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      "nts_long": "///A/212,///A/213"
    },
    {
      "index": 11,
      "num_nts": 2,
      "nts_short": "GC",
      "nts_long": "///A/215,///A/216"
    },
    {
      "index": 12,
      "num_nts": 3,
      "nts_short": "UUG",
      "nts_long": "///A/18,///A/19,///A/20"
    },
    {
      "index": 13,
      "num_nts": 3,
      "nts_short": "GAG",
      "nts_long": "///A/30,///A/28,///A/43"
    },
    {
      "index": 14,
      "num_nts": 3,
      "nts_short": "AGA",
      "nts_long": "///A/46,///A/210,///A/209"
    },
    {
      "index": 15,
      "num_nts": 3,
      "nts_short": "AAG",
      "nts_long": "///A/57,///A/58,///A/59"
    },
    {
      "index": 16,
      "num_nts": 3,
      "nts_short": "GAU",
      "nts_long": "///A/94,///A/95,///A/96"
    },
    {
      "index": 17,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///A/106,///A/107,///A/108"
    },
    {
      "index": 18,
      "num_nts": 3,
      "nts_short": "CCG",
      "nts_long": "///A/119,///A/120,///A/121"
    },
    {
      "index": 19,
      "num_nts": 3,
      "nts_short": "GCG",
      "nts_long": "///A/130,///A/131,///A/132"
    },
    {
      "index": 20,
      "num_nts": 3,
      "nts_short": "GAC",
      "nts_long": "///A/137,///A/184,///A/185"
    },
    {
      "index": 21,
      "num_nts": 3,
      "nts_short": "GGC",
      "nts_long": "///A/147,///A/174,///A/173"
    },
    {
      "index": 22,
      "num_nts": 3,
      "nts_short": "CGU",
      "nts_long": "///A/158,///A/159,///A/160"
    },
    {
      "index": 23,
      "num_nts": 3,
      "nts_short": "CAU",
      "nts_long": "///A/167,///A/168,///A/170"
    },
    {
      "index": 24,
      "num_nts": 3,
      "nts_short": "GGG",
      "nts_long": "///A/196,///A/197,///A/198"
    },
    {
      "index": 25,
      "num_nts": 4,
      "nts_short": "CAGG",
      "nts_long": "///A/51,///A/81,///A/199,///A/200"
    },
    {
      "index": 26,
      "num_nts": 4,
      "nts_short": "GGCA",
      "nts_long": "///A/63,///A/64,///A/65,///A/66"
    },
    {
      "index": 27,
      "num_nts": 4,
      "nts_short": "GUUC",
      "nts_long": "///A/69,///A/70,///A/71,///A/72"
    },
    {
      "index": 28,
      "num_nts": 4,
      "nts_short": "GAGC",
      "nts_long": "///A/83,///A/140,///A/101,///A/103"
    },
    {
      "index": 29,
      "num_nts": 4,
      "nts_short": "CGGG",
      "nts_long": "///A/115,///A/114,///A/113,///A/133"
    },
    {
      "index": 30,
      "num_nts": 4,
      "nts_short": "AGCC",
      "nts_long": "///A/138,///A/183,///A/182,///A/181"
    },
    {
      "index": 31,
      "num_nts": 4,
      "nts_short": "GCAU",
      "nts_long": "///A/144,///A/145,///A/146,///A/148"
    },
    {
      "index": 32,
      "num_nts": 4,
      "nts_short": "AAAG",
      "nts_long": "///A/161,///A/162,///A/163,///A/164"
    },
    {
      "index": 33,
      "num_nts": 4,
      "nts_short": "GCGC",
      "nts_long": "///A/188,///A/189,///A/190,///A/201"
    },
    {
      "index": 34,
      "num_nts": 5,
      "nts_short": "GCGGA",
      "nts_long": "///A/9,///A/12,///A/10,///A/211,///A/44"
    },
    {
      "index": 35,
      "num_nts": 5,
      "nts_short": "AAAAA",
      "nts_long": "///A/21,///A/22,///A/203,///A/23,///A/206"
    },
    {
      "index": 36,
      "num_nts": 5,
      "nts_short": "CAUGU",
      "nts_long": "///A/54,///A/55,///A/56,///A/77,///A/76"
    },
    {
      "index": 37,
      "num_nts": 5,
      "nts_short": "AAUCG",
      "nts_long": "///A/122,///A/123,///A/124,///A/125,///A/126"
    },
    {
      "index": 38,
      "num_nts": 6,
      "nts_short": "GAAACC",
      "nts_long": "///A/150,///A/149,///A/175,///A/176,///A/177,///A/178"
    },
    {
      "index": 39,
      "num_nts": 6,
      "nts_short": "GCGGAG",
      "nts_long": "///A/156,///A/155,///A/154,///A/153,///A/171,///A/172"
    },
    {
      "index": 40,
      "num_nts": 7,
      "nts_short": "GAUGAGU",
      "nts_long": "///A/79,///A/93,///A/193,///A/192,///A/191,///A/97,///A/98"
    }
  ],
  "nonStack": {
    "num_nts": 14,
    "nts_short": "UUUACUUUAAUGAA",
    "nts_long": "///A/11,///A/15,///A/29,///A/78,///A/80,///A/82,///A/85,///A/92,///A/99,///A/100,///A/102,///A/169,///A/202,///A/204"
  },
  "num_atom2bases": 12,
  "atom2bases": [
    {
      "index": 1,
      "type": "sugar",
      "atom": "///A/43/O4'",
      "nt": "///A/45",
      "vert_dist": 3.358
    },
    {
      "index": 2,
      "type": "sugar",
      "atom": "///A/69/O2'",
      "nt": "///A/68",
      "vert_dist": 3.019
    },
    {
      "index": 3,
      "type": "sugar",
      "atom": "///A/34/O4'",
      "nt": "///A/78",
      "vert_dist": 3.053
    },
    {
      "index": 4,
      "type": "sugar",
      "atom": "///A/78/O2'",
      "nt": "///A/79",
      "vert_dist": 2.923
    },
    {
      "index": 5,
      "type": "sugar",
      "atom": "///A/83/O4'",
      "nt": "///A/84",
      "vert_dist": 3.342
    },
    {
      "index": 6,
      "type": "sugar",
      "atom": "///A/93/O2'",
      "nt": "///A/92",
      "vert_dist": 3.161
    },
    {
      "index": 7,
      "type": "phosphate",
      "atom": "///A/100/OP2",
      "nt": "///A/98",
      "vert_dist": 3.324
    },
    {
      "index": 8,
      "type": "sugar",
      "atom": "///A/189/O4'",
      "nt": "///A/100",
      "vert_dist": 3.298
    },
    {
      "index": 9,
      "type": "sugar",
      "atom": "///A/103/O4'",
      "nt": "///A/101",
      "vert_dist": 3.163
    },
    {
      "index": 10,
      "type": "phosphate",
      "atom": "///A/123/OP2",
      "nt": "///A/121",
      "vert_dist": 3.035
    },
    {
      "index": 11,
      "type": "phosphate",
      "atom": "///A/203/O3'",
      "nt": "///A/205",
      "vert_dist": 3.496
    },
    {
      "index": 12,
      "type": "phosphate",
      "atom": "///A/204/O5'",
      "nt": "///A/205",
      "vert_dist": 3.409
    }
  ],
  "num_hairpins": 4,
  "hairpins": [
    {
      "index": 1,
      "type": "hairpin loop",
      "bridging_nts": [
        7
      ],
      "stem_indices": [
        5
      ],
      "summary": "[1] 7 [A.32 A.40] 3",
      "num_nts": 9,
      "nts_short": "CAGUCGCAG",
      "nts_long": "///A/32,///A/33,///A/34,///A/35,///A/36,///A/37,///A/38,///A/39,///A/40",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 7,
          "nts_short": "AGUCGCA",
          "nts_long": "///A/33,///A/34,///A/35,///A/36,///A/37,///A/38,///A/39"
        }
      ]
    },
    {
      "index": 2,
      "type": "hairpin loop",
      "bridging_nts": [
        3
      ],
      "stem_indices": [
        -1
      ],
      "summary": "[1] 3 [A.65 A.69] 1",
      "num_nts": 5,
      "nts_short": "CAAAG",
      "nts_long": "///A/65,///A/66,///A/67,///A/68,///A/69",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 3,
          "nts_short": "AAA",
          "nts_long": "///A/66,///A/67,///A/68"
        }
      ]
    },
    {
      "index": 3,
      "type": "hairpin loop",
      "bridging_nts": [
        6
      ],
      "stem_indices": [
        11
      ],
      "summary": "[1] 6 [A.119 A.126] 5",
      "num_nts": 8,
      "nts_short": "CCGAAUCG",
      "nts_long": "///A/119,///A/120,///A/121,///A/122,///A/123,///A/124,///A/125,///A/126",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 6,
          "nts_short": "CGAAUC",
          "nts_long": "///A/120,///A/121,///A/122,///A/123,///A/124,///A/125"
        }
      ]
    },
    {
      "index": 4,
      "type": "hairpin loop",
      "bridging_nts": [
        5
      ],
      "stem_indices": [
        14
      ],
      "summary": "[1] 5 [A.158 A.164] 3",
      "num_nts": 7,
      "nts_short": "CGUAAAG",
      "nts_long": "///A/158,///A/159,///A/160,///A/161,///A/162,///A/163,///A/164",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 5,
          "nts_short": "GUAAA",
          "nts_long": "///A/159,///A/160,///A/161,///A/162,///A/163"
        }
      ]
    }
  ],
  "num_bulges": 4,
  "bulges": [
    {
      "index": 1,
      "type": "bulge",
      "bridging_nts": [
        1,
        0
      ],
      "stem_indices": [
        -3,
        9
      ],
      "summary": "[2] 1 0 [A.101 A.189 A.103 A.188] 1 4",
      "num_nts": 5,
      "nts_short": "GUCGC",
      "nts_long": "///A/101,///A/102,///A/103,///A/188,///A/189",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///A/102"
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 2,
      "type": "bulge",
      "bridging_nts": [
        1,
        0
      ],
      "stem_indices": [
        -4,
        12
      ],
      "summary": "[2] 1 0 [A.139 A.182 A.141 A.181] 1 4",
      "num_nts": 5,
      "nts_short": "GAGCC",
      "nts_long": "///A/139,///A/140,///A/141,///A/181,///A/182",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///A/140"
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 3,
      "type": "bulge",
      "bridging_nts": [
        2,
        0
      ],
      "stem_indices": [
        1,
        2
      ],
      "summary": "[2] 2 0 [A.9 A.216 A.12 A.215] 8 3",
      "num_nts": 6,
      "nts_short": "GGUCGC",
      "nts_long": "///A/9,///A/10,///A/11,///A/12,///A/215,///A/216",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "GU",
          "nts_long": "///A/10,///A/11"
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 4,
      "type": "bulge",
      "bridging_nts": [
        0,
        3
      ],
      "stem_indices": [
        2,
        3
      ],
      "summary": "[2] 0 3 [A.14 A.213 A.15 A.209] 3 4",
      "num_nts": 7,
      "nts_short": "GUAGGUC",
      "nts_long": "///A/14,///A/15,///A/209,///A/210,///A/211,///A/212,///A/213",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 3,
          "nts_short": "GGU",
          "nts_long": "///A/210,///A/211,///A/212"
        }
      ]
    }
  ],
  "num_iloops": 6,
  "iloops": [
    {
      "index": 1,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        1,
        2
      ],
      "stem_indices": [
        8,
        -1
      ],
      "summary": "[2] 1 2 [A.63 A.72 A.65 A.69] 5 1",
      "num_nts": 7,
      "nts_short": "GGCGUUC",
      "nts_long": "///A/63,///A/64,///A/65,///A/69,///A/70,///A/71,///A/72",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///A/64"
        },
        {
          "index": 2,
          "num_nts": 2,
          "nts_short": "UU",
          "nts_long": "///A/70,///A/71"
        }
      ]
    },
    {
      "index": 2,
      "type": "symmetric internal loop",
      "bridging_nts": [
        2,
        2
      ],
      "stem_indices": [
        10,
        11
      ],
      "summary": "[2] 2 2 [A.112 A.133 A.115 A.130] 5 5",
      "num_nts": 8,
      "nts_short": "CGGCGCGG",
      "nts_long": "///A/112,///A/113,///A/114,///A/115,///A/130,///A/131,///A/132,///A/133",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "GG",
          "nts_long": "///A/113,///A/114"
        },
        {
          "index": 2,
          "num_nts": 2,
          "nts_short": "CG",
          "nts_long": "///A/131,///A/132"
        }
      ]
    },
    {
      "index": 3,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        4,
        1
      ],
      "stem_indices": [
        -2,
        -3
      ],
      "summary": "[2] 4 1 [A.96 A.191 A.101 A.189] 1 1",
      "num_nts": 9,
      "nts_short": "UGUAAGCGA",
      "nts_long": "///A/96,///A/97,///A/98,///A/99,///A/100,///A/101,///A/189,///A/190,///A/191",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "GUAA",
          "nts_long": "///A/97,///A/98,///A/99,///A/100"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///A/190"
        }
      ]
    },
    {
      "index": 4,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        2,
        4
      ],
      "stem_indices": [
        4,
        5
      ],
      "summary": "[2] 2 4 [A.27 A.47 A.30 A.42] 4 3",
      "num_nts": 10,
      "nts_short": "GAUGCGAAAC",
      "nts_long": "///A/27,///A/28,///A/29,///A/30,///A/42,///A/43,///A/44,///A/45,///A/46,///A/47",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "AU",
          "nts_long": "///A/28,///A/29"
        },
        {
          "index": 2,
          "num_nts": 4,
          "nts_short": "GAAA",
          "nts_long": "///A/43,///A/44,///A/45,///A/46"
        }
      ]
    },
    {
      "index": 5,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        5,
        4
      ],
      "stem_indices": [
        12,
        13
      ],
      "summary": "[2] 5 4 [A.144 A.178 A.150 A.173] 4 2",
      "num_nts": 13,
      "nts_short": "GCAGUAGCGAACC",
      "nts_long": "///A/144,///A/145,///A/146,///A/147,///A/148,///A/149,///A/150,///A/173,///A/174,///A/175,///A/176,///A/177,///A/178",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 5,
          "nts_short": "CAGUA",
          "nts_long": "///A/145,///A/146,///A/147,///A/148,///A/149"
        },
        {
          "index": 2,
          "num_nts": 4,
          "nts_short": "GAAC",
          "nts_long": "///A/174,///A/175,///A/176,///A/177"
        }
      ]
    },
    {
      "index": 6,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        4,
        5
      ],
      "stem_indices": [
        13,
        14
      ],
      "summary": "[2] 4 5 [A.151 A.172 A.156 A.166] 2 3",
      "num_nts": 13,
      "nts_short": "UGGGCGUCAGUAG",
      "nts_long": "///A/151,///A/152,///A/153,///A/154,///A/155,///A/156,///A/166,///A/167,///A/168,///A/169,///A/170,///A/171,///A/172",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "GGGC",
          "nts_long": "///A/152,///A/153,///A/154,///A/155"
        },
        {
          "index": 2,
          "num_nts": 5,
          "nts_short": "CAGUA",
          "nts_long": "///A/167,///A/168,///A/169,///A/170,///A/171"
        }
      ]
    }
  ],
  "num_junctions": 3,
  "junctions": [
    {
      "index": 1,
      "type": "3-way junction",
      "bridging_nts": [
        1,
        1,
        2
      ],
      "stem_indices": [
        9,
        10,
        -4
      ],
      "summary": "[3] 1 1 2 [A.106 A.185 A.108 A.137 A.139 A.182] 4 5 1",
      "num_nts": 10,
      "nts_short": "GUCGAGCGAC",
      "nts_long": "///A/106,///A/107,///A/108,///A/137,///A/138,///A/139,///A/182,///A/183,///A/184,///A/185",
      "num_stems": 3,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///A/107"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///A/138"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "GA",
          "nts_long": "///A/183,///A/184"
        }
      ]
    },
    {
      "index": 2,
      "type": "3-way junction",
      "bridging_nts": [
        5,
        1,
        9
      ],
      "stem_indices": [
        3,
        4,
        7
      ],
      "summary": "[3] 5 1 9 [A.18 A.206 A.24 A.50 A.52 A.196] 4 4 3",
      "num_nts": 21,
      "nts_short": "UUGAAAGUCCGGGGGCAAAAA",
      "nts_long": "///A/18,///A/19,///A/20,///A/21,///A/22,///A/23,///A/24,///A/50,///A/51,///A/52,///A/196,///A/197,///A/198,///A/199,///A/200,///A/201,///A/202,///A/203,///A/204,///A/205,///A/206",
      "num_stems": 3,
      "bridges": [
        {
          "index": 1,
          "num_nts": 5,
          "nts_short": "UGAAA",
          "nts_long": "///A/19,///A/20,///A/21,///A/22,///A/23"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "C",
          "nts_long": "///A/51"
        },
        {
          "index": 3,
          "num_nts": 9,
          "nts_short": "GGGGCAAAA",
          "nts_long": "///A/197,///A/198,///A/199,///A/200,///A/201,///A/202,///A/203,///A/204,///A/205"
        }
      ]
    },
    {
      "index": 3,
      "type": "6-way junction",
      "bridging_nts": [
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        5,
        2,
        4,
        8,
        0
      ],
      "stem_indices": [
        5,
        6,
        -2,
        7,
        8,
        6
      ],
      "summary": "[6] 1 5 2 4 8 0 [A.32 A.40 A.34 A.90 A.96 A.191 A.194 A.54 A.59 A.76 A.85 A.39] 3 6 1 3 5 6",
      "is_repeated": true,
      "num_nts": 32,
      "nts_short": "CAGCUUAGAUAGUGCAUAAGUGAGCAUGGUAG",
      "nts_long": "///A/32,///A/33,///A/34,///A/90,///A/91,///A/92,///A/93,///A/94,///A/95,///A/96,///A/191,///A/192,///A/193,///A/194,///A/54,///A/55,///A/56,///A/57,///A/58,///A/59,///A/76,///A/77,///A/78,///A/79,///A/80,///A/81,///A/82,///A/83,///A/84,///A/85,///A/39,///A/40",
      "num_stems": 6,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///A/33"
        },
        {
          "index": 2,
          "num_nts": 5,
          "nts_short": "UUAGA",
          "nts_long": "///A/91,///A/92,///A/93,///A/94,///A/95"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "GU",
          "nts_long": "///A/192,///A/193"
        },
        {
          "index": 4,
          "num_nts": 4,
          "nts_short": "AUAA",
          "nts_long": "///A/55,///A/56,///A/57,///A/58"
        },
        {
          "index": 5,
          "num_nts": 8,
          "nts_short": "GAGCAUGG",
          "nts_long": "///A/77,///A/78,///A/79,///A/80,///A/81,///A/82,///A/83,///A/84"
        },
        {
          "index": 6,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    }
  ],
  "num_ssSegments": 2,
  "ssSegments": [
    {
      "index": 1,
      "num_nts": 1,
      "nts_short": "G",
      "nts_long": "///A/1"
    },
    {
      "index": 2,
      "num_nts": 1,
      "nts_short": "A",
      "nts_long": "///A/224"
    }
  ],
  "num_Aminors": 1,
  "Aminors": [
    {
      "index": 1,
      "type": "I",
      "desc_short": "A vs G-C (WC)",
      "desc_long": "///A/58 vs ///A/34,///A/90",
      "A_nt1": {
        "desc": "///A/58 vs ///A/34",
        "face_type": "+",
        "hbonds_num": 2,
        "hbonds_desc": "N1-O2'(hydroxyl)[3.32],N3-N2(amino)[2.71]"
      },
      "A_nt2": {
        "desc": "///A/58 vs ///A/90",
        "face_type": "-",
        "hbonds_num": 0,
        "hbonds_desc": ""
      }
    }
  ],
  "num_splayUnits": 19,
  "splayUnits": [
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      "index": 1,
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      "nts_short": "GUC",
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    },
    {
      "index": 2,
      "num_nts": 2,
      "nts_short": "AG",
      "nts_long": "///A/23,///A/24"
    },
    {
      "index": 3,
      "num_nts": 3,
      "nts_short": "AUG",
      "nts_long": "///A/28,///A/29,///A/30"
    },
    {
      "index": 4,
      "num_nts": 3,
      "nts_short": "CAG",
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    },
    {
      "index": 5,
      "num_nts": 5,
      "nts_short": "GAAAC",
      "nts_long": "///A/43,///A/44,///A/45,///A/46,///A/47"
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    {
      "index": 6,
      "num_nts": 2,
      "nts_short": "UC",
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    {
      "index": 7,
      "num_nts": 2,
      "nts_short": "AA",
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    },
    {
      "index": 8,
      "num_nts": 2,
      "nts_short": "GA",
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    },
    {
      "index": 9,
      "num_nts": 2,
      "nts_short": "GU",
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    },
    {
      "index": 10,
      "num_nts": 2,
      "nts_short": "UA",
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    },
    {
      "index": 11,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///A/101,///A/102,///A/103"
    },
    {
      "index": 12,
      "num_nts": 5,
      "nts_short": "GAGAG",
      "nts_long": "///A/137,///A/138,///A/139,///A/140,///A/141"
    },
    {
      "index": 13,
      "num_nts": 2,
      "nts_short": "UA",
      "nts_long": "///A/160,///A/161"
    },
    {
      "index": 14,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///A/174,///A/175"
    },
    {
      "index": 15,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///A/183,///A/184"
    },
    {
      "index": 16,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///A/190,///A/191"
    },
    {
      "index": 17,
      "num_nts": 2,
      "nts_short": "UG",
      "nts_long": "///A/193,///A/194"
    },
    {
      "index": 18,
      "num_nts": 3,
      "nts_short": "AAA",
      "nts_long": "///A/202,///A/203,///A/204"
    },
    {
      "index": 19,
      "num_nts": 2,
      "nts_short": "AA",
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    {
      "index": 1,
      "symbols": "[]",
      "num_nts": 12,
      "nts_short": "GUCGCAUGCGGC",
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      "num_chars": 224,
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      "num_chars": 224,
      "bseq": "GGGAGUCGGGUCUGUGGUUGAAAGUCGAUGCCAGUCGCAGGCGAAACGAUCCACAUAAGCGGGGCAAAGUUCCCGUGAGCAUGGUGCGGCUUAGAUGUAAGUCCUGUCGUGCGGCAUUCCGAAUCGAAUGCGGUGCGAGAGUGGCAGUAGUGGGCGGCGUAAAGCUCAGUAGCGAACCCACCGACAGGCGAGUGUGGGGGCAAAAACCAGGUCAGCCGACUCCA",
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      "helical_rise_std": 3.350,
      "helical_axis": [
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      "point1": [
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      "point2": [
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      "num_chars": 670,
      "suite": "G1aG1aG1aA1aG1aU1aC1aG1aG1[G6pU6jC1aU1aG!!U1aG1cG1aU1aU1cG1gA1aA1tA0aG1aU1aC1aG!!A!!U!!G1aC1aC3aA3aG1aU1aC1aG1aC1aA1aG1aG1aC1mG7pA2[A!!A2aC1cG1aA1aU7dC!!C1aA1cC1aA1cU1aA1aA1aG1aC1aG1aG1aG1aG1aC1aA1gA1aA1cG1aU1aU1aC1aC1aC1aG1aU1aG1oA!!G2aC5pA!!U!!G6nG!!U1aG1aC1aG1aG1aC1cU1cU!!A6nG1cA1aU1cG1aU1gA1aA!!G!!U2hC1aC1aU1aG1aU1aC1aG1aU1aG1aC1aG1aG1aC1aA1aU1aU1aC1aC1aG!!A1aA1aU1aC1aG1aA1aA1aU1aG1aC1cG1aG1aU1aG1aC1aG!!A3aG1zA!!G1aU1aG1aG1aC5zA!!G0aU1cA1aG1aU1aG1eG1aG1aC1cG1aG1aC1cG1aU1gA1aA1aA1aG1aC1aU1aC!!A!!G0aU1cA1aG1aC1cG!!A1cA1aC1aC1aC1aA1aC1aC1tG0kA1cC1aA1aG1cG1aC1cG!!A1aG1aU!!G1aU1cG1aG1aG1aG1aG!!C!!A1oA!!A!!A0aA1aC1aC1aA1aG!!G0aU1aC1aA1aG1aC1aC1aG1aA1aC1aU1aC1aC1aA"
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      "puckering": "C3'-endo",
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        "x_axis": [
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      "    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": "9g7c",
    "num_naChains": 1,
    "naChains": "A=224",
    "num_atoms": 4826,
    "num_waters": 0,
    "num_notes": 52,
    "notes": [
      {
        "Aminors": "A-minor interactions (including types I and II)"
      },
      {
        "Cstem_index": "stem index of the 'Canonical' helix in k-turn"
      },
      {
        "Cstem_pair": "Cstem bp delineating the k-turn internal loop"
      },
      {
        "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond"
      },
      {
        "GA_pair": "sheared G-A pair in k-turn"
      },
      {
        "HtypePknot": "H-type pseudoknot"
      },
      {
        "Kturn": "kink-turn (k-turn)"
      },
      {
        "LW": "Leontis-Westhof"
      },
      {
        "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn"
      },
      {
        "NCstem_pair": "NCstem bp delineating the k-turn internal loop"
      },
      {
        "Uturn": "U-turn of the UNR- or GNRA-type"
      },
      {
        "aa": "amino acid"
      },
      {
        "atom_pair": "symbols of the two atoms involved in an H-bond"
      },
      {
        "auxfiles": "auxiliary files"
      },
      {
        "glyco_bond": "conformation of base related to sugar (syn or anti)"
      },
      {
        "bb_type": "backbone conformation, BI or BII"
      },
      {
        "bending_angle": "angle between two helical axes"
      },
      {
        "bp": "base pair"
      },
      {
        "bseq": "base sequence in one-letter code"
      },
      {
        "bulge": "bulge loop"
      },
      {
        "coaxStacks": "coaxial stacking of stems within a helix"
      },
      {
        "dbn": "dot bracket notation"
      },
      {
        "desc": "description"
      },
      {
        "donAcc_type": "donor/acceptor type of the atom pair in an H-bond"
      },
      {
        "epsilon_zeta": "difference between epsilon and zeta torsion angles"
      },
      {
        "hairpin": "hairpin loop"
      },
      {
        "hbond": "hydrogen bond (H-bond)"
      },
      {
        "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity"
      },
      {
        "id": "identifier"
      },
      {
        "iloop": "internal loop"
      },
      {
        "index": "serial number"
      },
      {
        "isoCanonPairs": "isolated canonical pairs"
      },
      {
        "junction": "(multi-branched) junction loop"
      },
      {
        "kissingLoop": "kissing loop"
      },
      {
        "multiplet": "3+ bases in a coplanar geometry"
      },
      {
        "na": "nucleic acid"
      },
      {
        "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions"
      },
      {
        "nonStack": "nucleotide not involved in stacking interactions"
      },
      {
        "nt": "nucleotide"
      },
      {
        "num": "number"
      },
      {
        "oArea": "overlap areas between two bases, including exocyclic atoms"
      },
      {
        "oArea_ring": "overlap areas between two bases, including only ring atoms"
      },
      {
        "phosContacts": "H-bonding and atom-capping interactions involving a phosphate"
      },
      {
        "residue_pair": "types of the two residues involved in an H-bond"
      },
      {
        "rmsd": "root-mean-squares deviation"
      },
      {
        "serNum": "serial number"
      },
      {
        "ssSegments": "single-stranded segments not involved in loops"
      },
      {
        "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane"
      },
      {
        "sstr": "secondary structure in dbn"
      },
      {
        "stem": "helix consisting of only canonical pairs, with a continuous backbone"
      },
      {
        "str_id": "structure identifier, derived from inpfile with extension removed"
      },
      {
        "vert_dist": "vertical distance from an atom to a base plane"
      }
    ],
    "num_auxfiles": 20,
    "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-stacks.pdb",
        "desc": "an ensemble of base stacks"
      },
      {
        "index": 16,
        "name": "dssr-atom2bases.pdb",
        "desc": "an ensemble of atom-base stacking interactions"
      },
      {
        "index": 17,
        "name": "dssr-rotmat.txt",
        "desc": "position vector and rotation matrix"
      },
      {
        "index": 18,
        "name": "dssr-viewV.pdb",
        "desc": "vertical view of the principal moment of inertia"
      },
      {
        "index": 19,
        "name": "dssr-viewH.pdb",
        "desc": "horizontal view of the principal moment of inertia"
      },
      {
        "index": 20,
        "name": "dssr-viewT.pdb",
        "desc": "top view of the principal moment of inertia"
      }
    ],
    "time_used": "999"
  }
}