g/502,///g/543", "A_nt1": { "desc": "///g/509 vs ///g/502", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/509 vs ///g/543", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.58]" } }, { "index": 25, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/510 vs ///g/503,///g/542", "A_nt1": { "desc": "///g/510 vs ///g/503", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.88]" }, "A_nt2": { "desc": "///g/510 vs ///g/542", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.86],N3-N2(amino)[3.19]" } }, { "index": 26, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/535 vs ///g/522,///g/527", "A_nt1": { "desc": "///g/535 vs ///g/522", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/535 vs ///g/527", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.22],N1-O2'(hydroxyl)[2.81],N3-N2(amino)[3.57]" } }, { "index": 27, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///g/572 vs ///g/19,///g/916", "A_nt1": { "desc": "///g/572 vs ///g/19", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.38]" }, "A_nt2": { "desc": "///g/572 vs ///g/916", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.94]" } }, { "index": 28, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/574 vs ///g/568,///g/882", "A_nt1": { "desc": "///g/574 vs ///g/568", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.05],N3-N2(amino)[3.35]" }, "A_nt2": { "desc": "///g/574 vs ///g/882", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.88]" } }, { "index": 29, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///g/607 vs ///g/291,///g/309", "A_nt1": { "desc": "///g/607 vs ///g/291", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/607 vs ///g/309", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.06],N6(amino)-N3[3.16],N1-O2'(hydroxyl)[2.98]" } }, { "index": 30, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/608 vs ///g/292,///g/308", "A_nt1": { "desc": "///g/608 vs ///g/292", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.26],N6(amino)-N3[2.93],N1-N2(amino)[3.12]" }, "A_nt2": { "desc": "///g/608 vs ///g/308", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 31, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/622 vs ///g/42,///g/400", "A_nt1": { "desc": "///g/622 vs ///g/42", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.25],N3-N2(amino)[3.44]" }, "A_nt2": { "desc": "///g/622 vs ///g/400", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 32, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///g/642 vs ///g/598,///g/640", "A_nt1": { "desc": "///g/642 vs ///g/598", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.98]" }, "A_nt2": { "desc": "///g/642 vs ///g/640", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 33, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/695 vs ///g/786,///g/796", "A_nt1": { "desc": "///g/695 vs ///g/786", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.11]" }, "A_nt2": { "desc": "///g/695 vs ///g/796", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 34, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/696 vs ///g/785,///g/797", "A_nt1": { "desc": "///g/696 vs ///g/785", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/696 vs ///g/797", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.28],N1-O2'(hydroxyl)[3.31]" } }, { "index": 35, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/704 vs ///g/688,///g/699", "A_nt1": { "desc": "///g/704 vs ///g/688", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.40],N3-N2(amino)[3.08]" }, "A_nt2": { "desc": "///g/704 vs ///g/699", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 36, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///g/728 vs ///g/578,///g/763", "A_nt1": { "desc": "///g/728 vs ///g/578", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.08],N3-O2'(hydroxyl)[3.10]" }, "A_nt2": { "desc": "///g/728 vs ///g/763", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 37, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/729 vs ///g/577,///g/764", "A_nt1": { "desc": "///g/729 vs ///g/577", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.58]" }, "A_nt2": { "desc": "///g/729 vs ///g/764", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 38, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/767 