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        43
      ]
    },
    {
      "index": 4,
      "helix_index": 4,
      "num_stems": 9,
      "stem_indices": [
        11,
        10,
        19,
        21,
        20,
        28,
        27,
        41,
        42
      ]
    },
    {
      "index": 5,
      "helix_index": 5,
      "num_stems": 8,
      "stem_indices": [
        13,
        12,
        17,
        18,
        31,
        30,
        29,
        40
      ]
    },
    {
      "index": 6,
      "helix_index": 6,
      "num_stems": 8,
      "stem_indices": [
        14,
        15,
        16,
        34,
        33,
        32,
        38,
        39
      ]
    }
  ],
  "num_stacks": 89,
  "stacks": [
    {
      "index": 1,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///B/1,///B/356"
    },
    {
      "index": 2,
      "num_nts": 2,
      "nts_short": "AA",
      "nts_long": "///B/16,///B/51"
    },
    {
      "index": 3,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///B/77,///B/78"
    },
    {
      "index": 4,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///B/102,///B/337"
    },
    {
      "index": 5,
      "num_nts": 2,
      "nts_short": "AU",
      "nts_long": "///B/125,///B/126"
    },
    {
      "index": 6,
      "num_nts": 2,
      "nts_short": "AG",
      "nts_long": "///B/128,///B/306"
    },
    {
      "index": 7,
      "num_nts": 2,
      "nts_short": "AG",
      "nts_long": "///B/132,///B/274"
    },
    {
      "index": 8,
      "num_nts": 2,
      "nts_short": "CA",
      "nts_long": "///B/156,///B/273"
    },
    {
      "index": 9,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/158,///B/159"
    },
    {
      "index": 10,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/182,///B/242"
    },
    {
      "index": 11,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/183,///B/213"
    },
    {
      "index": 12,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/199,///B/200"
    },
    {
      "index": 13,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/244,///B/245"
    },
    {
      "index": 14,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///B/276,///B/277"
    },
    {
      "index": 15,
      "num_nts": 2,
      "nts_short": "CA",
      "nts_long": "///B/285,///B/286"
    },
    {
      "index": 16,
      "num_nts": 2,
      "nts_short": "AU",
      "nts_long": "///B/287,///B/421"
    },
    {
      "index": 17,
      "num_nts": 2,
      "nts_short": "CU",
      "nts_long": "///B/370,///B/676"
    },
    {
      "index": 18,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/371,///B/675"
    },
    {
      "index": 19,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/374,///B/649"
    },
    {
      "index": 20,
      "num_nts": 2,
      "nts_short": "CG",
      "nts_long": "///B/405,///B/648"
    },
    {
      "index": 21,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/408,///B/622"
    },
    {
      "index": 22,
      "num_nts": 2,
      "nts_short": "CA",
      "nts_long": "///B/418,///B/419"
    },
    {
      "index": 23,
      "num_nts": 2,
      "nts_short": "CU",
      "nts_long": "///B/439,///B/621"
    },
    {
      "index": 24,
      "num_nts": 2,
      "nts_short": "AG",
      "nts_long": "///B/442,///B/595"
    },
    {
      "index": 25,
      "num_nts": 2,
      "nts_short": "UG",
      "nts_long": "///B/447,///B/448"
    },
    {
      "index": 26,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/449,///B/466"
    },
    {
      "index": 27,
      "num_nts": 2,
      "nts_short": "CA",
      "nts_long": "///B/473,///B/594"
    },
    {
      "index": 28,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/475,///B/476"
    },
    {
      "index": 29,
      "num_nts": 2,
      "nts_short": "UU",
      "nts_long": "///B/499,///B/500"
    },
    {
      "index": 30,
      "num_nts": 2,
      "nts_short": "CC",
      "nts_long": "///B/506,///B/568"
    },
    {
      "index": 31,
      "num_nts": 2,
      "nts_short": "CU",
      "nts_long": "///B/543,///B/544"
    },
    {
      "index": 32,
      "num_nts": 2,
      "nts_short": "GC",
      "nts_long": "///B/557,///B/558"
    },
    {
      "index": 33,
      "num_nts": 2,
      "nts_short": "CG",
      "nts_long": "///B/565,///B/566"
    },
    {
      "index": 34,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/570,///B/571"
    },
    {
      "index": 35,
      "num_nts": 2,
      "nts_short": "GC",
      "nts_long": "///B/584,///B/585"
    },
    {
      "index": 36,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/589,///B/590"
    },
    {
      "index": 37,
      "num_nts": 2,
      "nts_short": "GA",
      "nts_long": "///B/597,///B/598"
    },
    {
      "index": 38,
      "num_nts": 2,
      "nts_short": "GC",
      "nts_long": "///B/624,///B/625"
    },
    {
      "index": 39,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/665,///B/666"
    },
    {
      "index": 40,
      "num_nts": 2,
      "nts_short": "GC",
      "nts_long": "///B/692,///B/693"
    },
    {
      "index": 41,
      "num_nts": 2,
      "nts_short": "GG",
      "nts_long": "///B/705,///B/706"
    },
    {
      "index": 42,
      "num_nts": 3,
      "nts_short": "UCC",
      "nts_long": "///B/14,///B/15,///B/75"
    },
    {
      "index": 43,
      "num_nts": 3,
      "nts_short": "CAC",
      "nts_long": "///B/28,///B/29,///B/523"
    },
    {
      "index": 44,
      "num_nts": 3,
      "nts_short": "GAU",
      "nts_long": "///B/31,///B/529,///B/530"
    },
    {
      "index": 45,
      "num_nts": 3,
      "nts_short": "GAG",
      "nts_long": "///B/36,///B/37,///B/38"
    },
    {
      "index": 46,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/60,///B/61,///B/63"
    },
    {
      "index": 47,
      "num_nts": 3,
      "nts_short": "UGA",
      "nts_long": "///B/62,///B/64,///B/65"
    },
    {
      "index": 48,
      "num_nts": 3,
      "nts_short": "AUC",
      "nts_long": "///B/87,///B/88,///B/90"
    },
    {
      "index": 49,
      "num_nts": 3,
      "nts_short": "UGU",
      "nts_long": "///B/89,///B/91,///B/92"
    },
    {
      "index": 50,
      "num_nts": 3,
      "nts_short": "UGG",
      "nts_long": "///B/108,///B/107,///B/127"
    },
    {
      "index": 51,
      "num_nts": 3,
      "nts_short": "CUC",
      "nts_long": "///B/114,///B/115,///B/117"
    },
    {
      "index": 52,
      "num_nts": 3,
      "nts_short": "UGG",
      "nts_long": "///B/116,///B/118,///B/119"
    },
    {
      "index": 53,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/141,///B/142,///B/144"
    },
    {
      "index": 54,
      "num_nts": 3,
      "nts_short": "UGG",
      "nts_long": "///B/143,///B/145,///B/146"
    },
    {
      "index": 55,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///B/168,///B/169,///B/171"
    },
    {
      "index": 56,
      "num_nts": 3,
      "nts_short": "UGC",
      "nts_long": "///B/170,///B/172,///B/173"
    },
    {
      "index": 57,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///B/195,///B/196,///B/198"
    },
    {
      "index": 58,
      "num_nts": 3,
      "nts_short": "GAG",
      "nts_long": "///B/225,///B/495,///B/496"
    },
    {
      "index": 59,
      "num_nts": 3,
      "nts_short": "AAC",
      "nts_long": "///B/230,///B/231,///B/232"
    },
    {
      "index": 60,
      "num_nts": 3,
      "nts_short": "CAC",
      "nts_long": "///B/254,///B/255,///B/455"
    },
    {
      "index": 61,
      "num_nts": 3,
      "nts_short": "AAC",
      "nts_long": "///B/257,///B/461,///B/462"
    },
    {
      "index": 62,
      "num_nts": 3,
      "nts_short": "GAG",
      "nts_long": "///B/262,///B/263,///B/264"
    },
    {
      "index": 63,
      "num_nts": 3,
      "nts_short": "GAG",
      "nts_long": "///B/289,///B/427,///B/428"
    },
    {
      "index": 64,
      "num_nts": 3,
      "nts_short": "GGA",
      "nts_long": "///B/290,///B/291,///B/292"
    },
    {
      "index": 65,
      "num_nts": 3,
      "nts_short": "GAC",
      "nts_long": "///B/318,///B/319,///B/387"
    },
    {
      "index": 66,
      "num_nts": 3,
      "nts_short": "GAC",
      "nts_long": "///B/326,///B/327,///B/328"
    },
    {
      "index": 67,
      "num_nts": 3,
      "nts_short": "CAA",
      "nts_long": "///B/384,///B/385,///B/386"
    },
    {
      "index": 68,
      "num_nts": 3,
      "nts_short": "GAG",
      "nts_long": "///B/392,///B/393,///B/394"
    },
    {
      "index": 69,
      "num_nts": 3,
      "nts_short": "UCC",
      "nts_long": "///B/423,///B/424,///B/425"
    },
    {
      "index": 70,
      "num_nts": 3,
      "nts_short": "AGA",
      "nts_long": "///B/483,///B/482,///B/501"
    },
    {
      "index": 71,
      "num_nts": 3,
      "nts_short": "AGC",
      "nts_long": "///B/515,///B/516,///B/517"
    },
    {
      "index": 72,
      "num_nts": 3,
      "nts_short": "GUU",
      "nts_long": "///B/533,///B/534,///B/535"
    },
    {
      "index": 73,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///B/553,///B/554,///B/556"
    },
    {
      "index": 74,
      "num_nts": 3,
      "nts_short": "CGG",
      "nts_long": "///B/576,///B/575,///B/591"
    },
    {
      "index": 75,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///B/580,///B/581,///B/583"
    },
    {
      "index": 76,
      "num_nts": 3,
      "nts_short": "GGU",
      "nts_long": "///B/626,///B/627,///B/628"
    },
    {
      "index": 77,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///B/634,///B/635,///B/637"
    },
    {
      "index": 78,
      "num_nts": 3,
      "nts_short": "UGC",
      "nts_long": "///B/636,///B/638,///B/639"
    },
    {
      "index": 79,
      "num_nts": 3,
      "nts_short": "AUC",
      "nts_long": "///B/645,///B/646,///B/647"
    },
    {
      "index": 80,
      "num_nts": 3,
      "nts_short": "AUC",
      "nts_long": "///B/661,///B/662,///B/664"
    },
    {
      "index": 81,
      "num_nts": 3,
      "nts_short": "GUC",
      "nts_long": "///B/688,///B/689,///B/691"
    },
    {
      "index": 82,
      "num_nts": 4,
      "nts_short": "AAAA",
      "nts_long": "///B/30,///B/522,///B/521,///B/520"
    },
    {
      "index": 83,
      "num_nts": 4,
      "nts_short": "AAAG",
      "nts_long": "///B/256,///B/454,///B/453,///B/452"
    },
    {
      "index": 84,
      "num_nts": 4,
      "nts_short": "AAUG",
      "nts_long": "///B/294,///B/295,///B/296,///B/297"
    },
    {
      "index": 85,
      "num_nts": 4,
      "nts_short": "GGGA",
      "nts_long": "///B/340,///B/341,///B/342,///B/343"
    },
    {
      "index": 86,
      "num_nts": 4,
      "nts_short": "GAUG",
      "nts_long": "///B/507,///B/567,///B/545,///B/546"
    },
    {
      "index": 87,
      "num_nts": 5,
      "nts_short": "GUUUC",
      "nts_long": "///B/605,///B/606,///B/607,///B/608,///B/610"
    },
    {
      "index": 88,
      "num_nts": 5,
      "nts_short": "UGAGC",
      "nts_long": "///B/609,///B/611,///B/612,///B/613,///B/614"
    },
    {
      "index": 89,
      "num_nts": 6,
      "nts_short": "GAAAAC",
      "nts_long": "///B/222,///B/223,///B/224,///B/488,///B/487,///B/486"
    }
  ],
  "nonStack": {
    "num_nts": 19,
    "nts_short": "CUUAACCCCUCCAUCUCUU",
    "nts_long": "///B/129,///B/197,///B/215,///B/288,///B/320,///B/321,///B/338,///B/351,///B/353,///B/359,///B/360,///B/362,///B/420,///B/504,///B/550,///B/582,///B/603,///B/663,///B/690"
  },
  "num_atom2bases": 27,
  "atom2bases": [
    {
      "index": 1,
      "type": "sugar",
      "atom": "///B/62/O2'",
      "nt": "///B/64",
      "vert_dist": 3.188
    },
    {
      "index": 2,
      "type": "sugar",
      "atom": "///B/89/O2'",
      "nt": "///B/91",
      "vert_dist": 2.972
    },
    {
      "index": 3,
      "type": "sugar",
      "atom": "///B/92/O4'",
      "nt": "///B/91",
      "vert_dist": 3.444
    },
    {
      "index": 4,
      "type": "sugar",
      "atom": "///B/116/O2'",
      "nt": "///B/118",
      "vert_dist": 3.157
    },
    {
      "index": 5,
      "type": "sugar",
      "atom": "///B/119/O4'",
      "nt": "///B/118",
      "vert_dist": 3.430
    },
    {
      "index": 6,
      "type": "sugar",
      "atom": "///B/143/O2'",
      "nt": "///B/145",
      "vert_dist": 3.235
    },
    {
      "index": 7,
      "type": "sugar",
      "atom": "///B/146/O4'",
      "nt": "///B/145",
      "vert_dist": 3.476
    },
    {
      "index": 8,
      "type": "sugar",
      "atom": "///B/274/O4'",
      "nt": "///B/155",
      "vert_dist": 3.280
    },
    {
      "index": 9,
      "type": "sugar",
      "atom": "///B/170/O2'",
      "nt": "///B/172",
      "vert_dist": 3.114
    },
    {
      "index": 10,
      "type": "sugar",
      "atom": "///B/173/O4'",
      "nt": "///B/172",
      "vert_dist": 3.461
    },
    {
      "index": 11,
      "type": "sugar",
      "atom": "///B/186/O4'",
      "nt": "///B/185",
      "vert_dist": 3.318
    },
    {
      "index": 12,
      "type": "sugar",
      "atom": "///B/197/O2'",
      "nt": "///B/199",
      "vert_dist": 3.041
    },
    {
      "index": 13,
      "type": "sugar",
      "atom": "///B/200/O4'",
      "nt": "///B/199",
      "vert_dist": 3.325
    },
    {
      "index": 14,
      "type": "sugar",
      "atom": "///B/421/O4'",
      "nt": "///B/287",
      "vert_dist": 3.217
    },
    {
      "index": 15,
      "type": "sugar",
      "atom": "///B/287/O2'",
      "nt": "///B/288",
      "vert_dist": 3.395
    },
    {
      "index": 16,
      "type": "sugar",
      "atom": "///B/676/O4'",
      "nt": "///B/370",
      "vert_dist": 3.468
    },
    {
      "index": 17,
      "type": "sugar",
      "atom": "///B/289/O4'",
      "nt": "///B/419",
      "vert_dist": 3.063
    },
    {
      "index": 18,
      "type": "sugar",
      "atom": "///B/487/O4'",
      "nt": "///B/488",
      "vert_dist": 3.065
    },
    {
      "index": 19,
      "type": "sugar",
      "atom": "///B/555/O2'",
      "nt": "///B/557",
      "vert_dist": 3.026
    },
    {
      "index": 20,
      "type": "sugar",
      "atom": "///B/582/O2'",
      "nt": "///B/584",
      "vert_dist": 3.113
    },
    {
      "index": 21,
      "type": "sugar",
      "atom": "///B/585/O4'",
      "nt": "///B/584",
      "vert_dist": 3.434
    },
    {
      "index": 22,
      "type": "sugar",
      "atom": "///B/609/O2'",
      "nt": "///B/611",
      "vert_dist": 3.149
    },
    {
      "index": 23,
      "type": "sugar",
      "atom": "///B/612/O4'",
      "nt": "///B/611",
      "vert_dist": 3.459
    },
    {
      "index": 24,
      "type": "sugar",
      "atom": "///B/636/O2'",
      "nt": "///B/638",
      "vert_dist": 3.143
    },
    {
      "index": 25,
      "type": "sugar",
      "atom": "///B/639/O4'",
      "nt": "///B/638",
      "vert_dist": 3.473
    },
    {
      "index": 26,
      "type": "sugar",
      "atom": "///B/663/O2'",
      "nt": "///B/665",
      "vert_dist": 3.156
    },
    {
      "index": 27,
      "type": "sugar",
      "atom": "///B/690/O2'",
      "nt": "///B/692",
      "vert_dist": 3.232
    }
  ],
  "num_hairpins": 23,
  "hairpins": [
    {
      "index": 1,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        2
      ],
      "summary": "[1] 9 [B.28 B.38] 13",
      "num_nts": 11,
      "nts_short": "CAAGUUCAGAG",
      "nts_long": "///B/28,///B/29,///B/30,///B/31,///B/32,///B/33,///B/34,///B/35,///B/36,///B/37,///B/38",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AAGUUCAGA",
          "nts_long": "///B/29,///B/30,///B/31,///B/32,///B/33,///B/34,///B/35,///B/36,///B/37"
        }
      ]
    },
    {
      "index": 2,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        4
      ],
      "summary": "[1] 4 [B.60 B.65] 10",
      "num_nts": 6,
      "nts_short": "UUUCGA",
      "nts_long": "///B/60,///B/61,///B/62,///B/63,///B/64,///B/65",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/61,///B/62,///B/63,///B/64"
        }
      ]
    },
    {
      "index": 3,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        6
      ],
      "summary": "[1] 4 [B.87 B.92] 10",
      "num_nts": 6,
      "nts_short": "AUUCGU",
      "nts_long": "///B/87,///B/88,///B/89,///B/90,///B/91,///B/92",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/88,///B/89,///B/90,///B/91"
        }
      ]
    },
    {
      "index": 4,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        9
      ],
      "summary": "[1] 4 [B.114 B.119] 7",
      "num_nts": 6,
      "nts_short": "CUUCGG",
      "nts_long": "///B/114,///B/115,///B/116,///B/117,///B/118,///B/119",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/115,///B/116,///B/117,///B/118"
        }
      ]
    },
    {
      "index": 5,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        11
      ],
      "summary": "[1] 4 [B.141 B.146] 10",
      "num_nts": 6,
      "nts_short": "UUUCGG",
      "nts_long": "///B/141,///B/142,///B/143,///B/144,///B/145,///B/146",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/142,///B/143,///B/144,///B/145"
        }
      ]
    },
    {
      "index": 6,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        13
      ],
      "summary": "[1] 4 [B.168 B.173] 10",
      "num_nts": 6,
      "nts_short": "GUUCGC",
      "nts_long": "///B/168,///B/169,///B/170,///B/171,///B/172,///B/173",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/169,///B/170,///B/171,///B/172"
        }
      ]
    },
    {
      "index": 7,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        14
      ],
      "summary": "[1] 4 [B.195 B.200] 13",
      "num_nts": 6,
      "nts_short": "GUUCGU",
      "nts_long": "///B/195,///B/196,///B/197,///B/198,///B/199,///B/200",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/196,///B/197,///B/198,///B/199"
        }
      ]
    },
    {
      "index": 8,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        15
      ],
      "summary": "[1] 9 [B.222 B.232] 10",
      "num_nts": 11,
      "nts_short": "GAAGAGGUAAC",
      "nts_long": "///B/222,///B/223,///B/224,///B/225,///B/226,///B/227,///B/228,///B/229,///B/230,///B/231,///B/232",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AAGAGGUAA",
          "nts_long": "///B/223,///B/224,///B/225,///B/226,///B/227,///B/228,///B/229,///B/230,///B/231"
        }
      ]
    },
    {
      "index": 9,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        17
      ],
      "summary": "[1] 9 [B.254 B.264] 10",
      "num_nts": 11,
      "nts_short": "CAAAGGUAGAG",
      "nts_long": "///B/254,///B/255,///B/256,///B/257,///B/258,///B/259,///B/260,///B/261,///B/262,///B/263,///B/264",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AAAGGUAGA",
          "nts_long": "///B/255,///B/256,///B/257,///B/258,///B/259,///B/260,///B/261,///B/262,///B/263"
        }
      ]
    },
    {
      "index": 10,
      "type": "hairpin loop",
      "bridging_nts": [
        11
      ],
      "stem_indices": [
        19
      ],
      "summary": "[1] 11 [B.285 B.297] 9",
      "num_nts": 13,
      "nts_short": "CAAAGGGAUAAUG",
      "nts_long": "///B/285,///B/286,///B/287,///B/288,///B/289,///B/290,///B/291,///B/292,///B/293,///B/294,///B/295,///B/296,///B/297",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 11,
          "nts_short": "AAAGGGAUAAU",
          "nts_long": "///B/286,///B/287,///B/288,///B/289,///B/290,///B/291,///B/292,///B/293,///B/294,///B/295,///B/296"
        }
      ]
    },
    {
      "index": 11,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        22
      ],
      "summary": "[1] 9 [B.318 B.328] 10",
      "num_nts": 11,
      "nts_short": "GAACUCACGAC",
      "nts_long": "///B/318,///B/319,///B/320,///B/321,///B/322,///B/323,///B/324,///B/325,///B/326,///B/327,///B/328",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AACUCACGA",
          "nts_long": "///B/319,///B/320,///B/321,///B/322,///B/323,///B/324,///B/325,///B/326,///B/327"
        }
      ]
    },
    {
      "index": 12,
      "type": "hairpin loop",
      "bridging_nts": [
        60
      ],
      "stem_indices": [
        23
      ],
      "summary": "[1] 60 [B.326 B.387] 6",
      "num_nts": 62,
      "nts_short": "GACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAAC",
      "nts_long": "///B/326,///B/327,///B/328,///B/329,///B/330,///B/331,///B/332,///B/333,///B/334,///B/335,///B/336,///B/337,///B/338,///B/339,///B/340,///B/341,///B/342,///B/343,///B/344,///B/345,///B/346,///B/347,///B/348,///B/349,///B/350,///B/351,///B/352,///B/353,///B/354,///B/355,///B/356,///B/357,///B/358,///B/359,///B/360,///B/361,///B/362,///B/363,///B/364,///B/365,///B/366,///B/367,///B/368,///B/369,///B/370,///B/371,///B/372,///B/373,///B/374,///B/375,///B/376,///B/377,///B/378,///B/379,///B/380,///B/381,///B/382,///B/383,///B/384,///B/385,///B/386,///B/387",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 60,
          "nts_short": "ACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAA",
          "nts_long": "///B/327,///B/328,///B/329,///B/330,///B/331,///B/332,///B/333,///B/334,///B/335,///B/336,///B/337,///B/338,///B/339,///B/340,///B/341,///B/342,///B/343,///B/344,///B/345,///B/346,///B/347,///B/348,///B/349,///B/350,///B/351,///B/352,///B/353,///B/354,///B/355,///B/356,///B/357,///B/358,///B/359,///B/360,///B/361,///B/362,///B/363,///B/364,///B/365,///B/366,///B/367,///B/368,///B/369,///B/370,///B/371,///B/372,///B/373,///B/374,///B/375,///B/376,///B/377,///B/378,///B/379,///B/380,///B/381,///B/382,///B/383,///B/384,///B/385,///B/386"
        }
      ]
    },
    {
      "index": 13,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        26
      ],
      "summary": "[1] 9 [B.384 B.394] 11",
      "num_nts": 11,
      "nts_short": "CAACGUGAGAG",
      "nts_long": "///B/384,///B/385,///B/386,///B/387,///B/388,///B/389,///B/390,///B/391,///B/392,///B/393,///B/394",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AACGUGAGA",
          "nts_long": "///B/385,///B/386,///B/387,///B/388,///B/389,///B/390,///B/391,///B/392,///B/393"
        }
      ]
    },
    {
      "index": 14,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        28
      ],
      "summary": "[1] 9 [B.418 B.428] 11",
      "num_nts": 11,
      "nts_short": "CAAUAUCCCAG",
      "nts_long": "///B/418,///B/419,///B/420,///B/421,///B/422,///B/423,///B/424,///B/425,///B/426,///B/427,///B/428",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AAUAUCCCA",
          "nts_long": "///B/419,///B/420,///B/421,///B/422,///B/423,///B/424,///B/425,///B/426,///B/427"
        }
      ]
    },
    {
      "index": 15,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        31
      ],
      "summary": "[1] 9 [B.452 B.462] 4",
      "num_nts": 11,
      "nts_short": "GAACUACCUAC",
      "nts_long": "///B/452,///B/453,///B/454,///B/455,///B/456,///B/457,///B/458,///B/459,///B/460,///B/461,///B/462",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AACUACCUA",
          "nts_long": "///B/453,///B/454,///B/455,///B/456,///B/457,///B/458,///B/459,///B/460,///B/461"
        }
      ]
    },
    {
      "index": 16,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        34
      ],
      "summary": "[1] 9 [B.486 B.496] 4",
      "num_nts": 11,
      "nts_short": "CAAUACCUCAG",
      "nts_long": "///B/486,///B/487,///B/488,///B/489,///B/490,///B/491,///B/492,///B/493,///B/494,///B/495,///B/496",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AAUACCUCA",
          "nts_long": "///B/487,///B/488,///B/489,///B/490,///B/491,///B/492,///B/493,///B/494,///B/495"
        }
      ]
    },
    {
      "index": 17,
      "type": "hairpin loop",
      "bridging_nts": [
        9
      ],
      "stem_indices": [
        36
      ],
      "summary": "[1] 9 [B.520 B.530] 4",
      "num_nts": 11,
      "nts_short": "AAACUGAACAU",
      "nts_long": "///B/520,///B/521,///B/522,///B/523,///B/524,///B/525,///B/526,///B/527,///B/528,///B/529,///B/530",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 9,
          "nts_short": "AACUGAACA",
          "nts_long": "///B/521,///B/522,///B/523,///B/524,///B/525,///B/526,///B/527,///B/528,///B/529"
        }
      ]
    },
    {
      "index": 18,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        37
      ],
      "summary": "[1] 4 [B.553 B.558] 8",
      "num_nts": 6,
      "nts_short": "GUUCGC",
      "nts_long": "///B/553,///B/554,///B/555,///B/556,///B/557,///B/558",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/554,///B/555,///B/556,///B/557"
        }
      ]
    },
    {
      "index": 19,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        39
      ],
      "summary": "[1] 4 [B.580 B.585] 5",
      "num_nts": 6,
      "nts_short": "GUUCGC",
      "nts_long": "///B/580,///B/581,///B/582,///B/583,///B/584,///B/585",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/581,///B/582,///B/583,///B/584"
        }
      ]
    },
    {
      "index": 20,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        -3
      ],
      "summary": "[1] 4 [B.607 B.612] 1",
      "num_nts": 6,
      "nts_short": "UUUCGA",
      "nts_long": "///B/607,///B/608,///B/609,///B/610,///B/611,///B/612",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/608,///B/609,///B/610,///B/611"
        }
      ]
    },
    {
      "index": 21,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        42
      ],
      "summary": "[1] 4 [B.634 B.639] 7",
      "num_nts": 6,
      "nts_short": "GUUCGC",
      "nts_long": "///B/634,///B/635,///B/636,///B/637,///B/638,///B/639",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/635,///B/636,///B/637,///B/638"
        }
      ]
    },
    {
      "index": 22,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        43
      ],
      "summary": "[1] 4 [B.661 B.666] 10",
      "num_nts": 6,
      "nts_short": "AUUCGU",
      "nts_long": "///B/661,///B/662,///B/663,///B/664,///B/665,///B/666",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/662,///B/663,///B/664,///B/665"
        }
      ]
    },
    {
      "index": 23,
      "type": "hairpin loop",
      "bridging_nts": [
        4
      ],
      "stem_indices": [
        44
      ],
      "summary": "[1] 4 [B.688 B.693] 13",
      "num_nts": 6,
      "nts_short": "GUUCGC",
      "nts_long": "///B/688,///B/689,///B/690,///B/691,///B/692,///B/693",
      "num_stems": 1,
      "bridges": [
        {
          "index": 1,
          "num_nts": 4,
          "nts_short": "UUCG",
          "nts_long": "///B/689,///B/690,///B/691,///B/692"
        }
      ]
    }
  ],
  "num_iloops": 10,
  "iloops": [
    {
      "index": 1,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        1,
        -1
      ],
      "summary": "[2] 1 1 [B.13 B.343 B.15 B.341] 13 1",
      "num_nts": 6,
      "nts_short": "UUCGGA",
      "nts_long": "///B/13,///B/14,///B/15,///B/341,///B/342,///B/343",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/14"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/342"
        }
      ]
    },
    {
      "index": 2,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        8,
        9
      ],
      "summary": "[2] 1 1 [B.106 B.127 B.108 B.125] 2 7",
      "num_nts": 6,
      "nts_short": "UGUAUG",
      "nts_long": "///B/106,///B/107,///B/108,///B/125,///B/126,///B/127",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/107"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/126"
        }
      ]
    },
    {
      "index": 3,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        20,
        21
      ],
      "summary": "[2] 1 1 [B.290 B.425 B.292 B.423] 2 3",
      "num_nts": 6,
      "nts_short": "GGAUCC",
      "nts_long": "///B/290,///B/291,///B/292,///B/423,///B/424,///B/425",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/291"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "C",
          "nts_long": "///B/424"
        }
      ]
    },
    {
      "index": 4,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        30,
        31
      ],
      "summary": "[2] 1 1 [B.447 B.467 B.449 B.465] 6 4",
      "num_nts": 6,
      "nts_short": "UGGCUA",
      "nts_long": "///B/447,///B/448,///B/449,///B/465,///B/466,///B/467",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/448"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/466"
        }
      ]
    },
    {
      "index": 5,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        33,
        34
      ],
      "summary": "[2] 1 1 [B.481 B.501 B.483 B.499] 6 4",
      "num_nts": 6,
      "nts_short": "UGAUUA",
      "nts_long": "///B/481,///B/482,///B/483,///B/499,///B/500,///B/501",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/482"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/500"
        }
      ]
    },
    {
      "index": 6,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        35,
        36
      ],
      "summary": "[2] 1 1 [B.515 B.535 B.517 B.533] 9 4",
      "num_nts": 6,
      "nts_short": "AGCGUU",
      "nts_long": "///B/515,///B/516,///B/517,///B/533,///B/534,///B/535",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/516"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/534"
        }
      ]
    },
    {
      "index": 7,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        -2,
        37
      ],
      "summary": "[2] 1 1 [B.544 B.567 B.546 B.565] 1 8",
      "num_nts": 6,
      "nts_short": "UUGCGA",
      "nts_long": "///B/544,///B/545,///B/546,///B/565,///B/566,///B/567",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/545"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/566"
        }
      ]
    },
    {
      "index": 8,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        38,
        39
      ],
      "summary": "[2] 1 1 [B.574 B.591 B.576 B.589] 4 5",
      "num_nts": 6,
      "nts_short": "CGCGUG",
      "nts_long": "///B/574,///B/575,///B/576,///B/589,///B/590,///B/591",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/575"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/590"
        }
      ]
    },
    {
      "index": 9,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        40,
        -3
      ],
      "summary": "[2] 1 1 [B.605 B.614 B.607 B.612] 8 1",
      "num_nts": 6,
      "nts_short": "GUUAGC",
      "nts_long": "///B/605,///B/606,///B/607,///B/612,///B/613,///B/614",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/606"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/613"
        }
      ]
    },
    {
      "index": 10,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        41,
        42
      ],
      "summary": "[2] 1 1 [B.626 B.647 B.628 B.645] 2 7",
      "num_nts": 6,
      "nts_short": "GGUAUC",
      "nts_long": "///B/626,///B/627,///B/628,///B/645,///B/646,///B/647",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///B/627"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///B/646"
        }
      ]
    }
  ],
  "num_junctions": 15,
  "junctions": [
    {
      "index": 1,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        -1,
        2,
        4,
        5
      ],
      "summary": "[4] 0 0 0 0 [B.15 B.341 B.16 B.50 B.51 B.74 B.75 B.340] 1 13 10 3",
      "num_nts": 8,
      "nts_short": "CAUAUCGG",
      "nts_long": "///B/15,///B/16,///B/50,///B/51,///B/74,///B/75,///B/340,///B/341",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 2,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        5,
        6,
        7,
        22
      ],
      "summary": "[4] 0 0 0 0 [B.77 B.338 B.78 B.101 B.102 B.308 B.309 B.337] 3 10 3 10",
      "num_nts": 8,
      "nts_short": "GAUGCUAC",
      "nts_long": "///B/77,///B/78,///B/101,///B/102,///B/308,///B/309,///B/337,///B/338",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 3,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        7,
        8,
        10,
        19
      ],
      "summary": "[4] 0 0 0 0 [B.104 B.306 B.105 B.128 B.129 B.276 B.277 B.305] 3 2 3 9",
      "num_nts": 8,
      "nts_short": "CUACGAUG",
      "nts_long": "///B/104,///B/105,///B/128,///B/129,///B/276,///B/277,///B/305,///B/306",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 4,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        10,
        11,
        12,
        17
      ],
      "summary": "[4] 0 0 0 0 [B.131 B.274 B.132 B.155 B.156 B.244 B.245 B.273] 3 10 3 10",
      "num_nts": 8,
      "nts_short": "CAUCGUAG",
      "nts_long": "///B/131,///B/132,///B/155,///B/156,///B/244,///B/245,///B/273,///B/274",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 5,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        12,
        13,
        14,
        15
      ],
      "summary": "[4] 0 0 0 0 [B.158 B.242 B.159 B.182 B.183 B.212 B.213 B.241] 3 10 13 10",
      "num_nts": 8,
      "nts_short": "GGUGCGCC",
      "nts_long": "///B/158,///B/159,///B/182,///B/183,///B/212,///B/213,///B/241,///B/242",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 6,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        24,
        25,
        43,
        44
      ],
      "summary": "[4] 0 0 0 0 [B.370 B.706 B.371 B.651 B.652 B.675 B.676 B.705] 15 3 10 13",
      "num_nts": 8,
      "nts_short": "CGCCGUGG",
      "nts_long": "///B/370,///B/371,///B/651,///B/652,///B/675,///B/676,///B/705,///B/706",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 7,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        25,
        26,
        27,
        41
      ],
      "summary": "[4] 0 0 0 0 [B.373 B.649 B.374 B.404 B.405 B.624 B.625 B.648] 3 11 3 2",
      "num_nts": 8,
      "nts_short": "CGCCGCGG",
      "nts_long": "///B/373,///B/374,///B/404,///B/405,///B/624,///B/625,///B/648,///B/649",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 8,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        27,
        28,
        29,
        40
      ],
      "summary": "[4] 0 0 0 0 [B.407 B.622 B.408 B.438 B.439 B.597 B.598 B.621] 3 11 3 8",
      "num_nts": 8,
      "nts_short": "CGCCGAUG",
      "nts_long": "///B/407,///B/408,///B/438,///B/439,///B/597,///B/598,///B/621,///B/622",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 9,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        29,
        30,
        32,
        38
      ],
      "summary": "[4] 0 0 0 0 [B.441 B.595 B.442 B.472 B.473 B.570 B.571 B.594] 3 6 3 4",
      "num_nts": 8,
      "nts_short": "CAUCGUAG",
      "nts_long": "///B/441,///B/442,///B/472,///B/473,///B/570,///B/571,///B/594,///B/595",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 10,
      "type": "4-way junction",
      "bridging_nts": [
        0,
        0,
        0,
        0
      ],
      "stem_indices": [
        32,
        33,
        35,
        -2
      ],
      "summary": "[4] 0 0 0 0 [B.475 B.568 B.476 B.506 B.507 B.543 B.544 B.567] 3 6 9 1",
      "num_nts": 8,
      "nts_short": "GGCGCUAC",
      "nts_long": "///B/475,///B/476,///B/506,///B/507,///B/543,///B/544,///B/567,///B/568",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 3,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 4,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        }
      ]
    },
    {
      "index": 11,
      "type": "4-way junction",
      "bridging_nts": [
        2,
        1,
        2,
        1
      ],
      "stem_indices": [
        2,
        3,
        36,
        3
      ],
      "summary": "[4] 2 1 2 1 [B.28 B.38 B.31 B.528 B.530 B.520 B.523 B.36] 13 6 4 6",
      "is_repeated": true,
      "num_nts": 14,
      "nts_short": "CAAGCAUAAACGAG",
      "nts_long": "///B/28,///B/29,///B/30,///B/31,///B/528,///B/529,///B/530,///B/520,///B/521,///B/522,///B/523,///B/36,///B/37,///B/38",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/29,///B/30"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/529"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/521,///B/522"
        },
        {
          "index": 4,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/37"
        }
      ]
    },
    {
      "index": 12,
      "type": "4-way junction",
      "bridging_nts": [
        2,
        1,
        2,
        1
      ],
      "stem_indices": [
        15,
        16,
        34,
        16
      ],
      "summary": "[4] 2 1 2 1 [B.222 B.232 B.225 B.494 B.496 B.486 B.489 B.230] 10 6 4 6",
      "is_repeated": true,
      "num_nts": 14,
      "nts_short": "GAAGCAGCAAUAAC",
      "nts_long": "///B/222,///B/223,///B/224,///B/225,///B/494,///B/495,///B/496,///B/486,///B/487,///B/488,///B/489,///B/230,///B/231,///B/232",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/223,///B/224"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/495"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/487,///B/488"
        },
        {
          "index": 4,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/231"
        }
      ]
    },
    {
      "index": 13,
      "type": "4-way junction",
      "bridging_nts": [
        2,
        1,
        2,
        1
      ],
      "stem_indices": [
        17,
        18,
        31,
        18
      ],
      "summary": "[4] 2 1 2 1 [B.254 B.264 B.257 B.460 B.462 B.452 B.455 B.262] 10 6 4 6",
      "is_repeated": true,
      "num_nts": 14,
      "nts_short": "CAAAUACGAACGAG",
      "nts_long": "///B/254,///B/255,///B/256,///B/257,///B/460,///B/461,///B/462,///B/452,///B/453,///B/454,///B/455,///B/262,///B/263,///B/264",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/255,///B/256"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/461"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/453,///B/454"
        },
        {
          "index": 4,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/263"
        }
      ]
    },
    {
      "index": 14,
      "type": "4-way junction",
      "bridging_nts": [
        2,
        1,
        2,
        1
      ],
      "stem_indices": [
        22,
        23,
        26,
        23
      ],
      "summary": "[4] 2 1 2 1 [B.318 B.328 B.321 B.392 B.394 B.384 B.387 B.326] 10 6 11 6",
      "is_repeated": true,
      "num_nts": 14,
      "nts_short": "GAACGAGCAACGAC",
      "nts_long": "///B/318,///B/319,///B/320,///B/321,///B/392,///B/393,///B/394,///B/384,///B/385,///B/386,///B/387,///B/326,///B/327,///B/328",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/319,///B/320"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/393"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/385,///B/386"
        },
        {
          "index": 4,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/327"
        }
      ]
    },
    {
      "index": 15,
      "type": "4-way junction",
      "bridging_nts": [
        3,
        1,
        2,
        2
      ],
      "stem_indices": [
        19,
        20,
        28,
        21
      ],
      "summary": "[4] 3 1 2 2 [B.285 B.297 B.289 B.426 B.428 B.418 B.421 B.294] 9 2 11 3",
      "num_nts": 16,
      "nts_short": "CAAAGCAGCAAUAAUG",
      "nts_long": "///B/285,///B/286,///B/287,///B/288,///B/289,///B/426,///B/427,///B/428,///B/418,///B/419,///B/420,///B/421,///B/294,///B/295,///B/296,///B/297",
      "num_stems": 4,
      "bridges": [
        {
          "index": 1,
          "num_nts": 3,
          "nts_short": "AAA",
          "nts_long": "///B/286,///B/287,///B/288"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///B/427"
        },
        {
          "index": 3,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///B/419,///B/420"
        },
        {
          "index": 4,
          "num_nts": 2,
          "nts_short": "AU",
          "nts_long": "///B/295,///B/296"
        }
      ]
    }
  ],
  "num_kissingLoops": 6,
  "kissingLoops": [
    {
      "index": 1,
      "stem_index": 3,
      "hairpin_indices": [
        1,
        17
      ]
    },
    {
      "index": 2,
      "stem_index": 16,
      "hairpin_indices": [
        8,
        16
      ]
    },
    {
      "index": 3,
      "stem_index": 18,
      "hairpin_indices": [
        9,
        15
      ]
    },
    {
      "index": 4,
      "stem_index": 20,
      "hairpin_indices": [
        10,
        14
      ]
    },
    {
      "index": 5,
      "stem_index": 21,
      "hairpin_indices": [
        10,
        14
      ]
    },
    {
      "index": 6,
      "stem_index": 23,
      "hairpin_indices": [
        11,
        13
      ]
    }
  ],
  "num_splayUnits": 31,
  "splayUnits": [
    {
      "index": 1,
      "num_nts": 2,
      "nts_short": "CA",
      "nts_long": "///B/15,///B/16"
    },
    {
      "index": 2,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/62,///B/63"
    },
    {
      "index": 3,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/74,///B/75"
    },
    {
      "index": 4,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/88,///B/89,///B/90"
    },
    {
      "index": 5,
      "num_nts": 2,
      "nts_short": "UG",
      "nts_long": "///B/101,///B/102"
    },
    {
      "index": 6,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/115,///B/116,///B/117"
    },
    {
      "index": 7,
      "num_nts": 2,
      "nts_short": "AC",
      "nts_long": "///B/128,///B/129"
    },
    {
      "index": 8,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/143,///B/144"
    },
    {
      "index": 9,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/155,///B/156"
    },
    {
      "index": 10,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/169,///B/170,///B/171"
    },
    {
      "index": 11,
      "num_nts": 2,
      "nts_short": "UG",
      "nts_long": "///B/182,///B/183"
    },
    {
      "index": 12,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/196,///B/197,///B/198"
    },
    {
      "index": 13,
      "num_nts": 2,
      "nts_short": "CC",
      "nts_long": "///B/241,///B/242"
    },
    {
      "index": 14,
      "num_nts": 2,
      "nts_short": "AG",
      "nts_long": "///B/273,///B/274"
    },
    {
      "index": 15,
      "num_nts": 2,
      "nts_short": "UG",
      "nts_long": "///B/305,///B/306"
    },
    {
      "index": 16,
      "num_nts": 2,
      "nts_short": "AC",
      "nts_long": "///B/337,///B/338"
    },
    {
      "index": 17,
      "num_nts": 2,
      "nts_short": "CG",
      "nts_long": "///B/370,///B/371"
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    {
      "index": 18,
      "num_nts": 2,
      "nts_short": "AC",
      "nts_long": "///B/386,///B/387"
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    {
      "index": 19,
      "num_nts": 2,
      "nts_short": "CC",
      "nts_long": "///B/404,///B/405"
    },
    {
      "index": 20,
      "num_nts": 2,
      "nts_short": "CC",
      "nts_long": "///B/438,///B/439"
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    {
      "index": 21,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/472,///B/473"
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      "index": 22,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/554,///B/555,///B/556"
    },
    {
      "index": 23,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/581,///B/582,///B/583"
    },
    {
      "index": 24,
      "num_nts": 2,
      "nts_short": "AG",
      "nts_long": "///B/594,///B/595"
    },
    {
      "index": 25,
      "num_nts": 2,
      "nts_short": "UC",
      "nts_long": "///B/609,///B/610"
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    {
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      "num_nts": 2,
      "nts_short": "UG",
      "nts_long": "///B/621,///B/622"
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      "num_nts": 3,
      "nts_short": "UUC",
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      "num_nts": 2,
      "nts_short": "GG",
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      "num_nts": 2,
      "nts_short": "UU",
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    {
      "index": 30,
      "num_nts": 2,
      "nts_short": "GU",
      "nts_long": "///B/675,///B/676"
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    {
      "index": 31,
      "num_nts": 3,
      "nts_short": "UUC",
      "nts_long": "///B/689,///B/690,///B/691"
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    {
      "index": 2,
      "desc": "stem#22(hairpin#11) vs stem#23(hairpin#12) L2 groove=----- nts=1 A ///B/327"
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      "index": 3,
      "desc": "stem#22(hairpin#11) vs stem#23(hairpin#12) L3 groove=----- nts=49 CGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAA ///B/338,///B/339,///B/340,///B/341,///B/342,///B/343,///B/344,///B/345,///B/346,///B/347,///B/348,///B/349,///B/350,///B/351,///B/352,///B/353,///B/354,///B/355,///B/356,///B/357,///B/358,///B/359,///B/360,///B/361,///B/362,///B/363,///B/364,///B/365,///B/366,///B/367,///B/368,///B/369,///B/370,///B/371,///B/372,///B/373,///B/374,///B/375,///B/376,///B/377,///B/378,///B/379,///B/380,///B/381,///B/382,///B/383,///B/384,///B/385,///B/386"
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      "helical_rise_std": 2.863,
      "helical_axis": [
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      "point1": [
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      "point2": [
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      "    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": "7ptk",
    "num_naChains": 1,
    "naChains": "B=720",
    "num_atoms": 23080,
    "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": 18,
    "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-iloops.pdb",
        "desc": "an ensemble of internal loops"
      },
      {
        "index": 7,
        "name": "dssr-junctions.pdb",
        "desc": "an ensemble of junctions (multi-branch)"
      },
      {
        "index": 8,
        "name": "dssr-2ndstrs.bpseq",
        "desc": "secondary structure in bpseq format"
      },
      {
        "index": 9,
        "name": "dssr-2ndstrs.ct",
        "desc": "secondary structure in connectivity table format"
      },
      {
        "index": 10,
        "name": "dssr-2ndstrs.dbn",
        "desc": "secondary structure in dot-bracket notation"
      },
      {
        "index": 11,
        "name": "dssr-torsions.txt",
        "desc": "backbone torsion angles and suite names"
      },
      {
        "index": 12,
        "name": "dssr-splays.pdb",
        "desc": "an ensemble of splayed-apart units"
      },
      {
        "index": 13,
        "name": "dssr-stacks.pdb",
        "desc": "an ensemble of base stacks"
      },
      {
        "index": 14,
        "name": "dssr-atom2bases.pdb",
        "desc": "an ensemble of atom-base stacking interactions"
      },
      {
        "index": 15,
        "name": "dssr-rotmat.txt",
        "desc": "position vector and rotation matrix"
      },
      {
        "index": 16,
        "name": "dssr-viewV.pdb",
        "desc": "vertical view of the principal moment of inertia"
      },
      {
        "index": 17,
        "name": "dssr-viewH.pdb",
        "desc": "horizontal view of the principal moment of inertia"
      },
      {
        "index": 18,
        "name": "dssr-viewT.pdb",
        "desc": "top view of the principal moment of inertia"
      }
    ],
    "time_used": "999"
  }
}