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132, "type": "sugar", "atom": "///1/1570/O4'", "nt": "///1/1569", "vert_dist": 3.399 }, { "index": 133, "type": "other", "atom": "///U/56/SD", "nt": "///1/1580", "vert_dist": 3.447 }, { "index": 134, "type": "sugar", "atom": "///1/1586/O2'", "nt": "///1/1587", "vert_dist": 3.394 }, { "index": 135, "type": "other", "atom": "///1/1599/P", "nt": "///1/1600", "vert_dist": 3.356 }, { "index": 136, "type": "phosphate", "atom": "///1/1599/OP1", "nt": "///1/1600", "vert_dist": 2.661 }, { "index": 137, "type": "sugar", "atom": "///1/1601/O2'", "nt": "///1/1602", "vert_dist": 2.975 }, { "index": 138, "type": "other", "atom": "///1/1619/P", "nt": "///1/1617", "vert_dist": 3.384 }, { "index": 139, "type": "phosphate", "atom": "///1/1619/OP2", "nt": "///1/1617", "vert_dist": 2.782 }, { "index": 140, "type": "phosphate", "atom": "///1/1619/O5'", "nt": "///1/1617", "vert_dist": 2.974 }, { "index": 141, "type": "phosphate", "atom": "///1/1624/O5'", "nt": "///1/1624", "vert_dist": 2.557 }, { "index": 142, "type": "phosphate", "atom": "///1/1638/OP2", "nt": "///1/1638", "vert_dist": 2.623 }, { "index": 143, "type": "sugar", "atom": "///1/1205/O2'", "nt": "///1/1700", "vert_dist": 2.864 }, { "index": 144, "type": "sugar", "atom": "///1/1722/O4'", "nt": "///1/1720", "vert_dist": 3.261 }, { "index": 145, "type": "sugar", "atom": "///1/1769/O4'", "nt": "///1/1768", "vert_dist": 3.042 }, { "index": 146, "type": "sugar", "atom": "///1/1206/O4'", "nt": "///1/1834", "vert_dist": 2.772 }, { "index": 147, "type": "phosphate", "atom": "///1/1208/OP2", "nt": "///1/1835", "vert_dist": 2.473 }, { "index": 148, "type": "sugar", "atom": "///1/1063/O2'", "nt": "///1/1838", "vert_dist": 2.962 }, { "index": 149, "type": "sugar", "atom": "///j/6036/O4'", "nt": "///j/6035", "vert_dist": 3.064 }, { "index": 150, "type": "phosphate", "atom": "///j/6074/OP1", "nt": "///j/6073", "vert_dist": 2.990 }, { "index": 151, "type": "sugar", "atom": "///j/6090/O4'", "nt": "///j/6089", "vert_dist": 3.210 }, { "index": 152, "type": "other", "atom": "///j/6098/P", "nt": "///j/6096", "vert_dist": 3.387 }, { "index": 153, "type": "phosphate", "atom": "///j/6098/OP1", "nt": "///j/6096", "vert_dist": 2.808 }, { "index": 154, "type": "phosphate", "atom": "///j/6098/OP2", "nt": "///j/6096", "vert_dist": 3.006 }, { "index": 155, "type": "sugar", "atom": "///j/6098/O4'", "nt": "///j/6097", "vert_dist": 3.202 }, { "index": 156, "type": "sugar", "atom": "///j/6101/O4'", "nt": "///j/6100", "vert_dist": 3.132 }, { "index": 157, "type": "phosphate", "atom": "///j/6113/OP2", "nt": "///j/6111", "vert_dist": 2.961 }, { "index": 158, "type": "sugar", "atom": "///j/6115/O4'", "nt": "///j/6114", "vert_dist": 3.168 }, { "index": 159, "type": "phosphate", "atom": "///j/6120/OP2", "nt": "///j/6118", "vert_dist": 3.016 }, { "index": 160, "type": "phosphate", "atom": "///j/6144/OP2", "nt": "///j/6142", "vert_dist": 2.969 }, { "index": 161, "type": "sugar", "atom": "///j/6158/O4'", "nt": "///j/6157", "vert_dist": 3.339 }, { "index": 162, "type": "phosphate", "atom": "///j/6164/O3'", "nt": "///j/6166", "vert_dist": 3.477 }, { "index": 163, "type": "sugar", "atom": "///j/6179/O4'", "nt": "///j/6178", "vert_dist": 3.446 }, { "index": 164, "type": "sugar", "atom": "///j/6182/O2'", "nt": "///j/6181", "vert_dist": 3.050 }, { "index": 165, "type": "phosphate", "atom": "///j/6188/OP2", "nt": "///j/6186", "vert_dist": 3.300 }, { "index": 166, "type": "sugar", "atom": "///j/6198/O4'", "nt": "///j/6197", "vert_dist": 3.463 }, { "index": 167, "type": "sugar", "atom": "///j/6202/O2'", "nt": "///j/6203", "vert_dist": 2.777 }, { "index": 168, "type": "sugar", "atom": "///j/6172/O2'", "nt": "///j/6205", "vert_dist": 2.874 }, { "index": 169, "type": "phosphate", "atom": "///j/6173/O3'", "nt": "///j/6207", "vert_dist": 2.976 }, { "index": 170, "type": "phosphate", "atom": "///1/1701/O3'", "nt": "///j/6216", "vert_dist": 3.426 } ], "num_hairpins": 38, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 1 ], "summary": "[1] 9 [1.7 1.17] 4", "num_nts": 11, "nts_short": "GUUGAUCCUGC", "nts_long": "///1/7,///1/8,///1/9,///1/10,///1/11,///1/12,///1/13,///1/14,///1/15,///1/16,///1/17", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UUGAUCCUG", "nts_long": "///1/8,///1/9,///1/10,///1/11,///1/12,///1/13,///1/14,///1/15,///1/16" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 21 ], "stem_indices": [ 8 ], "summary": "[1] 21 [1.63 1.85] 3", "num_nts": 23, "nts_short": "UACGCACGGCCGGUACAGUGAAA", "nts_long": "///1/63,///1/64,///1/65,///1/66,///1/67,///1/68,///1/69,///1/70,///1/71,///1/72,///1/73,///1/74,///1/75,///1/76,///1/77,///1/78,///1/79,///1/80,///1/81,///1/82,///1/83,///1/84,///1/85", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 21, "nts_short": "ACGCACGGCCGGUACAGUGAA", "nts_long": "///1/64,///1/65,///1/66,///1/67,///1/68,///1/69,///1/70,///1/71,///1/72,///1/73,///1/74,///1/75,///1/76,///1/77,///1/78,///1/79,///1/80,///1/81,///1/82,///1/83,///1/84" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 13 ], "summary": "[1] 5 [1.156 1.162] 3", "num_nts": 7, "nts_short": "GUAAUUC", "nts_long": "///1/156,///1/157,///1/158,///1/159,///1/160,///1/161,///1/162", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAAUU", "nts_long": "///1/157,///1/158,///1/159,///1/160,///1/161" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 16 ], "summary": "[1] 4 [1.197 1.202] 3", "num_nts": 6, "nts_short": "UUCGCG", "nts_long": "///1/197,///1/198,///1/199,///1/200,///1/201,///1/202", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UCGC", "nts_long": "///1/198,///1/199,///1/200,///1/201" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 21 ], "summary": "[1] 6 [1.322 1.329] 2", "num_nts": 8, "nts_short": "CCCCCGUG", "nts_long": "///1/322,///1/323,///1/324,///1/325,///1/326,///1/327,///1/328,///1/329", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CCCCGU", "nts_long": "///1/323,///1/324,///1/325,///1/326,///1/327,///1/328" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 24 ], "summary": "[1] 9 [1.377 1.387] 7", "num_nts": 11, "nts_short": "GUCGCCGUGCC", "nts_long": "///1/377,///1/378,///1/379,///1/380,///1/381,///1/382,///1/383,///1/384,///1/385,///1/386,///1/387", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UCGCCGUGC", "nts_long": "///1/378,///1/379,///1/380,///1/381,///1/382,///1/383,///1/384,///1/385,///1/386" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 26 ], "summary": "[1] 4 [1.416 1.421] 4", "num_nts": 6, "nts_short": "UCAGGG", "nts_long": "///1/416,///1/417,///1/418,///1/419,///1/420,///1/421", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAGG", "nts_long": "///1/417,///1/418,///1/419,///1/420" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 28 ], "summary": "[1] 10 [1.441 1.452] 3", "num_nts": 12, "nts_short": "CCUGAGAAACGG", "nts_long": "///1/441,///1/442,///1/443,///1/444,///1/445,///1/446,///1/447,///1/448,///1/449,///1/450,///1/451,///1/452", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "CUGAGAAACG", "nts_long": "///1/442,///1/443,///1/444,///1/445,///1/446,///1/447,///1/448,///1/449,///1/450,///1/451" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 29 ], "summary": "[1] 4 [1.462 1.467] 2", "num_nts": 6, "nts_short": "CCAAGG", "nts_long": "///1/462,///1/463,///1/464,///1/465,///1/466,///1/467", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAAG", "nts_long": "///1/463,///1/464,///1/465,///1/466" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 31 ], "summary": "[1] 5 [1.498 1.504] 3", "num_nts": 7, "nts_short": "CGACCCG", "nts_long": "///1/498,///1/499,///1/500,///1/501,///1/502,///1/503,///1/504", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GACCC", "nts_long": "///1/499,///1/500,///1/501,///1/502,///1/503" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 34 ], "summary": "[1] 4 [1.539 1.544] 2", "num_nts": 6, "nts_short": "CUUUCG", "nts_long": "///1/539,///1/540,///1/541,///1/542,///1/543,///1/544", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUUC", "nts_long": "///1/540,///1/541,///1/542,///1/543" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ -16 ], "summary": "[1] 11 [1.569 1.581] 1", "num_nts": 13, "nts_short": "ACUUUAAAUCCUU", "nts_long": "///1/569,///1/570,///1/571,///1/572,///1/573,///1/574,///1/575,///1/576,///1/577,///1/578,///1/579,///1/580,///1/581", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "CUUUAAAUCCU", "nts_long": "///1/570,///1/571,///1/572,///1/573,///1/574,///1/575,///1/576,///1/577,///1/578,///1/579,///1/580" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 19 ], "stem_indices": [ 36 ], "summary": "[1] 19 [1.601 1.621] 2", "num_nts": 21, "nts_short": "GGCAAGUCUGGUGCCAGCAGC", "nts_long": "///1/601,///1/602,///1/603,///1/604,///1/605,///1/606,///1/607,///1/608,///1/609,///1/610,///1/611,///1/612,///1/613,///1/614,///1/615,///1/616,///1/617,///1/618,///1/619,///1/620,///1/621", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 19, "nts_short": "GCAAGUCUGGUGCCAGCAG", "nts_long": "///1/602,///1/603,///1/604,///1/605,///1/606,///1/607,///1/608,///1/609,///1/610,///1/611,///1/612,///1/613,///1/614,///1/615,///1/616,///1/617,///1/618,///1/619,///1/620" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 38 ], "summary": "[1] 4 [1.618 1.623] 2", "num_nts": 6, "nts_short": "CAGCCG", "nts_long": "///1/618,///1/619,///1/620,///1/621,///1/622,///1/623", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGCC", "nts_long": "///1/619,///1/620,///1/621,///1/622" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ -23 ], "summary": "[1] 9 [1.819 1.829] 1", "num_nts": 11, "nts_short": "GUGUUCAAAGC", "nts_long": "///1/819,///1/820,///1/821,///1/822,///1/823,///1/824,///1/825,///1/826,///1/827,///1/828,///1/829", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UGUUCAAAG", "nts_long": "///1/820,///1/821,///1/822,///1/823,///1/824,///1/825,///1/826,///1/827,///1/828" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 48 ], "summary": "[1] 7 [1.833 1.841] 3", "num_nts": 9, "nts_short": "CCCGAGCCG", "nts_long": "///1/833,///1/834,///1/835,///1/836,///1/837,///1/838,///1/839,///1/840,///1/841", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CCGAGCC", "nts_long": "///1/834,///1/835,///1/836,///1/837,///1/838,///1/839,///1/840" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 17 ], "stem_indices": [ 49 ], "summary": "[1] 17 [1.884 1.902] 4", "num_nts": 19, "nts_short": "CUAUUUUGUUGGUUUUCGG", "nts_long": "///1/884,///1/885,///1/886,///1/887,///1/888,///1/889,///1/890,///1/891,///1/892,///1/893,///1/894,///1/895,///1/896,///1/897,///1/898,///1/899,///1/900,///1/901,///1/902", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 17, "nts_short": "UAUUUUGUUGGUUUUCG", "nts_long": "///1/885,///1/886,///1/887,///1/888,///1/889,///1/890,///1/891,///1/892,///1/893,///1/894,///1/895,///1/896,///1/897,///1/898,///1/899,///1/900,///1/901" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 55 ], "summary": "[1] 8 [1.957 1.966] 2", "num_nts": 10, "nts_short": "AGGUGAAAUU", "nts_long": "///1/957,///1/958,///1/959,///1/960,///1/961,///1/962,///1/963,///1/964,///1/965,///1/966", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GGUGAAAU", "nts_long": "///1/958,///1/959,///1/960,///1/961,///1/962,///1/963,///1/964,///1/965" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 56 ], "summary": "[1] 4 [1.994 1.999] 2", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///1/994,///1/995,///1/996,///1/997,///1/998,///1/999", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/995,///1/996,///1/997,///1/998" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ -30 ], "summary": "[1] 9 [1.1054 1.1064] 1", "num_nts": 11, "nts_short": "GAUCAGAUACC", "nts_long": "///1/1054,///1/1055,///1/1056,///1/1057,///1/1058,///1/1059,///1/1060,///1/1061,///1/1062,///1/1063,///1/1064", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AUCAGAUAC", "nts_long": "///1/1055,///1/1056,///1/1057,///1/1058,///1/1059,///1/1060,///1/1061,///1/1062,///1/1063" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 63 ], "summary": "[1] 10 [1.1111 1.1122] 2", "num_nts": 12, "nts_short": "UUAUUCCCAUGA", "nts_long": "///1/1111,///1/1112,///1/1113,///1/1114,///1/1115,///1/1116,///1/1117,///1/1118,///1/1119,///1/1120,///1/1121,///1/1122", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "UAUUCCCAUG", "nts_long": "///1/1112,///1/1113,///1/1114,///1/1115,///1/1116,///1/1117,///1/1118,///1/1119,///1/1120,///1/1121" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 64 ], "summary": "[1] 4 [1.1141 1.1146] 2", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///1/1141,///1/1142,///1/1143,///1/1144,///1/1145,///1/1146", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/1142,///1/1143,///1/1144,///1/1145" } ] }, { "index": 23, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 66 ], "summary": "[1] 4 [1.1178 1.1183] 4", "num_nts": 6, "nts_short": "UGCAAA", "nts_long": "///1/1178,///1/1179,///1/1180,///1/1181,///1/1182,///1/1183", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///1/1179,///1/1180,///1/1181,///1/1182" } ] }, { "index": 24, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ -35 ], "summary": "[1] 8 [1.1245 1.1254] 1", "num_nts": 