**************************************************************************** File name: 7qh7.pdb no. of DNA/RNA chains: 2 [A=1256,B=56] no. of nucleotides: 1312 no. of atoms: 85397 no. of waters: 14 no. of metals: 53 [Mg=50,Zn=3] **************************************************************************** List of 543 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1671 A.C1817 G-C WC 19-XIX cWW cW-W 2 A.C1672 A.G1816 C-G WC 19-XIX cWW cW-W 3 A.U1673 A.A1815 U-A -- -- tWH tW-M 4 A.C1678 A.G1797 C-G WC 19-XIX cWW cW-W 5 A.U1679 A.A1773 U-A rHoogsteen 24-XXIV tWH tW-M 6 A.A1680 A.A1775 A+A -- 01-I tWW tW+W 7 A.G1681 A.C1771 G-C WC 19-XIX cWW cW-W 8 A.G1681 A.G1776 G+G -- 04-IV tSS tm+m 9 A.C1682 A.G1770 C-G WC 19-XIX cWW cW-W 10 A.C1683 A.G1768 C-G WC 19-XIX cWW cW-W 11 A.C1684 A.G1767 C-G WC 19-XIX cWW cW-W 12 A.C1685 A.U1766 C-U -- 18-XVIII cWW cW-W 13 A.A1697 A.C1703 A-C -- -- cSS cm-m 14 A.C1698 A.A1702 C-A -- -- cSS cm-m 15 A.U1717 A.A1718 U+A Platform -- cSH cm+M 16 A.C1721 A.U1730 C-U -- 18-XVIII cWW cW-W 17 A.A1722 A.U1729 A-U WC 20-XX cWW cW-W 18 A.A1723 A.G1750 A-G -- -- cSW cm-W 19 A.A1724 A.G2040 A+G -- 10-X tWS tW+m 20 A.C1726 A.G1748 C-G WC 19-XIX cWW cW-W 21 A.U1729 A.G1750 U+G -- -- tSW tm+W 22 A.A1737 A.G1760 A-G Sheared 11-XI tHS tM-m 23 A.U1738 A.U1759 U-U -- 16-XVI cWW cW-W 24 A.A1739 A.U1758 A-U WC 20-XX cWW cW-W 25 A.A1740 A.A1757 A-A ~Sheared -- tSH tm-M 26 A.A1741 A.A1756 A+A -- 02-II tHH tM+M 27 A.G1742 A.U1743 G+U Platform -- cSH cm+M 28 A.U1743 A.A1755 U-A rHoogsteen 24-XXIV tWH tW-M 29 A.A1744 A.G1754 A-G Sheared 11-XI tHS tM-m 30 A.U1745 A.A1753 U-A WC 20-XX cWW cW-W 31 A.A1746 A.U1752 A-U WC 20-XX cWW cW-W 32 A.G1747 A.A1751 G-A Sheared 11-XI tSH tm-M 33 A.G1748 A.A2919 G+A -- -- tSH tm+M 34 A.C1769 A.G2289 C+G -- -- tWS tW+m 35 A.C1771 A.A1775 C-A -- -- cSS cm-m 36 A.U1774 A.U2302 U-U -- -- cWS cW-m 37 A.A1781 A.A1795 A+A -- 02-II tHH tM+M 38 A.A1781 A.A1796 A+A -- -- tHW tM+W 39 A.G1782 A.U1783 G+U Platform -- cSH cm+M 40 A.U1783 A.A1794 U-A rHoogsteen 24-XXIV tWH tW-M 41 A.A1784 A.G1793 A-G Sheared 11-XI tHS tM-m 42 A.C1785 A.G1792 C-G WC 19-XIX cWW cW-W 43 A.C1786 A.G1791 C-G WC 19-XIX cWW cW-W 44 A.G1787 A.A1790 G-A -- -- tSH tm-M 45 A.A1789 A.C1915 A-C -- -- cSS cm-m 46 A.A1790 A.C2005 A+C -- -- tWS tW+m 47 A.A1815 A.G2304 A+G Linker -- tSS tm+m 48 A.A1825 A.U2705 A+U Hoogsteen 23-XXIII cHW cM+W 49 A.G1826 A.A2704 G-A Imino 08-VIII cWW cW-W 50 A.C1827 A.G2681 C-G WC 19-XIX cWW cW-W 51 A.A1828 A.C2683 A-C -- -- cWS cW-m 52 A.A1828 A.G2698 A+G -- -- .W. .W+. 53 A.A1829 A.U1841 A-U WC 20-XX cWW cW-W 54 A.G1830 A.C1840 G-C WC 19-XIX cWW cW-W 55 A.G1831 A.C1839 G-C WC 19-XIX cWW cW-W 56 A.A1835 A.C1837 A+C -- -- tSH tm+M 57 A.U1843 A.A2696 U-A WC 20-XX cWW cW-W 58 A.A1844 A.U1854 A-U -- -- cHH cM-M 59 A.A1844 A.A1859 A-A -- -- cWW cW-W 60 A.C1845 A.G1858 C-G WC 19-XIX cWW cW-W 61 A.C1846 A.U1857 C-U -- 18-XVIII cWW cW-W 62 A.U1847 A.A1856 U-A WC 20-XX cWW cW-W 63 A.U1848 A.A1855 U-A WC 20-XX cWW cW-W 64 A.U1850 A.A2134 U-A -- -- cWW cW-W 65 A.A1853 A.G2692 A-G -- -- cWS cW-m 66 A.U1854 A.A1859 U+A -- -- -- -- 67 A.G1858 A.A2297 G-A -- -- cSS cm-m 68 A.A1860 A.U2305 A-U WC 20-XX cWW cW-W 69 A.U1861 A.G2304 U-G Wobble 28-XXVIII cWW cW-W 70 A.U1862 A.A2303 U-A WC 20-XX cWW cW-W 71 A.A1863 A.U2302 A-U WC 20-XX cWW cW-W 72 A.A1864 A.U2301 A-U WC 20-XX cWW cW-W 73 A.C1865 A.G2300 C-G WC 19-XIX cWW cW-W 74 A.U1866 A.A2298 U-A -- -- tWH tW-M 75 A.A1867 A.G2019 A+G Linker -- tSS tm+m 76 A.A1867 A.C2295 A-C ~rHoogsteen 25-XXV tHW tM-W 77 A.G1868 A.U2020 G-U -- -- cW. cW-. 78 A.A1871 A.C1901 A-C ~rHoogsteen -- tHW tM-W 79 A.A1873 A.A1900 A-A -- -- t.W t.-W 80 A.C1875 A.G1899 C-G WC 19-XIX cWW cW-W 81 A.U1876 A.A1898 U-A WC 20-XX cWW cW-W 82 A.U1877 A.A1897 U-A WC 20-XX cWW cW-W 83 A.U1878 A.U1896 U-U -- -- cWW cW-W 84 A.G1879 A.C1895 G-C WC 19-XIX cWW cW-W 85 A.C1880 A.G1894 C-G WC 19-XIX cWW cW-W 86 A.G1883 A.C1890 G-C WC 19-XIX cWW cW-W 87 A.G1884 A.C1889 G-C WC 19-XIX cWW cW-W 88 A.C1903 A.G2019 C-G WC 19-XIX cWW cW-W 89 A.C1904 A.G2018 C-G WC 19-XIX cWW cW-W 90 A.C1904 A.A2298 C+A -- -- tSW tm+W 91 A.C1905 A.U2017 C-U -- 18-XVIII cWW cW-W 92 A.G1906 A.C2016 G-C WC 19-XIX cWW cW-W 93 A.A1907 A.U2013 A-U rHoogsteen 24-XXIV tHW tM-W 94 A.A1907 A.U2930 A-U -- -- cSS cm-m 95 A.A1908 A.A2012 A-A -- 05-V tHW tM-W 96 A.A1908 A.G2732 A+G Linker -- tSS tm+m 97 A.A1909 A.U2010 A+U rWC 21-XXI tWW tW+W 98 A.C1910 A.G2009 C-G WC 19-XIX cWW cW-W 99 A.C1911 A.G2008 C-G WC 19-XIX cWW cW-W 100 A.A1912 A.U2007 A-U WC 20-XX cWW cW-W 101 A.G1913 A.C2006 G-C WC 19-XIX cWW cW-W 102 A.A1914 A.C2005 A-C ~Wobble -- cWW cW-W 103 A.C1915 A.G2004 C-G WC 19-XIX cWW cW-W 104 A.G1916 A.G1985 G-G -- 07-VII tWH tW-M 105 A.A1917 A.U1920 A+U -- -- tSW tm+W 106 A.A1917 A.G1988 A+G -- 10-X tWS tW+m 107 A.C1919 A.A2500 C-A -- -- cSW cm-W 108 A.A1921 A.U1983 A-U WC 20-XX cWW cW-W 109 A.C1922 A.G1982 C-G WC 19-XIX cWW cW-W 110 A.C1923 A.G1981 C-G WC 19-XIX cWW cW-W 111 A.U1924 A.A1980 U-A WC 20-XX cWW cW-W 112 A.A1925 A.U1979 A-U WC 20-XX cWW cW-W 113 A.A1926 A.A1978 A-A -- -- cWW cW-W 114 A.G1927 A.U1977 G-U Wobble 28-XXVIII cWW cW-W 115 A.A1928 A.U1976 A-U WC 20-XX cWW cW-W 116 A.A1929 A.U1975 A-U WC 20-XX cWW cW-W 117 A.C1930 A.G1973 C-G WC 19-XIX cWW cW-W 118 A.A1931 A.A1943 A-A ~Sheared -- tHS tM-m 119 A.G1932 A.C1942 G-C WC 19-XIX cWW cW-W 120 A.C1933 A.G1941 C-G WC 19-XIX cWW cW-W 121 A.U1934 A.A1940 U-A WC 20-XX cWW cW-W 122 A.A1935 A.A1938 A-A -- -- cSW cm-W 123 A.A1937 A.U2392 A-U WC 20-XX cWW cW-W 124 A.G1939 A.C2494 G-C WC 19-XIX cWW cW-W 125 A.A1945 A.A1971 A-A ~Sheared -- tHS tM-m 126 A.C1946 A.G1970 C-G WC 19-XIX cWW cW-W 127 A.C1947 A.G1969 C-G WC 19-XIX cWW cW-W 128 A.C1948 A.G1968 C-G WC 19-XIX cWW cW-W 129 A.G1949 A.U1950 G+U Platform -- cSH cm+M 130 A.G1949 A.U1967 G-U -- -- c.W c.-W 131 A.U1950 A.U1967 U-U -- 16-XVI cWW cW-W 132 A.C1951 A.G1966 C-G WC 19-XIX cWW cW-W 133 A.U1952 A.A1965 U-A WC 20-XX cWW cW-W 134 A.A1953 A.U1964 A-U WC 20-XX cWW cW-W 135 A.U1954 A.A1963 U-A WC 20-XX cWW cW-W 136 A.G1955 A.A1960 G+A -- 10-X tSW tm+W 137 A.C1959 A.A1963 C-A -- -- cWS cW-m 138 A.A1962 A.U3096 A-U WC 20-XX cWW cW-W 139 A.G1968 A.A2644 G-A -- -- cSW cm-W 140 A.A1974 A.U2495 A+U Hoogsteen 23-XXIII cHW cM+W 141 A.A1974 A.A2509 A-A -- -- cWS cW-m 142 A.A1984 A.G1987 A-G -- -- cSS cm-m 143 A.A1984 A.C1997 A+C -- -- tWS tW+m 144 A.G1985 A.C2001 G-C WC 19-XIX cWW cW-W 145 A.G1985 A.A2003 G+A Linker -- .SS .m+m 146 A.G1987 A.C1997 G-C WC 19-XIX cWW cW-W 147 A.G1988 A.C1996 G-C WC 19-XIX cWW cW-W 148 A.C1989 A.A1995 C-A -- -- cWW cW-W 149 A.G1990 A.A1993 G+A -- -- tSW tm+W 150 A.A1991 A.G2496 A+G Linker -- tSS tm+m 151 A.G2018 A.A2298 G-A -- -- cSS cm-m 152 A.G2022 A.C2271 G-C WC 19-XIX cWW cW-W 153 A.U2023 A.A2270 U-A WC 20-XX cWW cW-W 154 A.C2024 A.G2269 C-G WC 19-XIX cWW cW-W 155 A.C2025 A.G2268 C-G WC 19-XIX cWW cW-W 156 A.A2026 A.U2267 A-U WC 20-XX cWW cW-W 157 A.A2027 A.U2266 A-U WC 20-XX cWW cW-W 158 A.G2028 A.A2265 G-A Sheared 11-XI tSH tm-M 159 A.A2029 A.C2263 A-C ~rHoogsteen -- tHW tM-W 160 A.U2030 A.A2124 U-A -- -- tHW tM-W 161 A.A2031 A.A2044 A-A ~Sheared -- tHS tM-m 162 A.G2032 A.C2043 G-C WC 19-XIX cWW cW-W 163 A.A2033 A.U2042 A-U WC 20-XX cWW cW-W 164 A.A2034 A.U2041 A-U WC 20-XX cWW cW-W 165 A.U2035 A.G2040 U-G Wobble 28-XXVIII cWW cW-W 166 A.U2037 A.U2038 U+U Platform -- cSH cm+M 167 A.A2039 A.U2729 A+U -- -- cHS cM+m 168 A.A2039 A.G2932 A-G -- -- cWS cW-m 169 A.A2044 A.U2096 A-U -- -- cWW cW-W 170 A.A2045 A.U2095 A-U WC 20-XX cWW cW-W 171 A.C2046 A.G2094 C-G WC 19-XIX cWW cW-W 172 A.U2047 A.C2092 U-C -- -- cWW cW-W 173 A.U2048 A.A2091 U-A WC 20-XX cWW cW-W 174 A.U2049 A.A2090 U-A WC 20-XX cWW cW-W 175 A.A2050 A.U2089 A-U WC 20-XX cWW cW-W 176 A.A2051 A.U2088 A-U WC 20-XX cWW cW-W 177 A.A2052 A.U2087 A-U WC 20-XX cWW cW-W 178 A.U2053 A.A2086 U-A WC 20-XX cWW cW-W 179 A.U2054 A.A2085 U-A WC 20-XX cWW cW-W 180 A.U2055 A.A2084 U-A WC 20-XX cWW cW-W 181 A.G2056 A.U2083 G-U Wobble 28-XXVIII cWW cW-W 182 A.C2057 A.G2082 C-G WC 19-XIX cWW cW-W 183 A.C2058 A.U2081 C-U -- 18-XVIII cWW cW-W 184 A.C2059 A.C2079 C-C -- -- tWH tW-M 185 A.A2060 A.C2078 A-C ~rHoogsteen -- tHW tM-W 186 A.C2061 A.C2078 C-C -- -- tHW tM-W 187 A.A2062 A.C2077 A-C -- -- cWW cW-W 188 A.G2063 A.C2076 G-C WC 19-XIX cWW cW-W 189 A.A2064 A.U2075 A-U WC 20-XX cWW cW-W 190 A.A2073 A.A2832 A+A -- -- tHH tM+M 191 A.G2098 A.C2123 G-C WC 19-XIX cWW cW-W 192 A.U2099 A.A2122 U-A WC 20-XX cWW cW-W 193 A.C2100 A.G2121 C-G WC 19-XIX cWW cW-W 194 A.C2101 A.G2120 C-G WC 19-XIX cWW cW-W 195 A.A2102 A.U2119 A-U WC 20-XX cWW cW-W 196 A.A2103 A.U2118 A-U WC 20-XX cWW cW-W 197 A.A2104 A.U2117 A-U WC 20-XX cWW cW-W 198 A.G2105 A.C2116 G-C WC 19-XIX cWW cW-W 199 A.G2105 A.A2837 G+A -- -- t.W t.