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2.918 }, { "index": 95, "type": "phosphate", "atom": "///6/72/OP1", "nt": "///6/72", "vert_dist": 2.824 }, { "index": 96, "type": "sugar", "atom": "///6/73/O2'", "nt": "///6/74", "vert_dist": 2.842 } ], "num_hairpins": 22, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 5 ], "summary": "[1] 4 [1.69 1.74] 2", "num_nts": 6, "nts_short": "UAACCA", "nts_long": "///1/69,///1/70,///1/71,///1/72,///1/73,///1/74", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AACC", "nts_long": "///1/70,///1/71,///1/72,///1/73" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 10 ], "summary": "[1] 7 [1.133 1.141] 7", "num_nts": 9, "nts_short": "AUUUCUUUU", "nts_long": "///1/133,///1/134,///1/135,///1/136,///1/137,///1/138,///1/139,///1/140,///1/141", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUUCUUU", "nts_long": "///1/134,///1/135,///1/136,///1/137,///1/138,///1/139,///1/140" 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"///1/223,///1/224,///1/225,///1/226,///1/227,///1/228,///1/229,///1/230,///1/231", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGAGAAC", "nts_long": "///1/224,///1/225,///1/226,///1/227,///1/228,///1/229,///1/230" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 24 ], "summary": "[1] 4 [1.365 1.370] 2", "num_nts": 6, "nts_short": "AGUGAU", "nts_long": "///1/365,///1/366,///1/367,///1/368,///1/369,///1/370", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///1/366,///1/367,///1/368,///1/369" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 26 ], "summary": "[1] 4 [1.390 1.395] 4", "num_nts": 6, "nts_short": "UGAAAA", "nts_long": "///1/390,///1/391,///1/392,///1/393,///1/394,///1/395", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/391,///1/392,///1/393,///1/394" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 38 ], "summary": "[1] 5 [1.623 1.629] 3", "num_nts": 7, "nts_short": "CUUCGUG", "nts_long": "///1/623,///1/624,///1/625,///1/626,///1/627,///1/628,///1/629", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UUCGU", "nts_long": "///1/624,///1/625,///1/626,///1/627,///1/628" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 39 ], "summary": "[1] 8 [1.665 1.674] 4", "num_nts": 10, "nts_short": "UCUUGAAACA", "nts_long": "///1/665,///1/666,///1/667,///1/668,///1/669,///1/670,///1/671,///1/672,///1/673,///1/674", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "CUUGAAAC", "nts_long": "///1/666,///1/667,///1/668,///1/669,///1/670,///1/671,///1/672,///1/673" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 44 ], "summary": "[1] 9 [1.711 1.721] 3", "num_nts": 11, "nts_short": "GUGAUGAAAAC", "nts_long": "///1/711,///1/712,///1/713,///1/714,///1/715,///1/716,///1/717,///1/718,///1/719,///1/720,///1/721", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UGAUGAAAA", "nts_long": "///1/712,///1/713,///1/714,///1/715,///1/716,///1/717,///1/718,///1/719,///1/720" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -18 ], "summary": "[1] 4 [1.758 1.763] 1", "num_nts": 6, "nts_short": "CCCUUG", "nts_long": "///1/758,///1/759,///1/760,///1/761,///1/762,///1/763", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CCUU", "nts_long": "///1/759,///1/760,///1/761,///1/762" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 55 ], "summary": "[1] 5 [1.1157 1.1163] 2", "num_nts": 7, "nts_short": "GGUAAGC", "nts_long": "///1/1157,///1/1158,///1/1159,///1/1160,///1/1161,///1/1162,///1/1163", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GUAAG", "nts_long": "///1/1158,///1/1159,///1/1160,///1/1161,///1/1162" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 56 ], "summary": "[1] 6 [1.1179 1.1186] 3", "num_nts": 8, "nts_short": "GGAUGAAC", "nts_long": "///1/1179,///1/1180,///1/1181,///1/1182,///1/1183,///1/1184,///1/1185,///1/1186", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAUGAA", "nts_long": "///1/1180,///1/1181,///1/1182,///1/1183,///1/1184,///1/1185" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 12 ], "stem_indices": [ 63 ], "summary": "[1] 12 [1.1378 1.1391] 9", "num_nts": 14, "nts_short": "UUAGCUUUGAGAAG", "nts_long": "///1/1378,///1/1379,///1/1380,///1/1381,///1/1382,///1/1383,///1/1384,///1/1385,///1/1386,///1/1387,///1/1388,///1/1389,///1/1390,///1/1391", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 12, "nts_short": "UAGCUUUGAGAA", "nts_long": "///1/1379,///1/1380,///1/1381,///1/1382,///1/1383,///1/1384,///1/1385,///1/1386,///1/1387,///1/1388,///1/1389,///1/1390" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 67 ], "summary": "[1] 4 [1.1437 1.1442] 4", "num_nts": 6, "nts_short": "CGUGAG", "nts_long": "///1/1437,///1/1438,///1/1439,///1/1440,///1/1441,///1/1442", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///1/1438,///1/1439,///1/1440,///1/1441" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ -27 ], "summary": "[1] 13 [1.2450 1.2464] 1", "num_nts": 15, "nts_short": "CAGCCUGGGGAACGG", "nts_long": "///1/2450,///1/2451,///1/2452,///1/2453,///1/2454,///1/2455,///1/2456,///1/2457,///1/2458,///1/2459,///1/2460,///1/2461,///1/2462,///1/2463,///1/2464", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "AGCCUGGGGAACG", "nts_long": "///1/2451,///1/2452,///1/2453,///1/2454,///1/2455,///1/2456,///1/2457,///1/2458,///1/2459,///1/2460,///1/2461,///1/2462,///1/2463" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 70 ], "summary": "[1] 8 [1.2457 1.2466] 5", "num_nts": 10, "nts_short": "GGGAACGGGC", "nts_long": "///1/2457,///1/2458,///1/2459,///1/2460,///1/2461,///1/2462,///1/2463,///1/2464,///1/2465,///1/2466", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GGAACGGG", "nts_long": "///1/2458,///1/2459,///1/2460,///1/2461,///1/2462,///1/2463,///1/2464,///1/2465" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -29 ], "summary": "[1] 4 [1.3121 1.3126] 1", "num_nts": 6, "nts_short": "CGAGAG", "nts_long": "///1/3121,///1/3122,///1/3123,///1/3124,///1/3125,///1/3126", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///1/3122,///1/3123,///1/3124,///1/3125" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 77 ], "summary": "[1] 13 [1.3206 1.3220] 3", "num_nts": 15, "nts_short": "CUGAACGCCUCUAAG", "nts_long": "///1/3206,///1/3207,///1/3208,///1/3209,///1/3210,///1/3211,///1/3212,///1/3213,///1/3214,///1/3215,///1/3216,///1/3217,///1/3218,///1/3219,///1/3220", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "UGAACGCCUCUAA", "nts_long": "///1/3207,///1/3208,///1/3209,///1/3210,///1/3211,///1/3212,///1/3213,///1/3214,///1/3215,///1/3216,///1/3217,///1/3218,///1/3219" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 82 ], "summary": "[1] 6 [1.3340 1.3347] 11", "num_nts": 8, "nts_short": "CGGAAGUG", "nts_long": "///1/3340,///1/3341,///1/3342,///1/3343,///1/3344,///1/3345,///1/3346,///1/3347", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GGAAGU", "nts_long": "///1/3341,///1/3342,///1/3343,///1/3344,///1/3345,///1/3346" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -37 ], "summary": "[1] 7 [1.3404 1.3412] 1", "num_nts": 9, "nts_short": "GCAUACGAC", "nts_long": "///1/3404,///1/3405,///1/3406,///1/3407,///1/3408,///1/3409,///1/3410,///1/3411,///1/3412", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CAUACGA", "nts_long": "///1/3405,///1/3406,///1/3407,///1/3408,///1/3409,///1/3410,///1/3411" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 88 ], "summary": "[1] 6 [2.56 2.63] 4", "num_nts": 8, "nts_short": "AGCGAAAU", "nts_long": "///2/56,///2/57,///2/58,///2/59,///2/60,///2/61,///2/62,///2/63", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GCGAAA", "nts_long": "///2/57,///2/58,///2/59,///2/60,///2/61,///2/62" } ] } ], "num_bulges": 20, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 1, 2 ], "summary": "[2] 0 1 [1.7 2.160 1.8 2.158] 4 6", "num_nts": 5, "nts_short": "CCGUG", "nts_long": "///1/7,///1/8,///2/158,///2/159,///2/160", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/159" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 2, 3 ], "summary": "[2] 1 0 [1.13 2.153 1.15 2.152] 6 6", "num_nts": 5, "nts_short": "AUCGU", "nts_long": "///1/13,///1/14,///1/15,///2/152,///2/153", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/14" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 11, 12 ], "summary": "[2] 0 1 [1.165 1.270 1.166 1.268] 2 2", "num_nts": 5, "nts_short": "AAUUU", "nts_long": "///1/165,///1/166,///1/268,///1/269,///1/270", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/269" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -5, 14 ], "summary": "[2] 1 0 [1.175 1.256 1.177 1.255] 1 5", "num_nts": 5, "nts_short": "GAGCC", "nts_long": "///1/175,///1/176,///1/177,///1/255,///1/256", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/176" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -6, 17 ], "summary": "[2] 1 0 [1.196 1.212 1.198 1.211] 1 4", "num_nts": 5, "nts_short": "GUUAC", "nts_long": "///1/196,///1/197,///1/198,///1/211,///1/212", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/197" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 6, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 22, 23 ], "summary": "[2] 1 0 [1.345 2.34 1.347 2.33] 7 2", "num_nts": 5, "nts_short": "GACGC", "nts_long": "///1/345,///1/346,///1/347,///2/33,///2/34", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/346" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 7, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 29, 30 ], "summary": "[2] 0 1 [1.452 1.501 1.453 1.499] 3 5", "num_nts": 5, "nts_short": "CUGUG", "nts_long": "///1/452,///1/453,///1/499,///1/500,///1/501", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/500" } ] }, { "index": 8, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 32, 33 ], "summary": "[2] 1 0 [1.464 1.485 1.466 1.484] 2 7", "num_nts": 5, "nts_short": "AGUAU", "nts_long": "///1/464,///1/465,///1/466,///1/484,///1/485", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/465" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 9, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 35, 36 ], "summary": "[2] 0 1 [1.523 1.603 1.524 1.601] 10 5", "num_nts": 5, "nts_short": "GGCAC", "nts_long": "///1/523,///1/524,///1/601,///1/602,///1/603", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/602" } ] }, { "index": 10, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -21, 49 ], "summary": "[2] 0 1 [1.1001 1.1144 1.1002 1.1142] 1 7", "num_nts": 5, "nts_short": "CAUAG", "nts_long": "///1/1001,///1/1002,///1/1142,///1/1143,///1/1144", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/1143" } ] }, { "index": 11, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 50, 51 ], "summary": "[2] 1 0 [1.1015 1.1132 1.1017 1.1131] 3 2", "num_nts": 5, "nts_short": "AGUAU", "nts_long": "///1/1015,///1/1016,///1/1017,///1/1131,///1/1132", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1016" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 12, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -23, 60 ], "summary": "[2] 1 0 [1.1211 1.1356 1.1213 1.1355] 1 6", "num_nts": 5, "nts_short": "AUGCU", "nts_long": "///1/1211,///1/1212,///1/1213,///1/1355,///1/1356", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1212" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 13, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 61, -25 ], "summary": "[2] 1 0 [1.1238 1.1328 1.1240 1.1327] 3 1", "num_nts": 5, "nts_short": "GUGCC", "nts_long": "///1/1238,///1/1239,///1/1240,///1/1327,///1/1328", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1239" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 14, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 64, 65 ], "summary": "[2] 1 0 [1.1419 1.1455 1.1421 1.1454] 8 2", "num_nts": 5, "nts_short": "UUGCA", "nts_long": "///1/1419,///1/1420,///1/1421,///1/1454,///1/1455", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1420" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 15, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 66, 67 ], "summary": "[2] 1 0 [1.1432 1.1446 1.1434 1.1445] 4 4", "num_nts": 5, "nts_short": "UUGUG", "nts_long": "///1/1432,///1/1433,///1/1434,///1/1445,///1/1446", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1433" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 16, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -33, 79 ], "summary": "[2] 1 0 [1.3271 1.3312 1.3273 1.3311] 1 2", "num_nts": 5, "nts_short": "GUAUC", "nts_long": "///1/3271,///1/3272,///1/3273,///1/3311,///1/3312", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3272" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 17, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 84, 85 ], "summary": "[2] 0 1 [1.3425 1.3484 1.3426 1.3482] 4 3", "num_nts": 5, "nts_short": "CGUUG", "nts_long": "///1/3425,///1/3426,///1/3482,///1/3483,///1/3484", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3483" } ] }, { "index": 18, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 89, -39 ], "summary": "[2] 0 1 [2.76 2.99 2.77 2.97] 3 1", "num_nts": 5, "nts_short": "GUAUC", "nts_long": "///2/76,///2/77,///2/97,///2/98,///2/99", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/98" } ] }, { "index": 19, "type": "bulge", "bridging_nts": [ 0, 4 ], "stem_indices": [ -4, 9 ], "summary": "[2] 0 4 [1.123 1.155 1.124 1.150] 1 2", "num_nts": 8, "nts_short": "AUAGUUGU", "nts_long": "///1/123,///1/124,///1/150,///1/151,///1/152,///1/153,///1/154,///1/155", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "GUUG", "nts_long": "///1/151,///1/152,///1/153,///1/154" } ] }, { "index": 20, "type": "bulge", "bridging_nts": [ 0, 4 ], "stem_indices": [ 13, -5 ], "summary": "[2] 0 4 [1.174 1.261 1.175 1.256] 5 1", "num_nts": 8, "nts_short": "UGCAUAUA", "nts_long": "///1/174,///1/175,///1/256,///1/257,///1/258,///1/259,///1/260,///1/261", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "AUAU", "nts_long": "///1/257,///1/258,///1/259,///1/260" } ] } ], "num_iloops": 46, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 9, 10 ], "summary": "[2] 1 1 [1.125 1.149 1.127 1.147] 2 7", "num_nts": 6, "nts_short": "CUGCCG", "nts_long": "///1/125,///1/126,///1/127,///1/147,///1/148,///1/149", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/126" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/148" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -9, 20 ], "summary": "[2] 1 1 [1.280 1.301 1.282 1.299] 1 5", "num_nts": 6, "nts_short": "GAGCUC", "nts_long": "///1/280,///1/281,///1/282,///1/299,///1/300,///1/301", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/281" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/300" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 41, 42 ], "summary": "[2] 1 1 [1.693 1.826 1.695 1.824] 6 6", "num_nts": 6, "nts_short": "AUCGCU", "nts_long": "///1/693,///1/694,///1/695,///1/824,///1/825,///1/826", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/694" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/825" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -17, -18 ], "summary": "[2] 1 1 [1.756 1.765 1.758 1.763] 1 1", "num_nts": 6, "nts_short": "CGCGUG", "nts_long": "///1/756,///1/757,///1/758,///1/763,///1/764,///1/765", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/757" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/764" } ] }, { "index": 5, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 45, -19 ], "summary": "[2] 1 1 [1.835 1.972 1.837 1.970] 2 1", "num_nts": 6, "nts_short": "CCGCUG", "nts_long": "///1/835,///1/836,///1/837,///1/970,///1/971,///1/972", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/836" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/971" } ] }, { "index": 6, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -20, 48 ], "summary": "[2] 1 1 [1.986 1.999 1.988 1.997] 1 2", "num_nts": 6, "nts_short": "UUUAUA", "nts_long": "///1/986,///1/987,///1/988,///1/997,///1/998,///1/999", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/987" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/998" } ] }, { "index": 7, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 52, -22 ], "summary": "[2] 1 1 [1.1021 1.1092 1.1023 1.1090] 3 1", "num_nts": 6, "nts_short": "AUGUGU", "nts_long": "///1/1021,///1/1022,///1/1023,///1/1090,///1/1091,///1/1092", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1022" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1091" } ] }, { "index": 8, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 53, 54 ], "summary": "[2] 1 1 [1.1151 1.1169 1.1153 1.1167] 4 2", "num_nts": 6, "nts_short": "AUUACU", "nts_long": "///1/1151,///1/1152,///1/1153,///1/1167,///1/1168,///1/1169", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1152" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///1/1168" } ] }, { "index": 9, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 54, 55 ], "summary": "[2] 1 1 [1.1154 1.1166 1.1156 1.1164] 2 2", "num_nts": 6, "nts_short": "UUUAGA", "nts_long": "///1/1154,///1/1155,///1/1156,///1/1164,///1/1165,///1/1166", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1155" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1165" } ] }, { "index": 10, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -25, 62 ], "summary": "[2] 1 1 [1.1240 1.1327 1.1242 1.1325] 1 6", "num_nts": 6, "nts_short": "GUUAGC", "nts_long": "///1/1240,///1/1241,///1/1242,///1/1325,///1/1326,///1/1327", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/1241" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1326" } ] }, { "index": 11, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -28, 73 ], "summary": "[2] 1 1 [1.3108 1.3138 1.3110 1.3136] 1 5", "num_nts": 6, "nts_short": "AUUAUU", "nts_long": "///1/3108,///1/3109,///1/3110,///1/3136,///1/3137,///1/3138", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3109" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3137" } ] }, { "index": 12, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -30, 74 ], "summary": "[2] 1 1 [1.3139 1.3194 1.3141 1.3192] 1 3", "num_nts": 6, "nts_short": "CAGCUG", "nts_long": "///1/3139,///1/3140,///1/3141,///1/3192,///1/3193,///1/3194", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/3140" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3193" } ] }, { "index": 13, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -32, 78 ], "summary": "[2] 1 1 [1.3253 1.3393 1.3255 1.3391] 1 7", "num_nts": 6, "nts_short": "GGUAAU", "nts_long": "///1/3253,///1/3254,///1/3255,///1/3391,///1/3392,///1/3393", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/3254" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///1/3392" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -35, 83 ], "summary": "[2] 1 1 [1.3394 1.3497 