10, "nts_short": "GACUCAACAC", "nts_long": "///1/1245,///1/1246,///1/1247,///1/1248,///1/1249,///1/1250,///1/1251,///1/1252,///1/1253,///1/1254", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "ACUCAACA", "nts_long": "///1/1246,///1/1247,///1/1248,///1/1249,///1/1250,///1/1251,///1/1252,///1/1253" } ] }, { "index": 25, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 78 ], "summary": "[1] 8 [1.1295 1.1304] 3", "num_nts": 10, "nts_short": "AUUGAUAGCU", "nts_long": "///1/1295,///1/1296,///1/1297,///1/1298,///1/1299,///1/1300,///1/1301,///1/1302,///1/1303,///1/1304", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UUGAUAGC", "nts_long": "///1/1296,///1/1297,///1/1298,///1/1299,///1/1300,///1/1301,///1/1302,///1/1303" } ] }, { "index": 26, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -38 ], "summary": "[1] 4 [1.1353 1.1358] 1", "num_nts": 6, "nts_short": "AGCGAU", "nts_long": "///1/1353,///1/1354,///1/1355,///1/1356,///1/1357,///1/1358", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCGA", "nts_long": "///1/1354,///1/1355,///1/1356,///1/1357" } ] }, { "index": 27, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 86 ], "summary": "[1] 6 [1.1366 1.1373] 2", "num_nts": 8, "nts_short": "GUUAAUUC", "nts_long": "///1/1366,///1/1367,///1/1368,///1/1369,///1/1370,///1/1371,///1/1372,///1/1373", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUAAUU", "nts_long": "///1/1367,///1/1368,///1/1369,///1/1370,///1/1371,///1/1372" } ] }, { "index": 28, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 91 ], "summary": "[1] 4 [1.1421 1.1426] 3", "num_nts": 6, "nts_short": "AGCGGU", "nts_long": "///1/1421,///1/1422,///1/1423,///1/1424,///1/1425,///1/1426", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCGG", "nts_long": "///1/1422,///1/1423,///1/1424,///1/1425" } ] }, { "index": 29, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 92 ], "summary": "[1] 7 [1.1459 1.1467] 4", "num_nts": 9, "nts_short": "GCGUUCAGC", "nts_long": "///1/1459,///1/1460,///1/1461,///1/1462,///1/1463,///1/1464,///1/1465,///1/1466,///1/1467", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CGUUCAG", "nts_long": "///1/1460,///1/1461,///1/1462,///1/1463,///1/1464,///1/1465,///1/1466" } ] }, { "index": 30, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 96 ], "summary": "[1] 4 [1.1565 1.1570] 2", "num_nts": 6, "nts_short": "CGGCAG", "nts_long": "///1/1565,///1/1566,///1/1567,///1/1568,///1/1569,///1/1570", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGCA", "nts_long": "///1/1566,///1/1567,///1/1568,///1/1569" } ] }, { "index": 31, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 97 ], "summary": "[1] 10 [1.1614 1.1625] 5", "num_nts": 12, "nts_short": "AUUGCAAUUAUU", "nts_long": "///1/1614,///1/1615,///1/1616,///1/1617,///1/1618,///1/1619,///1/1620,///1/1621,///1/1622,///1/1623,///1/1624,///1/1625", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "UUGCAAUUAU", "nts_long": "///1/1615,///1/1616,///1/1617,///1/1618,///1/1619,///1/1620,///1/1621,///1/1622,///1/1623,///1/1624" } ] }, { "index": 32, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -46 ], "summary": "[1] 7 [1.1658 1.1666] 1", "num_nts": 9, "nts_short": "GUCAUAAGC", "nts_long": "///1/1658,///1/1659,///1/1660,///1/1661,///1/1662,///1/1663,///1/1664,///1/1665,///1/1666", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UCAUAAG", "nts_long": "///1/1659,///1/1660,///1/1661,///1/1662,///1/1663,///1/1664,///1/1665" } ] }, { "index": 33, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 111 ], "summary": "[1] 5 [1.1763 1.1769] 2", "num_nts": 7, "nts_short": "GGCCCAC", "nts_long": "///1/1763,///1/1764,///1/1765,///1/1766,///1/1767,///1/1768,///1/1769", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GCCCA", "nts_long": "///1/1764,///1/1765,///1/1766,///1/1767,///1/1768" } ] }, { "index": 34, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 112 ], "summary": "[1] 4 [1.1847 1.1852] 9", "num_nts": 6, "nts_short": "GUGAAC", "nts_long": "///1/1847,///1/1848,///1/1849,///1/1850,///1/1851,///1/1852", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UGAA", "nts_long": "///1/1848,///1/1849,///1/1850,///1/1851" } ] }, { "index": 35, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 117 ], "summary": "[1] 4 [j.6110 j.6115] 2", "num_nts": 6, "nts_short": "UAUUUA", "nts_long": "///j/6110,///j/6111,///j/6112,///j/6113,///j/6114,///j/6115", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUUU", "nts_long": "///j/6111,///j/6112,///j/6113,///j/6114" } ] }, { "index": 36, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 120 ], "summary": "[1] 5 [j.6141 j.6147] 3", "num_nts": 7, "nts_short": "GCAGCCC", "nts_long": "///j/6141,///j/6142,///j/6143,///j/6144,///j/6145,///j/6146,///j/6147", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CAGCC", "nts_long": "///j/6142,///j/6143,///j/6144,///j/6145,///j/6146" } ] }, { "index": 37, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 122 ], "summary": "[1] 8 [j.6184 j.6193] 2", "num_nts": 10, "nts_short": "AUUAGGUAGU", "nts_long": "///j/6184,///j/6185,///j/6186,///j/6187,///j/6188,///j/6189,///j/6190,///j/6191,///j/6192,///j/6193", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UUAGGUAG", "nts_long": "///j/6185,///j/6186,///j/6187,///j/6188,///j/6189,///j/6190,///j/6191,///j/6192" } ] }, { "index": 38, "type": "hairpin loop", "bridging_nts": [ 22 ], "stem_indices": [ 123 ], "summary": "[1] 22 [j.6190 j.6213] 4", "num_nts": 24, "nts_short": "UAGUCGAAAAACCUAAGAAAUUUA", "nts_long": "///j/6190,///j/6191,///j/6192,///j/6193,///j/6194,///j/6195,///j/6196,///j/6197,///j/6198,///j/6199,///j/6200,///j/6201,///j/6202,///j/6203,///j/6204,///j/6205,///j/6206,///j/6207,///j/6208,///j/6209,///j/6210,///j/6211,///j/6212,///j/6213", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 22, "nts_short": "AGUCGAAAAACCUAAGAAAUUU", "nts_long": 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2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -11, 30 ], "summary": "[2] 1 0 [1.487 1.512 1.489 1.511] 1 3", "num_nts": 5, "nts_short": "UUAUA", "nts_long": "///1/487,///1/488,///1/489,///1/511,///1/512", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/488" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -12, 31 ], "summary": "[2] 0 1 [1.495 1.508 1.496 1.506] 1 3", "num_nts": 5, "nts_short": "UCGGA", "nts_long": "///1/495,///1/496,///1/506,///1/507,///1/508", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/507" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -13, 33 ], "summary": "[2] 0 1 [1.530 1.555 1.531 1.553] 1 5", 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"///1/877,///1/878,///1/879,///1/907,///1/908,///1/909", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/878" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/908" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -25, 49 ], "summary": "[2] 1 1 [1.879 1.907 1.881 1.905] 1 4", "num_nts": 6, "nts_short": "CGGCUG", "nts_long": "///1/879,///1/880,///1/881,///1/905,///1/906,///1/907", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/880" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/906" } ] }, { "index": 15, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 54, -28 ], "summary": "[2] 1 1 [1.950 1.976 1.952 1.974] 6 1", "num_nts": 6, "nts_short": "CCGCGG", "nts_long": "///1/950,///1/951,///1/952,///1/974,///1/975,///1/976", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/951" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/975" } ] }, { "index": 16, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 58, -30 ], "summary": "[2] 1 1 [1.1052 1.1066 1.1054 1.1064] 2 1", "num_nts": 6, "nts_short": "ACGCGU", "nts_long": "///1/1052,///1/1053,///1/1054,///1/1064,///1/1065,///1/1066", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1053" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1065" } ] }, { "index": 17, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -32, 62 ], "summary": "[2] 1 1 [1.1101 1.1131 1.1103 1.1129] 1 6", "num_nts": 6, "nts_short": "UGCGGG", "nts_long": "///1/1101,///1/1102,///1/1103,///1/1129,///1/1130,///1/1131", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1102" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1130" } ] }, { "index": 18, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 72, 73 ], "summary": "[2] 1 1 [1.1230 1.1528 1.1232 1.1526] 3 4", "num_nts": 6, "nts_short": "CCUGCG", "nts_long": "///1/1230,///1/1231,///1/1232,///1/1526,///1/1527,///1/1528", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1231" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1527" } ] }, { "index": 19, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 75, -36 ], "summary": "[2] 1 1 [1.1270 1.1512 1.1272 1.1510] 5 1", "num_nts": 6, "nts_short": "GCCGUC", "nts_long": "///1/1270,///1/1271,///1/1272,///1/1510,///1/1511,///1/1512", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1271" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1511" } ] }, { "index": 20, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 77, 78 ], "summary": "[2] 1 1 [1.1291 1.1308 1.1293 1.1306] 2 3", "num_nts": 6, "nts_short": "ACAUUU", "nts_long": "///1/1291,///1/1292,///1/1293,///1/1306,///1/1307,///1/1308", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1292" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1307" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 84, 85 ], "summary": "[2] 1 1 [1.1347 1.1382 1.1349 1.1380] 3 2", "num_nts": 6, "nts_short": "UGGCGA", "nts_long": "///1/1347,///1/1348,///1/1349,///1/1380,///1/1381,///1/1382", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1348" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1381" } ] }, { "index": 22, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -37, -38 ], "summary": "[2] 1 1 [1.1351 1.1360 1.1353 1.1358] 1 1", "num_nts": 6, "nts_short": "GGAUUU", "nts_long": "///1/1351,///1/1352,///1/1353,///1/1358,///1/1359,///1/1360", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1352" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1359" } ] }, { "index": 23, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -39, -40 ], "summary": "[2] 1 1 [1.1395 1.1450 1.1397 1.1448] 1 1", "num_nts": 6, "nts_short": "CAUAGG", "nts_long": "///1/1395,///1/1396,///1/1397,///1/1448,///1/1449,///1/1450", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1396" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1449" } ] }, { "index": 24, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 89, -41 ], "summary": "[2] 1 1 [1.1406 1.1440 1.1408 1.1438] 2 1", "num_nts": 6, "nts_short": "GUUAAC", "nts_long": "///1/1406,///1/1407,///1/1408,///1/1438,///1/1439,///1/1440", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1407" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1439" } ] }, { "index": 25, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 93, 94 ], "summary": "[2] 1 1 [1.1537 1.1596 1.1539 1.1594] 2 3", "num_nts": 6, "nts_short": "ACUAUU", "nts_long": "///1/1537,///1/1538,///1/1539,///1/1594,///1/1595,///1/1596", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1538" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1595" } ] }, { "index": 26, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 95, -44 ], "summary": "[2] 1 1 [1.1560 1.1575 1.1562 1.1573] 3 1", "num_nts": 6, "nts_short": "UACGCG", "nts_long": "///1/1560,///1/1561,///1/1562,///1/1573,///1/1574,///1/1575", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1561" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1574" } ] }, { "index": 27, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -44, 96 ], "summary": "[2] 1 1 [1.1562 1.1573 1.1564 1.1571] 1 2", "num_nts": 6, "nts_short": "CGCGCG", "nts_long": "///1/1562,///1/1563,///1/1564,///1/1571,///1/1572,///1/1573", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1563" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1572" } ] }, { "index": 28, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 98, 99 ], "summary": "[2] 1 1 [1.1652 1.1672 1.1654 1.1670] 2 2", "num_nts": 6, "nts_short": "GUGCGU", "nts_long": "///1/1652,///1/1653,///1/1654,///1/1670,///1/1671,///1/1672", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1653" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1671" } ] }, { "index": 29, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 100, -49 ], "summary": "[2] 1 1 [1.1706 1.1828 1.1708 1.1826] 2 1", "num_nts": 6, "nts_short": "GUCGUC", "nts_long": "///1/1706,///1/1707,///1/1708,///1/1826,///1/1827,///1/1828", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1707" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1827" } ] }, { "index": 30, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 101, 102 ], "summary": "[2] 1 1 [1.1714 1.1819 1.1716 1.1817] 4 2", "num_nts": 6, "nts_short": "UACGAA", "nts_long": "///1/1714,///1/1715,///1/1716,///1/1817,///1/1818,///1/1819", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1715" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1818" } ] }, { "index": 31, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 103, 104 ], "summary": "[2] 1 1 [1.1725 1.1809 1.1727 1.1807] 4 3", "num_nts": 6, "nts_short": "UGGCUA", "nts_long": "///1/1725,///1/1726,///1/1727,///1/1807,///1/1808,///1/1809", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1726" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1808" } ] }, { "index": 32, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 104, 105 ], "summary": "[2] 1 1 [1.1729 1.1805 1.1731 1.1803] 3 3", "num_nts": 6, "nts_short": "UUAUUG", "nts_long": "///1/1729,///1/1730,///1/1731,///1/1803,///1/1804,///1/1805", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1730" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1804" } ] }, { "index": 33, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -51, 106 ], "summary": "[2] 1 1 [1.1736 1.1798 1.1738 1.1796] 1 2", "num_nts": 6, "nts_short": "GGCGUC", "nts_long": "///1/1736,///1/1737,///1/1738,///1/1796,///1/1797,///1/1798", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1737" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1797" } ] }, { "index": 34, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 107, 108 ], "summary": "[2] 1 1 [1.1747 1.1787 1.1749 1.1785] 2 2", "num_nts": 6, "nts_short": "CGGCUG", "nts_long": "///1/1747,///1/1748,///1/1749,///1/1785,///1/1786,///1/1787", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1748" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1786" } ] }, { "index": 35, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 109, 110 ], "summary": "[2] 1 1 [1.1757 1.1775 1.1759 1.1773] 6 2", "num_nts": 6, "nts_short": "GGGCUC", "nts_long": "///1/1757,///1/1758,///1/1759,///1/1773,///1/1774,///1/1775", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1758" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1774" } ] }, { "index": 36, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 110, 111 ], "summary": "[2] 1 1 [1.1760 1.1772 1.1762 1.1770] 2 2", "num_nts": 6, "nts_short": "GUCGGC", "nts_long": "///1/1760,///1/1761,///1/1762,///1/1770,///1/1771,///1/1772", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1761" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1771" } ] }, { "index": 37, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 118, 119 ], "summary": "[2] 1 1 [j.6127 j.6159 j.6129 j.6157] 4 2", "num_nts": 6, "nts_short": "CAGCAG", "nts_long": "///j/6127,///j/6128,///j/6129,///j/6157,///j/6158,///j/6159", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///j/6128" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///j/6158" } ] }, { "index": 38, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 119, -54 ], "summary": "[2] 1 1 [j.6130 j.6156 j.6132 j.6154] 2 1", "num_nts": 6, "nts_short": "GAUAUC", "nts_long": "///j/6130,///j/6131,///j/6132,///j/6154,///j/6155,///j/6156", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///j/6131" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///j/6155" } ] }, { "index": 39, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 33, -14 ], "summary": "[2] 1 2 [1.535 1.549 1.537 1.546] 5 1", "num_nts": 7, "nts_short": "GACGGCC", "nts_long": "///1/535,///1/536,///1/537,///1/546,///1/547,///1/548,///1/549", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/536" }, { "index": 2, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/547,///1/548" } ] }, { "index": 40, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 50, 51 ], "summary": "[2] 1 2 [1.924 1.1018 1.926 1.1015] 2 3", "num_nts": 7, "nts_short": "GGAUUUU", "nts_long": "///1/924,///1/925,///1/926,///1/1015,///1/1016,///1/1017,///1/1018", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/925" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/1016,///1/1017" } ] }, { "index": 41, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -33, 67 ], "summary": "[2] 1 2 [1.1202 1.1697 1.1204 1.1694] 1 3", "num_nts": 7, "nts_short": "UGAUACA", "nts_long": "///1/1202,///1/1203,///1/1204,///1/1694,///1/1695,///1/1696,///1/1697", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1203" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///1/1695,///1/1696" } ] }, { "index": 42, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -47, -48 ], "summary": "[2] 1 2 [1.1700 1.1836 1.1702 1.1833] 1 1", "num_nts": 7, "nts_short": "CCGCAAG", "nts_long": "///1/1700,///1/1701,///1/1702,///1/1833,///1/1834,///1/1835,///1/1836", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1701" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/1834,///1/1835" } ] }, { "index": 43, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 51, -27 ], "summary": "[2] 2 2 [1.928 1.1013 1.931 1.1010] 3 1", "num_nts": 8, "nts_short": "GGCCGAAU", "nts_long": "///1/928,///1/929,///1/930,///1/931,///1/1010,///1/1011,///1/1012,///1/1013", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/929,///1/930" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/1011,///1/1012" } ] }, { "index": 44, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 53, 54 ], "summary": "[2] 2 2 [1.942 1.984 1.945 1.981] 2 6", "num_nts": 8, "nts_short": "GUAUAGAC", "nts_long": "///1/942,///1/943,///1/944,///1/945,///1/981,///1/982,///1/983,///1/984", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/943,///1/944" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/982,///1/983" } ] }, { "index": 45, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 61, -32 ], "summary": "[2] 2 2 [1.1098 1.1134 1.1101 1.1131] 2 1", "num_nts": 8, "nts_short": "CGAUGCAG", "nts_long": "///1/1098,///1/1099,///1/1100,///1/1101,///1/1131,///1/1132,///1/1133,///1/1134", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1099,///1/1100" }, { "index": 2, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/1132,///1/1133" } ] }, { "index": 46, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 99, -46 ], "summary": "[2] 2 2 [1.1655 1.1669 1.1658 1.1666] 2 1", "num_nts": 8, "nts_short": "CGGGCUUG", "nts_long": "///1/1655,///1/1656,///1/1657,///1/1658,///1/1666,///1/1667,///1/1668,///1/1669", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1656,///1/1657" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/1667,///1/1668" } ] }, { "index": 47, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 102, -50 ], "summary": "[2] 2 2 [1.1717 1.1816 1.1720 1.1813] 2 1", "num_nts": 8, "nts_short": "CGAUAGAG", "nts_long": "///1/1717,///1/1718,///1/1719,///1/1720,///1/1813,///1/1814,///1/1815,///1/1816", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1718,///1/1719" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1814,///1/1815" } ] }, { "index": 48, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 105, -51 ], "summary": "[2] 2 2 [1.1733 1.1801 1.1736 1.1798] 3 1", "num_nts": 8, "nts_short": "UGAGCGAA", "nts_long": "///1/1733,///1/1734,///1/1735,///1/1736,///1/1798,///1/1799,///1/1800,///1/1801", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1734,///1/1735" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1799,///1/1800" } ] }, { "index": 49, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 106, -52 ], "summary": "[2] 2 2 [1.1739 1.1795 1.1742 1.1792] 2 1", "num_nts": 8, "nts_short": "CCUCGACG", "nts_long": "///1/1739,///1/1740,///1/1741,///1/1742,///1/1792,///1/1793,///1/1794,///1/1795", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/1740,///1/1741" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///1/1793,///1/1794" } ] }, { "index": 50, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 108, 109 ], "summary": "[2] 1 3 [1.1750 1.1784 1.1752 1.1780] 2 6", "num_nts": 8, "nts_short": "CCCGAGCG", "nts_long": "///1/1750,///1/1751,///1/1752,///1/1780,///1/1781,///1/1782,///1/1783,///1/1784", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1751" }, { "index": 2, "num_nts": 3, "nts_short": "AGC", "nts_long": "///1/1781,///1/1782,///1/1783" } ] }, { "index": 51, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ -5, 8 ], "summary": "[2] 4 1 [1.56 1.89 1.61 1.87] 1 3", "num_nts": 9, "nts_short": "GUCUAAUGC", "nts_long": "///1/56,///1/57,///1/58,///1/59,///1/60,///1/61,///1/87,///1/88,///1/89", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UCUA", "nts_long": "///1/57,///1/58,///1/59,///1/60" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/88" } ] }, { "index": 52, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 18, 19 ], "summary": "[2] 2 3 [1.232 1.897 1.235 1.893] 2 3", "num_nts": 9, "nts_short": "ACCAUGGUU", "nts_long": "///1/232,///1/233,///1/234,///1/235,///1/893,///1/894,///1/895,///1/896,///1/897", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/233,///1/234" }, { "index": 2, "num_nts": 3, "nts_short": "GGU", "nts_long": "///1/894,///1/895,///1/896" } ] }, { "index": 53, "type": "asymmetric internal loop", "bridging_nts": [ 1, 4 ], "stem_indices": [ 25, 26 ], "summary": "[2] 1 4 [1.411 1.429 1.413 1.424] 2 4", "num_nts": 9, "nts_short": "GGGCGAUUC", "nts_long": "///1/411,///1/412,///1/413,///1/424,///1/425,///1/426,///1/427,///1/428,///1/429", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/412" }, { "index": 2, "num_nts": 4, "nts_short": "GAUU", "nts_long": "///1/425,///1/426,///1/427,///1/428" } ] }, { "index": 54, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ -27, 52 ], "summary": "[2] 3 2 [1.931 1.1010 1.935 1.1007] 1 4", "num_nts": 9, "nts_short": "CGGGGCAAG", "nts_long": "///1/931,///1/932,///1/933,///1/934,///1/935,///1/1007,///1/1008,///1/1009,///1/1010", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGG", "nts_long": "///1/932,///1/933,///1/934" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/1008,///1/1009" } ] }, { "index": 55, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 57, -29 ], "summary": "[2] 4 1 [1.1042 1.1073 1.1047 1.1071] 6 1", "num_nts": 9, "nts_short": "AGGUUCGUU", "nts_long": "///1/1042,///1/1043,///1/1044,///1/1045,///1/1046,///1/1047,///1/1071,///1/1072,///1/1073", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGUU", "nts_long": "///1/1043,///1/1044,///1/1045,///1/1046" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1072" } ] }, { "index": 56, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 90, 91 ], "summary": "[2] 3 2 [1.1415 1.1431 1.1419 1.1428] 3 3", "num_nts": 9, "nts_short": "CCCCCGGCG", "nts_long": "///1/1415,///1/1416,///1/1417,///1/1418,///1/1419,///1/1428,///1/1429,///1/1430,///1/1431", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CCC", "nts_long": "///1/1416,///1/1417,///1/1418" }, { "index": 2, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/1429,///1/1430" } ] }, { "index": 57, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ -48, 100 ], "summary": "[2] 2 3 [1.1702 1.1833 1.1705 1.1829] 1 2", "num_nts": 9, "nts_short": "GCCCGUAAC", "nts_long": "///1/1702,///1/1703,///1/1704,///1/1705,///1/1829,///1/1830,///1/1831,///1/1832,///1/1833", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/1703,///1/1704" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///1/1830,///1/1831,///1/1832" } ] }, { "index": 58, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ -49, 101 ], "summary": "[2] 2 3 [1.1708 1.1826 1.1711 1.1822] 1 4", "num_nts": 9, "nts_short": "CGCUAAAAG", "nts_long": "///1/1708,///1/1709,///1/1710,///1/1711,///1/1822,///1/1823,///1/1824,///1/1825,///1/1826", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/1709,///1/1710" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/1823,///1/1824,///1/1825" } ] }, { "index": 59, "type": "asymmetric internal loop", "bridging_nts": [ 5, 1 ], "stem_indices": [ -4, 6 ], "summary": "[2] 5 1 [1.41 1.481 1.47 1.479] 1 3", "num_nts": 10, "nts_short": "GAUUAAGCGC", "nts_long": "///1/41,///1/42,///1/43,///1/44,///1/45,///1/46,///1/47,///1/479,///1/480,///1/481", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AUUAA", "nts_long": "///1/42,///1/43,///1/44,///1/45,///1/46" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/480" } ] }, { "index": 60, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 10, -6 ], "summary": "[2] 3 3 [1.108 1.353 1.112 1.349] 3 1", "num_nts": 10, "nts_short": "GUUAUACGUC", "nts_long": "///1/108,///1/109,///1/110,///1/111,///1/112,///1/349,///1/350,///1/351,///1/352,///1/353", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUA", "nts_long": "///1/109,///1/110,///1/111" }, { "index": 2, "num_nts": 3, "nts_short": "CGU", "nts_long": "///1/350,///1/351,///1/352" } ] }, { "index": 61, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 14, 15 ], "summary": "[2] 3 3 [1.188 1.211 1.192 1.207] 3 2", "num_nts": 10, "nts_short": "CUGACGGAUG", "nts_long": "///1/188,///1/189,///1/190,///1/191,///1/192,///1/207,///1/208,///1/209,///1/210,///1/211", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGA", "nts_long": "///1/189,///1/190,///1/191" }, { "index": 2, "num_nts": 3, "nts_short": "GAU", "nts_long": "///1/208,///1/209,///1/210" } ] }, { "index": 62, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -15, -16 ], "summary": "[2] 3 3 [1.565 1.585 1.569 1.581] 1 1", "num_nts": 10, "nts_short": "GUCCAUUAAC", "nts_long": "///1/565,///1/566,///1/567,///1/568,///1/569,///1/581,///1/582,///1/583,///1/584,///1/585", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UCC", "nts_long": "///1/566,///1/567,///1/568" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///1/582,///1/583,///1/584" } ] }, { "index": 63, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -29, 58 ], "summary": "[2] 3 3 [1.1047 1.1071 1.1051 1.1067] 1 2", "num_nts": 10, "nts_short": "CGAAGCGUAG", "nts_long": "///1/1047,///1/1048,///1/1049,///1/1050,///1/1051,///1/1067,///1/1068,///1/1069,///1/1070,///1/1071", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///1/1048,///1/1049,///1/1050" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///1/1068,///1/1069,///1/1070" } ] }, { "index": 64, "type": "asymmetric internal loop", "bridging_nts": [ 1, 5 ], "stem_indices": [ 59, 60 ], "summary": "[2] 1 5 [1.1091 1.1158 1.1093 1.1152] 3 2", "num_nts": 10, "nts_short": "CGAUCUUUGG", "nts_long": "///1/1091,///1/1092,///1/1093,///1/1152,///1/1153,///1/1154,///1/1155,///1/1156,///1/1157,///1/1158", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1092" }, { "index": 2, "num_nts": 5, "nts_short": "CUUUG", "nts_long": "///1/1153,///1/1154,///1/1155,///1/1156,///1/1157" } ] }, { "index": 65, "type": "asymmetric internal loop", "bridging_nts": [ 1, 5 ], "stem_indices": [ 81, 82 ], "summary": "[2] 1 5 [1.1333 1.1498 1.1335 1.1492] 2 3", "num_nts": 10, "nts_short": "UGGUCUGUGA", "nts_long": "///1/1333,///1/1334,///1/1335,///1/1492,///1/1493,///1/1494,///1/1495,///1/1496,///1/1497,///1/1498", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1334" }, { "index": 2, "num_nts": 5, "nts_short": "CUGUG", "nts_long": "///1/1493,///1/1494,///1/1495,///1/1496,///1/1497" } ] }, { "index": 66, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 88, 89 ], "summary": "[2] 3 3 [1.1401 1.1445 1.1405 1.1441] 3 2", "num_nts": 10, "nts_short": "AACUAUUCUU", "nts_long": "///1/1401,///1/1402,///1/1403,///1/1404,///1/1405,///1/1441,///1/1442,///1/1443,///1/1444,///1/1445", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACU", "nts_long": "///1/1402,///1/1403,///1/1404" }, { "index": 2, "num_nts": 3, "nts_short": "UCU", "nts_long": "///1/1442,///1/1443,///1/1444" } ] }, { "index": 67, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -52, 107 ], "summary": "[2] 3 3 [1.1742 1.1792 1.1746 1.1788] 1 2", "num_nts": 10, "nts_short": "CGGAUAGAAG", "nts_long": "///1/1742,///1/1743,///1/1744,///1/1745,///1/1746,///1/1788,///1/1789,///1/1790,///1/1791,///1/1792", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/1743,///1/1744,///1/1745" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///1/1789,///1/1790,///1/1791" } ] }, { "index": 68, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -55, 121 ], "summary": "[2] 3 3 [j.6175 j.6201 j.6179 j.6197] 1 3", "num_nts": 10, "nts_short": "GUUAUAAAAC", "nts_long": "///j/6175,///j/6176,///j/6177,///j/6178,///j/6179,///j/6197,///j/6198,///j/6199,///j/6200,///j/6201", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUA", "nts_long": "///j/6176,///j/6177,///j/6178" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///j/6198,///j/6199,///j/6200" } ] }, { "index": 69, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ -34, 70 ], "summary": "[2] 3 4 [1.1213 1.1686 1.1217 1.1681] 1 2", "num_nts": 11, "nts_short": "CACCAUCCCUG", "nts_long": "///1/1213,///1/1214,///1/1215,///1/1216,///1/1217,///1/1681,///1/1682,///1/1683,///1/1684,///1/1685,///1/1686", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACC", "nts_long": "///1/1214,///1/1215,///1/1216" }, { "index": 2, "num_nts": 4, "nts_short": "CCCU", "nts_long": "///1/1682,///1/1683,///1/1684,///1/1685" } ] }, { "index": 70, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 40, 41 ], "summary": "[2] 4 4 [1.676 1.1029 1.681 1.1024] 2 2", "num_nts": 12, "nts_short": "CGUAGUAUCAAG", "nts_long": "///1/676,///1/677,///1/678,///1/679,///1/680,///1/681,///1/1024,///1/1025,///1/1026,///1/1027,///1/1028,///1/1029", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAG", "nts_long": "///1/677,///1/678,///1/679,///1/680" }, { "index": 2, "num_nts": 4, "nts_short": "UCAA", "nts_long": "///1/1025,///1/1026,///1/1027,///1/1028" } ] }, { "index": 71, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -41, 90 ], "summary": "[2] 4 4 [1.1408 1.1438 1.1413 1.1433] 1 3", "num_nts": 12, "nts_short": "UACGCGCCCCCA", "nts_long": "///1/1408,///1/1409,///1/1410,///1/1411,///1/1412,///1/1413,///1/1433,///1/1434,///1/1435,///1/1436,///1/1437,///1/1438", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "ACGC", "nts_long": "///1/1409,///1/1410,///1/1411,///1/1412" }, { "index": 2, "num_nts": 4, "nts_short": "CCCC", "nts_long": "///1/1434,///1/1435,///1/1436,///1/1437" } ] }, { "index": 72, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ -7, 11 ], "summary": "[2] 5 4 [1.115 1.348 1.121 1.343] 1 3", "num_nts": 13, "nts_short": "UUCCUUUAUUCGA", "nts_long": "///1/115,///1/116,///1/117,///1/118,///1/119,///1/120,///1/121,///1/343,///1/344,///1/345,///1/346,///1/347,///1/348", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UCCUU", "nts_long": "///1/116,///1/117,///1/118,///1/119,///1/120" }, { "index": 2, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///1/344,///1/345,///1/346,///1/347" } ] }, { "index": 73, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ -28, 55 ], "summary": "[2] 3 6 [1.952 1.974 1.956 1.967] 1 2", "num_nts": 13, "nts_short": "GCUAGCUUGGACC", "nts_long": "///1/952,///1/953,///1/954,///1/955,///1/956,///1/967,///1/968,///1/969,///1/970,///1/971,///1/972,///1/973,///1/974", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CUA", "nts_long": "///1/953,///1/954,///1/955" }, { "index": 2, "num_nts": 6, "nts_short": "UUGGAC", "nts_long": "///1/968,///1/969,///1/970,///1/971,///1/972,///1/973" } ] }, { "index": 74, "type": "asymmetric internal loop", "bridging_nts": [ 4, 6 ], "stem_indices": [ -8, 12 ], "summary": "[2] 4 6 [1.146 1.174 1.151 1.167] 1 2", "num_nts": 14, "nts_short": "GAUAACGCUAAUAC", "nts_long": "///1/146,///1/147,///1/148,///1/149,///1/150,///1/151,///1/167,///1/168,///1/169,///1/170,///1/171,///1/172,///1/173,///1/174", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUAA", "nts_long": "///1/147,///1/148,///1/149,///1/150" }, { "index": 2, "num_nts": 6, "nts_short": "CUAAUA", "nts_long": "///1/168,///1/169,///1/170,///1/171,///1/172,///1/173" } ] }, { "index": 75, "type": "asymmetric internal loop", "bridging_nts": [ 4, 6 ], "stem_indices": [ 22, 23 ], "summary": "[2] 4 6 [1.359 1.403 1.364 1.396] 3 3", "num_nts": 14, "nts_short": "UAUCAAUGACCACG", "nts_long": "///1/359,///1/360,///1/361,///1/362,///1/363,///1/364,///1/396,///1/397,///1/398,///1/399,///1/400,///1/401,///1/402,///1/403", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUCA", "nts_long": "///1/360,///1/361,///1/362,///1/363" }, { "index": 2, "num_nts": 6, "nts_short": "GACCAC", "nts_long": "///1/397,///1/398,///1/399,///1/400,///1/401,///1/402" } ] }, { "index": 76, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 65, 66 ], "summary": "[2] 6 4 [1.1168 1.1191 1.1175 1.1186] 2 4", "num_nts": 14, "nts_short": "GGAGUAUGUGAAAC", "nts_long": "///1/1168,///1/1169,///1/1170,///1/1171,///1/1172,///1/1173,///1/1174,///1/1175,///1/1186,///1/1187,///1/1188,///1/1189,///1/1190,///1/1191", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAGUAU", "nts_long": "///1/1169,///1/1170,///1/1171,///1/1172,///1/1173,///1/1174" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/1187,///1/1188,///1/1189,///1/1190" } ] }, { "index": 77, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ -45, 97 ], "summary": "[2] 5 5 [1.1604 1.1635 1.1610 1.1629] 1 5", "num_nts": 14, "nts_short": "GGGAUCGCAUGAAC", "nts_long": "///1/1604,///1/1605,///1/1606,///1/1607,///1/1608,///1/1609,///1/1610,///1/1629,///1/1630,///1/1631,///1/1632,///1/1633,///1/1634,///1/1635", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGAUC", "nts_long": "///1/1605,///1/1606,///1/1607,///1/1608,///1/1609" }, { "index": 2, "num_nts": 5, "nts_short": "AUGAA", "nts_long": "///1/1630,///1/1631,///1/1632,///1/1633,///1/1634" } ] }, { "index": 78, "type": "asymmetric internal loop", "bridging_nts": [ 5, 6 ], "stem_indices": [ -2, -3 ], "summary": "[2] 5 6 [1.34 1.521 1.40 1.514] 1 1", "num_nts": 15, "nts_short": "UCUCAAAUGACGAAA", "nts_long": "///1/34,///1/35,///1/36,///1/37,///1/38,///1/39,///1/40,///1/514,///1/515,///1/516,///1/517,///1/518,///1/519,///1/520,///1/521", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CUCAA", "nts_long": "///1/35,///1/36,///1/37,///1/38,///1/39" }, { "index": 2, "num_nts": 6, "nts_short": "GACGAA", "nts_long": "///1/515,///1/516,///1/517,///1/518,///1/519,///1/520" } ] }, { "index": 79, "type": "asymmetric internal loop", "bridging_nts": [ 7, 4 ], "stem_indices": [ -43, 95 ], "summary": "[2] 7 4 [1.1550 1.1582 1.1558 1.1577] 1 3", "num_nts": 15, "nts_short": "GUGCCUACCGUAACC", "nts_long": "///1/1550,///1/1551,///1/1552,///1/1553,///1/1554,///1/1555,///1/1556,///1/1557,///1/1558,///1/1577,///1/1578,///1/1579,///1/1580,///1/1581,///1/1582", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGCCUAC", "nts_long": "///1/1551,///1/1552,///1/1553,///1/1554,///1/1555,///1/1556,///1/1557" }, { "index": 2, "num_nts": 4, "nts_short": "UAAC", "nts_long": "///1/1578,///1/1579,///1/1580,///1/1581" } ] }, { "index": 80, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 37, 38 ], "summary": "[2] 5 7 [1.611 1.632 1.617 1.624] 4 2", "num_nts": 16, "nts_short": "GUGCCAGCGGUAAUUC", "nts_long": "///1/611,///1/612,///1/613,///1/614,///1/615,///1/616,///1/617,///1/624,///1/625,///1/626,///1/627,///1/628,///1/629,///1/630,///1/631,///1/632", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGCCA", "nts_long": "///1/612,///1/613,///1/614,///1/615,///1/616" }, { "index": 2, "num_nts": 7, "nts_short": "GGUAAUU", "nts_long": "///1/625,///1/626,///1/627,///1/628,///1/629,///1/630,///1/631" } ] }, { "index": 81, "type": "asymmetric internal loop", "bridging_nts": [ 7, 6 ], "stem_indices": [ -22, 47 ], "summary": "[2] 7 6 [1.807 1.856 1.815 1.849] 1 2", "num_nts": 17, "nts_short": "GAAAAAAUUACCGCAGC", "nts_long": "///1/807,///1/808,///1/809,///1/810,///1/811,///1/812,///1/813,///1/814,///1/815,///1/849,///1/850,///1/851,///1/852,///1/853,///1/854,///1/855,///1/856", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AAAAAAU", "nts_long": "///1/808,///1/809,///1/810,///1/811,///1/812,///1/813,///1/814" }, { "index": 2, "num_nts": 6, "nts_short": "CCGCAG", "nts_long": "///1/850,///1/851,///1/852,///1/853,///1/854,///1/855" } ] }, { "index": 82, "type": "asymmetric internal loop", "bridging_nts": [ 9, 7 ], "stem_indices": [ 76, 77 ], "summary": "[2] 9 7 [1.1280 1.1317 1.1290 1.1309] 4 2", "num_nts": 20, "nts_short": "GGACAGGAUUGCUCGAUUCC", "nts_long": "///1/1280,///1/1281,///1/1282,///1/1283,///1/1284,///1/1285,///1/1286,///1/1287,///1/1288,///1/1289,///1/1290,///1/1309,///1/1310,///1/1311,///1/1312,///1/1313,///1/1314,///1/1315,///1/1316,///1/1317", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "GACAGGAUU", "nts_long": "///1/1281,///1/1282,///1/1283,///1/1284,///1/1285,///1/1286,///1/1287,///1/1288,///1/1289" }, { "index": 2, "num_nts": 7, "nts_short": "UCGAUUC", "nts_long": "///1/1310,///1/1311,///1/1312,///1/1313,///1/1314,///1/1315,///1/1316" } ] }, { "index": 83, "type": "asymmetric internal loop", "bridging_nts": [ 8, 9 ], "stem_indices": [ 94, -43 ], "summary": "[2] 8 9 [1.1541 1.1592 1.1550 1.1582] 3 1", "num_nts": 21, "nts_short": "GCUCAGCGUGCCGUUGAACCC", "nts_long": "///1/1541,///1/1542,///1/1543,///1/1544,///1/1545,///1/1546,///1/1547,///1/1548,///1/1549,///1/1550,///1/1582,///1/1583,///1/1584,///1/1585,///1/1586,///1/1587,///1/1588,///1/1589,///1/1590,///1/1591,///1/1592", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "CUCAGCGU", "nts_long": "///1/1542,///1/1543,///1/1544,///1/1545,///1/1546,///1/1547,///1/1548,///1/1549" }, { "index": 2, "num_nts": 9, "nts_short": "CGUUGAACC", "nts_long": "///1/1583,///1/1584,///1/1585,///1/1586,///1/1587,///1/1588,///1/1589,///1/1590,///1/1591" } ] }, { "index": 84, "type": "asymmetric internal loop", "bridging_nts": [ 13, 11 ], "stem_indices": [ 113, 114 ], "summary": "[2] 13 11 [j.6031 j.6094 j.6045 j.6082] 2 7", "num_nts": 28, "nts_short": "AAAAUGUGAUCUUGCGUAGUGCUAUUUU", "nts_long": "///j/6031,///j/6032,///j/6033,///j/6034,///j/6035,///j/6036,///j/6037,///j/6038,///j/6039,///j/6040,///j/6041,///j/6042,///j/6043,///j/6044,///j/6045,///j/6082,///j/6083,///j/6084,///j/6085,///j/6086,///j/6087,///j/6088,///j/6089,///j/6090,///j/6091,///j/6092,///j/6093,///j/6094", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "AAAUGUGAUCUUG", "nts_long": "///j/6032,///j/6033,///j/6034,///j/6035,///j/6036,///j/6037,///j/6038,///j/6039,///j/6040,///j/6041,///j/6042,///j/6043,///j/6044" }, { "index": 2, "num_nts": 11, "nts_short": "UAGUGCUAUUU", "nts_long": "///j/6083,///j/6084,///j/6085,///j/6086,///j/6087,///j/6088,///j/6089,///j/6090,///j/6091,///j/6092,///j/6093" } ] } ], "num_junctions": 19, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 3, 0 ], "stem_indices": [ 41, -21, -26 ], "summary": "[3] 1 3 0 [1.682 1.1023 1.684 1.918 1.922 1.1022] 2 1 1", "num_nts": 10, "nts_short": "UGGUAAGAUA", "nts_long": "///1/682,///1/683,///1/684,///1/918,///1/919,///1/920,///1/921,///1/922,///1/1022,///1/1023", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/683" }, { "index": 2, "num_nts": 3, "nts_short": "AAG", "nts_long": "///1/919,///1/920,///1/921" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 2, 1, 2 ], "stem_indices": [ 71, 72, -42 ], "summary": "[3] 2 1 2 [1.1225 1.1641 1.1228 1.1530 1.1532 1.1638] 5 3 1", "num_nts": 11, "nts_short": "UGGAUACGGAA", "nts_long": "///1/1225,///1/1226,///1/1227,///1/1228,///1/1530,///1/1531,///1/1532,///1/1638,///1/1639,///1/1640,///1/1641", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1226,///1/1227" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1531" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1639,///1/1640" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 0, 5, 1 ], "stem_indices": [ -3, -4, -11 ], "summary": "[3] 0 5 1 [1.40 1.514 1.41 1.481 1.487 1.512] 1 1 1", "num_nts": 12, "nts_short": "AGCGCAAAUAGU", "nts_long": "///1/40,///1/41,///1/481,///1/482,///1/483,///1/484,///1/485,///1/486,///1/487,///1/512,///1/513,///1/514", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "GCAAA", "nts_long": "///1/482,///1/483,///1/484,///1/485,///1/486" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///1/513" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 2, 1, 4 ], "stem_indices": [ 47, -23, 48 ], "summary": "[3] 2 1 4 [1.816 1.848 1.819 1.829 1.831 1.843] 2 1 3", "num_nts": 13, "nts_short": "AGAGCAGCUGGAU", "nts_long": "///1/816,///1/817,///1/818,///1/819,///1/829,///1/830,///1/831,///1/843,///1/844,///1/845,///1/846,///1/847,///1/848", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/817,///1/818" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/830" }, { "index": 3, "num_nts": 4, "nts_short": "UGGA", "nts_long": "///1/844,///1/845,///1/846,///1/847" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 0, 4, 4 ], "stem_indices": [ 85, -37, 86 ], "summary": "[3] 0 4 4 [1.1350 1.1379 1.1351 1.1360 1.1365 1.1374] 2 1 2", "num_nts": 14, "nts_short": "UGUGUCUGCGAUAA", "nts_long": "///1/1350,///1/1351,///1/1360,///1/1361,///1/1362,///1/1363,///1/1364,///1/1365,///1/1374,///1/1375,///1/1376,///1/1377,///1/1378,///1/1379", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "GUCU", "nts_long": "///1/1361,///1/1362,///1/1363,///1/1364" }, { "index": 3, "num_nts": 4, "nts_short": "GAUA", "nts_long": "///1/1375,///1/1376,///1/1377,///1/1378" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 2, 4, 3 ], "stem_indices": [ 60, 61, 64 ], "summary": "[3] 2 4 3 [1.1094 1.1151 1.1097 1.1135 1.1140 1.1147] 2 2 2", "num_nts": 15, "nts_short": "CCGGCUUCCGCAAAG", "nts_long": "///1/1094,///1/1095,///1/1096,///1/1097,///1/1135,///1/1136,///1/1137,///1/1138,///1/1139,///1/1140,///1/1147,///1/1148,///1/1149,///1/1150,///1/1151", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/1095,///1/1096" }, { "index": 2, "num_nts": 4, "nts_short": "UUCC", "nts_long": "///1/1136,///1/1137,///1/1138,///1/1139" }, { "index": 3, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/1148,///1/1149,///1/1150" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 3, 6, 2 ], "stem_indices": [ -42, 93, -45 ], "summary": "[3] 3 6 2 [1.1532 1.1638 1.1536 1.1597 1.1604 1.1635] 1 2 1", "num_nts": 17, "nts_short": "CACUGCGUGAUGGCGAG", "nts_long": "///1/1532,///1/1533,///1/1534,///1/1535,///1/1536,///1/1597,///1/1598,///1/1599,///1/1600,///1/1601,///1/1602,///1/1603,///1/1604,///1/1635,///1/1636,///1/1637,///1/1638", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACU", "nts_long": "///1/1533,///1/1534,///1/1535" }, { "index": 2, "num_nts": 6, "nts_short": "GUGAUG", "nts_long": "///1/1598,///1/1599,///1/1600,///1/1601,///1/1602,///1/1603" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1636,///1/1637" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 2, 7, 3 ], "stem_indices": [ 52, 53, 56 ], "summary": "[3] 2 7 3 [1.938 1.1004 1.941 1.985 1.993 1.1000] 4 2 2", "num_nts": 18, "nts_short": "AUUCGGACCAGAGCAUUU", "nts_long": "///1/938,///1/939,///1/940,///1/941,///1/985,///1/986,///1/987,///1/988,///1/989,///1/990,///1/991,///1/992,///1/993,///1/1000,///1/1001,///1/1002,///1/1003,///1/1004", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/939,///1/940" }, { "index": 2, "num_nts": 7, "nts_short": "GACCAGA", "nts_long": "///1/986,///1/987,///1/988,///1/989,///1/990,///1/991,///1/992" }, { "index": 3, "num_nts": 3, "nts_short": "AUU", "nts_long": "///1/1001,///1/1002,///1/1003" } ] }, { "index": 9, "type": "3-way junction", "bridging_nts": [ 4, 3, 5 ], "stem_indices": [ -36, 76, 79 ], "summary": "[3] 4 3 5 [1.1272 1.1510 1.1277 1.1320 1.1324 1.1504] 1 4 2", "num_nts": 18, "nts_short": "CCGGACGGGUGUUAGAUG", "nts_long": "///1/1272,///1/1273,///1/1274,///1/1275,///1/1276,///1/1277,///1/1320,///1/1321,///1/1322,///1/1323,///1/1324,///1/1504,///1/1505,///1/1506,///1/1507,///1/1508,///1/1509,///1/1510", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CGGA", "nts_long": "///1/1273,///1/1274,///1/1275,///1/1276" }, { "index": 2, "num_nts": 3, "nts_short": "GGU", "nts_long": "///1/1321,///1/1322,///1/1323" }, { "index": 3, "num_nts": 5, "nts_short": "UAGAU", "nts_long": "///1/1505,///1/1506,///1/1507,///1/1508,///1/1509" } ] }, { "index": 10, "type": "3-way junction", "bridging_nts": [ 4, 4, 4 ], "stem_indices": [ 83, 84, 87 ], "summary": "[3] 4 4 4 [1.1340 1.1486 1.1345 1.1384 1.1389 1.1481] 3 3 3", "num_nts": 18, "nts_short": "UCUUAGCGAGACGCAAUA", "nts_long": "///1/1340,///1/1341,///1/1342,///1/1343,///1/1344,///1/1345,///1/1384,///1/1385,///1/1386,///1/1387,///1/1388,///1/1389,///1/1481,///1/1482,///1/1483,///1/1484,///1/1485,///1/1486", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUUA", "nts_long": "///1/1341,///1/1342,///1/1343,///1/1344" }, { "index": 2, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///1/1385,///1/1386,///1/1387,///1/1388" }, { "index": 3, "num_nts": 4, "nts_short": "CAAU", "nts_long": "///1/1482,///1/1483,///1/1484,///1/1485" } ] }, { "index": 11, "type": "3-way junction", "bridging_nts": [ 2, 5, 6 ], "stem_indices": [ 70, 71, 98 ], "summary": "[3] 2 5 6 [1.1218 1.1680 1.1221 1.1645 1.1651 1.1673] 2 5 2", "num_nts": 19, "nts_short": "CCAGCCAGUAAUGAUUAAG", "nts_long": "///1/1218,///1/1219,///1/1220,///1/1221,///1/1645,///1/1646,///1/1647,///1/1648,///1/1649,///1/1650,///1/1651,///1/1673,///1/1674,///1/1675,///1/1676,///1/1677,///1/1678,///1/1679,///1/1680", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/1219,///1/1220" }, { "index": 2, "num_nts": 5, "nts_short": "CAGUA", "nts_long": "///1/1646,///1/1647,///1/1648,///1/1649,///1/1650" }, { "index": 3, "num_nts": 6, "nts_short": "GAUUAA", "nts_long": "///1/1674,///1/1675,///1/1676,///1/1677,///1/1678,///1/1679" } ] }, { "index": 12, "type": "3-way junction", "bridging_nts": [ 3, 5, 8 ], "stem_indices": [ 87, -39, 92 ], "summary": "[3] 3 5 8 [1.1391 1.1479 1.1395 1.1450 1.1456 1.1470] 3 1 4", "num_nts": 22, "nts_short": "CUGGCGGACAAGCCCGAGAUUG", "nts_long": "///1/1391,///1/1392,///1/1393,///1/1394,///1/1395,///1/1450,///1/1451,///1/1452,///1/1453,///1/1454,///1/1455,///1/1456,///1/1470,///1/1471,///1/1472,///1/1473,///1/1474,///1/1475,///1/1476,///1/1477,///1/1478,///1/1479", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGG", "nts_long": "///1/1392,///1/1393,///1/1394" }, { "index": 2, "num_nts": 5, "nts_short": "GACAA", "nts_long": "///1/1451,///1/1452,///1/1453,///1/1454,///1/1455" }, { "index": 3, "num_nts": 8, "nts_short": "CCGAGAUU", "nts_long": "///1/1471,///1/1472,///1/1473,///1/1474,///1/1475,///1/1476,///1/1477,///1/1478" } ] }, { "index": 13, "type": "3-way junction", "bridging_nts": [ 7, 11, 3 ], "stem_indices": [ 74, -35, 75 ], "summary": "[3] 7 11 3 [1.1237 1.1520 1.1245 1.1254 1.1266 1.1516] 2 1 5", "num_nts": 27, "nts_short": "CUUAAUUUGCGGGAAACCUCACGGCUG", "nts_long": "///1/1237,///1/1238,///1/1239,///1/1240,///1/1241,///1/1242,///1/1243,///1/1244,///1/1245,///1/1254,///1/1255,///1/1256,///1/1257,///1/1258,///1/1259,///1/1260,///1/1261,///1/1262,///1/1263,///1/1264,///1/1265,///1/1266,///1/1516,///1/1517,///1/1518,///1/1519,///1/1520", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUAAUUU", "nts_long": "///1/1238,///1/1239,///1/1240,///1/1241,///1/1242,///1/1243,///1/1244" }, { "index": 2, "num_nts": 11, "nts_short": "GGGAAACCUCA", "nts_long": "///1/1255,///1/1256,///1/1257,///1/1258,///1/1259,///1/1260,///1/1261,///1/1262,///1/1263,///1/1264,///1/1265" }, { "index": 3, "num_nts": 3, "nts_short": "GCU", "nts_long": "///1/1517,///1/1518,///1/1519" } ] }, { "index": 14, "type": "4-way junction", "bridging_nts": [ 7, 1, 4, 1 ], "stem_indices": [ 9, 10, 22, 25 ], "summary": "[4] 7 1 4 1 [1.98 1.432 1.106 1.355 1.357 1.405 1.410 1.430] 3 3 3 2", "num_nts": 21, "nts_short": "CAUUAAAUCGCCGUGACGCGG", "nts_long": "///1/98,///1/99,///1/100,///1/101,///1/102,///1/103,///1/104,///1/105,///1/106,///1/355,///1/356,///1/357,///1/405,///1/406,///1/407,///1/408,///1/409,///1/410,///1/430,///1/431,///1/432", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AUUAAAU", "nts_long": "///1/99,///1/100,///1/101,///1/102,///1/103,///1/104,///1/105" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/356" }, { "index": 3, "num_nts": 4, "nts_short": "UGAC", "nts_long": "///1/406,///1/407,///1/408,///1/409" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///1/431" } ] }, { "index": 15, "type": "5-way junction", "bridging_nts": [ 0, 0, 2, 6, 1 ], "stem_indices": [ 35, 36, 38, 36, 37 ], "summary": "[5] 0 0 2 6 1 [1.599 1.637 1.600 1.622 1.623 1.618 1.621 1.601 1.608 1.635] 5 2 2 2 4", "is_repeated": true, "num_nts": 19, "nts_short": "AGCGCAGCGGCAAGUCGCU", "nts_long": "///1/599,///1/600,///1/622,///1/623,///1/618,///1/619,///1/620,///1/621,///1/601,///1/602,///1/603,///1/604,///1/605,///1/606,///1/607,///1/608,///1/635,///1/636,///1/637", "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": "AG", "nts_long": "///1/619,///1/620" }, { "index": 4, "num_nts": 6, "nts_short": "GCAAGU", "nts_long": "///1/602,///1/603,///1/604,///1/605,///1/606,///1/607" }, { "index": 5, "num_nts": 1, "nts_short": "C", "nts_long": "///1/636" } ] }, { "index": 16, "type": "5-way junction", "bridging_nts": [ 2, 6, 1, 1, 3 ], "stem_indices": [ 7, -5, 9, 27, -10 ], "summary": "[5] 2 6 1 1 3 [1.53 1.474 1.56 1.89 1.96 1.434 1.436 1.457 1.459 1.470] 3 1 3 2 1", "num_nts": 23, "nts_short": "CAUGCGAAUGGCGAGCACGGCAG", "nts_long": "///1/53,///1/54,///1/55,///1/56,///1/89,///1/90,///1/91,///1/92,///1/93,///1/94,///1/95,///1/96,///1/434,///1/435,///1/436,///1/457,///1/458,///1/459,///1/470,///1/471,///1/472,///1/473,///1/474", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/54,///1/55" }, { "index": 2, "num_nts": 6, "nts_short": "GAAUGG", "nts_long": "///1/90,///1/91,///1/92,///1/93,///1/94,///1/95" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///1/435" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///1/458" }, { "index": 5, "num_nts": 3, "nts_short": "GCA", "nts_long": "///1/471,///1/472,///1/473" } ] }, { "index": 17, "type": "5-way junction", "bridging_nts": [ 3, 5, 6, 9, 2 ], "stem_indices": [ 5, -2, 32, -15, 35 ], "summary": "[5] 3 5 6 9 2 [1.30 1.644 1.34 1.521 1.527 1.558 1.565 1.585 1.595 1.641] 2 1 2 1 5", "num_nts": 35, "nts_short": "CUUGUAAAUAACGGAAUGAGCGAGGAUCCAUAUAG", "nts_long": "///1/30,///1/31,///1/32,///1/33,///1/34,///1/521,///1/522,///1/523,///1/524,///1/525,///1/526,///1/527,///1/558,///1/559,///1/560,///1/561,///1/562,///1/563,///1/564,///1/565,///1/585,///1/586,///1/587,///1/588,///1/589,///1/590,///1/591,///1/592,///1/593,///1/594,///1/595,///1/641,///1/642,///1/643,///1/644", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUG", "nts_long": "///1/31,///1/32,///1/33" }, { "index": 2, "num_nts": 5, "nts_short": "AAUAA", "nts_long": "///1/522,///1/523,///1/524,///1/525,///1/526" }, { "index": 3, "num_nts": 6, "nts_short": "GAAUGA", "nts_long": "///1/559,///1/560,///1/561,///1/562,///1/563,///1/564" }, { "index": 4, "num_nts": 9, "nts_short": "GAGGAUCCA", "nts_long": "///1/586,///1/587,///1/588,///1/589,///1/590,///1/591,///1/592,///1/593,///1/594" }, { "index": 5, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/642,///1/643" } ] }, { "index": 18, "type": "5-way junction", "bridging_nts": [ 6, 8, 8, 16, 8 ], "stem_indices": [ -21, 42, 44, 46, -24 ], "summary": "[5] 6 8 8 16 8 [1.684 1.918 1.691 1.740 1.749 1.794 1.803 1.860 1.877 1.909] 1 2 4 3 1", "num_nts": 56, "nts_short": "GAUCUUGGCCUUGCCUCUAAGCGUUUACGAAUAAUGGAAUAGGACCGGCCAUGAUU", "nts_long": "///1/684,///1/685,///1/686,///1/687,///1/688,///1/689,///1/690,///1/691,///1/740,///1/741,///1/742,///1/743,///1/744,///1/745,///1/746,///1/747,///1/748,///1/749,///1/794,///1/795,///1/796,///1/797,///1/798,///1/799,///1/800,///1/801,///1/802,///1/803,///1/860,///1/861,///1/862,///1/863,///1/864,///1/865,///1/866,///1/867,///1/868,///1/869,///1/870,///1/871,///1/872,///1/873,///1/874,///1/875,///1/876,///1/877,///1/909,///1/910,///1/911,///1/912,///1/913,///1/914,///1/915,///1/916,///1/917,///1/918", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AUCUUG", "nts_long": "///1/685,///1/686,///1/687,///1/688,///1/689,///1/690" }, { "index": 2, "num_nts": 8, "nts_short": "CUUGCCUC", "nts_long": "///1/741,///1/742,///1/743,///1/744,///1/745,///1/746,///1/747,///1/748" }, { "index": 3, "num_nts": 8, "nts_short": "AGCGUUUA", "nts_long": "///1/795,///1/796,///1/797,///1/798,///1/799,///1/800,///1/801,///1/802" }, { "index": 4, "num_nts": 16, "nts_short": "AAUAAUGGAAUAGGAC", "nts_long": "///1/861,///1/862,///1/863,///1/864,///1/865,///1/866,///1/867,///1/868,///1/869,///1/870,///1/871,///1/872,///1/873,///1/874,///1/875,///1/876" }, { "index": 5, "num_nts": 8, "nts_short": "GCCAUGAU", "nts_long": "///1/910,///1/911,///1/912,///1/913,///1/914,///1/915,///1/916,///1/917" } ] }, { "index": 