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122, "type": "phosphate", "atom": "///B/43/OP2", "nt": "///B/40", "vert_dist": 3.067 }, { "index": 123, "type": "sugar", "atom": "///B/15/O4'", "nt": "///B/109", "vert_dist": 2.947 } ], "num_hairpins": 70, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 9 ], "summary": "[1] 8 [A.59 A.68] 3", "num_nts": 10, "nts_short": "UGCUAAUCUG", "nts_long": "///A/59,///A/60,///A/61,///A/62,///A/63,///A/64,///A/65,///A/66,///A/67,///A/68", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GCUAAUCU", "nts_long": "///A/60,///A/61,///A/62,///A/63,///A/64,///A/65,///A/66,///A/67" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 21 ], "stem_indices": [ 10 ], "summary": "[1] 21 [A.66 A.88] 3", "num_nts": 23, "nts_short": "CUGCGAUAAGCGUCGGUAAGGUG", "nts_long": "///A/66,///A/67,///A/68,///A/69,///A/70,///A/71,///A/72,///A/73,///A/74,///A/75,///A/76,///A/77,///A/78,///A/79,///A/80,///A/81,///A/82,///A/83,///A/84,///A/85,///A/86,///A/87,///A/88", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 21, "nts_short": "UGCGAUAAGCGUCGGUAAGGU", "nts_long": "///A/67,///A/68,///A/69,///A/70,///A/71,///A/72,///A/73,///A/74,///A/75,///A/76,///A/77,///A/78,///A/79,///A/80,///A/81,///A/82,///A/83,///A/84,///A/85,///A/86,///A/87" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 12 ], "summary": "[1] 7 [A.87 A.95] 3", "num_nts": 9, "nts_short": "UGAUAUGAA", "nts_long": "///A/87,///A/88,///A/89,///A/90,///A/91,///A/92,///A/93,///A/94,///A/95", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GAUAUGA", "nts_long": "///A/88,///A/89,///A/90,///A/91,///A/92,///A/93,///A/94" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 13 ], "summary": "[1] 4 [A.123 A.128] 3", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///A/123,///A/124,///A/125,///A/126,///A/127,///A/128", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/124,///A/125,///A/126,///A/127" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 14 ], "summary": "[1] 4 [A.137 A.142] 7", "num_nts": 6, "nts_short": "UUUCGA", "nts_long": "///A/137,///A/138,///A/139,///A/140,///A/141,///A/142", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///A/138,///A/139,///A/140,///A/141" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 15 ], "summary": "[1] 9 [A.158 A.168] 9", "num_nts": 11, "nts_short": "UGAAUCCAUAG", "nts_long": "///A/158,///A/159,///A/160,///A/161,///A/162,///A/163,///A/164,///A/165,///A/166,///A/167,///A/168", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "GAAUCCAUA", "nts_long": "///A/159,///A/160,///A/161,///A/162,///A/163,///A/164,///A/165,///A/166,///A/167" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ -4 ], "summary": "[1] 6 [A.194 A.201] 1", "num_nts": 8, "nts_short": "GAAACAUC", "nts_long": "///A/194,///A/195,///A/196,///A/197,///A/198,///A/199,///A/200,///A/201", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AAACAU", "nts_long": "///A/195,///A/196,///A/197,///A/198,///A/199,///A/200" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 17 ], "summary": "[1] 4 [A.225 A.230] 2", "num_nts": 6, "nts_short": "CAACCG", "nts_long": "///A/225,///A/226,///A/227,///A/228,///A/229,///A/230", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/226,///A/227,///A/228,///A/229" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 19 ], "summary": "[1] 5 [A.246 A.252] 2", "num_nts": 7, "nts_short": "CGGCGAG", "nts_long": "///A/246,///A/247,///A/248,///A/249,///A/250,///A/251,///A/252", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGCGA", "nts_long": "///A/247,///A/248,///A/249,///A/250,///A/251" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 24 ], "summary": "[1] 6 [A.305 A.312] 5", "num_nts": 8, "nts_short": "CUGGAAAG", "nts_long": "///A/305,///A/306,///A/307,///A/308,///A/309,///A/310,///A/311,///A/312", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UGGAAA", "nts_long": "///A/306,///A/307,///A/308,///A/309,///A/310,///A/311" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ -6 ], "summary": "[1] 3 [A.319 A.323] 1", "num_nts": 5, "nts_short": "GAUAC", "nts_long": "///A/319,///A/320,///A/321,///A/322,///A/323", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/320,///A/321,///A/322" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 26 ], "summary": "[1] 7 [A.327 A.335] 3", "num_nts": 9, "nts_short": "GUGACAGCC", "nts_long": "///A/327,///A/328,///A/329,///A/330,///A/331,///A/332,///A/333,///A/334,///A/335", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGACAGC", "nts_long": "///A/328,///A/329,///A/330,///A/331,///A/332,///A/333,///A/334" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ 27 ], "summary": "[1] 11 [A.381 A.393] 7", "num_nts": 13, "nts_short": "GACACGUGGUAUC", "nts_long": "///A/381,///A/382,///A/383,///A/384,///A/385,///A/386,///A/387,///A/388,///A/389,///A/390,///A/391,///A/392,///A/393", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "ACACGUGGUAU", "nts_long": "///A/382,///A/383,///A/384,///A/385,///A/386,///A/387,///A/388,///A/389,///A/390,///A/391,///A/392" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 25 ], "stem_indices": [ -7 ], "summary": "[1] 25 [A.385 A.411] 1", "num_nts": 27, "nts_short": "CGUGGUAUCCUGUCUGAAUAUGGGGGG", "nts_long": "///A/385,///A/386,///A/387,///A/388,///A/389,///A/390,///A/391,///A/392,///A/393,///A/394,///A/395,///A/396,///A/397,///A/398,///A/399,///A/400,///A/401,///A/402,///A/403,///A/404,///A/405,///A/406,///A/407,///A/408,///A/409,///A/410,///A/411", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 25, "nts_short": "GUGGUAUCCUGUCUGAAUAUGGGGG", "nts_long": "///A/386,///A/387,///A/388,///A/389,///A/390,///A/391,///A/392,///A/393,///A/394,///A/395,///A/396,///A/397,///A/398,///A/399,///A/400,///A/401,///A/402,///A/403,///A/404,///A/405,///A/406,///A/407,///A/408,///A/409,///A/410" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 28 ], "summary": "[1] 6 [A.410 A.417] 5", "num_nts": 8, "nts_short": "GGACCAUC", "nts_long": "///A/410,///A/411,///A/412,///A/413,///A/414,///A/415,///A/416,///A/417", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GACCAU", "nts_long": "///A/411,///A/412,///A/413,///A/414,///A/415,///A/416" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 30 ], "summary": "[1] 4 [A.462 A.467] 2", "num_nts": 6, "nts_short": "CGUGAG", "nts_long": "///A/462,///A/463,///A/464,///A/465,///A/466,///A/467", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///A/463,///A/464,///A/465,///A/466" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 31 ], "summary": "[1] 5 [A.487 A.493] 4", "num_nts": 7, "nts_short": "CGGCGAG", "nts_long": "///A/487,///A/488,///A/489,///A/490,///A/491,///A/492,///A/493", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGCGA", "nts_long": "///A/488,///A/489,///A/490,///A/491,///A/492" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 33 ], "summary": "[1] 6 [A.543 A.550] 5", "num_nts": 8, "nts_short": "GCUUAGGC", "nts_long": "///A/543,///A/544,///A/545,///A/546,///A/547,///A/548,///A/549,///A/550", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CUUAGG", "nts_long": "///A/544,///A/545,///A/546,///A/547,///A/548,///A/549" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ -11 ], "summary": "[1] 8 [A.566 A.575] 1", "num_nts": 10, "nts_short": "UUUUGUAUAA", "nts_long": "///A/566,///A/567,///A/568,///A/569,///A/570,///A/571,///A/572,///A/573,///A/574,///A/575", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UUUGUAUA", "nts_long": "///A/567,///A/568,///A/569,///A/570,///A/571,///A/572,///A/573,///A/574" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 37 ], "summary": "[1] 5 [A.611 A.617] 2", "num_nts": 7, "nts_short": "CGAAUAG", "nts_long": "///A/611,///A/612,///A/613,///A/614,///A/615,///A/616,///A/617", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAAUA", "nts_long": "///A/612,///A/613,///A/614,///A/615,///A/616" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 38 ], "summary": "[1] 4 [A.629 A.634] 2", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///A/629,///A/630,///A/631,///A/632,///A/633,///A/634", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/630,///A/631,///A/632,///A/633" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 39 ], "summary": "[1] 5 [A.641 A.647] 4", "num_nts": 7, "nts_short": "UUAACUG", "nts_long": "///A/641,///A/642,///A/643,///A/644,///A/645,///A/646,///A/647", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAACU", "nts_long": "///A/642,///A/643,///A/644,///A/645,///A/646" } ] }, { "index": 23, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 44 ], "summary": "[1] 6 [A.712 A.719] 6", "num_nts": 8, "nts_short": "GGUAACAC", "nts_long": "///A/712,///A/713,///A/714,///A/715,///A/716,///A/717,///A/718,///A/719", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GUAACA", "nts_long": "///A/713,///A/714,///A/715,///A/716,///A/717,///A/718" } ] }, { "index": 24, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 46 ], "summary": "[1] 8 [A.744 A.753] 5", "num_nts": 10, "nts_short": "UGUUGAAAAA", "nts_long": "///A/744,///A/745,///A/746,///A/747,///A/748,///A/749,///A/750,///A/751,///A/752,///A/753", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GUUGAAAA", "nts_long": "///A/745,///A/746,///A/747,///A/748,///A/749,///A/750,///A/751,///A/752" } ] }, { "index": 25, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 47 ], "summary": "[1] 7 [A.778 A.786] 2", "num_nts": 9, "nts_short": "GUGAAAGGC", "nts_long": "///A/778,///A/779,///A/780,///A/781,///A/782,///A/783,///A/784,///A/785,///A/786", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGAAAGG", "nts_long": "///A/779,///A/780,///A/781,///A/782,///A/783,///A/784,///A/785" } ] }, { "index": 26, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 49 ], "summary": "[1] 4 [A.826 A.831] 5", "num_nts": 6, "nts_short": "UUUAGG", "nts_long": "///A/826,///A/827,///A/828,///A/829,///A/830,///A/831", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUAG", "nts_long": "///A/827,///A/828,///A/829,///A/830" } ] }, { "index": 27, "type": "hairpin loop", "bridging_nts": [ 26 ], "stem_indices": [ 55 ], "summary": "[1] 26 [A.875 A.902] 4", "num_nts": 28, "nts_short": "GCAAGGGGGUCAUCCCGACUUACCAACC", "nts_long": "///A/875,///A/876,///A/877,///A/878,///A/879,///A/880,///A/881,///A/882,///A/883,///A/884,///A/885,///A/886,///A/887,///A/888,///A/889,///A/890,///A/891,///A/892,///A/893,///A/894,///A/895,///A/896,///A/897,///A/898,///A/899,///A/900,///A/901,///A/902", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 26, "nts_short": "CAAGGGGGUCAUCCCGACUUACCAAC", "nts_long": "///A/876,///A/877,///A/878,///A/879,///A/880,///A/881,///A/882,///A/883,///A/884,///A/885,///A/886,///A/887,///A/888,///A/889,///A/890,///A/891,///A/892,///A/893,///A/894,///A/895,///A/896,///A/897,///A/898,///A/899,///A/900,///A/901" } ] }, { "index": 28, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 56 ], "summary": "[1] 8 [A.954 A.963] 8", "num_nts": 10, "nts_short": "GUGCUAACGU", "nts_long": "///A/954,///A/955,///A/956,///A/957,///A/958,///A/959,///A/960,///A/961,///A/962,///A/963", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UGCUAACG", "nts_long": "///A/955,///A/956,///A/957,///A/958,///A/959,///A/960,///A/961,///A/962" } ] }, { "index": 29, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 57 ], "summary": "[1] 6 [A.978 A.985] 3", "num_nts": 8, "nts_short": "GAAACAAC", "nts_long": "///A/978,///A/979,///A/980,///A/981,///A/982,///A/983,///A/984,///A/985", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AAACAA", "nts_long": "///A/979,///A/980,///A/981,///A/982,///A/983,///A/984" } ] }, { "index": 30, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ -22 ], "summary": "[1] 13 [A.1062 A.1076] 1", "num_nts": 15, "nts_short": "GGCUUAGAAGCAGCC", "nts_long": "///A/1062,///A/1063,///A/1064,///A/1065,///A/1066,///A/1067,///A/1068,///A/1069,///A/1070,///A/1071,///A/1072,///A/1073,///A/1074,///A/1075,///A/1076", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "GCUUAGAAGCAGC", "nts_long": "///A/1063,///A/1064,///A/1065,///A/1066,///A/1067,///A/1068,///A/1069,///A/1070,///A/1071,///A/1072,///A/1073,///A/1074,///A/1075" } ] }, { "index": 31, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ -24 ], "summary": "[1] 6 [A.1092 A.1099] 1", "num_nts": 8, "nts_short": "CGUAAUAG", "nts_long": "///A/1092,///A/1093,///A/1094,///A/1095,///A/1096,///A/1097,///A/1098,///A/1099", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GUAAUA", "nts_long": "///A/1093,///A/1094,///A/1095,///A/1096,///A/1097,///A/1098" } ] }, { "index": 32, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ -26 ], "summary": "[1] 6 [A.1171 A.1178] 1", "num_nts": 8, "nts_short": "GCUUAUGC", "nts_long": "///A/1171,///A/1172,///A/1173,///A/1174,///A/1175,///A/1176,///A/1177,///A/1178", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CUUAUG", "nts_long": "///A/1172,///A/1173,///A/1174,///A/1175,///A/1176,///A/1177" } ] }, { "index": 33, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 71 ], "summary": "[1] 4 [A.1222 A.1227] 8", "num_nts": 6, "nts_short": "UGUGAG", "nts_long": "///A/1222,///A/1223,///A/1224,///A/1225,///A/1226,///A/1227", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///A/1223,///A/1224,///A/1225,///A/1226" } ] }, { "index": 34, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 73 ], "summary": "[1] 7 [A.1281 A.1289] 6", "num_nts": 9, "nts_short": "GUGAAAAGC", "nts_long": "///A/1281,///A/1282,///A/1283,///A/1284,///A/1285,///A/1286,///A/1287,///A/1288,///A/1289", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGAAAAG", "nts_long": "///A/1282,///A/1283,///A/1284,///A/1285,///A/1286,///A/1287,///A/1288" } ] }, { "index": 35, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 78 ], "summary": "[1] 5 [A.1324 A.1330] 2", "num_nts": 7, "nts_short": "GUUAAUC", "nts_long": "///A/1324,///A/1325,///A/1326,///A/1327,///A/1328,///A/1329,///A/1330", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UUAAU", "nts_long": "///A/1325,///A/1326,///A/1327,///A/1328,///A/1329" } ] }, { "index": 36, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 83 ], "summary": "[1] 4 [A.1363 A.1368] 3", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/1363,///A/1364,///A/1365,///A/1366,///A/1367,///A/1368", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/1364,///A/1365,///A/1366,///A/1367" } ] }, { "index": 37, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 84 ], "summary": "[1] 8 [A.1389 A.1398] 5", "num_nts": 10, "nts_short": "GUUAAUAUUC", "nts_long": "///A/1389,///A/1390,///A/1391,///A/1392,///A/1393,///A/1394,///A/1395,///A/1396,///A/1397,///A/1398", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UUAAUAUU", "nts_long": "///A/1390,///A/1391,///A/1392,///A/1393,///A/1394,///A/1395,///A/1396,///A/1397" } ] }, { "index": 38, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -31 ], "summary": "[1] 7 [A.1451 A.1459] 1", "num_nts": 9, "nts_short": "CGACGGUUG", "nts_long": "///A/1451,///A/1452,///A/1453,///A/1454,///A/1455,///A/1456,///A/1457,///A/1458,///A/1459", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GACGGUU", "nts_long": "///A/1452,///A/1453,///A/1454,///A/1455,///A/1456,///A/1457,///A/1458" } ] }, { "index": 39, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 97 ], "summary": "[1] 5 [A.1492 A.1498] 2", "num_nts": 7, "nts_short": "GCAAAUC", "nts_long": "///A/1492,///A/1493,///A/1494,///A/1495,///A/1496,///A/1497,///A/1498", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CAAAU", "nts_long": "///A/1493,///A/1494,///A/1495,///A/1496,///A/1497" } ] }, { "index": 40, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 98 ], "summary": "[1] 4 [A.1533 A.1538] 4", "num_nts": 6, "nts_short": "CUACGG", "nts_long": "///A/1533,///A/1534,///A/1535,///A/1536,///A/1537,///A/1538", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UACG", "nts_long": "///A/1534,///A/1535,///A/1536,///A/1537" } ] }, { "index": 41, "type": "hairpin loop", "bridging_nts": [ 2 ], "stem_indices": [ -33 ], "summary": "[1] 2 [A.1565 A.1568] 1", "num_nts": 4, "nts_short": "CAGG", "nts_long": "///A/1565,///A/1566,///A/1567,///A/1568", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/1566,///A/1567" } ] }, { "index": 42, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 99 ], "summary": "[1] 6 [A.1612 A.1619] 2", "num_nts": 8, "nts_short": "CGACACAG", "nts_long": "///A/1612,///A/1613,///A/1614,///A/1615,///A/1616,///A/1617,///A/1618,///A/1619", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GACACA", "nts_long": "///A/1613,///A/1614,///A/1615,///A/1616,///A/1617,///A/1618" } ] }, { "index": 43, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 100 ], "summary": "[1] 5 [A.1630 A.1636] 4", "num_nts": 7, "nts_short": "AGAGAAU", "nts_long": "///A/1630,///A/1631,///A/1632,///A/1633,///A/1634,///A/1635,///A/1636", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAGAA", "nts_long": "///A/1631,///A/1632,///A/1633,///A/1634,///A/1635" } ] }, { "index": 44, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -35 ], "summary": "[1] 4 [A.1691 A.1696] 1", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///A/1691,///A/1692,///A/1693,///A/1694,///A/1695,///A/1696", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///A/1692,///A/1693,///A/1694,///A/1695" } ] }, { "index": 45, "type": "hairpin loop", "bridging_nts": [ 2 ], "stem_indices": [ -37 ], "summary": "[1] 2 [A.1728 A.1731] 1", "num_nts": 4, "nts_short": "CUCG", "nts_long": "///A/1728,///A/1729,///A/1730,///A/1731", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/1729,///A/1730" } ] }, { "index": 46, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ -38 ], "summary": "[1] 3 [A.1752 A.1756] 1", "num_nts": 5, "nts_short": "CGAAG", "nts_long": "///A/1752,///A/1753,///A/1754,///A/1755,///A/1756", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1753,///A/1754,///A/1755" } ] }, { "index": 47, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 110 ], "summary": "[1] 9 [A.1777 A.1787] 2", "num_nts": 11, "nts_short": "UUUAUUAAAAA", "nts_long": "///A/1777,///A/1778,///A/1779,///A/1780,///A/1781,///A/1782,///A/1783,///A/1784,///A/1785,///A/1786,///A/1787", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UUAUUAAAA", "nts_long": "///A/1778,///A/1779,///A/1780,///A/1781,///A/1782,///A/1783,///A/1784,///A/1785,///A/1786" } ] }, { "index": 48, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 113 ], "summary": "[1] 4 [A.1806 A.1811] 3", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/1806,///A/1807,///A/1808,///A/1809,///A/1810,///A/1811", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/1807,///A/1808,///A/1809,///A/1810" } ] }, { "index": 49, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 120 ], "summary": "[1] 4 [A.1868 A.1873] 2", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///A/1868,///A/1869,///A/1870,///A/1871,///A/1872,///A/1873", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/1869,///A/1870,///A/1871,///A/1872" } ] }, { "index": 50, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 121 ], "summary": "[1] 9 [A.1910 A.1920] 5", "num_nts": 11, "nts_short": "GUAACUAUAAC", "nts_long": "///A/1910,///A/1911,///A/1912,///A/1913,///A/1914,///A/1915,///A/1916,///A/1917,///A/1918,///A/1919,///A/1920", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UAACUAUAA", "nts_long": "///A/1911,///A/1912,///A/1913,///A/1914,///A/1915,///A/1916,///A/1917,///A/1918,///A/1919" } ] }, { "index": 51, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ -39 ], "summary": "[1] 13 [A.2020 A.2034] 1", "num_nts": 15, "nts_short": "ACUCGCUGUGAAGAU", "nts_long": "///A/2020,///A/2021,///A/2022,///A/2023,///A/2024,///A/2025,///A/2026,///A/2027,///A/2028,///A/2029,///A/2030,///A/2031,///A/2032,///A/2033,///A/2034", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "CUCGCUGUGAAGA", "nts_long": "///A/2021,///A/2022,///A/2023,///A/2024,///A/2025,///A/2026,///A/2027,///A/2028,///A/2029,///A/2030,///A/2031,///A/2032,///A/2033" } ] }, { "index": 52, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 122 ], "summary": "[1] 8 [A.2027 A.2036] 5", "num_nts": 10, "nts_short": "GUGAAGAUGC", "nts_long": "///A/2027,///A/2028,///A/2029,///A/2030,///A/2031,///A/2032,///A/2033,///A/2034,///A/2035,///A/2036", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UGAAGAUG", "nts_long": "///A/2028,///A/2029,///A/2030,///A/2031,///A/2032,///A/2033,///A/2034,///A/2035" } ] }, { "index": 53, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 135 ], "summary": "[1] 4 [A.2143 A.2148] 7", "num_nts": 6, "nts_short": "CGCCAG", "nts_long": "///A/2143,///A/2144,///A/2145,///A/2146,///A/2147,///A/2148", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCCA", "nts_long": "///A/2144,///A/2145,///A/2146,///A/2147" } ] }, { "index": 54, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 137 ], "summary": "[1] 5 [A.2209 A.2215] 6", "num_nts": 7, "nts_short": "GUAAUCC", "nts_long": "///A/2209,///A/2210,///A/2211,///A/2212,///A/2213,///A/2214,///A/2215", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAAUC", "nts_long": "///A/2210,///A/2211,///A/2212,///A/2213,///A/2214" } ] }, { "index": 55, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 138 ], "summary": "[1] 7 [A.2248 A.2256] 3", "num_nts": 9, "nts_short": "CUGGGGCGG", "nts_long": "///A/2248,///A/2249,///A/2250,///A/2251,///A/2252,///A/2253,///A/2254,///A/2255,///A/2256", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGGGGCG", "nts_long": "///A/2249,///A/2250,///A/2251,///A/2252,///A/2253,///A/2254,///A/2255" } ] }, { "index": 56, "type": "hairpin loop", "bridging_nts": [ 19 ], "stem_indices": [ -42 ], "summary": "[1] 19 [A.2255 A.2275] 1", "num_nts": 21, "nts_short": "GGUCUCCUCCUAAAGAGUAAC", "nts_long": "///A/2255,///A/2256,///A/2257,///A/2258,///A/2259,///A/2260,///A/2261,///A/2262,///A/2263,///A/2264,///A/2265,///A/2266,///A/2267,///A/2268,///A/2269,///A/2270,///A/2271,///A/2272,///A/2273,///A/2274,///A/2275", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 