vs ///g/1511,///g/1524", "A_nt1": { "desc": "///g/767 vs ///g/1511", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.18]" }, "A_nt2": { "desc": "///g/767 vs ///g/1524", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.77],O2'(hydroxyl)-O2(carbonyl)[3.17]" } }, { "index": 39, "type": "X", "desc_short": "A vs A-G (Imino)", "desc_long": "///g/777 vs ///g/676,///g/714", "A_nt1": { "desc": "///g/777 vs ///g/676", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/777 vs ///g/714", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.92]" } }, { "index": 40, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/864 vs ///g/18,///g/917", "A_nt1": { "desc": "///g/864 vs ///g/18", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.45]" }, "A_nt2": { "desc": "///g/864 vs ///g/917", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.56],N3-N2(amino)[3.12]" } }, { "index": 41, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/873 vs ///g/862,///g/867", "A_nt1": { "desc": "///g/873 vs ///g/862", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/873 vs ///g/867", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.21],N1-O2'(hydroxyl)[2.78]" } }, { "index": 42, "type": "X", "desc_short": "A vs A-C (--)", "desc_long": "///g/901 vs ///g/768,///g/811", "A_nt1": { "desc": "///g/901 vs ///g/768", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/901 vs ///g/811", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.84]" } }, { "index": 43, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/914 vs ///g/885,///g/912", "A_nt1": { "desc": "///g/914 vs ///g/885", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.21],N3-N2(amino)[3.39]" }, "A_nt2": { "desc": "///g/914 vs ///g/912", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 44, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///g/958 vs ///g/985,///g/1220", "A_nt1": { "desc": "///g/958 vs ///g/985", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.98]" }, "A_nt2": { "desc": "///g/958 vs ///g/1220", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 45, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/959 vs ///g/984,///g/1221", "A_nt1": { "desc": "///g/959 vs ///g/984", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.80]" }, "A_nt2": { "desc": "///g/959 vs ///g/1221", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.03],N3-N2(amino)[2.99]" } }, { "index": 46, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1014 vs ///g/987,///g/1218", "A_nt1": { "desc": "///g/1014 vs ///g/987", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.23]" }, "A_nt2": { "desc": "///g/1014 vs ///g/1218", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 47, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1016 vs ///g/988,///g/1217", "A_nt1": { "desc": "///g/1016 vs ///g/988", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.29]" }, "A_nt2": { "desc": "///g/1016 vs ///g/1217", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.03]" } }, { "index": 48, "type": "X", "desc_short": "A vs A-A (--)", "desc_long": "///g/1080 vs ///g/16,///g/919", "A_nt1": { "desc": "///g/1080 vs ///g/16", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N3[3.16]" }, "A_nt2": { "desc": "///g/1080 vs ///g/919", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.79]" } }, { "index": 49, "type": "I", "desc_short": "A vs G-U (Wobble)", "desc_long": "///g/1101 vs ///g/1074,///g/1083", "A_nt1": { "desc": "///g/1101 vs ///g/1074", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.12],N3-N2(amino)[3.06]" }, "A_nt2": { "desc": "///g/1101 vs ///g/1083", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 50, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1169 vs ///g/1088,///g/1097", "A_nt1": { "desc": "///g/1169 vs ///g/1088", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1169 vs ///g/1097", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.87],N3-O2'(hydroxyl)[3.18]" } }, { "index": 51, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1170 vs ///g/1089,///g/1096", "A_nt1": { "desc": "///g/1170 vs ///g/1089", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.15]" }, "A_nt2": { "desc": "///g/1170 vs ///g/1096", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.86],O2'(hydroxyl)-O2(carbonyl)[2.90]" } }, { "index": 52, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1191 vs ///g/1068,///g/1107", "A_nt1": { "desc": "///g/1191 vs ///g/1068", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.20],N3-N2(amino)[3.06]" }, "A_nt2": { "desc": "///g/1191 vs ///g/1107", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.08]" } }, { "index": 53, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1227 vs ///g/954,///g/1226", "A_nt1": { "desc": "///g/1227 vs ///g/954", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.99]" }, "A_nt2": { "desc": "///g/1227 vs ///g/1226", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1*O2(carbonyl)[3.35]" } }, { "index": 54, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1238 vs ///g/1241,///g/1296", "A_nt1": { "desc": "///g/1238 vs ///g/1241", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1-N2(amino)[3.23],N3-O2'(hydroxyl)[2.86]" }, "A_nt2": { "desc": "///g/1238 vs ///g/1296", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 55, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1269 vs ///g/1312,///g/1325", "A_nt1": { "desc": "///g/1269 vs ///g/1312", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.19],N3-N2(amino)[3.24]" }, "A_nt2": { "desc": "///g/1269 vs ///g/1325", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.96]" } }, { "index": 56, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1280 vs ///g/1124,///g/1149", "A_nt1": { "desc": "///g/1280 vs ///g/1124", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1280 vs ///g/1149", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.88],N1-O2'(hydroxyl)[3.40]" } }, { "index": 57, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///g/1288 vs ///g/1351,///g/1371", "A_nt1": { "desc": "///g/1288 vs ///g/1351", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1288 vs ///g/1371", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.00]" } }, { "index": 58, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/1288 vs ///g/1352,///g/1370", "A_nt1": { "desc": "///g/1288 vs ///g/1352", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.39]" }, "A_nt2": { "desc": "///g/1288 vs ///g/1370", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 59, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///g/1319 vs ///g/1314,///g/1323", "A_nt1": { "desc": "///g/1319 vs ///g/1314", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1319 vs ///g/1323", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O6(carbonyl)[3.30]" } }, { "index": 60, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///g/1333 vs ///g/946,///g/1235", "A_nt1": { "desc": "///g/1333 vs ///g/946", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.01],N3-O2'(hydroxyl)[3.22]" }, "A_nt2": { "desc": "///g/1333 vs ///g/1235", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 61, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1339 vs ///v/31,///v/41", "A_nt1": { "desc": "///g/1339 vs ///v/31", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1339 vs ///v/41", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.21]" } }, { "index": 62, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1433 vs ///g/318,///g/335", "A_nt1": { "desc": "///g/1433 vs ///g/318", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1433 vs ///g/335", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.24]" } }, { "index": 63, "type": "X", "desc_short": "A vs G-A (Imino)", "desc_long": "///g/1446 vs ///g/148,///g/174", "A_nt1": { "desc": "///g/1446 vs ///g/148", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.75],N1-N2(amino)[3.07],N3-O2'(hydroxyl)[2.79]" }, "A_nt2": { "desc": "///g/1446 vs ///g/174", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 64, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///g/1447 vs ///g/147,///g/175", "A_nt1": { "desc": "///g/1447 vs ///g/147", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1447 vs ///g/175", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.09]" } }, { "index": 65, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/1502 vs ///g/924,///g/1392", "A_nt1": { "desc": "///g/1502 vs ///g/924", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.03]" }, "A_nt2": { "desc": "///g/1502 vs ///g/1392", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 66, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/1518 vs ///g/1404,///g/1497", "A_nt1": { "desc": "///g/1518 vs ///g/1404", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///g/1518 vs ///g/1497", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.18]" } }, { "index": 67, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///g/1519 vs ///g/1404,///g/1497", "A_nt1": { "desc": "///g/1519 vs ///g/1404", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.20]" }, "A_nt2": { "desc": "///g/1519 vs ///g/1497", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.31],N3-N2(amino)[3.00]" } } ], "num_riboseZippers": 11, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "AUGA", "nts_long": "///g/16,///g/17,///g/1079,///g/1080" }, { "index": 2, "num_nts": 4, "nts_short": "ACAA", "nts_long": "///g/66,///g/67,///g/171,///g/172" }, { "index": 3, "num_nts": 4, "nts_short": "AAGU", "nts_long": "///g/509,///g/510,///g/542,///g/543" }, { "index": 4, "num_nts": 4, "nts_short": "AUGG", "nts_long": "///g/696,///g/697,///g/785,///g/786" }, { "index": 5, "num_nts": 4, "nts_short": "AGAU", "nts_long": "///g/938,///g/939,///g/1375,///g/1376" }, { "index": 6, "num_nts": 4, "nts_short": "AACC", "nts_long": "///g/958,///g/959,///g/984,///g/985" }, { "index": 7, "num_nts": 4, "nts_short": "GACC", "nts_long": "///g/1015,///g/1016,///g/1217,///g/1218" }, { "index": 8, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///g/1096,///g/1097,///g/1169,///g/1170" }, { "index": 9, "num_nts": 4, "nts_short": "GACU", "nts_long": "///g/1268,///g/1269,///g/1325,///g/1326" }, { "index": 10, "num_nts": 4, "nts_short": "GACC", "nts_long": "///g/1338,///g/1339,///v/41,///v/42" }, { "index": 11, "num_nts": 6, "nts_short": "CGUGAA", "nts_long": "///g/1404,///g/1405,///g/1406,///g/1517,///g/1518,///g/1519" } ], "num_Kturns": 3, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 30, "bounding_stems": [ 52, 51 ], "Cstem_index": 52, "NCstem_index": 51, "Cstem_pair": "C-G (///g/699,///g/688) WC", "NCstem_pair": "A-U (///g/706,///g/684) WC", "GA_pair": "G-A (///g/703,///g/687) Sheared", "bending_angle": 53.121, "strand1": { "num_nts": 15, "nts_short": "GCGUAGAGAUCUGGA", "nts_long": "///g/698,///g/699,///g/700,///g/701,///g/702,///g/703,///g/704,///g/705,///g/706,///g/707,///g/708,///g/709,///g/710,///g/711,///g/712" }, "strand2": { "num_nts": 12, "nts_short": "UCCAGGUGUAGC", "nts_long": "///g/678,///g/679,///g/680,///g/681,///g/682,///g/683,///g/684,///g/685,///g/686,///g/687,///g/688,///g/689" } }, { "index": 2, "type": "Normal k-turn", "iloop_index": 32, "bounding_stems": [ 24, 23 ], "Cstem_index": 24, "NCstem_index": 23, "Cstem_pair": "C-G (///g/277,///g/247) WC", "NCstem_pair": "C-G (///g/284,///g/242) WC", "GA_pair": "G-A (///g/281,///g/246) Sheared", "bending_angle": 54.755, "strand1": { "num_nts": 12, "nts_short": "GGCGACGAUCCC", "nts_long": "///g/275,///g/276,///g/277,///g/278,///g/279,///g/280,///g/281,///g/282,///g/283,///g/284,///g/285,///g/286" }, "strand2": { "num_nts": 10, "nts_short": "GGGAUUAGCU", "nts_long": "///g/240,///g/241,///g/242,///g/243,///g/244,///g/245,///g/246,///g/247,///g/248,///g/249" } }, { "index": 3, "type": "Undecided case", "iloop_index": 37, "bounding_stems": [ 32, 33 ], "Cstem_index": 32, "NCstem_index": 33, "Cstem_pair": "U-G (///g/409,///g/433) Wobble", "NCstem_pair": "G-U (///g/416,///g/427) Wobble", "GA_pair": "G-A (///g/410,///g/432) Sheared", "bending_angle": 52.466, "strand1": { "num_nts": 14, "nts_short": "GUAUGAAGAAGGCC", "nts_long": "///g/406,///g/407,///g/408,///g/409,///g/410,///g/411,///g/412,///g/413,///g/414,///g/415,///g/416,///g/417,///g/418,///g/419" }, "strand2": { "num_nts": 13, "nts_short": "GGUUGUAAAGUAC", "nts_long": "///g/424,///g/425,///g/426,///g/427,///g/428,///g/429,///g/430,///g/431,///g/432,///g/433,///g/434,///g/435,///g/436" } } ], "num_splayUnits": 116, 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"donAcc_type": "standard", "distance": 2.837, "atom1_id": "///v/57/OP1", "atom2_id": "///v/58/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 6363, "atom1_serNum": 57215, "atom2_serNum": 57226, "donAcc_type": "acceptable", "distance": 2.700, "atom1_id": "///v/57/O2'", "atom2_id": "///v/58/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6364, "atom1_serNum": 57235, "atom2_serNum": 57250, "donAcc_type": "acceptable", "distance": 2.871, "atom1_id": "///v/58/O2'", "atom2_id": "///v/59/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6365, "atom1_serNum": 57257, "atom2_serNum": 57292, "donAcc_type": "acceptable", "distance": 2.681, "atom1_id": "///v/59/O2'", "atom2_id": "///v/61/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6366, "atom1_serNum": 57267, "atom2_serNum": 57279, "donAcc_type": "acceptable", "distance": 3.386, "atom1_id": "///v/59/N3", "atom2_id": "///v/60/O2'", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 6367, "atom1_serNum": 57279, "atom2_serNum": 57293, "donAcc_type": "acceptable", "distance": 2.652, "atom1_id": "///v/60/O2'", "atom2_id": "///v/61/OP2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6368, "atom1_serNum": 57301, "atom2_serNum": 57312, "donAcc_type": "acceptable", "distance": 2.666, "atom1_id": "///v/61/O2'", "atom2_id": "///v/62/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6369, "atom1_serNum": 57427, "atom2_serNum": 57443, "donAcc_type": "acceptable", "distance": 2.868, "atom1_id": "///v/67/O2'", "atom2_id": "///v/68/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6370, "atom1_serNum": 57447, "atom2_serNum": 57463, "donAcc_type": "acceptable", "distance": 2.901, "atom1_id": "///v/68/O2'", "atom2_id": "///v/69/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6371, "atom1_serNum": 57542, "atom2_serNum": 57579, "donAcc_type": "standard", "distance": 2.860, "atom1_id": "///v/73/OP2", "atom2_id": 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"distance": 3.174, "atom1_id": "///v/74/N3", "atom2_id": "///v/75/N4", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6377, "atom1_serNum": 57614, "atom2_serNum": 57626, "donAcc_type": "acceptable", "distance": 2.705, "atom1_id": "///v/76/O2'", "atom2_id": "///v/77/OP2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6378, "atom1_serNum": 57654, "atom2_serNum": 57667, "donAcc_type": "acceptable", "distance": 2.705, "atom1_id": "///N/13/O2'", "atom2_id": "///N/14/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6379, "atom1_serNum": 57676, "atom2_serNum": 57689, "donAcc_type": "acceptable", "distance": 2.651, "atom1_id": "///N/14/O2'", "atom2_id": "///N/15/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6380, "atom1_serNum": 57698, "atom2_serNum": 57710, "donAcc_type": "acceptable", "distance": 2.655, "atom1_id": "///N/15/O2'", "atom2_id": "///N/16/OP2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6381, "atom1_serNum": 57698, "atom2_serNum": 57722, "donAcc_type": "acceptable", "distance": 3.294, "atom1_id": "///N/15/O2'", "atom2_id": "///N/16/N7", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 6382, "atom1_serNum": 57718, "atom2_serNum": 57733, "donAcc_type": "acceptable", "distance": 2.992, "atom1_id": "///N/16/O2'", "atom2_id": "///N/17/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6383, "atom1_serNum": 57718, "atom2_serNum": 57736, "donAcc_type": "acceptable", "distance": 3.014, "atom1_id": "///N/16/O2'", "atom2_id": "///N/17/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6384, "atom1_serNum": 57740, "atom2_serNum": 57756, "donAcc_type": "acceptable", "distance": 2.910, "atom1_id": "///N/17/O2'", "atom2_id": "///N/18/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" } ], "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": "6o7k", "num_aaChains": 22, "aaChains": "1=55,2=51,3=85,5=71,P=80,f=509,h=206,j=218,k=150,l=205,m=151,n=100,o=127,p=129,q=117,r=98,s=114,t=123,u=88,w=96,y=82,z=79", "num_naChains": 3, "naChains": "N=6,g=1539,v=77", "num_atoms": 57748, "num_waters": 0, "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": 21, "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-Kturns.pdb", "desc": "an ensemble of kink-turn motifs" }, { "index": 16, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 17, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 18, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 19, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 20, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 21, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }