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"[1] 4 [A.133 A.138] 5", "num_nts": 6, "nts_short": "CGUAAG", "nts_long": "///A/133,///A/134,///A/135,///A/136,///A/137,///A/138", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/134,///A/135,///A/136,///A/137" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 16 ], "summary": "[1] 4 [A.146 A.151] 4", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///A/146,///A/147,///A/148,///A/149,///A/150,///A/151", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/147,///A/148,///A/149,///A/150" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 18 ], "summary": "[1] 4 [A.172 A.177] 2", "num_nts": 6, "nts_short": "AAACAU", "nts_long": "///A/172,///A/173,///A/174,///A/175,///A/176,///A/177", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AACA", "nts_long": "///A/173,///A/174,///A/175,///A/176" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 19 ], "summary": "[1] 4 [A.202 A.207] 2", "num_nts": 6, "nts_short": "AGAAUU", "nts_long": "///A/202,///A/203,///A/204,///A/205,///A/206,///A/207", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///A/203,///A/204,///A/205,///A/206" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 21 ], "summary": "[1] 5 [A.223 A.229] 2", "num_nts": 7, "nts_short": "CGGCGAG", "nts_long": "///A/223,///A/224,///A/225,///A/226,///A/227,///A/228,///A/229", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGCGA", "nts_long": "///A/224,///A/225,///A/226,///A/227,///A/228" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 25 ], "summary": "[1] 6 [A.316 A.323] 5", "num_nts": 8, "nts_short": "CUGGAAAG", "nts_long": "///A/316,///A/317,///A/318,///A/319,///A/320,///A/321,///A/322,///A/323", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UGGAAA", "nts_long": "///A/317,///A/318,///A/319,///A/320,///A/321,///A/322" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ -11 ], "summary": "[1] 3 [A.330 A.334] 1", "num_nts": 5, "nts_short": "CUCAG", "nts_long": "///A/330,///A/331,///A/332,///A/333,///A/334", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UCA", "nts_long": "///A/331,///A/332,///A/333" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 27 ], "summary": "[1] 7 [A.338 A.346] 3", "num_nts": 9, "nts_short": "GUGAGAGUC", "nts_long": "///A/338,///A/339,///A/340,///A/341,///A/342,///A/343,///A/344,///A/345,///A/346", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGAGAGU", "nts_long": "///A/339,///A/340,///A/341,///A/342,///A/343,///A/344,///A/345" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 29 ], "summary": "[1] 7 [A.396 A.404] 4", "num_nts": 9, "nts_short": "UUCGUGAAA", "nts_long": "///A/396,///A/397,///A/398,///A/399,///A/400,///A/401,///A/402,///A/403,///A/404", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UCGUGAA", "nts_long": "///A/397,///A/398,///A/399,///A/400,///A/401,///A/402,///A/403" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 30 ], "summary": "[1] 6 [A.423 A.430] 5", "num_nts": 8, "nts_short": "GGACCACC", "nts_long": "///A/423,///A/424,///A/425,///A/426,///A/427,///A/428,///A/429,///A/430", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GACCAC", "nts_long": "///A/424,///A/425,///A/426,///A/427,///A/428,///A/429" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 32 ], "summary": "[1] 4 [A.473 A.478] 2", "num_nts": 6, "nts_short": "CGUGAG", "nts_long": "///A/473,///A/474,///A/475,///A/476,///A/477,///A/478", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///A/474,///A/475,///A/476,///A/477" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 33 ], "summary": "[1] 4 [A.498 A.503] 4", "num_nts": 6, "nts_short": "CGGGAG", "nts_long": "///A/498,///A/499,///A/500,///A/501,///A/502,///A/503", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGGA", "nts_long": "///A/499,///A/500,///A/501,///A/502" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 34 ], "summary": "[1] 7 [A.552 A.560] 10", "num_nts": 9, "nts_short": "CCUUAUGCG", "nts_long": "///A/552,///A/553,///A/554,///A/555,///A/556,///A/557,///A/558,///A/559,///A/560", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CUUAUGC", "nts_long": "///A/553,///A/554,///A/555,///A/556,///A/557,///A/558,///A/559" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ -13 ], "summary": "[1] 8 [A.575 A.584] 1", "num_nts": 10, "nts_short": "UAUUGAAGCA", "nts_long": "///A/575,///A/576,///A/577,///A/578,///A/579,///A/580,///A/581,///A/582,///A/583,///A/584", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "AUUGAAGC", "nts_long": "///A/576,///A/577,///A/578,///A/579,///A/580,///A/581,///A/582,///A/583" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 38 ], "summary": "[1] 4 [A.622 A.627] 2", "num_nts": 6, "nts_short": "UGAAAA", "nts_long": "///A/622,///A/623,///A/624,///A/625,///A/626,///A/627", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/623,///A/624,///A/625,///A/626" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 39 ], "summary": "[1] 4 [A.640 A.645] 2", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/640,///A/641,///A/642,///A/643,///A/644,///A/645", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/641,///A/642,///A/643,///A/644" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 40 ], "summary": "[1] 6 [A.651 A.658] 2", "num_nts": 8, "nts_short": "CCGAAUAG", "nts_long": "///A/651,///A/652,///A/653,///A/654,///A/655,///A/656,///A/657,///A/658", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CGAAUA", "nts_long": "///A/652,///A/653,///A/654,///A/655,///A/656,///A/657" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 45 ], "summary": "[1] 6 [A.725 A.732] 5", "num_nts": 8, "nts_short": "CGUGACAG", "nts_long": "///A/725,///A/726,///A/727,///A/728,///A/729,///A/730,///A/731,///A/732", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GUGACA", "nts_long": "///A/726,///A/727,///A/728,///A/729,///A/730,///A/731" } ] }, { "index": 23, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 47 ], "summary": "[1] 8 [A.757 A.766] 2", "num_nts": 10, "nts_short": "UGCUGAAACA", "nts_long": "///A/757,///A/758,///A/759,///A/760,///A/761,///A/762,///A/763,///A/764,///A/765,///A/766", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GCUGAAAC", "nts_long": "///A/758,///A/759,///A/760,///A/761,///A/762,///A/763,///A/764,///A/765" } ] }, { "index": 24, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 48 ], "summary": "[1] 5 [A.792 A.798] 3", "num_nts": 7, "nts_short": "UGAAAAG", "nts_long": "///A/792,///A/793,///A/794,///A/795,///A/796,///A/797,///A/798", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAAAA", "nts_long": "///A/793,///A/794,///A/795,///A/796,///A/797" } ] }, { "index": 25, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 50 ], "summary": "[1] 4 [A.839 A.844] 5", "num_nts": 6, "nts_short": "UUGAGG", "nts_long": "///A/839,///A/840,///A/841,///A/842,///A/843,///A/844", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UGAG", "nts_long": "///A/840,///A/841,///A/842,///A/843" } ] }, { "index": 26, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 57 ], "summary": "[1] 6 [A.966 A.973] 2", "num_nts": 8, "nts_short": "AGCUAACU", "nts_long": "///A/966,///A/967,///A/968,///A/969,///A/970,///A/971,///A/972,///A/973", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GCUAAC", "nts_long": "///A/967,///A/968,///A/969,///A/970,///A/971,///A/972" } ] }, { "index": 27, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 58 ], "summary": "[1] 6 [A.989 A.996] 3", "num_nts": 8, "nts_short": "GAAACAAC", "nts_long": "///A/989,///A/990,///A/991,///A/992,///A/993,///A/994,///A/995,///A/996", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AAACAA", "nts_long": "///A/990,///A/991,///A/992,///A/993,///A/994,///A/995" } ] }, { "index": 28, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 67 ], "summary": "[1] 9 [A.1075 A.1085] 3", "num_nts": 11, "nts_short": "CUUAGAAGCAG", "nts_long": "///A/1075,///A/1076,///A/1077,///A/1078,///A/1079,///A/1080,///A/1081,///A/1082,///A/1083,///A/1084,///A/1085", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UUAGAAGCA", "nts_long": "///A/1076,///A/1077,///A/1078,///A/1079,///A/1080,///A/1081,///A/1082,///A/1083,///A/1084" } ] }, { "index": 29, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 68 ], "summary": "[1] 6 [A.1103 A.1110] 2", "num_nts": 8, "nts_short": "CGUAAUAG", "nts_long": "///A/1103,///A/1104,///A/1105,///A/1106,///A/1107,///A/1108,///A/1109,///A/1110", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GUAAUA", "nts_long": "///A/1104,///A/1105,///A/1106,///A/1107,///A/1108,///A/1109" } ] }, { "index": 30, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ 70 ], "summary": "[1] 3 [A.1185 A.1189] 3", "num_nts": 5, "nts_short": "CGAAG", "nts_long": "///A/1185,///A/1186,///A/1187,///A/1188,///A/1189", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1186,///A/1187,///A/1188" } ] }, { "index": 31, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 74 ], "summary": "[1] 4 [A.1235 A.1240] 2", "num_nts": 6, "nts_short": "CGGAAG", "nts_long": "///A/1235,///A/1236,///A/1237,///A/1238,///A/1239,///A/1240", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///A/1236,///A/1237,///A/1238,///A/1239" } ] }, { "index": 32, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 76 ], "summary": "[1] 7 [A.1294 A.1302] 6", "num_nts": 9, "nts_short": "GUGAGAAUC", "nts_long": "///A/1294,///A/1295,///A/1296,///A/1297,///A/1298,///A/1299,///A/1300,///A/1301,///A/1302", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGAGAAU", "nts_long": "///A/1295,///A/1296,///A/1297,///A/1298,///A/1299,///A/1300,///A/1301" } ] }, { "index": 33, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 81 ], "summary": "[1] 5 [A.1337 A.1343] 2", "num_nts": 7, "nts_short": "GGUCGUC", "nts_long": "///A/1337,///A/1338,///A/1339,///A/1340,///A/1341,///A/1342,///A/1343", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GUCGU", "nts_long": "///A/1338,///A/1339,///A/1340,///A/1341,///A/1342" } ] }, { "index": 34, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 86 ], "summary": "[1] 4 [A.1376 A.1381] 3", "num_nts": 6, "nts_short": "CGAACG", "nts_long": "///A/1376,///A/1377,///A/1378,///A/1379,///A/1380,///A/1381", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAC", "nts_long": "///A/1377,///A/1378,///A/1379,///A/1380" } ] }, { "index": 35, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 87 ], "summary": "[1] 8 [A.1402 A.1411] 5", "num_nts": 10, "nts_short": "GUCAAGAUUC", "nts_long": "///A/1402,///A/1403,///A/1404,///A/1405,///A/1406,///A/1407,///A/1408,///A/1409,///A/1410,///A/1411", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UCAAGAUU", "nts_long": "///A/1403,///A/1404,///A/1405,///A/1406,///A/1407,///A/1408,///A/1409,///A/1410" } ] }, { "index": 36, "type": "hairpin loop", "bridging_nts": [ 14 ], "stem_indices": [ 94 ], "summary": "[1] 14 [A.1463 A.1478] 4", "num_nts": 16, "nts_short": "AAGCUAUGGCUAUGCU", "nts_long": "///A/1463,///A/1464,///A/1465,///A/1466,///A/1467,///A/1468,///A/1469,///A/1470,///A/1471,///A/1472,///A/1473,///A/1474,///A/1475,///A/1476,///A/1477,///A/1478", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 14, "nts_short": "AGCUAUGGCUAUGC", "nts_long": "///A/1464,///A/1465,///A/1466,///A/1467,///A/1468,///A/1469,///A/1470,///A/1471,///A/1472,///A/1473,///A/1474,///A/1475,///A/1476,///A/1477" } ] }, { "index": 37, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 97 ], "summary": "[1] 13 [A.1503 A.1517] 3", "num_nts": 15, "nts_short": "GGUCAGAAAAUCUAC", "nts_long": "///A/1503,///A/1504,///A/1505,///A/1506,///A/1507,///A/1508,///A/1509,///A/1510,///A/1511,///A/1512,///A/1513,///A/1514,///A/1515,///A/1516,///A/1517", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "GUCAGAAAAUCUA", "nts_long": "///A/1504,///A/1505,///A/1506,///A/1507,///A/1508,///A/1509,///A/1510,///A/1511,///A/1512,///A/1513,///A/1514,///A/1515,///A/1516" } ] }, { "index": 38, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ -34 ], "summary": "[1] 3 [A.1549 A.1553] 1", "num_nts": 5, "nts_short": "CCUCG", "nts_long": "///A/1549,///A/1550,///A/1551,///A/1552,///A/1553", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CUC", "nts_long": "///A/1550,///A/1551,///A/1552" } ] }, { "index": 39, "type": "hairpin loop", "bridging_nts": [ 2 ], "stem_indices": [ -35 ], "summary": "[1] 2 [A.1581 A.1584] 1", "num_nts": 4, "nts_short": "CAAG", "nts_long": "///A/1581,///A/1582,///A/1583,///A/1584", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1582,///A/1583" } ] }, { "index": 40, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 99 ], "summary": "[1] 6 [A.1628 A.1635] 2", "num_nts": 8, "nts_short": "CGACACAG", "nts_long": "///A/1628,///A/1629,///A/1630,///A/1631,///A/1632,///A/1633,///A/1634,///A/1635", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GACACA", "nts_long": "///A/1629,///A/1630,///A/1631,///A/1632,///A/1633,///A/1634" } ] }, { "index": 41, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 100 ], "summary": "[1] 4 [A.1647 A.1652] 5", "num_nts": 6, "nts_short": "UCAAUG", "nts_long": "///A/1647,///A/1648,///A/1649,///A/1650,///A/1651,///A/1652", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAAU", "nts_long": "///A/1648,///A/1649,///A/1650,///A/1651" } ] }, { "index": 42, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -38 ], "summary": "[1] 4 [A.1708 A.1713] 1", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///A/1708,///A/1709,///A/1710,///A/1711,///A/1712,///A/1713", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///A/1709,///A/1710,///A/1711,///A/1712" } ] }, { "index": 43, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ 106 ], "summary": "[1] 3 [A.1731 A.1735] 3", "num_nts": 5, "nts_short": "CUUCG", "nts_long": "///A/1731,///A/1732,///A/1733,///A/1734,///A/1735", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUC", "nts_long": "///A/1732,///A/1733,///A/1734" } ] }, { "index": 44, "type": "hairpin loop", "bridging_nts": [ 3 ], "stem_indices": [ -40 ], "summary": "[1] 3 [A.1743 A.1747] 1", "num_nts": 5, "nts_short": "CGCAG", "nts_long": "///A/1743,///A/1744,///A/1745,///A/1746,///A/1747", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GCA", "nts_long": "///A/1744,///A/1745,///A/1746" } ] }, { "index": 45, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ -41 ], "summary": "[1] 11 [A.1767 A.1779] 1", "num_nts": 13, "nts_short": "GUUUACCAAAAUC", "nts_long": "///A/1767,///A/1768,///A/1769,///A/1770,///A/1771,///A/1772,///A/1773,///A/1774,///A/1775,///A/1776,///A/1777,///A/1778,///A/1779", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "UUUACCAAAAU", "nts_long": "///A/1768,///A/1769,///A/1770,///A/1771,///A/1772,///A/1773,///A/1774,///A/1775,///A/1776,///A/1777,///A/1778" } ] }, { "index": 46, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 110 ], "summary": "[1] 5 [A.1797 A.1803] 3", "num_nts": 7, "nts_short": "CGAACAG", "nts_long": "///A/1797,///A/1798,///A/1799,///A/1800,///A/1801,///A/1802,///A/1803", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAACA", "nts_long": "///A/1798,///A/1799,///A/1800,///A/1801,///A/1802" } ] }, { "index": 47, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -42 ], "summary": "[1] 7 [A.1854 A.1862] 1", "num_nts": 9, "nts_short": "GGUGCAAGC", "nts_long": "///A/1854,///A/1855,///A/1856,///A/1857,///A/1858,///A/1859,///A/1860,///A/1861,///A/1862", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUGCAAG", "nts_long": "///A/1855,///A/1856,///A/1857,///A/1858,///A/1859,///A/1860,///A/1861" } ] }, { "index": 48, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 116 ], "summary": "[1] 9 [A.1893 A.1903] 2", "num_nts": 11, "nts_short": "GUAACUAUAAC", "nts_long": "///A/1893,///A/1894,///A/1895,///A/1896,///A/1897,///A/1898,///A/1899,///A/1900,///A/1901,///A/1902,///A/1903", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UAACUAUAA", "nts_long": "///A/1894,///A/1895,///A/1896,///A/1897,///A/1898,///A/1899,///A/1900,///A/1901,///A/1902" } ] }, { "index": 49, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 117 ], "summary": "[1] 7 [A.1932 A.1940] 3", "num_nts": 9, "nts_short": "GGUAAGUUC", "nts_long": "///A/1932,///A/1933,///A/1934,///A/1935,///A/1936,///A/1937,///A/1938,///A/1939,///A/1940", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUAAGUU", "nts_long": "///A/1933,///A/1934,///A/1935,///A/1936,///A/1937,///A/1938,///A/1939" } ] }, { "index": 50, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 118 ], "summary": "[1] 8 [A.2010 A.2019] 5", "num_nts": 10, "nts_short": "GUAAAGAUGC", "nts_long": "///A/2010,///A/2011,///A/2012,///A/2013,///A/2014,///A/2015,///A/2016,///A/2017,///A/2018,///A/2019", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "UAAAGAUG", "nts_long": "///A/2011,///A/2012,///A/2013,///A/2014,///A/2015,///A/2016,///A/2017,///A/2018" } ] }, { "index": 51, "type": "hairpin loop", "bridging_nts": [ 12 ], "stem_indices": [ 129 ], "summary": "[1] 12 [A.2186 A.2199] 4", "num_nts": 14, "nts_short": "GAAAAAUCACUUUC", "nts_long": "///A/2186,///A/2187,///A/2188,///A/2189,///A/2190,///A/2191,///A/2192,///A/2193,///A/2194,///A/2195,///A/2196,///A/2197,///A/2198,///A/2199", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 12, "nts_short": "AAAAAUCACUUU", "nts_long": "///A/2187,///A/2188,///A/2189,///A/2190,///A/2191,///A/2192,///A/2193,///A/2194,///A/2195,///A/2196,///A/2197,///A/2198" } ] }, { "index": 52, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 130 ], "summary": "[1] 7 [A.2227 A.2235] 2", "num_nts": 9, "nts_short": "CUGGGGCGG", "nts_long": "///A/2227,///A/2228,///A/2229,///A/2230,///A/2231,///A/2232,///A/2233,///A/2234,///A/2235", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGGGGCG", "nts_long": "///A/2228,///A/2229,///A/2230,///A/2231,///A/2232,///A/2233,///A/2234" } ] }, { "index": 53, "type": "hairpin loop", "bridging_nts": [ 19 ], "stem_indices": [ -45 ], "summary": "[1] 19 [A.2234 A.2254] 1", "num_nts": 21, "nts_short": "GGUCGCCUCCCAAAAUGUAAC", "nts_long": "///A/2234,///A/2235,///A/2236,///A/2237,///A/2238,///A/2239,///A/2240,///A/2241,///A/2242,///A/2243,///A/2244,///A/2245,///A/2246,///A/2247,///A/2248,///A/2249,///A/2250,///A/2251,///A/2252,///A/2253,///A/2254", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 19, "nts_short": "GUCGCCUCCCAAAAUGUAA", "nts_long": "///A/2235,///A/2236,///A/2237,///A/2238,///A/2239,///A/2240,///A/2241,///A/2242,///A/2243,///A/2244,///A/2245,///A/2246,///A/2247,///A/2248,///A/2249,///A/2250,///A/2251,///A/2252,///A/2253" } ] }, { "index": 54, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ 131 ], "summary": "[1] 11 [A.2243 A.2255] 6", "num_nts": 13, "nts_short": "CCAAAAUGUAACG", "nts_long": "///A/2243,///A/2244,///A/2245,///A/2246,///A/2247,///A/2248,///A/2249,///A/2250,///A/2251,///A/2252,///A/2253,///A/2254,///A/2255", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "CAAAAUGUAAC", "nts_long": "///A/2244,///A/2245,///A/2246,///A/2247,///A/2248,///A/2249,///A/2250,///A/2251,///A/2252,///A/2253,///A/2254" } ] }, { "index": 55, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 134 ], "summary": "[1] 9 [A.2282 A.2292] 5", "num_nts": 11, "nts_short": "GGUUGGAAAUC", "nts_long": "///A/2282,///A/2283,///A/2284,///A/2285,///A/2286,///A/2287,///A/2288,///A/2289,///A/2290,///A/2291,///A/2292", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "GUUGGAAAU", "nts_long": "///A/2283,///A/2284,///A/2285,///A/2286,///A/2287,///A/2288,///A/2289,///A/2290,///A/2291" } ] }, { "index": 56, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 135 ], "summary": "[1] 6 [A.2303 A.2310] 2", "num_nts": 8, "nts_short": "CGCAAAGG", "nts_long": "///A/2303,///A/2304,///A/2305,///A/2306,///A/2307,///A/2308,///A/2309,///A/2310", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GCAAAG", "nts_long": "///A/2304,///A/2305,///A/2306,///A/2307,///A/2308,///A/2309" } ] }, { "index": 57, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ -50 ], "summary": "[1] 5 [A.2335 A.2341] 1", "num_nts": 7, "nts_short": "UGACACG", "nts_long": "///A/2335,///A/2336,///A/2337,///A/2338,///A/2339,///A/2340,///A/2341", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GACAC", "nts_long": "///A/2336,///A/2337,///A/2338,///A/2339,///A/2340" } ] }, { "index": 58, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 138 ], "summary": "[1] 4 [A.2353 A.2358] 3", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///A/2353,///A/2354,///A/2355,///A/2356,///A/2357,///A/2358", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/2354,///A/2355,///A/2356,///A/2357" } ] }, { "index": 59, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 140 ], "summary": "[1] 8 [A.2383 A.2392] 2", "num_nts": 10, "nts_short": "CGUGUGGAAG", "nts_long": "///A/2383,///A/2384,///A/2385,///A/2386,///A/2387,///A/2388,///A/2389,///A/2390,///A/2391,///A/2392", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GUGUGGAA", "nts_long": "///A/2384,///A/2385,///A/2386,///A/2387,///A/2388,///A/2389,///A/2390,///A/2391" } ] }, { "index": 60, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -55 ], "summary": "[1] 7 [A.2450 A.2458] 1", "num_nts": 9, "nts_short": "AGUCCAUAU", "nts_long": "///A/2450,///A/2451,///A/2452,///A/2453,///A/2454,///A/2455,///A/2456,///A/2457,///A/2458", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUCCAUA", "nts_long": "///A/2451,///A/2452,///A/2453,///A/2454,///A/2455,///A/2456,///A/2457" } ] }, { "index": 61, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 146 ], "summary": "[1] 6 [A.2507 A.2514] 6", "num_nts": 8, "nts_short": "UGAAGAAG", "nts_long": "///A/2507,///A/2508,///A/2509,///A/2510,///A/2511,///A/2512,///A/2513,///A/2514", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAAGAA", "nts_long": "///A/2508,///A/2509,///A/2510,///A/2511,///A/2512,///A/2513" } ] }, { "index": 62, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 147 ], "summary": "[1] 5 [A.2530 A.2536] 5", "num_nts": 7, "nts_short": "CUGUUCG", "nts_long": "///A/2530,///A/2531,///A/2532,///A/2533,///A/2534,///A/2535,///A/2536", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGUUC", "nts_long": "///A/2531,///A/2532,///A/2533,///A/2534,///A/2535" } ] }, { "index": 63, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 149 ], "summary": "[1] 4 [A.2573 A.2578] 3", "num_nts": 6, "nts_short": "CGUGAG", "nts_long": "///A/2573,///A/2574,///A/2575,///A/2576,///A/2577,///A/2578", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUGA", "nts_long": "///A/2574,///A/2575,///A/2576,///A/2577" } ] }, { "index": 64, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -59 ], "summary": "[1] 4 [A.2637 A.2642] 1", "num_nts": 6, "nts_short": "CGAGAG", "nts_long": "///A/2637,///A/2638,///A/2639,///A/2640,///A/2641,///A/2642", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///A/2638,///A/2639,///A/2640,///A/2641" } ] }, { "index": 65, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 156 ], "summary": "[1] 4 [A.2680 A.2685] 6", "num_nts": 6, "nts_short": "UACCAA", "nts_long": "///A/2680,///A/2681,///A/2682,///A/2683,///A/2684,///A/2685", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "ACCA", "nts_long": "///A/2681,///A/2682,///A/2683,///A/2684" } ] }, { "index": 66, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 158 ], "summary": "[1] 13 [A.2725 A.2739] 2", "num_nts": 15, "nts_short": "CUGAAAGCAUCUAAG", "nts_long": 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"nts_long": "///A/2831,///A/2832,///A/2833,///A/2834,///A/2835,///A/2836", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/2832,///A/2833,///A/2834,///A/2835" } ] } ], "num_bulges": 27, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 4, -3 ], "summary": "[2] 0 1 [A.36 A.456 A.37 A.454] 2 1", "num_nts": 5, "nts_short": "GCGAC", "nts_long": "///A/36,///A/37,///A/454,///A/455,///A/456", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/455" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 5, 6 ], "summary": "[2] 0 1 [A.42 A.449 A.43 A.447] 4 2", "num_nts": 5, "nts_short": "GAUCC", "nts_long": "///A/42,///A/43,///A/447,///A/448,///A/449", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, 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A.1024 A.1160] 1 5", "num_nts": 5, "nts_short": "AUGCU", "nts_long": "///A/1022,///A/1023,///A/1024,///A/1160,///A/1161", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1023" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 11, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 98, -33 ], "summary": "[2] 0 1 [A.1546 A.1557 A.1547 A.1555] 2 1", "num_nts": 5, "nts_short": "CUAAG", "nts_long": "///A/1546,///A/1547,///A/1555,///A/1556,///A/1557", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1556" } ] }, { "index": 12, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 119, 120 ], "summary": "[2] 1 0 [A.2033 A.2597 A.2035 A.2596] 8 3", "num_nts": 5, "nts_short": "CAGCG", "nts_long": "///A/2033,///A/2034,///A/2035,///A/2596,///A/2597", "num_stems": 2, "bridges": [ { "index": 1, 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"stem_indices": [ -12, -13 ], "summary": "[2] 1 1 [A.573 A.586 A.575 A.584] 1 1", "num_nts": 6, "nts_short": "CCUAUG", "nts_long": "///A/573,///A/574,///A/575,///A/584,///A/585,///A/586", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/574" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/585" } ] }, { "index": 5, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 41, -15 ], "summary": "[2] 1 1 [A.685 A.821 A.687 A.819] 2 1", "num_nts": 6, "nts_short": "UCGCUA", "nts_long": "///A/685,///A/686,///A/687,///A/819,///A/820,///A/821", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/686" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/820" } ] }, { "index": 6, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -16, 43 ], "summary": "[2] 1 1 [A.700 A.788 A.702 A.786] 1 9", "num_nts": 6, "nts_short": "CUAUAG", "nts_long": "///A/700,///A/701,///A/702,///A/786,///A/787,///A/788", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/701" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/787" } ] }, { "index": 7, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -19, 47 ], "summary": "[2] 1 1 [A.754 A.769 A.756 A.767] 1 2", "num_nts": 6, "nts_short": "GCCGUC", "nts_long": "///A/754,///A/755,///A/756,///A/767,///A/768,///A/769", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/755" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/768" } ] }, { "index": 8, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -21, 52 ], "summary": "[2] 1 1 [A.864 A.938 A.866 A.936] 1 6", "num_nts": 6, "nts_short": "CAUACG", "nts_long": "///A/864,///A/865,///A/866,///A/936,///A/937,///A/938", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/865" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/937" } ] }, { "index": 9, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 54, 55 ], "summary": "[2] 1 1 [A.883 A.919 A.885 A.917] 3 4", "num_nts": 6, "nts_short": "ACAUAU", "nts_long": "///A/883,///A/884,///A/885,///A/917,///A/918,///A/919", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/884" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/918" } ] }, { "index": 10, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 56, 57 ], "summary": "[2] 1 1 [A.963 A.976 A.965 A.974] 7 2", "num_nts": 6, "nts_short": "GAGUCC", "nts_long": "///A/963,///A/964,///A/965,///A/974,///A/975,///A/976", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/964" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/975" } ] }, { "index": 11, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 64, -27 ], "summary": "[2] 1 1 [A.1052 A.1125 A.1054 A.1123] 8 1", "num_nts": 6, "nts_short": "CGCGUG", "nts_long": "///A/1052,///A/1053,///A/1054,///A/1123,///A/1124,///A/1125", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1053" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1124" } ] }, { "index": 12, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 69, 70 ], "summary": "[2] 1 1 [A.1181 A.1193 A.1183 A.1191] 4 3", "num_nts": 6, "nts_short": "CUCGAG", "nts_long": "///A/1181,///A/1182,///A/1183,///A/1191,///A/1192,///A/1193", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1182" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1192" } ] }, { "index": 13, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 71, 72 ], "summary": "[2] 1 1 [A.1218 A.1254 A.1220 A.1252] 7 2", "num_nts": 6, "nts_short": "CCGCCG", "nts_long": "///A/1218,///A/1219,///A/1220,///A/1252,///A/1253,///A/1254", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1219" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1253" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -30, 88 ], "summary": "[2] 1 1 [A.1418 A.1613 A.1420 A.1611] 1 7", "num_nts": 6, "nts_short": "CGAUUG", "nts_long": "///A/1418,///A/1419,///A/1420,///A/1611,///A/1612,///A/1613", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1419" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1612" } ] }, { "index": 15, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 96, 97 ], "summary": "[2] 1 1 [A.1499 A.1521 A.1501 A.1519] 2 3", "num_nts": 6, "nts_short": "AUCGGU", "nts_long": "///A/1499,///A/1500,///A/1501,///A/1519,///A/1520,///A/1521", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1500" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1520" } ] }, { "index": 16, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -33, -34 ], "summary": "[2] 1 1 [A.1547 A.1555 A.1549 A.1553] 1 1", "num_nts": 6, "nts_short": "UUCGGA", "nts_long": "///A/1547,///A/1548,///A/1549,///A/1553,///A/1554,///A/1555", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1548" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1554" } ] }, { "index": 17, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 102, 103 ], "summary": "[2] 1 1 [A.1680 A.1980 A.1682 A.1978] 8 2", "num_nts": 6, "nts_short": "UAAUCA", "nts_long": "///A/1680,///A/1681,///A/1682,///A/1978,///A/1979,///A/1980", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1681" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1979" } ] }, { "index": 18, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 105, 106 ], "summary": "[2] 1 1 [A.1727 A.1739 A.1729 A.1737] 4 3", "num_nts": 6, "nts_short": "CACGUG", "nts_long": "///A/1727,///A/1728,///A/1729,///A/1737,///A/1738,///A/1739", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1728" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1738" } ] }, { "index": 19, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -48, 136 ], "summary": "[2] 1 1 [A.2305 A.2368 A.2307 A.2366] 1 3", "num_nts": 6, "nts_short": "CAAUAG", "nts_long": "///A/2305,///A/2306,///A/2307,///A/2366,///A/2367,///A/2368", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2306" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2367" } ] }, { "index": 20, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -60, 154 ], "summary": "[2] 1 1 [A.2663 A.2705 A.2665 A.2703] 1 2", "num_nts": 6, "nts_short": "UGGCUA", "nts_long": "///A/2663,///A/2664,///A/2665,///A/2703,///A/2704,///A/2705", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2664" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2704" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -61, 158 ], "summary": "[2] 1 1 [A.2722 A.2742 A.2724 A.2740] 1 2", "num_nts": 6, "nts_short": "CCGCGG", "nts_long": "///A/2722,///A/2723,///A/2724,///A/2740,///A/2741,///A/2742", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2723" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2741" } ] }, { "index": 22, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -62, -63 ], "summary": "[2] 1 1 [A.2771 A.2781 A.2773 A.2779] 1 1", "num_nts": 6, "nts_short": "CUGCAG", "nts_long": "///A/2771,///A/2772,///A/2773,///A/2779,///A/2780,///A/2781", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2772" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2780" } ] }, { "index": 23, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -23, -24 ], "summary": "[2] 1 2 [A.1003 A.1174 A.1005 A.1171] 1 1", "num_nts": 7, "nts_short": "CAUAUGG", "nts_long": "///A/1003,///A/1004,///A/1005,///A/1171,///A/1172,///A/1173,///A/1174", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1004" }, { "index": 2, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/1172,///A/1173" } ] }, { "index": 24, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 63, 64 ], "summary": "[2] 2 1 [A.1042 A.1134 A.1045 A.1132] 2 8", "num_nts": 7, "nts_short": "GAUGCGC", "nts_long": "///A/1042,///A/1043,///A/1044,///A/1045,///A/1132,///A/1133,///A/1134", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1043,///A/1044" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1133" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -29, 71 ], "summary": "[2] 1 2 [A.1210 A.1263 A.1212 A.1260] 1 7", "num_nts": 7, "nts_short": "CGUAGUG", "nts_long": "///A/1210,///A/1211,///A/1212,///A/1260,///A/1261,///A/1262,///A/1263", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1211" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/1261,///A/1262" } ] }, { "index": 26, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 107, 108 ], "summary": "[2] 1 2 [A.1760 A.1966 A.1762 A.1963] 6 2", "num_nts": 7, "nts_short": "GGCGAUC", "nts_long": "///A/1760,///A/1761,///A/1762,///A/1963,///A/1964,///A/1965,///A/1966", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1761" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1964,///A/1965" } ] }, { "index": 27, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ -49, -50 ], "summary": "[2] 2 1 [A.2332 A.2343 A.2335 A.2341] 1 1", "num_nts": 7, "nts_short": "GACUGUC", "nts_long": "///A/2332,///A/2333,///A/2334,///A/2335,///A/2341,///A/2342,///A/2343", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2333,///A/2334" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2342" } ] }, { "index": 28, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 162, 163 ], "summary": "[2] 1 2 [A.2818 A.2849 A.2820 A.2846] 5 3", "num_nts": 7, "nts_short": "GGCGGAC", "nts_long": "///A/2818,///A/2819,///A/2820,///A/2846,///A/2847,///A/2848,///A/2849", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2819" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2847,///A/2848" } ] }, { "index": 29, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 10, 11 ], "summary": "[2] 2 2 [A.61 A.91 A.64 A.88] 2 2", "num_nts": 8, "nts_short": "UUACGAGA", "nts_long": "///A/61,///A/62,///A/63,///A/64,///A/88,///A/89,///A/90,///A/91", "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": "AG", "nts_long": "///A/89,///A/90" } ] }, { "index": 30, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 66, 67 ], "summary": "[2] 2 2 [A.1070 A.1090 A.1073 A.1087] 3 3", "num_nts": 8, "nts_short": "GUUGCACC", "nts_long": "///A/1070,///A/1071,///A/1072,///A/1073,///A/1087,///A/1088,///A/1089,///A/1090", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/1071,///A/1072" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/1088,///A/1089" } ] }, { "index": 31, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ -28, 68 ], "summary": "[2] 3 1 [A.1098 A.1113 A.1102 A.1111] 1 2", "num_nts": 8, "nts_short": "GAGUGCUC", "nts_long": "///A/1098,///A/1099,///A/1100,///A/1101,///A/1102,///A/1111,///A/1112,///A/1113", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AGU", "nts_long": "///A/1099,///A/1100,///A/1101" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1112" } ] }, { "index": 32, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 73, 74 ], "summary": "[2] 2 2 [A.1231 A.1244 A.1234 A.1241] 4 2", "num_nts": 8, "nts_short": "AUACGAGU", "nts_long": "///A/1231,///A/1232,///A/1233,///A/1234,///A/1241,///A/1242,///A/1243,///A/1244", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1232,///A/1233" }, { "index": 2, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/1242,///A/1243" } ] }, { "index": 33, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 80, 81 ], "summary": "[2] 3 1 [A.1332 A.1346 A.1336 A.1344] 6 2", "num_nts": 8, "nts_short": "GGAAGCGC", "nts_long": "///A/1332,///A/1333,///A/1334,///A/1335,///A/1336,///A/1344,///A/1345,///A/1346", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1333,///A/1334,///A/1335" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1345" } ] }, { "index": 34, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 113, 114 ], "summary": "[2] 1 3 [A.1833 A.1884 A.1835 A.1880] 2 4", "num_nts": 8, "nts_short": "UGCGUGAA", "nts_long": "///A/1833,///A/1834,///A/1835,///A/1880,///A/1881,///A/1882,///A/1883,///A/1884", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1834" }, { "index": 2, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/1881,///A/1882,///A/1883" } ] }, { "index": 35, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 114, 115 ], "summary": "[2] 3 1 [A.1838 A.1877 A.1842 A.1875] 4 2", "num_nts": 8, "nts_short": "GAAGGCCC", "nts_long": "///A/1838,///A/1839,///A/1840,///A/1841,///A/1842,///A/1875,///A/1876,///A/1877", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/1839,///A/1840,///A/1841" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1876" } ] }, { "index": 36, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 125, 126 ], "summary": "[2] 2 2 [A.2068 A.2213 A.2071 A.2210] 3 3", "num_nts": 8, "nts_short": "CUGGCUUG", "nts_long": "///A/2068,///A/2069,///A/2070,///A/2071,///A/2210,///A/2211,///A/2212,///A/2213", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2069,///A/2070" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2211,///A/2212" } ] }, { "index": 37, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ -47, 134 ], "summary": "[2] 1 3 [A.2276 A.2300 A.2278 A.2296] 1 5", "num_nts": 8, "nts_short": "CAAUGUAG", "nts_long": "///A/2276,///A/2277,///A/2278,///A/2296,///A/2297,///A/2298,///A/2299,///A/2300", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2277" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/2297,///A/2298,///A/2299" } ] }, { "index": 38, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 137, -49 ], "summary": "[2] 2 2 [A.2329 A.2346 A.2332 A.2343] 4 1", "num_nts": 8, "nts_short": "CGAGCGAG", "nts_long": "///A/2329,///A/2330,///A/2331,///A/2332,///A/2343,///A/2344,///A/2345,///A/2346", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2330,///A/2331" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2344,///A/2345" } ] }, { "index": 39, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ -54, 142 ], "summary": "[2] 1 3 [A.2438 A.2472 A.2440 A.2468] 1 6", "num_nts": 8, "nts_short": "AUCGGUUU", "nts_long": "///A/2438,///A/2439,///A/2440,///A/2468,///A/2469,///A/2470,///A/2471,///A/2472", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2439" }, { "index": 2, "num_nts": 3, "nts_short": "GUU", "nts_long": "///A/2469,///A/2470,///A/2471" } ] }, { "index": 40, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 143, -57 ], "summary": "[2] 1 3 [A.2489 A.2557 A.2491 A.2553] 3 1", "num_nts": 8, "nts_short": "CUCGCGAG", "nts_long": "///A/2489,///A/2490,///A/2491,///A/2553,///A/2554,///A/2555,///A/2556,///A/2557", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2490" }, { "index": 2, "num_nts": 3, "nts_short": "CGA", "nts_long": "///A/2554,///A/2555,///A/2556" } ] }, { "index": 41, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 153, -60 ], "summary": "[2] 3 1 [A.2659 A.2707 A.2663 A.2705] 5 1", "num_nts": 8, "nts_short": "CCGCUAUG", "nts_long": "///A/2659,///A/2660,///A/2661,///A/2662,///A/2663,///A/2705,///A/2706,///A/2707", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CGC", "nts_long": "///A/2660,///A/2661,///A/2662" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2706" } ] }, { "index": 42, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 46, -19 ], "summary": "[2] 3 2 [A.750 A.772 A.754 A.769] 2 1", "num_nts": 9, "nts_short": "CGGUGCUCG", "nts_long": "///A/750,///A/751,///A/752,///A/753,///A/754,///A/769,///A/770,///A/771,///A/772", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGU", "nts_long": "///A/751,///A/752,///A/753" }, { "index": 2, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/770,///A/771" } ] }, { "index": 43, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 53, 54 ], "summary": "[2] 3 2 [A.877 A.924 A.881 A.921] 2 3", "num_nts": 9, "nts_short": "GCACUAAAC", "nts_long": "///A/877,///A/878,///A/879,///A/880,///A/881,///A/921,///A/922,///A/923,///A/924", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAC", "nts_long": "///A/878,///A/879,///A/880" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/922,///A/923" } ] }, { "index": 44, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 91, 92 ], "summary": "[2] 2 3 [A.1446 A.1577 A.1449 A.1573] 4 3", "num_nts": 9, "nts_short": "UUACGACGG", "nts_long": "///A/1446,///A/1447,///A/1448,///A/1449,///A/1573,///A/1574,///A/1575,///A/1576,///A/1577", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1447,///A/1448" }, { "index": 2, "num_nts": 3, "nts_short": "ACG", "nts_long": "///A/1574,///A/1575,///A/1576" } ] }, { "index": 45, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 92, 93 ], "summary": "[2] 2 3 [A.1451 A.1571 A.1454 A.1567] 3 5", "num_nts": 9, "nts_short": "CUAUAAACG", "nts_long": "///A/1451,///A/1452,///A/1453,///A/1454,///A/1567,///A/1568,///A/1569,///A/1570,///A/1571", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1452,///A/1453" }, { "index": 2, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/1568,///A/1569,///A/1570" } ] }, { "index": 46, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 101, 102 ], "summary": "[2] 4 1 [A.1668 A.1989 A.1673 A.1987] 4 8", "num_nts": 9, "nts_short": "GAGAACGAC", "nts_long": "///A/1668,///A/1669,///A/1670,///A/1671,///A/1672,///A/1673,///A/1987,///A/1988,///A/1989", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///A/1669,///A/1670,///A/1671,///A/1672" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1988" } ] }, { "index": 47, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 124, 125 ], "summary": "[2] 2 3 [A.2063 A.2219 A.2066 A.2215] 4 3", "num_nts": 9, "nts_short": "AUAGCGGGU", "nts_long": "///A/2063,///A/2064,///A/2065,///A/2066,///A/2215,///A/2216,///A/2217,///A/2218,///A/2219", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2064,///A/2065" }, { "index": 2, "num_nts": 3, "nts_short": "GGG", "nts_long": "///A/2216,///A/2217,///A/2218" } ] }, { "index": 48, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 23, -10 ], "summary": "[2] 3 3 [A.299 A.363 A.303 A.359] 5 1", "num_nts": 10, "nts_short": "CCCUCGAGCG", "nts_long": "///A/299,///A/300,///A/301,///A/302,///A/303,///A/359,///A/360,///A/361,///A/362,///A/363", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CCU", "nts_long": "///A/300,///A/301,///A/302" }, { "index": 2, "num_nts": 3, "nts_short": "AGC", "nts_long": "///A/360,///A/361,///A/362" } ] }, { "index": 49, "type": "asymmetric internal loop", "bridging_nts": [ 2, 4 ], "stem_indices": [ -10, 24 ], "summary": "[2] 2 4 [A.303 A.359 A.306 A.354] 1 3", "num_nts": 10, "nts_short": "CAAGCGAACG", "nts_long": "///A/303,///A/304,///A/305,///A/306,///A/354,///A/355,///A/356,///A/357,///A/358,///A/359", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/304,///A/305" }, { "index": 2, "num_nts": 4, "nts_short": "GAAC", "nts_long": "///A/355,///A/356,///A/357,///A/358" } ] }, { "index": 50, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 52, -22 ], "summary": "[2] 3 3 [A.871 A.931 A.875 A.927] 6 1", "num_nts": 10, "nts_short": "UGUAGCGAAG", "nts_long": "///A/871,///A/872,///A/873,///A/874,///A/875,///A/927,///A/928,///A/929,///A/930,///A/931", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/872,///A/873,///A/874" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/928,///A/929,///A/930" } ] }, { "index": 51, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 59, 60 ], "summary": "[2] 3 3 [A.1009 A.1168 A.1013 A.1164] 3 3", "num_nts": 10, "nts_short": "CUAAGCGAAG", "nts_long": "///A/1009,///A/1010,///A/1011,///A/1012,///A/1013,///A/1164,///A/1165,///A/1166,///A/1167,///A/1168", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1010,///A/1011,///A/1012" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/1165,///A/1166,///A/1167" } ] }, { "index": 52, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 84, 85 ], "summary": "[2] 3 3 [A.1364 A.1393 A.1368 A.1389] 2 2 k-turn:undecided", "num_nts": 10, "nts_short": "CUAAGCGAUG", "nts_long": "///A/1364,///A/1365,///A/1366,///A/1367,///A/1368,///A/1389,///A/1390,///A/1391,///A/1392,///A/1393", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1365,///A/1366,///A/1367" }, { "index": 2, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/1390,///A/1391,///A/1392" } ] }, { "index": 53, "type": "asymmetric internal loop", "bridging_nts": [ 4, 2 ], "stem_indices": [ -36, -37 ], "summary": "[2] 4 2 [A.1686 A.1976 A.1691 A.1973] 1 1", "num_nts": 10, "nts_short": "ACUUUGCUGU", "nts_long": "///A/1686,///A/1687,///A/1688,///A/1689,///A/1690,///A/1691,///A/1973,///A/1974,///A/1975,///A/1976", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUUU", "nts_long": "///A/1687,///A/1688,///A/1689,///A/1690" }, { "index": 2, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/1974,///A/1975" } ] }, { "index": 54, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 154, 155 ], "summary": "[2] 3 3 [A.2666 A.2702 A.2670 A.2698] 2 5", "num_nts": 10, "nts_short": "UCUCCGGUAG", "nts_long": "///A/2666,///A/2667,///A/2668,///A/2669,///A/2670,///A/2698,///A/2699,///A/2700,///A/2701,///A/2702", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CUC", "nts_long": "///A/2667,///A/2668,///A/2669" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/2699,///A/2700,///A/2701" } ] }, { "index": 55, "type": "asymmetric internal loop", "bridging_nts": [ 2, 5 ], "stem_indices": [ -32, 96 ], "summary": "[2] 2 5 [A.1495 A.1528 A.1498 A.1522] 1 2", "num_nts": 11, "nts_short": "GGCGCACAUGC", "nts_long": "///A/1495,///A/1496,///A/1497,///A/1498,///A/1522,///A/1523,///A/1524,///A/1525,///A/1526,///A/1527,///A/1528", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/1496,///A/1497" }, { "index": 2, "num_nts": 5, "nts_short": "ACAUG", "nts_long": "///A/1523,///A/1524,///A/1525,///A/1526,///A/1527" } ] }, { "index": 56, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 163, 164 ], "summary": "[2] 4 3 [A.2822 A.2844 A.2827 A.2840] 3 5", "num_nts": 11, "nts_short": "UGCACGUUCAG", "nts_long": "///A/2822,///A/2823,///A/2824,///A/2825,///A/2826,///A/2827,///A/2840,///A/2841,///A/2842,///A/2843,///A/2844", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAC", "nts_long": "///A/2823,///A/2824,///A/2825,///A/2826" }, { "index": 2, "num_nts": 3, "nts_short": "UCA", "nts_long": "///A/2841,///A/2842,///A/2843" } ] }, { "index": 57, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -9, 23 ], "summary": "[2] 4 4 [A.290 A.372 A.295 A.367] 1 5", "num_nts": 12, "nts_short": "AGAUUCGACUGU", "nts_long": "///A/290,///A/291,///A/292,///A/293,///A/294,///A/295,///A/367,///A/368,///A/369,///A/370,///A/371,///A/372", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAUU", "nts_long": "///A/291,///A/292,///A/293,///A/294" }, { "index": 2, "num_nts": 4, "nts_short": "ACUG", "nts_long": "///A/368,///A/369,///A/370,///A/371" } ] }, { "index": 58, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -17, 45 ], "summary": "[2] 4 4 [A.716 A.741 A.721 A.736] 1 5", "num_nts": 12, "nts_short": "UGAAACGCGGAG", "nts_long": "///A/716,///A/717,///A/718,///A/719,///A/720,///A/721,///A/736,///A/737,///A/738,///A/739,///A/740,///A/741", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/717,///A/718,///A/719,///A/720" }, { "index": 2, "num_nts": 4, "nts_short": "CGGA", "nts_long": "///A/737,///A/738,///A/739,///A/740" } ] }, { "index": 59, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 85, 86 ], "summary": "[2] 4 4 [A.1369 A.1388 A.1374 A.1383] 2 3", "num_nts": 12, "nts_short": "GUGAGGCGCAGC", "nts_long": "///A/1369,///A/1370,///A/1371,///A/1372,///A/1373,///A/1374,///A/1383,///A/1384,///A/1385,///A/1386,///A/1387,///A/1388", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UGAG", "nts_long": "///A/1370,///A/1371,///A/1372,///A/1373" }, { "index": 2, "num_nts": 4, "nts_short": "GCAG", "nts_long": "///A/1384,///A/1385,///A/1386,///A/1387" } ] }, { "index": 60, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 89, 90 ], "summary": "[2] 4 4 [A.1431 A.1597 A.1436 A.1592] 2 3", "num_nts": 12, "nts_short": "UGAUGGUCUAAA", "nts_long": "///A/1431,///A/1432,///A/1433,///A/1434,///A/1435,///A/1436,///A/1592,///A/1593,///A/1594,///A/1595,///A/1596,///A/1597", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAUG", "nts_long": "///A/1432,///A/1433,///A/1434,///A/1435" }, { "index": 2, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///A/1593,///A/1594,///A/1595,///A/1596" } ] }, { "index": 61, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -31, -32 ], "summary": "[2] 4 4 [A.1490 A.1533 A.1495 A.1528] 1 1", "num_nts": 12, "nts_short": "UCAAGGCCUCAG", "nts_long": "///A/1490,///A/1491,///A/1492,///A/1493,///A/1494,///A/1495,///A/1528,///A/1529,///A/1530,///A/1531,///A/1532,///A/1533", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAAG", "nts_long": "///A/1491,///A/1492,///A/1493,///A/1494" }, { "index": 2, "num_nts": 4, "nts_short": "CUCA", "nts_long": "///A/1529,///A/1530,///A/1531,///A/1532" } ] }, { "index": 62, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 142, -55 ], "summary": "[2] 4 4 [A.2445 A.2463 A.2450 A.2458] 6 1", "num_nts": 12, "nts_short": "CCGAGAUCGGCG", "nts_long": "///A/2445,///A/2446,///A/2447,///A/2448,///A/2449,///A/2450,///A/2458,///A/2459,///A/2460,///A/2461,///A/2462,///A/2463", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CGAG", "nts_long": "///A/2446,///A/2447,///A/2448,///A/2449" }, { "index": 2, "num_nts": 4, "nts_short": "CGGC", "nts_long": "///A/2459,///A/2460,///A/2461,///A/2462" } ] }, { "index": 63, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ 157, -61 ], "summary": "[2] 4 4 [A.2717 A.2747 A.2722 A.2742] 2 1", "num_nts": 12, "nts_short": "GAUAACGGAAGC", "nts_long": "///A/2717,///A/2718,///A/2719,///A/2720,///A/2721,///A/2722,///A/2742,///A/2743,///A/2744,///A/2745,///A/2746,///A/2747", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUAA", "nts_long": "///A/2718,///A/2719,///A/2720,///A/2721" }, { "index": 2, "num_nts": 4, "nts_short": "GAAG", "nts_long": "///A/2743,///A/2744,///A/2745,///A/2746" } ] }, { "index": 64, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ 12, 13 ], "summary": "[2] 3 6 [A.80 A.103 A.84 A.96] 6 2 k-turn:normal", "num_nts": 13, "nts_short": "ACGAGCUUUGACU", "nts_long": "///A/80,///A/81,///A/82,///A/83,///A/84,///A/96,///A/97,///A/98,///A/99,///A/100,///A/101,///A/102,///A/103", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CGA", "nts_long": "///A/81,///A/82,///A/83" }, { "index": 2, "num_nts": 6, "nts_short": "UUUGAC", "nts_long": "///A/97,///A/98,///A/99,///A/100,///A/101,///A/102" } ] }, { "index": 65, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ -14, 38 ], "summary": "[2] 5 4 [A.615 A.633 A.621 A.628] 1 2", "num_nts": 13, "nts_short": "CUUAAGUACGGAG", "nts_long": "///A/615,///A/616,///A/617,///A/618,///A/619,///A/620,///A/621,///A/628,///A/629,///A/630,///A/631,///A/632,///A/633", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UUAAG", "nts_long": "///A/616,///A/617,///A/618,///A/619,///A/620" }, { "index": 2, "num_nts": 4, "nts_short": "CGGA", "nts_long": "///A/629,///A/630,///A/631,///A/632" } ] }, { "index": 66, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ -15, 42 ], "summary": "[2] 3 6 [A.687 A.819 A.691 A.812] 1 6", "num_nts": 13, "nts_short": "GAAACGAGAUAGC", "nts_long": "///A/687,///A/688,///A/689,///A/690,///A/691,///A/812,///A/813,///A/814,///A/815,///A/816,///A/817,///A/818,///A/819", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/688,///A/689,///A/690" }, { "index": 2, "num_nts": 6, "nts_short": "AGAUAG", "nts_long": "///A/813,///A/814,///A/815,///A/816,///A/817,///A/818" } ] }, { "index": 67, "type": "asymmetric internal loop", "bridging_nts": [ 6, 3 ], "stem_indices": [ 72, 73 ], "summary": "[2] 6 3 [A.1221 A.1251 A.1228 A.1247] 2 4 k-turn:normal", "num_nts": 13, "nts_short": "CGGAGAAGUGGAG", "nts_long": "///A/1221,///A/1222,///A/1223,///A/1224,///A/1225,///A/1226,///A/1227,///A/1228,///A/1247,///A/1248,///A/1249,///A/1250,///A/1251", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GGAGAA", "nts_long": "///A/1222,///A/1223,///A/1224,///A/1225,///A/1226,///A/1227" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/1248,///A/1249,///A/1250" } ] }, { "index": 68, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ 88, 89 ], "summary": "[2] 3 6 [A.1426 A.1605 A.1430 A.1598] 7 2 k-turn:normal", "num_nts": 13, "nts_short": "UGGAGCGUUGAAA", "nts_long": "///A/1426,///A/1427,///A/1428,///A/1429,///A/1430,///A/1598,///A/1599,///A/1600,///A/1601,///A/1602,///A/1603,///A/1604,///A/1605", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/1427,///A/1428,///A/1429" }, { "index": 2, "num_nts": 6, "nts_short": "GUUGAA", "nts_long": "///A/1599,///A/1600,///A/1601,///A/1602,///A/1603,///A/1604" } ] }, { "index": 69, "type": "asymmetric internal loop", "bridging_nts": [ 4, 5 ], "stem_indices": [ 104, -38 ], "summary": "[2] 4 5 [A.1703 A.1719 A.1708 A.1713] 4 1", "num_nts": 13, "nts_short": "CGUAACGAAGAAG", "nts_long": "///A/1703,///A/1704,///A/1705,///A/1706,///A/1707,///A/1708,///A/1713,///A/1714,///A/1715,///A/1716,///A/1717,///A/1718,///A/1719", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/1704,///A/1705,///A/1706,///A/1707" }, { "index": 2, "num_nts": 5, "nts_short": "AAGAA", "nts_long": "///A/1714,///A/1715,///A/1716,///A/1717,///A/1718" } ] }, { "index": 70, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ 152, -59 ], "summary": "[2] 5 4 [A.2631 A.2647 A.2637 A.2642] 7 1", "num_nts": 13, "nts_short": "CUAGUACGGACCG", "nts_long": "///A/2631,///A/2632,///A/2633,///A/2634,///A/2635,///A/2636,///A/2637,///A/2642,///A/2643,///A/2644,///A/2645,///A/2646,///A/2647", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAGUA", "nts_long": "///A/2632,///A/2633,///A/2634,///A/2635,///A/2636" }, { "index": 2, "num_nts": 4, "nts_short": "GACC", "nts_long": "///A/2643,///A/2644,///A/2645,///A/2646" } ] }, { "index": 71, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ 2, -2 ], "summary": "[2] 5 5 [A.24 A.526 A.30 A.520] 8 1", "num_nts": 14, "nts_short": "GUGGAUGCUGAAAC", "nts_long": "///A/24,///A/25,///A/26,///A/27,///A/28,///A/29,///A/30,///A/520,///A/521,///A/522,///A/523,///A/524,///A/525,///A/526", "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/521,///A/522,///A/523,///A/524,///A/525" } ] }, { "index": 72, "type": "asymmetric internal loop", "bridging_nts": [ 3, 7 ], "stem_indices": [ 150, 151 ], "summary": "[2] 3 7 [A.2615 A.2762 A.2619 A.2754] 7 4", "num_nts": 14, "nts_short": "UUGAGCAAGAUGAG", "nts_long": "///A/2615,///A/2616,///A/2617,///A/2618,///A/2619,///A/2754,///A/2755,///A/2756,///A/2757,///A/2758,///A/2759,///A/2760,///A/2761,///A/2762", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/2616,///A/2617,///A/2618" }, { "index": 2, "num_nts": 7, "nts_short": "AAGAUGA", "nts_long": "///A/2755,///A/2756,///A/2757,///A/2758,///A/2759,///A/2760,///A/2761" } ] }, { "index": 73, "type": "asymmetric internal loop", "bridging_nts": [ 5, 6 ], "stem_indices": [ 17, 18 ], "summary": "[2] 5 6 [A.165 A.185 A.171 A.178] 5 2", "num_nts": 15, "nts_short": "GGAACUGCUCAGUAC", "nts_long": "///A/165,///A/166,///A/167,///A/168,///A/169,///A/170,///A/171,///A/178,///A/179,///A/180,///A/181,///A/182,///A/183,///A/184,///A/185", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAACU", "nts_long": "///A/166,///A/167,///A/168,///A/169,///A/170" }, { "index": 2, "num_nts": 6, "nts_short": "UCAGUA", "nts_long": "///A/179,///A/180,///A/181,///A/182,///A/183,///A/184" } ] }, { "index": 74, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 20, 21 ], "summary": "[2] 6 5 [A.215 A.236 A.222 A.230] 4 2", "num_nts": 15, "nts_short": "GUUAGUAGCGAACCC", "nts_long": "///A/215,///A/216,///A/217,///A/218,///A/219,///A/220,///A/221,///A/222,///A/230,///A/231,///A/232,///A/233,///A/234,///A/235,///A/236", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUAGUA", "nts_long": "///A/216,///A/217,///A/218,///A/219,///A/220,///A/221" }, { "index": 2, "num_nts": 5, "nts_short": "GAACC", "nts_long": "///A/231,///A/232,///A/233,///A/234,///A/235" } ] }, { "index": 75, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 62, -26 ], "summary": "[2] 6 5 [A.1028 A.1156 A.1035 A.1150] 5 1", "num_nts": 15, "nts_short": "GCUCAGUGCUCAAGU", "nts_long": "///A/1028,///A/1029,///A/1030,///A/1031,///A/1032,///A/1033,///A/1034,///A/1035,///A/1150,///A/1151,///A/1152,///A/1153,///A/1154,///A/1155,///A/1156", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CUCAGU", "nts_long": "///A/1029,///A/1030,///A/1031,///A/1032,///A/1033,///A/1034" }, { "index": 2, "num_nts": 5, "nts_short": "UCAAG", "nts_long": "///A/1151,///A/1152,///A/1153,///A/1154,///A/1155" } ] }, { "index": 76, "type": "symmetric internal loop", "bridging_nts": [ 6, 6 ], "stem_indices": [ 51, -21 ], "summary": "[2] 6 6 [A.857 A.945 A.864 A.938] 7 1", "num_nts": 16, "nts_short": "UGUUGACCGCGUUUAG", "nts_long": "///A/857,///A/858,///A/859,///A/860,///A/861,///A/862,///A/863,///A/864,///A/938,///A/939,///A/940,///A/941,///A/942,///A/943,///A/944,///A/945", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GUUGAC", "nts_long": "///A/858,///A/859,///A/860,///A/861,///A/862,///A/863" }, { "index": 2, "num_nts": 6, "nts_short": "CGUUUA", "nts_long": "///A/939,///A/940,///A/941,///A/942,///A/943,///A/944" } ] }, { "index": 77, "type": "asymmetric internal loop", "bridging_nts": [ 8, 4 ], "stem_indices": [ -27, 65 ], "summary": "[2] 8 4 [A.1054 A.1123 A.1063 A.1118] 1 4", "num_nts": 16, "nts_short": "CAUAGACAGCGUCGAG", "nts_long": "///A/1054,///A/1055,///A/1056,///A/1057,///A/1058,///A/1059,///A/1060,///A/1061,///A/1062,///A/1063,///A/1118,///A/1119,///A/1120,///A/1121,///A/1122,///A/1123", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "AUAGACAG", "nts_long": "///A/1055,///A/1056,///A/1057,///A/1058,///A/1059,///A/1060,///A/1061,///A/1062" }, { "index": 2, "num_nts": 4, "nts_short": "UCGA", "nts_long": "///A/1119,///A/1120,///A/1121,///A/1122" } ] }, { "index": 78, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 109, 110 ], "summary": "[2] 5 7 [A.1789 A.1813 A.1795 A.1805] 7 3 k-turn:undecided", "num_nts": 16, "nts_short": "UGCCAACGGACGUAUA", "nts_long": "///A/1789,///A/1790,///A/1791,///A/1792,///A/1793,///A/1794,///A/1795,///A/1805,///A/1806,///A/1807,///A/1808,///A/1809,///A/1810,///A/1811,///A/1812,///A/1813", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GCCAA", "nts_long": "///A/1790,///A/1791,///A/1792,///A/1793,///A/1794" }, { "index": 2, "num_nts": 7, "nts_short": "GACGUAU", "nts_long": "///A/1806,///A/1807,///A/1808,///A/1809,///A/1810,///A/1811,///A/1812" } ] }, { "index": 79, "type": "asymmetric internal loop", "bridging_nts": [ 12, 4 ], "stem_indices": [ -44, 117 ], "summary": "[2] 12 4 [A.1917 A.1947 A.1930 A.1942] 1 3", "num_nts": 20, "nts_short": "CGAAAUUCCUUGUCGACCUG", "nts_long": "///A/1917,///A/1918,///A/1919,///A/1920,///A/1921,///A/1922,///A/1923,///A/1924,///A/1925,///A/1926,///A/1927,///A/1928,///A/1929,///A/1930,///A/1942,///A/1943,///A/1944,///A/1945,///A/1946,///A/1947", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 12, "nts_short": "GAAAUUCCUUGU", "nts_long": "///A/1918,///A/1919,///A/1920,///A/1921,///A/1922,///A/1923,///A/1924,///A/1925,///A/1926,///A/1927,///A/1928,///A/1929" }, { "index": 2, "num_nts": 4, "nts_short": "ACCU", "nts_long": "///A/1943,///A/1944,///A/1945,///A/1946" } ] }, { "index": 80, "type": "asymmetric internal loop", "bridging_nts": [ 10, 11 ], "stem_indices": [ 115, -42 ], "summary": "[2] 10 11 [A.1843 A.1874 A.1854 A.1862] 2 1", "num_nts": 25, "nts_short": "UCAAGUGGAGCGCUGCGAAAUGAAG", "nts_long": "///A/1843,///A/1844,///A/1845,///A/1846,///A/1847,///A/1848,///A/1849,///A/1850,///A/1851,///A/1852,///A/1853,///A/1854,///A/1862,///A/1863,///A/1864,///A/1865,///A/1866,///A/1867,///A/1868,///A/1869,///A/1870,///A/1871,///A/1872,///A/1873,///A/1874", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "CAAGUGGAGC", "nts_long": "///A/1844,///A/1845,///A/1846,///A/1847,///A/1848,///A/1849,///A/1850,///A/1851,///A/1852,///A/1853" }, { "index": 2, "num_nts": 11, "nts_short": "UGCGAAAUGAA", "nts_long": "///A/1863,///A/1864,///A/1865,///A/1866,///A/1867,///A/1868,///A/1869,///A/1870,///A/1871,///A/1872,///A/1873" } ] } ], "num_junctions": 31, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 1, 4 ], "stem_indices": [ 133, -47, 135 ], "summary": "[3] 1 1 4 [A.2274 A.2316 A.2276 A.2300 A.2302 A.2311] 6 1 2", "num_nts": 12, "nts_short": "CUCGAGUAGAAG", "nts_long": "///A/2274,///A/2275,///A/2276,///A/2300,///A/2301,///A/2302,///A/2311,///A/2312,///A/2313,///A/2314,///A/2315,///A/2316", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2275" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2301" }, { "index": 3, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///A/2312,///A/2313,///A/2314,///A/2315" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 1, 5, 1 ], "stem_indices": [ 65, 66, -28 ], "summary": "[3] 1 5 1 [A.1066 A.1115 A.1068 A.1092 A.1098 A.1113] 4 3 1", "num_nts": 13, "nts_short": "GGAUUCAAAGCAC", "nts_long": "///A/1066,///A/1067,///A/1068,///A/1092,///A/1093,///A/1094,///A/1095,///A/1096,///A/1097,///A/1098,///A/1113,///A/1114,///A/1115", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1067" }, { "index": 2, "num_nts": 5, "nts_short": "UCAAA", "nts_long": "///A/1093,///A/1094,///A/1095,///A/1096,///A/1097" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1114" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 4, 1, 2 ], "stem_indices": [ 77, 78, 100 ], "summary": "[3] 4 1 2 [A.1311 A.1659 A.1316 A.1641 A.1643 A.1656] 4 4 5", "num_nts": 13, "nts_short": "CGUAAGCGAUAAG", "nts_long": "///A/1311,///A/1312,///A/1313,///A/1314,///A/1315,///A/1316,///A/1641,///A/1642,///A/1643,///A/1656,///A/1657,///A/1658,///A/1659", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/1312,///A/1313,///A/1314,///A/1315" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1642" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1657,///A/1658" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 0, 4, 3 ], "stem_indices": [ 159, 160, 161 ], "summary": "[3] 0 4 3 [A.2789 A.2861 A.2790 A.2806 A.2811 A.2857] 4 5 3", "num_nts": 13, "nts_short": "UCGUUAAGCAUCA", "nts_long": "///A/2789,///A/2790,///A/2806,///A/2807,///A/2808,///A/2809,///A/2810,///A/2811,///A/2857,///A/2858,///A/2859,///A/2860,///A/2861", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 4, "nts_short": "UUAA", "nts_long": "///A/2807,///A/2808,///A/2809,///A/2810" }, { "index": 3, "num_nts": 3, "nts_short": "AUC", "nts_long": "///A/2858,///A/2859,///A/2860" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 2, 5, 1 ], "stem_indices": [ 78, 79, 99 ], "summary": "[3] 2 5 1 [A.1319 A.1638 A.1322 A.1621 A.1627 A.1636] 4 2 2", "num_nts": 14, "nts_short": "CAAGCGCAAACGUG", "nts_long": "///A/1319,///A/1320,///A/1321,///A/1322,///A/1621,///A/1622,///A/1623,///A/1624,///A/1625,///A/1626,///A/1627,///A/1636,///A/1637,///A/1638", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1320,///A/1321" }, { "index": 2, "num_nts": 5, "nts_short": "GCAAA", "nts_long": "///A/1622,///A/1623,///A/1624,///A/1625,///A/1626" }, { "index": 3, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1637" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 2, 1, 5 ], "stem_indices": [ 144, 145, 147 ], "summary": "[3] 2 1 5 [A.2496 A.2546 A.2499 A.2524 A.2526 A.2540] 5 3 5", "num_nts": 14, "nts_short": "CAUCGUUAUUAAAG", "nts_long": "///A/2496,///A/2497,///A/2498,///A/2499,///A/2524,///A/2525,///A/2526,///A/2540,///A/2541,///A/2542,///A/2543,///A/2544,///A/2545,///A/2546", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/2497,///A/2498" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2525" }, { "index": 3, "num_nts": 5, "nts_short": "UUAAA", "nts_long": "///A/2541,///A/2542,///A/2543,///A/2544,///A/2545" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 2, 3, 4 ], "stem_indices": [ 43, 44, 46 ], "summary": "[3] 2 3 4 [A.710 A.778 A.713 A.745 A.749 A.773] 9 3 2", "num_nts": 15, "nts_short": "CCAGCGAACGAUGAG", "nts_long": "///A/710,///A/711,///A/712,///A/713,///A/745,///A/746,///A/747,///A/748,///A/749,///A/773,///A/774,///A/775,///A/776,///A/777,///A/778", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/711,///A/712" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/746,///A/747,///A/748" }, { "index": 3, "num_nts": 4, "nts_short": "AUGA", "nts_long": "///A/774,///A/775,///A/776,///A/777" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 4, 0, 5 ], "stem_indices": [ 90, 91, -35 ], "summary": "[3] 4 0 5 [A.1438 A.1590 A.1443 A.1580 A.1581 A.1584] 3 4 1", "num_nts": 15, "nts_short": "GGGACGCCGAAAAGC", "nts_long": "///A/1438,///A/1439,///A/1440,///A/1441,///A/1442,///A/1443,///A/1580,///A/1581,///A/1584,///A/1585,///A/1586,///A/1587,///A/1588,///A/1589,///A/1590", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAC", "nts_long": "///A/1439,///A/1440,///A/1441,///A/1442" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 5, "nts_short": "AAAAG", "nts_long": "///A/1585,///A/1586,///A/1587,///A/1588,///A/1589" } ] }, { "index": 9, "type": "3-way junction", "bridging_nts": [ 3, 1, 6 ], "stem_indices": [ 42, -16, 48 ], "summary": "[3] 3 1 6 [A.696 A.807 A.700 A.788 A.790 A.800] 6 1 3", "num_nts": 16, "nts_short": "UGAGCGGAUAACCGAA", "nts_long": "///A/696,///A/697,///A/698,///A/699,///A/700,///A/788,///A/789,///A/790,///A/800,///A/801,///A/802,///A/803,///A/804,///A/805,///A/806,///A/807", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/697,///A/698,///A/699" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/789" }, { "index": 3, "num_nts": 6, "nts_short": "AACCGA", "nts_long": "///A/801,///A/802,///A/803,///A/804,///A/805,///A/806" } ] }, { "index": 10, "type": "3-way junction", "bridging_nts": [ 5, 6, 5 ], "stem_indices": [ 126, 127, 129 ], "summary": "[3] 5 6 5 [A.2073 A.2208 A.2079 A.2176 A.2183 A.2202] 3 2 4", "num_nts": 22, "nts_short": "AUUGGGAUUUCUAACGGACCGU", "nts_long": "///A/2073,///A/2074,///A/2075,///A/2076,///A/2077,///A/2078,///A/2079,///A/2176,///A/2177,///A/2178,///A/2179,///A/2180,///A/2181,///A/2182,///A/2183,///A/2202,///A/2203,///A/2204,///A/2205,///A/2206,///A/2207,///A/2208", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UUGGG", "nts_long": "///A/2074,///A/2075,///A/2076,///A/2077,///A/2078" }, { "index": 2, "num_nts": 6, "nts_short": "UUCUAA", "nts_long": "///A/2177,///A/2178,///A/2179,///A/2180,///A/2181,///A/2182" }, { "index": 3, "num_nts": 5, "nts_short": "GACCG", "nts_long": "///A/2203,///A/2204,///A/2205,///A/2206,///A/2207" } ] }, { "index": 11, "type": "3-way junction", "bridging_nts": [ 2, 14, 4 ], "stem_indices": [ 3, 4, 32 ], "summary": "[3] 2 14 4 [A.32 A.484 A.35 A.457 A.472 A.479] 2 2 2", "num_nts": 26, "nts_short": "CCUGCGAUAGCGCAUAGUACGGAAAG", "nts_long": "///A/32,///A/33,///A/34,///A/35,///A/457,///A/458,///A/459,///A/460,///A/461,///A/462,///A/463,///A/464,///A/465,///A/466,///A/467,///A/468,///A/469,///A/470,///A/471,///A/472,///A/479,///A/480,///A/481,///A/482,///A/483,///A/484", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/33,///A/34" }, { "index": 2, "num_nts": 14, "nts_short": "GAUAGCGCAUAGUA", "nts_long": "///A/458,///A/459,///A/460,///A/461,///A/462,///A/463,///A/464,///A/465,///A/466,///A/467,///A/468,///A/469,///A/470,///A/471" }, { "index": 3, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/480,///A/481,///A/482,///A/483" } ] }, { "index": 12, "type": "3-way junction", "bridging_nts": [ 0, 9, 13 ], "stem_indices": [ -2, 3, 33 ], "summary": "[3] 0 9 13 [A.30 A.520 A.31 A.485 A.495 A.506] 1 2 4", "num_nts": 28, "nts_short": "GCGUGAAAAGAACGAGUGAAAGAGAACC", "nts_long": "///A/30,///A/31,///A/485,///A/486,///A/487,///A/488,///A/489,///A/490,///A/491,///A/492,///A/493,///A/494,///A/495,///A/506,///A/507,///A/508,///A/509,///A/510,///A/511,///A/512,///A/513,///A/514,///A/515,///A/516,///A/517,///A/518,///A/519,///A/520", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 9, "nts_short": "UGAAAAGAA", "nts_long": "///A/486,///A/487,///A/488,///A/489,///A/490,///A/491,///A/492,///A/493,///A/494" }, { "index": 3, "num_nts": 13, "nts_short": "AGUGAAAGAGAAC", "nts_long": "///A/507,///A/508,///A/509,///A/510,///A/511,///A/512,///A/513,///A/514,///A/515,///A/516,///A/517,///A/518,///A/519" } ] }, { "index": 13, "type": "4-way junction", "bridging_nts": [ 1, 2, 1, 1 ], "stem_indices": [ -4, 10, 13, 11 ], "summary": "[4] 1 2 1 1 [A.58 A.67 A.60 A.92 A.95 A.85 A.87 A.65] 1 2 2 2", "num_nts": 13, "nts_short": "CGAUACGCUGCUG", "nts_long": "///A/58,///A/59,///A/60,///A/92,///A/93,///A/94,///A/95,///A/85,///A/86,///A/87,///A/65,///A/66,///A/67", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/59" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/93,///A/94" }, { "index": 3, "num_nts": 1, "nts_short": "U", "nts_long": "///A/86" }, { "index": 4, "num_nts": 1, "nts_short": "U", "nts_long": "///A/66" } ] }, { "index": 14, "type": "4-way junction", "bridging_nts": [ 2, 2, 2, 0 ], "stem_indices": [ 30, 31, 140, 31 ], "summary": "[4] 2 2 2 0 [A.423 A.430 A.426 A.2389 A.2392 A.2383 A.2386 A.429] 5 4 2 4", "is_repeated": true, "num_nts": 14, "nts_short": "GGACGAAGCGUGCC", "nts_long": "///A/423,///A/424,///A/425,///A/426,///A/2389,///A/2390,///A/2391,///A/2392,///A/2383,///A/2384,///A/2385,///A/2386,///A/429,///A/430", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/424,///A/425" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2390,///A/2391" }, { "index": 3, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/2384,///A/2385" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 15, "type": "4-way junction", "bridging_nts": [ 5, 0, 2, 0 ], "stem_indices": [ 75, 76, 77, 101 ], "summary": "[4] 5 0 2 0 [A.1283 A.1993 A.1289 A.1307 A.1308 A.1662 A.1665 A.1992] 2 6 4 4", "num_nts": 15, "nts_short": "CGAUAAAUCGCGCGG", "nts_long": "///A/1283,///A/1284,///A/1285,///A/1286,///A/1287,///A/1288,///A/1289,///A/1307,///A/1308,///A/1662,///A/1663,///A/1664,///A/1665,///A/1992,///A/1993", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUAA", "nts_long": "///A/1284,///A/1285,///A/1286,///A/1287,///A/1288" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/1663,///A/1664" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 16, "type": "4-way junction", "bridging_nts": [ 2, 1, 4, 2 ], "stem_indices": [ 151, 152, 153, 157 ], "summary": "[4] 2 1 4 2 [A.2622 A.2751 A.2625 A.2653 A.2655 A.2711 A.2716 A.2748] 4 7 5 2", "num_nts": 17, "nts_short": "GAGUAACGGAACGCAGC", "nts_long": "///A/2622,///A/2623,///A/2624,///A/2625,///A/2653,///A/2654,///A/2655,///A/2711,///A/2712,///A/2713,///A/2714,///A/2715,///A/2716,///A/2748,///A/2749,///A/2750,///A/2751", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2623,///A/2624" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2654" }, { "index": 3, "num_nts": 4, "nts_short": "GAAC", "nts_long": "///A/2712,///A/2713,///A/2714,///A/2715" }, { "index": 4, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2749,///A/2750" } ] }, { "index": 17, "type": "4-way junction", "bridging_nts": [ 4, 4, 1, 1 ], "stem_indices": [ 132, 133, 137, 138 ], "summary": "[4] 4 4 1 1 [A.2264 A.2362 A.2269 A.2321 A.2326 A.2349 A.2351 A.2360] 2 6 4 3", "num_nts": 18, "nts_short": "CAAAGGCUUGACGGGCGG", "nts_long": "///A/2264,///A/2265,///A/2266,///A/2267,///A/2268,///A/2269,///A/2321,///A/2322,///A/2323,///A/2324,///A/2325,///A/2326,///A/2349,///A/2350,///A/2351,///A/2360,///A/2361,///A/2362", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AAAG", "nts_long": "///A/2265,///A/2266,///A/2267,///A/2268" }, { "index": 2, "num_nts": 4, "nts_short": "UUGA", "nts_long": "///A/2322,///A/2323,///A/2324,///A/2325" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2350" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///A/2361" } ] }, { "index": 18, "type": "4-way junction", "bridging_nts": [ 6, 1, 1, 6 ], "stem_indices": [ 94, 95, 156, 95 ], "summary": "[4] 6 1 1 6 [A.1463 A.1478 A.1470 A.2683 A.2685 A.2680 A.2682 A.1471] 4 2 6 2", "is_repeated": true, "num_nts": 22, "nts_short": "AAGCUAUGCAAUACGCUAUGCU", "nts_long": "///A/1463,///A/1464,///A/1465,///A/1466,///A/1467,///A/1468,///A/1469,///A/1470,///A/2683,///A/2684,///A/2685,///A/2680,///A/2681,///A/2682,///A/1471,///A/1472,///A/1473,///A/1474,///A/1475,///A/1476,///A/1477,///A/1478", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AGCUAU", "nts_long": "///A/1464,///A/1465,///A/1466,///A/1467,///A/1468,///A/1469" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2684" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2681" }, { "index": 4, "num_nts": 6, "nts_short": "CUAUGC", "nts_long": "///A/1472,///A/1473,///A/1474,///A/1475,///A/1476,///A/1477" } ] }, { "index": 19, "type": "4-way junction", "bridging_nts": [ 3, 5, 3, 9 ], "stem_indices": [ 37, -14, 39, 40 ], "summary": "[4] 3 5 3 9 [A.611 A.669 A.615 A.633 A.639 A.646 A.650 A.659] 10 1 2 2", "num_nts": 28, "nts_short": "CGAGCGGCGGAGCGAGUGGCGGCAUUAG", "nts_long": "///A/611,///A/612,///A/613,///A/614,///A/615,///A/633,///A/634,///A/635,///A/636,///A/637,///A/638,///A/639,///A/646,///A/647,///A/648,///A/649,///A/650,///A/659,///A/660,///A/661,///A/662,///A/663,///A/664,///A/665,///A/666,///A/667,///A/668,///A/669", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/612,///A/613,///A/614" }, { "index": 2, "num_nts": 5, "nts_short": "GCGGA", "nts_long": "///A/634,///A/635,///A/636,///A/637,///A/638" }, { "index": 3, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/647,///A/648,///A/649" }, { "index": 4, "num_nts": 9, "nts_short": "GCGGCAUUA", "nts_long": "///A/660,///A/661,///A/662,///A/663,///A/664,///A/665,///A/666,///A/667,///A/668" } ] }, { "index": 20, "type": "4-way junction", "bridging_nts": [ 2, 3, 11, 5 ], "stem_indices": [ 111, 112, 116, -43 ], "summary": "[4] 2 3 11 5 [A.1824 A.1956 A.1827 A.1888 A.1892 A.1904 A.1916 A.1950] 3 3 2 1", "num_nts": 29, "nts_short": "CCUGCGGCCGGUCCUAAGGUAGCGAAAGG", "nts_long": "///A/1824,///A/1825,///A/1826,///A/1827,///A/1888,///A/1889,///A/1890,///A/1891,///A/1892,///A/1904,///A/1905,///A/1906,///A/1907,///A/1908,///A/1909,///A/1910,///A/1911,///A/1912,///A/1913,///A/1914,///A/1915,///A/1916,///A/1950,///A/1951,///A/1952,///A/1953,///A/1954,///A/1955,///A/1956", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/1825,///A/1826" }, { "index": 2, "num_nts": 3, "nts_short": "GGC", "nts_long": "///A/1889,///A/1890,///A/1891" }, { "index": 3, "num_nts": 11, "nts_short": "GUCCUAAGGUA", "nts_long": "///A/1905,///A/1906,///A/1907,///A/1908,///A/1909,///A/1910,///A/1911,///A/1912,///A/1913,///A/1914,///A/1915" }, { "index": 4, "num_nts": 5, "nts_short": "GAAAG", "nts_long": "///A/1951,///A/1952,///A/1953,///A/1954,///A/1955" } ] }, { "index": 21, "type": "4-way junction", "bridging_nts": [ 1, 8, 11, 4 ], "stem_indices": [ 93, 94, -31, 98 ], "summary": "[4] 1 8 11 4 [A.1458 A.1563 A.1460 A.1481 A.1490 A.1533 A.1545 A.1558] 5 4 1 2", "num_nts": 32, "nts_short": "AUGUUGGUACGCUGACGUAUCGGGAGCGAAGU", "nts_long": "///A/1458,///A/1459,///A/1460,///A/1481,///A/1482,///A/1483,///A/1484,///A/1485,///A/1486,///A/1487,///A/1488,///A/1489,///A/1490,///A/1533,///A/1534,///A/1535,///A/1536,///A/1537,///A/1538,///A/1539,///A/1540,///A/1541,///A/1542,///A/1543,///A/1544,///A/1545,///A/1558,///A/1559,///A/1560,///A/1561,///A/1562,///A/1563", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1459" }, { "index": 2, "num_nts": 8, "nts_short": "UGGUACGC", "nts_long": "///A/1482,///A/1483,///A/1484,///A/1485,///A/1486,///A/1487,///A/1488,///A/1489" }, { "index": 3, "num_nts": 11, "nts_short": "ACGUAUCGGGA", "nts_long": "///A/1534,///A/1535,///A/1536,///A/1537,///A/1538,///A/1539,///A/1540,///A/1541,///A/1542,///A/1543,///A/1544" }, { "index": 4, "num_nts": 4, "nts_short": "GAAG", "nts_long": "///A/1559,///A/1560,///A/1561,///A/1562" } ] }, { "index": 22, "type": "5-way junction", "bridging_nts": [ 6, 4, 0, 0, 0 ], "stem_indices": [ 7, 8, 14, 15, 16 ], "summary": "[5] 6 4 0 0 0 [A.46 A.155 A.53 A.114 A.119 A.128 A.129 A.142 A.143 A.154] 2 3 3 5 4", "num_nts": 20, "nts_short": "CGAUGAAGCGAAUGCAUAUG", "nts_long": "///A/46,///A/47,///A/48,///A/49,///A/50,///A/51,///A/52,///A/53,///A/114,///A/115,///A/116,///A/117,///A/118,///A/119,///A/128,///A/129,///A/142,///A/143,///A/154,///A/155", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAUGAA", "nts_long": "///A/47,///A/48,///A/49,///A/50,///A/51,///A/52" }, { "index": 2, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///A/115,///A/116,///A/117,///A/118" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 23, "type": "5-way junction", "bridging_nts": [ 4, 2, 2, 0, 5 ], "stem_indices": [ 35, 36, 41, 49, -29 ], "summary": "[5] 4 2 2 0 5 [A.593 A.1269 A.598 A.681 A.684 A.822 A.825 A.1209 A.1210 A.1263] 6 3 2 6 1", "num_nts": 23, "nts_short": "CGACUUAGACGUUCGCGCGGAUG", "nts_long": "///A/593,///A/594,///A/595,///A/596,///A/597,///A/598,///A/681,///A/682,///A/683,///A/684,///A/822,///A/823,///A/824,///A/825,///A/1209,///A/1210,///A/1263,///A/1264,///A/1265,///A/1266,///A/1267,///A/1268,///A/1269", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GACU", "nts_long": "///A/594,///A/595,///A/596,///A/597" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/682,///A/683" }, { "index": 3, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/823,///A/824" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 5, "num_nts": 5, "nts_short": "CGGAU", "nts_long": "///A/1264,///A/1265,///A/1266,///A/1267,///A/1268" } ] }, { "index": 24, "type": "5-way junction", "bridging_nts": [ 8, 1, 0, 7, 1 ], "stem_indices": [ -37, 104, 105, -40, 107 ], "summary": "[5] 8 1 0 7 1 [A.1691 A.1973 A.1700 A.1722 A.1724 A.1742 A.1743 A.1747 A.1755 A.1971] 1 4 4 1 6", "num_nts": 27, "nts_short": "GCAAUCUCACGUCGCGUGAAUAGGCGC", "nts_long": "///A/1691,///A/1692,///A/1693,///A/1694,///A/1695,///A/1696,///A/1697,///A/1698,///A/1699,///A/1700,///A/1722,///A/1723,///A/1724,///A/1742,///A/1743,///A/1747,///A/1748,///A/1749,///A/1750,///A/1751,///A/1752,///A/1753,///A/1754,///A/1755,///A/1971,///A/1972,///A/1973", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "CAAUCUCA", "nts_long": "///A/1692,///A/1693,///A/1694,///A/1695,///A/1696,///A/1697,///A/1698,///A/1699" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1723" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 7, "nts_short": "UGAAUAG", "nts_long": "///A/1748,///A/1749,///A/1750,///A/1751,///A/1752,///A/1753,///A/1754" }, { "index": 5, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1972" } ] }, { "index": 25, "type": "5-way junction", "bridging_nts": [ 9, 6, 6, 7, 10 ], "stem_indices": [ 120, 121, -52, -56, 148 ], "summary": "[5] 9 6 6 7 10 [A.2037 A.2594 A.2047 A.2425 A.2432 A.2479 A.2486 A.2561 A.2569 A.2583] 3 4 1 1 2", "num_nts": 48, "nts_short": "ACGAAAAGACCGGAUAACAUCGAUGUCGGUUCAGAAUUCGGUCUCUAU", "nts_long": "///A/2037,///A/2038,///A/2039,///A/2040,///A/2041,///A/2042,///A/2043,///A/2044,///A/2045,///A/2046,///A/2047,///A/2425,///A/2426,///A/2427,///A/2428,///A/2429,///A/2430,///A/2431,///A/2432,///A/2479,///A/2480,///A/2481,///A/2482,///A/2483,///A/2484,///A/2485,///A/2486,///A/2561,///A/2562,///A/2563,///A/2564,///A/2565,///A/2566,///A/2567,///A/2568,///A/2569,///A/2583,///A/2584,///A/2585,///A/2586,///A/2587,///A/2588,///A/2589,///A/2590,///A/2591,///A/2592,///A/2593,///A/2594", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "CGAAAAGAC", "nts_long": "///A/2038,///A/2039,///A/2040,///A/2041,///A/2042,///A/2043,///A/2044,///A/2045,///A/2046" }, { "index": 2, "num_nts": 6, "nts_short": "GAUAAC", "nts_long": "///A/2426,///A/2427,///A/2428,///A/2429,///A/2430,///A/2431" }, { "index": 3, "num_nts": 6, "nts_short": "CGAUGU", "nts_long": "///A/2480,///A/2481,///A/2482,///A/2483,///A/2484,///A/2485" }, { "index": 4, "num_nts": 7, "nts_short": "GUUCAGA", "nts_long": "///A/2562,///A/2563,///A/2564,///A/2565,///A/2566,///A/2567,///A/2568" }, { "index": 5, "num_nts": 10, "nts_short": "UCGGUCUCUA", "nts_long": "///A/2584,///A/2585,///A/2586,///A/2587,///A/2588,///A/2589,///A/2590,///A/2591,///A/2592,///A/2593" } ] }, { "index": 26, "type": "6-way junction", "bridging_nts": [ 1, 0, 0, 1, 5, 5 ], "stem_indices": [ -46, 132, 136, 135, -48, 139 ], "summary": "[6] 1 0 0 1 5 5 [A.2261 A.2406 A.2263 A.2363 A.2364 A.2309 A.2310 A.2303 A.2305 A.2368 A.2374 A.2400] 1 2 3 2 1 7", "num_nts": 24, "nts_short": "GCCGCGGCGCGUGAACCGAUCAAC", "nts_long": 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A.1018 A.1022 A.1161] 3 3 1 2 3 1", "is_repeated": true, "num_nts": 31, "nts_short": "UCGGCGGUUAAGCGAAAAUGAUCGCUAAAUA", "nts_long": "///A/1015,///A/1016,///A/1148,///A/1149,///A/1150,///A/1035,///A/1036,///A/1037,///A/1038,///A/1039,///A/1040,///A/1041,///A/1135,///A/1136,///A/1137,///A/1138,///A/1139,///A/1140,///A/1141,///A/1142,///A/1143,///A/1144,///A/1145,///A/1146,///A/1018,///A/1019,///A/1020,///A/1021,///A/1022,///A/1161,///A/1162", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1149" }, { "index": 3, "num_nts": 5, "nts_short": "GUUAA", "nts_long": "///A/1036,///A/1037,///A/1038,///A/1039,///A/1040" }, { "index": 4, "num_nts": 10, "nts_short": "GAAAAUGAUC", "nts_long": "///A/1136,///A/1137,///A/1138,///A/1139,///A/1140,///A/1141,///A/1142,///A/1143,///A/1144,///A/1145" }, { "index": 5, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1019,///A/1020,///A/1021" }, { "index": 6, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 28, "type": "6-way junction", "bridging_nts": [ 0, 3, 9, 3, 3, 6 ], "stem_indices": [ 6, 7, -7, 19, 20, 22 ], "summary": "[6] 0 3 9 3 3 6 [A.44 A.446 A.45 A.156 A.160 A.191 A.201 A.208 A.212 A.239 A.243 A.439] 2 2 1 2 4 3", "num_nts": 36, "nts_short": "GCGGAACGGAGAAGAAAGCGAUUAUCAGCUAAAUAC", "nts_long": "///A/44,///A/45,///A/156,///A/157,///A/158,///A/159,///A/160,///A/191,///A/192,///A/193,///A/194,///A/195,///A/196,///A/197,///A/198,///A/199,///A/200,///A/201,///A/208,///A/209,///A/210,///A/211,///A/212,///A/239,///A/240,///A/241,///A/242,///A/243,///A/439,///A/440,///A/441,///A/442,///A/443,///A/444,///A/445,///A/446", "num_stems": 6, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/157,///A/158,///A/159" }, { "index": 3, "num_nts": 9, "nts_short": "GAGAAGAAA", "nts_long": 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"num_nts": 7, "nts_short": "UCUGGUA", "nts_long": "///A/1197,///A/1198,///A/1199,///A/1200,///A/1201,///A/1202,///A/1203" } ] }, { "index": 31, "type": "9-way junction", "bridging_nts": [ 3, 4, 0, 0, 1, 3, 0, 0, 2 ], "stem_indices": [ 79, 80, 82, -30, 83, 84, 87, 82, 83 ], "summary": "[9] 3 4 0 0 1 3 0 0 2 [A.1323 A.1620 A.1327 A.1351 A.1356 A.1417 A.1418 A.1613 A.1614 A.1361 A.1363 A.1394 A.1398 A.1415 A.1416 A.1357 A.1358 A.1617] 2 6 2 1 4 2 5 2 4", "is_repeated": true, "num_nts": 31, "nts_short": "GGUUCGGAAAGCCGCGACGACAGCAUCGUAC", "nts_long": "///A/1323,///A/1324,///A/1325,///A/1326,///A/1327,///A/1351,///A/1352,///A/1353,///A/1354,///A/1355,///A/1356,///A/1417,///A/1418,///A/1613,///A/1614,///A/1361,///A/1362,///A/1363,///A/1394,///A/1395,///A/1396,///A/1397,///A/1398,///A/1415,///A/1416,///A/1357,///A/1358,///A/1617,///A/1618,///A/1619,///A/1620", "num_stems": 9, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUU", "nts_long": "///A/1324,///A/1325,///A/1326" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/1352,///A/1353,///A/1354,///A/1355" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 5, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1362" }, { "index": 6, "num_nts": 3, "nts_short": "ACA", "nts_long": "///A/1395,///A/1396,///A/1397" }, { "index": 7, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 8, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 9, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1618,///A/1619" } ] } ], "num_ssSegments": 31, "ssSegments": [ { "index": 1, "num_nts": 6, "nts_short": "UAGUAA", "nts_long": "///A/9,///A/10,///A/11,///A/12,///A/13,///A/14" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/73" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///A/111" }, { "index": 4, "num_nts": 3, "nts_short": "CAA", "nts_long": "///A/246,///A/247,///A/248" }, { "index": 5, "is_broken": true, "num_nts": 5, "nts_short": "AAGUA", "nts_long": "///A/373,///A/384,///A/385,///A/386,///A/387" }, { "index": 6, "num_nts": 6, "nts_short": "GAAUCC", "nts_long": "///A/413,///A/414,///A/415,///A/416,///A/417,///A/418" }, { "index": 7, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/435,///A/436" }, { "index": 8, "num_nts": 7, "nts_short": "ACAAGCA", "nts_long": "///A/536,///A/537,///A/538,///A/539,///A/540,///A/541,///A/542" }, { "index": 9, "num_nts": 3, "nts_short": "GUG", "nts_long": "///A/570,///A/571,///A/572" }, { "index": 10, "num_nts": 1, "nts_short": "A", "nts_long": "///A/587" }, { "index": 11, "is_broken": true, "num_nts": 9, "nts_short": "CUAGCCAAA", "nts_long": "///A/889,///A/890,///A/891,///A/892,///A/909,///A/910,///A/911,///A/912,///A/913" }, { "index": 12, "num_nts": 7, "nts_short": "AUGAGUA", "nts_long": "///A/1275,///A/1276,///A/1277,///A/1278,///A/1279,///A/1280,///A/1281" }, { "index": 13, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1764" }, { "index": 14, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1766" }, { "index": 15, "num_nts": 3, "nts_short": "ACA", "nts_long": "///A/1780,///A/1781,///A/1782" }, { "index": 16, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1820" }, { "index": 17, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/1959,///A/1960,///A/1961" }, { "index": 18, "num_nts": 11, "nts_short": "GAAAUUGAAUU", "nts_long": "///A/1995,///A/1996,///A/1997,///A/1998,///A/1999,///A/2000,///A/2001,///A/2002,///A/2003,///A/2004,///A/2005" }, { "index": 19, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2024,///A/2025" }, { "index": 20, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2058,///A/2059" }, { "index": 21, "num_nts": 17, "nts_short": "UCGGGUUUCUCUGCGUA", "nts_long": "///A/2081,///A/2082,///A/2083,///A/2084,///A/2085,///A/2086,///A/2087,///A/2088,///A/2089,///A/2090,///A/2091,///A/2092,///A/2093,///A/2094,///A/2095,///A/2096,///A/2097" }, { "index": 22, "is_broken": true, "num_nts": 25, "nts_short": "GGGAGAAACUGGCCGGUCGGUGGCC", "nts_long": "///A/2106,///A/2107,///A/2108,///A/2109,///A/2110,///A/2117,///A/2118,///A/2119,///A/2120,///A/2121,///A/2122,///A/2123,///A/2124,///A/2125,///A/2132,///A/2133,///A/2134,///A/2135,///A/2136,///A/2137,///A/2138,///A/2139,///A/2140,///A/2157,///A/2158" }, { "index": 23, "num_nts": 13, "nts_short": "CUGAGAAACUUGG", "nts_long": "///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" }, { "index": 24, "num_nts": 3, "nts_short": "UUG", "nts_long": "///A/2223,///A/2224,///A/2225" }, { "index": 25, "num_nts": 6, "nts_short": "GAUAAA", "nts_long": "///A/2408,///A/2409,///A/2410,///A/2411,///A/2412,///A/2413" }, { "index": 26, "num_nts": 3, "nts_short": "GCA", "nts_long": "///A/2606,///A/2607,///A/2608" }, { "index": 27, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2769,///A/2770" }, { "index": 28, "is_broken": true, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2774,///A/2778" }, { "index": 29, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/2782,///A/2783,///A/2784,///A/2785" }, { "index": 30, "num_nts": 4, "nts_short": "GAGG", "nts_long": "///A/2865,///A/2866,///A/2867,///A/2868" }, { "index": 31, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2877" } ], "num_kissingLoops": 6, "kissingLoops": [ { "index": 1, "stem_index": -45, "is_isoCanonPair": true, "hairpin_indices": [ 52, 54 ] }, { "index": 2, "stem_index": -8, "is_isoCanonPair": true, "hairpin_indices": [ 7, 9 ] }, { "index": 3, "stem_index": 10, "hairpin_indices": [ 1, 3 ] }, { "index": 4, "stem_index": 11, "hairpin_indices": [ 1, 3 ] }, { "index": 5, "stem_index": 31, "hairpin_indices": [ 14, 59 ] }, { "index": 6, "stem_index": 95, "hairpin_indices": [ 36, 65 ] } ], "num_Aminors": 115, "Aminors": [ { "index": 1, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/51 vs ///A/46,///A/155", "A_nt1": { "desc": "///A/51 vs ///A/46", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.56]" }, "A_nt2": { "desc": "///A/51 vs ///A/155", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.18]" } }, { "index": 2, "type": "X", "desc_short": "A vs A-G (--)", "desc_long": "///A/70 vs ///A/55,///A/69", "A_nt1": { "desc": "///A/70 vs ///A/55", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/70 vs ///A/69", "face_type": "-", "hbonds_num": 4, "hbonds_desc": "OP1-O2'(hydroxyl)[2.67],O5'-O2'(hydroxyl)[2.39],O4'-O2'(hydroxyl)[2.98],N1-N2(amino)[3.12]" } }, { "index": 3, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/70 vs ///A/56,///A/69", "A_nt1": { "desc": "///A/70 vs ///A/56", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/70 vs ///A/69", "face_type": "-", "hbonds_num": 4, "hbonds_desc": "OP1-O2'(hydroxyl)[2.67],O5'-O2'(hydroxyl)[2.39],O4'-O2'(hydroxyl)[2.98],N1-N2(amino)[3.12]" } }, { "index": 4, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/124 vs ///A/53,///A/114", "A_nt1": { "desc": "///A/124 vs ///A/53", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/124 vs ///A/114", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.96],N3-O2'(hydroxyl)[2.77]" } }, { "index": 5, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/125 vs ///A/54,///A/113", "A_nt1": { "desc": "///A/125 vs ///A/54", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.86],N3-N2(amino)[2.90]" }, "A_nt2": { "desc": "///A/125 vs ///A/113", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.90],O2'(hydroxyl)-O2(carbonyl)[3.18]" } }, { "index": 6, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/167 vs ///A/692,///A/811", "A_nt1": { "desc": "///A/167 vs ///A/692", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.90],N3-O2'(hydroxyl)[2.79]" }, "A_nt2": { "desc": "///A/167 vs ///A/811", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 7, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/168 vs ///A/691,///A/812", "A_nt1": { "desc": "///A/168 vs ///A/691", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.57],O2'(hydroxyl)-O2(carbonyl)[2.94]" }, "A_nt2": { "desc": "///A/168 vs ///A/812", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.03]" } }, { "index": 8, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/173 vs ///A/839,///A/844", "A_nt1": { "desc": "///A/173 vs ///A/839", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/173 vs ///A/844", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)*N2(amino)[3.12],N6(amino)-N3[3.41],N1-N2(amino)[3.39]" } }, { "index": 9, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/176 vs ///A/2061,///A/2221", "A_nt1": { "desc": "///A/176 vs ///A/2061", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/176 vs ///A/2221", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O5'-O2'(hydroxyl)[3.58]" } }, { "index": 10, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/200 vs ///A/420,///A/433", "A_nt1": { "desc": "///A/200 vs ///A/420", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.76]" }, "A_nt2": { "desc": "///A/200 vs ///A/433", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.88],O2'(hydroxyl)-N3[2.76],N3-N2(amino)[3.36]" } }, { "index": 11, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/228 vs ///A/171,///A/178", "A_nt1": { "desc": "///A/228 vs ///A/171", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.16]" }, "A_nt2": { "desc": "///A/228 vs ///A/178", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 12, "type": "X", "desc_short": "A vs A-C (--)", "desc_long": "///A/228 vs ///A/172,///A/178", "A_nt1": { "desc": "///A/228 vs ///A/172", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O4'-O2'(hydroxyl)[2.85],O2'(hydroxyl)-O4'[2.99]" }, "A_nt2": { "desc": "///A/228 vs ///A/178", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 13, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/310 vs ///A/330,///A/334", "A_nt1": { "desc": "///A/310 vs ///A/330", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.95]" }, "A_nt2": { "desc": "///A/310 vs ///A/334", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 14, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/311 vs ///A/329,///A/344", "A_nt1": { "desc": "///A/311 vs ///A/329", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.86],O2'(hydroxyl)-O2(carbonyl)[2.71]" }, "A_nt2": { "desc": "///A/311 vs ///A/344", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.59],N3-N2(amino)[3.03]" } }, { "index": 15, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/415 vs ///A/419,///A/434", "A_nt1": { "desc": "///A/415 vs ///A/419", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.10]" }, "A_nt2": { "desc": "///A/415 vs ///A/434", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 16, "type": "X", "desc_short": "A vs A-G (Imino)", "desc_long": "///A/445 vs ///A/159,///A/192", "A_nt1": { "desc": "///A/445 vs ///A/159", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/445 vs ///A/192", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.40]" } }, { "index": 17, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/445 vs ///A/160,///A/191", "A_nt1": { "desc": "///A/445 vs ///A/160", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.94]" }, "A_nt2": { "desc": "///A/445 vs ///A/191", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 18, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/455 vs ///A/1214,///A/1258", "A_nt1": { "desc": "///A/455 vs ///A/1214", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.07]" }, "A_nt2": { "desc": "///A/455 vs ///A/1258", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.98],N3-N2(amino)[2.97]" } }, { "index": 19, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/461 vs ///A/35,///A/457", "A_nt1": { "desc": "///A/461 vs ///A/35", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/461 vs ///A/457", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.80],N3-O2'(hydroxyl)[2.81]" } }, { "index": 20, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/477 vs ///A/695,///A/808", "A_nt1": { "desc": "///A/477 vs ///A/695", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.16]" }, "A_nt2": { "desc": "///A/477 vs ///A/808", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.99]" } }, { "index": 21, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/524 vs ///A/590,///A/1272", "A_nt1": { "desc": "///A/524 vs ///A/590", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.16],O2'(hydroxyl)-O2'(hydroxyl)[2.72],N3-O2'(hydroxyl)[2.69]" }, "A_nt2": { "desc": "///A/524 vs ///A/1272", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 22, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/525 vs ///A/589,///A/1273", "A_nt1": { "desc": "///A/525 vs ///A/589", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.90],O2'(hydroxyl)-O2(carbonyl)[3.04]" }, "A_nt2": { "desc": "///A/525 vs ///A/1273", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.08],N3-N2(amino)[2.88]" } }, { "index": 23, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/536 vs ///A/2026,///A/2604", "A_nt1": { "desc": "///A/536 vs ///A/2026", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.82],O2'(hydroxyl)-O2(carbonyl)[3.01]" }, "A_nt2": { "desc": "///A/536 vs ///A/2604", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 24, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/595 vs ///A/684,///A/822", "A_nt1": { "desc": "///A/595 vs ///A/684", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.22]" }, "A_nt2": { "desc": "///A/595 vs ///A/822", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.78],N3-N2(amino)[3.59]" } }, { "index": 25, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/618 vs ///A/214,///A/237", "A_nt1": { "desc": "///A/618 vs ///A/214", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.71],O2'(hydroxyl)-O2(carbonyl)[2.82]" }, "A_nt2": { "desc": "///A/618 vs ///A/237", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.73],N3-N2(amino)[3.00]" } }, { "index": 26, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/626 vs ///A/622,///A/627", "A_nt1": { "desc": "///A/626 vs ///A/622", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.14]" }, "A_nt2": { "desc": "///A/626 vs ///A/627", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 27, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/632 vs ///A/215,///A/236", "A_nt1": { "desc": "///A/632 vs ///A/215", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.52]" }, "A_nt2": { "desc": "///A/632 vs ///A/236", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[3.04],O2'(hydroxyl)-O2'(hydroxyl)[2.77],O2'(hydroxyl)-O2(carbonyl)[2.66]" } }, { "index": 28, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/683 vs ///A/598,///A/681", "A_nt1": { "desc": "///A/683 vs ///A/598", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/683 vs ///A/681", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.86]" } }, { "index": 29, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/688 vs ///A/2050,///A/2422", "A_nt1": { "desc": "///A/688 vs ///A/2050", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/688 vs ///A/2422", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.76],N3-O2'(hydroxyl)[2.95]" } }, { "index": 30, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/762 vs ///A/757,///A/766", "A_nt1": { "desc": "///A/762 vs ///A/757", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/762 vs ///A/766", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.56]" } }, { "index": 31, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/794 vs ///A/1767,///A/1779", "A_nt1": { "desc": "///A/794 vs ///A/1767", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.19],N3-N2(amino)[3.10]" }, "A_nt2": { "desc": "///A/794 vs ///A/1779", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.63],O2'(hydroxyl)-O2(carbonyl)[3.04]" } }, { "index": 32, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/832 vs ///A/850,///A/953", "A_nt1": { "desc": "///A/832 vs ///A/850", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.71],O2'(hydroxyl)-O2(carbonyl)[3.10]" }, "A_nt2": { "desc": "///A/832 vs ///A/953", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.72]" } }, { "index": 33, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/879 vs ///A/877,///A/924", "A_nt1": { "desc": "///A/879 vs ///A/877", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.35]" }, "A_nt2": { "desc": "///A/879 vs ///A/924", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 34, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/922 vs ///A/2243,///A/2255", "A_nt1": { "desc": "///A/922 vs ///A/2243", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.64],O2'(hydroxyl)-O2'(hydroxyl)[2.75],N3-O2'(hydroxyl)[2.92]" }, "A_nt2": { "desc": "///A/922 vs ///A/2255", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 35, "type": "X", "desc_short": "A vs U-U (--)", "desc_long": "///A/944 vs ///A/859,///A/943", "A_nt1": { "desc": "///A/944 vs ///A/859", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1*O2(carbonyl)[2.80]" }, "A_nt2": { "desc": "///A/944 vs ///A/943", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O4'-O2'(hydroxyl)[2.62]" } }, { "index": 36, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/970 vs ///A/2436,///A/2473", "A_nt1": { "desc": "///A/970 vs ///A/2436", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.63],O2'(hydroxyl)-O2'(hydroxyl)[3.03],N3-O2'(hydroxyl)[2.66]" }, "A_nt2": { "desc": "///A/970 vs ///A/2473", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 37, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/971 vs ///A/2435,///A/2474", "A_nt1": { "desc": "///A/971 vs ///A/2435", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.77]" }, "A_nt2": { "desc": "///A/971 vs ///A/2474", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.94]" } }, { "index": 38, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/991 vs ///A/2009,///A/2020", "A_nt1": { "desc": "///A/991 vs ///A/2009", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/991 vs ///A/2020", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1-N2(amino)[3.13],N3-O2'(hydroxyl)[2.95]" } }, { "index": 39, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/992 vs ///A/2010,///A/2019", "A_nt1": { "desc": "///A/992 vs ///A/2010", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.80],N3-N2(amino)[3.36]" }, "A_nt2": { "desc": "///A/992 vs ///A/2019", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[2.75]" } }, { "index": 40, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/994 vs ///A/957,///A/982", "A_nt1": { "desc": "///A/994 vs ///A/957", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/994 vs ///A/982", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O3'[3.07],N3-O2'(hydroxyl)[2.53]" } }, { "index": 41, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1011 vs ///A/987,///A/998", "A_nt1": { "desc": "///A/1011 vs ///A/987", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1011 vs ///A/998", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.88],O2'(hydroxyl)-O2'(hydroxyl)[2.69],N3-O2'(hydroxyl)[2.66]" } }, { "index": 42, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1012 vs ///A/988,///A/997", "A_nt1": { "desc": "///A/1012 vs ///A/988", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.85],N3-N2(amino)[2.99]" }, "A_nt2": { "desc": "///A/1012 vs ///A/997", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.18]" } }, { "index": 43, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1020 vs ///A/1013,///A/1164", "A_nt1": { "desc": "///A/1020 vs ///A/1013", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1020 vs ///A/1164", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.13]" } }, { "index": 44, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1021 vs ///A/1014,///A/1163", "A_nt1": { "desc": "///A/1021 vs ///A/1014", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.71],N3-N2(amino)[3.15]" }, "A_nt2": { "desc": "///A/1021 vs ///A/1163", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.06],O2'(hydroxyl)-O2(carbonyl)[2.71]" } }, { "index": 45, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1039 vs ///A/2443,///A/2465", "A_nt1": { "desc": "///A/1039 vs ///A/2443", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1039 vs ///A/2465", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.94],N3-O2'(hydroxyl)[2.86]" } }, { "index": 46, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1040 vs ///A/2444,///A/2464", "A_nt1": { "desc": "///A/1040 vs ///A/2444", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.13]" }, "A_nt2": { "desc": "///A/1040 vs ///A/2464", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 47, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1059 vs ///A/1054,///A/1123", "A_nt1": { "desc": "///A/1059 vs ///A/1054", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1059 vs ///A/1123", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.08]" } }, { "index": 48, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1095 vs ///A/1065,///A/1116", "A_nt1": { "desc": "///A/1095 vs ///A/1065", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1095 vs ///A/1116", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.48]" } }, { "index": 49, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1096 vs ///A/1066,///A/1115", "A_nt1": { "desc": "///A/1096 vs ///A/1066", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.39],N3-N2(amino)[2.84]" }, "A_nt2": { "desc": "///A/1096 vs ///A/1115", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[2.98]" } }, { "index": 50, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1138 vs ///A/2442,///A/2466", "A_nt1": { "desc": "///A/1138 vs ///A/2442", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.16]" }, "A_nt2": { "desc": "///A/1138 vs ///A/2466", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 51, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1140 vs ///A/2494,///A/2548", "A_nt1": { "desc": "///A/1140 vs ///A/2494", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.79],O2'(hydroxyl)-O2(carbonyl)[2.79]" }, "A_nt2": { "desc": "///A/1140 vs ///A/2548", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.77]" } }, { "index": 52, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1143 vs ///A/2008,///A/2021", "A_nt1": { "desc": "///A/1143 vs ///A/2008", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N7-O2'(hydroxyl)[3.09],N6(amino)-O2'(hydroxyl)[2.75],N6(amino)-O2(carbonyl)[3.29]" }, "A_nt2": { "desc": "///A/1143 vs ///A/2021", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 53, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1233 vs ///A/552,///A/560", "A_nt1": { "desc": "///A/1233 vs ///A/552", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1233 vs ///A/560", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.86]" } }, { "index": 54, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1238 vs ///A/826,///A/1208", "A_nt1": { "desc": "///A/1238 vs ///A/826", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.16],O2'(hydroxyl)-O2'(hydroxyl)[2.77],N3-O2'(hydroxyl)[3.34]" }, "A_nt2": { "desc": "///A/1238 vs ///A/1208", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 55, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1239 vs ///A/825,///A/1209", "A_nt1": { "desc": "///A/1239 vs ///A/825", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.55],O2'(hydroxyl)-O2(carbonyl)[3.18]" }, "A_nt2": { "desc": "///A/1239 vs ///A/1209", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.94],N3-N2(amino)[3.13]" } }, { "index": 56, "type": "I", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1267 vs ///A/685,///A/821", "A_nt1": { "desc": "///A/1267 vs ///A/685", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1267 vs ///A/821", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.63]" } }, { "index": 57, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1287 vs ///A/1309,///A/1661", "A_nt1": { "desc": "///A/1287 vs ///A/1309", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.58]" }, "A_nt2": { "desc": "///A/1287 vs ///A/1661", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.66]" } }, { "index": 58, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1288 vs ///A/1308,///A/1662", "A_nt1": { "desc": "///A/1288 vs ///A/1308", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.92]" }, "A_nt2": { "desc": "///A/1288 vs ///A/1662", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 59, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1300 vs ///A/1665,///A/1992", "A_nt1": { "desc": "///A/1300 vs ///A/1665", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///A/1300 vs ///A/1992", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 60, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1315 vs ///A/1310,///A/1660", "A_nt1": { "desc": "///A/1315 vs ///A/1310", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.72]" }, "A_nt2": { "desc": "///A/1315 vs ///A/1660", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 61, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1335 vs ///A/1332,///A/1346", "A_nt1": { "desc": "///A/1335 vs ///A/1332", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1335 vs ///A/1346", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.18],N1-O2'(hydroxyl)[2.95]" } }, { "index": 62, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1366 vs ///A/706,///A/782", "A_nt1": { "desc": "///A/1366 vs ///A/706", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.14],N3-O2'(hydroxyl)[2.80]" }, "A_nt2": { "desc": "///A/1366 vs ///A/782", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 63, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1367 vs ///A/705,///A/783", "A_nt1": { "desc": "///A/1367 vs ///A/705", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[2.88]" }, "A_nt2": { "desc": "///A/1367 vs ///A/783", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.88],N3-N2(amino)[2.92]" } }, { "index": 64, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1397 vs ///A/1356,///A/1417", "A_nt1": { "desc": "///A/1397 vs ///A/1356", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.34]" }, "A_nt2": { "desc": "///A/1397 vs ///A/1417", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.15]" } }, { "index": 65, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1405 vs ///A/1328,///A/1350", "A_nt1": { "desc": "///A/1405 vs ///A/1328", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.76],O2'(hydroxyl)-O2'(hydroxyl)[3.09],N3-O2'(hydroxyl)[2.81]" }, "A_nt2": { "desc": "///A/1405 vs ///A/1350", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 66, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1406 vs ///A/1327,///A/1351", "A_nt1": { "desc": "///A/1406 vs ///A/1327", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.37]" }, "A_nt2": { "desc": "///A/1406 vs ///A/1351", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.88],N3-N2(amino)[3.01]" } }, { "index": 67, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1493 vs ///A/1449,///A/1573", "A_nt1": { "desc": "///A/1493 vs ///A/1449", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[2.83]" }, "A_nt2": { "desc": "///A/1493 vs ///A/1573", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-N2(amino)[3.28],N1-O2'(hydroxyl)[2.89],N3-N2(amino)[3.16]" } }, { "index": 68, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1556 vs ///A/1547,///A/1555", "A_nt1": { "desc": "///A/1556 vs ///A/1547", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.23]" }, "A_nt2": { "desc": "///A/1556 vs ///A/1555", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "O4'-O2'(hydroxyl)[3.07]" } }, { "index": 69, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1561 vs ///A/1461,///A/1480", "A_nt1": { "desc": "///A/1561 vs ///A/1461", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.89],O2'(hydroxyl)-O2(carbonyl)[3.04]" }, "A_nt2": { "desc": "///A/1561 vs ///A/1480", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.41],N3-N2(amino)[3.33]" } }, { "index": 70, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1586 vs ///A/1364,///A/1393", "A_nt1": { "desc": "///A/1586 vs ///A/1364", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1586 vs ///A/1393", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.79]" } }, { "index": 71, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1587 vs ///A/1364,///A/1393", "A_nt1": { "desc": "///A/1587 vs ///A/1364", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.81],N3-O2'(hydroxyl)[3.28]" }, "A_nt2": { "desc": "///A/1587 vs ///A/1393", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 72, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1588 vs ///A/1363,///A/1394", "A_nt1": { "desc": "///A/1588 vs ///A/1363", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.03]" }, "A_nt2": { "desc": "///A/1588 vs ///A/1394", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.39]" } }, { "index": 73, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1626 vs ///A/1323,///A/1620", "A_nt1": { "desc": "///A/1626 vs ///A/1323", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1626 vs ///A/1620", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.85]" } }, { "index": 74, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1632 vs ///A/1337,///A/1343", "A_nt1": { "desc": "///A/1632 vs ///A/1337", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[2.77]" }, "A_nt2": { "desc": "///A/1632 vs ///A/1343", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 75, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1649 vs ///A/713,///A/745", "A_nt1": { "desc": "///A/1649 vs ///A/713", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O3'[3.22],N3-O2'(hydroxyl)[2.72]" }, "A_nt2": { "desc": "///A/1649 vs ///A/745", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 76, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1694 vs ///A/1691,///A/1973", "A_nt1": { "desc": "///A/1694 vs ///A/1691", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.89]" }, "A_nt2": { "desc": "///A/1694 vs ///A/1973", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 77, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1746 vs ///A/2673,///A/2695", "A_nt1": { "desc": "///A/1746 vs ///A/2673", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.88],N6(amino)-N3[3.30],N1-N2(amino)[2.88]" }, "A_nt2": { "desc": "///A/1746 vs ///A/2695", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 78, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1751 vs ///A/1646,///A/1653", "A_nt1": { "desc": "///A/1751 vs ///A/1646", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1751 vs ///A/1653", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.85],N3-O2'(hydroxyl)[2.93]" } }, { "index": 79, "type": "X", "desc_short": "A vs G-C (~Wobble)", "desc_long": "///A/1776 vs ///A/2567,///A/2585", "A_nt1": { "desc": "///A/1776 vs ///A/2567", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.23]" }, "A_nt2": { "desc": "///A/1776 vs ///A/2585", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 80, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1793 vs ///A/1789,///A/1813", "A_nt1": { "desc": "///A/1793 vs ///A/1789", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.06],N3-O2'(hydroxyl)[3.10]" }, "A_nt2": { "desc": "///A/1793 vs ///A/1813", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 81, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1794 vs ///A/1788,///A/1814", "A_nt1": { "desc": "///A/1794 vs ///A/1788", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.03]" }, "A_nt2": { "desc": "///A/1794 vs ///A/1814", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.14],N3-N2(amino)[3.06]" } }, { "index": 82, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1800 vs ///A/1375,///A/1382", "A_nt1": { "desc": "///A/1800 vs ///A/1375", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1800 vs ///A/1382", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.36],N1-O2'(hydroxyl)[2.97]" } }, { "index": 83, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1800 vs ///A/1376,///A/1381", "A_nt1": { "desc": "///A/1800 vs ///A/1376", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O4'-O2'(hydroxyl)[3.07],N3-O2'(hydroxyl)[3.18]" }, "A_nt2": { "desc": "///A/1800 vs ///A/1381", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 84, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1802 vs ///A/1375,///A/1382", "A_nt1": { "desc": "///A/1802 vs ///A/1375", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.71],O2'(hydroxyl)-O2(carbonyl)[3.35]" }, "A_nt2": { "desc": "///A/1802 vs ///A/1382", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.45]" } }, { "index": 85, "type": "X", "desc_short": "A vs U-U (--)", "desc_long": "///A/1845 vs ///A/2069,///A/2212", "A_nt1": { "desc": "///A/1845 vs ///A/2069", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1845 vs ///A/2212", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.19],O2'(hydroxyl)-O2'(hydroxyl)[2.74],N3-O2'(hydroxyl)[2.84]" } }, { "index": 86, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1873 vs ///A/2068,///A/2213", "A_nt1": { "desc": "///A/1873 vs ///A/2068", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.39]" }, "A_nt2": { "desc": "///A/1873 vs ///A/2213", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.59]" } }, { "index": 87, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1883 vs ///A/1784,///A/1818", "A_nt1": { "desc": "///A/1883 vs ///A/1784", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.36],N1-O2'(hydroxyl)[2.92]" }, "A_nt2": { "desc": "///A/1883 vs ///A/1818", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 88, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1910 vs ///A/1829,///A/1886", "A_nt1": { "desc": "///A/1910 vs ///A/1829", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.87],N3-O2'(hydroxyl)[2.75]" }, "A_nt2": { "desc": "///A/1910 vs ///A/1886", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 89, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1911 vs ///A/1828,///A/1887", "A_nt1": { "desc": "///A/1911 vs ///A/1828", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1911 vs ///A/1887", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.74],N3-N2(amino)[3.18]" } }, { "index": 90, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1920 vs ///A/1917,///A/1947", "A_nt1": { "desc": "///A/1920 vs ///A/1917", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1920 vs ///A/1947", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.98]" } }, { "index": 91, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1921 vs ///A/2569,///A/2583", "A_nt1": { "desc": "///A/1921 vs ///A/2569", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1921 vs ///A/2583", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O3'-O2'(hydroxyl)[2.98]" } }, { "index": 92, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1935 vs ///A/2527,///A/2539", "A_nt1": { "desc": "///A/1935 vs ///A/2527", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1935 vs ///A/2539", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.95],N3-O2'(hydroxyl)[2.80]" } }, { "index": 93, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1936 vs ///A/2528,///A/2538", "A_nt1": { "desc": "///A/1936 vs ///A/2528", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.08],N3-N2(amino)[2.94]" }, "A_nt2": { "desc": "///A/1936 vs ///A/2538", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.66],O2'(hydroxyl)-O2(carbonyl)[3.04]" } }, { "index": 94, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1949 vs ///A/2571,///A/2580", "A_nt1": { "desc": "///A/1949 vs ///A/2571", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.41]" }, "A_nt2": { "desc": "///A/1949 vs ///A/2580", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 95, "type": "X", "desc_short": "A vs G-C (--)", "desc_long": "///A/1964 vs ///A/751,///A/771", "A_nt1": { "desc": "///A/1964 vs ///A/751", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1964 vs ///A/771", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.22]" } }, { "index": 96, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2014 vs ///A/2434,///A/2475", "A_nt1": { "desc": "///A/2014 vs ///A/2434", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O4'[2.79],O2'(hydroxyl)-O2'(hydroxyl)[3.03],N3-O2'(hydroxyl)[3.12]" }, "A_nt2": { "desc": "///A/2014 vs ///A/2475", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 97, "type": "X", "desc_short": "A vs C-U (--)", "desc_long": "///A/2043 vs ///A/686,///A/820", "A_nt1": { "desc": "///A/2043 vs ///A/686", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2043 vs ///A/820", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.34],N1-O2'(hydroxyl)[2.85]" } }, { "index": 98, "type": "X", "desc_short": "A vs G-C (--)", "desc_long": "///A/2181 vs ///A/2076,///A/2179", "A_nt1": { "desc": "///A/2181 vs ///A/2076", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.98],N1-O2'(hydroxyl)[3.04]" }, "A_nt2": { "desc": "///A/2181 vs ///A/2179", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 99, "type": "II", "desc_short": "A vs A-C (~Wobble)", "desc_long": "///A/2252 vs ///A/964,///A/975", "A_nt1": { "desc": "///A/2252 vs ///A/964", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2252 vs ///A/975", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.83]" } }, { "index": 100, "type": "I", "desc_short": "A vs G-U (Wobble)", "desc_long": "///A/2253 vs ///A/965,///A/974", "A_nt1": { "desc": "///A/2253 vs ///A/965", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.94],N3-N2(amino)[3.23]" }, "A_nt2": { "desc": "///A/2253 vs ///A/974", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 101, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2306 vs ///A/2240,///A/2258", "A_nt1": { "desc": "///A/2306 vs ///A/2240", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.56]" }, "A_nt2": { "desc": "///A/2306 vs ///A/2258", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.18]" } }, { "index": 102, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2367 vs ///A/2239,///A/2259", "A_nt1": { "desc": "///A/2367 vs ///A/2239", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.82]" }, "A_nt2": { "desc": "///A/2367 vs ///A/2259", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.08],N3-N2(amino)[3.14]" } }, { "index": 103, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2413 vs ///A/2060,///A/2222", "A_nt1": { "desc": "///A/2413 vs ///A/2060", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.93],O2'(hydroxyl)-N3[2.78]" }, "A_nt2": { "desc": "///A/2413 vs ///A/2222", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.94]" } }, { "index": 104, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2543 vs ///A/2500,///A/2523", "A_nt1": { "desc": "///A/2543 vs ///A/2500", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.79],N3-O2'(hydroxyl)[3.19]" }, "A_nt2": { "desc": "///A/2543 vs ///A/2523", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 105, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2544 vs ///A/2499,///A/2524", "A_nt1": { "desc": "///A/2544 vs ///A/2499", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.73],O2'(hydroxyl)-O2(carbonyl)[3.25]" }, "A_nt2": { "desc": "///A/2544 vs ///A/2524", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.37],N3-N2(amino)[2.84]" } }, { "index": 106, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2551 vs ///A/2432,///A/2479", "A_nt1": { "desc": "///A/2551 vs ///A/2432", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.46]" }, "A_nt2": { "desc": "///A/2551 vs ///A/2479", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 107, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2577 vs ///A/2056,///A/2415", "A_nt1": { "desc": "///A/2577 vs ///A/2056", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.87]" }, "A_nt2": { "desc": "///A/2577 vs ///A/2415", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.80],N3-N2(amino)[3.08]" } }, { "index": 108, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2720 vs ///A/2502,///A/2519", "A_nt1": { "desc": "///A/2720 vs ///A/2502", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2720 vs ///A/2519", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[2.93],O2'(hydroxyl)-O2'(hydroxyl)[2.73],N3-O2'(hydroxyl)[2.79]" } }, { "index": 109, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2721 vs ///A/2503,///A/2518", "A_nt1": { "desc": "///A/2721 vs ///A/2503", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.93],N3-N2(amino)[2.94]" }, "A_nt2": { "desc": "///A/2721 vs ///A/2518", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2(carbonyl)[3.24]" } }, { "index": 110, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2785 vs ///A/2610,///A/2767", "A_nt1": { "desc": "///A/2785 vs ///A/2610", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.06],N3-N2(amino)[3.13]" }, "A_nt2": { "desc": "///A/2785 vs ///A/2767", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 111, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/2798 vs ///A/2030,///A/2600", "A_nt1": { "desc": "///A/2798 vs ///A/2030", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.16],N1-O2'(hydroxyl)[3.24]" }, "A_nt2": { "desc": "///A/2798 vs ///A/2600", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 112, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2834 vs ///A/1726,///A/1740", "A_nt1": { "desc": "///A/2834 vs ///A/1726", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.78],N3-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///A/2834 vs ///A/1740", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 113, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2835 vs ///A/1725,///A/1741", "A_nt1": { "desc": "///A/2835 vs ///A/1725", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.10]" }, "A_nt2": { "desc": "///A/2835 vs ///A/1741", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.02],N3-N2(amino)[3.13]" } }, { "index": 114, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2858 vs ///A/2791,///A/2805", "A_nt1": { "desc": "///A/2858 vs ///A/2791", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.97],O2'(hydroxyl)-O2(carbonyl)[2.73]" }, "A_nt2": { "desc": "///A/2858 vs ///A/2805", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.72],N3-N2(amino)[3.48]" } }, { "index": 115, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2866 vs ///A/2609,///A/2768", "A_nt1": { "desc": "///A/2866 vs ///A/2609", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-N2(amino)[3.11],O2'(hydroxyl)-N3[2.64],N3-N2(amino)[3.09]" }, "A_nt2": { "desc": "///A/2866 vs ///A/2768", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } } ], "num_riboseZippers": 34, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "CGGA", "nts_long": "///A/46,///A/47,///A/50,///A/51" }, { "index": 2, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/113,///A/114,///A/124,///A/125" }, { "index": 3, "num_nts": 4, "nts_short": "ACAC", "nts_long": "///A/159,///A/160,///A/445,///A/446" }, { "index": 4, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/167,///A/168,///A/691,///A/692" }, { "index": 5, "num_nts": 4, "nts_short": "AGAU", "nts_long": "///A/196,///A/197,///A/210,///A/211" }, { "index": 6, "num_nts": 4, "nts_short": "CGUA", "nts_long": "///A/214,///A/215,///A/617,///A/618" }, { "index": 7, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/310,///A/311,///A/329,///A/330" }, { "index": 8, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/524,///A/525,///A/589,///A/590" }, { "index": 9, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/688,///A/689,///A/2421,///A/2422" }, { "index": 10, "num_nts": 4, "nts_short": "CAAA", "nts_long": "///A/705,///A/706,///A/1366,///A/1367" }, { "index": 11, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///A/712,///A/713,///A/1649,///A/1650" }, { "index": 12, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///A/825,///A/826,///A/1238,///A/1239" }, { "index": 13, "num_nts": 4, "nts_short": "GACC", "nts_long": "///A/831,///A/832,///A/850,///A/851" }, { "index": 14, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/952,///A/953,///A/1203,///A/1204" }, { "index": 15, "num_nts": 4, "nts_short": "AACU", "nts_long": "///A/970,///A/971,///A/2435,///A/2436" }, { "index": 16, "num_nts": 4, "nts_short": "CCUA", "nts_long": "///A/975,///A/976,///A/2251,///A/2252" }, { "index": 17, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/981,///A/982,///A/994,///A/995" }, { "index": 18, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/997,///A/998,///A/1011,///A/1012" }, { "index": 19, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/1020,///A/1021,///A/1163,///A/1164" }, { "index": 20, "num_nts": 4, "nts_short": "AACG", "nts_long": "///A/1139,///A/1140,///A/2494,///A/2495" }, { "index": 21, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1327,///A/1328,///A/1405,///A/1406" }, { "index": 22, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1363,///A/1364,///A/1587,///A/1588" }, { "index": 23, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///A/1435,///A/1507,///A/1508,///A/1509" }, { "index": 24, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1461,///A/1462,///A/1560,///A/1561" }, { "index": 25, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/1725,///A/1726,///A/2834,///A/2835" }, { "index": 26, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///A/1788,///A/1789,///A/1793,///A/1794" }, { "index": 27, "num_nts": 4, "nts_short": "AACU", "nts_long": "///A/1872,///A/1873,///A/2068,///A/2069" }, { "index": 28, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/1935,///A/1936,///A/2538,///A/2539" }, { "index": 29, "num_nts": 4, "nts_short": "CUGA", "nts_long": "///A/2056,///A/2057,///A/2576,///A/2577" }, { "index": 30, "num_nts": 4, "nts_short": "ACAA", "nts_long": "///A/2060,///A/2061,///A/2412,///A/2413" }, { "index": 31, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/2499,///A/2500,///A/2543,///A/2544" }, { "index": 32, "num_nts": 4, "nts_short": "GGGA", "nts_long": "///A/2502,///A/2503,///A/2743,///A/2744" }, { "index": 33, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/2518,///A/2519,///A/2720,///A/2721" }, { "index": 34, "num_nts": 4, "nts_short": "GGGA", "nts_long": "///A/2609,///A/2610,///A/2865,///A/2866" } ], "num_Kturns": 5, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 64, "bounding_stems": [ 13, 12 ], "Cstem_index": 13, "NCstem_index": 12, "Cstem_pair": "C-G (///A/96,///A/84) WC", "NCstem_pair": "U-A (///A/103,///A/80) WC", "GA_pair": "G-A (///A/100,///A/83) Sheared", "bending_angle": 51.595, "strand1": { "num_nts": 14, "nts_short": "GCUUUGACUCGGGG", "nts_long": "///A/95,///A/96,///A/97,///A/98,///A/99,///A/100,///A/101,///A/102,///A/103,///A/104,///A/105,///A/106,///A/107,///A/108" }, "strand2": { "num_nts": 11, "nts_short": "CCCCGACGAGC", "nts_long": "///A/75,///A/76,///A/77,///A/78,///A/79,///A/80,///A/81,///A/82,///A/83,///A/84,///A/85" } }, { "index": 2, "type": "Normal k-turn [A-G]", "iloop_index": 67, "bounding_stems": [ 72, 73 ], "Cstem_index": 72, "NCstem_index": 73, "Cstem_pair": "C-G (///A/1221,///A/1251) WC", "NCstem_pair": "G-U (///A/1228,///A/1247) Wobble", "GA_pair": "A-G (///A/1226,///A/1249) Sheared", "bending_angle": 35.907, "strand1": { "num_nts": 12, "nts_short": "GCGGAGAAGCCA", "nts_long": "///A/1220,///A/1221,///A/1222,///A/1223,///A/1224,///A/1225,///A/1226,///A/1227,///A/1228,///A/1229,///A/1230,///A/1231" }, "strand2": { "num_nts": 9, "nts_short": "UGGUGGAGC", "nts_long": "///A/1244,///A/1245,///A/1246,///A/1247,///A/1248,///A/1249,///A/1250,///A/1251,///A/1252" } }, { "index": 3, "type": "Normal k-turn [A-G]", "iloop_index": 68, "bounding_stems": [ 89, 88 ], "Cstem_index": 89, "NCstem_index": 88, "Cstem_pair": "C-G (///A/1598,///A/1430) WC", "NCstem_pair": "A-U (///A/1605,///A/1426) WC", "GA_pair": "A-G (///A/1604,///A/1427) Sheared", "bending_angle": 38.888, "strand1": { "num_nts": 15, "nts_short": "ACGUUGAAACAUGAU", "nts_long": "///A/1597,///A/1598,///A/1599,///A/1600,///A/1601,///A/1602,///A/1603,///A/1604,///A/1605,///A/1606,///A/1607,///A/1608,///A/1609,///A/1610,///A/1611" }, "strand2": { "num_nts": 12, "nts_short": "AUCAUGUGGAGU", "nts_long": "///A/1420,///A/1421,///A/1422,///A/1423,///A/1424,///A/1425,///A/1426,///A/1427,///A/1428,///A/1429,///A/1430,///A/1431" } }, { "index": 4, "type": "Undecided case [A-G]", "iloop_index": 52, "bounding_stems": [ 84, 85 ], "Cstem_index": 84, "NCstem_index": 85, "Cstem_pair": "C-G (///A/1364,///A/1393) WC", "NCstem_pair": "G-C (///A/1368,///A/1389) WC", "GA_pair": "A-G (///A/1367,///A/1390) Sheared", "bending_angle": 39.824, "strand1": { "num_nts": 7, "nts_short": "CCUAAGG", "nts_long": "///A/1363,///A/1364,///A/1365,///A/1366,///A/1367,///A/1368,///A/1369" }, "strand2": { "num_nts": 7, "nts_short": "CCGAUGG", "nts_long": "///A/1388,///A/1389,///A/1390,///A/1391,///A/1392,///A/1393,///A/1394" } }, { "index": 5, "type": "Undecided case", "iloop_index": 78, "bounding_stems": [ 110, 109 ], "Cstem_index": 110, "NCstem_index": 109, "Cstem_pair": "G-C (///A/1805,///A/1795) WC", "NCstem_pair": "A-U (///A/1813,///A/1789) WC", "GA_pair": "G-A (///A/1806,///A/1794) Sheared", "bending_angle": 75.181, "strand1": { "num_nts": 17, "nts_short": "GUGGACGUAUAGGGUGU", "nts_long": "///A/1803,///A/1804,///A/1805,///A/1806,///A/1807,///A/1808,///A/1809,///A/1810,///A/1811,///A/1812,///A/1813,///A/1814,///A/1815,///A/1816,///A/1817,///A/1818,///A/1819" }, "strand2": { "num_nts": 15, "nts_short": "GCACUCUGCCAACAC", "nts_long": "///A/1783,///A/1784,///A/1785,///A/1786,///A/1787,///A/1788,///A/1789,///A/1790,///A/1791,///A/1792,///A/1793,///A/1794,///A/1795,///A/1796,///A/1797" } } ], "num_splayUnits": 255, "splayUnits": [ { "index": 1, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/34,///A/35" }, { "index": 2, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/44,///A/45" }, { "index": 3, "num_nts": 4, "nts_short": "AUGA", "nts_long": "///A/48,///A/49,///A/50,///A/51" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/70,///A/71,///A/72" }, { "index": 5, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/73,///A/74" }, { "index": 6, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/86,///A/87" }, { "index": 7, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/90,///A/91" }, { "index": 8, "num_nts": 3, "nts_short": "UUG", "nts_long": "///A/98,///A/99,///A/100" }, { "index": 9, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/111,///A/112" }, { "index": 10, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/118,///A/119" }, { "index": 11, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/122,///A/123,///A/124" }, { "index": 12, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/125,///A/126" }, { "index": 13, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/134,///A/135" }, { "index": 14, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/142,///A/143" }, { "index": 15, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/148,///A/149" }, { "index": 16, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/154,///A/155" }, { "index": 17, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/172,///A/173,///A/174" }, { "index": 18, "num_nts": 4, "nts_short": "AAAG", "nts_long": "///A/198,///A/199,///A/200,///A/201" }, { "index": 19, "num_nts": 3, "nts_short": "AUU", "nts_long": "///A/205,///A/206,///A/207" }, { "index": 20, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/209,///A/210" }, { "index": 21, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/225,///A/226" }, { "index": 22, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/241,///A/242" }, { "index": 23, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/311,///A/312" }, { "index": 24, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/322,///A/323" }, { "index": 25, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/331,///A/332" }, { "index": 26, "num_nts": 2, "nts_short": "GA", "nts_long": 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"nt:nt" }, { "index": 5215, "atom1_serNum": 58907, "atom2_serNum": 58920, "donAcc_type": "acceptable", "distance": 3.083, "atom1_id": "///A/2848/O2'", "atom2_id": "///A/2849/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5216, "atom1_serNum": 59035, "atom2_serNum": 59051, "donAcc_type": "acceptable", "distance": 3.058, "atom1_id": "///A/2854/O2'", "atom2_id": "///A/2855/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5217, "atom1_serNum": 59035, "atom2_serNum": 59070, "donAcc_type": "acceptable", "distance": 3.626, "atom1_id": "///A/2854/O2'", "atom2_id": "///A/2856/OP2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5218, "atom1_serNum": 59132, "atom2_serNum": 59167, "donAcc_type": "standard", "distance": 2.756, "atom1_id": "///A/2859/OP2", "atom2_id": "///A/2860/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 5219, "atom1_serNum": 59180, "atom2_serNum": 59198, "donAcc_type": "acceptable", "distance": 2.630, "atom1_id": "///A/2861/O2'", "atom2_id": "///A/2862/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5220, "atom1_serNum": 59202, "atom2_serNum": 59221, "donAcc_type": "acceptable", "distance": 3.107, "atom1_id": "///A/2862/O2'", "atom2_id": "///A/2863/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5221, "atom1_serNum": 59310, "atom2_serNum": 59326, "donAcc_type": "acceptable", "distance": 2.446, "atom1_id": "///A/2867/O2'", "atom2_id": "///A/2868/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5222, "atom1_serNum": 59310, "atom2_serNum": 59329, "donAcc_type": "acceptable", "distance": 2.391, "atom1_id": "///A/2867/O2'", "atom2_id": "///A/2868/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5223, "atom1_serNum": 59416, "atom2_serNum": 59432, "donAcc_type": "acceptable", "distance": 3.224, "atom1_id": "///A/2872/O2'", "atom2_id": "///A/2873/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5224, "atom1_serNum": 59459, "atom2_serNum": 59477, "donAcc_type": "acceptable", "distance": 3.150, "atom1_id": "///A/2874/O2'", "atom2_id": "///A/2875/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 5225, "atom1_serNum": 59935, "atom2_serNum": 59943, "donAcc_type": "acceptable", "distance": 3.082, "atom1_id": "///A/2881/O11", "atom2_id": "///A/2881/O12", "atom_pair": "O:O", "residue_pair": "ligand:ligand" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "1j5a", "num_aaChains": 3, "aaChains": "K=197,L=130,M=58", "num_naChains": 1, "naChains": "A=2774", "num_atoms": 59971, "num_waters": 0, "num_metals": 2, "metals_desc": "Mg=2", "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" } }