19, "nts_short": "GUCUCCUCCUAAAGAGUAA", "nts_long": "///A/2256,///A/2257,///A/2258,///A/2259,///A/2260,///A/2261,///A/2262,///A/2263,///A/2264,///A/2265,///A/2266,///A/2267,///A/2268,///A/2269,///A/2270,///A/2271,///A/2272,///A/2273,///A/2274" } ] }, { "index": 57, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ 139 ], "summary": "[1] 11 [A.2264 A.2276] 6", "num_nts": 13, "nts_short": "CUAAAGAGUAACG", "nts_long": "///A/2264,///A/2265,///A/2266,///A/2267,///A/2268,///A/2269,///A/2270,///A/2271,///A/2272,///A/2273,///A/2274,///A/2275,///A/2276", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "UAAAGAGUAAC", "nts_long": "///A/2265,///A/2266,///A/2267,///A/2268,///A/2269,///A/2270,///A/2271,///A/2272,///A/2273,///A/2274,///A/2275" } ] }, { "index": 58, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 142 ], "summary": "[1] 9 [A.2303 A.2313] 5", "num_nts": 11, "nts_short": "GGUCGGACAUC", "nts_long": "///A/2303,///A/2304,///A/2305,///A/2306,///A/2307,///A/2308,///A/2309,///A/2310,///A/2311,///A/2312,///A/2313", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "GUCGGACAU", "nts_long": "///A/2304,///A/2305,///A/2306,///A/2307,///A/2308,///A/2309,///A/2310,///A/2311,///A/2312" } ] }, { "index": 59, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 143 ], "summary": "[1] 6 [A.2324 A.2331] 2", "num_nts": 8, "nts_short": "UGCAAUGG", "nts_long": "///A/2324,///A/2325,///A/2326,///A/2327,///A/2328,///A/2329,///A/2330,///A/2331", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GCAAUG", "nts_long": "///A/2325,///A/2326,///A/2327,///A/2328,///A/2329,///A/2330" } ] }, { "index": 60, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 146 ], "summary": "[1] 4 [A.2356 A.2361] 4", "num_nts": 6, "nts_short": "UGACGG", "nts_long": "///A/2356,///A/2357,///A/2358,///A/2359,///A/2360,///A/2361", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GACG", "nts_long": "///A/2357,///A/2358,///A/2359,///A/2360" } ] }, { "index": 61, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 147 ], "summary": "[1] 4 [A.2374 A.2379] 3", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/2374,///A/2375,///A/2376,///A/2377,///A/2378,///A/2379", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/2375,///A/2376,///A/2377,///A/2378" } ] }, { "index": 62, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ -46 ], "summary": "[1] 10 [A.2403 A.2414] 1", "num_nts": 12, "nts_short": "CUGAAUGGAAGG", "nts_long": "///A/2403,///A/2404,///A/2405,///A/2406,///A/2407,///A/2408,///A/2409,///A/2410,///A/2411,///A/2412,///A/2413,///A/2414", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "UGAAUGGAAG", "nts_long": "///A/2404,///A/2405,///A/2406,///A/2407,///A/2408,///A/2409,///A/2410,///A/2411,///A/2412,///A/2413" } ] }, { "index": 63, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -48 ], "summary": "[1] 4 [A.2658 A.2663] 1", "num_nts": 6, "nts_short": "CGAGAG", "nts_long": "///A/2658,///A/2659,///A/2660,///A/2661,///A/2662,///A/2663", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///A/2659,///A/2660,///A/2661,///A/2662" } ] }, { "index": 64, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 155 ], "summary": "[1] 4 [A.2701 A.2706] 6", "num_nts": 6, "nts_short": "UGCCAA", "nts_long": "///A/2701,///A/2702,///A/2703,///A/2704,///A/2705,///A/2706", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCCA", "nts_long": "///A/2702,///A/2703,///A/2704,///A/2705" } ] }, { "index": 65, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 157 ], "summary": "[1] 13 [A.2745 A.2759] 4", "num_nts": 15, "nts_short": "CUGAAAGCAUCUAAG", "nts_long": "///A/2745,///A/2746,///A/2747,///A/2748,///A/2749,///A/2750,///A/2751,///A/2752,///A/2753,///A/2754,///A/2755,///A/2756,///A/2757,///A/2758,///A/2759", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "UGAAAGCAUCUAA", "nts_long": "///A/2746,///A/2747,///A/2748,///A/2749,///A/2750,///A/2751,///A/2752,///A/2753,///A/2754,///A/2755,///A/2756,///A/2757,///A/2758" } ] }, { "index": 66, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 158 ], "summary": "[1] 5 [A.2795 A.2801] 5", "num_nts": 7, "nts_short": "CUUUAAG", "nts_long": "///A/2795,///A/2796,///A/2797,///A/2798,///A/2799,///A/2800,///A/2801", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UUUAA", "nts_long": "///A/2796,///A/2797,///A/2798,///A/2799,///A/2800" } ] }, { "index": 67, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 160 ], "summary": "[1] 7 [A.2819 A.2827] 5", "num_nts": 9, "nts_short": "GAAGACGAC", "nts_long": "///A/2819,///A/2820,///A/2821,///A/2822,///A/2823,///A/2824,///A/2825,///A/2826,///A/2827", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AAGACGA", "nts_long": "///A/2820,///A/2821,///A/2822,///A/2823,///A/2824,///A/2825,///A/2826" } ] }, { "index": 68, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 164 ], "summary": "[1] 4 [A.2856 A.2861] 5", "num_nts": 6, "nts_short": "AGCGAU", "nts_long": "///A/2856,///A/2857,///A/2858,///A/2859,///A/2860,///A/2861", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCGA", "nts_long": "///A/2857,///A/2858,///A/2859,///A/2860" } ] }, { "index": 69, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 169 ], "summary": "[1] 13 [B.34 B.48] 3", "num_nts": 15, "nts_short": "ACCCCAUGCCGAACU", "nts_long": "///B/34,///B/35,///B/36,///B/37,///B/38,///B/39,///B/40,///B/41,///B/42,///B/43,///B/44,///B/45,///B/46,///B/47,///B/48", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "CCCCAUGCCGAAC", "nts_long": "///B/35,///B/36,///B/37,///B/38,///B/39,///B/40,///B/41,///B/42,///B/43,///B/44,///B/45,///B/46,///B/47" } ] }, { "index": 70, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ 171 ], "summary": "[1] 3 [B.86 B.90] 6", "num_nts": 5, "nts_short": "GUCUC", "nts_long": "///B/86,///B/87,///B/88,///B/89,///B/90", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UCU", "nts_long": "///B/87,///B/88,///B/89" } ] } ], "num_bulges": 31, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 4, 5 ], "summary": "[2] 0 1 [A.36 A.444 A.37 A.442] 2 7", "num_nts": 5, "nts_short": "GCGAC", "nts_long": "///A/36,///A/37,///A/442,///A/443,///A/444", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/443" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 5, 6 ], "summary": "[2] 0 1 [A.43 A.436 A.44 A.434] 7 2", "num_nts": 5, "nts_short": "GAUCC", "nts_long": "///A/43,///A/44,///A/434,///A/435,///A/436", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/435" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -3, 16 ], "summary": "[2] 0 1 [A.183 A.214 A.184 A.212] 1 5", "num_nts": 5, "nts_short": "CCGAG", "nts_long": "///A/183,///A/184,///A/212,///A/213,///A/214", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/213" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 42, -13 ], "summary": "[2] 0 1 [A.697 A.765 A.698 A.763] 9 1", "num_nts": 5, "nts_short": "GCGAC", "nts_long": "///A/697,///A/698,///A/763,///A/764,///A/765", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/764" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 43, -14 ], "summary": "[2] 0 1 [A.702 A.730 A.703 A.728] 3 1", "num_nts": 5, "nts_short": "UUGGA", "nts_long": "///A/702,///A/703,///A/728,///A/729,///A/730", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/729" } ] }, { "index": 6, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -17, 50 ], "summary": "[2] 0 1 [A.837 A.942 A.838 A.940] 1 7", "num_nts": 5, "nts_short": "CCGAG", "nts_long": "///A/837,///A/838,///A/940,///A/941,///A/942", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/941" } ] }, { "index": 7, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 51, 52 ], "summary": "[2] 0 1 [A.850 A.928 A.851 A.926] 3 6", "num_nts": 5, "nts_short": "UCGAA", "nts_long": "///A/850,///A/851,///A/926,///A/927,///A/928", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/927" } ] }, { "index": 8, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -19, 53 ], "summary": "[2] 0 1 [A.862 A.915 A.863 A.913] 1 2", "num_nts": 5, "nts_short": "GAUGC", "nts_long": "///A/862,///A/863,///A/913,///A/914,///A/915", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/914" } ] }, { "index": 9, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 58, 59 ], "summary": "[2] 1 0 [A.994 A.1160 A.996 A.1159] 4 3", "num_nts": 5, "nts_short": "CCAUG", "nts_long": "///A/994,///A/995,///A/996,///A/1159,///A/1160", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/995" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 10, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -20, 62 ], "summary": "[2] 1 0 [A.1011 A.1150 A.1013 A.1149] 1 6", "num_nts": 5, "nts_short": "GUCGC", "nts_long": "///A/1011,///A/1012,///A/1013,///A/1149,///A/1150", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1012" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 11, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 81, -30 ], "summary": "[2] 1 0 [A.1351 A.1380 A.1353 A.1379] 3 1", "num_nts": 5, "nts_short": "CUAUG", "nts_long": "///A/1351,///A/1352,///A/1353,///A/1379,///A/1380", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1352" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 12, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 91, -31 ], "summary": "[2] 0 1 [A.1450 A.1461 A.1451 A.1459] 6 1", "num_nts": 5, "nts_short": "GCGUC", "nts_long": "///A/1450,///A/1451,///A/1459,///A/1460,///A/1461", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1460" } ] }, { "index": 13, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 96, 97 ], "summary": "[2] 1 0 [A.1489 A.1500 A.1491 A.1499] 8 2", "num_nts": 5, "nts_short": "CAGCG", "nts_long": "///A/1489,///A/1490,///A/1491,///A/1499,///A/1500", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1490" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 14, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 107, -37 ], "summary": "[2] 0 1 [A.1727 A.1733 A.1728 A.1731] 4 1", "num_nts": 5, "nts_short": "CCGCG", "nts_long": "///A/1727,///A/1728,///A/1731,///A/1732,///A/1733", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1732" } ] }, { "index": 15, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 108, 109 ], "summary": "[2] 0 1 [A.1770 A.1982 A.1771 A.1980] 7 2", "num_nts": 5, "nts_short": "GCGAU", "nts_long": "///A/1770,///A/1771,///A/1980,///A/1981,///A/1982", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1981" } ] }, { "index": 16, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 123, 124 ], "summary": "[2] 1 0 [A.2050 A.2618 A.2052 A.2617] 8 3", "num_nts": 5, "nts_short": "CAAUG", "nts_long": "///A/2050,///A/2051,///A/2052,///A/2617,///A/2618", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2051" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 17, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 125, 126 ], "summary": "[2] 1 0 [A.2067 A.2443 A.2069 A.2442] 5 2", "num_nts": 5, "nts_short": "GUGCC", "nts_long": "///A/2067,///A/2068,///A/2069,///A/2442,///A/2443", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2068" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 18, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 136, 137 ], "summary": "[2] 1 0 [A.2202 A.2221 A.2204 A.2220] 3 6", "num_nts": 5, "nts_short": "UUGUG", "nts_long": "///A/2202,///A/2203,///A/2204,///A/2220,///A/2221", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2203" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 19, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 148, -46 ], "summary": "[2] 1 0 [A.2401 A.2415 A.2403 A.2414] 7 1", "num_nts": 5, "nts_short": "UUCGG", "nts_long": "///A/2401,///A/2402,///A/2403,///A/2414,///A/2415", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2402" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 20, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 161, 162 ], "summary": "[2] 0 1 [A.2838 A.2880 A.2839 A.2878] 3 5", "num_nts": 5, "nts_short": "GGUAC", "nts_long": "///A/2838,///A/2839,///A/2878,///A/2879,///A/2880", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2879" } ] }, { "index": 21, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 50, -18 ], "summary": "[2] 2 0 [A.844 A.934 A.847 A.933] 7 1", "num_nts": 6, "nts_short": "AAUUAU", "nts_long": "///A/844,///A/845,///A/846,///A/847,///A/933,///A/934", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/845,///A/846" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 22, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ -18, 51 ], "summary": "[2] 0 2 [A.847 A.933 A.848 A.930] 1 3", "num_nts": 6, "nts_short": "UCGUUA", "nts_long": "///A/847,///A/848,///A/930,///A/931,///A/932,///A/933", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/931,///A/932" } ] }, { "index": 23, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 76, -29 ], "summary": "[2] 2 0 [A.1310 A.1604 A.1313 A.1603] 2 1", "num_nts": 6, "nts_short": "GGUUAC", "nts_long": "///A/1310,///A/1311,///A/1312,///A/1313,///A/1603,///A/1604", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/1311,///A/1312" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 24, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 95, 96 ], "summary": "[2] 0 2 [A.1481 A.1510 A.1482 A.1507] 4 8", "num_nts": 6, "nts_short": "UGCAAG", "nts_long": "///A/1481,///A/1482,///A/1507,///A/1508,///A/1509,///A/1510", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1508,///A/1509" } ] }, { "index": 25, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 115, 116 ], "summary": "[2] 2 0 [A.1837 A.1903 A.1840 A.1902] 3 2", "num_nts": 6, "nts_short": "CCGGCG", "nts_long": "///A/1837,///A/1838,///A/1839,///A/1840,///A/1902,///A/1903", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/1838,///A/1839" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 26, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 116, 117 ], "summary": "[2] 0 2 [A.1841 A.1901 A.1842 A.1898] 2 5", "num_nts": 6, "nts_short": "UGUAAA", "nts_long": "///A/1841,///A/1842,///A/1898,///A/1899,///A/1900,///A/1901", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, 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"index": 29, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 154, 155 ], "summary": "[2] 0 2 [A.2695 A.2714 A.2696 A.2711] 5 6", "num_nts": 6, "nts_short": "UUACUG", "nts_long": "///A/2695,///A/2696,///A/2711,///A/2712,///A/2713,///A/2714", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/2712,///A/2713" } ] }, { "index": 30, "type": "bulge", "bridging_nts": [ 0, 4 ], "stem_indices": [ 85, 86 ], "summary": "[2] 0 4 [A.1415 A.1587 A.1416 A.1582] 11 2", "num_nts": 8, "nts_short": "UGCAUCAG", "nts_long": "///A/1415,///A/1416,///A/1582,///A/1583,///A/1584,///A/1585,///A/1586,///A/1587", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "AUCA", "nts_long": "///A/1583,///A/1584,///A/1585,///A/1586" } ] }, { "index": 31, "type": "bulge", "bridging_nts": [ 9, 0 ], "stem_indices": [ -41, 133 ], "summary": "[2] 9 0 [A.2110 A.2179 A.2120 A.2178] 1 5", "num_nts": 13, "nts_short": "GUGUAGGAUAGCC", "nts_long": "///A/2110,///A/2111,///A/2112,///A/2113,///A/2114,///A/2115,///A/2116,///A/2117,///A/2118,///A/2119,///A/2120,///A/2178,///A/2179", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UGUAGGAUA", "nts_long": "///A/2111,///A/2112,///A/2113,///A/2114,///A/2115,///A/2116,///A/2117,///A/2118,///A/2119" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] } ], "num_iloops": 70, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -10, -11 ], "summary": "[2] 1 1 [A.564 A.577 A.566 A.575] 1 1", "num_nts": 6, "nts_short": "CCUAUG", "nts_long": "///A/564,///A/565,///A/566,///A/575,///A/576,///A/577", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/565" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/576" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 40, -12 ], "summary": "[2] 1 1 [A.672 A.808 A.674 A.806] 2 1", "num_nts": 6, "nts_short": "CCGCUG", "nts_long": "///A/672,///A/673,///A/674,///A/806,///A/807,///A/808", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/673" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/807" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 54, 55 ], "summary": "[2] 1 1 [A.870 A.907 A.872 A.905] 3 4", "num_nts": 6, "nts_short": "UUUAUG", "nts_long": "///A/870,///A/871,///A/872,///A/905,///A/906,///A/907", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/871" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/906" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 68, -25 ], "summary": "[2] 1 1 [A.1167 A.1182 A.1169 A.1180] 4 1", "num_nts": 6, "nts_short": "CGAUUG", "nts_long": "///A/1167,///A/1168,///A/1169,///A/1180,///A/1181,///A/1182", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1168" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1181" } ] }, { "index": 5, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -25, -26 ], "summary": "[2] 1 1 [A.1169 A.1180 A.1171 A.1178] 1 1", "num_nts": 6, "nts_short": "ACGCGU", "nts_long": "///A/1169,///A/1170,///A/1171,///A/1178,///A/1179,///A/1180", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1170" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1179" } ] }, { "index": 6, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 102, 103 ], "summary": "[2] 1 1 [A.1663 A.1997 A.1665 A.1995] 8 2", "num_nts": 6, "nts_short": "GAAUCC", "nts_long": "///A/1663,///A/1664,///A/1665,///A/1995,///A/1996,///A/1997", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1664" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1996" } ] }, { "index": 7, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 111, 112 ], "summary": "[2] 1 1 [A.1795 A.1824 A.1797 A.1822] 4 2", "num_nts": 6, "nts_short": "CUGCGG", "nts_long": "///A/1795,///A/1796,///A/1797,///A/1822,///A/1823,///A/1824", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1796" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1823" } ] }, { "index": 8, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 129, 130 ], "summary": "[2] 1 1 [A.2085 A.2234 A.2087 A.2232] 3 5", "num_nts": 6, "nts_short": "UUGCUG", "nts_long": "///A/2085,///A/2086,///A/2087,///A/2232,///A/2233,///A/2234", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2086" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2233" } ] }, { "index": 9, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 131, 132 ], "summary": "[2] 1 1 [A.2103 A.2186 A.2105 A.2184] 11 4", "num_nts": 6, "nts_short": "CCUAUG", "nts_long": "///A/2103,///A/2104,///A/2105,///A/2184,///A/2185,///A/2186", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2104" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2185" } ] }, { "index": 10, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 132, -41 ], "summary": "[2] 1 1 [A.2108 A.2181 A.2110 A.2179] 4 1", "num_nts": 6, "nts_short": "AUGCUU", "nts_long": "///A/2108,///A/2109,///A/2110,///A/2179,///A/2180,///A/2181", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2109" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2180" } ] }, { "index": 11, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -44, 144 ], "summary": "[2] 1 1 [A.2326 A.2389 A.2328 A.2387] 1 3", "num_nts": 6, "nts_short": "CAAUAG", "nts_long": "///A/2326,///A/2327,///A/2328,///A/2387,///A/2388,///A/2389", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2327" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2388" } ] }, { "index": 12, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -51, 171 ], "summary": "[2] 1 1 [B.79 B.97 B.81 B.95] 1 6", "num_nts": 6, "nts_short": "GUGUGC", "nts_long": "///B/79,///B/80,///B/81,///B/95,///B/96,///B/97", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///B/80" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///B/96" } ] }, { "index": 13, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 45, 46 ], "summary": "[2] 2 1 [A.737 A.759 A.740 A.757] 2 5", "num_nts": 7, "nts_short": "CGACGCG", "nts_long": "///A/737,///A/738,///A/739,///A/740,///A/757,///A/758,///A/759", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/738,///A/739" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/758" } ] }, { "index": 14, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 63, 64 ], "summary": "[2] 2 1 [A.1031 A.1123 A.1034 A.1121] 2 5", "num_nts": 7, "nts_short": "GAUGCGC", "nts_long": "///A/1031,///A/1032,///A/1033,///A/1034,///A/1121,///A/1122,///A/1123", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1032,///A/1033" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1122" } ] }, { "index": 15, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -27, 69 ], "summary": "[2] 1 2 [A.1196 A.1250 A.1198 A.1247] 1 5", "num_nts": 7, "nts_short": "CGUAGUG", "nts_long": "///A/1196,///A/1197,///A/1198,///A/1247,///A/1248,///A/1249,///A/1250", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1197" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/1248,///A/1249" } ] }, { "index": 16, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -30, 82 ], "summary": "[2] 1 2 [A.1353 A.1379 A.1355 A.1376] 1 3 k-turn:undecided", "num_nts": 7, "nts_short": "AAGCGAU", "nts_long": "///A/1353,///A/1354,///A/1355,///A/1376,///A/1377,///A/1378,///A/1379", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1354" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/1377,///A/1378" } ] }, { "index": 17, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 128, 129 ], "summary": "[2] 1 2 [A.2081 A.2239 A.2083 A.2236] 5 3", "num_nts": 7, "nts_short": "UAGUGGG", "nts_long": "///A/2081,///A/2082,///A/2083,///A/2236,///A/2237,///A/2238,///A/2239", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2082" }, { "index": 2, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/2237,///A/2238" } ] }, { "index": 18, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 166, 167 ], "summary": "[2] 1 2 [B.17 B.67 B.19 B.64] 2 5", "num_nts": 7, "nts_short": "CGCGUAG", "nts_long": "///B/17,///B/18,///B/19,///B/64,///B/65,///B/66,///B/67", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///B/18" }, { "index": 2, "num_nts": 2, "nts_short": "UA", "nts_long": "///B/65,///B/66" } ] }, { "index": 19, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ -2, 10 ], "summary": "[2] 2 2 [A.61 A.93 A.64 A.90] 1 3", "num_nts": 8, "nts_short": "CUAAUAUG", "nts_long": "///A/61,///A/62,///A/63,///A/64,///A/90,///A/91,///A/92,///A/93", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/62,///A/63" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/91,///A/92" } ] }, { "index": 20, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 22, 23 ], "summary": "[2] 1 3 [A.293 A.347 A.295 A.343] 13 3", "num_nts": 8, "nts_short": "UAGCAAAA", "nts_long": "///A/293,///A/294,///A/295,///A/343,///A/344,///A/345,///A/346,///A/347", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/294" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/344,///A/345,///A/346" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 32, 33 ], "summary": "[2] 2 2 [A.536 A.557 A.539 A.554] 4 5", "num_nts": 8, "nts_short": "GGAGUGAC", "nts_long": "///A/536,///A/537,///A/538,///A/539,///A/554,///A/555,///A/556,///A/557", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/537,///A/538" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/555,///A/556" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ -16, 47 ], "summary": "[2] 1 3 [A.775 A.791 A.777 A.787] 1 2", "num_nts": 8, "nts_short": "GGGCAAUC", "nts_long": "///A/775,///A/776,///A/777,///A/787,///A/788,///A/789,///A/790,///A/791", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/776" }, { "index": 2, "num_nts": 3, "nts_short": "AAU", "nts_long": "///A/788,///A/789,///A/790" } ] }, { "index": 23, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 64, 65 ], "summary": "[2] 2 2 [A.1038 A.1117 A.1041 A.1114] 5 3", "num_nts": 8, "nts_short": "GAAGCGGC", "nts_long": "///A/1038,///A/1039,///A/1040,///A/1041,///A/1114,///A/1115,///A/1116,///A/1117", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1039,///A/1040" }, { "index": 2, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/1115,///A/1116" } ] }, { "index": 24, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 67, -22 ], "summary": "[2] 2 2 [A.1059 A.1079 A.1062 A.1076] 2 1", "num_nts": 8, "nts_short": "GUUGCAUC", "nts_long": "///A/1059,///A/1060,///A/1061,///A/1062,///A/1076,///A/1077,///A/1078,///A/1079", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/1060,///A/1061" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1077,///A/1078" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 77, 78 ], "summary": "[2] 3 1 [A.1319 A.1333 A.1323 A.1331] 6 2", "num_nts": 8, "nts_short": "CCAACGGG", "nts_long": "///A/1319,///A/1320,///A/1321,///A/1322,///A/1323,///A/1331,///A/1332,///A/1333", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAA", "nts_long": "///A/1320,///A/1321,///A/1322" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1332" } ] }, { "index": 26, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 145, 146 ], "summary": "[2] 2 2 [A.2350 A.2367 A.2353 A.2364] 4 4", "num_nts": 8, "nts_short": "CGAGCGAG", "nts_long": "///A/2350,///A/2351,///A/2352,///A/2353,///A/2364,///A/2365,///A/2366,///A/2367", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2351,///A/2352" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2365,///A/2366" } ] }, { "index": 27, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 152, 153 ], "summary": "[2] 3 1 [A.2680 A.2727 A.2684 A.2725] 5 4", "num_nts": 8, "nts_short": "UCACUAAA", "nts_long": "///A/2680,///A/2681,///A/2682,///A/2683,///A/2684,///A/2725,///A/2726,///A/2727", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAC", "nts_long": "///A/2681,///A/2682,///A/2683" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2726" } ] }, { "index": 28, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 168, 169 ], "summary": "[2] 1 3 [B.30 B.54 B.32 B.50] 3 3", "num_nts": 8, "nts_short": "CCUAGAAG", "nts_long": "///B/30,///B/31,///B/32,///B/50,///B/51,///B/52,///B/53,///B/54", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///B/31" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///B/51,///B/52,///B/53" } ] }, { "index": 29, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 53, 54 ], "summary": "[2] 3 2 [A.864 A.912 A.868 A.909] 2 3", "num_nts": 9, "nts_short": "GCACUAAAC", "nts_long": "///A/864,///A/865,///A/866,///A/867,///A/868,///A/909,///A/910,///A/911,///A/912", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAC", "nts_long": "///A/865,///A/866,///A/867" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/910,///A/911" } ] }, { "index": 30, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 69, 70 ], "summary": "[2] 3 2 [A.1202 A.1243 A.1206 A.1240] 5 3", "num_nts": 9, "nts_short": "GUAAGUAUC", "nts_long": "///A/1202,///A/1203,///A/1204,///A/1205,///A/1206,///A/1240,///A/1241,///A/1242,///A/1243", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1203,///A/1204,///A/1205" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1241,///A/1242" } ] }, { "index": 31, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 88, 89 ], "summary": "[2] 2 3 [A.1432 A.1561 A.1435 A.1557] 4 3", "num_nts": 9, "nts_short": "GAAGCCUGC", "nts_long": "///A/1432,///A/1433,///A/1434,///A/1435,///A/1557,///A/1558,///A/1559,///A/1560,///A/1561", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1433,///A/1434" }, { "index": 2, "num_nts": 3, "nts_short": "CUG", "nts_long": "///A/1558,///A/1559,///A/1560" } ] }, { "index": 32, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 89, 90 ], "summary": "[2] 2 3 [A.1437 A.1555 A.1440 A.1551] 3 5", "num_nts": 9, "nts_short": "CUAUAAAUG", "nts_long": "///A/1437,///A/1438,///A/1439,///A/1440,///A/1551,///A/1552,///A/1553,///A/1554,///A/1555", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1438,///A/1439" }, { "index": 2, "num_nts": 3, "nts_short": "AAU", "nts_long": "///A/1552,///A/1553,///A/1554" } ] }, { "index": 33, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 93, 94 ], "summary": "[2] 2 3 [A.1468 A.1524 A.1471 A.1520] 2 4 k-turn:undecided", "num_nts": 9, "nts_short": "UAAGUGAUG", "nts_long": "///A/1468,///A/1469,///A/1470,///A/1471,///A/1520,///A/1521,///A/1522,///A/1523,///A/1524", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1469,///A/1470" }, { "index": 2, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/1521,///A/1522,///A/1523" } ] }, { "index": 34, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 101, 102 ], "summary": "[2] 4 1 [A.1651 A.2006 A.1656 A.2004] 4 8", "num_nts": 9, "nts_short": "GAGAACGAC", "nts_long": "///A/1651,///A/1652,///A/1653,///A/1654,///A/1655,///A/1656,///A/2004,///A/2005,///A/2006", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///A/1652,///A/1653,///A/1654,///A/1655" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2005" } ] }, { "index": 35, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 119, 120 ], "summary": "[2] 2 3 [A.1864 A.1878 A.1867 A.1874] 5 2", "num_nts": 9, "nts_short": "UUAGCGAAG", "nts_long": "///A/1864,///A/1865,///A/1866,///A/1867,///A/1874,///A/1875,///A/1876,///A/1877,///A/1878", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1865,///A/1866" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1875,///A/1876,///A/1877" } ] }, { "index": 36, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 124, -40 ], "summary": "[2] 2 3 [A.2054 A.2615 A.2057 A.2611] 3 1", "num_nts": 9, "nts_short": "ACGGCCUAU", "nts_long": "///A/2054,///A/2055,///A/2056,///A/2057,///A/2611,///A/2612,///A/2613,///A/2614,///A/2615", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/2055,///A/2056" }, { "index": 2, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/2612,///A/2613,///A/2614" } ] }, { "index": 37, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 162, 163 ], "summary": "[2] 2 3 [A.2843 A.2874 A.2846 A.2870] 5 2", "num_nts": 9, "nts_short": "GGUGCUAAC", "nts_long": "///A/2843,///A/2844,///A/2845,///A/2846,///A/2870,///A/2871,///A/2872,///A/2873,///A/2874", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/2844,///A/2845" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/2871,///A/2872,///A/2873" } ] }, { "index": 38, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 36, 37 ], "summary": "[2] 3 3 [A.606 A.622 A.610 A.618] 3 2", "num_nts": 10, "nts_short": "UUAACGGGAG", "nts_long": "///A/606,///A/607,///A/608,///A/609,///A/610,///A/618,///A/619,///A/620,///A/621,///A/622", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/607,///A/608,///A/609" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/619,///A/620,///A/621" } ] }, { "index": 39, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -14, 44 ], "summary": "[2] 3 3 [A.703 A.728 A.707 A.724] 1 6", "num_nts": 10, "nts_short": "UGAAGUGGAG", "nts_long": "///A/703,///A/704,///A/705,///A/706,///A/707,///A/724,///A/725,///A/726,///A/727,///A/728", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/704,///A/705,///A/706" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/725,///A/726,///A/727" } ] }, { "index": 40, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 59, 60 ], "summary": "[2] 3 3 [A.998 A.1157 A.1002 A.1153] 3 3 k-turn:undecided", "num_nts": 10, "nts_short": "CUAAGCGAAG", "nts_long": "///A/998,///A/999,///A/1000,///A/1001,///A/1002,///A/1153,///A/1154,///A/1155,///A/1156,///A/1157", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/999,///A/1000,///A/1001" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1154,///A/1155,///A/1156" } ] }, { "index": 41, "type": "asymmetric internal loop", "bridging_nts": [ 4, 2 ], "stem_indices": [ -23, -24 ], "summary": "[2] 4 2 [A.1087 A.1102 A.1092 A.1099] 1 1", "num_nts": 10, "nts_short": "GAAAGCGCUC", "nts_long": "///A/1087,///A/1088,///A/1089,///A/1090,///A/1091,///A/1092,///A/1099,///A/1100,///A/1101,///A/1102", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AAAG", "nts_long": "///A/1088,///A/1089,///A/1090,///A/1091" }, { "index": 2, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/1100,///A/1101" } ] }, { "index": 42, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 82, 83 ], "summary": "[2] 3 3 [A.1357 A.1374 A.1361 A.1370] 3 3", "num_nts": 10, "nts_short": "CGAGGCGUAG", "nts_long": "///A/1357,///A/1358,///A/1359,///A/1360,///A/1361,///A/1370,///A/1371,///A/1372,///A/1373,///A/1374", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/1358,///A/1359,///A/1360" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/1371,///A/1372,///A/1373" } ] }, { "index": 43, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 86, 87 ], "summary": "[2] 3 3 [A.1417 A.1581 A.1421 A.1577] 2 4", "num_nts": 10, "nts_short": "CGAAGCUAAG", "nts_long": "///A/1417,///A/1418,///A/1419,///A/1420,///A/1421,///A/1577,///A/1578,///A/1579,///A/1580,///A/1581", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1418,///A/1419,///A/1420" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1578,///A/1579,///A/1580" } ] }, { "index": 44, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 106, 107 ], "summary": "[2] 3 3 [A.1720 A.1740 A.1724 A.1736] 3 4", "num_nts": 10, "nts_short": "UGAGGUGGAG", "nts_long": "///A/1720,///A/1721,///A/1722,///A/1723,///A/1724,///A/1736,///A/1737,///A/1738,///A/1739,///A/1740", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/1721,///A/1722,///A/1723" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/1737,///A/1738,///A/1739" } ] }, { "index": 45, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 153, 154 ], "summary": "[2] 3 3 [A.2687 A.2722 A.2691 A.2718] 4 5", "num_nts": 10, "nts_short": "UGUUCGGUAG", "nts_long": "///A/2687,///A/2688,///A/2689,///A/2690,///A/2691,///A/2718,///A/2719,///A/2720,///A/2721,///A/2722", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUU", "nts_long": "///A/2688,///A/2689,///A/2690" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/2719,///A/2720,///A/2721" } ] }, { "index": 46, "type": "asymmetric internal loop", "bridging_nts": [ 4, 2 ], "stem_indices": [ -50, 159 ], "summary": "[2] 4 2 [A.2806 A.2892 A.2811 A.2889] 1 2", "num_nts": 10, "nts_short": "CUGAAGCGUG", "nts_long": "///A/2806,///A/2807,///A/2808,///A/2809,///A/2810,///A/2811,///A/2889,///A/2890,///A/2891,///A/2892", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UGAA", "nts_long": "///A/2807,///A/2808,///A/2809,///A/2810" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/2890,///A/2891" } ] }, { "index": 47, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 163, 164 ], "summary": "[2] 4 3 [A.2847 A.2869 A.2852 A.2865] 2 5", "num_nts": 11, "nts_short": "UGUAAGUUGAG", "nts_long": "///A/2847,///A/2848,///A/2849,///A/2850,///A/2851,///A/2852,///A/2865,///A/2866,///A/2867,///A/2868,///A/2869", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/2848,///A/2849,///A/2850,///A/2851" }, { "index": 2, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/2866,///A/2867,///A/2868" } ] }, { "index": 48, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 167, 168 ], "summary": "[2] 4 3 [B.23 B.60 B.28 B.56] 5 3", "num_nts": 11, "nts_short": "GGUCCCGAAAC", "nts_long": "///B/23,///B/24,///B/25,///B/26,///B/27,///B/28,///B/56,///B/57,///B/58,///B/59,///B/60", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUCC", "nts_long": "///B/24,///B/25,///B/26,///B/27" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///B/57,///B/58,///B/59" } ] }, { "index": 49, "type": "asymmetric internal loop", "bridging_nts": [ 5, 3 ], "stem_indices": [ 62, -21 ], "summary": "[2] 5 3 [A.1018 A.1144 A.1024 A.1140] 6 1", "num_nts": 12, "nts_short": "UUAAGUGCUAAA", "nts_long": "///A/1018,///A/1019,///A/1020,///A/1021,///A/1022,///A/1023,///A/1024,///A/1140,///A/1141,///A/1142,///A/1143,///A/1144", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAAGU", "nts_long": "///A/1019,///A/1020,///A/1021,///A/1022,///A/1023" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1141,///A/1142,///A/1143" } ] }, { "index": 50, "type": "asymmetric internal loop", "bridging_nts": [ 5, 3 ], "stem_indices": [ 105, 106 ], "summary": "[2] 5 3 [A.1712 A.1746 A.1718 A.1742] 6 3", "num_nts": 12, "nts_short": "UAUGUAGUGAAA", "nts_long": "///A/1712,///A/1713,///A/1714,///A/1715,///A/1716,///A/1717,///A/1718,///A/1742,///A/1743,///A/1744,///A/1745,///A/1746", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AUGUA", "nts_long": "///A/1713,///A/1714,///A/1715,///A/1716,///A/1717" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1743,///A/1744,///A/1745" } ] }, { "index": 51, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 156, 157 ], "summary": "[2] 4 4 [A.2737 A.2767 A.2742 A.2762] 3 4", "num_nts": 12, "nts_short": "GAUAAGCGAAAC", "nts_long": "///A/2737,///A/2738,///A/2739,///A/2740,///A/2741,///A/2742,///A/2762,///A/2763,///A/2764,///A/2765,///A/2766,///A/2767", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUAA", "nts_long": "///A/2738,///A/2739,///A/2740,///A/2741" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/2763,///A/2764,///A/2765,///A/2766" } ] }, { "index": 52, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ 18, 19 ], "summary": "[2] 5 4 [A.239 A.258 A.245 A.253] 5 2", "num_nts": 13, "nts_short": "CCAGUAGCGAACG", "nts_long": "///A/239,///A/240,///A/241,///A/242,///A/243,///A/244,///A/245,///A/253,///A/254,///A/255,///A/256,///A/257,///A/258", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CAGUA", "nts_long": "///A/240,///A/241,///A/242,///A/243,///A/244" }, { "index": 2, "num_nts": 4, "nts_short": "GAAC", "nts_long": "///A/254,///A/255,///A/256,///A/257" } ] }, { "index": 53, "type": "asymmetric internal loop", "bridging_nts": [ 6, 3 ], "stem_indices": [ 21, 22 ], "summary": "[2] 6 3 [A.274 A.363 A.281 A.359] 4 13 k-turn:reverse", "num_nts": 13, "nts_short": "CCUGAAUCGUGAG", "nts_long": "///A/274,///A/275,///A/276,///A/277,///A/278,///A/279,///A/280,///A/281,///A/359,///A/360,///A/361,///A/362,///A/363", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CUGAAU", "nts_long": "///A/275,///A/276,///A/277,///A/278,///A/279,///A/280" }, { "index": 2, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/360,///A/361,///A/362" } ] }, { "index": 54, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ -12, 41 ], "summary": "[2] 3 6 [A.674 A.806 A.678 A.799] 1 6", "num_nts": 13, "nts_short": "GAAACGAGAUAGC", "nts_long": "///A/674,///A/675,///A/676,///A/677,///A/678,///A/799,///A/800,///A/801,///A/802,///A/803,///A/804,///A/805,///A/806", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/675,///A/676,///A/677" }, { "index": 2, "num_nts": 6, "nts_short": "AGAUAG", "nts_long": "///A/800,///A/801,///A/802,///A/803,///A/804,///A/805" } ] }, { "index": 55, "type": "asymmetric internal loop", "bridging_nts": [ 6, 3 ], "stem_indices": [ 70, 71 ], "summary": "[2] 6 3 [A.1208 A.1238 A.1215 A.1234] 3 8 k-turn:normal", "num_nts": 13, "nts_short": "CUGCGAAGUGGAG", "nts_long": "///A/1208,///A/1209,///A/1210,///A/1211,///A/1212,///A/1213,///A/1214,///A/1215,///A/1234,///A/1235,///A/1236,///A/1237,///A/1238", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UGCGAA", "nts_long": "///A/1209,///A/1210,///A/1211,///A/1212,///A/1213,///A/1214" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/1235,///A/1236,///A/1237" } ] }, { "index": 56, "type": "asymmetric internal loop", "bridging_nts": [ 4, 5 ], "stem_indices": [ 104, -35 ], "summary": "[2] 4 5 [A.1686 A.1702 A.1691 A.1696] 5 1", "num_nts": 13, "nts_short": "CGUAACGGAGAAG", "nts_long": "///A/1686,///A/1687,///A/1688,///A/1689,///A/1690,///A/1691,///A/1696,///A/1697,///A/1698,///A/1699,///A/1700,///A/1701,///A/1702", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/1687,///A/1688,///A/1689,///A/1690" }, { "index": 2, "num_nts": 5, "nts_short": "GAGAA", "nts_long": "///A/1697,///A/1698,///A/1699,///A/1700,///A/1701" } ] }, { "index": 57, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ 151, -48 ], "summary": "[2] 5 4 [A.2652 A.2668 A.2658 A.2663] 7 1", "num_nts": 13, "nts_short": "CUAGUACGGACCG", "nts_long": "///A/2652,///A/2653,///A/2654,///A/2655,///A/2656,///A/2657,///A/2658,///A/2663,///A/2664,///A/2665,///A/2666,///A/2667,///A/2668", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAGUA", "nts_long": "///A/2653,///A/2654,///A/2655,///A/2656,///A/2657" }, { "index": 2, "num_nts": 4, "nts_short": "GACC", "nts_long": "///A/2664,///A/2665,///A/2666,///A/2667" } ] }, { "index": 58, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ 2, -1 ], "summary": "[2] 5 5 [A.24 A.516 A.30 A.510] 10 1", "num_nts": 14, "nts_short": "GUGGAUGCUGAAAC", "nts_long": "///A/24,///A/25,///A/26,///A/27,///A/28,///A/29,///A/30,///A/510,///A/511,///A/512,///A/513,///A/514,///A/515,///A/516", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGGAU", "nts_long": "///A/25,///A/26,///A/27,///A/28,///A/29" }, { "index": 2, "num_nts": 5, "nts_short": "UGAAA", "nts_long": "///A/511,///A/512,///A/513,///A/514,///A/515" } ] }, { "index": 59, "type": "asymmetric internal loop", "bridging_nts": [ 3, 7 ], "stem_indices": [ 11, 12 ], "summary": "[2] 3 7 [A.81 A.105 A.85 A.97] 6 3", "num_nts": 14, "nts_short": "GUAAGCGUUAUAAC", "nts_long": "///A/81,///A/82,///A/83,///A/84,///A/85,///A/97,///A/98,///A/99,///A/100,///A/101,///A/102,///A/103,///A/104,///A/105", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/82,///A/83,///A/84" }, { "index": 2, "num_nts": 7, "nts_short": "GUUAUAA", "nts_long": "///A/98,///A/99,///A/100,///A/101,///A/102,///A/103,///A/104" } ] }, { "index": 60, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ 52, -19 ], "summary": "[2] 5 5 [A.856 A.921 A.862 A.915] 6 1", "num_nts": 14, "nts_short": "GGGGUAGCGAAUAC", "nts_long": "///A/856,///A/857,///A/858,///A/859,///A/860,///A/861,///A/862,///A/915,///A/916,///A/917,///A/918,///A/919,///A/920,///A/921", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGGUA", "nts_long": "///A/857,///A/858,///A/859,///A/860,///A/861" }, { "index": 2, "num_nts": 5, "nts_short": "GAAUA", "nts_long": "///A/916,///A/917,///A/918,///A/919,///A/920" } ] }, { "index": 61, "type": "asymmetric internal loop", "bridging_nts": [ 7, 3 ], "stem_indices": [ 65, 66 ], "summary": "[2] 7 3 [A.1043 A.1112 A.1051 A.1108] 3 5 k-turn:normal", "num_nts": 14, "nts_short": "CCCAGACAGUCGAG", "nts_long": "///A/1043,///A/1044,///A/1045,///A/1046,///A/1047,///A/1048,///A/1049,///A/1050,///A/1051,///A/1108,///A/1109,///A/1110,///A/1111,///A/1112", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CCAGACA", "nts_long": "///A/1044,///A/1045,///A/1046,///A/1047,///A/1048,///A/1049,///A/1050" }, { "index": 2, "num_nts": 3, "nts_short": "CGA", "nts_long": "///A/1109,///A/1110,///A/1111" } ] }, { "index": 62, "type": "asymmetric internal loop", "bridging_nts": [ 7, 3 ], "stem_indices": [ 103, -34 ], "summary": "[2] 7 3 [A.1666 A.1994 A.1674 A.1990] 2 1", "num_nts": 14, "nts_short": "GGAACUAGGCUGUC", "nts_long": "///A/1666,///A/1667,///A/1668,///A/1669,///A/1670,///A/1671,///A/1672,///A/1673,///A/1674,///A/1990,///A/1991,///A/1992,///A/1993,///A/1994", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GAACUAG", "nts_long": "///A/1667,///A/1668,///A/1669,///A/1670,///A/1671,///A/1672,///A/1673" }, { "index": 2, "num_nts": 3, "nts_short": "UGU", "nts_long": "///A/1991,///A/1992,///A/1993" } ] }, { "index": 63, "type": "asymmetric internal loop", "bridging_nts": [ 3, 7 ], "stem_indices": [ 149, 150 ], "summary": "[2] 3 7 [A.2636 A.2782 A.2640 A.2774] 7 4", "num_nts": 14, "nts_short": "CUGAGCGAGAUGAG", "nts_long": "///A/2636,///A/2637,///A/2638,///A/2639,///A/2640,///A/2774,///A/2775,///A/2776,///A/2777,///A/2778,///A/2779,///A/2780,///A/2781,///A/2782", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/2637,///A/2638,///A/2639" }, { "index": 2, "num_nts": 7, "nts_short": "GAGAUGA", "nts_long": "///A/2775,///A/2776,///A/2777,///A/2778,///A/2779,///A/2780,///A/2781" } ] }, { "index": 64, "type": "asymmetric internal loop", "bridging_nts": [ 5, 6 ], "stem_indices": [ 16, -4 ], "summary": "[2] 5 6 [A.188 A.208 A.194 A.201] 5 1", "num_nts": 15, "nts_short": "GGAACUGCUAAGUAC", "nts_long": "///A/188,///A/189,///A/190,///A/191,///A/192,///A/193,///A/194,///A/201,///A/202,///A/203,///A/204,///A/205,///A/206,///A/207,///A/208", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAACU", "nts_long": "///A/189,///A/190,///A/191,///A/192,///A/193" }, { "index": 2, "num_nts": 6, "nts_short": "UAAGUA", "nts_long": "///A/202,///A/203,///A/204,///A/205,///A/206,///A/207" } ] }, { "index": 65, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ -28, 72 ], "summary": "[2] 6 5 [A.1262 A.2017 A.1269 A.2011] 1 2", "num_nts": 15, "nts_short": "AUAAGUAAUGAAAUU", "nts_long": "///A/1262,///A/1263,///A/1264,///A/1265,///A/1266,///A/1267,///A/1268,///A/1269,///A/2011,///A/2012,///A/2013,///A/2014,///A/2015,///A/2016,///A/2017", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UAAGUA", "nts_long": "///A/1263,///A/1264,///A/1265,///A/1266,///A/1267,///A/1268" }, { "index": 2, "num_nts": 5, "nts_short": "GAAAU", "nts_long": "///A/2012,///A/2013,///A/2014,///A/2015,///A/2016" } ] }, { "index": 66, "type": "asymmetric internal loop", "bridging_nts": [ 7, 4 ], "stem_indices": [ 134, 135 ], "summary": "[2] 7 4 [A.2129 A.2159 A.2137 A.2154] 2 7 k-turn:normal", "num_nts": 15, "nts_short": "CUUUGAAGUAUGGAG", "nts_long": "///A/2129,///A/2130,///A/2131,///A/2132,///A/2133,///A/2134,///A/2135,///A/2136,///A/2137,///A/2154,///A/2155,///A/2156,///A/2157,///A/2158,///A/2159", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUUGAAG", "nts_long": "///A/2130,///A/2131,///A/2132,///A/2133,///A/2134,///A/2135,///A/2136" }, { "index": 2, "num_nts": 4, "nts_short": "UGGA", "nts_long": "///A/2155,///A/2156,///A/2157,///A/2158" } ] }, { "index": 67, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 112, 113 ], "summary": "[2] 5 7 [A.1798 A.1821 A.1804 A.1813] 2 3 k-turn:undecided", "num_nts": 16, "nts_short": "UGCAAACGGACGUAUA", "nts_long": "///A/1798,///A/1799,///A/1800,///A/1801,///A/1802,///A/1803,///A/1804,///A/1813,///A/1814,///A/1815,///A/1816,///A/1817,///A/1818,///A/1819,///A/1820,///A/1821", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GCAAA", "nts_long": "///A/1799,///A/1800,///A/1801,///A/1802,///A/1803" }, { "index": 2, "num_nts": 7, "nts_short": "GACGUAU", "nts_long": "///A/1814,///A/1815,///A/1816,///A/1817,///A/1818,///A/1819,///A/1820" } ] }, { "index": 68, "type": "symmetric internal loop", "bridging_nts": [ 7, 7 ], "stem_indices": [ 170, -51 ], "summary": "[2] 7 7 [B.71 B.105 B.79 B.97] 2 1", "num_nts": 18, "nts_short": "CGAUGGUAGCGAGAGUAG", "nts_long": "///B/71,///B/72,///B/73,///B/74,///B/75,///B/76,///B/77,///B/78,///B/79,///B/97,///B/98,///B/99,///B/100,///B/101,///B/102,///B/103,///B/104,///B/105", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GAUGGUA", "nts_long": "///B/72,///B/73,///B/74,///B/75,///B/76,///B/77,///B/78" }, { "index": 2, "num_nts": 7, "nts_short": "GAGAGUA", "nts_long": "///B/98,///B/99,///B/100,///B/101,///B/102,///B/103,///B/104" } ] }, { "index": 69, "type": "symmetric internal loop", "bridging_nts": [ 8, 8 ], "stem_indices": [ 118, 119 ], "summary": "[2] 8 8 [A.1851 A.1891 A.1860 A.1882] 3 5", "num_nts": 20, "nts_short": "UUAAUUGAUGUUGAUCGAAG", "nts_long": "///A/1851,///A/1852,///A/1853,///A/1854,///A/1855,///A/1856,///A/1857,///A/1858,///A/1859,///A/1860,///A/1882,///A/1883,///A/1884,///A/1885,///A/1886,///A/1887,///A/1888,///A/1889,///A/1890,///A/1891", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UAAUUGAU", "nts_long": "///A/1852,///A/1853,///A/1854,///A/1855,///A/1856,///A/1857,///A/1858,///A/1859" }, { "index": 2, "num_nts": 8, "nts_short": "UGAUCGAA", "nts_long": "///A/1883,///A/1884,///A/1885,///A/1886,///A/1887,///A/1888,///A/1889,///A/1890" } ] }, { "index": 70, "type": "asymmetric internal loop", "bridging_nts": [ 3, 13 ], "stem_indices": [ 133, 134 ], "summary": "[2] 3 13 [A.2124 A.2174 A.2128 A.2160] 5 2", "num_nts": 20, "nts_short": "GGAGGCCGACCUUGAAAUAC", "nts_long": "///A/2124,///A/2125,///A/2126,///A/2127,///A/2128,///A/2160,///A/2161,///A/2162,///A/2163,///A/2164,///A/2165,///A/2166,///A/2167,///A/2168,///A/2169,///A/2170,///A/2171,///A/2172,///A/2173,///A/2174", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/2125,///A/2126,///A/2127" }, { "index": 2, "num_nts": 13, "nts_short": "CGACCUUGAAAUA", "nts_long": "///A/2161,///A/2162,///A/2163,///A/2164,///A/2165,///A/2166,///A/2167,///A/2168,///A/2169,///A/2170,///A/2171,///A/2172,///A/2173" } ] } ], "num_junctions": 33, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 0, 1 ], "stem_indices": [ -49, 158, -50 ], "summary": "[3] 1 0 1 [A.2789 A.2894 A.2791 A.2805 A.2806 A.2892] 1 5 1", "num_nts": 8, "nts_short": "CUGCCGAG", "nts_long": "///A/2789,///A/2790,///A/2791,///A/2805,///A/2806,///A/2892,///A/2893,///A/2894", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2790" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2893" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 1, 3, 2 ], "stem_indices": [ -13, 43, 45 ], "summary": "[3] 1 3 2 [A.698 A.763 A.700 A.732 A.736 A.760] 1 3 2", "num_nts": 12, "nts_short": "CAGCGAACGAUG", "nts_long": "///A/698,///A/699,///A/700,///A/732,///A/733,///A/734,///A/735,///A/736,///A/760,///A/761,///A/762,///A/763", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/699" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/733,///A/734,///A/735" }, { "index": 3, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/761,///A/762" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 4, 1, 2 ], "stem_indices": [ 74, 75, 100 ], "summary": "[3] 4 1 2 [A.1298 A.1642 A.1303 A.1625 A.1627 A.1639] 4 4 4", "num_nts": 13, "nts_short": "CGGAAGCAGCAAG", "nts_long": "///A/1298,///A/1299,///A/1300,///A/1301,///A/1302,///A/1303,///A/1625,///A/1626,///A/1627,///A/1639,///A/1640,///A/1641,///A/1642", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///A/1299,///A/1300,///A/1301,///A/1302" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1626" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1640,///A/1641" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 0, 5, 3 ], "stem_indices": [ 8, 9, 11 ], "summary": "[3] 0 5 3 [A.56 A.114 A.57 A.70 A.76 A.110] 3 3 6", "num_nts": 14, "nts_short": "ACGAUAAGCGAUUU", "nts_long": "///A/56,///A/57,///A/70,///A/71,///A/72,///A/73,///A/74,///A/75,///A/76,///A/110,///A/111,///A/112,///A/113,///A/114", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "AUAAG", "nts_long": "///A/71,///A/72,///A/73,///A/74,///A/75" }, { "index": 3, "num_nts": 3, "nts_short": "AUU", "nts_long": "///A/111,///A/112,///A/113" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 5, 1, 2 ], "stem_indices": [ 41, 42, -16 ], "summary": "[3] 5 1 2 [A.683 A.794 A.689 A.773 A.775 A.791] 6 9 1", "num_nts": 14, "nts_short": "UGAUCUAUGGCAAA", "nts_long": "///A/683,///A/684,///A/685,///A/686,///A/687,///A/688,///A/689,///A/773,///A/774,///A/775,///A/791,///A/792,///A/793,///A/794", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUCU", "nts_long": "///A/684,///A/685,///A/686,///A/687,///A/688" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/774" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/792,///A/793" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 2, 5, 1 ], "stem_indices": [ 75, 76, 99 ], "summary": "[3] 2 5 1 [A.1306 A.1622 A.1309 A.1605 A.1611 A.1620] 4 2 2", "num_nts": 14, "nts_short": "CAAGCCCAAACGUG", "nts_long": "///A/1306,///A/1307,///A/1308,///A/1309,///A/1605,///A/1606,///A/1607,///A/1608,///A/1609,///A/1610,///A/1611,///A/1620,///A/1621,///A/1622", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1307,///A/1308" }, { "index": 2, "num_nts": 5, "nts_short": "CCAAA", "nts_long": "///A/1606,///A/1607,///A/1608,///A/1609,///A/1610" }, { "index": 3, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1621" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 1, 3, 4 ], "stem_indices": [ 130, 131, 136 ], "summary": "[3] 1 3 4 [A.2091 A.2228 A.2093 A.2196 A.2200 A.2223] 5 11 3", "num_nts": 14, "nts_short": "CUGCUAACGGACAG", "nts_long": "///A/2091,///A/2092,///A/2093,///A/2196,///A/2197,///A/2198,///A/2199,///A/2200,///A/2223,///A/2224,///A/2225,///A/2226,///A/2227,///A/2228", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2092" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/2197,///A/2198,///A/2199" }, { "index": 3, "num_nts": 4, "nts_short": "GACA", "nts_long": "///A/2224,///A/2225,///A/2226,///A/2227" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 2, 6, 1 ], "stem_indices": [ 66, 67, -23 ], "summary": "[3] 2 6 1 [A.1055 A.1104 A.1058 A.1080 A.1087 A.1102] 5 2 1", "num_nts": 15, "nts_short": "GGAUAUUUAAAGCAC", "nts_long": "///A/1055,///A/1056,///A/1057,///A/1058,///A/1080,///A/1081,///A/1082,///A/1083,///A/1084,///A/1085,///A/1086,///A/1087,///A/1102,///A/1103,///A/1104", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/1056,///A/1057" }, { "index": 2, "num_nts": 6, "nts_short": "UUUAAA", "nts_long": "///A/1081,///A/1082,///A/1083,///A/1084,///A/1085,///A/1086" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1103" } ] }, { "index": 9, "type": "3-way junction", "bridging_nts": [ 4, 0, 5 ], "stem_indices": [ 87, 88, -33 ], "summary": "[3] 4 0 5 [A.1424 A.1574 A.1429 A.1564 A.1565 A.1568] 4 4 1", "num_nts": 15, "nts_short": "GGGACGCCGAAAAGC", "nts_long": "///A/1424,///A/1425,///A/1426,///A/1427,///A/1428,///A/1429,///A/1564,///A/1565,///A/1568,///A/1569,///A/1570,///A/1571,///A/1572,///A/1573,///A/1574", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAC", "nts_long": "///A/1425,///A/1426,///A/1427,///A/1428" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 5, "nts_short": "AAAAG", "nts_long": "///A/1569,///A/1570,///A/1571,///A/1572,///A/1573" } ] }, { "index": 10, "type": "3-way junction", "bridging_nts": [ 5, 1, 3 ], "stem_indices": [ 165, 166, 170 ], "summary": "[3] 5 1 3 [B.10 B.110 B.16 B.68 B.70 B.106] 10 2 2", "num_nts": 15, "nts_short": "GCCGUAGCGCGGAAC", "nts_long": "///B/10,///B/11,///B/12,///B/13,///B/14,///B/15,///B/16,///B/68,///B/69,///B/70,///B/106,///B/107,///B/108,///B/109,///B/110", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CCGUA", "nts_long": "///B/11,///B/12,///B/13,///B/14,///B/15" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///B/69" }, { "index": 3, "num_nts": 3, "nts_short": "GAA", "nts_long": "///B/107,///B/108,///B/109" } ] }, { "index": 11, "type": "3-way junction", "bridging_nts": [ 2, 4, 5 ], "stem_indices": [ 159, 160, 161 ], "summary": "[3] 2 4 5 [A.2812 A.2888 A.2815 A.2831 A.2836 A.2882] 2 5 3", "num_nts": 17, "nts_short": "GAACGUUGAUAAUGAAC", "nts_long": "///A/2812,///A/2813,///A/2814,///A/2815,///A/2831,///A/2832,///A/2833,///A/2834,///A/2835,///A/2836,///A/2882,///A/2883,///A/2884,///A/2885,///A/2886,///A/2887,///A/2888", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2813,///A/2814" }, { "index": 2, "num_nts": 4, "nts_short": "UUGA", "nts_long": "///A/2832,///A/2833,///A/2834,///A/2835" }, { "index": 3, "num_nts": 5, "nts_short": "AUGAA", "nts_long": "///A/2883,///A/2884,///A/2885,///A/2886,///A/2887" } ] }, { "index": 12, "type": "3-way junction", "bridging_nts": [ 3, 5, 4 ], "stem_indices": [ 141, 142, 143 ], "summary": "[3] 3 5 4 [A.2295 A.2337 A.2299 A.2317 A.2323 A.2332] 7 5 2", "num_nts": 18, "nts_short": "CUAAUAGGUUAGCAUAAG", "nts_long": "///A/2295,///A/2296,///A/2297,///A/2298,///A/2299,///A/2317,///A/2318,///A/2319,///A/2320,///A/2321,///A/2322,///A/2323,///A/2332,///A/2333,///A/2334,///A/2335,///A/2336,///A/2337", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/2296,///A/2297,///A/2298" }, { "index": 2, "num_nts": 5, "nts_short": "GGUUA", "nts_long": "///A/2318,///A/2319,///A/2320,///A/2321,///A/2322" }, { "index": 3, "num_nts": 4, "nts_short": "AUAA", "nts_long": "///A/2333,///A/2334,///A/2335,///A/2336" } ] }, { "index": 13, "type": "3-way junction", "bridging_nts": [ 2, 15, 4 ], "stem_indices": [ 3, 4, 30 ], "summary": "[3] 2 15 4 [A.32 A.473 A.35 A.445 A.461 A.468] 2 2 2", "num_nts": 27, "nts_short": "CCUGCGAUAGUGAACCAGUACGGAAAG", "nts_long": "///A/32,///A/33,///A/34,///A/35,///A/445,///A/446,///A/447,///A/448,///A/449,///A/450,///A/451,///A/452,///A/453,///A/454,///A/455,///A/456,///A/457,///A/458,///A/459,///A/460,///A/461,///A/468,///A/469,///A/470,///A/471,///A/472,///A/473", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/33,///A/34" }, { "index": 2, "num_nts": 15, "nts_short": "GAUAGUGAACCAGUA", "nts_long": "///A/446,///A/447,///A/448,///A/449,///A/450,///A/451,///A/452,///A/453,///A/454,///A/455,///A/456,///A/457,///A/458,///A/459,///A/460" }, { "index": 3, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/469,///A/470,///A/471,///A/472" } ] }, { "index": 14, "type": "3-way junction", "bridging_nts": [ 0, 9, 13 ], "stem_indices": [ -1, 3, 31 ], "summary": "[3] 0 9 13 [A.30 A.510 A.31 A.474 A.484 A.496] 1 2 4", "num_nts": 28, "nts_short": "GCGCGAAAAGAACGAGUGAAAAAGAACC", "nts_long": "///A/30,///A/31,///A/474,///A/475,///A/476,///A/477,///A/478,///A/479,///A/480,///A/481,///A/482,///A/483,///A/484,///A/496,///A/497,///A/498,///A/499,///A/500,///A/501,///A/502,///A/503,///A/504,///A/505,///A/506,///A/507,///A/508,///A/509,///A/510", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 9, "nts_short": "CGAAAAGAA", "nts_long": "///A/475,///A/476,///A/477,///A/478,///A/479,///A/480,///A/481,///A/482,///A/483" }, { "index": 3, "num_nts": 13, "nts_short": "AGUGAAAAAGAAC", "nts_long": "///A/497,///A/498,///A/499,///A/500,///A/501,///A/502,///A/503,///A/504,///A/505,///A/506,///A/507,///A/508,///A/509" } ] }, { "index": 15, "type": "4-way junction", "bridging_nts": [ 1, 1, 0, 1 ], "stem_indices": [ 9, -2, 12, 10 ], "summary": "[4] 1 1 0 1 [A.59 A.68 A.61 A.93 A.95 A.87 A.88 A.66] 3 1 3 3", "num_nts": 11, "nts_short": "UGCGAAUGCUG", "nts_long": "///A/59,///A/60,///A/61,///A/93,///A/94,///A/95,///A/87,///A/88,///A/66,///A/67,///A/68", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/60" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/94" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 1, "nts_short": "U", "nts_long": "///A/67" } ] }, { "index": 16, "type": "4-way junction", "bridging_nts": [ 3, 1, 0, 1 ], "stem_indices": [ -31, 92, 155, 92 ], "summary": "[4] 3 1 0 1 [A.1451 A.1459 A.1455 A.2704 A.2706 A.2701 A.2702 A.1457] 1 3 6 3", "is_repeated": true, "num_nts": 13, "nts_short": "CGACGCAAUGUUG", "nts_long": "///A/1451,///A/1452,///A/1453,///A/1454,///A/1455,///A/2704,///A/2705,///A/2706,///A/2701,///A/2702,///A/1457,///A/1458,///A/1459", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAC", "nts_long": "///A/1452,///A/1453,///A/1454" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2705" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1458" } ] }, { "index": 17, "type": "4-way junction", "bridging_nts": [ 5, 0, 2, 0 ], "stem_indices": [ 72, 73, 74, 101 ], "summary": "[4] 5 0 2 0 [A.1270 A.2010 A.1276 A.1294 A.1295 A.1645 A.1648 A.2009] 2 6 4 4", "num_nts": 15, "nts_short": "CGAUAAAUCGCUUAG", "nts_long": "///A/1270,///A/1271,///A/1272,///A/1273,///A/1274,///A/1275,///A/1276,///A/1294,///A/1295,///A/1645,///A/1646,///A/1647,///A/1648,///A/2009,///A/2010", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUAA", "nts_long": "///A/1271,///A/1272,///A/1273,///A/1274,///A/1275" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/1646,///A/1647" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 18, "type": "4-way junction", "bridging_nts": [ 2, 1, 3, 1 ], "stem_indices": [ 150, 151, 152, 156 ], "summary": "[4] 2 1 3 1 [A.2643 A.2771 A.2646 A.2674 A.2676 A.2731 A.2735 A.2769] 4 7 5 3", "num_nts": 15, "nts_short": "GGGCGACGGAAGUGC", "nts_long": "///A/2643,///A/2644,///A/2645,///A/2646,///A/2674,///A/2675,///A/2676,///A/2731,///A/2732,///A/2733,///A/2734,///A/2735,///A/2769,///A/2770,///A/2771", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/2644,///A/2645" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2675" }, { "index": 3, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/2732,///A/2733,///A/2734" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2770" } ] }, { "index": 19, "type": "4-way junction", "bridging_nts": [ 2, 3, 3, 0 ], "stem_indices": [ 28, 29, -46, 29 ], "summary": "[4] 2 3 3 0 [A.410 A.417 A.413 A.2410 A.2414 A.2403 A.2407 A.416] 5 4 1 4", "is_repeated": true, "num_nts": 16, "nts_short": "GGACGAAGGCUGAAUC", "nts_long": "///A/410,///A/411,///A/412,///A/413,///A/2410,///A/2411,///A/2412,///A/2413,///A/2414,///A/2403,///A/2404,///A/2405,///A/2406,///A/2407,///A/416,///A/417", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/411,///A/412" }, { "index": 2, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/2411,///A/2412,///A/2413" }, { "index": 3, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/2404,///A/2405,///A/2406" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 20, "type": "4-way junction", "bridging_nts": [ 3, 3, 1, 1 ], "stem_indices": [ 140, 141, 145, 147 ], "summary": "[4] 3 3 1 1 [A.2285 A.2383 A.2289 A.2343 A.2347 A.2370 A.2372 A.2381] 2 7 4 3", "num_nts": 16, "nts_short": "CGAAGUUGACGGUAGG", "nts_long": "///A/2285,///A/2286,///A/2287,///A/2288,///A/2289,///A/2343,///A/2344,///A/2345,///A/2346,///A/2347,///A/2370,///A/2371,///A/2372,///A/2381,///A/2382,///A/2383", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/2286,///A/2287,///A/2288" }, { "index": 2, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/2344,///A/2345,///A/2346" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2371" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2382" } ] }, { "index": 21, "type": "4-way junction", "bridging_nts": [ 0, 0, 4, 5 ], "stem_indices": [ 90, 91, 93, 98 ], "summary": "[4] 0 0 4 5 [A.1444 A.1547 A.1445 A.1466 A.1467 A.1525 A.1530 A.1541] 5 6 2 4", "num_nts": 17, "nts_short": "GGUUACGAGGCUGAAGC", "nts_long": "///A/1444,///A/1445,///A/1466,///A/1467,///A/1525,///A/1526,///A/1527,///A/1528,///A/1529,///A/1530,///A/1541,///A/1542,///A/1543,///A/1544,///A/1545,///A/1546,///A/1547", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 4, "nts_short": "CGAG", "nts_long": "///A/1526,///A/1527,///A/1528,///A/1529" }, { "index": 4, "num_nts": 5, "nts_short": "UGAAG", "nts_long": "///A/1542,///A/1543,///A/1544,///A/1545,///A/1546" } ] }, { "index": 22, "type": "4-way junction", "bridging_nts": [ 2, 3, 2, 5 ], "stem_indices": [ 35, 36, 38, 39 ], "summary": "[4] 2 3 2 5 [A.601 A.656 A.604 A.624 A.628 A.635 A.638 A.650] 13 3 2 4", "num_nts": 20, "nts_short": "CAAGCGAAGCGAGCGUUAAG", "nts_long": "///A/601,///A/602,///A/603,///A/604,///A/624,///A/625,///A/626,///A/627,///A/628,///A/635,///A/636,///A/637,///A/638,///A/650,///A/651,///A/652,///A/653,///A/654,///A/655,///A/656", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/602,///A/603" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/625,///A/626,///A/627" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/636,///A/637" }, { "index": 4, "num_nts": 5, "nts_short": "GUUAA", "nts_long": "///A/651,///A/652,///A/653,///A/654,///A/655" } ] }, { "index": 23, "type": "4-way junction", "bridging_nts": [ 2, 8, 6, 2 ], "stem_indices": [ 20, 21, 27, 28 ], "summary": "[4] 2 8 6 2 [A.268 A.424 A.271 A.366 A.375 A.399 A.406 A.421] 3 4 7 5", "num_nts": 26, "nts_short": "CCAGCGAUGAGUAGUGAAUAUGCAAG", "nts_long": "///A/268,///A/269,///A/270,///A/271,///A/366,///A/367,///A/368,///A/369,///A/370,///A/371,///A/372,///A/373,///A/374,///A/375,///A/399,///A/400,///A/401,///A/402,///A/403,///A/404,///A/405,///A/406,///A/421,///A/422,///A/423,///A/424", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/269,///A/270" }, { "index": 2, "num_nts": 8, "nts_short": "GAUGAGUA", "nts_long": "///A/367,///A/368,///A/369,///A/370,///A/371,///A/372,///A/373,///A/374" }, { "index": 3, "num_nts": 6, "nts_short": "GAAUAU", "nts_long": "///A/400,///A/401,///A/402,///A/403,///A/404,///A/405" }, { "index": 4, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/422,///A/423" } ] }, { "index": 24, "type": "5-way junction", "bridging_nts": [ 6, 4, 0, 1, 1 ], "stem_indices": [ 7, 8, 13, 14, 15 ], "summary": "[5] 6 4 0 1 1 [A.47 A.178 A.54 A.116 A.121 A.130 A.131 A.148 A.150 A.176] 2 3 3 7 9", "num_nts": 22, "nts_short": "CGAUGAAGCGAAUGCAUAUAGG", "nts_long": "///A/47,///A/48,///A/49,///A/50,///A/51,///A/52,///A/53,///A/54,///A/116,///A/117,///A/118,///A/119,///A/120,///A/121,///A/130,///A/131,///A/148,///A/149,///A/150,///A/176,///A/177,///A/178", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAUGAA", "nts_long": "///A/48,///A/49,///A/50,///A/51,///A/52,///A/53" }, { "index": 2, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///A/117,///A/118,///A/119,///A/120" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///A/149" }, { "index": 5, "num_nts": 1, "nts_short": "G", "nts_long": "///A/177" } ] }, { "index": 25, "type": "5-way junction", "bridging_nts": [ 4, 2, 2, 0, 5 ], "stem_indices": [ 34, 35, 40, 48, -27 ], "summary": "[5] 4 2 2 0 5 [A.584 A.1256 A.589 A.668 A.671 A.809 A.812 A.1195 A.1196 A.1250] 6 13 2 6 1", "num_nts": 23, "nts_short": "CGACUUAGACGUUCGCGCGAAUG", "nts_long": "///A/584,///A/585,///A/586,///A/587,///A/588,///A/589,///A/668,///A/669,///A/670,///A/671,///A/809,///A/810,///A/811,///A/812,///A/1195,///A/1196,///A/1250,///A/1251,///A/1252,///A/1253,///A/1254,///A/1255,///A/1256", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GACU", "nts_long": "///A/585,///A/586,///A/587,///A/588" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/669,///A/670" }, { "index": 3, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/810,///A/811" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 5, "num_nts": 5, "nts_short": "CGAAU", "nts_long": "///A/1251,///A/1252,///A/1253,///A/1254,///A/1255" } ] }, { "index": 26, "type": "5-way junction", "bridging_nts": [ 7, 0, 0, 7, 1 ], "stem_indices": [ -34, 104, 105, -38, 108 ], "summary": "[5] 7 0 0 7 1 [A.1674 A.1990 A.1682 A.1706 A.1707 A.1751 A.1752 A.1756 A.1764 A.1988] 1 5 6 1 7", "num_nts": 25, "nts_short": "GCAAAAUGGCGUCGAUACCAGCGGC", "nts_long": "///A/1674,///A/1675,///A/1676,///A/1677,///A/1678,///A/1679,///A/1680,///A/1681,///A/1682,///A/1706,///A/1707,///A/1751,///A/1752,///A/1756,///A/1757,///A/1758,///A/1759,///A/1760,///A/1761,///A/1762,///A/1763,///A/1764,///A/1988,///A/1989,///A/1990", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CAAAAUG", "nts_long": "///A/1675,///A/1676,///A/1677,///A/1678,///A/1679,///A/1680,///A/1681" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 7, "nts_short": "AUACCAG", "nts_long": "///A/1757,///A/1758,///A/1759,///A/1760,///A/1761,///A/1762,///A/1763" }, { "index": 5, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1989" } ] }, { "index": 27, "type": "6-way junction", "bridging_nts": [ 1, 1, 0, 2, 1, 5 ], "stem_indices": [ -9, -10, 34, -28, -39, 122 ], "summary": "[6] 1 1 0 2 1 5 [A.562 A.2033 A.564 A.577 A.579 A.1261 A.1262 A.2017 A.2020 A.2034 A.2036 A.2027] 1 1 6 1 1 5", "num_nts": 22, "nts_short": "UACGGGCAUGAAUGCGUGAAGA", "nts_long": "///A/562,///A/563,///A/564,///A/577,///A/578,///A/579,///A/1261,///A/1262,///A/2017,///A/2018,///A/2019,///A/2020,///A/2034,///A/2035,///A/2036,///A/2027,///A/2028,///A/2029,///A/2030,///A/2031,///A/2032,///A/2033", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/563" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/578" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2018,///A/2019" }, { "index": 5, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2035" }, { "index": 6, "num_nts": 5, "nts_short": "UGAAG", "nts_long": "///A/2028,///A/2029,///A/2030,///A/2031,///A/2032" } ] }, { "index": 28, "type": "6-way junction", "bridging_nts": [ 1, 0, 0, 1, 5, 5 ], "stem_indices": [ -43, 140, 144, 143, -44, 148 ], "summary": "[6] 1 0 0 1 5 5 [A.2282 A.2427 A.2284 A.2384 A.2385 A.2330 A.2331 A.2324 A.2326 A.2389 A.2395 A.2421] 1 2 3 2 1 7", "num_nts": 24, "nts_short": "GCAUCGGUGCGUGAUCCGCUCAAC", "nts_long": "///A/2282,///A/2283,///A/2284,///A/2384,///A/2385,///A/2330,///A/2331,///A/2324,///A/2325,///A/2326,///A/2389,///A/2390,///A/2391,///A/2392,///A/2393,///A/2394,///A/2395,///A/2421,///A/2422,///A/2423,///A/2424,///A/2425,///A/2426,///A/2427", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2283" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2325" }, { "index": 5, "num_nts": 5, "nts_short": "UGAUC", "nts_long": "///A/2390,///A/2391,///A/2392,///A/2393,///A/2394" }, { "index": 6, "num_nts": 5, "nts_short": "CUCAA", "nts_long": "///A/2422,///A/2423,///A/2424,///A/2425,///A/2426" } ] }, { "index": 29, "type": "6-way junction", "bridging_nts": [ 0, 1, 5, 11, 3, 0 ], "stem_indices": [ 60, 61, -21, 63, 61, -20 ], "summary": "[6] 0 1 5 11 3 0 [A.1004 A.1151 A.1005 A.1138 A.1140 A.1024 A.1030 A.1124 A.1136 A.1007 A.1011 A.1150] 3 3 1 2 3 1", "is_repeated": true, "num_nts": 32, "nts_short": "UCGGCGGGAAACGGAAGAUGUAACGCAAAGCA", "nts_long": "///A/1004,///A/1005,///A/1138,///A/1139,///A/1140,///A/1024,///A/1025,///A/1026,///A/1027,///A/1028,///A/1029,///A/1030,///A/1124,///A/1125,///A/1126,///A/1127,///A/1128,///A/1129,///A/1130,///A/1131,///A/1132,///A/1133,///A/1134,///A/1135,///A/1136,///A/1007,///A/1008,///A/1009,///A/1010,///A/1011,///A/1150,///A/1151", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1139" }, { "index": 3, "num_nts": 5, "nts_short": "GGAAA", "nts_long": "///A/1025,///A/1026,///A/1027,///A/1028,///A/1029" }, { "index": 4, "num_nts": 11, "nts_short": "GAAGAUGUAAC", "nts_long": "///A/1125,///A/1126,///A/1127,///A/1128,///A/1129,///A/1130,///A/1131,///A/1132,///A/1133,///A/1134,///A/1135" }, { "index": 5, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1008,///A/1009,///A/1010" }, { "index": 6, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 30, "type": "6-way junction", "bridging_nts": [ 0, 3, 9, 3, 3, 6 ], "stem_indices": [ 6, 7, -3, 17, 18, 20 ], "summary": "[6] 0 3 9 3 3 6 [A.45 A.433 A.46 A.179 A.183 A.214 A.224 A.231 A.235 A.262 A.266 A.426] 2 2 1 2 5 3", "num_nts": 36, "nts_short": "GGCGAACGGAAAAGAAAUAGAUUAGCAGCUAAAUAC", "nts_long": "///A/45,///A/46,///A/179,///A/180,///A/181,///A/182,///A/183,///A/214,///A/215,///A/216,///A/217,///A/218,///A/219,///A/220,///A/221,///A/222,///A/223,///A/224,///A/231,///A/232,///A/233,///A/234,///A/235,///A/262,///A/263,///A/264,///A/265,///A/266,///A/426,///A/427,///A/428,///A/429,///A/430,///A/431,///A/432,///A/433", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/180,///A/181,///A/182" }, { "index": 3, "num_nts": 9, "nts_short": "GAAAAGAAA", "nts_long": "///A/215,///A/216,///A/217,///A/218,///A/219,///A/220,///A/221,///A/222,///A/223" }, { "index": 4, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/232,///A/233,///A/234" }, { "index": 5, "num_nts": 3, "nts_short": "GCA", "nts_long": "///A/263,///A/264,///A/265" }, { "index": 6, "num_nts": 6, "nts_short": "UAAAUA", "nts_long": "///A/427,///A/428,///A/429,///A/430,///A/431,///A/432" } ] }, { "index": 31, "type": "7-way junction", "bridging_nts": [ 3, 0, 0, 5, 0, 1, 3 ], "stem_indices": [ 23, 24, 25, 26, 25, -6, 26 ], "summary": "[7] 3 0 0 5 0 1 3 [A.297 A.341 A.301 A.316 A.317 A.334 A.335 A.327 A.333 A.318 A.319 A.323 A.325 A.337] 3 5 2 3 2 1 3", "is_repeated": true, "num_nts": 26, "nts_short": "GGAAGCGCCGUGACAGCGCAGCGUAC", "nts_long": "///A/297,///A/298,///A/299,///A/300,///A/301,///A/316,///A/317,///A/334,///A/335,///A/327,///A/328,///A/329,///A/330,///A/331,///A/332,///A/333,///A/318,///A/319,///A/323,///A/324,///A/325,///A/337,///A/338,///A/339,///A/340,///A/341", "num_stems": 7, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/298,///A/299,///A/300" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 5, "nts_short": "UGACA", "nts_long": "///A/328,///A/329,///A/330,///A/331,///A/332" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 6, "num_nts": 1, "nts_short": "A", "nts_long": "///A/324" }, { "index": 7, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/338,///A/339,///A/340" } ] }, { "index": 32, "type": "7-way junction", "bridging_nts": [ 4, 1, 4, 5, 3, 0, 4 ], "stem_indices": [ 48, 49, -17, 56, 57, 58, 68 ], "summary": "[7] 4 1 4 5 3 0 4 [A.817 A.1190 A.822 A.835 A.837 A.942 A.947 A.970 A.976 A.987 A.991 A.1163 A.1164 A.1185] 6 5 1 8 3 4 4", "num_nts": 35, "nts_short": "CGAAAGCGCGACACAUGAAGAGCAGACGCGGGUAG", "nts_long": "///A/817,///A/818,///A/819,///A/820,///A/821,///A/822,///A/835,///A/836,///A/837,///A/942,///A/943,///A/944,///A/945,///A/946,///A/947,///A/970,///A/971,///A/972,///A/973,///A/974,///A/975,///A/976,///A/987,///A/988,///A/989,///A/990,///A/991,///A/1163,///A/1164,///A/1185,///A/1186,///A/1187,///A/1188,///A/1189,///A/1190", "num_stems": 7, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/818,///A/819,///A/820,///A/821" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/836" }, { "index": 3, "num_nts": 4, "nts_short": "ACAC", "nts_long": "///A/943,///A/944,///A/945,///A/946" }, { "index": 4, "num_nts": 5, "nts_short": "GAAGA", "nts_long": "///A/971,///A/972,///A/973,///A/974,///A/975" }, { "index": 5, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/988,///A/989,///A/990" }, { "index": 6, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 7, "num_nts": 4, "nts_short": "GGUA", "nts_long": "///A/1186,///A/1187,///A/1188,///A/1189" } ] }, { "index": 33, "type": "9-way junction", "bridging_nts": [ 0, 4, 0, 1, 1, 2, 0, 0, 1 ], "stem_indices": [ -29, 77, 79, 85, 80, 81, 84, 79, 80 ], "summary": "[9] 0 4 0 1 1 2 0 0 1 [A.1313 A.1603 A.1314 A.1338 A.1343 A.1404 A.1405 A.1597 A.1599 A.1347 A.1349 A.1382 A.1385 A.1402 A.1403 A.1344 A.1345 A.1601] 1 6 2 11 3 3 5 2 3", "is_repeated": true, "num_nts": 27, "nts_short": "UCGGUGAGCUAAUACCGAAAUAUCGUA", "nts_long": "///A/1313,///A/1314,///A/1338,///A/1339,///A/1340,///A/1341,///A/1342,///A/1343,///A/1404,///A/1405,///A/1597,///A/1598,///A/1599,///A/1347,///A/1348,///A/1349,///A/1382,///A/1383,///A/1384,///A/1385,///A/1402,///A/1403,///A/1344,///A/1345,///A/1601,///A/1602,///A/1603", "num_stems": 9, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///A/1339,///A/1340,///A/1341,///A/1342" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1598" }, { "index": 5, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1348" }, { "index": 6, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1383,///A/1384" }, { "index": 7, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 8, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 9, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1602" } ] } ], "num_ssSegments": 21, "ssSegments": [ { "index": 1, "num_nts": 6, "nts_short": "GACUAA", "nts_long": "///A/9,///A/10,///A/11,///A/12,///A/13,///A/14" }, { "index": 2, "num_nts": 5, "nts_short": "ACAAG", "nts_long": "///A/526,///A/527,///A/528,///A/529,///A/530" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/532" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///A/561" }, { "index": 5, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/1475,///A/1476,///A/1477" }, { "index": 6, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/1514,///A/1515" }, { "index": 7, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1773" }, { "index": 8, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1775" }, { "index": 9, "num_nts": 3, "nts_short": "ACA", "nts_long": "///A/1789,///A/1790,///A/1791" }, { "index": 10, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1828" }, { "index": 11, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1834" }, { "index": 12, "is_broken": true, "num_nts": 32, "nts_short": "CUAAGGUAGCGAAAUUCCUUGCCUGCACGAAU", "nts_long": "///A/1925,///A/1926,///A/1927,///A/1928,///A/1929,///A/1930,///A/1931,///A/1932,///A/1933,///A/1934,///A/1935,///A/1936,///A/1937,///A/1938,///A/1939,///A/1940,///A/1941,///A/1942,///A/1943,///A/1944,///A/1945,///A/1961,///A/1962,///A/1963,///A/1964,///A/1965,///A/1966,///A/1967,///A/1968,///A/1969,///A/1970,///A/1971" }, { "index": 13, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1976,///A/1977,///A/1978" }, { "index": 14, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2041,///A/2042" }, { "index": 15, "num_nts": 5, "nts_short": "AAAGA", "nts_long": "///A/2058,///A/2059,///A/2060,///A/2061,///A/2062" }, { "index": 16, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2075,///A/2076" }, { "index": 17, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2244,///A/2245" }, { "index": 18, "num_nts": 6, "nts_short": "GAUAAA", "nts_long": "///A/2429,///A/2430,///A/2431,///A/2432,///A/2433,///A/2434" }, { "index": 19, "is_broken": true, "num_nts": 4, "nts_short": "AGUC", "nts_long": "///A/2448,///A/2608,///A/2609,///A/2610" }, { "index": 20, "num_nts": 3, "nts_short": "GCU", "nts_long": "///A/2627,///A/2628,///A/2629" }, { "index": 21, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2903" } ], "num_kissingLoops": 7, "kissingLoops": [ { "index": 1, "stem_index": -42, "is_isoCanonPair": true, "hairpin_indices": [ 55, 57 ] }, { "index": 2, "stem_index": -7, "is_isoCanonPair": true, "hairpin_indices": [ 13, 15 ] }, { "index": 3, "stem_index": -5, "is_isoCanonPair": true, "hairpin_indices": [ 7, 9 ] }, { "index": 4, "stem_index": -2, "is_isoCanonPair": true, "hairpin_indices": [ 1, 3 ] }, { "index": 5, "stem_index": 10, "hairpin_indices": [ 1, 3 ] }, { "index": 6, "stem_index": 29, "hairpin_indices": [ 15, 62 ] }, { "index": 7, "stem_index": 92, "hairpin_indices": [ 38, 64 ] } ], "num_Aminors": 120, "Aminors": [ { "index": 1, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/52 vs ///A/47,///A/178", "A_nt1": { "desc": "///A/52 vs ///A/47", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.81],O2'(hydroxyl)-O2(carbonyl)[3.34]" }, "A_nt2": { "desc": "///A/52 vs ///A/178", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.84],N3-N2(amino)[2.91]" } }, { "index": 2, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/71 vs ///A/57,///A/70", "A_nt1": { "desc": "///A/71 vs ///A/57", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/71 vs ///A/70", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.47]" } }, { "index": 3, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/73 vs ///A/58,///A/69", "A_nt1": { "desc": "///A/73 vs ///A/58", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.64],N3-N2(amino)[3.25]" }, "A_nt2": { "desc": "///A/73 vs ///A/69", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.78],O2'(hydroxyl)-O2(carbonyl)[2.62]" } }, { "index": 4, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/103 vs ///A/85,///A/97", "A_nt1": { "desc": "///A/103 vs ///A/85", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.95],N3-N2(amino)[3.20]" }, "A_nt2": { "desc": "///A/103 vs ///A/97", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.34]" } }, { "index": 5, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/126 vs ///A/54,///A/116", "A_nt1": { "desc": "///A/126 vs ///A/54", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/126 vs ///A/116", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O3'[3.02],N3-O2'(hydroxyl)[2.52]" } }, { "index": 6, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/127 vs ///A/55,///A/115", "A_nt1": { "desc": "///A/127 vs ///A/55", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.50],N3-N2(amino)[3.34]" }, "A_nt2": { "desc": "///A/127 vs ///A/115", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.45]" } }, { "index": 7, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/160 vs ///A/2208,///A/2216", "A_nt1": { "desc": "///A/160 vs ///A/2208", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.04],N3-O2'(hydroxyl)[2.45]" }, "A_nt2": { "desc": "///A/160 vs ///A/2216", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 8, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/161 vs ///A/2207,///A/2217", "A_nt1": { "desc": "///A/161 vs ///A/2207", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.55],O2'(hydroxyl)-O2(carbonyl)[3.20]" }, "A_nt2": { "desc": "///A/161 vs ///A/2217", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.87],N3-N2(amino)[3.03]" } }, { "index": 9, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/182 vs ///A/45,///A/433", "A_nt1": { "desc": "///A/182 vs ///A/45", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/182 vs ///A/433", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.14],N3-O2'(hydroxyl)[2.44]" } }, { "index": 10, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/190 vs ///A/679,///A/798", "A_nt1": { "desc": "///A/190 vs ///A/679", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.80]" }, "A_nt2": { "desc": "///A/190 vs ///A/798", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 11, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/191 vs ///A/678,///A/799", "A_nt1": { "desc": "///A/191 vs ///A/678", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.81],O2'(hydroxyl)-O2(carbonyl)[2.62]" }, "A_nt2": { "desc": "///A/191 vs ///A/799", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.80]" } }, { "index": 12, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/196 vs ///A/826,///A/831", "A_nt1": { "desc": "///A/196 vs ///A/826", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/196 vs ///A/831", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.27]" } }, { "index": 13, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/199 vs ///A/2078,///A/2242", "A_nt1": { "desc": "///A/199 vs ///A/2078", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.34]" }, "A_nt2": { "desc": "///A/199 vs ///A/2242", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "OP1-O2'(hydroxyl)[3.47]" } }, { "index": 14, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/223 vs ///A/407,///A/420", "A_nt1": { "desc": "///A/223 vs ///A/407", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.41]" }, "A_nt2": { "desc": "///A/223 vs ///A/420", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91],O2'(hydroxyl)-O2(carbonyl)[2.73]" } }, { "index": 15, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/226 vs ///A/409,///A/418", "A_nt1": { "desc": "///A/226 vs ///A/409", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/226 vs ///A/418", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.12],N1-O2'(hydroxyl)[3.08]" } }, { "index": 16, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/227 vs ///A/410,///A/417", "A_nt1": { "desc": "///A/227 vs ///A/410", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.05],N6(amino)-N3[2.95],N1-N2(amino)[3.05]" }, "A_nt2": { "desc": "///A/227 vs ///A/417", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 17, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/251 vs ///A/194,///A/201", "A_nt1": { "desc": "///A/251 vs ///A/194", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.97],N3-N2(amino)[2.98]" }, "A_nt2": { "desc": "///A/251 vs ///A/201", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.73]" } }, { "index": 18, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/294 vs ///A/80,///A/106", "A_nt1": { "desc": "///A/294 vs ///A/80", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.91],N3-N2(amino)[3.20]" }, "A_nt2": { "desc": "///A/294 vs ///A/106", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.64],O2'(hydroxyl)-O2(carbonyl)[2.98]" } }, { "index": 19, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/299 vs ///A/319,///A/323", "A_nt1": { "desc": "///A/299 vs ///A/319", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.69]" }, "A_nt2": { "desc": "///A/299 vs ///A/323", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 20, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/300 vs ///A/318,///A/333", "A_nt1": { "desc": "///A/300 vs ///A/318", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.78]" }, "A_nt2": { "desc": "///A/300 vs ///A/333", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.58],N3-N2(amino)[3.26]" } }, { "index": 21, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/346 vs ///A/79,///A/107", "A_nt1": { "desc": "///A/346 vs ///A/79", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.13],N3-O2'(hydroxyl)[2.48]" }, "A_nt2": { "desc": "///A/346 vs ///A/107", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.11]" } }, { "index": 22, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/384 vs ///A/245,///A/253", "A_nt1": { "desc": "///A/384 vs ///A/245", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.16]" }, "A_nt2": { "desc": "///A/384 vs ///A/253", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 23, "type": "X", "desc_short": "A vs A-G (Imino)", "desc_long": "///A/432 vs ///A/182,///A/215", "A_nt1": { "desc": "///A/432 vs ///A/182", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/432 vs ///A/215", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.47]" } }, { "index": 24, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/432 vs ///A/183,///A/214", "A_nt1": { "desc": "///A/432 vs ///A/183", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.13],N3-O2'(hydroxyl)[2.56]" }, "A_nt2": { "desc": "///A/432 vs ///A/214", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 25, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/443 vs ///A/1200,///A/1245", "A_nt1": { "desc": "///A/443 vs ///A/1200", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.73],O2'(hydroxyl)-O2(carbonyl)[3.11]" }, "A_nt2": { "desc": "///A/443 vs ///A/1245", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.28],N3-N2(amino)[3.18]" } }, { "index": 26, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/449 vs ///A/35,///A/445", "A_nt1": { "desc": "///A/449 vs ///A/35", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.32]" }, "A_nt2": { "desc": "///A/449 vs ///A/445", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.88],N3-O2'(hydroxyl)[2.72]" } }, { "index": 27, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/466 vs ///A/682,///A/795", "A_nt1": { "desc": "///A/466 vs ///A/682", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/466 vs ///A/795", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.77]" } }, { "index": 28, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/514 vs ///A/581,///A/1259", "A_nt1": { "desc": "///A/514 vs ///A/581", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.09],N3-O2'(hydroxyl)[2.48]" }, "A_nt2": { "desc": "///A/514 vs ///A/1259", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 29, "type": "I", "desc_short": "A vs U-A (WC)", "desc_long": "///A/515 vs ///A/580,///A/1260", "A_nt1": { "desc": "///A/515 vs ///A/580", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.47]" }, "A_nt2": { "desc": "///A/515 vs ///A/1260", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.27]" } }, { "index": 30, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/526 vs ///A/2043,///A/2625", "A_nt1": { "desc": "///A/526 vs ///A/2043", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.90],O2'(hydroxyl)-O2(carbonyl)[2.40]" }, "A_nt2": { "desc": "///A/526 vs ///A/2625", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.95]" } }, { "index": 31, "type": "X", "desc_short": "A vs A-G (Imino)", "desc_long": "///A/532 vs ///A/2019,///A/2035", "A_nt1": { "desc": "///A/532 vs ///A/2019", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/532 vs ///A/2035", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.14]" } }, { "index": 32, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/532 vs ///A/2020,///A/2034", "A_nt1": { "desc": "///A/532 vs ///A/2020", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.14]" }, "A_nt2": { "desc": "///A/532 vs ///A/2034", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 33, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/586 vs ///A/671,///A/809", "A_nt1": { "desc": "///A/586 vs ///A/671", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.67],O2'(hydroxyl)-O2(carbonyl)[3.04]" }, "A_nt2": { "desc": "///A/586 vs ///A/809", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.47],N3-N2(amino)[3.45]" } }, { "index": 34, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/608 vs ///A/238,///A/259", "A_nt1": { "desc": "///A/608 vs ///A/238", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.18],O2'(hydroxyl)-O2'(hydroxyl)[3.10],N3-O2'(hydroxyl)[2.47]" }, "A_nt2": { "desc": "///A/608 vs ///A/259", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 35, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/609 vs ///A/237,///A/260", "A_nt1": { "desc": "///A/609 vs ///A/237", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.66],O2'(hydroxyl)-O2(carbonyl)[2.95]" }, "A_nt2": { "desc": "///A/609 vs ///A/260", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.49]" } }, { "index": 36, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/631 vs ///A/2401,///A/2415", "A_nt1": { "desc": "///A/631 vs ///A/2401", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/631 vs ///A/2415", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1-N2(amino)[3.12],N3-O2'(hydroxyl)[3.20]" } }, { "index": 37, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/643 vs ///A/2348,///A/2369", "A_nt1": { "desc": "///A/643 vs ///A/2348", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/643 vs ///A/2369", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.15],N1-O2'(hydroxyl)[2.68]" } }, { "index": 38, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/644 vs ///A/2349,///A/2368", "A_nt1": { "desc": "///A/644 vs ///A/2349", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.03],N1-N2(amino)[3.35]" }, "A_nt2": { "desc": "///A/644 vs ///A/2368", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 39, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/675 vs ///A/2067,///A/2443", "A_nt1": { "desc": "///A/675 vs ///A/2067", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/675 vs ///A/2443", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.65]" } }, { "index": 40, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/676 vs ///A/2069,///A/2442", "A_nt1": { "desc": "///A/676 vs ///A/2069", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.77]" }, "A_nt2": { "desc": "///A/676 vs ///A/2442", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.81],O2'(hydroxyl)-O2(carbonyl)[3.06]" } }, { "index": 41, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/685 vs ///A/778,///A/786", "A_nt1": { "desc": "///A/685 vs ///A/778", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.95],N6(amino)-N3[3.13],N1-N2(amino)[3.35]" }, "A_nt2": { "desc": "///A/685 vs ///A/786", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 42, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/749 vs ///A/744,///A/753", "A_nt1": { "desc": "///A/749 vs ///A/744", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/749 vs ///A/753", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.52],N1-O2'(hydroxyl)[3.27]" } }, { "index": 43, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/781 vs ///A/1776,///A/1788", "A_nt1": { "desc": "///A/781 vs ///A/1776", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N2(amino)[3.55]" }, "A_nt2": { "desc": "///A/781 vs ///A/1788", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.25]" } }, { "index": 44, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/792 vs ///A/2072,///A/2437", "A_nt1": { "desc": "///A/792 vs ///A/2072", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.13]" }, "A_nt2": { "desc": "///A/792 vs ///A/2437", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 45, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/819 vs ///A/837,///A/942", "A_nt1": { "desc": "///A/819 vs ///A/837", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.98]" }, "A_nt2": { "desc": "///A/819 vs ///A/942", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.19]" } }, { "index": 46, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/910 vs ///A/2264,///A/2276", "A_nt1": { "desc": "///A/910 vs ///A/2264", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O3'[2.45]" }, "A_nt2": { "desc": "///A/910 vs ///A/2276", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 47, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/911 vs ///A/2264,///A/2276", "A_nt1": { "desc": "///A/911 vs ///A/2264", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O4'-O2'(hydroxyl)[3.34]" }, "A_nt2": { "desc": "///A/911 vs ///A/2276", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 48, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/917 vs ///B/79,///B/97", "A_nt1": { "desc": "///A/917 vs ///B/79", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.07]" }, "A_nt2": { "desc": "///A/917 vs ///B/97", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 49, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/980 vs ///A/2026,///A/2037", "A_nt1": { "desc": "///A/980 vs ///A/2026", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/980 vs ///A/2037", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.70]" } }, { "index": 50, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/981 vs ///A/2027,///A/2036", "A_nt1": { "desc": "///A/981 vs ///A/2027", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.48],N3-N2(amino)[3.59]" }, "A_nt2": { "desc": "///A/981 vs ///A/2036", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.68],O2'(hydroxyl)-O2(carbonyl)[3.16]" } }, { "index": 51, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1000 vs ///A/976,///A/987", "A_nt1": { "desc": "///A/1000 vs ///A/976", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1000 vs ///A/987", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.55]" } }, { "index": 52, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1001 vs ///A/977,///A/986", "A_nt1": { "desc": "///A/1001 vs ///A/977", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.81],N3-N2(amino)[3.42]" }, "A_nt2": { "desc": "///A/1001 vs ///A/986", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.98]" } }, { "index": 53, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1009 vs ///A/1002,///A/1153", "A_nt1": { "desc": "///A/1009 vs ///A/1002", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1009 vs ///A/1153", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.57]" } }, { "index": 54, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1010 vs ///A/1003,///A/1152", "A_nt1": { "desc": "///A/1010 vs ///A/1003", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1010 vs ///A/1152", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.73],O2'(hydroxyl)-O2(carbonyl)[3.09]" } }, { "index": 55, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1048 vs ///A/1043,///A/1112", "A_nt1": { "desc": "///A/1048 vs ///A/1043", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.14]" }, "A_nt2": { "desc": "///A/1048 vs ///A/1112", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.46],N3-N2(amino)[3.41]" } }, { "index": 56, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1084 vs ///A/1054,///A/1105", "A_nt1": { "desc": "///A/1084 vs ///A/1054", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1084 vs ///A/1105", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.29]" } }, { "index": 57, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1085 vs ///A/1055,///A/1104", "A_nt1": { "desc": "///A/1085 vs ///A/1055", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.23]" }, "A_nt2": { "desc": "///A/1085 vs ///A/1104", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.88]" } }, { "index": 58, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1155 vs ///A/976,///A/987", "A_nt1": { "desc": "///A/1155 vs ///A/976", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.22],N3-N2(amino)[3.06]" }, "A_nt2": { "desc": "///A/1155 vs ///A/987", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 59, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1226 vs ///A/812,///A/1195", "A_nt1": { "desc": "///A/1226 vs ///A/812", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.79]" }, "A_nt2": { "desc": "///A/1226 vs ///A/1195", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.11],N3-N2(amino)[3.28]" } }, { "index": 60, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1253 vs ///A/564,///A/577", "A_nt1": { "desc": "///A/1253 vs ///A/564", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.95]" }, "A_nt2": { "desc": "///A/1253 vs ///A/577", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 61, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1254 vs ///A/672,///A/808", "A_nt1": { "desc": "///A/1254 vs ///A/672", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1254 vs ///A/808", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.55]" } }, { "index": 62, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1274 vs ///A/1296,///A/1644", "A_nt1": { "desc": "///A/1274 vs ///A/1296", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1274 vs ///A/1644", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.41]" } }, { "index": 63, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1275 vs ///A/1295,///A/1645", "A_nt1": { "desc": "///A/1275 vs ///A/1295", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.89]" }, "A_nt2": { "desc": "///A/1275 vs ///A/1645", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N3[3.44]" } }, { "index": 64, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1287 vs ///A/1648,///A/2009", "A_nt1": { "desc": "///A/1287 vs ///A/1648", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.25]" }, "A_nt2": { "desc": "///A/1287 vs ///A/2009", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 65, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1302 vs ///A/1297,///A/1643", "A_nt1": { "desc": "///A/1302 vs ///A/1297", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.92],N1-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///A/1302 vs ///A/1643", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 66, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1322 vs ///A/1319,///A/1333", "A_nt1": { "desc": "///A/1322 vs ///A/1319", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1322 vs ///A/1333", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.39],N1-O2'(hydroxyl)[2.72]" } }, { "index": 67, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1353 vs ///A/693,///A/769", "A_nt1": { "desc": "///A/1353 vs ///A/693", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.08],N3-O2'(hydroxyl)[2.73]" }, "A_nt2": { "desc": "///A/1353 vs ///A/769", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 68, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1354 vs ///A/692,///A/770", "A_nt1": { "desc": "///A/1354 vs ///A/692", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.74],O2'(hydroxyl)-O2(carbonyl)[2.62]" }, "A_nt2": { "desc": "///A/1354 vs ///A/770", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.49],N3-N2(amino)[3.25]" } }, { "index": 69, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1365 vs ///A/187,///A/209", "A_nt1": { "desc": "///A/1365 vs ///A/187", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1-N2(amino)[3.50],N3-O2'(hydroxyl)[3.09]" }, "A_nt2": { "desc": "///A/1365 vs ///A/209", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 70, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1383 vs ///A/1405,///A/1597", "A_nt1": { "desc": "///A/1383 vs ///A/1405", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.75],N3-O2'(hydroxyl)[3.37]" }, "A_nt2": { "desc": "///A/1383 vs ///A/1597", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 71, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1384 vs ///A/1343,///A/1404", "A_nt1": { "desc": "///A/1384 vs ///A/1343", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1384 vs ///A/1404", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.59],O2'(hydroxyl)-O2(carbonyl)[3.09]" } }, { "index": 72, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1392 vs ///A/1315,///A/1337", "A_nt1": { "desc": "///A/1392 vs ///A/1315", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.53]" }, "A_nt2": { "desc": "///A/1392 vs ///A/1337", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 73, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1469 vs ///A/1386,///A/1401", "A_nt1": { "desc": "///A/1469 vs ///A/1386", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91],N3-O2'(hydroxyl)[2.83]" }, "A_nt2": { "desc": "///A/1469 vs ///A/1401", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.56]" } }, { "index": 74, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1470 vs ///A/1385,///A/1402", "A_nt1": { "desc": "///A/1470 vs ///A/1385", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1470 vs ///A/1402", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.20]" } }, { "index": 75, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1477 vs ///A/1435,///A/1557", "A_nt1": { "desc": "///A/1477 vs ///A/1435", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1477 vs ///A/1557", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.32]" } }, { "index": 76, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1495 vs ///A/1421,///A/1577", "A_nt1": { "desc": "///A/1495 vs ///A/1421", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.34]" }, "A_nt2": { "desc": "///A/1495 vs ///A/1577", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 77, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1496 vs ///A/1421,///A/1577", "A_nt1": { "desc": "///A/1496 vs ///A/1421", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1496 vs ///A/1577", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O3'[3.50],N3-O2'(hydroxyl)[2.89]" } }, { "index": 78, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1515 vs ///A/1436,///A/1556", "A_nt1": { "desc": "///A/1515 vs ///A/1436", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.25]" }, "A_nt2": { "desc": "///A/1515 vs ///A/1556", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.92],O2'(hydroxyl)-O2(carbonyl)[2.90]" } }, { "index": 79, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1544 vs ///A/1447,///A/1464", "A_nt1": { "desc": "///A/1544 vs ///A/1447", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.10],N3-O2'(hydroxyl)[2.47]" }, "A_nt2": { "desc": "///A/1544 vs ///A/1464", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 80, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1545 vs ///A/1446,///A/1465", "A_nt1": { "desc": "///A/1545 vs ///A/1446", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.19],O2'(hydroxyl)-O2(carbonyl)[2.36]" }, "A_nt2": { "desc": "///A/1545 vs ///A/1465", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.81],N3-N2(amino)[3.06]" } }, { "index": 81, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1570 vs ///A/1351,///A/1380", "A_nt1": { "desc": "///A/1570 vs ///A/1351", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1570 vs ///A/1380", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.99]" } }, { "index": 82, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1571 vs ///A/1351,///A/1380", "A_nt1": { "desc": "///A/1571 vs ///A/1351", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.65],N3-O2'(hydroxyl)[3.35]" }, "A_nt2": { "desc": "///A/1571 vs ///A/1380", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 83, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1610 vs ///A/1310,///A/1604", "A_nt1": { "desc": "///A/1610 vs ///A/1310", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1610 vs ///A/1604", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.73]" } }, { "index": 84, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1616 vs ///A/1324,///A/1330", "A_nt1": { "desc": "///A/1616 vs ///A/1324", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.38]" }, "A_nt2": { "desc": "///A/1616 vs ///A/1330", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 85, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1632 vs ///A/700,///A/732", "A_nt1": { "desc": "///A/1632 vs ///A/700", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.99],O2'(hydroxyl)-O2'(hydroxyl)[3.02],N3-O2'(hydroxyl)[2.82]" }, "A_nt2": { "desc": "///A/1632 vs ///A/732", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 86, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1678 vs ///A/1674,///A/1990", "A_nt1": { "desc": "///A/1678 vs ///A/1674", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1678 vs ///A/1990", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.75]" } }, { "index": 87, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1754 vs ///A/2693,///A/2716", "A_nt1": { "desc": "///A/1754 vs ///A/2693", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1754 vs ///A/2716", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.46],N1-O2'(hydroxyl)[2.57]" } }, { "index": 88, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1755 vs ///A/2694,///A/2715", "A_nt1": { "desc": "///A/1755 vs ///A/2694", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.82],N6(amino)-N3[3.38],N1-N2(amino)[2.92]" }, "A_nt2": { "desc": "///A/1755 vs ///A/2715", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 89, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1802 vs ///A/1798,///A/1821", "A_nt1": { "desc": "///A/1802 vs ///A/1798", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.87],O2'(hydroxyl)-O2'(hydroxyl)[2.99],N3-O2'(hydroxyl)[2.64]" }, "A_nt2": { "desc": "///A/1802 vs ///A/1821", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 90, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1803 vs ///A/1797,///A/1822", "A_nt1": { "desc": "///A/1803 vs ///A/1797", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91],N3-N2(amino)[3.27]" }, "A_nt2": { "desc": "///A/1803 vs ///A/1822", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.66]" } }, { "index": 91, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1809 vs ///A/1363,///A/1368", "A_nt1": { "desc": "///A/1809 vs ///A/1363", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O3'[2.68],N3-O2'(hydroxyl)[2.41]" }, "A_nt2": { "desc": "///A/1809 vs ///A/1368", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 92, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1810 vs ///A/1362,///A/1369", "A_nt1": { "desc": "///A/1810 vs ///A/1362", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.20]" }, "A_nt2": { "desc": "///A/1810 vs ///A/1369", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.80]" } }, { "index": 93, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1848 vs ///A/1846,///A/1894", "A_nt1": { "desc": "///A/1848 vs ///A/1846", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1848 vs ///A/1894", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.07]" } }, { "index": 94, "type": "X", "desc_short": "A vs U-U (--)", "desc_long": "///A/1853 vs ///A/2086,///A/2233", "A_nt1": { "desc": "///A/1853 vs ///A/2086", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1853 vs ///A/2233", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.00],O2'(hydroxyl)-O2'(hydroxyl)[2.86],N3-O2'(hydroxyl)[2.71]" } }, { "index": 95, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1854 vs ///A/2087,///A/2232", "A_nt1": { "desc": "///A/1854 vs ///A/2087", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.89],N3-N2(amino)[3.44]" }, "A_nt2": { "desc": "///A/1854 vs ///A/2232", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91]" } }, { "index": 96, "type": "X", "desc_short": "A vs U-U (--)", "desc_long": "///A/1889 vs ///A/2086,///A/2233", "A_nt1": { "desc": "///A/1889 vs ///A/2086", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.05],N3-O2'(hydroxyl)[2.76]" }, "A_nt2": { "desc": "///A/1889 vs ///A/2233", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 97, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1900 vs ///A/1793,///A/1826", "A_nt1": { "desc": "///A/1900 vs ///A/1793", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///A/1900 vs ///A/1826", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 98, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1927 vs ///A/1837,///A/1903", "A_nt1": { "desc": "///A/1927 vs ///A/1837", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.02],N3-O2'(hydroxyl)[2.72]" }, "A_nt2": { "desc": "///A/1927 vs ///A/1903", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 99, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1928 vs ///A/1836,///A/1904", "A_nt1": { "desc": "///A/1928 vs ///A/1836", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.60]" }, "A_nt2": { "desc": "///A/1928 vs ///A/1904", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.66]" } }, { "index": 100, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1969 vs ///A/1833,///A/1972", "A_nt1": { "desc": "///A/1969 vs ///A/1833", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.88]" }, "A_nt2": { "desc": "///A/1969 vs ///A/1972", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.82],O2'(hydroxyl)-N3[3.03]" } }, { "index": 101, "type": "II", "desc_short": "A vs G-U (Wobble)", "desc_long": "///A/1970 vs ///A/1792,///A/1827", "A_nt1": { "desc": "///A/1970 vs ///A/1792", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.49]" }, "A_nt2": { "desc": "///A/1970 vs ///A/1827", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.58]" } }, { "index": 102, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2273 vs ///A/953,///A/964", "A_nt1": { "desc": "///A/2273 vs ///A/953", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2273 vs ///A/964", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.05],O2'(hydroxyl)-O2'(hydroxyl)[3.20],N3-O2'(hydroxyl)[2.41]" } }, { "index": 103, "type": "X", "desc_short": "A vs G-U (Wobble)", "desc_long": "///A/2274 vs ///A/954,///A/963", "A_nt1": { "desc": "///A/2274 vs ///A/954", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.02]" }, "A_nt2": { "desc": "///A/2274 vs ///A/963", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 104, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2288 vs ///A/2284,///A/2384", "A_nt1": { "desc": "///A/2288 vs ///A/2284", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.62]" }, "A_nt2": { "desc": "///A/2288 vs ///A/2384", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 105, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2327 vs ///A/2261,///A/2279", "A_nt1": { "desc": "///A/2327 vs ///A/2261", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.49]" }, "A_nt2": { "desc": "///A/2327 vs ///A/2279", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.35]" } }, { "index": 106, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2388 vs ///A/2260,///A/2280", "A_nt1": { "desc": "///A/2388 vs ///A/2260", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.53]" }, "A_nt2": { "desc": "///A/2388 vs ///A/2280", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.84]" } }, { "index": 107, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2434 vs ///A/2077,///A/2243", "A_nt1": { "desc": "///A/2434 vs ///A/2077", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N3[3.13]" }, "A_nt2": { "desc": "///A/2434 vs ///A/2243", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 108, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2682 vs ///A/2679,///A/2728", "A_nt1": { "desc": "///A/2682 vs ///A/2679", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2682 vs ///A/2728", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.24]" } }, { "index": 109, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/2682 vs ///A/2680,///A/2727", "A_nt1": { "desc": "///A/2682 vs ///A/2680", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.87]" }, "A_nt2": { "desc": "///A/2682 vs ///A/2727", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 110, "type": "X", "desc_short": "A vs U-A (--)", "desc_long": "///A/2764 vs ///A/2739,///A/2766", "A_nt1": { "desc": "///A/2764 vs ///A/2739", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "OP2*O4(carbonyl)[3.36],N6(amino)-O2(carbonyl)[2.96]" }, "A_nt2": { "desc": "///A/2764 vs ///A/2766", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 111, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2809 vs ///A/2630,///A/2788", "A_nt1": { "desc": "///A/2809 vs ///A/2630", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2809 vs ///A/2788", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.09],N3-O2'(hydroxyl)[2.49]" } }, { "index": 112, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2810 vs ///A/2631,///A/2787", "A_nt1": { "desc": "///A/2810 vs ///A/2631", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.99]" }, "A_nt2": { "desc": "///A/2810 vs ///A/2787", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.95]" } }, { "index": 113, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2823 vs ///A/2047,///A/2621", "A_nt1": { "desc": "///A/2823 vs ///A/2047", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.98],N1-O2'(hydroxyl)[2.67]" }, "A_nt2": { "desc": "///A/2823 vs ///A/2621", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 114, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2860 vs ///A/1708,///A/1750", "A_nt1": { "desc": "///A/2860 vs ///A/1708", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.48]" }, "A_nt2": { "desc": "///A/2860 vs ///A/1750", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.25],N3-N2(amino)[3.22]" } }, { "index": 115, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2883 vs ///A/2816,///A/2830", "A_nt1": { "desc": "///A/2883 vs ///A/2816", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.70],O2'(hydroxyl)-N3[3.29]" }, "A_nt2": { "desc": "///A/2883 vs ///A/2830", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.68]" } }, { "index": 116, "type": "X", "desc_short": "A vs C-A (--)", "desc_long": "///B/15 vs ///B/11,///B/109", "A_nt1": { "desc": "///B/15 vs ///B/11", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.79]" }, "A_nt2": { "desc": "///B/15 vs ///B/109", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 117, "type": "X", "desc_short": "A vs C-G (--)", "desc_long": "///B/53 vs ///B/31,///B/51", "A_nt1": { "desc": "///B/53 vs ///B/31", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.52]" }, "A_nt2": { "desc": "///B/53 vs ///B/51", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 118, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///B/57 vs ///B/30,///B/54", "A_nt1": { "desc": "///B/57 vs ///B/30", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.16],N1-O2'(hydroxyl)[2.66]" }, "A_nt2": { "desc": "///B/57 vs ///B/54", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 119, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///B/58 vs ///B/29,///B/55", "A_nt1": { "desc": "///B/58 vs ///B/29", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.18]" }, "A_nt2": { "desc": "///B/58 vs ///B/55", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 120, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///B/59 vs ///B/28,///B/56", "A_nt1": { "desc": "///B/59 vs ///B/28", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///B/59 vs ///B/56", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.54],N1-N2(amino)[3.29]" } } ], "num_riboseZippers": 33, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/115,///A/116,///A/126,///A/127" }, { "index": 2, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/160,///A/161,///A/2207,///A/2208" }, { "index": 3, "num_nts": 4, "nts_short": "ACAC", "nts_long": "///A/182,///A/183,///A/432,///A/433" }, { "index": 4, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/190,///A/191,///A/678,///A/679" }, { "index": 5, "num_nts": 4, "nts_short": "AGAU", "nts_long": "///A/219,///A/220,///A/233,///A/234" }, { "index": 6, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/237,///A/238,///A/608,///A/609" }, { "index": 7, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///A/262,///A/263,///A/429,///A/430" }, { "index": 8, "num_nts": 4, "nts_short": "AAUC", "nts_long": "///A/514,///A/515,///A/580,///A/581" }, { "index": 9, "num_nts": 4, "nts_short": "CAUG", "nts_long": "///A/527,///A/2778,///A/2779,///A/2780" }, { "index": 10, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/675,///A/676,///A/2442,///A/2443" }, { "index": 11, "num_nts": 4, "nts_short": "CAAA", "nts_long": "///A/692,///A/693,///A/1353,///A/1354" }, { "index": 12, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/699,///A/700,///A/1632,///A/1633" }, { "index": 13, "num_nts": 4, "nts_short": "CUGA", "nts_long": "///A/812,///A/813,///A/1225,///A/1226" }, { "index": 14, "num_nts": 4, "nts_short": "GACC", "nts_long": "///A/818,///A/819,///A/837,///A/838" }, { "index": 15, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/861,///A/862,///B/78,///B/79" }, { "index": 16, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/910,///A/911,///A/2263,///A/2264" }, { "index": 17, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/941,///A/942,///A/1189,///A/1190" }, { "index": 18, "num_nts": 4, "nts_short": "CCUA", "nts_long": "///A/964,///A/965,///A/2272,///A/2273" }, { "index": 19, "num_nts": 4, "nts_short": "GGGA", "nts_long": "///A/976,///A/977,///A/1154,///A/1155" }, { "index": 20, "num_nts": 4, "nts_short": "AACA", "nts_long": "///A/980,///A/981,///A/2036,///A/2037" }, { "index": 21, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/986,///A/987,///A/1000,///A/1001" }, { "index": 22, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/1009,///A/1010,///A/1152,///A/1153" }, { "index": 23, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1362,///A/1363,///A/1809,///A/1810" }, { "index": 24, "num_nts": 4, "nts_short": "AACU", "nts_long": "///A/1383,///A/1384,///A/1404,///A/1405" }, { "index": 25, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1446,///A/1447,///A/1544,///A/1545" }, { "index": 26, "num_nts": 4, "nts_short": "GACC", "nts_long": "///A/1514,///A/1515,///A/1556,///A/1557" }, { "index": 27, "num_nts": 4, "nts_short": "ACCU", "nts_long": "///A/1549,///A/1550,///A/1741,///A/1742" }, { "index": 28, "num_nts": 4, "nts_short": "CUGA", "nts_long": "///A/1708,///A/1709,///A/2859,///A/2860" }, { "index": 29, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/1797,///A/1798,///A/1802,///A/1803" }, { "index": 30, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1836,///A/1837,///A/1927,///A/1928" }, { "index": 31, "num_nts": 4, "nts_short": "AACU", "nts_long": "///A/1853,///A/1854,///A/2232,///A/2233" }, { "index": 32, "num_nts": 4, "nts_short": "ACAA", "nts_long": "///A/2077,///A/2078,///A/2433,///A/2434" }, { "index": 33, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/2787,///A/2788,///A/2809,///A/2810" } ], "num_Kturns": 8, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 55, "bounding_stems": [ 70, 71 ], "Cstem_index": 70, "NCstem_index": 71, "Cstem_pair": "C-G (///A/1208,///A/1238) WC", "NCstem_pair": "G-U (///A/1215,///A/1234) Wobble", "GA_pair": "G-A (///A/1212,///A/1237) Sheared", "bending_angle": 56.049, "strand1": { "num_nts": 17, "nts_short": "GCCUGCGAAGGUGUGCU", "nts_long": "///A/1206,///A/1207,///A/1208,///A/1209,///A/1210,///A/1211,///A/1212,///A/1213,///A/1214,///A/1215,///A/1216,///A/1217,///A/1218,///A/1219,///A/1220,///A/1221,///A/1222" }, "strand2": { "num_nts": 14, "nts_short": "GGCAUGCUGGAGGU", "nts_long": "///A/1227,///A/1228,///A/1229,///A/1230,///A/1231,///A/1232,///A/1233,///A/1234,///A/1235,///A/1236,///A/1237,///A/1238,///A/1239,///A/1240" } }, { "index": 2, "type": "Normal k-turn", "iloop_index": 61, "bounding_stems": [ 65, 66 ], "Cstem_index": 65, "NCstem_index": 66, "Cstem_pair": "C-G (///A/1043,///A/1112) WC", "NCstem_pair": "G-U (///A/1051,///A/1108) Wobble", "GA_pair": "G-A (///A/1047,///A/1111) Sheared", "bending_angle": 70.952, "strand1": { "num_nts": 15, "nts_short": "GGCCCAGACAGCCAG", "nts_long": "///A/1041,///A/1042,///A/1043,///A/1044,///A/1045,///A/1046,///A/1047,///A/1048,///A/1049,///A/1050,///A/1051,///A/1052,///A/1053,///A/1054,///A/1055" }, "strand2": { "num_nts": 11, "nts_short": "CUGGUCGAGUC", "nts_long": "///A/1104,///A/1105,///A/1106,///A/1107,///A/1108,///A/1109,///A/1110,///A/1111,///A/1112,///A/1113,///A/1114" } }, { "index": 3, "type": "Normal k-turn", "iloop_index": 66, "bounding_stems": [ 134, 135 ], "Cstem_index": 134, "NCstem_index": 135, "Cstem_pair": "C-G (///A/2129,///A/2159) WC", "NCstem_pair": "U-A (///A/2137,///A/2154) WC", "GA_pair": "G-A (///A/2133,///A/2158) Sheared", "bending_angle": 67.966, "strand1": { "num_nts": 16, "nts_short": "GCUUUGAAGUGUGGAC", "nts_long": "///A/2128,///A/2129,///A/2130,///A/2131,///A/2132,///A/2133,///A/2134,///A/2135,///A/2136,///A/2137,///A/2138,///A/2139,///A/2140,///A/2141,///A/2142,///A/2143" }, "strand2": { "num_nts": 13, "nts_short": "GUCUGCAUGGAGC", "nts_long": "///A/2148,///A/2149,///A/2150,///A/2151,///A/2152,///A/2153,///A/2154,///A/2155,///A/2156,///A/2157,///A/2158,///A/2159,///A/2160" } }, { "index": 4, "type": "REVERSE k-turn [A-G]", "iloop_index": 53, "bounding_stems": [ 21, 22 ], "Cstem_index": 21, "NCstem_index": 22, "Cstem_pair": "C-G (///A/274,///A/363) WC", "NCstem_pair": "C-G (///A/281,///A/359) WC", "GA_pair": "A-G (///A/279,///A/361) Sheared", "bending_angle": 75.474, "strand1": { "num_nts": 23, "nts_short": "GAGCCUGAAUCAGUGUGUGUGUU", "nts_long": "///A/271,///A/272,///A/273,///A/274,///A/275,///A/276,///A/277,///A/278,///A/279,///A/280,///A/281,///A/282,///A/283,///A/284,///A/285,///A/286,///A/287,///A/288,///A/289,///A/290,///A/291,///A/292,///A/293" }, "strand2": { "num_nts": 20, "nts_short": "AAUGCACAUGCUGUGAGCUC", "nts_long": "///A/347,///A/348,///A/349,///A/350,///A/351,///A/352,///A/353,///A/354,///A/355,///A/356,///A/357,///A/358,///A/359,///A/360,///A/361,///A/362,///A/363,///A/364,///A/365,///A/366" } }, { "index": 5, "type": "Undecided case [A-G]", "iloop_index": 16, "bounding_stems": [ -30, 82 ], "Cstem_index": -30, "NCstem_index": 82, "Cstem_pair": "A-U (///A/1353,///A/1379) WC", "NCstem_pair": "G-C (///A/1355,///A/1376) WC", "GA_pair": "A-G (///A/1354,///A/1377) Sheared", "bending_angle": 51.917, "strand1": { "num_nts": 5, "nts_short": "AAGGC", "nts_long": "///A/1353,///A/1354,///A/1355,///A/1356,///A/1357" }, "strand2": { "num_nts": 6, "nts_short": "GUCGAU", "nts_long": "///A/1374,///A/1375,///A/1376,///A/1377,///A/1378,///A/1379" } }, { "index": 6, "type": "Undecided case", "iloop_index": 33, "bounding_stems": [ 94, 93 ], "Cstem_index": 94, "NCstem_index": 93, "Cstem_pair": "U-G (///A/1520,///A/1471) Wobble", "NCstem_pair": "G-U (///A/1524,///A/1468) Wobble", "GA_pair": "G-A (///A/1521,///A/1470) Sheared", "bending_angle": 38.931, "strand1": { "num_nts": 9, "nts_short": "GCGUGAUGA", "nts_long": "///A/1517,///A/1518,///A/1519,///A/1520,///A/1521,///A/1522,///A/1523,///A/1524,///A/1525" }, "strand2": { "num_nts": 8, "nts_short": "UUAAGCGU", "nts_long": "///A/1467,///A/1468,///A/1469,///A/1470,///A/1471,///A/1472,///A/1473,///A/1474" } }, { "index": 7, "type": "Undecided case [A-G]", "iloop_index": 40, "bounding_stems": [ 59, 60 ], "Cstem_index": 59, "NCstem_index": 60, "Cstem_pair": "C-G (///A/998,///A/1157) WC", "NCstem_pair": "G-C (///A/1002,///A/1153) WC", "GA_pair": "A-G (///A/1001,///A/1154) Sheared", "bending_angle": 34.311, "strand1": { "num_nts": 9, "nts_short": "AGCUAAGGU", "nts_long": "///A/996,///A/997,///A/998,///A/999,///A/1000,///A/1001,///A/1002,///A/1003,///A/1004" }, "strand2": { "num_nts": 9, "nts_short": "ACCGAAGCU", "nts_long": 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"///A/1645,///A/1646,///A/1647,///A/1648" }, { "index": 146, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/1673,///A/1674" }, { "index": 147, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/1681,///A/1682" }, { "index": 148, "num_nts": 3, "nts_short": "UUC", "nts_long": "///A/1692,///A/1693,///A/1694" }, { "index": 149, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/1698,///A/1699,///A/1700" }, { "index": 150, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/1706,///A/1707" }, { "index": 151, "num_nts": 3, "nts_short": "AUG", "nts_long": "///A/1713,///A/1714,///A/1715" }, { "index": 152, "num_nts": 3, "nts_short": "GCG", "nts_long": "///A/1731,///A/1732,///A/1733" }, { "index": 153, "num_nts": 5, "nts_short": "AGAUA", "nts_long": "///A/1755,///A/1756,///A/1757,///A/1758,///A/1759" }, { "index": 154, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/1762,///A/1763" }, { "index": 155, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1779,///A/1780" }, { "index": 156, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/1781,///A/1782" }, { "index": 157, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1783,///A/1784" }, { "index": 158, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1785,///A/1786,///A/1787" }, { "index": 159, "num_nts": 3, "nts_short": "CAA", "nts_long": "///A/1800,///A/1801,///A/1802" }, { "index": 160, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/1807,///A/1808" }, { "index": 161, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/1816,///A/1817" }, { "index": 162, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/1819,///A/1820,///A/1821" }, { "index": 163, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/1828,///A/1829" }, { "index": 164, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/1834,///A/1835" }, { "index": 165, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/1869,///A/1870" }, { "index": 166, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1899,///A/1900,///A/1901" }, { "index": 167, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/1905,///A/1906" }, { "index": 168, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/1929,///A/1930" }, { "index": 169, "num_nts": 4, "nts_short": "UUCC", "nts_long": "///A/1939,///A/1940,///A/1941,///A/1942" }, { "index": 170, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/1962,///A/1963" }, { "index": 171, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/1964,///A/1965" }, { "index": 172, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/1966,///A/1967" }, { "index": 173, "num_nts": 4, "nts_short": "AAUG", "nts_long": "///A/1969,///A/1970,///A/1971,///A/1972" }, { "index": 174, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/1980,///A/1981,///A/1982" }, { "index": 175, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/1991,///A/1992" }, { "index": 176, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2017,///A/2018" }, { "index": 177, "num_nts": 4, "nts_short": "ACUC", "nts_long": "///A/2020,///A/2021,///A/2022,///A/2023" }, { "index": 178, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2029,///A/2030" }, { "index": 179, "num_nts": 4, "nts_short": "AGAU", "nts_long": "///A/2031,///A/2032,///A/2033,///A/2034" }, { "index": 180, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/2035,///A/2036" }, { "index": 181, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2042,///A/2043" }, { "index": 182, "num_nts": 3, "nts_short": "ACG", "nts_long": "///A/2054,///A/2055,///A/2056" }, { "index": 183, "num_nts": 3, "nts_short": "GUG", "nts_long": "///A/2067,///A/2068,///A/2069" }, { "index": 184, "num_nts": 3, "nts_short": "UUA", "nts_long": "///A/2075,///A/2076,///A/2077" }, { "index": 185, "num_nts": 3, "nts_short": "GUG", "nts_long": "///A/2110,///A/2111,///A/2112" }, { "index": 186, "num_nts": 4, "nts_short": "AUAG", "nts_long": "///A/2117,///A/2118,///A/2119,///A/2120" }, { "index": 187, "num_nts": 3, "nts_short": "UUG", "nts_long": "///A/2131,///A/2132,///A/2133" }, { "index": 188, "num_nts": 4, "nts_short": "GCCA", "nts_long": "///A/2144,///A/2145,///A/2146,///A/2147" }, { "index": 189, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/2171,///A/2172,///A/2173" }, { "index": 190, "num_nts": 3, "nts_short": "UUG", "nts_long": "///A/2202,///A/2203,///A/2204" }, { "index": 191, "num_nts": 5, "nts_short": "UAAUC", "nts_long": "///A/2210,///A/2211,///A/2212,///A/2213,///A/2214" }, { "index": 192, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/2237,///A/2238" }, { "index": 193, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2245,///A/2246" }, { "index": 194, "num_nts": 3, "nts_short": "UGG", "nts_long": "///A/2249,///A/2250,///A/2251" }, { "index": 195, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/2258,///A/2259" }, { "index": 196, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/2267,///A/2268,///A/2269" }, { "index": 197, "num_nts": 3, "nts_short": "ACG", "nts_long": "///A/2274,///A/2275,///A/2276" }, { "index": 198, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/2282,///A/2283" }, { "index": 199, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/2287,///A/2288,///A/2289" }, { "index": 200, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2321,///A/2322" }, { "index": 201, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2324,///A/2325" }, { "index": 202, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/2333,///A/2334,///A/2335" }, { "index": 203, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2336,///A/2337" }, { "index": 204, "num_nts": 4, "nts_short": "UGAC", "nts_long": "///A/2344,///A/2345,///A/2346,///A/2347" }, { "index": 205, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/2382,///A/2383" }, { "index": 206, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/2384,///A/2385" }, { "index": 207, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/2389,///A/2390" }, { "index": 208, "num_nts": 3, "nts_short": "UUC", "nts_long": "///A/2401,///A/2402,///A/2403" }, { "index": 209, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/2405,///A/2406,///A/2407" }, { "index": 210, "num_nts": 7, "nts_short": "CUCAACG", "nts_long": "///A/2422,///A/2423,///A/2424,///A/2425,///A/2426,///A/2427,///A/2428" }, { "index": 211, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2429,///A/2430" }, { "index": 212, "num_nts": 3, "nts_short": "UAC", "nts_long": "///A/2438,///A/2439,///A/2440" }, { "index": 213, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/2612,///A/2613,///A/2614" }, { "index": 214, "num_nts": 3, "nts_short": "CUG", "nts_long": "///A/2628,///A/2629,///A/2630" }, { "index": 215, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/2645,///A/2646" }, { "index": 216, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2659,///A/2660" }, { "index": 217, "num_nts": 4, "nts_short": "GUUC", "nts_long": "///A/2688,///A/2689,///A/2690,///A/2691" }, { "index": 218, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2711,///A/2712" }, { "index": 219, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2732,///A/2733" }, { "index": 220, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2750,///A/2751" }, { "index": 221, "num_nts": 3, "nts_short": "UCU", "nts_long": "///A/2754,///A/2755,///A/2756" }, { "index": 222, "num_nts": 7, "nts_short": "AGAUGAG", "nts_long": "///A/2776,///A/2777,///A/2778,///A/2779,///A/2780,///A/2781,///A/2782" }, { "index": 223, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2790,///A/2791" }, { "index": 224, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2797,///A/2798" }, { "index": 225, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/2799,///A/2800,///A/2801" }, { "index": 226, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/2819,///A/2820,///A/2821" }, { "index": 227, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2822,///A/2823" }, { "index": 228, "num_nts": 4, "nts_short": "GUUG", "nts_long": "///A/2831,///A/2832,///A/2833,///A/2834" }, { "index": 229, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2849,///A/2850" }, { "index": 230, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/2857,///A/2858" }, { "index": 231, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2873,///A/2874" }, { "index": 232, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/2883,///A/2884" }, { "index": 233, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2892,///A/2893" }, { "index": 234, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/2894,///A/2895" }, { "index": 235, "num_nts": 3, "nts_short": "CGU", "nts_long": "///B/12,///B/13,///B/14" }, { "index": 236, "num_nts": 2, "nts_short": "AG", "nts_long": "///B/15,///B/16" }, { "index": 237, "num_nts": 2, "nts_short": "AC", "nts_long": "///B/34,///B/35" }, { "index": 238, "num_nts": 3, "nts_short": "UGC", "nts_long": "///B/40,///B/41,///B/42" }, { "index": 239, "num_nts": 2, "nts_short": "CG", "nts_long": "///B/43,///B/44" }, { "index": 240, "num_nts": 4, "nts_short": "UCUC", "nts_long": "///B/87,///B/88,///B/89,///B/90" }, { "index": 241, "num_nts": 2, "nts_short": "AA", "nts_long": "///B/108,///B/109" } ], "num_HtypePknots": 3, "HtypePknots": [ { "index": 1, "desc": "stem#9(hairpin#1) vs stem#10(hairpin#2) L1 groove=MAJOR nts=4 GCUA ///A/60,///A/61,///A/62,///A/63" }, { "index": 2, "desc": "stem#9(hairpin#1) vs stem#10(hairpin#2) L2 groove=----- nts=1 U ///A/67" }, { "index": 3, "desc": "stem#9(hairpin#1) vs stem#10(hairpin#2) L3 groove=minor nts=17 AUAAGCGUCGGUAAGGU ///A/71,///A/72,///A/73,///A/74,///A/75,///A/76,///A/77,///A/78,///A/79,///A/80,///A/81,///A/82,///A/83,///A/84,///A/85,///A/86,///A/87" } ], "pseudoknot_order": 2, "pseudoknot_nts": [ { "index": 1, "symbols": "[]", "num_nts": 52, "nts_short": "CAUCGAUGCGGCGCCGCCAUUGCCCGGGGUACGCCAGCCAUGCAUGAUGGCG", "nts_long": "///A/61,///A/64,///A/65,///A/66,///A/88,///A/89,///A/90,///A/93,///A/198,///A/248,///A/317,///A/318,///A/333,///A/334,///A/385,///A/411,///A/413,///A/414,///A/415,///A/416,///A/562,///A/729,///A/1005,///A/1006,///A/1007,///A/1136,///A/1137,///A/1138,///A/1343,///A/1344,///A/1403,///A/1404,///A/1516,///A/1732,///A/1774,///A/2033,///A/2255,///A/2275,///A/2326,///A/2328,///A/2329,///A/2330,///A/2385,///A/2386,///A/2387,///A/2389,///A/2407,///A/2408,///A/2409,///A/2410,///A/2626,///A/2777" }, { "index": 2, "symbols": "{}", "num_nts": 12, "nts_short": "GGUUAAUCGGCC", "nts_long": "///A/1455,///A/1456,///A/1457,///A/1693,///A/1829,///A/2020,///A/2034,///A/2359,///A/2428,///A/2702,///A/2703,///A/2704" } ], "dbn": { "all_chains": { "num_nts": 2848, "num_chars": 2851, "bseq": 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0.361, 0.549 ], "quaternion": [ 0.683, -0.430, 0.203, -0.555 ] } }, { "index": 1957, "index_chain": 1957, "chain_name": "A", "nt_resnum": 1972, "nt_name": "G", "nt_code": "G", "nt_id": "///A/1972", "linked_nts": [ "///A/1971", "///A/1973" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,splayed-apart", "alpha": -177.236, "beta": 141.644, "gamma": -170.826, "delta": 80.606, "epsilon": -146.482, "zeta": -85.535, "epsilon_zeta": -60.947, "bb_type": "BI", "chi": -167.939, "glyco_bond": "anti", "C5prime_xyz": [ -1.393, 8.690, 0.989 ], "P_xyz": [ -1.258, 11.197, 0.233 ], "form": "A", "ssZp": 4.590, "Dp": 4.656, "splay_angle": 24.639, "splay_distance": 3.902, "splay_ratio": 0.216, "d22": null, "d64": null, "eta": -153.643, "theta": 152.826, "eta_prime": -124.769, "theta_prime": 168.237, "eta_base": -77.054, "theta_base": -172.614, "v0": 2.140, "v1": -24.472, "v2": 36.264, "v3": -36.031, "v4": 21.372, "amplitude": 37.619, "phase_angle": 15.424, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.002, "frame": { "rmsd": 0.002, "origin": [ 186.712, 127.856, 139.460 ], "x_axis": [ 0.448, 0.720, -0.530 ], "y_axis": [ -0.537, 0.691, 0.484 ], "z_axis": [ 0.714, 0.068, 0.696 ], "quaternion": [ 0.842, 0.123, 0.370, 0.373 ] } }, { "index": 1958, "index_chain": 1958, "chain_name": "A", "nt_resnum": 1973, "nt_name": "G", "nt_code": "G", "nt_id": "///A/1973", "linked_nts": [ "///A/1972", "///A/1974" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack", "alpha": -63.850, "beta": 175.789, "gamma": 47.436, "delta": 80.373, "epsilon": -136.052, "zeta": -81.600, "epsilon_zeta": -54.452, "bb_type": "BI", "chi": -165.113, "glyco_bond": "anti", "C5prime_xyz": [ -1.401, 8.717, 0.819 ], "P_xyz": [ 1.125, 9.174, 1.338 ], "form": "A", "ssZp": 4.527, "Dp": 4.712, 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"beta": 157.416, "gamma": 64.209, "delta": 81.131, "epsilon": -147.512, "zeta": -70.196, "epsilon_zeta": -77.315, "bb_type": "BI", "chi": -157.755, "glyco_bond": "anti", "C5prime_xyz": [ -1.426, 8.839, 0.382 ], "P_xyz": [ 1.123, 9.193, -0.104 ], "form": "A", "ssZp": 4.338, "Dp": 4.594, "splay_angle": 21.627, "splay_distance": 3.477, "splay_ratio": 0.188, "d22": null, "d64": null, "eta": 166.562, "theta": -140.128, "eta_prime": -176.548, "theta_prime": -143.848, "eta_base": -129.253, "theta_base": -113.936, "v0": 0.268, "v1": -22.546, "v2": 34.991, "v3": -35.783, "v4": 22.420, "amplitude": 36.832, "phase_angle": 18.191, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.681, "filter_rmsd": 0.066, "frame": { "rmsd": 0.005, "origin": [ 192.486, 127.755, 141.302 ], "x_axis": [ -0.411, 0.911, -0.027 ], "y_axis": [ -0.346, -0.128, 0.929 ], "z_axis": [ 0.844, 0.391, 0.368 ], "quaternion": [ 0.455, 0.296, 0.478, 0.690 ] } }, { "index": 1960, "index_chain": 1960, "chain_name": "A", "nt_resnum": 1975, "nt_name": "G", "nt_code": "G", "nt_id": "///A/1975", "linked_nts": [ "///A/1974", "///A/1976" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack", "alpha": -72.590, "beta": 171.675, "gamma": 56.083, "delta": 80.059, "epsilon": -140.741, "zeta": -77.931, "epsilon_zeta": -62.811, "bb_type": "BI", "chi": -161.983, "glyco_bond": "anti", "C5prime_xyz": [ -1.447, 8.770, 0.624 ], "P_xyz": [ 1.121, 9.267, 0.710 ], "form": "A", "ssZp": 4.462, "Dp": 4.687, "splay_angle": 22.505, "splay_distance": 3.596, "splay_ratio": 0.196, "d22": null, "d64": null, "eta": 161.876, "theta": -143.971, "eta_prime": 176.009, "theta_prime": -141.549, "eta_base": -136.319, "theta_base": -111.297, "v0": 1.707, "v1": -24.275, "v2": 36.339, "v3": -36.364, "v4": 21.843, "amplitude": 37.818, "phase_angle": 16.073, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": 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"z_axis": [ -0.259, 0.495, 0.830 ], "quaternion": [ -0.060, -0.119, 0.267, 0.955 ] } }, { "index": 1967, "index_chain": 1967, "chain_name": "A", "nt_resnum": 1982, "nt_name": "U", "nt_code": "U", "nt_id": "///A/1982", "linked_nts": [ "///A/1981", "///A/1983" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart", "alpha": 71.804, "beta": 125.133, "gamma": 60.466, "delta": 79.821, "epsilon": -142.483, "zeta": -76.205, "epsilon_zeta": -66.278, "bb_type": "BI", "chi": -157.124, "glyco_bond": "anti", "C5prime_xyz": [ -1.580, 8.797, 0.342 ], "P_xyz": [ 0.853, 8.699, -0.628 ], "form": ".", "ssZp": 4.324, "Dp": 4.646, "splay_angle": 32.735, "splay_distance": 5.261, "splay_ratio": 0.283, "d22": null, "d64": null, "eta": -116.570, "theta": -135.742, "eta_prime": -85.940, "theta_prime": -143.169, "eta_base": -103.890, "theta_base": -128.092, "v0": 0.434, "v1": -23.227, "v2": 35.903, "v3": -36.618, 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"x_axis": [ -0.843, 0.043, 0.537 ], "y_axis": [ 0.299, -0.792, 0.532 ], "z_axis": [ 0.448, 0.609, 0.654 ], "quaternion": [ -0.071, 0.272, 0.315, 0.907 ] } }, { "index": 1974, "index_chain": 1974, "chain_name": "A", "nt_resnum": 1989, "nt_name": "G", "nt_code": "G", "nt_id": "///A/1989", "linked_nts": [ "///A/1988", "///A/1990" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,junction-loop", "alpha": -66.847, "beta": 162.092, "gamma": 63.160, "delta": 80.143, "epsilon": -133.211, "zeta": -66.289, "epsilon_zeta": -66.922, "bb_type": "BI", "chi": -165.860, "glyco_bond": "anti", "C5prime_xyz": [ -1.378, 8.709, 0.852 ], "P_xyz": [ 1.202, 9.089, 0.594 ], "form": ".", "ssZp": 4.553, "Dp": 4.740, "splay_angle": 28.884, "splay_distance": 4.565, "splay_ratio": 0.250, "d22": null, "d64": null, "eta": 168.780, "theta": -126.607, "eta_prime": -178.616, "theta_prime": -124.046, "eta_base": -137.670, "theta_base": -78.594, "v0": 3.090, "v1": -25.636, "v2": 37.144, "v3": 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"amplitude": 37.070, "phase_angle": 17.018, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.729, "filter_rmsd": 0.036, "frame": { "rmsd": 0.005, "origin": [ 189.385, 185.226, 177.323 ], "x_axis": [ -0.010, 0.722, 0.691 ], "y_axis": [ -0.624, 0.536, -0.569 ], "z_axis": [ -0.781, -0.437, 0.446 ], "quaternion": [ 0.702, -0.047, -0.524, 0.479 ] } }, { "index": 2000, "index_chain": 2000, "chain_name": "A", "nt_resnum": 2015, "nt_name": "A", "nt_code": "A", "nt_id": "///A/2015", "linked_nts": [ "///A/2014", "///A/2016" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-pair-contact,internal-loop", "alpha": -55.479, "beta": 148.356, "gamma": 60.739, "delta": 81.351, "epsilon": -113.541, "zeta": -56.506, "epsilon_zeta": -57.035, "bb_type": "--", "chi": -137.851, "glyco_bond": "anti", "C5prime_xyz": [ -1.618, 8.699, -0.817 ], "P_xyz": [ 0.740, 8.744, -1.955 ], "form": ".", "ssZp": 3.073, "Dp": 4.695, "splay_angle": 51.700, "splay_distance": 8.349, "splay_ratio": 0.437, "d22": null, "d64": null, "eta": 179.191, "theta": -98.566, "eta_prime": -176.191, "theta_prime": -94.096, "eta_base": -165.348, "theta_base": -58.380, "v0": 0.253, "v1": -22.399, "v2": 34.769, "v3": -35.595, "v4": 22.329, "amplitude": 36.609, "phase_angle": 18.243, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.240, "filter_rmsd": 0.036, "frame": { "rmsd": 0.006, "origin": [ 186.786, 182.971, 179.039 ], "x_axis": [ -0.124, 0.876, 0.467 ], "y_axis": [ -0.770, 0.212, -0.602 ], "z_axis": [ -0.626, -0.434, 0.648 ], "quaternion": [ 0.659, -0.064, -0.415, 0.625 ] } }, { "index": 2001, "index_chain": 2001, "chain_name": "A", "nt_resnum": 2016, "nt_name": "U", "nt_code": "U", "nt_id": "///A/2016", "linked_nts": [ "///A/2015", "///A/2017" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": -68.164, "beta": 162.310, "gamma": 71.020, "delta": 81.590, "epsilon": -138.978, "zeta": -70.327, "epsilon_zeta": -68.651, "bb_type": "BI", "chi": -159.413, "glyco_bond": "anti", "C5prime_xyz": [ -1.499, 8.767, 0.492 ], "P_xyz": [ 1.046, 9.182, -0.008 ], "form": ".", "ssZp": 4.350, "Dp": 4.637, "splay_angle": 24.971, "splay_distance": 4.003, "splay_ratio": 0.216, "d22": 3.828, "d64": 3.681, "eta": 162.099, "theta": -133.360, "eta_prime": -160.674, "theta_prime": -134.312, "eta_base": -103.566, "theta_base": -95.490, "v0": 0.938, "v1": -23.091, "v2": 35.220, "v3": -35.587, "v4": 21.874, "amplitude": 36.857, "phase_angle": 17.141, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.214, "filter_rmsd": 0.107, "frame": { "rmsd": 0.005, "origin": [ 181.236, 189.202, 179.345 ], "x_axis": [ -0.236, 0.501, -0.833 ], "y_axis": [ -0.324, -0.848, -0.419 ], "z_axis": [ -0.916, 0.171, 0.363 ], "quaternion": [ 0.264, -0.559, -0.079, 0.782 ] } }, { "index": 2002, "index_chain": 2002, "chain_name": "A", "nt_resnum": 2017, "nt_name": "U", "nt_code": "U", "nt_id": "///A/2017", "linked_nts": [ "///A/2016", "///A/2018" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,cap-acceptor,splayed-apart", "alpha": -65.244, "beta": 165.318, "gamma": 59.626, "delta": 82.037, "epsilon": -95.201, "zeta": -139.257, "epsilon_zeta": 44.056, "bb_type": "--", "chi": -156.615, "glyco_bond": "anti", "C5prime_xyz": [ -1.559, 8.796, 0.312 ], "P_xyz": [ 1.011, 9.293, 0.123 ], "form": ".", "ssZp": 3.786, "Dp": 4.592, "splay_angle": 135.434, "splay_distance": 17.242, "splay_ratio": 0.926, "d22": null, "d64": null, "eta": 179.149, "theta": -144.236, "eta_prime": -165.681, "theta_prime": -173.459, "eta_base": -114.089, "theta_base": 145.916, "v0": -0.296, "v1": -21.577, "v2": 33.941, "v3": -35.045, "v4": 22.311, "amplitude": 35.908, "phase_angle": 19.053, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": 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"d64": null, "eta": -21.527, "theta": -138.743, "eta_prime": -1.978, "theta_prime": -137.130, "eta_base": 17.191, "theta_base": -104.001, "v0": 5.952, "v1": -27.575, "v2": 37.531, "v3": -35.080, "v4": 18.375, "amplitude": 38.086, "phase_angle": 9.789, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "3d", "suiteness": 0.313, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 171.080, 184.134, 192.652 ], "x_axis": [ 0.477, -0.872, -0.107 ], "y_axis": [ -0.020, 0.112, -0.994 ], "z_axis": [ 0.878, 0.476, 0.036 ], "quaternion": [ 0.637, -0.577, 0.387, -0.334 ] } }, { "index": 2004, "index_chain": 2004, "chain_name": "A", "nt_resnum": 2019, "nt_name": "A", "nt_code": "A", "nt_id": "///A/2019", "linked_nts": [ "///A/2018", "///A/2020" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,phosphate", "alpha": -66.959, "beta": 165.921, "gamma": 64.547, "delta": 82.803, "epsilon": 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"nt_name": "A", "nt_code": "A", "nt_id": "///A/2020", "linked_nts": [ "///A/2019", "///A/2021" ], "nt_type": "RNA", "dbn": "{", "summary": "pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop,A-minor,phosphate,splayed-apart", "alpha": 131.666, "beta": 174.126, "gamma": -159.979, "delta": 82.335, "epsilon": -168.084, "zeta": -94.715, "epsilon_zeta": -73.369, "bb_type": "BI", "chi": -155.799, "glyco_bond": "anti", "C5prime_xyz": [ -1.230, 8.670, 0.279 ], "P_xyz": [ -0.600, 10.872, -0.987 ], "form": ".", "ssZp": 4.336, "Dp": 4.514, "splay_angle": 101.935, "splay_distance": 15.692, "splay_ratio": 0.781, "d22": null, "d64": null, "eta": 153.252, "theta": 135.016, "eta_prime": 169.418, "theta_prime": 120.591, "eta_base": -158.251, "theta_base": 94.598, "v0": 4.548, "v1": -25.923, "v2": 36.270, "v3": -34.668, "v4": 19.004, "amplitude": 37.045, "phase_angle": 11.742, "puckering": "C3'-endo", "sugar_class": 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"d22": 10.200, "d64": 12.738, "eta": 104.437, "theta": -42.699, "eta_prime": 89.912, "theta_prime": -48.426, "eta_base": 57.124, "theta_base": -38.612, "v0": -20.375, "v1": 35.338, "v2": -35.975, "v3": 25.128, "v4": -3.166, "amplitude": 37.062, "phase_angle": 166.091, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32m", "cluster": "1o", "suiteness": 0.227, "filter_rmsd": 0.063, "frame": { "rmsd": 0.002, "origin": [ 177.159, 193.869, 205.334 ], "x_axis": [ -0.702, 0.621, -0.349 ], "y_axis": [ 0.238, -0.258, -0.936 ], "z_axis": [ -0.671, -0.740, 0.033 ], "quaternion": [ 0.136, -0.362, -0.594, 0.706 ] } }, { "index": 2007, "index_chain": 2007, "chain_name": "A", "nt_resnum": 2022, "nt_name": "U", "nt_code": "U", "nt_id": "///A/2022", "linked_nts": [ "///A/2021", "///A/2023" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart", "alpha": 101.105, "beta": 115.159, "gamma": -53.244, "delta": 147.149, "epsilon": -82.596, 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"nt_name": "C", "nt_code": "C", "nt_id": "///A/2023", "linked_nts": [ "///A/2022", "///A/2024" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,splayed-apart", "alpha": -116.098, "beta": -134.932, "gamma": 177.939, "delta": 79.980, "epsilon": -148.501, "zeta": -93.474, "epsilon_zeta": -55.028, "bb_type": "BI", "chi": -159.805, "glyco_bond": "anti", "C5prime_xyz": [ -1.420, 8.836, 0.502 ], "P_xyz": [ -0.028, 9.820, -1.481 ], "form": ".", "ssZp": 4.392, "Dp": 4.596, "splay_angle": 31.258, "splay_distance": 4.864, "splay_ratio": 0.269, "d22": null, "d64": null, "eta": -11.936, "theta": -178.951, "eta_prime": -27.197, "theta_prime": -179.426, "eta_base": 39.280, "theta_base": -159.514, "v0": 0.108, "v1": -22.722, "v2": 35.457, "v3": -36.356, "v4": 22.842, "amplitude": 37.374, "phase_angle": 18.432, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "23t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.066, "frame": { "rmsd": 0.006, "origin": [ 184.067, 179.149, 209.226 ], "x_axis": [ -0.886, 0.414, 0.210 ], "y_axis": [ -0.136, 0.200, -0.970 ], "z_axis": [ -0.444, -0.888, -0.121 ], "quaternion": [ -0.220, 0.094, 0.743, -0.625 ] } }, { "index": 2009, "index_chain": 2009, "chain_name": "A", "nt_resnum": 2024, "nt_name": "G", "nt_code": "G", "nt_id": "///A/2024", "linked_nts": [ "///A/2023", "///A/2025" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,hairpin-loop", "alpha": -45.803, "beta": 158.972, "gamma": 51.635, "delta": 81.344, "epsilon": -154.276, "zeta": -78.084, "epsilon_zeta": -76.192, "bb_type": "BI", "chi": -168.870, "glyco_bond": "anti", "C5prime_xyz": [ -1.355, 8.646, 1.052 ], "P_xyz": [ 1.251, 8.830, 1.226 ], "form": "A", "ssZp": 4.565, "Dp": 4.606, "splay_angle": 20.579, "splay_distance": 3.481, "splay_ratio": 0.188, "d22": null, "d64": null, "eta": 175.791, "theta": -117.663, "eta_prime": -174.659, "theta_prime": 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"z_axis": [ 0.388, 0.668, -0.636 ], "quaternion": [ 0.332, -0.323, 0.845, 0.268 ] } }, { "index": 2018, "index_chain": 2018, "chain_name": "A", "nt_resnum": 2033, "nt_name": "A", "nt_code": "A", "nt_id": "///A/2033", "linked_nts": [ "///A/2032", "///A/2034" ], "nt_type": "RNA", "dbn": "]", "summary": "pseudoknotted,anti,~C2'-endo,BII,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop,splayed-apart", "alpha": -68.821, "beta": -120.982, "gamma": 76.872, "delta": 146.764, "epsilon": -85.468, "zeta": -160.992, "epsilon_zeta": 75.524, "bb_type": "BII", "chi": -110.822, "glyco_bond": "anti", "C5prime_xyz": [ -2.302, 8.352, -1.659 ], "P_xyz": [ -0.097, 9.241, -0.539 ], "form": ".", "ssZp": 0.513, "Dp": 0.536, "splay_angle": 86.383, "splay_distance": 13.407, "splay_ratio": 0.685, "d22": null, "d64": null, "eta": -128.557, "theta": -106.440, "eta_prime": -77.801, "theta_prime": -162.765, "eta_base": -115.609, "theta_base": 162.126, "v0": -23.534, "v1": 37.563, "v2": -36.437, "v3": 23.802, "v4": -0.380, "amplitude": 38.360, "phase_angle": 161.779, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "2[", "suiteness": 0.213, "filter_rmsd": 0.037, "frame": { "rmsd": 0.006, "origin": [ 169.972, 174.396, 201.788 ], "x_axis": [ -0.529, -0.702, 0.478 ], "y_axis": [ 0.691, -0.683, -0.238 ], "z_axis": [ 0.493, 0.204, 0.846 ], "quaternion": [ -0.398, 0.278, -0.010, 0.874 ] } }, { "index": 2019, "index_chain": 2019, "chain_name": "A", "nt_resnum": 2034, "nt_name": "U", "nt_code": "U", "nt_id": "///A/2034", "linked_nts": [ "///A/2033", "///A/2035" ], "nt_type": "RNA", "dbn": "}", "summary": "pseudoknotted,turn,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop,A-minor,phosphate,splayed-apart", "alpha": 77.618, "beta": -158.673, "gamma": 60.335, "delta": 80.858, "epsilon": -126.845, "zeta": -91.990, "epsilon_zeta": -34.855, "bb_type": "--", "chi": -159.028, 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"atom2_id": "///3/46/NZ", "atom_pair": "N:N", "residue_pair": "aa:aa" }, { "index": 7871, "atom1_serNum": 83868, "atom2_serNum": 83942, "donAcc_type": "standard", "distance": 2.609, "atom1_id": "///3/27/O", "atom2_id": "///3/35/NZ", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7872, "atom1_serNum": 83913, "atom2_serNum": 83937, "donAcc_type": "questionable", "distance": 3.127, "atom1_id": "///3/32/O", "atom2_id": "///3/35/O", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 7873, "atom1_serNum": 83946, "atom2_serNum": 83975, "donAcc_type": "standard", "distance": 2.914, "atom1_id": "///3/36/O", "atom2_id": "///3/40/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7874, "atom1_serNum": 83951, "atom2_serNum": 83984, "donAcc_type": "standard", "distance": 2.645, "atom1_id": "///3/37/O", "atom2_id": "///3/41/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7875, "atom1_serNum": 83958, "atom2_serNum": 84001, "donAcc_type": "acceptable", "distance": 2.579, "atom1_id": "///3/38/O", "atom2_id": "///3/42/ND1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7876, "atom1_serNum": 83987, "atom2_serNum": 84013, "donAcc_type": "standard", "distance": 3.403, "atom1_id": "///3/41/O", "atom2_id": "///3/44/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7877, "atom1_serNum": 84069, "atom2_serNum": 84087, "donAcc_type": "standard", "distance": 3.366, "atom1_id": "///3/51/O", "atom2_id": "///3/54/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7878, "atom1_serNum": 84090, "atom2_serNum": 84107, "donAcc_type": "standard", "distance": 3.086, "atom1_id": "///3/54/O", "atom2_id": "///3/57/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7879, "atom1_serNum": 84090, "atom2_serNum": 84114, "donAcc_type": "standard", "distance": 3.247, "atom1_id": "///3/54/O", "atom2_id": "///3/58/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7880, "atom1_serNum": 84110, "atom2_serNum": 84133, "donAcc_type": "standard", "distance": 2.676, "atom1_id": "///3/57/O", "atom2_id": "///3/61/N", "atom_pair": "O:N", "residue_pair": "aa:aa" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "6gc0", "num_aaChains": 26, "aaChains": "0=56,1=50,2=46,3=64,C=271,D=209,E=201,F=177,G=176,H=50,J=142,K=122,L=143,N=120,O=116,P=114,Q=117,R=103,S=110,T=93,U=102,V=94,W=76,X=77,Y=63,Z=58", "num_naChains": 2, "naChains": "A=2729,B=119", "num_atoms": 84138, "num_waters": 0, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 21, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-bulges.pdb", "desc": "an ensemble of bulges" }, { "index": 7, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 8, "name": "dssr-junctions.pdb", "desc": "an ensemble of junctions (multi-branch)" }, { "index": 9, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 10, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 11, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 12, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 13, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 14, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 15, "name": "dssr-Kturns.pdb", "desc": "an ensemble of kink-turn motifs" }, { "index": 16, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 17, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 18, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 19, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 20, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 21, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }