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"atom": "///A/3064/O2'", "nt": "///A/3099", "vert_dist": 3.375 }, { "index": 62, "type": "other", "atom": "///A/3129/P", "nt": "///A/3127", "vert_dist": 3.420 }, { "index": 63, "type": "phosphate", "atom": "///A/3129/OP1", "nt": "///A/3127", "vert_dist": 2.651 }, { "index": 64, "type": "sugar", "atom": "///A/3130/O4'", "nt": "///A/3129", "vert_dist": 3.054 }, { "index": 65, "type": "sugar", "atom": "///B/1607/O4'", "nt": "///B/1606", "vert_dist": 3.486 }, { "index": 66, "type": "phosphate", "atom": "///B/1625/OP2", "nt": "///B/1625", "vert_dist": 2.908 } ], "num_hairpins": 29, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ -2 ], "summary": "[1] 6 [A.1722 A.1729] 1", "num_nts": 8, "nts_short": "AAACCAUU", "nts_long": "///A/1722,///A/1723,///A/1724,///A/1725,///A/1726,///A/1727,///A/1728,///A/1729", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AACCAU", "nts_long": "///A/1723,///A/1724,///A/1725,///A/1726,///A/1727,///A/1728" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 4 ], "summary": "[1] 5 [A.1746 A.1752] 2", "num_nts": 7, "nts_short": "AGGCGAU", "nts_long": "///A/1746,///A/1747,///A/1748,///A/1749,///A/1750,///A/1751,///A/1752", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGCGA", "nts_long": "///A/1747,///A/1748,///A/1749,///A/1750,///A/1751" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 5 ], "summary": "[1] 4 [A.1786 A.1791] 2", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///A/1786,///A/1787,///A/1788,///A/1789,///A/1790,///A/1791", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/1787,///A/1788,///A/1789,///A/1790" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 6 ], "summary": "[1] 7 [A.1831 A.1839] 3", "num_nts": 9, "nts_short": "GACUAACCC", "nts_long": "///A/1831,///A/1832,///A/1833,///A/1834,///A/1835,///A/1836,///A/1837,///A/1838,///A/1839", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "ACUAACC", "nts_long": "///A/1832,///A/1833,///A/1834,///A/1835,///A/1836,///A/1837,///A/1838" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 7 ], "summary": "[1] 6 [A.1848 A.1855] 2", "num_nts": 8, "nts_short": "UCUGCAUA", "nts_long": "///A/1848,///A/1849,///A/1850,///A/1851,///A/1852,///A/1853,///A/1854,///A/1855", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CUGCAU", "nts_long": "///A/1849,///A/1850,///A/1851,///A/1852,///A/1853,///A/1854" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 11 ], "summary": "[1] 4 [A.1884 A.1889] 2", "num_nts": 6, "nts_short": "GAGAGC", "nts_long": "///A/1884,///A/1885,///A/1886,///A/1887,///A/1888,///A/1889", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGAG", "nts_long": "///A/1885,///A/1886,///A/1887,///A/1888" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 16 ], "summary": "[1] 5 [A.1934 A.1940] 3", "num_nts": 7, "nts_short": "UAAAAGA", "nts_long": "///A/1934,///A/1935,///A/1936,///A/1937,///A/1938,///A/1939,///A/1940", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AAAAG", "nts_long": "///A/1935,///A/1936,///A/1937,///A/1938,///A/1939" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 18 ], "summary": "[1] 8 [A.1954 A.1963] 4", "num_nts": 10, "nts_short": "UGUAGCAAAA", "nts_long": "///A/1954,///A/1955,///A/1956,///A/1957,///A/1958,///A/1959,///A/1960,///A/1961,///A/1962,///A/1963", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GUAGCAAA", "nts_long": "///A/1955,///A/1956,///A/1957,///A/1958,///A/1959,///A/1960,///A/1961,///A/1962" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 19 ], "summary": "[1] 7 [A.1988 A.1996] 2", "num_nts": 9, "nts_short": "GCGACAAAC", "nts_long": "///A/1988,///A/1989,///A/1990,///A/1991,///A/1992,///A/1993,///A/1994,///A/1995,///A/1996", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "CGACAAA", "nts_long": "///A/1989,///A/1990,///A/1991,///A/1992,///A/1993,///A/1994,///A/1995" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 21 ], "summary": "[1] 4 [A.2035 A.2040] 4", "num_nts": 6, "nts_short": "UCUUAG", "nts_long": "///A/2035,///A/2036,///A/2037,///A/2038,///A/2039,///A/2040", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUUA", "nts_long": "///A/2036,///A/2037,///A/2038,///A/2039" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 26 ], "summary": "[1] 6 [A.2107 A.2114] 10", "num_nts": 8, "nts_short": "GGAACAGC", "nts_long": "///A/2107,///A/2108,///A/2109,///A/2110,///A/2111,///A/2112,///A/2113,///A/2114", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAACAG", "nts_long": "///A/2108,///A/2109,///A/2110,///A/2111,///A/2112,///A/2113" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 27 ], "summary": "[1] 6 [A.2129 A.2136] 3", "num_nts": 8, "nts_short": "GAAAAAAC", "nts_long": "///A/2129,///A/2130,///A/2131,///A/2132,///A/2133,///A/2134,///A/2135,///A/2136", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AAAAAA", "nts_long": "///A/2130,///A/2131,///A/2132,///A/2133,///A/2134,///A/2135" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 32 ], "summary": "[1] 4 [A.2319 A.2324] 3", "num_nts": 6, "nts_short": "AAACAU", "nts_long": "///A/2319,///A/2320,///A/2321,///A/2322,///A/2323,///A/2324", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AACA", "nts_long": "///A/2320,///A/2321,///A/2322,///A/2323" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 2 ], "stem_indices": [ -18 ], "summary": "[1] 2 [A.2400 A.2403] 1", "num_nts": 4, "nts_short": "CAAG", "nts_long": "///A/2400,///A/2401,///A/2402,///A/2403", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2401,///A/2402" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 44 ], "summary": "[1] 9 [A.2497 A.2507] 2", "num_nts": 11, "nts_short": "UUUACCAAAAA", "nts_long": "///A/2497,///A/2498,///A/2499,///A/2500,///A/2501,///A/2502,///A/2503,///A/2504,///A/2505,///A/2506,///A/2507", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UUACCAAAA", "nts_long": "///A/2498,///A/2499,///A/2500,///A/2501,///A/2502,///A/2503,///A/2504,///A/2505,///A/2506" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 45 ], "summary": "[1] 13 [A.2518 A.2532] 6", "num_nts": 15, "nts_short": "AGCAUCACCAGUAUU", "nts_long": "///A/2518,///A/2519,///A/2520,///A/2521,///A/2522,///A/2523,///A/2524,///A/2525,///A/2526,///A/2527,///A/2528,///A/2529,///A/2530,///A/2531,///A/2532", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "GCAUCACCAGUAU", "nts_long": "///A/2519,///A/2520,///A/2521,///A/2522,///A/2523,///A/2524,///A/2525,///A/2526,///A/2527,///A/2528,///A/2529,///A/2530,///A/2531" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 46 ], "summary": "[1] 7 [A.2612 A.2620] 2", "num_nts": 9, "nts_short": "CUUAAAUAG", "nts_long": "///A/2612,///A/2613,///A/2614,///A/2615,///A/2616,///A/2617,///A/2618,///A/2619,///A/2620", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUAAAUA", "nts_long": "///A/2613,///A/2614,///A/2615,///A/2616,///A/2617,///A/2618,///A/2619" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 56 ], "summary": "[1] 7 [A.2812 A.2820] 3", "num_nts": 9, "nts_short": "UUGGGGCGA", "nts_long": "///A/2812,///A/2813,///A/2814,///A/2815,///A/2816,///A/2817,///A/2818,///A/2819,///A/2820", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGGGGCG", "nts_long": "///A/2813,///A/2814,///A/2815,///A/2816,///A/2817,///A/2818,///A/2819" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ 57 ], "summary": "[1] 11 [A.2828 A.2840] 6", "num_nts": 13, "nts_short": "GCAGAACCCAACC", "nts_long": "///A/2828,///A/2829,///A/2830,///A/2831,///A/2832,///A/2833,///A/2834,///A/2835,///A/2836,///A/2837,///A/2838,///A/2839,///A/2840", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "CAGAACCCAAC", "nts_long": "///A/2829,///A/2830,///A/2831,///A/2832,///A/2833,///A/2834,///A/2835,///A/2836,///A/2837,///A/2838,///A/2839" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 59 ], "summary": "[1] 7 [A.2862 A.2870] 3", "num_nts": 9, "nts_short": "CUUCACCAG", "nts_long": "///A/2862,///A/2863,///A/2864,///A/2865,///A/2866,///A/2867,///A/2868,///A/2869,///A/2870", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUCACCA", "nts_long": "///A/2863,///A/2864,///A/2865,///A/2866,///A/2867,///A/2868,///A/2869" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 61 ], "summary": "[1] 7 [A.2958 A.2966] 2", "num_nts": 9, "nts_short": "AGUCCAUAU", "nts_long": "///A/2958,///A/2959,///A/2960,///A/2961,///A/2962,///A/2963,///A/2964,///A/2965,///A/2966", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUCCAUA", "nts_long": "///A/2959,///A/2960,///A/2961,///A/2962,///A/2963,///A/2964,///A/2965" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 66 ], "summary": "[1] 6 [A.3015 A.3022] 2", "num_nts": 8, "nts_short": "UGCAGCCG", "nts_long": "///A/3015,///A/3016,///A/3017,///A/3018,///A/3019,///A/3020,///A/3021,///A/3022", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GCAGCC", "nts_long": "///A/3016,///A/3017,///A/3018,///A/3019,///A/3020,///A/3021" } ] }, { "index": 23, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 67 ], "summary": "[1] 5 [A.3038 A.3044] 5", "num_nts": 7, "nts_short": "UUGUUCA", "nts_long": "///A/3038,///A/3039,///A/3040,///A/3041,///A/3042,///A/3043,///A/3044", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGUUC", "nts_long": "///A/3039,///A/3040,///A/3041,///A/3042,///A/3043" } ] }, { "index": 24, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 69 ], "summary": "[1] 4 [A.3081 A.3086] 3", "num_nts": 6, "nts_short": "AGUAAU", "nts_long": "///A/3081,///A/3082,///A/3083,///A/3084,///A/3085,///A/3086", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GUAA", "nts_long": "///A/3082,///A/3083,///A/3084,///A/3085" } ] }, { "index": 25, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -26 ], "summary": "[1] 4 [A.3126 A.3131] 1", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///A/3126,///A/3127,///A/3128,///A/3129,///A/3130,///A/3131", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/3127,///A/3128,///A/3129,///A/3130" } ] }, { "index": 26, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 73 ], "summary": "[1] 4 [A.3154 A.3159] 3", "num_nts": 6, "nts_short": "UCACAA", "nts_long": "///A/3154,///A/3155,///A/3156,///A/3157,///A/3158,///A/3159", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CACA", "nts_long": "///A/3155,///A/3156,///A/3157,///A/3158" } ] }, { "index": 27, "type": "hairpin loop", "bridging_nts": [ 16 ], "stem_indices": [ 74 ], "summary": "[1] 16 [A.3176 A.3193] 3", "num_nts": 18, "nts_short": "AAUGAUAUCAUCUCAACU", "nts_long": "///A/3176,///A/3177,///A/3178,///A/3179,///A/3180,///A/3181,///A/3182,///A/3183,///A/3184,///A/3185,///A/3186,///A/3187,///A/3188,///A/3189,///A/3190,///A/3191,///A/3192,///A/3193", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 16, "nts_short": "AUGAUAUCAUCUCAAC", "nts_long": "///A/3177,///A/3178,///A/3179,///A/3180,///A/3181,///A/3182,///A/3183,///A/3184,///A/3185,///A/3186,///A/3187,///A/3188,///A/3189,///A/3190,///A/3191,///A/3192" } ] }, { "index": 28, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 75 ], "summary": "[1] 7 [A.3216 A.3224] 4", "num_nts": 9, "nts_short": "CAAGAACAG", "nts_long": "///A/3216,///A/3217,///A/3218,///A/3219,///A/3220,///A/3221,///A/3222,///A/3223,///A/3224", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AAGAACA", "nts_long": "///A/3217,///A/3218,///A/3219,///A/3220,///A/3221,///A/3222,///A/3223" } ] }, { "index": 29, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ -28 ], "summary": "[1] 13 [B.1627 B.1641] 1", "num_nts": 15, "nts_short": "CCAACUUACACUUAG", "nts_long": "///B/1627,///B/1628,///B/1629,///B/1630,///B/1631,///B/1632,///B/1633,///B/1634,///B/1635,///B/1636,///B/1637,///B/1638,///B/1639,///B/1640,///B/1641", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "CAACUUACACUUA", "nts_long": "///B/1628,///B/1629,///B/1630,///B/1631,///B/1632,///B/1633,///B/1634,///B/1635,///B/1636,///B/1637,///B/1638,///B/1639,///B/1640" } ] } ], "num_bulges": 8, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 2, 3 ], "summary": "[2] 0 1 [A.1682 A.1770 A.1683 A.1768] 2 2", "num_nts": 5, "nts_short": "CCGCG", "nts_long": "///A/1682,///A/1683,///A/1768,///A/1769,///A/1770", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1769" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 15, -10 ], "summary": "[2] 0 1 [A.1929 A.1975 A.1930 A.1973] 3 1", "num_nts": 5, "nts_short": "ACGAU", "nts_long": "///A/1929,///A/1930,///A/1973,///A/1974,///A/1975", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1974" } ] }, { "index": 3, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 28, 29 ], "summary": "[2] 1 0 [A.2145 A.2255 A.2147 A.2254] 3 3", "num_nts": 5, "nts_short": "GAGCC", "nts_long": "///A/2145,///A/2146,///A/2147,///A/2254,///A/2255", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2146" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 4, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 42, 43 ], "summary": "[2] 0 1 [A.2490 A.2645 A.2491 A.2643] 4 2", "num_nts": 5, "nts_short": "CCGAG", "nts_long": "///A/2490,///A/2491,///A/2643,///A/2644,///A/2645", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2644" } ] }, { "index": 5, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 51, 52 ], "summary": "[2] 1 0 [A.2730 A.2930 A.2732 A.2929] 5 2", "num_nts": 5, "nts_short": "AUGCU", "nts_long": "///A/2730,///A/2731,///A/2732,///A/2929,///A/2930", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2731" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 6, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 68, 69 ], "summary": "[2] 0 1 [A.3078 A.3090 A.3079 A.3088] 4 3", "num_nts": 5, "nts_short": "CGCAG", "nts_long": "///A/3078,///A/3079,///A/3088,///A/3089,///A/3090", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/3089" } ] }, { "index": 7, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ 41, -19 ], "summary": "[2] 2 0 [A.2470 A.2657 A.2473 A.2656] 2 1", "num_nts": 6, "nts_short": "GGAAUC", "nts_long": "///A/2470,///A/2471,///A/2472,///A/2473,///A/2656,///A/2657", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2471,///A/2472" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 8, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 52, 53 ], "summary": "[2] 0 2 [A.2733 A.2928 A.2734 A.2925] 2 4", "num_nts": 6, "nts_short": "GAUACC", "nts_long": "///A/2733,///A/2734,///A/2925,///A/2926,///A/2927,///A/2928", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2926,///A/2927" } ] } ], "num_iloops": 32, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -7, 7 ], "summary": "[2] 1 1 [A.1845 A.1858 A.1847 A.1856] 1 2", "num_nts": 6, "nts_short": "CCUAUG", "nts_long": "///A/1845,///A/1846,///A/1847,///A/1856,///A/1857,///A/1858", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1846" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1857" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 9, 10 ], "summary": "[2] 1 1 [A.1877 A.1897 A.1879 A.1895] 3 2", "num_nts": 6, "nts_short": "UUGCUA", "nts_long": "///A/1877,///A/1878,///A/1879,///A/1895,///A/1896,///A/1897", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1878" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1896" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 12, -8 ], "summary": "[2] 1 1 [A.1904 A.2018 A.1906 A.2016] 2 1", "num_nts": 6, "nts_short": "CCGCUG", "nts_long": "///A/1904,///A/1905,///A/1906,///A/2016,///A/2017,///A/2018", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/1905" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2017" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 13, -9 ], "summary": "[2] 1 1 [A.1913 A.2006 A.1915 A.2004] 4 1", "num_nts": 6, "nts_short": "GACGCC", "nts_long": "///A/1913,///A/1914,///A/1915,///A/2004,///A/2005,///A/2006", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1914" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2005" } ] }, { "index": 5, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 14, 15 ], "summary": "[2] 1 1 [A.1925 A.1979 A.1927 A.1977] 5 3", "num_nts": 6, "nts_short": "AAGUAU", "nts_long": "///A/1925,///A/1926,///A/1927,///A/1977,///A/1978,///A/1979", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1926" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1978" } ] }, { "index": 6, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 40, 41 ], "summary": "[2] 1 1 [A.2467 A.2660 A.2469 A.2658] 7 2", "num_nts": 6, "nts_short": "AAAUCU", "nts_long": "///A/2467,///A/2468,///A/2469,///A/2658,///A/2659,///A/2660", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2468" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2659" } ] }, { "index": 7, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 65, 66 ], "summary": "[2] 1 1 [A.3012 A.3025 A.3014 A.3023] 3 2", "num_nts": 6, "nts_short": "UGGCUA", "nts_long": "///A/3012,///A/3013,///A/3014,///A/3023,///A/3024,///A/3025", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/3013" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/3024" } ] }, { "index": 8, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 70, 71 ], "summary": "[2] 1 1 [A.3115 A.3141 A.3117 A.3139] 3 3", "num_nts": 6, "nts_short": "UCCGAA", "nts_long": "///A/3115,///A/3116,///A/3117,///A/3139,///A/3140,///A/3141", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/3116" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/3140" } ] }, { "index": 9, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -29, -30 ], "summary": "[2] 1 1 [B.1649 B.1660 B.1651 B.1658] 1 1", "num_nts": 6, "nts_short": "CAAUUG", "nts_long": "///B/1649,///B/1650,///B/1651,///B/1658,///B/1659,///B/1660", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///B/1650" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///B/1659" } ] }, { "index": 10, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 17, 18 ], "summary": "[2] 2 1 [A.1948 A.1968 A.1951 A.1966] 3 4", "num_nts": 7, "nts_short": "CGUCGUG", "nts_long": "///A/1948,///A/1949,///A/1950,///A/1951,///A/1966,///A/1967,///A/1968", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/1949,///A/1950" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/1967" } ] }, { "index": 11, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 22, 23 ], "summary": "[2] 1 2 [A.2046 A.2094 A.2048 A.2091] 2 7", "num_nts": 7, "nts_short": "CUUACUG", "nts_long": "///A/2046,///A/2047,///A/2048,///A/2091,///A/2092,///A/2093,///A/2094", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2047" }, { "index": 2, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/2092,///A/2093" } ] }, { "index": 12, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 48, 49 ], "summary": "[2] 2 1 [A.2712 A.3106 A.2715 A.3104] 2 3", "num_nts": 7, "nts_short": "GCAAUAC", "nts_long": "///A/2712,///A/2713,///A/2714,///A/2715,///A/3104,///A/3105,///A/3106", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2713,///A/2714" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/3105" } ] }, { "index": 13, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 49, 50 ], "summary": "[2] 1 2 [A.2717 A.3102 A.2719 A.3099] 3 2", "num_nts": 7, "nts_short": "ACGCUAU", "nts_long": "///A/2717,///A/2718,///A/2719,///A/3099,///A/3100,///A/3101,///A/3102", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2718" }, { "index": 2, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/3100,///A/3101" } ] }, { "index": 14, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 54, 55 ], "summary": "[2] 2 1 [A.2744 A.2803 A.2747 A.2801] 5 7", "num_nts": 7, "nts_short": "UAUUAAA", "nts_long": "///A/2744,///A/2745,///A/2746,///A/2747,///A/2801,///A/2802,///A/2803", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/2745,///A/2746" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/2802" } ] }, { "index": 15, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ -14, 19 ], "summary": "[2] 1 3 [A.1985 A.2001 A.1987 A.1997] 1 2", "num_nts": 8, "nts_short": "GAGCUACC", "nts_long": "///A/1985,///A/1986,///A/1987,///A/1997,///A/1998,///A/1999,///A/2000,///A/2001", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1986" }, { "index": 2, "num_nts": 3, "nts_short": "UAC", "nts_long": "///A/1998,///A/1999,///A/2000" } ] }, { "index": 16, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 62, -25 ], "summary": "[2] 1 3 [A.2997 A.3065 A.2999 A.3061] 4 1", "num_nts": 8, "nts_short": "AUCGUGAU", "nts_long": "///A/2997,///A/2998,///A/2999,///A/3061,///A/3062,///A/3063,///A/3064,///A/3065", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2998" }, { "index": 2, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/3062,///A/3063,///A/3064" } ] }, { "index": 17, "type": "asymmetric internal loop", "bridging_nts": [ 1, 3 ], "stem_indices": [ 64, 65 ], "summary": "[2] 1 3 [A.3008 A.3031 A.3010 A.3027] 2 3", "num_nts": 8, "nts_short": "CCGUAAAG", "nts_long": "///A/3008,///A/3009,///A/3010,///A/3027,///A/3028,///A/3029,///A/3030,///A/3031", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/3009" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/3028,///A/3029,///A/3030" } ] }, { "index": 18, "type": "asymmetric internal loop", "bridging_nts": [ 3, 1 ], "stem_indices": [ 72, 73 ], "summary": "[2] 3 1 [A.3148 A.3163 A.3152 A.3161] 5 3", "num_nts": 8, "nts_short": "CCUACGCG", "nts_long": "///A/3148,///A/3149,///A/3150,///A/3151,///A/3152,///A/3161,///A/3162,///A/3163", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/3149,///A/3150,///A/3151" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///A/3162" } ] }, { "index": 19, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 10, 11 ], "summary": "[2] 2 3 [A.1880 A.1894 A.1883 A.1890] 2 2", "num_nts": 9, "nts_short": "CAAGCAAAG", "nts_long": "///A/1880,///A/1881,///A/1882,///A/1883,///A/1890,///A/1891,///A/1892,///A/1893,///A/1894", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1881,///A/1882" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1891,///A/1892,///A/1893" } ] }, { "index": 20, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 39, 40 ], "summary": "[2] 4 1 [A.2456 A.2668 A.2461 A.2666] 4 7", "num_nts": 9, "nts_short": "UAAAAAUUA", "nts_long": "///A/2456,///A/2457,///A/2458,///A/2459,///A/2460,///A/2461,///A/2666,///A/2667,///A/2668", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///A/2457,///A/2458,///A/2459,///A/2460" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2667" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 29, -15 ], "summary": "[2] 3 3 [A.2149 A.2252 A.2153 A.2248] 3 1", "num_nts": 10, "nts_short": "GUAAAUGAAC", "nts_long": "///A/2149,///A/2150,///A/2151,///A/2152,///A/2153,///A/2248,///A/2249,///A/2250,///A/2251,///A/2252", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/2150,///A/2151,///A/2152" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/2249,///A/2250,///A/2251" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 4, 2 ], "stem_indices": [ -19, -20 ], "summary": "[2] 4 2 [A.2473 A.2656 A.2478 A.2653] 1 1", "num_nts": 10, "nts_short": "ACUCGGCUGU", "nts_long": "///A/2473,///A/2474,///A/2475,///A/2476,///A/2477,///A/2478,///A/2653,///A/2654,///A/2655,///A/2656", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUCG", "nts_long": "///A/2474,///A/2475,///A/2476,///A/2477" }, { "index": 2, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2654,///A/2655" } ] }, { "index": 23, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 58, 59 ], "summary": "[2] 3 3 [A.2856 A.2876 A.2860 A.2872] 2 3", "num_nts": 10, "nts_short": "CUAAGCAAAG", "nts_long": "///A/2856,///A/2857,///A/2858,///A/2859,///A/2860,///A/2872,///A/2873,///A/2874,///A/2875,///A/2876", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/2857,///A/2858,///A/2859" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/2873,///A/2874,///A/2875" } ] }, { "index": 24, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 60, 61 ], "summary": "[2] 3 3 [A.2953 A.2971 A.2957 A.2967] 6 2", "num_nts": 10, "nts_short": "UCUAGCAACA", "nts_long": "///A/2953,///A/2954,///A/2955,///A/2956,///A/2957,///A/2967,///A/2968,///A/2969,///A/2970,///A/2971", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/2954,///A/2955,///A/2956" }, { "index": 2, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/2968,///A/2969,///A/2970" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 2, 5 ], "stem_indices": [ 33, 34 ], "summary": "[2] 2 5 [A.2330 A.2447 A.2333 A.2441] 4 4", "num_nts": 11, "nts_short": "UCCGCUCAUAA", "nts_long": "///A/2330,///A/2331,///A/2332,///A/2333,///A/2441,///A/2442,///A/2443,///A/2444,///A/2445,///A/2446,///A/2447", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///A/2331,///A/2332" }, { "index": 2, "num_nts": 5, "nts_short": "UCAUA", "nts_long": "///A/2442,///A/2443,///A/2444,///A/2445,///A/2446" } ] }, { "index": 26, "type": "asymmetric internal loop", "bridging_nts": [ 5, 4 ], "stem_indices": [ -4, 4 ], "summary": "[2] 5 4 [A.1739 A.1758 A.1745 A.1753] 1 2", "num_nts": 13, "nts_short": "AAAGUAUAGAAAU", "nts_long": "///A/1739,///A/1740,///A/1741,///A/1742,///A/1743,///A/1744,///A/1745,///A/1753,///A/1754,///A/1755,///A/1756,///A/1757,///A/1758", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AAGUA", "nts_long": "///A/1740,///A/1741,///A/1742,///A/1743,///A/1744" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/1754,///A/1755,///A/1756,///A/1757" } ] }, { "index": 27, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ -8, 13 ], "summary": "[2] 3 6 [A.1906 A.2016 A.1910 A.2009] 1 4", "num_nts": 13, "nts_short": "GAAACGUGAUAGC", "nts_long": "///A/1906,///A/1907,///A/1908,///A/1909,///A/1910,///A/2009,///A/2010,///A/2011,///A/2012,///A/2013,///A/2014,///A/2015,///A/2016", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1907,///A/1908,///A/1909" }, { "index": 2, "num_nts": 6, "nts_short": "UGAUAG", "nts_long": "///A/2010,///A/2011,///A/2012,///A/2013,///A/2014,///A/2015" } ] }, { "index": 28, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ 24, 25 ], "summary": "[2] 5 5 [A.2057 A.2082 A.2063 A.2076] 3 2", "num_nts": 14, "nts_short": "CCCACAGCCCCUUG", "nts_long": "///A/2057,///A/2058,///A/2059,///A/2060,///A/2061,///A/2062,///A/2063,///A/2076,///A/2077,///A/2078,///A/2079,///A/2080,///A/2081,///A/2082", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CCACA", "nts_long": "///A/2058,///A/2059,///A/2060,///A/2061,///A/2062" }, { "index": 2, "num_nts": 5, "nts_short": "CCCUU", "nts_long": "///A/2077,///A/2078,///A/2079,///A/2080,///A/2081" } ] }, { "index": 29, "type": "asymmetric internal loop", "bridging_nts": [ 3, 7 ], "stem_indices": [ 36, 37 ], "summary": "[2] 3 7 [A.2377 A.2419 A.2381 A.2411] 3 4", "num_nts": 14, "nts_short": "GCCCAUACCCUCAC", "nts_long": "///A/2377,///A/2378,///A/2379,///A/2380,///A/2381,///A/2411,///A/2412,///A/2413,///A/2414,///A/2415,///A/2416,///A/2417,///A/2418,///A/2419", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CCC", "nts_long": "///A/2378,///A/2379,///A/2380" }, { "index": 2, "num_nts": 7, "nts_short": "ACCCUCA", "nts_long": "///A/2412,///A/2413,///A/2414,///A/2415,///A/2416,///A/2417,///A/2418" } ] }, { "index": 30, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ -16, 31 ], "summary": "[2] 6 5 [A.2306 A.2680 A.2313 A.2674] 1 2", "num_nts": 15, "nts_short": "AUAAGUAAUGAAAUU", "nts_long": "///A/2306,///A/2307,///A/2308,///A/2309,///A/2310,///A/2311,///A/2312,///A/2313,///A/2674,///A/2675,///A/2676,///A/2677,///A/2678,///A/2679,///A/2680", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UAAGUA", "nts_long": "///A/2307,///A/2308,///A/2309,///A/2310,///A/2311,///A/2312" }, { "index": 2, "num_nts": 5, "nts_short": "GAAAU", "nts_long": "///A/2675,///A/2676,///A/2677,///A/2678,///A/2679" } ] }, { "index": 31, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 71, -26 ], "summary": "[2] 6 5 [A.3119 A.3137 A.3126 A.3131] 3 1", "num_nts": 15, "nts_short": "CCCUGUACGGACAAG", "nts_long": "///A/3119,///A/3120,///A/3121,///A/3122,///A/3123,///A/3124,///A/3125,///A/3126,///A/3131,///A/3132,///A/3133,///A/3134,///A/3135,///A/3136,///A/3137", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "CCUGUA", "nts_long": "///A/3120,///A/3121,///A/3122,///A/3123,///A/3124,///A/3125" }, { "index": 2, "num_nts": 5, "nts_short": "GACAA", "nts_long": "///A/3132,///A/3133,///A/3134,///A/3135,///A/3136" } ] }, { "index": 32, "type": "asymmetric internal loop", "bridging_nts": [ 8, 4 ], "stem_indices": [ -20, 42 ], "summary": "[2] 8 4 [A.2478 A.2653 A.2487 A.2648] 1 4", "num_nts": 16, "nts_short": "GCAAAUCUUAUUCAGC", "nts_long": "///A/2478,///A/2479,///A/2480,///A/2481,///A/2482,///A/2483,///A/2484,///A/2485,///A/2486,///A/2487,///A/2648,///A/2649,///A/2650,///A/2651,///A/2652,///A/2653", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "CAAAUCUU", "nts_long": "///A/2479,///A/2480,///A/2481,///A/2482,///A/2483,///A/2484,///A/2485,///A/2486" }, { "index": 2, "num_nts": 4, "nts_short": "UCAG", "nts_long": "///A/2649,///A/2650,///A/2651,///A/2652" } ] } ], "num_junctions": 10, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 3, 2 ], "stem_indices": [ -10, 16, 17 ], "summary": "[3] 1 3 2 [A.1930 A.1973 A.1932 A.1942 A.1946 A.1970] 1 3 3", "num_nts": 12, "nts_short": "CAGCACACGAAG", "nts_long": "///A/1930,///A/1931,///A/1932,///A/1942,///A/1943,///A/1944,///A/1945,///A/1946,///A/1970,///A/1971,///A/1972,///A/1973", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1931" }, { "index": 2, "num_nts": 3, "nts_short": "ACA", "nts_long": "///A/1943,///A/1944,///A/1945" }, { "index": 3, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1971,///A/1972" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 5, 1, 2 ], "stem_indices": [ -9, 14, -14 ], "summary": "[3] 5 1 2 [A.1915 A.2004 A.1921 A.1983 A.1985 A.2001] 1 5 1", "num_nts": 14, "nts_short": "CGAGCUAUAGCGAG", "nts_long": "///A/1915,///A/1916,///A/1917,///A/1918,///A/1919,///A/1920,///A/1921,///A/1983,///A/1984,///A/1985,///A/2001,///A/2002,///A/2003,///A/2004", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAGCU", "nts_long": "///A/1916,///A/1917,///A/1918,///A/1919,///A/1920" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/1984" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/2002,///A/2003" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 1, 6, 1 ], "stem_indices": [ -17, 35, 36 ], "summary": "[3] 1 6 1 [A.2343 A.2423 A.2345 A.2368 A.2375 A.2421] 1 5 3", "num_nts": 14, "nts_short": "GCGCAAUUAACGUC", "nts_long": "///A/2343,///A/2344,///A/2345,///A/2368,///A/2369,///A/2370,///A/2371,///A/2372,///A/2373,///A/2374,///A/2375,///A/2421,///A/2422,///A/2423", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///A/2344" }, { "index": 2, "num_nts": 6, "nts_short": "AAUUAA", "nts_long": "///A/2369,///A/2370,///A/2371,///A/2372,///A/2373,///A/2374" }, { "index": 3, "num_nts": 1, "nts_short": "U", "nts_long": "///A/2422" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 2, 1, 5 ], "stem_indices": [ 63, 64, 67 ], "summary": "[3] 2 1 5 [A.3004 A.3054 A.3007 A.3032 A.3034 A.3048] 5 2 5", "num_nts": 14, "nts_short": "CAUCGUUAUUAAAG", "nts_long": "///A/3004,///A/3005,///A/3006,///A/3007,///A/3032,///A/3033,///A/3034,///A/3048,///A/3049,///A/3050,///A/3051,///A/3052,///A/3053,///A/3054", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/3005,///A/3006" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/3033" }, { "index": 3, "num_nts": 5, "nts_short": "UUAAA", "nts_long": "///A/3049,///A/3050,///A/3051,///A/3052,///A/3053" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 6, 3, 1 ], "stem_indices": [ 34, -17, 38 ], "summary": "[3] 6 3 1 [A.2336 A.2438 A.2343 A.2423 A.2427 A.2436] 4 1 2", "num_nts": 16, "nts_short": "UAAGCCUGCAACCGCA", "nts_long": "///A/2336,///A/2337,///A/2338,///A/2339,///A/2340,///A/2341,///A/2342,///A/2343,///A/2423,///A/2424,///A/2425,///A/2426,///A/2427,///A/2436,///A/2437,///A/2438", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AAGCCU", "nts_long": 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junction", "bridging_nts": [ 3, 4, 4, 4 ], "stem_indices": [ 43, 44, 45, -21 ], "summary": "[4] 3 4 4 4 [A.2492 A.2642 A.2496 A.2508 A.2513 A.2537 A.2542 A.2637] 2 2 6 1", "num_nts": 23, "nts_short": "GCCUGCAUCACGCACCGCUCCAC", "nts_long": "///A/2492,///A/2493,///A/2494,///A/2495,///A/2496,///A/2508,///A/2509,///A/2510,///A/2511,///A/2512,///A/2513,///A/2537,///A/2538,///A/2539,///A/2540,///A/2541,///A/2542,///A/2637,///A/2638,///A/2639,///A/2640,///A/2641,///A/2642", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CCU", "nts_long": "///A/2493,///A/2494,///A/2495" }, { "index": 2, "num_nts": 4, "nts_short": "AUCA", "nts_long": "///A/2509,///A/2510,///A/2511,///A/2512" }, { "index": 3, "num_nts": 4, "nts_short": "CACC", "nts_long": "///A/2538,///A/2539,///A/2540,///A/2541" }, { "index": 4, "num_nts": 4, "nts_short": "UCCA", "nts_long": "///A/2638,///A/2639,///A/2640,///A/2641" } ] }, { "index": 9, "type": "5-way junction", "bridging_nts": [ 9, 3, 2, 3, 9 ], 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"nts_short": "UU", "nts_long": "///A/2738,///A/2739" }, { "index": 27, "is_broken": true, "num_nts": 5, "nts_short": "AAACC", "nts_long": "///A/2754,///A/2755,///A/2792,///A/2793,///A/2794" }, { "index": 28, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/2808,///A/2809" }, { "index": 29, "is_broken": true, "num_nts": 22, "nts_short": "GAAGAUCCAAUAACUUGACCAA", "nts_long": "///A/2878,///A/2879,///A/2880,///A/2896,///A/2897,///A/2898,///A/2899,///A/2900,///A/2901,///A/2902,///A/2903,///A/2904,///A/2905,///A/2906,///A/2907,///A/2908,///A/2909,///A/2910,///A/2911,///A/2912,///A/2913,///A/2914" }, { "index": 30, "num_nts": 5, "nts_short": "GAACA", "nts_long": "///A/2917,///A/2918,///A/2919,///A/2920,///A/2921" }, { "index": 31, "num_nts": 4, "nts_short": "CAAU", "nts_long": "///A/2944,///A/2945,///A/2946,///A/2947" }, { "index": 32, "num_nts": 6, "nts_short": "GUUUAC", "nts_long": "///A/2977,///A/2978,///A/2979,///A/2980,///A/2981,///A/2982" }, { "index": 33, "num_nts": 1, "nts_short": "C", "nts_long": "///A/3060" }, { "index": 34, "num_nts": 6, "nts_short": "AGUUCA", "nts_long": "///A/3069,///A/3070,///A/3071,///A/3072,///A/3073,///A/3074" }, { "index": 35, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/3094,///A/3095" }, { "index": 36, "num_nts": 1, "nts_short": "U", "nts_long": "///A/3097" }, { "index": 37, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/3108,///A/3109" }, { "index": 38, "num_nts": 1, "nts_short": "C", "nts_long": "///A/3168" }, { "index": 39, "num_nts": 12, "nts_short": "AUACCCACACCC", "nts_long": "///A/3201,///A/3202,///A/3203,///A/3204,///A/3205,///A/3206,///A/3207,///A/3208,///A/3209,///A/3210,///A/3211,///A/3212" }, { "index": 40, "num_nts": 1, "nts_short": "U", "nts_long": "///A/3228" }, { "index": 41, "num_nts": 3, "nts_short": "AGA", "nts_long": "///B/1603,///B/1604,///B/1605" }, { "index": 42, "num_nts": 4, "nts_short": "UGUA", "nts_long": "///B/1607,///B/1608,///B/1609,///B/1610" }, { "index": 43, "is_broken": true, "num_nts": 4, "nts_short": "UAAA", "nts_long": "///B/1614,///B/1615,///B/1616,///B/1621" }, { "index": 44, "num_nts": 2, "nts_short": "AC", "nts_long": "///B/1625,///B/1626" }, { "index": 45, "is_broken": true, "num_nts": 6, "nts_short": "GAGAUU", "nts_long": "///B/1642,///B/1643,///B/1644,///B/1645,///B/1646,///B/1648" }, { "index": 46, "is_broken": true, "num_nts": 3, "nts_short": "ACG", "nts_long": "///B/1661,///B/1663,///B/1664" }, { "index": 47, "num_nts": 5, "nts_short": "UCUGA", "nts_long": "///B/1666,///B/1667,///B/1668,///B/1669,///B/1670" } ], "num_kissingLoops": 1, "kissingLoops": [ { "index": 1, "stem_index": -3, "is_isoCanonPair": true, "hairpin_indices": [ 1, 2 ] } ], "num_Aminors": 45, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1718 vs ///A/1911,///A/2008", "A_nt1": { "desc": "///A/1718 vs ///A/1911", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.13]" }, "A_nt2": { "desc": "///A/1718 vs ///A/2008", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 2, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/1724 vs ///A/2035,///A/2040", "A_nt1": { "desc": "///A/1724 vs ///A/2035", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1724 vs ///A/2040", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.31],N6(amino)-N3[3.18],N1-N2(amino)[2.97]" } }, { "index": 3, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1727 vs ///A/2741,///A/2806", "A_nt1": { "desc": "///A/1727 vs ///A/2741", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.57]" }, "A_nt2": { "desc": "///A/1727 vs ///A/2806", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 4, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1751 vs ///A/1722,///A/1729", "A_nt1": { "desc": "///A/1751 vs ///A/1722", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.17]" }, "A_nt2": { "desc": "///A/1751 vs ///A/1729", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.03]" } }, { "index": 5, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1775 vs ///A/1681,///A/1771", "A_nt1": { "desc": "///A/1775 vs ///A/1681", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1775 vs ///A/1771", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.77],N3-O2'(hydroxyl)[2.75]" } }, { "index": 6, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1789 vs ///A/1915,///A/2004", "A_nt1": { "desc": "///A/1789 vs ///A/1915", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.13],O2'(hydroxyl)-O2'(hydroxyl)[2.80],N3-O2'(hydroxyl)[2.66]" }, "A_nt2": { "desc": "///A/1789 vs ///A/2004", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 7, "type": "X", "desc_short": "A vs A-C (~Wobble)", "desc_long": "///A/1790 vs ///A/1914,///A/2005", "A_nt1": { "desc": "///A/1790 vs ///A/1914", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.56]" }, "A_nt2": { "desc": "///A/1790 vs ///A/2005", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.64]" } }, { "index": 8, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/1814 vs ///A/1862,///A/2303", "A_nt1": { "desc": "///A/1814 vs ///A/1862", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.34],N3-O2'(hydroxyl)[2.86]" }, "A_nt2": { "desc": "///A/1814 vs ///A/2303", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 9, "type": "I", "desc_short": "A vs U-G (Wobble)", "desc_long": "///A/1815 vs ///A/1861,///A/2304", "A_nt1": { "desc": "///A/1815 vs ///A/1861", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.08]" }, "A_nt2": { "desc": "///A/1815 vs ///A/2304", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.99]" } }, { "index": 10, "type": "X", "desc_short": "A vs A-G (Imino)", "desc_long": "///A/1828 vs ///A/2682,///A/2698", "A_nt1": { "desc": "///A/1828 vs ///A/2682", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1828 vs ///A/2698", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.92]" } }, { "index": 11, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1828 vs ///A/2683,///A/2697", "A_nt1": { "desc": "///A/1828 vs ///A/2683", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.16]" }, "A_nt2": { "desc": "///A/1828 vs ///A/2697", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 12, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/1867 vs ///A/1903,///A/2019", "A_nt1": { "desc": "///A/1867 vs ///A/1903", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.52],O2'(hydroxyl)-O2(carbonyl)[2.67]" }, "A_nt2": { "desc": "///A/1867 vs ///A/2019", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.37],N3-N2(amino)[2.87]" } }, { "index": 13, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/1907 vs ///A/2730,///A/2930", "A_nt1": { "desc": "///A/1907 vs ///A/2730", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1907 vs ///A/2930", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.07],O2'(hydroxyl)-O2'(hydroxyl)[2.41],N3-O2'(hydroxyl)[2.75]" } }, { "index": 14, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1908 vs ///A/2732,///A/2929", "A_nt1": { "desc": "///A/1908 vs ///A/2732", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.92],N3-N2(amino)[2.98]" }, "A_nt2": { "desc": "///A/1908 vs ///A/2929", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.72],O2'(hydroxyl)-O2(carbonyl)[3.16]" } }, { "index": 15, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1917 vs ///A/1988,///A/1996", "A_nt1": { "desc": "///A/1917 vs ///A/1988", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.88],N1-N2(amino)[2.99]" }, "A_nt2": { "desc": "///A/1917 vs ///A/1996", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 16, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1984 vs ///A/1987,///A/1997", "A_nt1": { "desc": "///A/1984 vs ///A/1987", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.06]" }, "A_nt2": { "desc": "///A/1984 vs ///A/1997", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.87]" } }, { "index": 17, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1991 vs ///A/2496,///A/2508", "A_nt1": { "desc": "///A/1991 vs ///A/2496", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.31],N3-N2(amino)[3.11]" }, "A_nt2": { "desc": "///A/1991 vs ///A/2508", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[2.95],O2'(hydroxyl)-O2'(hydroxyl)[2.69],O2'(hydroxyl)-O2(carbonyl)[2.57]" } }, { "index": 18, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2039 vs ///A/2728,///A/2932", "A_nt1": { "desc": "///A/2039 vs ///A/2728", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2039 vs ///A/2932", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.35],N1-O2'(hydroxyl)[2.90]" } }, { "index": 19, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2131 vs ///A/2689,///A/2700", "A_nt1": { "desc": "///A/2131 vs ///A/2689", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2131 vs ///A/2700", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.05]" } }, { "index": 20, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2132 vs ///A/2690,///A/2699", "A_nt1": { "desc": "///A/2132 vs ///A/2690", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.25],N3-N2(amino)[3.17]" }, "A_nt2": { "desc": "///A/2132 vs ///A/2699", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.85],O2'(hydroxyl)-O2(carbonyl)[2.94]" } }, { "index": 21, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2134 vs ///A/2098,///A/2123", "A_nt1": { "desc": "///A/2134 vs ///A/2098", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2134 vs ///A/2123", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.73]" } }, { "index": 22, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2151 vs ///A/2127,///A/2138", "A_nt1": { "desc": "///A/2151 vs ///A/2127", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2151 vs ///A/2138", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.09],O2'(hydroxyl)-O2'(hydroxyl)[3.05],N3-O2'(hydroxyl)[2.63]" } }, { "index": 23, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2152 vs ///A/2128,///A/2137", "A_nt1": { "desc": "///A/2152 vs ///A/2128", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.17],N3-N2(amino)[3.20]" }, "A_nt2": { "desc": "///A/2152 vs ///A/2137", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.17],O2'(hydroxyl)-O2(carbonyl)[3.29]" } }, { "index": 24, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2232 vs ///A/3002,///A/3056", "A_nt1": { "desc": "///A/2232 vs ///A/3002", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.49],O2'(hydroxyl)-N3[3.00],N3-N2(amino)[3.20]" }, "A_nt2": { "desc": "///A/2232 vs ///A/3056", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.26]" } }, { "index": 25, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/2250 vs ///A/2127,///A/2138", "A_nt1": { "desc": "///A/2250 vs ///A/2127", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.86]" }, "A_nt2": { "desc": "///A/2250 vs ///A/2138", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 26, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2265 vs ///A/2046,///A/2094", "A_nt1": { "desc": "///A/2265 vs ///A/2046", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2265 vs ///A/2094", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.12],O2'(hydroxyl)-O2'(hydroxyl)[2.79],N3-O2'(hydroxyl)[2.67]" } }, { "index": 27, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2297 vs ///A/1845,///A/1858", "A_nt1": { "desc": "///A/2297 vs ///A/1845", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.23],N1-O2'(hydroxyl)[2.47]" }, "A_nt2": { "desc": "///A/2297 vs ///A/1858", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.51]" } }, { "index": 28, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2298 vs ///A/1904,///A/2018", "A_nt1": { "desc": "///A/2298 vs ///A/1904", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2298 vs ///A/2018", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.88],N3-N2(amino)[3.11]" } }, { "index": 29, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/2451 vs ///A/2327,///A/2450", "A_nt1": { "desc": "///A/2451 vs ///A/2327", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2451 vs ///A/2450", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.06]" } }, { "index": 30, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2451 vs ///A/2328,///A/2449", "A_nt1": { "desc": "///A/2451 vs ///A/2328", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.81]" }, "A_nt2": { "desc": "///A/2451 vs ///A/2449", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 31, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2481 vs ///A/2478,///A/2653", "A_nt1": { "desc": "///A/2481 vs ///A/2478", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.91]" }, "A_nt2": { "desc": "///A/2481 vs ///A/2653", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 32, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2482 vs ///A/2478,///A/2653", "A_nt1": { "desc": "///A/2482 vs ///A/2478", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2482 vs ///A/2653", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.77],N3-O2'(hydroxyl)[3.29]" } }, { "index": 33, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2505 vs ///A/3075,///A/3093", "A_nt1": { "desc": "///A/2505 vs ///A/3075", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.99]" }, "A_nt2": { "desc": "///A/2505 vs ///A/3093", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 34, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2615 vs ///A/3035,///A/3047", "A_nt1": { "desc": "///A/2615 vs ///A/3035", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2615 vs ///A/3047", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.49]" } }, { "index": 35, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2616 vs ///A/3036,///A/3046", "A_nt1": { "desc": "///A/2616 vs ///A/3036", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.11],N3-N2(amino)[3.38]" }, "A_nt2": { "desc": "///A/2616 vs ///A/3046", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.27],O2'(hydroxyl)-O2(carbonyl)[3.17]" } }, { "index": 36, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2644 vs ///A/1948,///A/1968", "A_nt1": { "desc": "///A/2644 vs ///A/1948", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2644 vs ///A/1968", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N1-N2(amino)[3.14],N3-O2'(hydroxyl)[2.60]" } }, { "index": 37, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/2745 vs ///A/2744,///A/2803", "A_nt1": { "desc": "///A/2745 vs ///A/2744", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.96]" }, "A_nt2": { "desc": "///A/2745 vs ///A/2803", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 38, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/2837 vs ///A/2105,///A/2116", "A_nt1": { "desc": "///A/2837 vs ///A/2105", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.00]" }, "A_nt2": { "desc": "///A/2837 vs ///A/2116", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.31]" } }, { "index": 39, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/2919 vs ///A/1726,///A/1748", "A_nt1": { "desc": "///A/2919 vs ///A/1726", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/2919 vs ///A/1748", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.41]" } }, { "index": 40, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/3051 vs ///A/3008,///A/3031", "A_nt1": { "desc": "///A/3051 vs ///A/3008", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.97]" }, "A_nt2": { "desc": "///A/3051 vs ///A/3031", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 41, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/3052 vs ///A/3007,///A/3032", "A_nt1": { "desc": "///A/3052 vs ///A/3007", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/3052 vs ///A/3032", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.65],N3-N2(amino)[3.14]" } }, { "index": 42, "type": "II", "desc_short": "A vs U-A (WC)", "desc_long": "///A/3084 vs ///A/2737,///A/2922", "A_nt1": { "desc": "///A/3084 vs ///A/2737", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.00],N3-O2'(hydroxyl)[2.63]" }, "A_nt2": { "desc": "///A/3084 vs ///A/2922", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 43, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/3085 vs ///A/2736,///A/2923", "A_nt1": { "desc": "///A/3085 vs ///A/2736", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.54],O2'(hydroxyl)-O2(carbonyl)[3.07]" }, "A_nt2": { "desc": "///A/3085 vs ///A/2923", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.36],N3-N2(amino)[2.80]" } }, { "index": 44, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/3151 vs ///A/3148,///A/3163", "A_nt1": { "desc": "///A/3151 vs ///A/3148", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/3151 vs ///A/3163", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.77],N1-O2'(hydroxyl)[2.99]" } }, { "index": 45, "type": "X", "desc_short": "A vs C-G (--)", "desc_long": "///A/3151 vs ///A/3149,///A/3163", "A_nt1": { "desc": "///A/3151 vs ///A/3149", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.56]" }, "A_nt2": { "desc": "///A/3151 vs ///A/3163", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.77],N1-O2'(hydroxyl)[2.99]" } } ], "num_riboseZippers": 8, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "ACAC", "nts_long": "///A/1697,///A/1698,///A/1702,///A/1703" }, { "index": 2, "num_nts": 4, "nts_short": "AAAC", "nts_long": "///A/1789,///A/1790,///A/1914,///A/1915" }, { "index": 3, "num_nts": 4, "nts_short": "AAUU", "nts_long": "///A/1814,///A/1815,///A/1861,///A/1862" }, { "index": 4, "num_nts": 4, "nts_short": "AACU", "nts_long": "///A/1907,///A/1908,///A/2929,///A/2930" }, { "index": 5, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///A/2137,///A/2138,///A/2151,///A/2152" }, { "index": 6, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///A/2231,///A/2232,///A/3002,///A/3003" }, { "index": 7, "num_nts": 4, "nts_short": "CAGG", "nts_long": "///A/2502,///A/2503,///A/3094,///A/3095" }, { "index": 8, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///A/2736,///A/2737,///A/3084,///A/3085" } ], "num_splayUnits": 141, "splayUnits": [ { "index": 1, "num_nts": 3, "nts_short": "CCU", "nts_long": "///A/1698,///A/1699,///A/1700" }, { "index": 2, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1701,///A/1702" }, { "index": 3, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/1703,///A/1704,///A/1705" }, { "index": 4, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/1716,///A/1717" }, { "index": 5, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/1723,///A/1724,///A/1725" }, { "index": 6, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1727,///A/1728" }, { "index": 7, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/1730,///A/1731" }, { "index": 8, "num_nts": 4, "nts_short": "GGCG", "nts_long": "///A/1747,///A/1748,///A/1749,///A/1750" }, { "index": 9, "num_nts": 3, "nts_short": "GCG", "nts_long": "///A/1768,///A/1769,///A/1770" }, { "index": 10, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/1773,///A/1774,///A/1775" }, { "index": 11, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1779,///A/1780" }, { "index": 12, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/1796,///A/1797" }, { "index": 13, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/1813,///A/1814" }, { "index": 14, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1820,///A/1821" }, { "index": 15, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/1823,///A/1824" }, { "index": 16, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/1826,///A/1827" }, { "index": 17, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/1842,///A/1843,///A/1844" }, { "index": 18, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1859,///A/1860" }, { "index": 19, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/1885,///A/1886,///A/1887" }, { "index": 20, "num_nts": 2, "nts_short": "GC", "nts_long": "///A/1888,///A/1889" }, { "index": 21, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1891,///A/1892,///A/1893" }, { "index": 22, "num_nts": 2, "nts_short": "CC", "nts_long": "///A/1902,///A/1903" }, { "index": 23, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/1917,///A/1918" }, { "index": 24, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/1930,///A/1931" }, { "index": 25, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/1938,///A/1939,///A/1940" }, { "index": 26, "num_nts": 3, "nts_short": "UAG", "nts_long": "///A/1956,///A/1957,///A/1958" }, { "index": 27, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/1960,///A/1961,///A/1962" }, { "index": 28, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/1971,///A/1972" }, { "index": 29, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/1973,///A/1974,///A/1975" }, { "index": 30, "num_nts": 3, "nts_short": "GAC", "nts_long": "///A/1990,///A/1991,///A/1992" }, { "index": 31, "num_nts": 3, "nts_short": "CUA", "nts_long": "///A/1997,///A/1998,///A/1999" }, { "index": 32, "num_nts": 3, "nts_short": "CCG", "nts_long": "///A/2000,///A/2001,///A/2002" }, { "index": 33, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2003,///A/2004" }, { "index": 34, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/2010,///A/2011,///A/2012" }, { "index": 35, "num_nts": 3, "nts_short": "AGC", "nts_long": "///A/2014,///A/2015,///A/2016" }, { "index": 36, "num_nts": 3, "nts_short": "UUG", "nts_long": "///A/2020,///A/2021,///A/2022" }, { "index": 37, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2030,///A/2031" }, { "index": 38, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/2035,///A/2036" }, { "index": 39, "num_nts": 3, "nts_short": "UAG", "nts_long": "///A/2038,///A/2039,///A/2040" }, { "index": 40, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2064,///A/2065" }, { "index": 41, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2097,///A/2098" }, { "index": 42, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2112,///A/2113" }, { "index": 43, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2124,///A/2125" }, { "index": 44, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2130,///A/2131" }, { "index": 45, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2133,///A/2134" }, { "index": 46, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/2142,///A/2143" }, { "index": 47, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/2145,///A/2146,///A/2147" }, { "index": 48, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2154,///A/2155" }, { "index": 49, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/2232,///A/2233" }, { "index": 50, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2236,///A/2237" }, { "index": 51, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2240,///A/2241" }, { "index": 52, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2242,///A/2243" }, { "index": 53, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2244,///A/2245" }, { "index": 54, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/2250,///A/2251,///A/2252" }, { "index": 55, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2259,///A/2260" }, { "index": 56, "num_nts": 3, "nts_short": "CCC", "nts_long": "///A/2261,///A/2262,///A/2263" }, { "index": 57, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/2291,///A/2292,///A/2293" }, { "index": 58, "num_nts": 3, "nts_short": "ACU", "nts_long": "///A/2294,///A/2295,///A/2296" }, { "index": 59, "num_nts": 4, "nts_short": "AAUG", "nts_long": "///A/2297,///A/2298,///A/2299,///A/2300" }, { "index": 60, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/2316,///A/2317" }, { "index": 61, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/2320,///A/2321,///A/2322" }, { "index": 62, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/2330,///A/2331" }, { "index": 63, "num_nts": 3, "nts_short": "GCG", "nts_long": "///A/2343,///A/2344,///A/2345" }, { "index": 64, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/2371,///A/2372" }, { "index": 65, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/2374,///A/2375" }, { "index": 66, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2380,///A/2381" }, { "index": 67, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/2387,///A/2388" }, { "index": 68, "num_nts": 2, "nts_short": "CA", "nts_long": "///A/2389,///A/2390" }, { "index": 69, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/2392,///A/2393" }, { "index": 70, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2401,///A/2402" }, { "index": 71, "num_nts": 2, "nts_short": "CC", "nts_long": "///A/2414,///A/2415" }, { "index": 72, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/2422,///A/2423" }, { "index": 73, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/2424,///A/2425,///A/2426,///A/2427" }, { "index": 74, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/2429,///A/2430" }, { 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"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": "7qh7", "num_aaChains": 47, "aaChains": "0=108,1=49,2=45,3=95,4=37,5=392,6=292,7=287,9=117,D=215,E=304,F=250,H=95,I=30,K=177,L=115,M=287,N=201,O=152,P=141,Q=217,R=139,S=156,T=155,U=125,V=48,W=100,X=243,Y=175,Z=115,a=80,b=148,c=275,d=157,f=17,g=129,h=101,i=97,j=86,o=81,p=125,q=101,r=129,s=370,u=111,v=69,w=79", "num_naChains": 2, "naChains": "A=1256,B=56", "num_atoms": 85397, "num_waters": 14, "num_metals": 53, "metals_desc": "Mg=50,Zn=3", "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" } }