1.3396 1.3495] 1 4", "num_nts": 6, "nts_short": "CGAUUG", "nts_long": "///1/3394,///1/3395,///1/3396,///1/3495,///1/3496,///1/3497", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/3395" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3496" } ] }, { "index": 15, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -2, 4 ], "summary": "[2] 1 2 [1.27 1.58 1.29 1.55] 1 3", "num_nts": 7, "nts_short": "CGCGCAG", "nts_long": "///1/27,///1/28,///1/29,///1/55,///1/56,///1/57,///1/58", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/28" }, { "index": 2, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/56,///1/57" } ] }, { "index": 16, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 12, 13 ], "summary": "[2] 2 1 [1.167 1.267 1.170 1.265] 2 5", "num_nts": 7, "nts_short": "GCUGCGC", "nts_long": "///1/167,///1/168,///1/169,///1/170,///1/265,///1/266,///1/267", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/168,///1/169" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/266" } ] }, { "index": 17, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 30, 31 ], "summary": "[2] 1 2 [1.457 1.495 1.459 1.492] 5 2", "num_nts": 7, "nts_short": "UGAUGAA", "nts_long": "///1/457,///1/458,///1/459,///1/492,///1/493,///1/494,///1/495", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/458" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/493,///1/494" } ] }, { "index": 18, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -26, 64 ], "summary": "[2] 1 2 [1.1410 1.1465 1.1412 1.1462] 1 8", "num_nts": 7, "nts_short": "CGUAGUG", "nts_long": "///1/1410,///1/1411,///1/1412,///1/1462,///1/1463,///1/1464,///1/1465", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1411" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/1463,///1/1464" } ] }, { "index": 19, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -38, 89 ], "summary": "[2] 1 2 [2.72 2.104 2.74 2.101] 1 3", "num_nts": 7, "nts_short": "UAAUCGA", "nts_long": "///2/72,///2/73,///2/74,///2/101,///2/102,///2/103,///2/104", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/73" }, { "index": 2, "num_nts": 2, "nts_short": "CG", "nts_long": "///2/102,///2/103" } ] }, { "index": 20, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 15, 16 ], "summary": "[2] 2 2 [1.187 1.245 1.190 1.242] 3 3", "num_nts": 8, "nts_short": "UCGGUCGA", "nts_long": "///1/187,///1/188,///1/189,///1/190,///1/242,///1/243,///1/244,///1/245", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/188,///1/189" }, { "index": 2, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/243,///1/244" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ -36, -37 ], "summary": "[2] 2 2 [1.3401 1.3415 1.3404 1.3412] 1 1", "num_nts": 8, "nts_short": "AUUGCUUU", "nts_long": "///1/3401,///1/3402,///1/3403,///1/3404,///1/3412,///1/3413,///1/3414,///1/3415", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/3402,///1/3403" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/3413,///1/3414" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 49, 50 ], "summary": "[2] 4 1 [1.1008 1.1136 1.1013 1.1134] 7 3", "num_nts": 9, "nts_short": "UCAGAUAGA", "nts_long": "///1/1008,///1/1009,///1/1010,///1/1011,///1/1012,///1/1013,///1/1134,///1/1135,///1/1136", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAGA", "nts_long": "///1/1009,///1/1010,///1/1011,///1/1012" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1135" } ] }, { "index": 23, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 74, 75 ], "summary": "[2] 3 2 [1.3143 1.3190 1.3147 1.3187] 3 3", "num_nts": 9, "nts_short": "UCAUUAUCA", "nts_long": "///1/3143,///1/3144,///1/3145,///1/3146,///1/3147,///1/3187,///1/3188,///1/3189,///1/3190", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAU", "nts_long": "///1/3144,///1/3145,///1/3146" }, { "index": 2, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/3188,///1/3189" } ] }, { "index": 24, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 14, 15 ], "summary": "[2] 3 3 [1.181 1.251 1.185 1.247] 5 3", "num_nts": 10, "nts_short": "AGACGUGGAU", "nts_long": "///1/181,///1/182,///1/183,///1/184,///1/185,///1/247,///1/248,///1/249,///1/250,///1/251", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAC", "nts_long": "///1/182,///1/183,///1/184" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/248,///1/249,///1/250" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 2, 4 ], "stem_indices": [ 31, 32 ], "summary": "[2] 2 4 [1.460 1.491 1.463 1.486] 2 2", "num_nts": 10, "nts_short": "GAUCGCACUC", "nts_long": "///1/460,///1/461,///1/462,///1/463,///1/486,///1/487,///1/488,///1/489,///1/490,///1/491", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/461,///1/462" }, { "index": 2, "num_nts": 4, "nts_short": "CACU", "nts_long": "///1/487,///1/488,///1/489,///1/490" } ] }, { "index": 26, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -12, 37 ], "summary": "[2] 3 3 [1.536 1.590 1.540 1.586] 1 3", "num_nts": 10, "nts_short": "AAUAAUUGUU", "nts_long": "///1/536,///1/537,///1/538,///1/539,///1/540,///1/586,///1/587,///1/588,///1/589,///1/590", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AUA", "nts_long": "///1/537,///1/538,///1/539" }, { "index": 2, "num_nts": 3, "nts_short": "UGU", "nts_long": "///1/587,///1/588,///1/589" } ] }, { "index": 27, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 43, 44 ], "summary": "[2] 3 3 [1.705 1.727 1.709 1.723] 3 3", "num_nts": 10, "nts_short": "GUUUGCAUCC", "nts_long": "///1/705,///1/706,///1/707,///1/708,///1/709,///1/723,///1/724,///1/725,///1/726,///1/727", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUU", "nts_long": "///1/706,///1/707,///1/708" }, { "index": 2, "num_nts": 3, "nts_short": "AUC", "nts_long": "///1/724,///1/725,///1/726" } ] }, { "index": 28, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 57, 58 ], "summary": "[2] 3 3 [1.1198 1.1363 1.1202 1.1359] 7 3", "num_nts": 10, "nts_short": "UUAAGCCAUA", "nts_long": "///1/1198,///1/1199,///1/1200,///1/1201,///1/1202,///1/1359,///1/1360,///1/1361,///1/1362,///1/1363", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///1/1199,///1/1200,///1/1201" }, { "index": 2, "num_nts": 3, "nts_short": "CAU", "nts_long": "///1/1360,///1/1361,///1/1362" } ] }, { "index": 29, "type": "asymmetric internal loop", "bridging_nts": [ 2, 4 ], "stem_indices": [ 71, 72 ], "summary": "[2] 2 4 [1.3100 1.3240 1.3103 1.3235] 7 4", "num_nts": 10, "nts_short": "CAAUAGAAAG", "nts_long": "///1/3100,///1/3101,///1/3102,///1/3103,///1/3235,///1/3236,///1/3237,///1/3238,///1/3239,///1/3240", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/3101,///1/3102" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/3236,///1/3237,///1/3238,///1/3239" } ] }, { "index": 30, "type": "asymmetric internal loop", "bridging_nts": [ 4, 2 ], "stem_indices": [ 81, 82 ], "summary": "[2] 4 2 [1.3325 1.3360 1.3330 1.3357] 6 11", "num_nts": 10, "nts_short": "CGAUGGCUUG", "nts_long": "///1/3325,///1/3326,///1/3327,///1/3328,///1/3329,///1/3330,///1/3357,///1/3358,///1/3359,///1/3360", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAUG", "nts_long": "///1/3326,///1/3327,///1/3328,///1/3329" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/3358,///1/3359" } ] }, { "index": 31, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ 80, -34 ], "summary": "[2] 3 4 [1.3284 1.3303 1.3288 1.3298] 3 1", "num_nts": 11, "nts_short": "GGUAGCUACUC", "nts_long": "///1/3284,///1/3285,///1/3286,///1/3287,///1/3288,///1/3298,///1/3299,///1/3300,///1/3301,///1/3302,///1/3303", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUA", "nts_long": "///1/3285,///1/3286,///1/3287" }, { "index": 2, "num_nts": 4, "nts_short": "UACU", "nts_long": "///1/3299,///1/3300,///1/3301,///1/3302" } ] }, { "index": 32, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ -40, -41 ], "summary": "[2] 4 3 [6.33 6.63 6.38 6.59] 1 1", "num_nts": 11, "nts_short": "AUAUUUAAUUU", "nts_long": "///6/33,///6/34,///6/35,///6/36,///6/37,///6/38,///6/59,///6/60,///6/61,///6/62,///6/63", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UAUU", "nts_long": "///6/34,///6/35,///6/36,///6/37" }, { "index": 2, "num_nts": 3, "nts_short": "AUU", "nts_long": "///6/60,///6/61,///6/62" } ] }, { "index": 33, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 76, 77 ], "summary": "[2] 4 4 [1.3199 1.3227 1.3204 1.3222] 4 3 k-turn:undecided", "num_nts": 12, "nts_short": "AUAACGCAGAAU", "nts_long": "///1/3199,///1/3200,///1/3201,///1/3202,///1/3203,///1/3204,///1/3222,///1/3223,///1/3224,///1/3225,///1/3226,///1/3227", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UAAC", "nts_long": "///1/3200,///1/3201,///1/3202,///1/3203" }, { "index": 2, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///1/3223,///1/3224,///1/3225,///1/3226" } ] }, { "index": 34, "type": "asymmetric internal loop", "bridging_nts": [ 4, 5 ], "stem_indices": [ -16, -17 ], "summary": "[2] 4 5 [1.751 1.771 1.756 1.765] 1 1", "num_nts": 13, "nts_short": "GGGAACGGCGUGC", "nts_long": "///1/751,///1/752,///1/753,///1/754,///1/755,///1/756,///1/765,///1/766,///1/767,///1/768,///1/769,///1/770,///1/771", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///1/752,///1/753,///1/754,///1/755" }, { "index": 2, "num_nts": 5, "nts_short": "GCGUG", "nts_long": "///1/766,///1/767,///1/768,///1/769,///1/770" } ] }, { "index": 35, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ -19, 46 ], "summary": "[2] 3 6 [1.837 1.970 1.841 1.963] 1 6", "num_nts": 13, "nts_short": "GAAAGCUAGUAGC", "nts_long": "///1/837,///1/838,///1/839,///1/840,///1/841,///1/963,///1/964,///1/965,///1/966,///1/967,///1/968,///1/969,///1/970", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/838,///1/839,///1/840" }, { "index": 2, "num_nts": 6, "nts_short": "UAGUAG", "nts_long": "///1/964,///1/965,///1/966,///1/967,///1/968,///1/969" } ] }, { "index": 36, "type": "asymmetric internal loop", "bridging_nts": [ 6, 3 ], "stem_indices": [ 65, 66 ], "summary": "[2] 6 3 [1.1422 1.1453 1.1429 1.1449] 2 4 k-turn:normal", "num_nts": 13, "nts_short": "UGACGAAGUCGAA", "nts_long": "///1/1422,///1/1423,///1/1424,///1/1425,///1/1426,///1/1427,///1/1428,///1/1429,///1/1449,///1/1450,///1/1451,///1/1452,///1/1453", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GACGAA", "nts_long": "///1/1423,///1/1424,///1/1425,///1/1426,///1/1427,///1/1428" }, { "index": 2, "num_nts": 3, "nts_short": "CGA", "nts_long": "///1/1450,///1/1451,///1/1452" } ] }, { "index": 37, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ 68, 69 ], "summary": "[2] 5 4 [1.1478 1.2447 1.1484 1.2442] 2 2", "num_nts": 13, "nts_short": "GAAGUAGCGAAAC", "nts_long": "///1/1478,///1/1479,///1/1480,///1/1481,///1/1482,///1/1483,///1/1484,///1/2442,///1/2443,///1/2444,///1/2445,///1/2446,///1/2447", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AAGUA", "nts_long": "///1/1479,///1/1480,///1/1481,///1/1482,///1/1483" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/2443,///1/2444,///1/2445,///1/2446" } ] }, { "index": 38, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ 75, -31 ], "summary": "[2] 5 4 [1.3149 1.3185 1.3155 1.3180] 3 1", "num_nts": 13, "nts_short": "GUAUUUGCGGAGC", "nts_long": "///1/3149,///1/3150,///1/3151,///1/3152,///1/3153,///1/3154,///1/3155,///1/3180,///1/3181,///1/3182,///1/3183,///1/3184,///1/3185", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAUUU", "nts_long": "///1/3150,///1/3151,///1/3152,///1/3153,///1/3154" }, { "index": 2, "num_nts": 4, "nts_short": "GGAG", "nts_long": "///1/3181,///1/3182,///1/3183,///1/3184" } ] }, { "index": 39, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ -11, 27 ], "summary": "[2] 5 5 [1.412 2.27 1.418 2.21] 1 10", "num_nts": 14, "nts_short": "GUGAAAUACGGAUC", "nts_long": "///1/412,///1/413,///1/414,///1/415,///1/416,///1/417,///1/418,///2/21,///2/22,///2/23,///2/24,///2/25,///2/26,///2/27", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGAAA", "nts_long": "///1/413,///1/414,///1/415,///1/416,///1/417" }, { "index": 2, "num_nts": 5, "nts_short": "CGGAU", "nts_long": "///2/22,///2/23,///2/24,///2/25,///2/26" } ] }, { "index": 40, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 60, -24 ], "summary": "[2] 6 4 [1.1218 1.1350 1.1225 1.1345] 6 1", "num_nts": 14, "nts_short": "CUCAUCAGCUUAAG", "nts_long": "///1/1218,///1/1219,///1/1220,///1/1221,///1/1222,///1/1223,///1/1224,///1/1225,///1/1345,///1/1346,///1/1347,///1/1348,///1/1349,///1/1350", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UCAUCA", "nts_long": "///1/1219,///1/1220,///1/1221,///1/1222,///1/1223,///1/1224" }, { "index": 2, "num_nts": 4, "nts_short": "UUAA", "nts_long": "///1/1346,///1/1347,///1/1348,///1/1349" } ] }, { "index": 41, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 6, 7 ], "summary": "[2] 6 5 [1.82 1.103 1.89 1.97] 4 2", "num_nts": 15, "nts_short": "CUCAGUAAUGAAGCG", "nts_long": "///1/82,///1/83,///1/84,///1/85,///1/86,///1/87,///1/88,///1/89,///1/97,///1/98,///1/99,///1/100,///1/101,///1/102,///1/103", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UCAGUA", "nts_long": "///1/83,///1/84,///1/85,///1/86,///1/87,///1/88" }, { "index": 2, "num_nts": 5, "nts_short": "GAAGC", "nts_long": "///1/98,///1/99,///1/100,///1/101,///1/102" } ] }, { "index": 42, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 73, -29 ], "summary": "[2] 6 5 [1.3114 1.3132 1.3121 1.3126] 5 1 k-turn:undecided", "num_nts": 15, "nts_short": "CUUAGUACGGAACCG", "nts_long": "///1/3114,///1/3115,///1/3116,///1/3117,///1/3118,///1/3119,///1/3120,///1/3121,///1/3126,///1/3127,///1/3128,///1/3129,///1/3130,///1/3131,///1/3132", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUAGUA", "nts_long": "///1/3115,///1/3116,///1/3117,///1/3118,///1/3119,///1/3120" }, { "index": 2, "num_nts": 5, "nts_short": "GAACC", "nts_long": "///1/3127,///1/3128,///1/3129,///1/3130,///1/3131" } ] }, { "index": 43, "type": "asymmetric internal loop", "bridging_nts": [ 7, 4 ], "stem_indices": [ 79, 80 ], "summary": "[2] 7 4 [1.3274 1.3310 1.3282 1.3305] 2 3", "num_nts": 15, "nts_short": "UAAAAAUAGCCUGUA", "nts_long": "///1/3274,///1/3275,///1/3276,///1/3277,///1/3278,///1/3279,///1/3280,///1/3281,///1/3282,///1/3305,///1/3306,///1/3307,///1/3308,///1/3309,///1/3310", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AAAAAUA", "nts_long": "///1/3275,///1/3276,///1/3277,///1/3278,///1/3279,///1/3280,///1/3281" }, { "index": 2, "num_nts": 4, "nts_short": "CUGU", "nts_long": "///1/3306,///1/3307,///1/3308,///1/3309" } ] }, { "index": 44, "type": "asymmetric internal loop", "bridging_nts": [ 7, 6 ], "stem_indices": [ 36, -12 ], "summary": "[2] 7 6 [1.528 1.597 1.536 1.590] 5 1", "num_nts": 17, "nts_short": "GGAAAAAGAUGUAAUAC", "nts_long": "///1/528,///1/529,///1/530,///1/531,///1/532,///1/533,///1/534,///1/535,///1/536,///1/590,///1/591,///1/592,///1/593,///1/594,///1/595,///1/596,///1/597", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GAAAAAG", "nts_long": "///1/529,///1/530,///1/531,///1/532,///1/533,///1/534,///1/535" }, { "index": 2, "num_nts": 6, "nts_short": "GUAAUA", "nts_long": "///1/591,///1/592,///1/593,///1/594,///1/595,///1/596" } ] }, { "index": 45, "type": "asymmetric internal loop", "bridging_nts": [ 2, 12 ], "stem_indices": [ -10, 26 ], "summary": "[2] 2 12 [1.384 1.411 1.387 1.398] 1 4", "num_nts": 18, "nts_short": "GAACGAGUUAAAUAGUAC", "nts_long": "///1/384,///1/385,///1/386,///1/387,///1/398,///1/399,///1/400,///1/401,///1/402,///1/403,///1/404,///1/405,///1/406,///1/407,///1/408,///1/409,///1/410,///1/411", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/385,///1/386" }, { "index": 2, "num_nts": 12, "nts_short": "AGUUAAAUAGUA", "nts_long": "///1/399,///1/400,///1/401,///1/402,///1/403,///1/404,///1/405,///1/406,///1/407,///1/408,///1/409,///1/410" } ] }, { "index": 46, "type": "asymmetric internal loop", "bridging_nts": [ 8, 9 ], "stem_indices": [ 37, -13 ], "summary": "[2] 8 9 [1.542 1.583 1.551 1.573] 3 1", "num_nts": 21, "nts_short": "GGAAGGUGGCGUGUUUAUAGC", "nts_long": "///1/542,///1/543,///1/544,///1/545,///1/546,///1/547,///1/548,///1/549,///1/550,///1/551,///1/573,///1/574,///1/575,///1/576,///1/577,///1/578,///1/579,///1/580,///1/581,///1/582,///1/583", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GAAGGUGG", "nts_long": "///1/543,///1/544,///1/545,///1/546,///1/547,///1/548,///1/549,///1/550" }, { "index": 2, "num_nts": 9, "nts_short": "UGUUUAUAG", "nts_long": "///1/574,///1/575,///1/576,///1/577,///1/578,///1/579,///1/580,///1/581,///1/582" } ] } ], "num_junctions": 15, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 2, 0 ], "stem_indices": [ -15, 41, 45 ], "summary": "[3] 1 2 0 [1.686 1.974 1.688 1.831 1.834 1.973] 1 6 2", "num_nts": 9, "nts_short": "GUCGGACGU", "nts_long": "///1/686,///1/687,///1/688,///1/831,///1/832,///1/833,///1/834,///1/973,///1/974", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/687" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/832,///1/833" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 6, 0, 0 ], "stem_indices": [ 25, -10, -11 ], "summary": "[3] 6 0 0 [1.377 2.28 1.384 1.411 1.412 2.27] 2 1 1", "num_nts": 12, "nts_short": "AUGAAAAGCGCU", "nts_long": "///1/377,///1/378,///1/379,///1/380,///1/381,///1/382,///1/383,///1/384,///1/411,///1/412,///2/27,///2/28", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UGAAAA", "nts_long": "///1/378,///1/379,///1/380,///1/381,///1/382,///1/383" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 0, 5, 3 ], "stem_indices": [ 87, 88, -38 ], "summary": "[3] 0 5 3 [2.52 2.108 2.53 2.66 2.72 2.104] 3 4 1", "num_nts": 14, "nts_short": "ACGAUACGUAAUCU", "nts_long": "///2/52,///2/53,///2/66,///2/67,///2/68,///2/69,///2/70,///2/71,///2/72,///2/104,///2/105,///2/106,///2/107,///2/108", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "AUACG", "nts_long": "///2/67,///2/68,///2/69,///2/70,///2/71" }, { "index": 3, "num_nts": 3, "nts_short": "AUC", "nts_long": "///2/105,///2/106,///2/107" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 5, 2, 4 ], "stem_indices": [ 28, 29, 34 ], "summary": "[3] 5 2 4 [1.444 1.648 1.450 1.503 1.506 1.643] 12 3 8", "num_nts": 17, "nts_short": "AGUCUUAUAGGCAUAAU", "nts_long": "///1/444,///1/445,///1/446,///1/447,///1/448,///1/449,///1/450,///1/503,///1/504,///1/505,///1/506,///1/643,///1/644,///1/645,///1/646,///1/647,///1/648", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GUCUU", "nts_long": "///1/445,///1/446,///1/447,///1/448,///1/449" }, { "index": 2, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/504,///1/505" }, { "index": 3, "num_nts": 4, "nts_short": "AUAA", "nts_long": "///1/644,///1/645,///1/646,///1/647" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 1, 6, 4 ], "stem_indices": [ 83, -36, 84 ], "summary": "[3] 1 6 4 [1.3399 1.3492 1.3401 1.3415 1.3422 1.3487] 4 1 4", "num_nts": 17, "nts_short": "CCAUAAUGUGGCCCAAG", "nts_long": "///1/3399,///1/3400,///1/3401,///1/3415,///1/3416,///1/3417,///1/3418,///1/3419,///1/3420,///1/3421,///1/3422,///1/3487,///1/3488,///1/3489,///1/3490,///1/3491,///1/3492", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///1/3400" }, { "index": 2, "num_nts": 6, "nts_short": "AAUGUG", "nts_long": "///1/3416,///1/3417,///1/3418,///1/3419,///1/3420,///1/3421" }, { "index": 3, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///1/3488,///1/3489,///1/3490,///1/3491" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 0, 8, 4 ], "stem_indices": [ 34, 35, 38 ], "summary": "[3] 0 8 4 [1.513 1.636 1.514 1.612 1.621 1.631] 8 10 3", "num_nts": 18, "nts_short": "UCGAGGACUGCGCAAGGA", "nts_long": "///1/513,///1/514,///1/612,///1/613,///1/614,///1/615,///1/616,///1/617,///1/618,///1/619,///1/620,///1/621,///1/631,///1/632,///1/633,///1/634,///1/635,///1/636", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 8, "nts_short": "AGGACUGC", "nts_long": "///1/613,///1/614,///1/615,///1/616,///1/617,///1/618,///1/619,///1/620" }, { "index": 3, "num_nts": 4, "nts_short": "AAGG", "nts_long": "///1/632,///1/633,///1/634,///1/635" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 9, 8, 3 ], "stem_indices": [ -3, -4, 11 ], "summary": "[3] 9 8 3 [1.113 1.275 1.123 1.155 1.164 1.271] 1 1 2", "num_nts": 26, "nts_short": "CAAAUUUGAAAUAAUUUCAAGCGAAG", "nts_long": "///1/113,///1/114,///1/115,///1/116,///1/117,///1/118,///1/119,///1/120,///1/121,///1/122,///1/123,///1/155,///1/156,///1/157,///1/158,///1/159,///1/160,///1/161,///1/162,///1/163,///1/164,///1/271,///1/272,///1/273,///1/274,///1/275", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AAAUUUGAA", "nts_long": "///1/114,///1/115,///1/116,///1/117,///1/118,///1/119,///1/120,///1/121,///1/122" }, { "index": 2, "num_nts": 8, "nts_short": "AAUUUCAA", "nts_long": "///1/156,///1/157,///1/158,///1/159,///1/160,///1/161,///1/162,///1/163" }, { "index": 3, "num_nts": 3, "nts_short": "GAA", "nts_long": "///1/272,///1/273,///1/274" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 15, 4, 2 ], "stem_indices": [ 23, 24, 25 ], "summary": "[3] 15 4 2 [1.348 2.32 1.364 1.371 1.376 2.29] 2 2 2", "num_nts": 27, "nts_short": "CGAUAGCGAACAAGUAGCGAAAGCUUG", "nts_long": "///1/348,///1/349,///1/350,///1/351,///1/352,///1/353,///1/354,///1/355,///1/356,///1/357,///1/358,///1/359,///1/360,///1/361,///1/362,///1/363,///1/364,///1/371,///1/372,///1/373,///1/374,///1/375,///1/376,///2/29,///2/30,///2/31,///2/32", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 15, "nts_short": "GAUAGCGAACAAGUA", "nts_long": "///1/349,///1/350,///1/351,///1/352,///1/353,///1/354,///1/355,///1/356,///1/357,///1/358,///1/359,///1/360,///1/361,///1/362,///1/363" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/372,///1/373,///1/374,///1/375" }, { "index": 3, "num_nts": 2, "nts_short": "UU", "nts_long": "///2/30,///2/31" } ] }, { "index": 9, "type": "4-way junction", "bridging_nts": [ 1, 0, 1, 1 ], "stem_indices": [ 72, -28, -30, 76 ], "summary": "[4] 1 0 1 1 [1.3106 1.3232 1.3108 1.3138 1.3139 1.3194 1.3196 1.3230] 4 1 1 4", "num_nts": 11, "nts_short": "UAAUCGCUGUG", "nts_long": "///1/3106,///1/3107,///1/3108,///1/3138,///1/3139,///1/3194,///1/3195,///1/3196,///1/3230,///1/3231,///1/3232", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///1/3107" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 1, "nts_short": "C", "nts_long": "///1/3195" }, { "index": 4, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3231" } ] }, { "index": 10, "type": "4-way junction", "bridging_nts": [ 2, 1, 0, 5 ], "stem_indices": [ 40, -15, 47, -26 ], "summary": "[4] 2 1 0 5 [1.683 1.1471 1.686 1.974 1.976 1.1409 1.1410 1.1465] 6 1 6 1", "num_nts": 16, "nts_short": "GGAGUUCGCGCAGAUC", "nts_long": "///1/683,///1/684,///1/685,///1/686,///1/974,///1/975,///1/976,///1/1409,///1/1410,///1/1465,///1/1466,///1/1467,///1/1468,///1/1469,///1/1470,///1/1471", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/684,///1/685" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///1/975" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 5, "nts_short": "CAGAU", "nts_long": "///1/1466,///1/1467,///1/1468,///1/1469,///1/1470" } ] }, { "index": 11, "type": "4-way junction", "bridging_nts": [ 0, 4, 5, 2 ], "stem_indices": [ 8, -3, -9, 21 ], "summary": "[4] 0 4 5 2 [1.112 1.327 1.113 1.275 1.280 1.301 1.307 1.324] 3 1 1 5", "num_nts": 19, "nts_short": "UCGAGUCGCUAAAUGUAAA", "nts_long": "///1/112,///1/113,///1/275,///1/276,///1/277,///1/278,///1/279,///1/280,///1/301,///1/302,///1/303,///1/304,///1/305,///1/306,///1/307,///1/324,///1/325,///1/326,///1/327", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "AGUC", "nts_long": "///1/276,///1/277,///1/278,///1/279" }, { "index": 3, "num_nts": 5, "nts_short": "UAAAU", "nts_long": "///1/302,///1/303,///1/304,///1/305,///1/306" }, { "index": 4, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/325,///1/326" } ] }, { "index": 12, "type": "5-way junction", "bridging_nts": [ 1, 6, 4, 0, 1 ], "stem_indices": [ 3, -1, 87, 90, 91 ], "summary": "[5] 1 6 4 0 1 [1.20 2.147 1.22 2.43 2.50 2.110 2.115 2.123 2.124 2.145] 6 1 3 3 5", "num_nts": 22, "nts_short": "AGGCGAUGAAGUGAACGCGCAU", "nts_long": "///1/20,///1/21,///1/22,///2/43,///2/44,///2/45,///2/46,///2/47,///2/48,///2/49,///2/50,///2/110,///2/111,///2/112,///2/113,///2/114,///2/115,///2/123,///2/124,///2/145,///2/146,///2/147", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///1/21" }, { "index": 2, "num_nts": 6, "nts_short": "GAUGAA", "nts_long": "///2/44,///2/45,///2/46,///2/47,///2/48,///2/49" }, { "index": 3, "num_nts": 4, "nts_short": "GAAC", "nts_long": "///2/111,///2/112,///2/113,///2/114" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 5, "num_nts": 1, "nts_short": "A", "nts_long": "///2/146" } ] }, { "index": 13, "type": "6-way junction", "bridging_nts": [ 0, 0, 0, 1, 1, 5 ], "stem_indices": [ -14, 39, 40, 68, -27, 70 ], "summary": "[6] 0 0 0 1 1 5 [1.661 1.2463 1.662 1.677 1.678 1.1476 1.1477 1.2448 1.2450 1.2464 1.2466 1.2457] 1 4 6 2 1 5", "num_nts": 19, "nts_short": "CCGAUGCACGGCGGGAACG", "nts_long": "///1/661,///1/662,///1/677,///1/678,///1/1476,///1/1477,///1/2448,///1/2449,///1/2450,///1/2464,///1/2465,///1/2466,///1/2457,///1/2458,///1/2459,///1/2460,///1/2461,///1/2462,///1/2463", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "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": "A", "nts_long": "///1/2449" }, { "index": 5, "num_nts": 1, "nts_short": "G", "nts_long": "///1/2465" }, { "index": 6, "num_nts": 5, "nts_short": "GGAAC", "nts_long": "///1/2458,///1/2459,///1/2460,///1/2461,///1/2462" } ] }, { "index": 14, "type": "6-way junction", "bridging_nts": [ 4, 9, 3, 3, 9, 2 ], "stem_indices": [ -1, -2, 5, 6, 8, 22 ], "summary": "[6] 4 9 3 3 9 2 [1.22 2.43 1.27 1.58 1.68 1.75 1.79 1.106 1.110 1.329 1.339 2.40] 1 1 2 4 3 7", "num_nts": 42, "nts_short": "GACUACGGAAAAGAAAAUGAUUAAAAGCUAAAUAUUGGCAUC", "nts_long": "///1/22,///1/23,///1/24,///1/25,///1/26,///1/27,///1/58,///1/59,///1/60,///1/61,///1/62,///1/63,///1/64,///1/65,///1/66,///1/67,///1/68,///1/75,///1/76,///1/77,///1/78,///1/79,///1/106,///1/107,///1/108,///1/109,///1/110,///1/329,///1/330,///1/331,///1/332,///1/333,///1/334,///1/335,///1/336,///1/337,///1/338,///1/339,///2/40,///2/41,///2/42,///2/43", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "ACUA", "nts_long": "///1/23,///1/24,///1/25,///1/26" }, { "index": 2, "num_nts": 9, "nts_short": "GAAAAGAAA", "nts_long": "///1/59,///1/60,///1/61,///1/62,///1/63,///1/64,///1/65,///1/66,///1/67" }, { "index": 3, "num_nts": 3, "nts_short": "GAU", "nts_long": "///1/76,///1/77,///1/78" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/107,///1/108,///1/109" }, { "index": 5, "num_nts": 9, "nts_short": "UAAAUAUUG", "nts_long": "///1/330,///1/331,///1/332,///1/333,///1/334,///1/335,///1/336,///1/337,///1/338" }, { "index": 6, "num_nts": 2, "nts_short": "AU", "nts_long": "///2/41,///2/42" } ] }, { "index": 15, "type": "7-way junction", "bridging_nts": [ 4, 1, 3, 4, 3, 0, 4 ], "stem_indices": [ 47, -20, -21, 53, 56, 57, 63 ], "summary": "[7] 4 1 3 4 3 0 4 [1.981 1.1404 1.986 1.999 1.1001 1.1144 1.1148 1.1172 1.1177 1.1188 1.1192 1.1369 1.1370 1.1399] 6 1 1 4 3 7 9", "num_nts": 33, "nts_short": "CGAAGUAGCGUGGGCGAUGCGAACGCCGAGUAG", "nts_long": "///1/981,///1/982,///1/983,///1/984,///1/985,///1/986,///1/999,///1/1000,///1/1001,///1/1144,///1/1145,///1/1146,///1/1147,///1/1148,///1/1172,///1/1173,///1/1174,///1/1175,///1/1176,///1/1177,///1/1188,///1/1189,///1/1190,///1/1191,///1/1192,///1/1369,///1/1370,///1/1399,///1/1400,///1/1401,///1/1402,///1/1403,///1/1404", "num_stems": 7, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAG", "nts_long": "///1/982,///1/983,///1/984,///1/985" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1000" }, { "index": 3, "num_nts": 3, "nts_short": "UGG", "nts_long": "///1/1145,///1/1146,///1/1147" }, { "index": 4, "num_nts": 4, "nts_short": "GAUG", "nts_long": "///1/1173,///1/1174,///1/1175,///1/1176" }, { "index": 5, "num_nts": 3, "nts_short": "AAC", "nts_long": "///1/1189,///1/1190,///1/1191" }, { "index": 6, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 7, "num_nts": 4, "nts_short": "AGUA", "nts_long": "///1/1400,///1/1401,///1/1402,///1/1403" } ] } ], "num_ssSegments": 39, "ssSegments": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3" }, { "index": 2, "is_broken": true, "num_nts": 10, "nts_short": "UGAACAAUAA", "nts_long": "///1/32,///1/33,///1/34,///1/35,///1/36,///1/48,///1/49,///1/50,///1/51,///1/52" }, { "index": 3, "is_broken": true, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/91,///1/94,///1/95" }, { "index": 4, "num_nts": 3, "nts_short": "UAA", "nts_long": "///1/193,///1/194,///1/195" }, { "index": 5, "num_nts": 1, "nts_short": "A", "nts_long": "///1/220" }, { "index": 6, "num_nts": 6, "nts_short": "GUCUUU", "nts_long": "///1/234,///1/235,///1/236,///1/237,///1/238,///1/239" }, { "index": 7, "is_broken": true, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/287,///1/294" }, { "index": 8, "is_broken": true, "num_nts": 4, "nts_short": "GUAU", "nts_long": "///1/312,///1/313,///1/314,///1/319" }, { "index": 9, "num_nts": 5, "nts_short": "GGAAG", "nts_long": "///1/428,///1/429,///1/430,///1/431,///1/432" }, { "index": 10, "is_broken": true, "num_nts": 2, "nts_short": "UC", "nts_long": "///1/473,///1/477" }, { "index": 11, "num_nts": 1, "nts_short": "G", "nts_long": "///1/660" }, { "index": 12, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/701,///1/702" }, { "index": 13, "is_broken": true, "num_nts": 5, "nts_short": "GAAGU", "nts_long": "///1/730,///1/731,///1/732,///1/749,///1/750" }, { "index": 14, "is_broken": true, "num_nts": 6, "nts_short": "ACCAGA", "nts_long": "///1/772,///1/773,///1/774,///1/816,///1/817,///1/818" }, { "index": 15, "is_broken": true, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///1/847,///1/848,///1/956,///1/957" }, { "index": 16, "is_broken": true, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/990,///1/995" }, { "index": 17, "is_broken": true, "num_nts": 4, "nts_short": "AGUA", "nts_long": "///1/1024,///1/1025,///1/1088,///1/1089" }, { "index": 18, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/1208,///1/1209,///1/1210" }, { "index": 19, "is_broken": true, "num_nts": 6, "nts_short": "ACGAAA", "nts_long": "///1/1226,///1/1227,///1/1232,///1/1233,///1/1234,///1/1235" }, { "index": 20, "is_broken": true, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/1248,///1/1319" }, { "index": 21, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1331" }, { "index": 22, "num_nts": 1, "nts_short": "G", "nts_long": "///1/1344" }, { "index": 23, "num_nts": 4, "nts_short": "UCUA", "nts_long": "///1/2437,///1/2438,///1/2439,///1/2440" }, { "index": 24, "is_broken": true, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/3156,///1/3179" }, { "index": 25, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/3269,///1/3270" }, { "index": 26, "num_nts": 1, "nts_short": "G", "nts_long": "///1/3289" }, { "index": 27, "num_nts": 7, "nts_short": "GUAGAAG", "nts_long": "///1/3313,///1/3314,///1/3315,///1/3316,///1/3317,///1/3318,///1/3319" }, { "index": 28, "num_nts": 10, "nts_short": "GAAAUUCCAU", "nts_long": "///1/3366,///1/3367,///1/3368,///1/3369,///1/3370,///1/3371,///1/3372,///1/3373,///1/3374,///1/3375" }, { "index": 29, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/3429,///1/3430" }, { "index": 30, "is_broken": true, "num_nts": 4, "nts_short": "UGAG", "nts_long": "///1/3433,///1/3434,///1/3471,///1/3472" }, { "index": 31, "num_nts": 1, "nts_short": "U", "nts_long": "///1/3475" }, { "index": 32, "num_nts": 3, "nts_short": "AAA", "nts_long": "///2/9,///2/10,///2/11" }, { "index": 33, "is_broken": true, "num_nts": 7, "nts_short": "GAAUUGA", "nts_long": "///2/78,///2/79,///2/80,///2/81,///2/82,///2/95,///2/96" }, { "index": 34, "num_nts": 1, "nts_short": "C", "nts_long": "///2/118" }, { "index": 35, "num_nts": 1, "nts_short": "U", "nts_long": "///2/164" }, { "index": 36, "num_nts": 11, "nts_short": "ACAAUCUUCUC", "nts_long": "///6/1,///6/2,///6/3,///6/4,///6/5,///6/6,///6/7,///6/8,///6/9,///6/10,///6/11" }, { "index": 37, "num_nts": 10, "nts_short": "UUUUUUUUAA", "nts_long": "///6/23,///6/24,///6/25,///6/26,///6/27,///6/28,///6/29,///6/30,///6/31,///6/32" }, { "index": 38, "is_broken": true, "num_nts": 7, "nts_short": "UUGAGAA", "nts_long": "///6/39,///6/40,///6/41,///6/42,///6/56,///6/57,///6/58" }, { "index": 39, "num_nts": 11, "nts_short": "GUUUUUUUUUU", "nts_long": "///6/64,///6/65,///6/66,///6/67,///6/68,///6/69,///6/70,///6/71,///6/72,///6/73,///6/74" } ], "num_Aminors": 39, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/34 vs ///1/841,///1/963", "A_nt1": { "desc": "///1/34 vs ///1/841", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/34 vs ///1/963", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.05],N1*O2(carbonyl)[3.25]" } }, { "index": 2, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///1/34 vs ///1/842,///1/962", "A_nt1": { "desc": "///1/34 vs ///1/842", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.11],N3-O2'(hydroxyl)[2.31]" }, "A_nt2": { "desc": "///1/34 vs ///1/962", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 3, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/35 vs ///1/841,///1/963", "A_nt1": { "desc": "///1/35 vs ///1/841", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-N3[3.01],N3-N2(amino)[3.17]" }, "A_nt2": { "desc": "///1/35 vs ///1/963", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 4, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/67 vs ///1/308,///1/323", "A_nt1": { "desc": "///1/67 vs ///1/308", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.52],N3-N2(amino)[3.19]" }, "A_nt2": { "desc": "///1/67 vs ///1/323", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[2.86],O2'(hydroxyl)-O2'(hydroxyl)[2.62],O2'(hydroxyl)-O2(carbonyl)[2.68]" } }, { "index": 5, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///1/70 vs ///1/310,///1/321", "A_nt1": { "desc": "///1/70 vs ///1/310", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/70 vs ///1/321", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.82],N1-O2'(hydroxyl)[2.46]" } }, { "index": 6, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/71 vs ///1/311,///1/320", "A_nt1": { "desc": "///1/71 vs ///1/311", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.80],N6(amino)-N3[3.03],N1-N2(amino)[3.04]" }, "A_nt2": { "desc": "///1/71 vs ///1/320", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 7, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///1/194 vs ///1/215,///1/219", "A_nt1": { "desc": "///1/194 vs ///1/215", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.61]" }, "A_nt2": { "desc": "///1/194 vs ///1/219", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 8, "type": "I", "desc_short": "A vs U-A (WC)", "desc_long": "///1/195 vs ///1/214,///1/229", "A_nt1": { "desc": "///1/195 vs ///1/214", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.51],O2'(hydroxyl)-O2(carbonyl)[2.75]" }, "A_nt2": { "desc": "///1/195 vs ///1/229", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.62]" } }, { "index": 9, "type": "II", "desc_short": "A vs G-U (Wobble)", "desc_long": "///1/304 vs ///1/307,///1/324", "A_nt1": { "desc": "///1/304 vs ///1/307", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.07],N3-O2'(hydroxyl)[2.84]" }, "A_nt2": { "desc": "///1/304 vs ///1/324", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 10, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///1/335 vs ///1/27,///1/58", "A_nt1": { "desc": "///1/335 vs ///1/27", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91],N3-O2'(hydroxyl)[2.45]" }, "A_nt2": { "desc": "///1/335 vs ///1/58", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 11, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/346 vs ///1/1414,///1/1460", "A_nt1": { "desc": "///1/346 vs ///1/1414", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O3'-O2'(hydroxyl)[3.05],N3-N2(amino)[3.47]" }, "A_nt2": { "desc": "///1/346 vs ///1/1460", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.00]" } }, { "index": 12, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///1/352 vs ///1/348,///2/32", "A_nt1": { "desc": "///1/352 vs ///1/348", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.70],N3-O2'(hydroxyl)[2.82]" }, "A_nt2": { "desc": "///1/352 vs ///2/32", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 13, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/369 vs ///1/845,///1/959", "A_nt1": { "desc": "///1/369 vs ///1/845", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.01],N3-N2(amino)[3.30]" }, "A_nt2": { "desc": "///1/369 vs ///1/959", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.54]" } }, { "index": 14, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///1/416 vs ///1/680,///1/1474", "A_nt1": { "desc": "///1/416 vs ///1/680", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.83],N3-O2'(hydroxyl)[2.64]" }, "A_nt2": { "desc": "///1/416 vs ///1/1474", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 15, "type": "X", "desc_short": "A vs U-U (--)", "desc_long": "///1/579 vs ///1/548,///1/576", "A_nt1": { "desc": "///1/579 vs ///1/548", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/579 vs ///1/576", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.27]" } }, { "index": 16, "type": "X", "desc_short": "A vs G-U (--)", "desc_long": "///1/579 vs ///1/549,///1/576", "A_nt1": { "desc": "///1/579 vs ///1/549", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/579 vs ///1/576", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.27]" } }, { "index": 17, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/644 vs ///1/506,///1/643", "A_nt1": { "desc": "///1/644 vs ///1/506", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/644 vs ///1/643", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "O5'-O2'(hydroxyl)[3.03],O4'-O2'(hydroxyl)[2.90]" } }, { "index": 18, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/685 vs ///1/834,///1/973", "A_nt1": { "desc": "///1/685 vs ///1/834", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.70],O2'(hydroxyl)-O2(carbonyl)[2.52]" }, "A_nt2": { "desc": "///1/685 vs ///1/973", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.39],N3-N2(amino)[2.99]" } }, { "index": 19, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/718 vs ///1/343,///2/36", "A_nt1": { "desc": "///1/718 vs ///1/343", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/718 vs ///2/36", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.98],N1-O2'(hydroxyl)[2.64]" } }, { "index": 20, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/833 vs ///1/688,///1/831", "A_nt1": { "desc": "///1/833 vs ///1/688", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/833 vs ///1/831", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-N7[3.28]" } }, { "index": 21, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/983 vs ///1/1001,///1/1144", "A_nt1": { "desc": "///1/983 vs ///1/1001", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O3'-O2'(hydroxyl)[2.88],O2'(hydroxyl)-O2'(hydroxyl)[3.12]" }, "A_nt2": { "desc": "///1/983 vs ///1/1144", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.97],N3-N2(amino)[3.14]" } }, { "index": 22, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1181 vs ///1/2456,///1/2467", "A_nt1": { "desc": "///1/1181 vs ///1/2456", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1181 vs ///1/2467", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.30]" } }, { "index": 23, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1181 vs ///1/2457,///1/2466", "A_nt1": { "desc": "///1/1181 vs ///1/2457", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.43]" }, "A_nt2": { "desc": "///1/1181 vs ///1/2466", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 24, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1185 vs ///1/1149,///1/1171", "A_nt1": { "desc": "///1/1185 vs ///1/1149", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.94],N1-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///1/1185 vs ///1/1171", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 25, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1200 vs ///1/1178,///1/1187", "A_nt1": { "desc": "///1/1200 vs ///1/1178", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.13]" }, "A_nt2": { "desc": "///1/1200 vs ///1/1187", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 26, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1201 vs ///1/1178,///1/1187", "A_nt1": { "desc": "///1/1201 vs ///1/1178", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.30],N3-N2(amino)[3.04]" }, "A_nt2": { "desc": "///1/1201 vs ///1/1187", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[2.97],O2'(hydroxyl)-O2'(hydroxyl)[2.62],O2'(hydroxyl)-O2(carbonyl)[2.88]" } }, { "index": 27, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1210 vs ///1/1203,///1/1358", "A_nt1": { "desc": "///1/1210 vs ///1/1203", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.82],N3-N2(amino)[3.07]" }, "A_nt2": { "desc": "///1/1210 vs ///1/1358", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.34],O2'(hydroxyl)-O2(carbonyl)[3.31]" } }, { "index": 28, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1361 vs ///1/1177,///1/1188", "A_nt1": { "desc": "///1/1361 vs ///1/1177", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.89]" }, "A_nt2": { "desc": "///1/1361 vs ///1/1188", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 29, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///1/1428 vs ///1/412,///2/27", "A_nt1": { "desc": "///1/1428 vs ///1/412", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1428 vs ///2/27", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.99],N3-O2'(hydroxyl)[2.80]" } }, { "index": 30, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1441 vs ///1/976,///1/1409", "A_nt1": { "desc": "///1/1441 vs ///1/976", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.73],O2'(hydroxyl)-O2(carbonyl)[3.10]" }, "A_nt2": { "desc": "///1/1441 vs ///1/1409", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.11],N3-N2(amino)[3.33]" } }, { "index": 31, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/1469 vs ///1/835,///1/972", "A_nt1": { "desc": "///1/1469 vs ///1/835", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/1469 vs ///1/972", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.76],O2'(hydroxyl)-N3[3.28],N3-N2(amino)[3.55]" } }, { "index": 32, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///1/3107 vs ///1/3139,///1/3194", "A_nt1": { "desc": "///1/3107 vs ///1/3139", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.23]" }, "A_nt2": { "desc": "///1/3107 vs ///1/3194", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O3'-O2'(hydroxyl)[3.48]" } }, { "index": 33, "type": "X", "desc_short": "A vs A-C (--)", "desc_long": "///1/3129 vs ///1/3117,///1/3130", "A_nt1": { "desc": "///1/3129 vs ///1/3117", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-OP1[3.24]" }, "A_nt2": { "desc": "///1/3129 vs ///1/3130", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 34, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///1/3145 vs ///1/3143,///1/3190", "A_nt1": { "desc": "///1/3145 vs ///1/3143", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/3145 vs ///1/3190", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.01],N6(amino)-N3[2.33]" } }, { "index": 35, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///1/3279 vs ///1/3282,///1/3305", "A_nt1": { "desc": "///1/3279 vs ///1/3282", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.31]" }, "A_nt2": { "desc": "///1/3279 vs ///1/3305", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 36, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///1/3374 vs ///1/508,///1/641", "A_nt1": { "desc": "///1/3374 vs ///1/508", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///1/3374 vs ///1/641", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.73],N6(amino)-N3[2.99],N1-N2(amino)[2.74]" } }, { "index": 37, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/48 vs ///1/22,///2/43", "A_nt1": { "desc": "///2/48 vs ///1/22", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.71],N3-N2(amino)[3.23]" }, "A_nt2": { "desc": "///2/48 vs ///2/43", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.97]" } }, { "index": 38, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/67 vs ///2/53,///2/66", "A_nt1": { "desc": "///2/67 vs ///2/53", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/67 vs ///2/66", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.04]" } }, { "index": 39, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/69 vs ///2/54,///2/65", "A_nt1": { "desc": "///2/69 vs ///2/54", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.63],N3-N2(amino)[2.87]" }, "A_nt2": { "desc": "///2/69 vs ///2/65", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.70],O2'(hydroxyl)-O2(carbonyl)[2.48]" } } ], "num_riboseZippers": 11, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "ACAU", "nts_long": "///1/26,///1/27,///1/335,///1/336" }, { "index": 2, "num_nts": 4, "nts_short": "AAGA", "nts_long": "///1/34,///1/35,///1/841,///1/842" }, { "index": 3, "num_nts": 4, "nts_short": "AGAU", "nts_long": "///1/63,///1/64,///1/77,///1/78" }, { "index": 4, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///1/106,///1/107,///1/332,///1/333" }, { "index": 5, "num_nts": 4, "nts_short": "AAUC", "nts_long": "///1/194,///1/195,///1/214,///1/215" }, { "index": 6, "num_nts": 4, "nts_short": "GAGU", "nts_long": "///1/368,///1/369,///1/845,///1/846" }, { "index": 7, "num_nts": 4, "nts_short": "AACC", "nts_long": "///1/416,///1/417,///1/679,///1/680" }, { "index": 8, "num_nts": 4, "nts_short": "CCGA", "nts_long": "///1/976,///1/977,///1/1440,///1/1441" }, { "index": 9, "num_nts": 4, "nts_short": "CGAA", "nts_long": "///1/1187,///1/1188,///1/1200,///1/1201" }, { "index": 10, "num_nts": 4, "nts_short": "GACC", "nts_long": "///1/1209,///1/1210,///1/1358,///1/1359" }, { "index": 11, "num_nts": 4, "nts_short": "AGUC", "nts_long": "///1/1428,///1/1429,///2/26,///2/27" } ], "num_Kturns": 3, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 36, "bounding_stems": [ 65, 66 ], "Cstem_index": 65, "NCstem_index": 66, "Cstem_pair": "U-A (///1/1422,///1/1453) WC", "NCstem_pair": "G-U (///1/1429,///1/1449) Wobble", "GA_pair": "G-A (///1/1426,///1/1452) Sheared", "bending_angle": 45.082, "strand1": { "num_nts": 12, "nts_short": "GUGACGAAGCCU", "nts_long": "///1/1421,///1/1422,///1/1423,///1/1424,///1/1425,///1/1426,///1/1427,///1/1428,///1/1429,///1/1430,///1/1431,///1/1432" }, "strand2": { "num_nts": 9, "nts_short": "GGGUCGAAC", "nts_long": "///1/1446,///1/1447,///1/1448,///1/1449,///1/1450,///1/1451,///1/1452,///1/1453,///1/1454" } }, { "index": 2, "type": "Undecided case", "iloop_index": 