+W 200 A.A2106 A.U2115 A-U WC 20-XX cWW cW-W 201 A.G2107 A.C2114 G-C WC 19-XIX cWW cW-W 202 A.G2108 A.C2114 G-C -- -- cSW cm-W 203 A.C2116 A.A2837 C-A -- -- cSW cm-W 204 A.U2126 A.U2139 U-U -- 16-XVI cWW cW-W 205 A.A2127 A.U2138 A-U WC 20-XX cWW cW-W 206 A.G2128 A.C2137 G-C WC 19-XIX cWW cW-W 207 A.G2128 A.A2152 G+A Linker -- tSS tm+m 208 A.G2129 A.C2136 G-C WC 19-XIX cWW cW-W 209 A.A2132 A.G2690 A+G Linker -- tSS tm+m 210 A.G2143 A.C2257 G-C WC 19-XIX cWW cW-W 211 A.A2144 A.U2256 A-U WC 20-XX cWW cW-W 212 A.G2145 A.C2255 G-C WC 19-XIX cWW cW-W 213 A.G2147 A.C2254 G-C WC 19-XIX cWW cW-W 214 A.A2148 A.U2253 A-U WC 20-XX cWW cW-W 215 A.G2149 A.C2252 G-C WC 19-XIX cWW cW-W 216 A.U2150 A.A2250 U-A rHoogsteen 24-XXIV tWH tW-M 217 A.A2152 A.G2249 A-G Sheared 11-XI tHS tM-m 218 A.A2153 A.U2248 A-U WC 20-XX cWW cW-W 219 A.A2232 A.G3002 A-G -- -- cSS cm-m 220 A.A2251 A.C2262 A-C -- -- cHH cM-M 221 A.C2272 A.A2294 C-A -- -- cWW cW-W 222 A.A2273 A.A2293 A-A -- -- cWS cW-m 223 A.A2274 A.A2291 A-A -- -- cWW cW-W 224 A.U2275 A.A2290 U-A WC 20-XX cWW cW-W 225 A.C2276 A.G2289 C-G WC 19-XIX cWW cW-W 226 A.U2277 A.A2288 U-A WC 20-XX cWW cW-W 227 A.A2278 A.U2287 A-U WC 20-XX cWW cW-W 228 A.U2279 A.A2286 U-A WC 20-XX cWW cW-W 229 A.C2280 A.U2285 C-U -- -- cWW cW-W 230 A.A2306 A.U2680 A-U WC 20-XX cWW cW-W 231 A.U2307 A.U2679 U-U -- 16-XVI cWW cW-W 232 A.A2308 A.A2678 A-A ~Sheared -- tSH tm-M 233 A.A2309 A.A2677 A+A -- 02-II tHH tM+M 234 A.G2310 A.U2311 G+U Platform -- cSH cm+M 235 A.U2311 A.A2676 U-A rHoogsteen 24-XXIV tWH tW-M 236 A.A2312 A.G2675 A-G Sheared 11-XI tHS tM-m 237 A.A2313 A.U2674 A-U WC 20-XX cWW cW-W 238 A.C2314 A.G2673 C-G WC 19-XIX cWW cW-W 239 A.A2315 A.A2672 A-A -- -- cWW cW-W 240 A.G2317 A.C2326 G-C WC 19-XIX cWW cW-W 241 A.A2318 A.U2325 A-U WC 20-XX cWW cW-W 242 A.A2319 A.U2324 A-U WC 20-XX cWW cW-W 243 A.U2327 A.A2450 U-A WC 20-XX cWW cW-W 244 A.C2328 A.G2449 C-G WC 19-XIX cWW cW-W 245 A.C2329 A.G2448 C-G WC 19-XIX cWW cW-W 246 A.U2330 A.A2447 U-A WC 20-XX cWW cW-W 247 A.C2332 A.U2442 C-U -- 18-XVIII cWW cW-W 248 A.C2332 A.A2444 C+A -- -- cWH cW+M 249 A.G2333 A.C2441 G-C WC 19-XIX cWW cW-W 250 A.C2334 A.G2440 C-G WC 19-XIX cWW cW-W 251 A.A2335 A.U2439 A-U WC 20-XX cWW cW-W 252 A.U2336 A.A2438 U-A WC 20-XX cWW cW-W 253 A.G2339 A.C2426 G-C -- -- cWW cW-W 254 A.C2340 A.G2343 C+G -- -- c.H c.+M 255 A.U2342 A.U2371 U+U -- 12-XII tWW tW+W 256 A.G2343 A.C2423 G-C WC 19-XIX cWW cW-W 257 A.G2345 A.C2368 G-C WC 19-XIX cWW cW-W 258 A.U2346 A.A2367 U-A WC 20-XX cWW cW-W 259 A.C2347 A.G2366 C-G WC 19-XIX cWW cW-W 260 A.A2348 A.U2365 A-U WC 20-XX cWW cW-W 261 A.G2349 A.C2364 G-C WC 19-XIX cWW cW-W 262 A.A2373 A.U2422 A-U rHoogsteen 24-XXIV tHW tM-W 263 A.C2375 A.G2421 C-G WC 19-XIX cWW cW-W 264 A.A2376 A.U2420 A-U WC 20-XX cWW cW-W 265 A.G2377 A.C2419 G-C WC 19-XIX cWW cW-W 266 A.C2378 A.A2418 C-A ~Wobble -- cWW cW-W 267 A.A2381 A.U2411 A-U WC 20-XX cWW cW-W 268 A.A2382 A.U2410 A-U WC 20-XX cWW cW-W 269 A.U2383 A.A2409 U-A WC 20-XX cWW cW-W 270 A.A2384 A.U2408 A-U WC 20-XX cWW cW-W 271 A.U2385 A.U2408 U-U -- -- cWW cW-W 272 A.C2386 A.U2407 C-U -- 18-XVIII cWW cW-W 273 A.A2390 A.A2399 A-A -- 05-V tHW tM-W 274 A.U2392 A.A2398 U-A -- -- c.W c.-W 275 A.A2394 A.C2396 A+C -- -- cWH cW+M 276 A.C2400 A.G2403 C-G WC 19-XIX cWW cW-W 277 A.C2427 A.G2436 C-G WC 19-XIX cWW cW-W 278 A.C2428 A.G2435 C-G WC 19-XIX cWW cW-W 279 A.U2442 A.A2444 U-A ~Wobble -- cWW cW-W 280 A.A2450 A.A2451 A+A Platform -- cSH cm+M 281 A.G2453 A.C2671 G-C WC 19-XIX cWW cW-W 282 A.G2454 A.C2670 G-C WC 19-XIX cWW cW-W 283 A.U2455 A.A2669 U-A WC 20-XX cWW cW-W 284 A.U2456 A.A2668 U-A WC 20-XX cWW cW-W 285 A.A2460 A.U2667 A-U -- -- cWW cW-W 286 A.A2461 A.U2666 A-U WC 20-XX cWW cW-W 287 A.A2462 A.U2665 A-U WC 20-XX cWW cW-W 288 A.A2463 A.U2664 A-U WC 20-XX cWW cW-W 289 A.G2464 A.C2663 G-C WC 19-XIX cWW cW-W 290 A.U2465 A.A2662 U-A WC 20-XX cWW cW-W 291 A.A2466 A.U2661 A-U WC 20-XX cWW cW-W 292 A.A2467 A.U2660 A-U WC 20-XX cWW cW-W 293 A.A2468 A.G2655 A-G -- -- .HH .M-M 294 A.A2468 A.C2659 A+C ~rWobble 26-XXVI tWW tW+W 295 A.A2469 A.U2658 A-U WC 20-XX cWW cW-W 296 A.G2470 A.C2657 G-C WC 19-XIX cWW cW-W 297 A.G2471 A.U2656 G-U ~Sheared -- tSH tm-M 298 A.A2472 A.A2480 A+A -- 01-I tWW tW+W 299 A.A2472 A.U2654 A-U rHoogsteen 24-XXIV tHW tM-W 300 A.A2473 A.U2656 A-U WC 20-XX cWW cW-W 301 A.G2478 A.A2481 G+A -- -- tSW tm+W 302 A.G2478 A.C2653 G-C WC 19-XIX cWW cW-W 303 A.A2482 A.C2653 A-C -- -- cSS cm-m 304 A.U2483 A.G2652 U-G -- -- cSS cm-m 305 A.U2485 A.C2650 U-C -- 18-XVIII cWW cW-W 306 A.A2487 A.U2648 A-U WC 20-XX cWW cW-W 307 A.C2488 A.G2647 C-G WC 19-XIX cWW cW-W 308 A.C2489 A.G2646 C-G WC 19-XIX cWW cW-W 309 A.C2490 A.G2645 C-G WC 19-XIX cWW cW-W 310 A.C2491 A.G2643 C-G WC 19-XIX cWW cW-W 311 A.G2492 A.C2642 G-C WC 19-XIX cWW cW-W 312 A.C2493 A.C2511 C+C -- -- tHH tM+M 313 A.C2494 A.U2510 C-U -- -- tHW tM-W 314 A.U2495 A.A2509 U-A -- -- tHW tM-W 315 A.G2496 A.C2508 G-C WC 19-XIX cWW cW-W 316 A.U2497 A.A2507 U-A WC 20-XX cWW cW-W 317 A.U2498 A.A2505 U-A rHoogsteen 24-XXIV tWH tW-M 318 A.U2499 A.A2504 U-A rHoogsteen 24-XXIV tWH tW-M 319 A.C2502 A.C3073 C+C -- -- tWW tW+W 320 A.A2503 A.G3094 A-G -- -- cSS cm-m 321 A.C2511 A.A2539 C+A -- -- tWS tW+m 322 A.A2512 A.C2538 A-C ~Wobble -- cWW cW-W 323 A.C2513 A.G2537 C-G WC 19-XIX cWW cW-W 324 A.C2514 A.G2536 C-G WC 19-XIX cWW cW-W 325 A.U2515 A.A2535 U-A WC 20-XX cWW cW-W 326 A.C2516 A.G2534 C-G WC 19-XIX cWW cW-W 327 A.U2517 A.A2533 U-A WC 20-XX cWW cW-W 328 A.A2518 A.U2532 A-U WC 20-XX cWW cW-W 329 A.G2519 A.U2529 G+U -- -- tWS tW+m 330 A.C2520 A.G2528 C+G rWC 22-XXII tWW tW+W 331 A.C2520 A.A2530 C+A -- -- tHH tM+M 332 A.C2541 A.C2639 C-C -- -- cW. cW-. 333 A.G2542 A.C2637 G-C WC 19-XIX cWW cW-W 334 A.C2611 A.G2621 C-G WC 19-XIX cWW cW-W 335 A.C2612 A.G2620 C-G WC 19-XIX cWW cW-W 336 A.U2613 A.A2619 U-A -- -- cWW cW-W 337 A.A2616 A.G3036 A+G Linker -- tSS tm+m 338 A.C2637 A.U2638 C+U Platform -- cWH cW+M 339 A.A2676 A.U3100 A+U rWC 21-XXI tWW tW+W 340 A.A2682 A.G2698 A-G Imino 08-VIII cWW cW-W 341 A.C2683 A.G2697 C-G WC 19-XIX cWW cW-W 342 A.G2686 A.C2703 G-C WC 19-XIX cWW cW-W 343 A.C2687 A.G2702 C-G WC 19-XIX cWW cW-W 344 A.C2688 A.G2701 C-G WC 19-XIX cWW cW-W 345 A.C2689 A.G2700 C-G WC 19-XIX cWW cW-W 346 A.G2690 A.C2699 G-C WC 19-XIX cWW cW-W 347 A.U2691 A.A2696 U-A rHoogsteen 24-XXIV tWH tW-M 348 A.C2710 A.A3220 C-A -- -- cSW cm-W 349 A.A2711 A.U3107 A-U WC 20-XX cWW cW-W 350 A.G2712 A.C3106 G-C WC 19-XIX cWW cW-W 351 A.C2713 A.A3105 C-A ~Wobble -- cWW cW-W 352 A.A2714 A.A2715 A+A Platform -- cSH cm+M 353 A.A2715 A.U3104 A-U WC 20-XX cWW cW-W 354 A.G2716 A.C3103 G-C WC 19-XIX cWW cW-W 355 A.A2717 A.A3064 A-A -- 05-V tHW tM-W 356 A.A2717 A.U3102 A-U WC 20-XX cWW cW-W 357 A.G2719 A.C3099 G-C WC 19-XIX cWW cW-W 358 A.A2720 A.U3098 A-U WC 20-XX cWW cW-W 359 A.C2726 A.G2934 C-G WC 19-XIX cWW cW-W 360 A.C2727 A.G2933 C-G WC 19-XIX cWW cW-W 361 A.C2728 A.G2932 C-G WC 19-XIX cWW cW-W 362 A.U2729 A.A2931 U-A WC 20-XX cWW cW-W 363 A.A2730 A.U2930 A-U WC 20-XX cWW cW-W 364 A.U2731 A.A2918 U+A rWC 21-XXI tWW tW+W 365 A.G2732 A.C2929 G-C WC 19-XIX cWW cW-W 366 A.G2733 A.C2928 G-C WC 19-XIX cWW cW-W 367 A.A2734 A.U2925 A-U WC 20-XX cWW cW-W 368 A.G2735 A.U2924 G-U Wobble 28-XXVIII cWW cW-W 369 A.C2736 A.G2923 C-G WC 19-XIX cWW cW-W 370 A.U2737 A.A2922 U-A WC 20-XX cWW cW-W 371 A.U2737 A.A3084 U-A -- -- cSS cm-m 372 A.U2738 A.A2740 U+A Hoogsteen 23-XXIII cWH cW+M 373 A.A2740 A.U2807 A-U WC 20-XX cWW cW-W 374 A.A2741 A.U2806 A-U WC 20-XX cWW cW-W 375 A.U2742 A.A2805 U-A WC 20-XX cWW cW-W 376 A.U2743 A.A2804 U-A WC 20-XX cWW cW-W 377 A.U2744 A.A2745 U+A Platform -- cSH cm+M 378 A.U2744 A.A2803 U-A WC 20-XX cWW cW-W 379 A.U2746 A.A2802 U-A -- -- cWW cW-W 380 A.U2747 A.A2801 U-A WC 20-XX cWW cW-W 381 A.A2748 A.U2800 A-U WC 20-XX cWW cW-W 382 A.A2749 A.U2799 A-U WC 20-XX cWW cW-W 383 A.U2750 A.A2798 U-A WC 20-XX cWW cW-W 384 A.G2751 A.C2797 G-C WC 19-XIX cWW cW-W 385 A.C2752 A.G2796 C-G WC 19-XIX cWW cW-W 386 A.A2753 A.U2795 A-U WC 20-XX cWW cW-W 387 A.A2754 A.C2794 A-C -- -- cWW cW-W 388 A.A2755 A.C2793 A-C -- -- cWW cW-W 389 A.U2808 A.A2922 U+A Hoogsteen 23-XXIII cWH cW+M 390 A.C2809 A.G2923 C+G ~Hoogsteen -- cWH cW+M 391 A.G2810 A.C2822 G-C WC 19-XIX cWW cW-W 392 A.G2811 A.C2821 G-C WC 19-XIX cWW cW-W 393 A.U2812 A.A2820 U-A WC 20-XX cWW cW-W 394 A.U2813 A.G2819 U-G -- -- cWW cW-W 395 A.G2814 A.G2816 G-G -- -- cHH cM-M 396 A.G2817 A.C2982 G+C -- -- cWH cW+M 397 A.U2823 A.A2845 U-A WC 20-XX cWW cW-W 398 A.C2824 A.G2844 C-G WC 19-XIX cWW cW-W 399 A.G2825 A.C2843 G-C WC 19-XIX cWW cW-W 400 A.G2826 A.C2842 G-C WC 19-XIX cWW cW-W 401 A.A2827 A.U2841 A-U WC 20-XX cWW cW-W 402 A.G2828 A.C2840 G-C WC 19-XIX cWW cW-W 403 A.C2829 A.A2838 C-A -- -- cWW cW-W 404 A.A2830 A.A2837 A+A -- 02-II tHH tM+M 405 A.G2846 A.C2915 G-C WC 19-XIX cWW cW-W 406 A.G2855 A.C2877 G-C WC 19-XIX cWW cW-W 407 A.C2856 A.G2876 C-G WC 19-XIX cWW cW-W 408 A.U2857 A.A2875 U-A -- -- cWW cW-W 409 A.A2858 A.A2874 A-A ~Sheared -- tSH tm-M 410 A.A2859 A.A2873 A-A ~Sheared -- tHS tM-m 411 A.G2860 A.C2872 G-C WC 19-XIX cWW cW-W 412 A.A2861 A.U2871 A-U WC 20-XX cWW cW-W 413 A.C2862 A.G2870 C-G WC 19-XIX cWW cW-W 414 A.U2863 A.A2869 U-A -- -- cWW cW-W 415 A.C2867 A.G2916 C-G WC 19-XIX cWW cW-W 416 A.G2896 A.A2913 G+A -- -- tHH tM+M 417 A.G2896 A.G2917 G+G -- 04-IV tSS tm+m 418 A.A2897 A.C2912 A-C ~rHoogsteen -- tHW tM-W 419 A.C2900 A.G2909 C-G -- -- cW. cW-. 420 A.A2901 A.U2908 A-U -- -- .HW .M-W 421 A.G2923 A.A3085 G+A Linker -- tSS tm+m 422 A.A2945 A.A2946 A+A Platform -- cSH cm+M 423 A.U2947 A.G2977 U-G sWobble -- cWW cW-W 424 A.C2948 A.G2976 C-G WC 19-XIX cWW cW-W 425 A.C2949 A.G2975 C-G WC 19-XIX cWW cW-W 426 A.U2950 A.A2974 U-A WC 20-XX cWW cW-W 427 A.A2951 A.U2973 A-U WC 20-XX cWW cW-W 428 A.U2952 A.A2972 U-A WC 20-XX cWW cW-W 429 A.U2953 A.C2954 U+C Platform -- cSH cm+M 430 A.U2953 A.A2971 U-A WC 20-XX cWW cW-W 431 A.C2954 A.A2971 C-A -- -- cWW cW-W 432 A.G2957 A.C2967 G-C WC 19-XIX cWW cW-W 433 A.G2957 A.A2968 G-A -- -- cWS cW-m 434 A.A2958 A.U2966 A-U WC 20-XX cWW cW-W 435 A.U2994 A.G3068 U-G Wobble 28-XXVIII cWW cW-W 436 A.G2995 A.G3063 G-G -- -- tHW tM-W 437 A.G2995 A.U3067 G-U Wobble 28-XXVIII cWW cW-W 438 A.G2996 A.C3060 G+C -- -- cHW cM+W 439 A.G2996 A.C3066 G-C WC 19-XIX cWW cW-W 440 A.A2997 A.U3065 A-U WC 20-XX cWW cW-W 441 A.U2998 A.U3062 U-U -- 16-XVI cWW cW-W 442 A.C2999 A.G3061 C-G WC 19-XIX cWW cW-W 443 A.A3000 A.U3058 A-U WC 20-XX cWW cW-W 444 A.G3001 A.C3057 G-C WC 19-XIX cWW cW-W 445 A.G3002 A.C3056 G-C WC 19-XIX cWW cW-W 446 A.A3003 A.U3055 A-U WC 20-XX cWW cW-W 447 A.C3004 A.G3054 C-G WC 19-XIX cWW cW-W 448 A.U3006 A.C3008 U+C -- -- cWH cW+M 449 A.C3007 A.A3029 C-A -- -- t.W t.-W 450 A.C3007 A.G3032 C-G WC 19-XIX cWW cW-W 451 A.C3008 A.G3031 C-G WC 19-XIX cWW cW-W 452 A.C3008 A.A3051 C-A -- -- cSS cm-m 453 A.G3010 A.U3027 G-U Wobble 28-XXVIII cWW cW-W 454 A.A3011 A.U3026 A-U WC 20-XX cWW cW-W 455 A.U3012 A.A3025 U-A WC 20-XX cWW cW-W 456 A.G3014 A.C3023 G-C WC 19-XIX cWW cW-W 457 A.G3014 A.U3024 G-U -- -- cWW cW-W 458 A.U3015 A.G3022 U-G Wobble 28-XXVIII cWW cW-W 459 A.U3015 A.C3023 U-C -- 18-XVIII cWW cW-W 460 A.C3017 A.C3021 C-C -- -- .SW .m-W 461 A.G3032 A.A3052 G+A Linker -- tSS tm+m 462 A.U3033 A.G3054 U+G -- -- cWH cW+M 463 A.U3034 A.A3048 U-A WC 20-XX cWW cW-W 464 A.C3035 A.G3047 C-G WC 19-XIX cWW cW-W 465 A.G3036 A.C3046 G-C WC 19-XIX cWW cW-W 466 A.U3037 A.A3045 U-A WC 20-XX cWW cW-W 467 A.U3037 A.C3046 U-C -- 18-XVIII cWW cW-W 468 A.U3038 A.A3044 U-A WC 20-XX cWW cW-W 469 A.U3038 A.A3045 U-A -- -- cWW cW-W 470 A.U3039 A.C3043 U-C -- -- tWH tW-M 471 A.U3049 A.A3053 U-A rHoogsteen 24-XXIV tWH tW-M 472 A.G3063 A.U3067 G+U -- -- tSH tm+M 473 A.A3074 A.G3095 A-G Sheared 11-XI tHS tM-m 474 A.G3075 A.C3093 G-C WC 19-XIX cWW cW-W 475 A.A3076 A.U3092 A-U WC 20-XX cWW cW-W 476 A.C3077 A.G3091 C-G WC 19-XIX cWW cW-W 477 A.C3078 A.G3090 C-G WC 19-XIX cWW cW-W 478 A.G3079 A.C3088 G-C WC 19-XIX cWW cW-W 479 A.G3080 A.C3087 G-C WC 19-XIX cWW cW-W 480 A.A3081 A.U3086 A-U WC 20-XX cWW cW-W 481 A.G3082 A.A3085 G-A Sheared 11-XI tSH tm-M 482 A.A3101 A.C3103 A+C -- -- cSH cm+M 483 A.A3113 A.U3143 A-U WC 20-XX cWW cW-W 484 A.U3114 A.A3142 U-A WC 20-XX cWW cW-W 485 A.U3115 A.A3141 U-A WC 20-XX cWW cW-W 486 A.C3116 A.A3140 C-A -- -- cWW cW-W 487 A.C3117 A.G3139 C-G WC 19-XIX cWW cW-W 488 A.U3118 A.A3138 U-A WC 20-XX cWW cW-W 489 A.C3119 A.G3137 C-G WC 19-XIX cWW cW-W 490 A.C3120 A.A3136 C-A ~Wobble -- cWW cW-W 491 A.C3121 A.A3135 C-A -- -- cWW cW-W 492 A.A3125 A.G3132 A-G Sheared 11-XI tHS tM-m 493 A.C3126 A.G3131 C-G WC 19-XIX cWW cW-W 494 A.G3127 A.A3130 G-A Sheared 11-XI tSH tm-M 495 A.A3144 A.U3167 A-U WC 20-XX cWW cW-W 496 A.A3145 A.U3166 A-U WC 20-XX cWW cW-W 497 A.G3146 A.C3165 G-C WC 19-XIX cWW cW-W 498 A.G3147 A.C3164 G-C WC 19-XIX cWW cW-W 499 A.C3148 A.G3163 C-G WC 19-XIX cWW cW-W 500 A.C3149 A.A3151 C+A -- -- cSH cm+M 501 A.C3149 A.G3163 C-G -- -- cWW cW-W 502 A.U3150 A.G3163 U-G -- -- .WS .W-m 503 A.A3151 A.G3163 A-G -- -- cWS cW-m 504 A.C3152 A.G3161 C-G WC 19-XIX cWW cW-W 505 A.U3153 A.A3160 U-A WC 20-XX cWW cW-W 506 A.U3154 A.A3159 U-A WC 20-XX cWW cW-W 507 A.C3155 A.A3158 C-A -- -- cSW cm-W 508 A.U3174 A.A3195 U-A WC 20-XX cWW cW-W 509 A.A3175 A.U3194 A-U WC 20-XX cWW cW-W 510 A.A3176 A.U3193 A-U WC 20-XX cWW cW-W 511 A.U3178 A.U3188 U-U Calcutta -- tWH tW-M 512 A.G3179 A.A3190 G-A Sheared 11-XI tSH tm-M 513 A.G3179 A.A3191 G-A Sheared 11-XI tSH tm-M 514 A.A3180 A.U3186 A-U rHoogsteen 24-XXIV tHW tM-W 515 A.U3181 A.A3185 U-A -- -- tH. tM-. 516 A.U3188 A.A3191 U+A Hoogsteen 23-XXIII cWH cW+M 517 A.A3213 A.U3227 A-U WC 20-XX cWW cW-W 518 A.C3214 A.G3226 C-G WC 19-XIX cWW cW-W 519 A.C3215 A.G3225 C-G WC 19-XIX cWW cW-W 520 A.C3216 A.G3224 C-G WC 19-XIX cWW cW-W 521 A.A3218 A.A3223 A-A -- -- cSW cm-W 522 B.A1603 B.U1668 A-U -- -- tHW tM-W 523 B.A1605 B.C1667 A-C -- -- cW. cW-. 524 B.G1606 B.C1665 G-C WC 19-XIX cWW cW-W 525 B.G1608 B.C1663 G-C -- -- cWW cW-W 526 B.U1609 B.A1622 U+A -- -- tWW tW+W 527 B.A1610 B.C1612 A-C -- -- cHH cM-M 528 B.A1610 B.A1622 A+A -- -- tHH tM+M 529 B.A1610 B.G1623 A+G -- -- cHH cM+M 530 B.G1611 B.C1624 G-C WC 19-XIX cWW cW-W 531 B.G1611 B.A1625 G-A -- -- cWW cW-W 532 B.G1611 B.G1644 G+G -- 06-VI cHW cM+W 533 B.C1612 B.G1623 C-G WC 19-XIX cWW cW-W 534 B.U1613 B.A1622 U-A WC 20-XX cWW cW-W 535 B.A1615 B.A1645 A+A -- -- tWW tW+W 536 B.A1616 B.U1646 A+U rWC 21-XXI tWW tW+W 537 B.A1622 B.A1645 A-A ~rHoogsteen -- tHW tM-W 538 B.C1627 B.G1641 C-G WC 19-XIX cWW cW-W 539 B.C1628 B.A1640 C-A -- -- tWH tW-M 540 B.C1631 B.U1638 C-U -- -- cWW cW-W 541 B.C1649 B.G1660 C-G WC 19-XIX cWW cW-W 542 B.A1650 B.U1659 A-U -- -- cWW cW-W 543 B.A1651 B.U1658 A-U WC 20-XX cWW cW-W **************************************************************************** List of 68 multiplets 1 nts=3 GCA A.G1681,A.C1771,A.A1775 2 nts=3 AUG A.A1723,A.U1729,A.G1750 3 nts=3 AUG A.A1724,A.U2035,A.G2040 4 nts=3 CGA A.C1726,A.G1748,A.A2919 5 nts=3 GUA A.G1742,A.U1743,A.A1755 6 nts=3 CCG A.C1769,A.C2276,A.G2289 7 nts=3 UAU A.U1774,A.A1863,A.U2302 8 nts=3 GUA A.G1782,A.U1783,A.A1794 9 nts=3 ACG A.A1789,A.C1915,A.G2004 10 nts=3 AAG A.A1828,A.A2682,A.G2698 11 nts=3 ACG A.A1828,A.C2683,A.G2697 12 nts=3 UUA A.U1843,A.U2691,A.A2696 13 nts=3 AUA A.A1844,A.U1854,A.A1859 14 nts=3 CGA A.C1845,A.G1858,A.A2297 15 nts=3 GGC A.G1916,A.G1985,A.C2001 16 nts=3 AUA A.A1937,A.U2392,A.A2398 17 nts=3 GCU A.G1939,A.C2494,A.U2510 18 nts=3 CGA A.C1948,A.G1968,A.A2644 19 nts=3 GUU A.G1949,A.U1950,A.U1967 20 nts=3 UCA A.U1954,A.C1959,A.A1963 21 nts=3 AUA A.A1974,A.U2495,A.A2509 22 nts=3 AGC A.A1984,A.G1987,A.C1997 23 nts=3 AGC A.A1991,A.G2496,A.C2508 24 nts=3 AAU A.A2031,A.A2044,A.U2096 25 nts=3 ACG A.A2039,A.C2728,A.G2932 26 nts=3 AUA A.A2039,A.U2729,A.A2931 27 nts=3 AGC A.A2132,A.G2690,A.C2699 28 nts=3 AGC A.A2232,A.G3002,A.C3056 29 nts=3 UAA A.U2327,A.A2450,A.A2451 30 nts=3 CUA A.C2332,A.U2442,A.A2444 31 nts=3 CGC A.C2340,A.G2343,A.C2423 32 nts=3 AGC A.A2468,A.G2655,A.C2659 33 nts=3 GAU A.G2471,A.A2473,A.U2656 34 nts=3 AAU A.A2472,A.A2480,A.U2654 35 nts=3 GAC A.G2478,A.A2482,A.C2653 36 nts=3 CCA A.C2493,A.C2511,A.A2539 37 nts=3 CGA A.C2520,A.G2528,A.A2530 38 nts=3 GCU A.G2542,A.C2637,A.U2638 39 nts=3 AGC A.A2616,A.G3036,A.C3046 40 nts=3 AAU A.A2714,A.A2715,A.U3104 41 nts=3 GAC A.G2716,A.A3101,A.C3103 42 nts=3 AAU A.A2717,A.A3064,A.U3102 43 nts=3 UAU A.U2738,A.A2740,A.U2807 44 nts=3 UAA A.U2744,A.A2745,A.A2803 45 nts=3 GAG A.G2896,A.A2913,A.G2917 46 nts=3 UCA A.U2953,A.C2954,A.A2971 47 nts=3 GGU A.G2995,A.G3063,A.U3067 48 nts=3 GCC A.G2996,A.C3060,A.C3066 49 nts=3 CUG A.C3004,A.U3033,A.G3054 50 nts=3 CAG A.C3149,A.A3151,A.G3163 51 nts=3 GUA A.G3179,A.U3188,A.A3191 52 nts=3 ACG B.A1610,B.C1612,B.G1623 53 nts=3 GCG B.G1611,B.C1624,B.G1644 54 nts=4 UAUG A.U1673,A.A1815,A.U1861,A.G2304 55 nts=4 GAAC A.G1787,A.A1790,A.A1914,A.C2005 56 nts=4 UCGA A.U1866,A.C1904,A.G2018,A.A2298 57 nts=4 ACGC A.A1867,A.C1903,A.G2019,A.C2295 58 nts=4 AUAU A.A1907,A.U2013,A.A2730,A.U2930 59 nts=4 AAGC A.A1908,A.A2012,A.G2732,A.C2929 60 nts=4 AUGC A.A1917,A.U1920,A.G1988,A.C1996 61 nts=4 GCAA A.G2105,A.C2116,A.A2830,A.A2837 62 nts=4 GCAG A.G2128,A.C2137,A.A2152,A.G2249 63 nts=4 GUAU A.G2310,A.U2311,A.A2676,A.U3100 64 nts=4 UUAA A.U2737,A.U2808,A.A2922,A.A3084 65 nts=4 UCGA A.U3006,A.C3008,A.G3031,A.A3051 66 nts=4 CAGA A.C3007,A.A3029,A.G3032,A.A3052 67 nts=4 UUAA B.U1609,B.U1613,B.A1622,B.A1645 68 nts=5 CCGGA A.C2736,A.C2809,A.G2923,A.G3082,A.A3085 **************************************************************************** List of 56 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=3 strand-1 5'-GCU-3' bp-type ||. strand-2 3'-CGA-5' helix-form .. 1 A.G1671 A.C1817 G-C WC 19-XIX cWW cW-W 2 A.C1672 A.G1816 C-G WC 19-XIX cWW cW-W 3 A.U1673 A.A1815 U-A -- -- tWH tW-M -------------------------------------------------------------------------- helix#2[2] bps=8 strand-1 5'-CUAGCCCC-3' bp-type |..||||. strand-2 3'-GAACGGGU-5' helix-form xxxAxA. 1 A.C1678 A.G1797 C-G WC 19-XIX cWW cW-W 2 A.U1679 A.A1773 U-A rHoogsteen 24-XXIV tWH tW-M 3 A.A1680 A.A1775 A+A -- 01-I tWW tW+W 4 A.G1681 A.C1771 G-C WC 19-XIX cWW cW-W 5 A.C1682 A.G1770 C-G WC 19-XIX cWW cW-W 6 A.C1683 A.G1768 C-G WC 19-XIX cWW cW-W 7 A.C1684 A.G1767 C-G WC 19-XIX cWW cW-W 8 A.C1685 A.U1766 C-U -- 18-XVIII cWW cW-W -------------------------------------------------------------------------- helix#3[0] bps=2 strand-1 5'-AC-3' bp-type .. strand-2 3'-CA-5' helix-form . 1 A.A1697 A.C1703 A-C -- -- cSS cm-m 2 A.C1698 A.A1702 C-A -- -- cSS cm-m -------------------------------------------------------------------------- helix#4[0] bps=4 strand-1 5'-CAAC-3' bp-type .|.| strand-2 3'-UUGG-5' helix-form .xx 1 A.C1721 A.U1730 C-U -- 18-XVIII cWW cW-W 2 A.A1722 A.U1729 A-U WC 20-XX cWW cW-W 3 A.A1723 A.G1750 A-G -- -- cSW cm-W 4 A.C1726 A.G1748 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#5[1] bps=10 strand-1 5'-AUAAAUAUAG-3' bp-type ..|....||. strand-2 3'-GUUAAAGAUA-5' helix-form ....x..A. 1 A.A1737 A.G1760 A-G Sheared 11-XI tHS tM-m 2 A.U1738 A.U1759 U-U -- 16-XVI cWW cW-W 3 A.A1739 A.U1758 A-U WC 20-XX cWW cW-W 4 A.A1740 A.A1757 A-A ~Sheared -- tSH tm-M 5 A.A1741 A.A1756 A+A -- 02-II tHH tM+M 6 A.U1743 A.A1755 U-A rHoogsteen 24-XXIV tWH tW-M 7 A.A1744 A.G1754 A-G Sheared 11-XI tHS tM-m 8 A.U1745 A.A1753 U-A WC 20-XX cWW cW-W 9 A.A1746 A.U1752 A-U WC 20-XX cWW cW-W 10 A.G1747 A.A1751 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#6[1] bps=5 strand-1 5'-UACCG-3' bp-type ..||. strand-2 3'-AGGGA-5' helix-form ..A. 1 A.U1783 A.A1794 U-A rHoogsteen 24-XXIV tWH tW-M 2 A.A1784 A.G1793 A-G Sheared 11-XI tHS tM-m 3 A.C1785 A.G1792 C-G WC 19-XIX cWW cW-W 4 A.C1786 A.G1791 C-G WC 19-XIX cWW cW-W 5 A.G1787 A.A1790 G-A -- -- tSH tm-M -------------------------------------------------------------------------- helix#7[1] bps=9 strand-1 5'-AGGCCCGUA-3' bp-type ..||||||. strand-2 3'-UACGGGCAG-5' helix-form .xAAAAxx 1 A.A1825 A.U2705 A+U Hoogsteen 23-XXIII cHW cM+W 2 A.G1826 A.A2704 G-A Imino 08-VIII cWW cW-W 3 A.G2686 A.C2703 G-C WC 19-XIX cWW cW-W 4 A.C2687 A.G2702 C-G WC 19-XIX cWW cW-W 5 A.C2688 A.G2701 C-G WC 19-XIX cWW cW-W 6 A.C2689 A.G2700 C-G WC 19-XIX cWW cW-W 7 A.G2690 A.C2699 G-C WC 19-XIX cWW cW-W 8 A.U1843 A.A2696 U-A WC 20-XX cWW cW-W 9 A.A1853 A.G2692 A-G -- -- cWS cW-m -------------------------------------------------------------------------- helix#8[1] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form AA 1 A.A1829 A.U1841 A-U WC 20-XX cWW cW-W 2 A.G1830 A.C1840 G-C WC 19-XIX cWW cW-W 3 A.G1831 A.C1839 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#9[1] bps=8 strand-1 5'-AAUGAGAC-3' bp-type ||.|.|.| strand-2 3'-UUCCACGG-5' helix-form A.AAxx. 1 A.A1855 A.U1848 A-U WC 20-XX cWW cW-W 2 A.A1856 A.U1847 A-U WC 20-XX cWW cW-W 3 A.U1857 A.C1846 U-C -- 18-XVIII cWW cW-W 4 A.G1858 A.C1845 G-C WC 19-XIX cWW cW-W 5 A.A1859 A.A1844 A-A -- -- cWW cW-W 6 A.G2681 A.C1827 G-C WC 19-XIX cWW cW-W 7 A.A2682 A.G2698 A-G Imino 08-VIII cWW cW-W 8 A.C2683 A.G2697 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#10[2] bps=14 strand-1 5'-GCCCGAAACCAGAC-3' bp-type .||.|...||||.| strand-2 3'-UGGUCUAUGGUCCG-5' helix-form xAA.x.x.AAA.. 1 A.G1868 A.U2020 G-U -- -- cW. cW-. 2 A.C1903 A.G2019 C-G WC 19-XIX cWW cW-W 3 A.C1904 A.G2018 C-G WC 19-XIX cWW cW-W 4 A.C1905 A.U2017 C-U -- 18-XVIII cWW cW-W 5 A.G1906 A.C2016 G-C WC 19-XIX cWW cW-W 6 A.A1907 A.U2013 A-U rHoogsteen 24-XXIV tHW tM-W 7 A.A1908 A.A2012 A-A -- 05-V tHW tM-W 8 A.A1909 A.U2010 A+U rWC 21-XXI tWW tW+W 9 A.C1910 A.G2009 C-G WC 19-XIX cWW cW-W 10 A.C1911 A.G2008 C-G WC 19-XIX cWW cW-W 11 A.A1912 A.U2007 A-U WC 20-XX cWW cW-W 12 A.G1913 A.C2006 G-C WC 19-XIX cWW cW-W 13 A.A1914 A.C2005 A-C ~Wobble -- cWW cW-W 14 A.C1915 A.G2004 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#11[2] bps=8 strand-1 5'-AACUUUGC-3' bp-type ..|||.|| strand-2 3'-CAGAAUCG-5' helix-form xxAAAAA 1 A.A1871 A.C1901 A-C ~rHoogsteen -- tHW tM-W 2 A.A1873 A.A1900 A-A -- -- t.W t.-W 3 A.C1875 A.G1899 C-G WC 19-XIX cWW cW-W 4 A.U1876 A.A1898 U-A WC 20-XX cWW cW-W 5 A.U1877 A.A1897 U-A WC 20-XX cWW cW-W 6 A.U1878 A.U1896 U-U -- -- cWW cW-W 7 A.G1879 A.C1895 G-C WC 19-XIX cWW cW-W 8 A.C1880 A.G1894 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#12[1] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 A.G1883 A.C1890 G-C WC 19-XIX cWW cW-W 2 A.G1884 A.C1889 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#13[2] bps=12 strand-1 5'-CUACCUAAGAAC-3' bp-type ..|||||.|||| strand-2 3'-AAUGGAUAUUUG-5' helix-form xxAAAA...Ax 1 A.C1919 A.A2500 C-A -- -- cSW cm-W 2 A.U1920 A.A1917 U+A -- -- tWS tW+m 3 A.A1921 A.U1983 A-U WC 20-XX cWW cW-W 4 A.C1922 A.G1982 C-G WC 19-XIX cWW cW-W 5 A.C1923 A.G1981 C-G WC 19-XIX cWW cW-W 6 A.U1924 A.A1980 U-A WC 20-XX cWW cW-W 7 A.A1925 A.U1979 A-U WC 20-XX cWW cW-W 8 A.A1926 A.A1978 A-A -- -- cWW cW-W 9 A.G1927 A.U1977 G-U Wobble 28-XXVIII cWW cW-W 10 A.A1928 A.U1976 A-U WC 20-XX cWW cW-W 11 A.A1929 A.U1975 A-U WC 20-XX cWW cW-W 12 A.C1930 A.G1973 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#14[0] bps=3 strand-1 5'-AAC-3' bp-type |.| strand-2 5'-UAG-3' helix-form xx 1 A.A1937 A.U2392 A-U WC 20-XX cWW cW-W 2 A.A2399 A.A2390 A-A -- 05-V tWH tW-M 3 A.C2400 A.G2403 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#15[3] bps=15 strand-1 5'-AAGCAACCCUCUAUG-3' bp-type .|||..|||.||||. strand-2 3'-AUCGAAGGGUGAUAA-5' helix-form xAA.x.AAx.AAAx 1 A.A1938 A.A1935 A-A -- -- cWS cW-m 2 A.A1940 A.U1934 A-U WC 20-XX cWW cW-W 3 A.G1941 A.C1933 G-C WC 19-XIX cWW cW-W 4 A.C1942 A.G1932 C-G WC 19-XIX cWW cW-W 5 A.A1943 A.A1931 A-A ~Sheared -- tSH tm-M 6 A.A1945 A.A1971 A-A ~Sheared -- tHS tM-m 7 A.C1946 A.G1970 C-G WC 19-XIX cWW cW-W 8 A.C1947 A.G1969 C-G WC 19-XIX cWW cW-W 9 A.C1948 A.G1968 C-G WC 19-XIX cWW cW-W 10 A.U1950 A.U1967 U-U -- 16-XVI cWW cW-W 11 A.C1951 A.G1966 C-G WC 19-XIX cWW cW-W 12 A.U1952 A.A1965 U-A WC 20-XX cWW cW-W 13 A.A1953 A.U1964 A-U WC 20-XX cWW cW-W 14 A.U1954 A.A1963 U-A WC 20-XX cWW cW-W 15 A.G1955 A.A1960 G+A -- 10-X tSW tm+W -------------------------------------------------------------------------- helix#16[1] bps=6 strand-1 5'-GACAAA-3' bp-type |.||.. strand-2 5'-CUGUUU-3' helix-form xx.x. 1 A.G1939 A.C2494 G-C WC 19-XIX cWW cW-W 2 A.A1974 A.U2495 A+U Hoogsteen 23-XXIII cHW cM+W 3 A.C2508 A.G2496 C-G WC 19-XIX cWW cW-W 4 A.A2507 A.U2497 A-U WC 20-XX cWW cW-W 5 A.A2505 A.U2498 A-U rHoogsteen 24-XXIV tHW tM-W 6 A.A2504 A.U2499 A-U rHoogsteen 24-XXIV tHW tM-W -------------------------------------------------------------------------- helix#17[1] bps=5 strand-1 5'-GGGCG-3' bp-type |||.. strand-2 3'-CCCAA-5' helix-form xA.x 1 A.G1985 A.C2001 G-C WC 19-XIX cWW cW-W 2 A.G1987 A.C1997 G-C WC 19-XIX cWW cW-W 3 A.G1988 A.C1996 G-C WC 19-XIX cWW cW-W 4 A.C1989 A.A1995 C-A -- -- cWW cW-W 5 A.G1990 A.A1993 G+A -- -- tSW tm+W -------------------------------------------------------------------------- helix#18[1] bps=11 strand-1 5'-UGUCCAAAGAG-3' bp-type .|||||||||| strand-2 3'-ACAGGUUUCUC-5' helix-form xAAAAAA.A. 1 A.U2030 A.A2124 U-A -- -- tHW tM-W 2 A.G2098 A.C2123 G-C WC 19-XIX cWW cW-W 3 A.U2099 A.A2122 U-A WC 20-XX cWW cW-W 4 A.C2100 A.G2121 C-G WC 19-XIX cWW cW-W 5 A.C2101 A.G2120 C-G WC 19-XIX cWW cW-W 6 A.A2102 A.U2119 A-U WC 20-XX cWW cW-W 7 A.A2103 A.U2118 A-U WC 20-XX cWW cW-W 8 A.A2104 A.U2117 A-U WC 20-XX cWW cW-W 9 A.G2105 A.C2116 G-C WC 19-XIX cWW cW-W 10 A.A2106 A.U2115 A-U WC 20-XX cWW cW-W 11 A.G2107 A.C2114 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#19[3] bps=15 strand-1 5'-GUUCAACUUUAAAUU-3' bp-type ||||.||.||||||| strand-2 3'-UAAGUUGCAAUUUAA-5' helix-form .AAx.Ax.AAAAAA 1 A.G2040 A.U2035 G-U Wobble 28-XXVIII cWW cW-W 2 A.U2041 A.A2034 U-A WC 20-XX cWW cW-W 3 A.U2042 A.A2033 U-A WC 20-XX cWW cW-W 4 A.C2043 A.G2032 C-G WC 19-XIX cWW cW-W 5 A.A2044 A.U2096 A-U -- -- cWW cW-W 6 A.A2045 A.U2095 A-U WC 20-XX cWW cW-W 7 A.C2046 A.G2094 C-G WC 19-XIX cWW cW-W 8 A.U2047 A.C2092 U-C -- -- cWW cW-W 9 A.U2048 A.A2091 U-A WC 20-XX cWW cW-W 10 A.U2049 A.A2090 U-A WC 20-XX cWW cW-W 11 A.A2050 A.U2089 A-U WC 20-XX cWW cW-W 12 A.A2051 A.U2088 A-U WC 20-XX cWW cW-W 13 A.A2052 A.U2087 A-U WC 20-XX cWW cW-W 14 A.U2053 A.A2086 U-A WC 20-XX cWW cW-W 15 A.U2054 A.A2085 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#20[2] bps=9 strand-1 5'-UGCCCCAGA-3' bp-type |||....|| strand-2 3'-AUGUCCCCU-5' helix-form ...xx..A 1 A.U2055 A.A2084 U-A WC 20-XX cWW cW-W 2 A.G2056 A.U2083 G-U Wobble 28-XXVIII cWW cW-W 3 A.C2057 A.G2082 C-G WC 19-XIX cWW cW-W 4 A.C2058 A.U2081 C-U -- 18-XVIII cWW cW-W 5 A.C2059 A.C2079 C-C -- -- tWH tW-M 6 A.C2061 A.C2078 C-C -- -- tHW tM-W 7 A.A2062 A.C2077 A-C -- -- cWW cW-W 8 A.G2063 A.C2076 G-C WC 19-XIX cWW cW-W 9 A.A2064 A.U2075 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#21[1] bps=4 strand-1 5'-UAGG-3' bp-type .||| strand-2 3'-UUCC-5' helix-form .AA 1 A.U2126 A.U2139 U-U -- 16-XVI cWW cW-W 2 A.A2127 A.U2138 A-U WC 20-XX cWW cW-W 3 A.G2128 A.C2137 G-C WC 19-XIX cWW cW-W 4 A.G2129 A.C2136 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#22[2] bps=9 strand-1 5'-GAGGAGUAA-3' bp-type ||||||..| strand-2 3'-CUCCUCAGU-5' helix-form A.xAAxx. 1 A.G2143 A.C2257 G-C WC 19-XIX cWW cW-W 2 A.A2144 A.U2256 A-U WC 20-XX cWW cW-W 3 A.G2145 A.C2255 G-C WC 19-XIX cWW cW-W 4 A.G2147 A.C2254 G-C WC 19-XIX cWW cW-W 5 A.A2148 A.U2253 A-U WC 20-XX cWW cW-W 6 A.G2149 A.C2252 G-C WC 19-XIX cWW cW-W 7 A.U2150 A.A2250 U-A rHoogsteen 24-XXIV tWH tW-M 8 A.A2152 A.G2249 A-G Sheared 11-XI tHS tM-m 9 A.A2153 A.U2248 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#23[2] bps=16 strand-1 5'-AUUGGACCAAUCUAUC-3' bp-type .||||||...|||||. strand-2 3'-GAACCUGAAAAGAUAU-5' helix-form .AAAA.x.x..AAA. 1 A.A2265 A.G2028 A-G Sheared 11-XI tHS tM-m 2 A.U2266 A.A2027 U-A WC 20-XX cWW cW-W 3 A.U2267 A.A2026 U-A WC 20-XX cWW cW-W 4 A.G2268 A.C2025 G-C WC 19-XIX cWW cW-W 5 A.G2269 A.C2024 G-C WC 19-XIX cWW cW-W 6 A.A2270 A.U2023 A-U WC 20-XX cWW cW-W 7 A.C2271 A.G2022 C-G WC 19-XIX cWW cW-W 8 A.C2272 A.A2294 C-A -- -- cWW cW-W 9 A.A2273 A.A2293 A-A -- -- cWS cW-m 10 A.A2274 A.A2291 A-A -- -- cWW cW-W 11 A.U2275 A.A2290 U-A WC 20-XX cWW cW-W 12 A.C2276 A.G2289 C-G WC 19-XIX cWW cW-W 13 A.U2277 A.A2288 U-A WC 20-XX cWW cW-W 14 A.A2278 A.U2287 A-U WC 20-XX cWW cW-W 15 A.U2279 A.A2286 U-A WC 20-XX cWW cW-W 16 A.C2280 A.U2285 C-U -- -- cWW cW-W -------------------------------------------------------------------------- helix#24[1] bps=13 strand-1 5'-CAGUUAGUAUAAU-3' bp-type ..|||||||.... strand-2 3'-AUCAAUUAUUAAA-5' helix-form xxAAA..x...x 1 A.C2295 A.A1867 C-A ~rHoogsteen 25-XXV tWH tW-M 2 A.A2298 A.U1866 A-U -- -- tHW tM-W 3 A.G2300 A.C1865 G-C WC 19-XIX cWW cW-W 4 A.U2301 A.A1864 U-A WC 20-XX cWW cW-W 5 A.U2302 A.A1863 U-A WC 20-XX cWW cW-W 6 A.A2303 A.U1862 A-U WC 20-XX cWW cW-W 7 A.G2304 A.U1861 G-U Wobble 28-XXVIII cWW cW-W 8 A.U2305 A.A1860 U-A WC 20-XX cWW cW-W 9 A.A2306 A.U2680 A-U WC 20-XX cWW cW-W 10 A.U2307 A.U2679 U-U -- 16-XVI cWW cW-W 11 A.A2308 A.A2678 A-A ~Sheared -- tSH tm-M 12 A.A2309 A.A2677 A+A -- 02-II tHH tM+M 13 A.U3100 A.A2676 U+A rWC 21-XXI tWW tW+W -------------------------------------------------------------------------- helix#25[3] bps=17 strand-1 5'-UAACAGGUUAAAAGUAA-3' bp-type ..||.||||.||||||| strand-2 3'-GGUGACCAAUUUUCAUU-5' helix-form x.A.xAA.x.AAAAAA 1 A.U2311 A.G2310 U+G Platform -- cHS cM+m 2 A.A2312 A.G2675 A-G Sheared 11-XI tHS tM-m 3 A.A2313 A.U2674 A-U WC 20-XX cWW cW-W 4 A.C2314 A.G2673 C-G WC 19-XIX cWW cW-W 5 A.A2315 A.A2672 A-A -- -- cWW cW-W 6 A.G2453 A.C2671 G-C WC 19-XIX cWW cW-W 7 A.G2454 A.C2670 G-C WC 19-XIX cWW cW-W 8 A.U2455 A.A2669 U-A WC 20-XX cWW cW-W 9 A.U2456 A.A2668 U-A WC 20-XX cWW cW-W 10 A.A2460 A.U2667 A-U -- -- cWW cW-W 11 A.A2461 A.U2666 A-U WC 20-XX cWW cW-W 12 A.A2462 A.U2665 A-U WC 20-XX cWW cW-W 13 A.A2463 A.U2664 A-U WC 20-XX cWW cW-W 14 A.G2464 A.C2663 G-C WC 19-XIX cWW cW-W 15 A.U2465 A.A2662 U-A WC 20-XX cWW cW-W 16 A.A2466 A.U2661 A-U WC 20-XX cWW cW-W 17 A.A2467 A.U2660 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#26[2] bps=7 strand-1 5'-UUCUCCU-3' bp-type ||||||| strand-2 3'-AAGAGGA-5' helix-form AAxA.A 1 A.U2324 A.A2319 U-A WC 20-XX cWW cW-W 2 A.U2325 A.A2318 U-A WC 20-XX cWW cW-W 3 A.C2326 A.G2317 C-G WC 19-XIX cWW cW-W 4 A.U2327 A.A2450 U-A WC 20-XX cWW cW-W 5 A.C2328 A.G2449 C-G WC 19-XIX cWW cW-W 6 A.C2329 A.G2448 C-G WC 19-XIX cWW cW-W 7 A.U2330 A.A2447 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#27[1] bps=5 strand-1 5'-CGCAU-3' bp-type .|||| strand-2 3'-UCGUA-5' helix-form AAAA 1 A.C2332 A.U2442 C-U -- 18-XVIII cWW cW-W 2 A.G2333 A.C2441 G-C WC 19-XIX cWW cW-W 3 A.C2334 A.G2440 C-G WC 19-XIX cWW cW-W 4 A.A2335 A.U2439 A-U WC 20-XX cWW cW-W 5 A.U2336 A.A2438 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#28[0] bps=2 strand-1 5'-UG-3' bp-type .| strand-2 5'-UC-3' helix-form x 1 A.U2342 A.U2371 U+U -- 12-XII tWW tW+W 2 A.G2343 A.C2423 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#29[1] bps=5 strand-1 5'-GUCAG-3' bp-type ||||| strand-2 3'-CAGUC-5' helix-form AAA. 1 A.G2345 A.C2368 G-C WC 19-XIX cWW cW-W 2 A.U2346 A.A2367 U-A WC 20-XX cWW cW-W 3 A.C2347 A.G2366 C-G WC 19-XIX cWW cW-W 4 A.A2348 A.U2365 A-U WC 20-XX cWW cW-W 5 A.G2349 A.C2364 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#30[1] bps=5 strand-1 5'-ACAGC-3' bp-type .|||. strand-2 3'-UGUCA-5' helix-form xAA. 1 A.A2373 A.U2422 A-U rHoogsteen 24-XXIV tHW tM-W 2 A.C2375 A.G2421 C-G WC 19-XIX cWW cW-W 3 A.A2376 A.U2420 A-U WC 20-XX cWW cW-W 4 A.G2377 A.C2419 G-C WC 19-XIX cWW cW-W 5 A.C2378 A.A2418 C-A ~Wobble -- cWW cW-W -------------------------------------------------------------------------- helix#31[1] bps=5 strand-1 5'-AAUAC-3' bp-type ||||. strand-2 3'-UUAUU-5' helix-form .A.x 1 A.A2381 A.U2411 A-U WC 20-XX cWW cW-W 2 A.A2382 A.U2410 A-U WC 20-XX cWW cW-W 3 A.U2383 A.A2409 U-A WC 20-XX cWW cW-W 4 A.A2384 A.U2408 A-U WC 20-XX cWW cW-W 5 A.C2386 A.U2407 C-U -- 18-XVIII cWW cW-W -------------------------------------------------------------------------- helix#32[1] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C2427 A.G2436 C-G WC 19-XIX cWW cW-W 2 A.C2428 A.G2435 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#33[3] bps=16 strand-1 5'-AAGAAGUUACCCCGCG-3' bp-type .|||.|..||||||.| strand-2 3'-CUCUUCGCUGGGGCCC-5' helix-form .AxxxxxxAAAxAxx 1 A.A2468 A.C2659 A+C ~rWobble 26-XXVI tWW tW+W 2 A.A2469 A.U2658 A-U WC 20-XX cWW cW-W 3 A.G2470 A.C2657 G-C WC 19-XIX cWW cW-W 4 A.A2473 A.U2656 A-U WC 20-XX cWW cW-W 5 A.A2472 A.U2654 A-U rHoogsteen 24-XXIV tHW tM-W 6 A.G2478 A.C2653 G-C WC 19-XIX cWW cW-W 7 A.U2483 A.G2652 U-G -- -- cSS cm-m 8 A.U2485 A.C2650 U-C -- 18-XVIII cWW cW-W 9 A.A2487 A.U2648 A-U WC 20-XX cWW cW-W 10 A.C2488 A.G2647 C-G WC 19-XIX cWW cW-W 11 A.C2489 A.G2646 C-G WC 19-XIX cWW cW-W 12 A.C2490 A.G2645 C-G WC 19-XIX cWW cW-W 13 A.C2491 A.G2643 C-G WC 19-XIX cWW cW-W 14 A.G2492 A.C2642 G-C WC 19-XIX cWW cW-W 15 A.C2541 A.C2639 C-C -- -- cW. cW-. 16 A.G2542 A.C2637 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#34[1] bps=8 strand-1 5'-CACCUCUA-3' bp-type ..|||||| strand-2 3'-ACGGAGAU-5' helix-form ..AAAAA 1 A.C2511 A.A2539 C+A -- -- tWS tW+m 2 A.A2512 A.C2538 A-C ~Wobble -- cWW cW-W 3 A.C2513 A.G2537 C-G WC 19-XIX cWW cW-W 4 A.C2514 A.G2536 C-G WC 19-XIX cWW cW-W 5 A.U2515 A.A2535 U-A WC 20-XX cWW cW-W 6 A.C2516 A.G2534 C-G WC 19-XIX cWW cW-W 7 A.U2517 A.A2533 U-A WC 20-XX cWW cW-W 8 A.A2518 A.U2532 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#35[0] bps=2 strand-1 5'-GC-3' bp-type .. strand-2 3'-UG-5' helix-form . 1 A.G2519 A.U2529 G+U -- -- tWS tW+m 2 A.C2520 A.G2528 C+G rWC 22-XXII tWW tW+W -------------------------------------------------------------------------- helix#36[1] bps=3 strand-1 5'-CCU-3' bp-type ||. strand-2 3'-GGA-5' helix-form A. 1 A.C2611 A.G2621 C-G WC 19-XIX cWW cW-W 2 A.C2612 A.G2620 C-G WC 19-XIX cWW cW-W 3 A.U2613 A.A2619 U-A -- -- cWW cW-W -------------------------------------------------------------------------- helix#37[2] bps=7 strand-1 5'-CAGCAGA-3' bp-type .||.||| strand-2 3'-AUCAUCU-5' helix-form x..xAA 1 A.C2710 A.A3220 C-A -- -- cSW cm-W 2 A.A2711 A.U3107 A-U WC 20-XX cWW cW-W 3 A.G2712 A.C3106 G-C WC 19-XIX cWW cW-W 4 A.C2713 A.A3105 C-A ~Wobble -- cWW cW-W 5 A.A2715 A.U3104 A-U WC 20-XX cWW cW-W 6 A.G2716 A.C3103 G-C WC 19-XIX cWW cW-W 7 A.A2717 A.U3102 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#38[1] bps=2 strand-1 5'-GA-3' bp-type || strand-2 3'-CU-5' helix-form . 1 A.G2719 A.C3099 G-C WC 19-XIX cWW cW-W 2 A.A2720 A.U3098 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#39[5] bps=26 strand-1 5'-CCCUAGGAGCUAAUUUUUAAUGCAAA-3' bp-type ||||||||||||||||.|||||||.. strand-2 3'-GGGAUCCUUGAUUAAAAAUUACGUCC-5' helix-form AA.AxAx..AxAAAAx.AAAAAA.. 1 A.C2726 A.G2934 C-G WC 19-XIX cWW cW-W 2 A.C2727 A.G2933 C-G WC 19-XIX cWW cW-W 3 A.C2728 A.G2932 C-G WC 19-XIX cWW cW-W 4 A.U2729 A.A2931 U-A WC 20-XX cWW cW-W 5 A.A2730 A.U2930 A-U WC 20-XX cWW cW-W 6 A.G2732 A.C2929 G-C WC 19-XIX cWW cW-W 7 A.G2733 A.C2928 G-C WC 19-XIX cWW cW-W 8 A.A2734 A.U2925 A-U WC 20-XX cWW cW-W 9 A.G2735 A.U2924 G-U Wobble 28-XXVIII cWW cW-W 10 A.C2736 A.G2923 C-G WC 19-XIX cWW cW-W 11 A.U2737 A.A2922 U-A WC 20-XX cWW cW-W 12 A.A2740 A.U2807 A-U WC 20-XX cWW cW-W 13 A.A2741 A.U2806 A-U WC 20-XX cWW cW-W 14 A.U2742 A.A2805 U-A WC 20-XX cWW cW-W 15 A.U2743 A.A2804 U-A WC 20-XX cWW cW-W 16 A.U2744 A.A2803 U-A WC 20-XX cWW cW-W 17 A.U2746 A.A2802 U-A -- -- cWW cW-W 18 A.U2747 A.A2801 U-A WC 20-XX cWW cW-W 19 A.A2748 A.U2800 A-U WC 20-XX cWW cW-W 20 A.A2749 A.U2799 A-U WC 20-XX cWW cW-W 21 A.U2750 A.A2798 U-A WC 20-XX cWW cW-W 22 A.G2751 A.C2797 G-C WC 19-XIX cWW cW-W 23 A.C2752 A.G2796 C-G WC 19-XIX cWW cW-W 24 A.A2753 A.U2795 A-U WC 20-XX cWW cW-W 25 A.A2754 A.C2794 A-C -- -- cWW cW-W 26 A.A2755 A.C2793 A-C -- -- cWW cW-W -------------------------------------------------------------------------- helix#40[1] bps=6 strand-1 5'-GGUUCG-3' bp-type |||... strand-2 3'-CCAGGG-5' helix-form .A.xx 1 A.G2810 A.C2822 G-C WC 19-XIX cWW cW-W 2 A.G2811 A.C2821 G-C WC 19-XIX cWW cW-W 3 A.U2812 A.A2820 U-A WC 20-XX cWW cW-W 4 A.U2813 A.G2819 U-G -- -- cWW cW-W 5 A.C2982 A.G2817 C+G -- -- cHW cM+W 6 A.G2814 A.G2816 G-G -- -- cHH cM-M -------------------------------------------------------------------------- helix#41[1] bps=9 strand-1 5'-AACUCCGAG-3' bp-type ..||||||| strand-2 3'-ACGAGGCUC-5' helix-form .x....Ax 1 A.A2837 A.A2830 A+A -- 02-II tHH tM+M 2 A.A2838 A.C2829 A-C -- -- cWW cW-W 3 A.C2840 A.G2828 C-G WC 19-XIX cWW cW-W 4 A.U2841 A.A2827 U-A WC 20-XX cWW cW-W 5 A.C2842 A.G2826 C-G WC 19-XIX cWW cW-W 6 A.C2843 A.G2825 C-G WC 19-XIX cWW cW-W 7 A.G2844 A.C2824 G-C WC 19-XIX cWW cW-W 8 A.A2845 A.U2823 A-U WC 20-XX cWW cW-W 9 A.G2846 A.C2915 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#42[2] bps=9 strand-1 5'-GCUAAGACU-3' bp-type ||...|||. strand-2 3'-CGAAACUGA-5' helix-form A.....A. 1 A.G2855 A.C2877 G-C WC 19-XIX cWW cW-W 2 A.C2856 A.G2876 C-G WC 19-XIX cWW cW-W 3 A.U2857 A.A2875 U-A -- -- cWW cW-W 4 A.A2858 A.A2874 A-A ~Sheared -- tSH tm-M 5 A.A2859 A.A2873 A-A ~Sheared -- tHS tM-m 6 A.G2860 A.C2872 G-C WC 19-XIX cWW cW-W 7 A.A2861 A.U2871 A-U WC 20-XX cWW cW-W 8 A.C2862 A.G2870 C-G WC 19-XIX cWW cW-W 9 A.U2863 A.A2869 U-A -- -- cWW cW-W -------------------------------------------------------------------------- helix#43[0] bps=4 strand-1 5'-GACA-3' bp-type .... strand-2 3'-GCGU-5' helix-form xx. 1 A.G2896 A.G2917 G+G -- 04-IV tSS tm+m 2 A.A2897 A.C2912 A-C ~rHoogsteen -- tHW tM-W 3 A.C2900 A.G2909 C-G -- -- cW. cW-. 4 A.A2901 A.U2908 A-U -- -- .HW .M-W -------------------------------------------------------------------------- helix#44[1] bps=8 strand-1 5'-AUCCUAUU-3' bp-type ..|||||| strand-2 3'-AGGGAUAA-5' helix-form x.AAA.A 1 A.A2946 A.A2945 A+A Platform -- cHS cM+m 2 A.U2947 A.G2977 U-G sWobble -- cWW cW-W 3 A.C2948 A.G2976 C-G WC 19-XIX cWW cW-W 4 A.C2949 A.G2975 C-G WC 19-XIX cWW cW-W 5 A.U2950 A.A2974 U-A WC 20-XX cWW cW-W 6 A.A2951 A.U2973 A-U WC 20-XX cWW cW-W 7 A.U2952 A.A2972 U-A WC 20-XX cWW cW-W 8 A.U2953 A.A2971 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#45[1] bps=2 strand-1 5'-GA-3' bp-type || strand-2 3'-CU-5' helix-form A 1 A.G2957 A.C2967 G-C WC 19-XIX cWW cW-W 2 A.A2958 A.U2966 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#46[5] bps=19 strand-1 5'-UGGAUCAGGACCCGAUGUC-3' bp-type ||||.|||||||||||||. strand-2 3'-GUCUUGUCCUGGGUUACGC-5' helix-form ..Ax.x.AAAxAx.Ax.x 1 A.U2994 A.G3068 U-G Wobble 28-XXVIII cWW cW-W 2 A.G2995 A.U3067 G-U Wobble 28-XXVIII cWW cW-W 3 A.G2996 A.C3066 G-C WC 19-XIX cWW cW-W 4 A.A2997 A.U3065 A-U WC 20-XX cWW cW-W 5 A.U2998 A.U3062 U-U -- 16-XVI cWW cW-W 6 A.C2999 A.G3061 C-G WC 19-XIX cWW cW-W 7 A.A3000 A.U3058 A-U WC 20-XX cWW cW-W 8 A.G3001 A.C3057 G-C WC 19-XIX cWW cW-W 9 A.G3002 A.C3056 G-C WC 19-XIX cWW cW-W 10 A.A3003 A.U3055 A-U WC 20-XX cWW cW-W 11 A.C3004 A.G3054 C-G WC 19-XIX cWW cW-W 12 A.C3007 A.G3032 C-G WC 19-XIX cWW cW-W 13 A.C3008 A.G3031 C-G WC 19-XIX cWW cW-W 14 A.G3010 A.U3027 G-U Wobble 28-XXVIII cWW cW-W 15 A.A3011 A.U3026 A-U WC 20-XX cWW cW-W 16 A.U3012 A.A3025 U-A WC 20-XX cWW cW-W 17 A.G3014 A.C3023 G-C WC 19-XIX cWW cW-W 18 A.U3015 A.G3022 U-G Wobble 28-XXVIII cWW cW-W 19 A.C3017 A.C3021 C-C -- -- .SW .m-W -------------------------------------------------------------------------- helix#47[1] bps=7 strand-1 5'-CAACGAU-3' bp-type .|||||. strand-2 3'-UUUGCUA-5' helix-form ....Ax 1 A.C3043 A.U3039 C-U -- -- tHW tM-W 2 A.A3044 A.U3038 A-U WC 20-XX cWW cW-W 3 A.A3045 A.U3037 A-U WC 20-XX cWW cW-W 4 A.C3046 A.G3036 C-G WC 19-XIX cWW cW-W 5 A.G3047 A.C3035 G-C WC 19-XIX cWW cW-W 6 A.A3048 A.U3034 A-U WC 20-XX cWW cW-W 7 A.U3049 A.A3053 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#48[2] bps=11 strand-1 5'-CAAGACCGGAG-3' bp-type ...|||||||. strand-2 3'-CGGCUGGCCUA-5' helix-form xxxAAAx.A. 1 A.C3073 A.C2502 C+C -- -- tWW tW+W 2 A.A3074 A.G3095 A-G Sheared 11-XI tHS tM-m 3 A.A2503 A.G3094 A-G -- -- cSS cm-m 4 A.G3075 A.C3093 G-C WC 19-XIX cWW cW-W 5 A.A3076 A.U3092 A-U WC 20-XX cWW cW-W 6 A.C3077 A.G3091 C-G WC 19-XIX cWW cW-W 7 A.C3078 A.G3090 C-G WC 19-XIX cWW cW-W 8 A.G3079 A.C3088 G-C WC 19-XIX cWW cW-W 9 A.G3080 A.C3087 G-C WC 19-XIX cWW cW-W 10 A.A3081 A.U3086 A-U WC 20-XX cWW cW-W 11 A.G3082 A.A3085 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#49[0] bps=3 strand-1 5'-ACG-3' bp-type .|. strand-2 3'-GGA-5' helix-form .. 1 A.A3125 A.G3132 A-G Sheared 11-XI tHS tM-m 2 A.C3126 A.G3131 C-G WC 19-XIX cWW cW-W 3 A.G3127 A.A3130 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#50[4] bps=19 strand-1 5'-AAGAGAAAUAAGGCACUUC-3' bp-type ..|||.||||||||.|||. strand-2 3'-CCCUCCUUAUUCCGCGAAA-5' helix-form ..AAAAA.xAA..xx... 1 A.A3135 A.C3121 A-C -- -- cWW cW-W 2 A.A3136 A.C3120 A-C ~Wobble -- cWW cW-W 3 A.G3137 A.C3119 G-C WC 19-XIX cWW cW-W 4 A.A3138 A.U3118 A-U WC 20-XX cWW cW-W 5 A.G3139 A.C3117 G-C WC 19-XIX cWW cW-W 6 A.A3140 A.C3116 A-C -- -- cWW cW-W 7 A.A3141 A.U3115 A-U WC 20-XX cWW cW-W 8 A.A3142 A.U3114 A-U WC 20-XX cWW cW-W 9 A.U3143 A.A3113 U-A WC 20-XX cWW cW-W 10 A.A3144 A.U3167 A-U WC 20-XX cWW cW-W 11 A.A3145 A.U3166 A-U WC 20-XX cWW cW-W 12 A.G3146 A.C3165 G-C WC 19-XIX cWW cW-W 13 A.G3147 A.C3164 G-C WC 19-XIX cWW cW-W 14 A.C3148 A.G3163 C-G WC 19-XIX cWW cW-W 15 A.A3151 A.C3149 A+C -- -- cHS cM+m 16 A.C3152 A.G3161 C-G WC 19-XIX cWW cW-W 17 A.U3153 A.A3160 U-A WC 20-XX cWW cW-W 18 A.U3154 A.A3159 U-A WC 20-XX cWW cW-W 19 A.C3155 A.A3158 C-A -- -- cSW cm-W -------------------------------------------------------------------------- helix#51[1] bps=7 strand-1 5'-UAAUGAU-3' bp-type |||.... strand-2 3'-AUUAAUA-5' helix-form ..xxx. 1 A.U3174 A.A3195 U-A WC 20-XX cWW cW-W 2 A.A3175 A.U3194 A-U WC 20-XX cWW cW-W 3 A.A3176 A.U3193 A-U WC 20-XX cWW cW-W 4 A.U3188 A.A3191 U+A Hoogsteen 23-XXIII cWH cW+M 5 A.G3179 A.A3190 G-A Sheared 11-XI tSH tm-M 6 A.A3180 A.U3186 A-U rHoogsteen 24-XXIV tHW tM-W 7 A.U3181 A.A3185 U-A -- -- tH. tM-. -------------------------------------------------------------------------- helix#52[1] bps=5 strand-1 5'-ACCCA-3' bp-type ||||. strand-2 3'-UGGGA-5' helix-form AAAx 1 A.A3213 A.U3227 A-U WC 20-XX cWW cW-W 2 A.C3214 A.G3226 C-G WC 19-XIX cWW cW-W 3 A.C3215 A.G3225 C-G WC 19-XIX cWW cW-W 4 A.C3216 A.G3224 C-G WC 19-XIX cWW cW-W 5 A.A3218 A.A3223 A-A -- -- cSW cm-W -------------------------------------------------------------------------- helix#53[0] bps=2 strand-1 5'-AG-3' bp-type .| strand-2 5'-CC-3' helix-form x 1 B.A1605 B.C1667 A-C -- -- cW. cW-. 2 B.G1606 B.C1665 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#54[1] bps=5 strand-1 5'-GCUAA-3' bp-type |||.. strand-2 3'-CGAAU-5' helix-form ..x. 1 B.G1611 B.C1624 G-C WC 19-XIX cWW cW-W 2 B.C1612 B.G1623 C-G WC 19-XIX cWW cW-W 3 B.U1613 B.A1622 U-A WC 20-XX cWW cW-W 4 B.A1615 B.A1645 A+A -- -- tWW tW+W 5 B.A1616 B.U1646 A+U rWC 21-XXI tWW tW+W -------------------------------------------------------------------------- helix#55[0] bps=2 strand-1 5'-CC-3' bp-type |. strand-2 3'-GA-5' helix-form . 1 B.C1627 B.G1641 C-G WC 19-XIX cWW cW-W 2 B.C1628 B.A1640 C-A -- -- tWH tW-M -------------------------------------------------------------------------- helix#56[0] bps=3 strand-1 5'-CAA-3' bp-type |.| strand-2 3'-GUU-5' helix-form .. 1 B.C1649 B.G1660 C-G WC 19-XIX cWW cW-W 2 B.A1650 B.U1659 A-U -- -- cWW cW-W 3 B.A1651 B.U1658 A-U WC 20-XX cWW cW-W **************************************************************************** List of 76 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G1671 A.C1817 G-C WC 19-XIX cWW cW-W 2 A.C1672 A.G1816 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G1681 A.C1771 G-C WC 19-XIX cWW cW-W 2 A.C1682 A.G1770 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C1683 A.G1768 C-G WC 19-XIX cWW cW-W 2 A.C1684 A.G1767 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#5] bps=2 strand-1 5'-UA-3' bp-type || strand-2 3'-AU-5' helix-form A 1 A.U1745 A.A1753 U-A WC 20-XX cWW cW-W 2 A.A1746 A.U1752 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#6] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C1785 A.G1792 C-G WC 19-XIX cWW cW-W 2 A.C1786 A.G1791 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#8] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form AA 1 A.A1829 A.U1841 A-U WC 20-XX cWW cW-W 2 A.G1830 A.C1840 G-C WC 19-XIX cWW cW-W 3 A.G1831 A.C1839 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#9] bps=2 strand-1 5'-UU-3' bp-type || strand-2 3'-AA-5' helix-form A 1 A.U1847 A.A1856 U-A WC 20-XX cWW cW-W 2 A.U1848 A.A1855 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#8[#24] bps=6 strand-1 5'-AUUAAC-3' bp-type |||||| strand-2 3'-UGAUUG-5' helix-form ..AAA 1 A.A1860 A.U2305 A-U WC 20-XX cWW cW-W 2 A.U1861 A.G2304 U-G Wobble 28-XXVIII cWW cW-W 3 A.U1862 A.A2303 U-A WC 20-XX cWW cW-W 4 A.A1863 A.U2302 A-U WC 20-XX cWW cW-W 5 A.A1864 A.U2301 A-U WC 20-XX cWW cW-W 6 A.C1865 A.G2300 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#11] bps=3 strand-1 5'-CUU-3' bp-type ||| strand-2 3'-GAA-5' helix-form AA 1 A.C1875 A.G1899 C-G WC 19-XIX cWW cW-W 2 A.U1876 A.A1898 U-A WC 20-XX cWW cW-W 3 A.U1877 