19, "type": "5-way junction", "bridging_nts": [ 22, 11, 5, 13, 6 ], "stem_indices": [ 11, -8, 14, 17, 20 ], "summary": "[5] 22 11 5 13 6 [1.123 1.341 1.146 1.174 1.186 1.213 1.219 1.302 1.316 1.334] 3 1 3 5 2", "num_nts": 67, "nts_short": "GUCGCUCGCUCCUCUCCCACUUGGCAUGCCGACGGGCGUGCAUUACCUCGGGCCGAUCGCGACGACC", "nts_long": "///1/123,///1/124,///1/125,///1/126,///1/127,///1/128,///1/129,///1/130,///1/131,///1/132,///1/133,///1/134,///1/135,///1/136,///1/137,///1/138,///1/139,///1/140,///1/141,///1/142,///1/143,///1/144,///1/145,///1/146,///1/174,///1/175,///1/176,///1/177,///1/178,///1/179,///1/180,///1/181,///1/182,///1/183,///1/184,///1/185,///1/186,///1/213,///1/214,///1/215,///1/216,///1/217,///1/218,///1/219,///1/302,///1/303,///1/304,///1/305,///1/306,///1/307,///1/308,///1/309,///1/310,///1/311,///1/312,///1/313,///1/314,///1/315,///1/316,///1/334,///1/335,///1/336,///1/337,///1/338,///1/339,///1/340,///1/341", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 22, "nts_short": "UCGCUCGCUCCUCUCCCACUUG", "nts_long": "///1/124,///1/125,///1/126,///1/127,///1/128,///1/129,///1/130,///1/131,///1/132,///1/133,///1/134,///1/135,///1/136,///1/137,///1/138,///1/139,///1/140,///1/141,///1/142,///1/143,///1/144,///1/145" }, { "index": 2, "num_nts": 11, "nts_short": "AUGCCGACGGG", "nts_long": "///1/175,///1/176,///1/177,///1/178,///1/179,///1/180,///1/181,///1/182,///1/183,///1/184,///1/185" }, { "index": 3, "num_nts": 5, "nts_short": "UGCAU", "nts_long": "///1/214,///1/215,///1/216,///1/217,///1/218" }, { "index": 4, "num_nts": 13, "nts_short": "CCUCGGGCCGAUC", "nts_long": "///1/303,///1/304,///1/305,///1/306,///1/307,///1/308,///1/309,///1/310,///1/311,///1/312,///1/313,///1/314,///1/315" }, { "index": 5, "num_nts": 6, "nts_short": "GACGAC", "nts_long": "///1/335,///1/336,///1/337,///1/338,///1/339,///1/340" } ] } ], "num_ssSegments": 29, "ssSegments": [ { "index": 1, "num_nts": 3, "nts_short": "UAC", "nts_long": "///1/1,///1/2,///1/3" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/21" }, { "index": 3, "num_nts": 7, "nts_short": "AGAUCAA", "nts_long": "///1/224,///1/225,///1/226,///1/227,///1/228,///1/229,///1/230" }, { "index": 4, "is_broken": true, "num_nts": 5, "nts_short": "CCGUA", "nts_long": "///1/238,///1/239,///1/240,///1/296,///1/297" }, { "index": 5, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/653,///1/654,///1/655" }, { "index": 6, "num_nts": 6, "nts_short": "UUGCUG", "nts_long": "///1/657,///1/658,///1/659,///1/660,///1/661,///1/662" }, { "index": 7, "num_nts": 5, "nts_short": "AAAAA", "nts_long": "///1/668,///1/669,///1/670,///1/671,///1/672" }, { "index": 8, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/1033,///1/1034,///1/1035,///1/1036" }, { "index": 9, "num_nts": 6, "nts_short": "CAUAAA", "nts_long": "///1/1079,///1/1080,///1/1081,///1/1082,///1/1083,///1/1084" }, { "index": 10, "num_nts": 3, "nts_short": "GAU", "nts_long": "///1/1086,///1/1087,///1/1088" }, { "index": 11, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1161" }, { "index": 12, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1165,///1/1166" }, { "index": 13, "num_nts": 4, "nts_short": "UAAA", "nts_long": "///1/1193,///1/1194,///1/1195,///1/1196" }, { "index": 14, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/1698,///1/1699" }, { "index": 15, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/1837,///1/1838" }, { "index": 16, "num_nts": 8, "nts_short": "GAUCAUUA", "nts_long": "///1/1862,///1/1863,///1/1864,///1/1865,///1/1866,///1/1867,///1/1868,///1/1869" }, { "index": 17, "num_nts": 10, "nts_short": "AUACAAUUUU", "nts_long": "///j/6052,///j/6053,///j/6054,///j/6055,///j/6056,///j/6057,///j/6058,///j/6059,///j/6060,///j/6061" }, { "index": 18, "num_nts": 1, "nts_short": "A", "nts_long": "///j/6065" }, { "index": 19, "is_broken": true, "num_nts": 9, "nts_short": "GUUAAUAAA", "nts_long": "///j/6067,///j/6068,///j/6069,///j/6070,///j/6071,///j/6072,///j/6073,///j/6074,///j/6075" }, { "index": 20, "num_nts": 6, "nts_short": "GUAUUU", "nts_long": "///j/6096,///j/6097,///j/6098,///j/6099,///j/6100,///j/6101" }, { "index": 21, "is_broken": true, "num_nts": 4, "nts_short": "UUAG", "nts_long": "///j/6105,///j/6106,///j/6107,///j/6108" }, { "index": 22, "num_nts": 7, "nts_short": "CUUUACG", "nts_long": "///j/6117,///j/6118,///j/6119,///j/6120,///j/6121,///j/6122,///j/6123" }, { "index": 23, "num_nts": 1, "nts_short": "G", "nts_long": "///j/6133" }, { "index": 24, "num_nts": 2, "nts_short": "AG", "nts_long": "///j/6137,///j/6138" }, { "index": 25, "is_broken": true, "num_nts": 4, "nts_short": "CAAU", "nts_long": "///j/6150,///j/6151,///j/6152,///j/6153" }, { "index": 26, "num_nts": 3, "nts_short": "GCC", "nts_long": "///j/6163,///j/6164,///j/6165" }, { "index": 27, "num_nts": 1, "nts_short": "U", "nts_long": "///j/6167" }, { "index": 28, "num_nts": 4, "nts_short": "UGCG", "nts_long": "///j/6171,///j/6172,///j/6173,///j/6174" }, { "index": 29, "num_nts": 14, "nts_short": "UAAGGCUUCCUCGA", "nts_long": "///j/6217,///j/6218,///j/6219,///j/6220,///j/6221,///j/6222,///j/6223,///j/6224,///j/6225,///j/6226,///j/6227,///j/6228,///j/6229,///j/6230" } ], "num_Aminors": 53, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///1/46 vs ///1/97,///1/433", "A_nt1": { "desc": "///1/46 vs ///1/97", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N7-O2'(hydroxyl)[2.97]" }, "A_nt2": { "desc": "///1/46 vs ///1/433", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 2, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/99 vs ///1/98,///1/432", "A_nt1": { "desc": "///1/99 vs ///1/98", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.69]" }, "A_nt2": { "desc": "///1/99 vs ///1/432", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 3, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///1/149 vs ///1/63,///1/85", "A_nt1": { "desc": "///1/149 vs ///1/63", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/149 vs ///1/85", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.11],N3-O2'(hydroxyl)[2.52]" } }, { "index": 4, "type": "X", "desc_short": "A vs A-A (--)", "desc_long": "///1/150 vs ///1/64,///1/84", "A_nt1": { "desc": "///1/150 vs ///1/64", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/150 vs ///1/84", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N3[2.87]" } }, { "index": 5, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/158 vs ///1/462,///1/467", "A_nt1": { "desc": "///1/158 vs ///1/462", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/158 vs ///1/467", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.79],N1*N3[3.38]" } }, { "index": 6, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/159 vs ///1/462,///1/467", "A_nt1": { "desc": "///1/159 vs ///1/462", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/159 vs ///1/467", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.38]" } }, { "index": 7, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/170 vs ///1/62,///1/86", "A_nt1": { "desc": "///1/170 vs ///1/62", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/170 vs ///1/86", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.08]" } }, { "index": 8, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///1/170 vs ///1/63,///1/85", "A_nt1": { "desc": "///1/170 vs ///1/63", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.02],N3-O2'(hydroxyl)[2.98]" }, "A_nt2": { "desc": "///1/170 vs ///1/85", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 9, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/171 vs ///1/62,///1/86", "A_nt1": { "desc": "///1/171 vs ///1/62", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O3'-O2'(hydroxyl)[2.51]" }, "A_nt2": { "desc": "///1/171 vs ///1/86", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.26]" } }, { "index": 10, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///1/401 vs ///1/364,///1/396", "A_nt1": { "desc": "///1/401 vs ///1/364", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.49]" }, "A_nt2": { "desc": "///1/401 vs ///1/396", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.16]" } }, { "index": 11, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/473 vs ///1/96,///1/434", "A_nt1": { "desc": "///1/473 vs ///1/96", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[2.58]" }, "A_nt2": { "desc": "///1/473 vs ///1/434", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.85],N3-N2(amino)[3.10]" } }, { "index": 12, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/493 vs ///1/490,///1/510", "A_nt1": { "desc": "///1/493 vs ///1/490", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/493 vs ///1/510", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.27],N1-O2'(hydroxyl)[3.01]" } }, { "index": 13, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/493 vs ///1/491,///1/509", "A_nt1": { "desc": "///1/493 vs ///1/491", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[2.94],N6(amino)-O2(carbonyl)[2.92]" }, "A_nt2": { "desc": "///1/493 vs ///1/509", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)*N2(amino)[2.96]" } }, { "index": 14, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/536 vs ///1/537,///1/546", "A_nt1": { "desc": "///1/536 vs ///1/537", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-OP2[2.74],O2'(hydroxyl)-O5'[2.72],O2'(hydroxyl)-O4'[2.99]" }, "A_nt2": { "desc": "///1/536 vs ///1/546", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 15, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/605 vs ///1/598,///1/638", "A_nt1": { "desc": "///1/605 vs ///1/598", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.03]" }, "A_nt2": { "desc": "///1/605 vs ///1/638", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[3.01],O2'(hydroxyl)-O2'(hydroxyl)[2.74],O2'(hydroxyl)-O2(carbonyl)[2.89]" } }, { "index": 16, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/616 vs ///1/617,///1/624", "A_nt1": { "desc": "///1/616 vs ///1/617", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-OP1[2.80]" }, "A_nt2": { "desc": "///1/616 vs ///1/624", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 17, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/668 vs ///1/14,///1/1197", "A_nt1": { "desc": "///1/668 vs ///1/14", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///1/668 vs ///1/1197", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[3.12],O2'(hydroxyl)-N3[3.52],N3-N2(amino)[3.43]" } }, { "index": 18, "type": "I", "desc_short": "A vs A-C (--)", "desc_long": "///1/670 vs ///1/664,///1/1163", "A_nt1": { "desc": "///1/670 vs ///1/664", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/670 vs ///1/1163", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.69],O2'(hydroxyl)-O2(carbonyl)[2.91]" } }, { "index": 19, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/693 vs ///1/692,///1/739", "A_nt1": { "desc": "///1/693 vs ///1/692", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N7-N2(amino)[2.84]" }, "A_nt2": { "desc": "///1/693 vs ///1/739", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 20, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/811 vs ///1/411,///1/429", "A_nt1": { "desc": "///1/811 vs ///1/411", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/811 vs ///1/429", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.12],N1-O2'(hydroxyl)[2.91]" } }, { "index": 21, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/854 vs ///1/108,///1/353", "A_nt1": { "desc": "///1/854 vs ///1/108", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.84]" }, "A_nt2": { "desc": "///1/854 vs ///1/353", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.58]" } }, { "index": 22, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/862 vs ///1/803,///1/860", "A_nt1": { "desc": "///1/862 vs ///1/803", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.59]" }, "A_nt2": { "desc": "///1/862 vs ///1/860", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 23, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/972 vs ///1/956,///1/967", "A_nt1": { "desc": "///1/972 vs ///1/956", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/972 vs ///1/967", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.16]" } }, { "index": 24, "type": "II", "desc_short": "A vs C-A (~Wobble)", "desc_long": "///1/996 vs ///1/674,///1/1031", "A_nt1": { "desc": "///1/996 vs ///1/674", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.07],O2'(hydroxyl)-O2'(hydroxyl)[3.11],N3-O2'(hydroxyl)[2.58]" }, "A_nt2": { "desc": "///1/996 vs ///1/1031", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 25, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/997 vs ///1/673,///1/1032", "A_nt1": { "desc": "///1/997 vs ///1/673", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/997 vs ///1/1032", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.24]" } }, { "index": 26, "type": "X", "desc_short": "A vs C-G (--)", "desc_long": "///1/1011 vs ///1/930,///1/1010", "A_nt1": { "desc": "///1/1011 vs ///1/930", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1011 vs ///1/1010", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O4'-O2'(hydroxyl)[3.10]" } }, { "index": 27, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1034 vs ///1/1842,///1/1857", "A_nt1": { "desc": "///1/1034 vs ///1/1842", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1034 vs ///1/1857", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.17]" } }, { "index": 28, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1034 vs ///1/1843,///1/1856", "A_nt1": { "desc": "///1/1034 vs ///1/1843", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.46]" }, "A_nt2": { "desc": "///1/1034 vs ///1/1856", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 29, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1035 vs ///1/1843,///1/1856", "A_nt1": { "desc": "///1/1035 vs ///1/1843", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.84]" }, "A_nt2": { "desc": "///1/1035 vs ///1/1856", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.01],O2'(hydroxyl)-O2(carbonyl)[2.46]" } }, { "index": 30, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1143 vs ///1/13,///1/1198", "A_nt1": { "desc": "///1/1143 vs ///1/13", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1143 vs ///1/1198", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.55]" } }, { "index": 31, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1150 vs ///1/1141,///1/1146", "A_nt1": { "desc": "///1/1150 vs ///1/1141", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1150 vs ///1/1146", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.69]" } }, { "index": 32, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1181 vs ///1/1037,///1/1078", "A_nt1": { "desc": "///1/1181 vs ///1/1037", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.09]" }, "A_nt2": { "desc": "///1/1181 vs ///1/1078", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 33, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///1/1190 vs ///1/1714,///1/1819", "A_nt1": { "desc": "///1/1190 vs ///1/1714", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.07],N3-O2'(hydroxyl)[2.81]" }, "A_nt2": { "desc": "///1/1190 vs ///1/1819", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 34, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1240 vs ///1/1267,///1/1515", "A_nt1": { "desc": "///1/1240 vs ///1/1267", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.97]" }, "A_nt2": { "desc": "///1/1240 vs ///1/1515", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 35, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1241 vs ///1/1266,///1/1516", "A_nt1": { "desc": "///1/1241 vs ///1/1266", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91],O2'(hydroxyl)-O2(carbonyl)[3.14]" }, "A_nt2": { "desc": "///1/1241 vs ///1/1516", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.53],N3-N2(amino)[2.64]" } }, { "index": 36, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1465 vs ///1/1366,///1/1373", "A_nt1": { "desc": "///1/1465 vs ///1/1366", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.32],N3-N2(amino)[3.00]" }, "A_nt2": { "desc": "///1/1465 vs ///1/1373", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.73]" } }, { "index": 37, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1484 vs ///1/1345,///1/1384", "A_nt1": { "desc": "///1/1484 vs ///1/1345", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.45]" }, "A_nt2": { "desc": "///1/1484 vs ///1/1384", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.41]" } }, { "index": 38, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1522 vs ///1/1236,///1/1521", "A_nt1": { "desc": "///1/1522 vs ///1/1236", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.79]" }, "A_nt2": { "desc": "///1/1522 vs ///1/1521", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 39, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1533 vs ///1/1536,///1/1597", "A_nt1": { "desc": "///1/1533 vs ///1/1536", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1-N2(amino)[3.26],N3-O2'(hydroxyl)[2.73]" }, "A_nt2": { "desc": "///1/1533 vs ///1/1597", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 40, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1569 vs ///1/1613,///1/1626", "A_nt1": { "desc": "///1/1569 vs ///1/1613", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.06]" }, "A_nt2": { "desc": "///1/1569 vs ///1/1626", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.11],O2'(hydroxyl)-O2(carbonyl)[2.85]" } }, { "index": 41, "type": "X", "desc_short": "A vs U-G (--)", "desc_long": "///1/1588 vs ///1/1653,///1/1671", "A_nt1": { "desc": "///1/1588 vs ///1/1653", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1588 vs ///1/1671", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.15]" } }, { "index": 42, "type": "II", "desc_short": "A vs U-G (--)", "desc_long": "///1/1589 vs ///1/1653,///1/1671", "A_nt1": { "desc": "///1/1589 vs ///1/1653", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.00],O2'(hydroxyl)-O2'(hydroxyl)[2.80],N3-O2'(hydroxyl)[2.89]" }, "A_nt2": { "desc": "///1/1589 vs ///1/1671", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 43, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///1/1634 vs ///1/1228,///1/1530", "A_nt1": { "desc": "///1/1634 vs ///1/1228", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.00],N3-O2'(hydroxyl)[3.27]" }, "A_nt2": { "desc": "///1/1634 vs ///1/1530", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 44, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1834 vs ///1/1205,///1/1693", "A_nt1": { "desc": "///1/1834 vs ///1/1205", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N7*O2(carbonyl)[3.08],N6(amino)-O2'(hydroxyl)[2.58]" }, "A_nt2": { "desc": "///1/1834 vs ///1/1693", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "OP1-O2'(hydroxyl)[3.51],O4'-N2(amino)[3.01]" } }, { "index": 45, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1850 vs ///1/1705,///1/1829", "A_nt1": { "desc": "///1/1850 vs ///1/1705", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1850 vs ///1/1829", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.87]" } }, { "index": 46, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///j/6052 vs ///j/6130,///j/6156", "A_nt1": { "desc": "///j/6052 vs ///j/6130", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.08]" }, "A_nt2": { "desc": "///j/6052 vs ///j/6156", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 47, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///j/6056 vs ///j/6125,///j/6161", "A_nt1": { "desc": "///j/6056 vs ///j/6125", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///j/6056 vs ///j/6161", "face_type": "+", "hbonds_num": 4, "hbonds_desc": "OP2*O3'[2.68],N7-O2'(hydroxyl)[2.16],N6(amino)-O2'(hydroxyl)[3.22],N6(amino)-N3[2.88]" } }, { "index": 48, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///j/6056 vs ///j/6126,///j/6160", "A_nt1": { "desc": "///j/6056 vs ///j/6126", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.76],N1-O2'(hydroxyl)[3.20]" }, "A_nt2": { "desc": "///j/6056 vs ///j/6160", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 49, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///j/6057 vs ///j/6125,///j/6161", "A_nt1": { "desc": "///j/6057 vs ///j/6125", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.86],N1-O2'(hydroxyl)[2.72]" }, "A_nt2": { "desc": "///j/6057 vs ///j/6161", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 50, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///j/6151 vs ///j/6103,///j/6135", "A_nt1": { "desc": "///j/6151 vs ///j/6103", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.56]" }, "A_nt2": { "desc": "///j/6151 vs ///j/6135", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1*O2(carbonyl)[2.71],N3-O2'(hydroxyl)[3.13]" } }, { "index": 51, "type": "X", "desc_short": "A vs G-G (--)", "desc_long": "///j/6152 vs ///j/6104,///j/6133", "A_nt1": { "desc": "///j/6152 vs ///j/6104", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.44],N1-N2(amino)[3.01]" }, "A_nt2": { "desc": "///j/6152 vs ///j/6133", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 52, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///j/6152 vs ///j/6104,///j/6134", "A_nt1": { "desc": "///j/6152 vs ///j/6104", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.44],N1-N2(amino)[3.01]" }, "A_nt2": { "desc": "///j/6152 vs ///j/6134", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.86]" } }, { "index": 53, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///j/6182 vs ///j/6181,///j/6195", "A_nt1": { "desc": "///j/6182 vs ///j/6181", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///j/6182 vs ///j/6195", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.33]" } } ], "num_riboseZippers": 10, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "GCAG", "nts_long": "///1/95,///1/96,///1/473,///1/474" }, { "index": 2, "num_nts": 4, "nts_short": "UAAG", "nts_long": "///1/454,///1/455,///1/1735,///1/1736" }, { "index": 3, "num_nts": 4, "nts_short": "AACG", "nts_long": "///1/669,///1/670,///1/1163,///1/1164" }, { "index": 4, "num_nts": 4, "nts_short": "UCUU", "nts_long": "///1/1025,///1/1026,///1/1160,///1/1161" }, { "index": 5, "num_nts": 4, "nts_short": "UACG", "nts_long": "///1/1081,///1/1082,///1/1842,///1/1843" }, { "index": 6, "num_nts": 4, "nts_short": "AACC", "nts_long": "///1/1240,///1/1241,///1/1266,///1/1267" }, { "index": 7, "num_nts": 4, "nts_short": "AGCG", "nts_long": "///1/1545,///1/1546,///1/1670,///1/1671" }, { "index": 8, "num_nts": 4, "nts_short": "CACC", "nts_long": "///1/1568,///1/1569,///1/1626,///1/1627" }, { "index": 9, "num_nts": 4, "nts_short": "AAUG", "nts_long": "///1/1588,///1/1589,///1/1653,///1/1654" }, { "index": 10, "num_nts": 4, "nts_short": "CGAA", "nts_long": "///1/1705,///1/1706,///1/1850,///1/1851" } ], "num_splayUnits": 162, "splayUnits": [ { "index": 1, "num_nts": 2, "nts_short": "AC", "nts_long": "///1/2,///1/3" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/8,///1/9" }, { "index": 3, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/32,///1/33" }, { "index": 4, "num_nts": 3, "nts_short": "AGA", "nts_long": "///1/40,///1/41,///1/42" }, { "index": 5, "num_nts": 3, "nts_short": "AAG", "nts_long": "///1/45,///1/46,///1/47" }, { "index": 6, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/54,///1/55" }, { "index": 7, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/58,///1/59" }, { "index": 8, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/60,///1/61" }, { "index": 9, "num_nts": 5, "nts_short": "CGCAC", "nts_long": "///1/65,///1/66,///1/67,///1/68,///1/69" }, { "index": 10, "num_nts": 3, "nts_short": "CGG", "nts_long": "///1/73,///1/74,///1/75" }, { "index": 11, "num_nts": 3, "nts_short": "ACA", "nts_long": "///1/77,///1/78,///1/79" }, { "index": 12, "num_nts": 3, "nts_short": "UGG", "nts_long": "///1/112,///1/113,///1/114" }, { "index": 13, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/117,///1/118" }, { "index": 14, "num_nts": 5, "nts_short": "GUCGC", "nts_long": "///1/123,///1/124,///1/125,///1/126,///1/127" }, { "index": 15, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/131,///1/132" }, { "index": 16, "num_nts": 7, "nts_short": "CUCUCCC", "nts_long": "///1/134,///1/135,///1/136,///1/137,///1/138,///1/139,///1/140" }, { "index": 17, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/142,///1/143" }, { "index": 18, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/157,///1/158" }, { "index": 19, "num_nts": 3, "nts_short": "UUC", "nts_long": "///1/160,///1/161,///1/162" }, { "index": 20, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/172,///1/173" }, { "index": 21, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/199,///1/200" }, { "index": 22, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/214,///1/215" }, { "index": 23, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/227,///1/228" }, { "index": 24, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/305,///1/306" }, { "index": 25, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/307,///1/308" }, { "index": 26, "num_nts": 3, "nts_short": "CCG", "nts_long": "///1/310,///1/311,///1/312" }, { "index": 27, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/324,///1/325" }, { "index": 28, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/328,///1/329" }, { "index": 29, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/356,///1/357" }, { "index": 30, "num_nts": 3, "nts_short": "AUC", "nts_long": "///1/360,///1/361,///1/362" }, { "index": 31, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/384,///1/385" }, { "index": 32, "num_nts": 3, "nts_short": "ACC", "nts_long": "///1/398,///1/399,///1/400" }, { "index": 33, "num_nts": 3, "nts_short": "UGA", "nts_long": "///1/406,///1/407,///1/408" }, { "index": 34, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/417,///1/418" }, { "index": 35, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/425,///1/426" }, { "index": 36, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/435,///1/436" }, { "index": 37, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/447,///1/448,///1/449" }, { "index": 38, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/451,///1/452" }, { "index": 39, "num_nts": 3, "nts_short": "CAA", "nts_long": "///1/463,///1/464,///1/465" }, { "index": 40, "num_nts": 4, "nts_short": "GCAG", "nts_long": "///1/471,///1/472,///1/473,///1/474" }, { "index": 41, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/485,///1/486" }, { "index": 42, "num_nts": 3, "nts_short": "UUA", "nts_long": "///1/487,///1/488,///1/489" }, { "index": 43, "num_nts": 3, "nts_short": "ACC", "nts_long": "///1/500,///1/501,///1/502" }, { "index": 44, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/506,///1/507,///1/508" }, { "index": 45, "num_nts": 3, "nts_short": "GAC", "nts_long": "///1/515,///1/516,///1/517" }, { "index": 46, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/524,///1/525" }, { "index": 47, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/542,///1/543" }, { "index": 48, "num_nts": 3, "nts_short": "GGC", "nts_long": "///1/546,///1/547,///1/548" }, { "index": 49, "num_nts": 3, "nts_short": "UAA", "nts_long": "///1/553,///1/554,///1/555" }, { "index": 50, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/573,///1/574" }, { "index": 51, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/588,///1/589" }, { "index": 52, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/592,///1/593" }, { "index": 53, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/599,///1/600" }, { "index": 54, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/605,///1/606" }, { "index": 55, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/614,///1/615" }, { "index": 56, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/619,///1/620" }, { "index": 57, "num_nts": 5, "nts_short": "GUAAU", "nts_long": "///1/626,///1/627,///1/628,///1/629,///1/630" }, { "index": 58, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/631,///1/632" }, { "index": 59, "num_nts": 4, "nts_short": "AGUU", "nts_long": "///1/655,///1/656,///1/657,///1/658" }, { "index": 60, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/659,///1/660" }, { "index": 61, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/662,///1/663" }, { "index": 62, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/665,///1/666" }, { "index": 63, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/672,///1/673" }, { "index": 64, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/683,///1/684" }, { "index": 65, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/687,///1/688" }, { "index": 66, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/741,///1/742" }, { "index": 67, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/744,///1/745" }, { "index": 68, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/810,///1/811" }, { "index": 69, "num_nts": 4, "nts_short": "UGUU", "nts_long": "///1/820,///1/821,///1/822,///1/823" }, { "index": 70, "num_nts": 9, "nts_short": "CCCGAGCCG", "nts_long": "///1/833,///1/834,///1/835,///1/836,///1/837,///1/838,///1/839,///1/840,///1/841" }, { "index": 71, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/846,///1/847" }, { "index": 72, "num_nts": 5, "nts_short": "AUAGG", "nts_long": "///1/870,///1/871,///1/872,///1/873,///1/874" }, { "index": 73, "num_nts": 3, "nts_short": "CAU", "nts_long": "///1/912,///1/913,///1/914" }, { "index": 74, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/916,///1/917" }, { "index": 75, "num_nts": 5, "nts_short": "UAAGA", "nts_long": "///1/918,///1/919,///1/920,///1/921,///1/922" }, { "index": 76, "num_nts": 3, "nts_short": "GGG", "nts_long": "///1/932,///1/933,///1/934" }, { "index": 77, "num_nts": 3, "nts_short": "UGG", "nts_long": "///1/969,///1/970,///1/971" }, { "index": 78, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/985,///1/986" }, { "index": 79, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/991,///1/992" }, { "index": 80, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/1001,///1/1002" }, { "index": 81, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1033,///1/1034" }, { "index": 82, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/1044,///1/1045" }, { "index": 83, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/1057,///1/1058" }, { "index": 84, "num_nts": 3, "nts_short": "AUA", "nts_long": "///1/1060,///1/1061,///1/1062" }, { "index": 85, "num_nts": 6, "nts_short": "AAACGA", "nts_long": "///1/1082,///1/1083,///1/1084,///1/1085,///1/1086,///1/1087" }, { "index": 86, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/1088,///1/1089" }, { "index": 87, "num_nts": 3, "nts_short": "GCG", "nts_long": "///1/1108,///1/1109,///1/1110" }, { "index": 88, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/1115,///1/1116" }, { "index": 89, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1142,///1/1143" }, { "index": 90, "num_nts": 3, "nts_short": "AAG", "nts_long": "///1/1149,///1/1150,///1/1151" }, { "index": 91, "num_nts": 3, "nts_short": "UUU", "nts_long": "///1/1154,///1/1155,///1/1156" }, { "index": 92, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1157,///1/1158" }, { "index": 93, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1165,///1/1166" }, { "index": 94, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/1179,///1/1180" }, { "index": 95, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/1206,///1/1207,///1/1208" }, { "index": 96, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/1215,///1/1216" }, { "index": 97, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/1239,///1/1240" }, { "index": 98, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/1242,///1/1243" }, { "index": 99, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/1247,///1/1248" }, { "index": 100, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/1250,///1/1251" }, { "index": 101, "num_nts": 3, "nts_short": "CAC", "nts_long": "///1/1252,///1/1253,///1/1254" }, { "index": 102, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1257,///1/1258" }, { "index": 103, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/1259,///1/1260" }, { "index": 104, "num_nts": 3, "nts_short": "AGG", "nts_long": "///1/1284,///1/1285,///1/1286" }, { "index": 105, "num_nts": 3, "nts_short": "AUU", "nts_long": "///1/1287,///1/1288,///1/1289" }, { "index": 106, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/1297,///1/1298" }, { "index": 107, "num_nts": 4, "nts_short": "AUAG", "nts_long": "///1/1299,///1/1300,///1/1301,///1/1302" }, { "index": 108, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/1313,///1/1314" }, { "index": 109, "num_nts": 3, "nts_short": "GUG", "nts_long": "///1/1325,///1/1326,///1/1327" }, { "index": 110, "num_nts": 3, "nts_short": "GCA", "nts_long": "///1/1330,///1/1331,///1/1332" }, { "index": 111, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/1368,///1/1369" }, { "index": 112, "num_nts": 3, "nts_short": "AUU", "nts_long": "///1/1370,///1/1371,///1/1372" }, { "index": 113, "num_nts": 3, "nts_short": "UGC", "nts_long": "///1/1397,///1/1398,///1/1399" }, { "index": 114, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/1422,///1/1423" }, { "index": 115, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1424,///1/1425" }, { "index": 116, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/1462,///1/1463" }, { "index": 117, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1473,///1/1474" }, { "index": 118, "num_nts": 3, "nts_short": "CAA", "nts_long": "///1/1482,///1/1483,///1/1484" }, { "index": 119, "num_nts": 3, "nts_short": "CAG", "nts_long": "///1/1488,///1/1489,///1/1490" }, { "index": 120, "num_nts": 3, "nts_short": "CUG", "nts_long": "///1/1493,///1/1494,///1/1495" }, { "index": 121, "num_nts": 3, "nts_short": "UGA", "nts_long": "///1/1496,///1/1497,///1/1498" }, { "index": 122, "num_nts": 6, "nts_short": "UAGAUG", "nts_long": "///1/1505,///1/1506,///1/1507,///1/1508,///1/1509,///1/1510" }, { "index": 123, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/1519,///1/1520" }, { "index": 124, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/1532,///1/1533" }, { "index": 125, "num_nts": 3, "nts_short": "CUG", "nts_long": "///1/1534,///1/1535,///1/1536" }, { "index": 126, "num_nts": 4, "nts_short": "GCCU", "nts_long": "///1/1552,///1/1553,///1/1554,///1/1555" }, { "index": 127, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/1557,///1/1558" }, { "index": 128, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1566,///1/1567" }, { "index": 129, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/1578,///1/1579" }, { "index": 130, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1587,///1/1588" }, { "index": 131, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1600,///1/1601" }, { "index": 132, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1603,///1/1604" }, { "index": 133, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/1623,///1/1624" }, { "index": 134, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1636,///1/1637" }, { "index": 135, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1638,///1/1639" }, { "index": 136, "num_nts": 3, "nts_short": "AGU", "nts_long": "///1/1647,///1/1648,///1/1649" }, { "index": 137, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/1660,///1/1661" }, { "index": 138, "num_nts": 3, "nts_short": "AGC", "nts_long": "///1/1664,///1/1665,///1/1666" }, { "index": 139, "num_nts": 3, "nts_short": "AAG", "nts_long": "///1/1678,///1/1679,///1/1680" }, { "index": 140, "num_nts": 6, "nts_short": "ACACCG", "nts_long": "///1/1697,///1/1698,///1/1699,///1/1700,///1/1701,///1/1702" }, { "index": 141, "num_nts": 3, "nts_short": "UUG", "nts_long": "///1/1720,///1/1721,///1/1722" }, { "index": 142, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/1764,///1/1765" }, { "index": 143, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/1835,///1/1836" }, { "index": 144, "num_nts": 3, "nts_short": "GUU", "nts_long": "///1/1837,///1/1838,///1/1839" }, { "index": 145, "num_nts": 3, "nts_short": "AGG", "nts_long": "///1/1860,///1/1861,///1/1862" }, { "index": 146, "num_nts": 3, "nts_short": "CAU", "nts_long": "///1/1865,///1/1866,///1/1867" }, { "index": 147, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/1868,///1/1869" }, { "index": 148, "num_nts": 2, "nts_short": "AA", "nts_long": "///j/6032,///j/6033" }, { "index": 149, "num_nts": 2, "nts_short": "UG", "nts_long": "///j/6043,///j/6044" }, { "index": 150, "num_nts": 2, "nts_short": "UA", "nts_long": "///j/6053,///j/6054" }, { "index": 151, "num_nts": 3, "nts_short": "GUU", "nts_long": "///j/6067,///j/6068,///j/6069" }, { "index": 152, "num_nts": 2, "nts_short": "UG", "nts_long": "///j/6086,///j/6087" }, { "index": 153, "num_nts": 2, "nts_short": "CG", "nts_long": "///j/6122,///j/6123" }, { "index": 154, "num_nts": 2, "nts_short": "AG", "nts_long": "///j/6137,///j/6138" }, { "index": 155, "num_nts": 3, "nts_short": "CCC", "nts_long": "///j/6145,///j/6146,///j/6147" }, { "index": 156, "num_nts": 4, "nts_short": "GCCC", "nts_long": "///j/6163,///j/6164,///j/6165,///j/6166" }, { "index": 157, "num_nts": 2, "nts_short": "AG", "nts_long": "///j/6205,///j/6206" }, { "index": 158, "num_nts": 3, "nts_short": "UUU", "nts_long": "///j/6210,///j/6211,///j/6212" }, { "index": 159, "num_nts": 2, "nts_short": "UA", "nts_long": "///j/6217,///j/6218" }, { "index": 160, "num_nts": 2, "nts_short": "AG", "nts_long": "///j/6219,///j/6220" }, { "index": 161, "num_nts": 2, "nts_short": "CU", "nts_long": "///j/6222,///j/6223" }, { "index": 162, "num_nts": 5, "nts_short": "CUCGA", "nts_long": "///j/6226,///j/6227,///j/6228,///j/6229,///j/6230" } ], "num_HtypePknots": 3, "HtypePknots": [ { "index": 1, "desc": "stem#122(hairpin#37) vs stem#123(hairpin#38) L1 groove=MAJOR nts=2 UU ///j/6185,///j/6186" }, { "index": 2, "desc": "stem#122(hairpin#37) vs stem#123(hairpin#38) L2 groove=----- nts=2 AG ///j/6191,///j/6192" }, { "index": 3, "desc": "stem#122(hairpin#37) vs stem#123(hairpin#38) L3 groove=----- nts=18 GAAAAACCUAAGAAAUUU ///j/6195,///j/6196,///j/6197,///j/6198,///j/6199,///j/6200,///j/6201,///j/6202,///j/6203,///j/6204,///j/6205,///j/6206,///j/6207,///j/6208,///j/6209,///j/6210,///j/6211,///j/6212" } ], "pseudoknot_order": 3, "pseudoknot_nts": [ { "index": 1, "symbols": "[]", "num_nts": 48, "nts_short": "GUCCAAAACGGCCGUUUUGGAUGAGGAGGCCUCCUCGUUCGAUCGAAC", "nts_long": "///1/10,///1/12,///1/13,///1/14,///1/231,///1/232,///1/235,///1/236,///1/237,///1/600,///1/601,///1/621,///1/622,///1/891,///1/892,///1/893,///1/897,///1/898,///1/1197,///1/1198,///1/1199,///1/1201,///j/6062,///j/6063,///j/6064,///j/6066,///j/6102,///j/6103,///j/6104,///j/6134,///j/6135,///j/6136,///j/6166,///j/6168,///j/6169,///j/6170,///j/6175,///j/6179,///j/6180,///j/6181,///j/6183,///j/6184,///j/6193,///j/6194,///j/6195,///j/6196,///j/6197,///j/6201" }, { "index": 2, "symbols": "{}", "num_nts": 6, "nts_short": "GUUAAU", "nts_long": "///1/656,///1/666,///1/667,///1/1144,///1/1145,///1/1156" }, { "index": 3, "symbols": "<>", "num_nts": 2, "nts_short": "CG", "nts_long": "///1/1085,///1/1861" } ], "dbn": { "all_chains": { "num_nts": 1943, "num_chars": 1952, "bseq": "UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG&UAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCG&CGCCCCUUGCCUCUCGGCGC&GCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCUCGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA&AAAAAUGUGAUCUUGCUUGUAAAUACAAUUUUGAGA&GGUUAAUA&AAUUACAAGUAGUGCUAUUUUUGUAUUUAGGUU&AGCUAUUUAGCUUUACGUUCCAGGAUGCCU&AGUGGCAGCCCCAC&AAUAUCCAGGAAGCCCUCUCUGCGGUUAUUCAGAUUAGGUAGUCGAAAAACCUAAGAAAUUUACCUUAAGGCUUCCUCGA", 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"form": 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}, "chain_1": { "num_nts": 1742, "num_chars": 1745, "bseq": 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