33, "bounding_stems": [ 77, 76 ], "Cstem_index": 77, "NCstem_index": 76, "Cstem_pair": "C-G (///1/3222,///1/3204) WC", "NCstem_pair": "U-A (///1/3227,///1/3199) WC", "GA_pair": "G-A (///1/3224,///1/3202) Sheared", "bending_angle": 33.111, "strand1": { "num_nts": 11, "nts_short": "GCCAGAAUCCG", "nts_long": "///1/3220,///1/3221,///1/3222,///1/3223,///1/3224,///1/3225,///1/3226,///1/3227,///1/3228,///1/3229,///1/3230" }, "strand2": { "num_nts": 11, "nts_short": "UGGAUAACGGC", "nts_long": "///1/3196,///1/3197,///1/3198,///1/3199,///1/3200,///1/3201,///1/3202,///1/3203,///1/3204,///1/3205,///1/3206" } }, { "index": 3, "type": "Undecided case", "iloop_index": 42, "bounding_stems": [ -29, 73 ], "Cstem_index": -29, "NCstem_index": 73, "Cstem_pair": "G-C (///1/3126,///1/3121) WC", "NCstem_pair": "G-C (///1/3132,///1/3114) WC", "GA_pair": "G-A (///1/3127,///1/3120) Sheared", "bending_angle": 36.615, "strand1": { "num_nts": 11, "nts_short": "GGAACCGUUGA", "nts_long": "///1/3126,///1/3127,///1/3128,///1/3129,///1/3130,///1/3131,///1/3132,///1/3133,///1/3134,///1/3135,///1/3136" }, "strand2": { "num_nts": 12, "nts_short": "UCAACUUAGUAC", "nts_long": "///1/3110,///1/3111,///1/3112,///1/3113,///1/3114,///1/3115,///1/3116,///1/3117,///1/3118,///1/3119,///1/3120,///1/3121" } } ], "num_splayUnits": 143, "splayUnits": [ { "index": 1, "num_nts": 3, "nts_short": "AUC", "nts_long": "///1/13,///1/14,///1/15" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/49,///1/50" }, { "index": 3, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/66,///1/67,///1/68" }, { "index": 4, "num_nts": 3, "nts_short": "CCA", "nts_long": "///1/72,///1/73,///1/74" }, { "index": 5, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/76,///1/77" }, { "index": 6, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/108,///1/109" }, { "index": 7, "num_nts": 3, "nts_short": "AUU", "nts_long": "///1/116,///1/117,///1/118" }, { "index": 8, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/119,///1/120" }, { "index": 9, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/121,///1/122" }, { "index": 10, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/135,///1/136" }, { "index": 11, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/137,///1/138" }, { "index": 12, "num_nts": 3, "nts_short": "UUG", "nts_long": "///1/152,///1/153,///1/154" }, { "index": 13, "num_nts": 3, "nts_short": "CAA", "nts_long": "///1/161,///1/162,///1/163" }, { "index": 14, "num_nts": 4, "nts_short": "UGAG", "nts_long": "///1/174,///1/175,///1/176,///1/177" }, { "index": 15, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/193,///1/194" }, { "index": 16, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/195,///1/196" }, { "index": 17, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/197,///1/198" }, { "index": 18, "num_nts": 2, "nts_short": "CA", "nts_long": "///1/207,///1/208" }, { "index": 19, "num_nts": 3, "nts_short": "AGA", "nts_long": "///1/216,///1/217,///1/218" }, { "index": 20, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/219,///1/220" }, { "index": 21, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/224,///1/225" }, { "index": 22, "num_nts": 3, "nts_short": "GAA", "nts_long": "///1/227,///1/228,///1/229" }, { "index": 23, "num_nts": 2, "nts_short": "CC", "nts_long": "///1/230,///1/231" }, { "index": 24, "num_nts": 3, "nts_short": "UUG", "nts_long": "///1/238,///1/239,///1/240" }, { "index": 25, "num_nts": 4, "nts_short": "UAUA", "nts_long": "///1/258,///1/259,///1/260,///1/261" }, { "index": 26, "num_nts": 3, "nts_short": "UUU", "nts_long": "///1/268,///1/269,///1/270" }, { "index": 27, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/272,///1/273" }, { "index": 28, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/275,///1/276" }, { "index": 29, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/305,///1/306" }, { "index": 30, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/326,///1/327" }, { "index": 31, "num_nts": 3, "nts_short": "UUG", "nts_long": "///1/336,///1/337,///1/338" }, { "index": 32, "num_nts": 3, "nts_short": "GAC", "nts_long": "///1/345,///1/346,///1/347" }, { "index": 33, "num_nts": 3, "nts_short": "AUA", "nts_long": "///1/350,///1/351,///1/352" }, { "index": 34, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/356,///1/357" }, { "index": 35, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/375,///1/376" }, { "index": 36, "num_nts": 2, "nts_short": "AU", "nts_long": "///1/377,///1/378" }, { "index": 37, "num_nts": 2, "nts_short": "AA", "nts_long": "///1/385,///1/386" }, { "index": 38, "num_nts": 3, "nts_short": "AUA", "nts_long": "///1/405,///1/406,///1/407" }, { "index": 39, "num_nts": 4, "nts_short": "UACG", "nts_long": "///1/409,///1/410,///1/411,///1/412" }, { "index": 40, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/427,///1/428" }, { "index": 41, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/429,///1/430" }, { "index": 42, "num_nts": 2, "nts_short": "CU", "nts_long": "///1/447,///1/448" }, { "index": 43, "num_nts": 3, "nts_short": "AUC", "nts_long": "///1/461,///1/462,///1/463" }, { "index": 44, "num_nts": 3, "nts_short": "AGU", "nts_long": "///1/464,///1/465,///1/466" }, { "index": 45, "num_nts": 3, "nts_short": "UGA", "nts_long": "///1/492,///1/493,///1/494" }, { "index": 46, "num_nts": 3, "nts_short": "GUG", "nts_long": "///1/499,///1/500,///1/501" }, { "index": 47, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/504,///1/505" }, { "index": 48, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///1/529,///1/530,///1/531,///1/532" }, { "index": 49, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/545,///1/546" }, { "index": 50, "num_nts": 3, "nts_short": "CAC", "nts_long": "///1/601,///1/602,///1/603" }, { "index": 51, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/615,///1/616" }, { "index": 52, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/618,///1/619" }, { "index": 53, "num_nts": 3, "nts_short": "GUG", "nts_long": "///1/627,///1/628,///1/629" }, { "index": 54, "num_nts": 3, "nts_short": "CAA", "nts_long": "///1/631,///1/632,///1/633" }, { "index": 55, "num_nts": 3, "nts_short": "GGA", "nts_long": "///1/634,///1/635,///1/636" }, { "index": 56, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/645,///1/646" }, { "index": 57, "num_nts": 2, "nts_short": "GC", "nts_long": "///1/660,///1/661" }, { "index": 58, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/677,///1/678" }, { "index": 59, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/705,///1/706" }, { "index": 60, "num_nts": 2, "nts_short": "UU", "nts_long": "///1/707,///1/708" }, { "index": 61, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/713,///1/714" }, { "index": 62, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/715,///1/716" }, { "index": 63, "num_nts": 3, "nts_short": "AAA", "nts_long": "///1/717,///1/718,///1/719" }, { "index": 64, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/768,///1/769" }, { "index": 65, "num_nts": 2, "nts_short": "AC", "nts_long": "///1/833,///1/834" }, { "index": 66, "num_nts": 3, "nts_short": "UAG", "nts_long": "///1/964,///1/965,///1/966" }, { "index": 67, "num_nts": 3, "nts_short": "AGC", "nts_long": "///1/968,///1/969,///1/970" }, { "index": 68, "num_nts": 3, "nts_short": "UUC", "nts_long": "///1/974,///1/975,///1/976" }, { "index": 69, "num_nts": 2, "nts_short": "GU", "nts_long": "///1/985,///1/986" }, { "index": 70, "num_nts": 2, "nts_short": "AG", "nts_long": "///1/1010,///1/1011" }, { "index": 71, "num_nts": 3, "nts_short": "AGU", "nts_long": "///1/1015,///1/1016,///1/1017" }, { "index": 72, "num_nts": 2, "nts_short": "GG", "nts_long": "///1/1146,///1/1147" }, { "index": 73, "num_nts": 2, "nts_short": "UA", "nts_long": "///1/1159,///1/1160" }, { "index": 74, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1180,///1/1181" }, { "index": 75, "num_nts": 2, "nts_short": "GA", "nts_long": "///1/1183,///1/1184" }, { "index": 76, "num_nts": 2, "nts_short": "AC", "nts_long": "///1/1185,///1/1186" }, { "index": 77, "num_nts": 2, "nts_short": "CG", "nts_long": "///1/1191,///1/1192" }, { "index": 78, "num_nts": 2, "nts_short": "UG", "nts_long": "///1/1204,///1/1205" }, { "index": 79, "num_nts": 3, "nts_short": "AUG", "nts_long": "///1/1211,///1/1212,///1/1213" }, { "index": 80, "num_nts": 4, "nts_short": "AUCA", "nts_long": "///1/1221,///1/1222,///1/1223,///1/1224" }, { "index": 81, "num_nts": 3, "nts_short": "GUG", "nts_long": "///1/1238,///1/1239,///1/1240" }, { "index": 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"///T/142/OG", "atom2_id": "///T/144/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 9001, "atom1_serNum": 80192, "atom2_serNum": 80213, "donAcc_type": "standard", "distance": 3.173, "atom1_id": "///T/143/O", "atom2_id": "///T/146/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": "8euy", "num_aaChains": 37, "aaChains": "3=192,4=210,5=340,A=254,B=332,C=329,D=406,E=170,F=240,G=164,H=155,J=89,K=243,L=116,M=125,N=166,O=187,P=145,Q=135,S=168,T=19,V=113,Y=125,b=120,e=124,f=106,h=121,i=98,j=71,m=92,o=129,r=50,t=23,u=102,v=161,x=305,y=198", "num_naChains": 3, "naChains": "1=1433,2=130,6=56", "num_atoms": 80241, "num_waters": 0, "num_metals": 1, "metals_desc": "Zn=1", "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 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" } }