A.A1897 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#10[#11] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G1879 A.C1895 G-C WC 19-XIX cWW cW-W 2 A.C1880 A.G1894 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#12] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 A.G1883 A.C1890 G-C WC 19-XIX cWW cW-W 2 A.G1884 A.C1889 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#12[#10] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C1903 A.G2019 C-G WC 19-XIX cWW cW-W 2 A.C1904 A.G2018 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#13[#10] bps=4 strand-1 5'-CCAG-3' bp-type |||| strand-2 3'-GGUC-5' helix-form AAA 1 A.C1910 A.G2009 C-G WC 19-XIX cWW cW-W 2 A.C1911 A.G2008 C-G WC 19-XIX cWW cW-W 3 A.A1912 A.U2007 A-U WC 20-XX cWW cW-W 4 A.G1913 A.C2006 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#14[#13] bps=5 strand-1 5'-ACCUA-3' bp-type ||||| strand-2 3'-UGGAU-5' helix-form AAAA 1 A.A1921 A.U1983 A-U WC 20-XX cWW cW-W 2 A.C1922 A.G1982 C-G WC 19-XIX cWW cW-W 3 A.C1923 A.G1981 C-G WC 19-XIX cWW cW-W 4 A.U1924 A.A1980 U-A WC 20-XX cWW cW-W 5 A.A1925 A.U1979 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#15[#13] bps=3 strand-1 5'-GAA-3' bp-type ||| strand-2 3'-UUU-5' helix-form .A 1 A.G1927 A.U1977 G-U Wobble 28-XXVIII cWW cW-W 2 A.A1928 A.U1976 A-U WC 20-XX cWW cW-W 3 A.A1929 A.U1975 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#16[#15] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-CGA-5' helix-form AA 1 A.G1932 A.C1942 G-C WC 19-XIX cWW cW-W 2 A.C1933 A.G1941 C-G WC 19-XIX cWW cW-W 3 A.U1934 A.A1940 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#17[#15] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form AA 1 A.C1946 A.G1970 C-G WC 19-XIX cWW cW-W 2 A.C1947 A.G1969 C-G WC 19-XIX cWW cW-W 3 A.C1948 A.G1968 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#18[#15] bps=4 strand-1 5'-CUAU-3' bp-type |||| strand-2 3'-GAUA-5' helix-form AAA 1 A.C1951 A.G1966 C-G WC 19-XIX cWW cW-W 2 A.U1952 A.A1965 U-A WC 20-XX cWW cW-W 3 A.A1953 A.U1964 A-U WC 20-XX cWW cW-W 4 A.U1954 A.A1963 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#19[#17] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 A.G1987 A.C1997 G-C WC 19-XIX cWW cW-W 2 A.G1988 A.C1996 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#20[#23] bps=6 strand-1 5'-GUCCAA-3' bp-type |||||| strand-2 3'-CAGGUU-5' helix-form .AAAA 1 A.G2022 A.C2271 G-C WC 19-XIX cWW cW-W 2 A.U2023 A.A2270 U-A WC 20-XX cWW cW-W 3 A.C2024 A.G2269 C-G WC 19-XIX cWW cW-W 4 A.C2025 A.G2268 C-G WC 19-XIX cWW cW-W 5 A.A2026 A.U2267 A-U WC 20-XX cWW cW-W 6 A.A2027 A.U2266 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#21[#19] bps=4 strand-1 5'-GAAU-3' bp-type |||| strand-2 3'-CUUG-5' helix-form AA. 1 A.G2032 A.C2043 G-C WC 19-XIX cWW cW-W 2 A.A2033 A.U2042 A-U WC 20-XX cWW cW-W 3 A.A2034 A.U2041 A-U WC 20-XX cWW cW-W 4 A.U2035 A.G2040 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#22[#19] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A2045 A.U2095 A-U WC 20-XX cWW cW-W 2 A.C2046 A.G2094 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#23[#19] bps=7 strand-1 5'-UUAAAUU-3' bp-type ||||||| strand-2 3'-AAUUUAA-5' helix-form AAAAAA 1 A.U2048 A.A2091 U-A WC 20-XX cWW cW-W 2 A.U2049 A.A2090 U-A WC 20-XX cWW cW-W 3 A.A2050 A.U2089 A-U WC 20-XX cWW cW-W 4 A.A2051 A.U2088 A-U WC 20-XX cWW cW-W 5 A.A2052 A.U2087 A-U WC 20-XX cWW cW-W 6 A.U2053 A.A2086 U-A WC 20-XX cWW cW-W 7 A.U2054 A.A2085 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#24[#20] bps=3 strand-1 5'-UGC-3' bp-type ||| strand-2 3'-AUG-5' helix-form .. 1 A.U2055 A.A2084 U-A WC 20-XX cWW cW-W 2 A.G2056 A.U2083 G-U Wobble 28-XXVIII cWW cW-W 3 A.C2057 A.G2082 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#25[#20] bps=2 strand-1 5'-GA-3' bp-type || strand-2 3'-CU-5' helix-form A 1 A.G2063 A.C2076 G-C WC 19-XIX cWW cW-W 2 A.A2064 A.U2075 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#26[#18] bps=10 strand-1 5'-GUCCAAAGAG-3' bp-type |||||||||| strand-2 3'-CAGGUUUCUC-5' helix-form AAAAAA.A. 1 A.G2098 A.C2123 G-C WC 19-XIX cWW cW-W 2 A.U2099 A.A2122 U-A WC 20-XX cWW cW-W 3 A.C2100 A.G2121 C-G WC 19-XIX cWW cW-W 4 A.C2101 A.G2120 C-G WC 19-XIX cWW cW-W 5 A.A2102 A.U2119 A-U WC 20-XX cWW cW-W 6 A.A2103 A.U2118 A-U WC 20-XX cWW cW-W 7 A.A2104 A.U2117 A-U WC 20-XX cWW cW-W 8 A.G2105 A.C2116 G-C WC 19-XIX cWW cW-W 9 A.A2106 A.U2115 A-U WC 20-XX cWW cW-W 10 A.G2107 A.C2114 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#27[#21] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form AA 1 A.A2127 A.U2138 A-U WC 20-XX cWW cW-W 2 A.G2128 A.C2137 G-C WC 19-XIX cWW cW-W 3 A.G2129 A.C2136 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#28[#22] bps=3 strand-1 5'-GAG-3' bp-type ||| strand-2 3'-CUC-5' helix-form A. 1 A.G2143 A.C2257 G-C WC 19-XIX cWW cW-W 2 A.A2144 A.U2256 A-U WC 20-XX cWW cW-W 3 A.G2145 A.C2255 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#29[#22] bps=3 strand-1 5'-GAG-3' bp-type ||| strand-2 3'-CUC-5' helix-form AA 1 A.G2147 A.C2254 G-C WC 19-XIX cWW cW-W 2 A.A2148 A.U2253 A-U WC 20-XX cWW cW-W 3 A.G2149 A.C2252 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#30[#23] bps=5 strand-1 5'-UCUAU-3' bp-type ||||| strand-2 3'-AGAUA-5' helix-form .AAA 1 A.U2275 A.A2290 U-A WC 20-XX cWW cW-W 2 A.C2276 A.G2289 C-G WC 19-XIX cWW cW-W 3 A.U2277 A.A2288 U-A WC 20-XX cWW cW-W 4 A.A2278 A.U2287 A-U WC 20-XX cWW cW-W 5 A.U2279 A.A2286 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#31[#25] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A2313 A.U2674 A-U WC 20-XX cWW cW-W 2 A.C2314 A.G2673 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#32[#26] bps=3 strand-1 5'-GAA-3' bp-type ||| strand-2 3'-CUU-5' helix-form AA 1 A.G2317 A.C2326 G-C WC 19-XIX cWW cW-W 2 A.A2318 A.U2325 A-U WC 20-XX cWW cW-W 3 A.A2319 A.U2324 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#33[#26] bps=4 strand-1 5'-UCCU-3' bp-type |||| strand-2 3'-AGGA-5' helix-form A.A 1 A.U2327 A.A2450 U-A WC 20-XX cWW cW-W 2 A.C2328 A.G2449 C-G WC 19-XIX cWW cW-W 3 A.C2329 A.G2448 C-G WC 19-XIX cWW cW-W 4 A.U2330 A.A2447 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#34[#27] bps=4 strand-1 5'-GCAU-3' bp-type |||| strand-2 3'-CGUA-5' helix-form AAA 1 A.G2333 A.C2441 G-C WC 19-XIX cWW cW-W 2 A.C2334 A.G2440 C-G WC 19-XIX cWW cW-W 3 A.A2335 A.U2439 A-U WC 20-XX cWW cW-W 4 A.U2336 A.A2438 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#35[#29] bps=5 strand-1 5'-GUCAG-3' bp-type ||||| strand-2 3'-CAGUC-5' helix-form AAA. 1 A.G2345 A.C2368 G-C WC 19-XIX cWW cW-W 2 A.U2346 A.A2367 U-A WC 20-XX cWW cW-W 3 A.C2347 A.G2366 C-G WC 19-XIX cWW cW-W 4 A.A2348 A.U2365 A-U WC 20-XX cWW cW-W 5 A.G2349 A.C2364 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#36[#30] bps=3 strand-1 5'-CAG-3' bp-type ||| strand-2 3'-GUC-5' helix-form AA 1 A.C2375 A.G2421 C-G WC 19-XIX cWW cW-W 2 A.A2376 A.U2420 A-U WC 20-XX cWW cW-W 3 A.G2377 A.C2419 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#37[#31] bps=4 strand-1 5'-AAUA-3' bp-type |||| strand-2 3'-UUAU-5' helix-form .A. 1 A.A2381 A.U2411 A-U WC 20-XX cWW cW-W 2 A.A2382 A.U2410 A-U WC 20-XX cWW cW-W 3 A.U2383 A.A2409 U-A WC 20-XX cWW cW-W 4 A.A2384 A.U2408 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#38[#32] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C2427 A.G2436 C-G WC 19-XIX cWW cW-W 2 A.C2428 A.G2435 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#39[#25] bps=4 strand-1 5'-GGUU-3' bp-type |||| strand-2 3'-CCAA-5' helix-form AA. 1 A.G2453 A.C2671 G-C WC 19-XIX cWW cW-W 2 A.G2454 A.C2670 G-C WC 19-XIX cWW cW-W 3 A.U2455 A.A2669 U-A WC 20-XX cWW cW-W 4 A.U2456 A.A2668 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#40[#25] bps=7 strand-1 5'-AAAGUAA-3' bp-type ||||||| strand-2 3'-UUUCAUU-5' helix-form AAAAAA 1 A.A2461 A.U2666 A-U WC 20-XX cWW cW-W 2 A.A2462 A.U2665 A-U WC 20-XX cWW cW-W 3 A.A2463 A.U2664 A-U WC 20-XX cWW cW-W 4 A.G2464 A.C2663 G-C WC 19-XIX cWW cW-W 5 A.U2465 A.A2662 U-A WC 20-XX cWW cW-W 6 A.A2466 A.U2661 A-U WC 20-XX cWW cW-W 7 A.A2467 A.U2660 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#41[#33] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form A 1 A.A2469 A.U2658 A-U WC 20-XX cWW cW-W 2 A.G2470 A.C2657 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#42[#33] bps=4 strand-1 5'-ACCC-3' bp-type |||| strand-2 3'-UGGG-5' helix-form AAA 1 A.A2487 A.U2648 A-U WC 20-XX cWW cW-W 2 A.C2488 A.G2647 C-G WC 19-XIX cWW cW-W 3 A.C2489 A.G2646 C-G WC 19-XIX cWW cW-W 4 A.C2490 A.G2645 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#43[#33] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form A 1 A.C2491 A.G2643 C-G WC 19-XIX cWW cW-W 2 A.G2492 A.C2642 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#44[#16] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form A 1 A.G2496 A.C2508 G-C WC 19-XIX cWW cW-W 2 A.U2497 A.A2507 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#45[#34] bps=6 strand-1 5'-CCUCUA-3' bp-type |||||| strand-2 3'-GGAGAU-5' helix-form AAAAA 1 A.C2513 A.G2537 C-G WC 19-XIX cWW cW-W 2 A.C2514 A.G2536 C-G WC 19-XIX cWW cW-W 3 A.U2515 A.A2535 U-A WC 20-XX cWW cW-W 4 A.C2516 A.G2534 C-G WC 19-XIX cWW cW-W 5 A.U2517 A.A2533 U-A WC 20-XX cWW cW-W 6 A.A2518 A.U2532 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#46[#36] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C2611 A.G2621 C-G WC 19-XIX cWW cW-W 2 A.C2612 A.G2620 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#47[#7] bps=5 strand-1 5'-GCCCG-3' bp-type ||||| strand-2 3'-CGGGC-5' helix-form AAAA 1 A.G2686 A.C2703 G-C WC 19-XIX cWW cW-W 2 A.C2687 A.G2702 C-G WC 19-XIX cWW cW-W 3 A.C2688 A.G2701 C-G WC 19-XIX cWW cW-W 4 A.C2689 A.G2700 C-G WC 19-XIX cWW cW-W 5 A.G2690 A.C2699 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#48[#37] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form . 1 A.A2711 A.U3107 A-U WC 20-XX cWW cW-W 2 A.G2712 A.C3106 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#49[#37] bps=3 strand-1 5'-AGA-3' bp-type ||| strand-2 3'-UCU-5' helix-form AA 1 A.A2715 A.U3104 A-U WC 20-XX cWW cW-W 2 A.G2716 A.C3103 G-C WC 19-XIX cWW cW-W 3 A.A2717 A.U3102 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#50[#38] bps=2 strand-1 5'-GA-3' bp-type || strand-2 3'-CU-5' helix-form . 1 A.G2719 A.C3099 G-C WC 19-XIX cWW cW-W 2 A.A2720 A.U3098 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#51[#39] bps=5 strand-1 5'-CCCUA-3' bp-type ||||| strand-2 3'-GGGAU-5' helix-form AA.A 1 A.C2726 A.G2934 C-G WC 19-XIX cWW cW-W 2 A.C2727 A.G2933 C-G WC 19-XIX cWW cW-W 3 A.C2728 A.G2932 C-G WC 19-XIX cWW cW-W 4 A.U2729 A.A2931 U-A WC 20-XX cWW cW-W 5 A.A2730 A.U2930 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#52[#39] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 A.G2732 A.C2929 G-C WC 19-XIX cWW cW-W 2 A.G2733 A.C2928 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#53[#39] bps=4 strand-1 5'-AGCU-3' bp-type |||| strand-2 3'-UUGA-5' helix-form ..A 1 A.A2734 A.U2925 A-U WC 20-XX cWW cW-W 2 A.G2735 A.U2924 G-U Wobble 28-XXVIII cWW cW-W 3 A.C2736 A.G2923 C-G WC 19-XIX cWW cW-W 4 A.U2737 A.A2922 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#54[#39] bps=5 strand-1 5'-AAUUU-3' bp-type ||||| strand-2 3'-UUAAA-5' helix-form AAAA 1 A.A2740 A.U2807 A-U WC 20-XX cWW cW-W 2 A.A2741 A.U2806 A-U WC 20-XX cWW cW-W 3 A.U2742 A.A2805 U-A WC 20-XX cWW cW-W 4 A.U2743 A.A2804 U-A WC 20-XX cWW cW-W 5 A.U2744 A.A2803 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#55[#39] bps=7 strand-1 5'-UAAUGCA-3' bp-type ||||||| strand-2 3'-AUUACGU-5' helix-form AAAAAA 1 A.U2747 A.A2801 U-A WC 20-XX cWW cW-W 2 A.A2748 A.U2800 A-U WC 20-XX cWW cW-W 3 A.A2749 A.U2799 A-U WC 20-XX cWW cW-W 4 A.U2750 A.A2798 U-A WC 20-XX cWW cW-W 5 A.G2751 A.C2797 G-C WC 19-XIX cWW cW-W 6 A.C2752 A.G2796 C-G WC 19-XIX cWW cW-W 7 A.A2753 A.U2795 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#56[#40] bps=3 strand-1 5'-GGU-3' bp-type ||| strand-2 3'-CCA-5' helix-form .A 1 A.G2810 A.C2822 G-C WC 19-XIX cWW cW-W 2 A.G2811 A.C2821 G-C WC 19-XIX cWW cW-W 3 A.U2812 A.A2820 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#57[#41] bps=6 strand-1 5'-UCGGAG-3' bp-type |||||| strand-2 3'-AGCCUC-5' helix-form A.... 1 A.U2823 A.A2845 U-A WC 20-XX cWW cW-W 2 A.C2824 A.G2844 C-G WC 19-XIX cWW cW-W 3 A.G2825 A.C2843 G-C WC 19-XIX cWW cW-W 4 A.G2826 A.C2842 G-C WC 19-XIX cWW cW-W 5 A.A2827 A.U2841 A-U WC 20-XX cWW cW-W 6 A.G2828 A.C2840 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#58[#42] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G2855 A.C2877 G-C WC 19-XIX cWW cW-W 2 A.C2856 A.G2876 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#59[#42] bps=3 strand-1 5'-GAC-3' bp-type ||| strand-2 3'-CUG-5' helix-form .A 1 A.G2860 A.C2872 G-C WC 19-XIX cWW cW-W 2 A.A2861 A.U2871 A-U WC 20-XX cWW cW-W 3 A.C2862 A.G2870 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#60[#44] bps=6 strand-1 5'-CCUAUU-3' bp-type |||||| strand-2 3'-GGAUAA-5' helix-form AAA.A 1 A.C2948 A.G2976 C-G WC 19-XIX cWW cW-W 2 A.C2949 A.G2975 C-G WC 19-XIX cWW cW-W 3 A.U2950 A.A2974 U-A WC 20-XX cWW cW-W 4 A.A2951 A.U2973 A-U WC 20-XX cWW cW-W 5 A.U2952 A.A2972 U-A WC 20-XX cWW cW-W 6 A.U2953 A.A2971 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#61[#45] bps=2 strand-1 5'-GA-3' bp-type || strand-2 3'-CU-5' helix-form A 1 A.G2957 A.C2967 G-C WC 19-XIX cWW cW-W 2 A.A2958 A.U2966 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#62[#46] bps=4 strand-1 5'-UGGA-3' bp-type |||| strand-2 3'-GUCU-5' helix-form ..A 1 A.U2994 A.G3068 U-G Wobble 28-XXVIII cWW cW-W 2 A.G2995 A.U3067 G-U Wobble 28-XXVIII cWW cW-W 3 A.G2996 A.C3066 G-C WC 19-XIX cWW cW-W 4 A.A2997 A.U3065 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#63[#46] bps=5 strand-1 5'-AGGAC-3' bp-type ||||| strand-2 3'-UCCUG-5' helix-form .AAA 1 A.A3000 A.U3058 A-U WC 20-XX cWW cW-W 2 A.G3001 A.C3057 G-C WC 19-XIX cWW cW-W 3 A.G3002 A.C3056 G-C WC 19-XIX cWW cW-W 4 A.A3003 A.U3055 A-U WC 20-XX cWW cW-W 5 A.C3004 A.G3054 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#64[#46] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C3007 A.G3032 C-G WC 19-XIX cWW cW-W 2 A.C3008 A.G3031 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#65[#46] bps=3 strand-1 5'-GAU-3' bp-type ||| strand-2 3'-UUA-5' helix-form .A 1 A.G3010 A.U3027 G-U Wobble 28-XXVIII cWW cW-W 2 A.A3011 A.U3026 A-U WC 20-XX cWW cW-W 3 A.U3012 A.A3025 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#66[#46] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G3014 A.C3023 G-C WC 19-XIX cWW cW-W 2 A.U3015 A.G3022 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#67[#47] bps=5 strand-1 5'-UCGUU-3' bp-type ||||| strand-2 3'-AGCAA-5' helix-form A... 1 A.U3034 A.A3048 U-A WC 20-XX cWW cW-W 2 A.C3035 A.G3047 C-G WC 19-XIX cWW cW-W 3 A.G3036 A.C3046 G-C WC 19-XIX cWW cW-W 4 A.U3037 A.A3045 U-A WC 20-XX cWW cW-W 5 A.U3038 A.A3044 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#68[#48] bps=4 strand-1 5'-GACC-3' bp-type |||| strand-2 3'-CUGG-5' helix-form AAA 1 A.G3075 A.C3093 G-C WC 19-XIX cWW cW-W 2 A.A3076 A.U3092 A-U WC 20-XX cWW cW-W 3 A.C3077 A.G3091 C-G WC 19-XIX cWW cW-W 4 A.C3078 A.G3090 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#69[#48] bps=3 strand-1 5'-GGA-3' bp-type ||| strand-2 3'-CCU-5' helix-form .A 1 A.G3079 A.C3088 G-C WC 19-XIX cWW cW-W 2 A.G3080 A.C3087 G-C WC 19-XIX cWW cW-W 3 A.A3081 A.U3086 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#70[#50] bps=3 strand-1 5'-AUU-3' bp-type ||| strand-2 3'-UAA-5' helix-form .A 1 A.A3113 A.U3143 A-U WC 20-XX cWW cW-W 2 A.U3114 A.A3142 U-A WC 20-XX cWW cW-W 3 A.U3115 A.A3141 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#71[#50] bps=3 strand-1 5'-CUC-3' bp-type ||| strand-2 3'-GAG-5' helix-form AA 1 A.C3117 A.G3139 C-G WC 19-XIX cWW cW-W 2 A.U3118 A.A3138 U-A WC 20-XX cWW cW-W 3 A.C3119 A.G3137 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#72[#50] bps=5 strand-1 5'-AAGGC-3' bp-type ||||| strand-2 3'-UUCCG-5' helix-form AA.. 1 A.A3144 A.U3167 A-U WC 20-XX cWW cW-W 2 A.A3145 A.U3166 A-U WC 20-XX cWW cW-W 3 A.G3146 A.C3165 G-C WC 19-XIX cWW cW-W 4 A.G3147 A.C3164 G-C WC 19-XIX cWW cW-W 5 A.C3148 A.G3163 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#73[#50] bps=3 strand-1 5'-CUU-3' bp-type ||| strand-2 3'-GAA-5' helix-form .. 1 A.C3152 A.G3161 C-G WC 19-XIX cWW cW-W 2 A.U3153 A.A3160 U-A WC 20-XX cWW cW-W 3 A.U3154 A.A3159 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#74[#51] bps=3 strand-1 5'-UAA-3' bp-type ||| strand-2 3'-AUU-5' helix-form .. 1 A.U3174 A.A3195 U-A WC 20-XX cWW cW-W 2 A.A3175 A.U3194 A-U WC 20-XX cWW cW-W 3 A.A3176 A.U3193 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#75[#52] bps=4 strand-1 5'-ACCC-3' bp-type |||| strand-2 3'-UGGG-5' helix-form AAA 1 A.A3213 A.U3227 A-U WC 20-XX cWW cW-W 2 A.C3214 A.G3226 C-G WC 19-XIX cWW cW-W 3 A.C3215 A.G3225 C-G WC 19-XIX cWW cW-W 4 A.C3216 A.G3224 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#76[#54] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-CGA-5' helix-form .. 1 B.G1611 B.C1624 G-C WC 19-XIX cWW cW-W 2 B.C1612 B.G1623 C-G WC 19-XIX cWW cW-W 3 B.U1613 B.A1622 U-A WC 20-XX cWW cW-W **************************************************************************** List of 30 isolated WC/wobble pairs Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#2] -1 A.C1678 A.G1797 C-G WC 19-XIX cWW cW-W [#4] -2 A.A1722 A.U1729 A-U WC 20-XX cWW cW-W [#4] -3 A.C1726 A.G1748 C-G WC 19-XIX cWW cW-W [#5] -4 A.A1739 A.U1758 A-U WC 20-XX cWW cW-W [#9] -5 A.C1827 A.G2681 C-G WC 19-XIX cWW cW-W [#7] -6 A.U1843 A.A2696 U-A WC 20-XX cWW cW-W [#9] -7 A.C1845 A.G1858 C-G WC 19-XIX cWW cW-W [#10] -8 A.G1906 A.C2016 G-C WC 19-XIX cWW cW-W [#10] -9 A.C1915 A.G2004 C-G WC 19-XIX cWW cW-W [#13] -10 A.C1930 A.G1973 C-G WC 19-XIX cWW cW-W [#14] -11 A.A1937 A.U2392 A-U WC 20-XX cWW cW-W [#16] -12 A.G1939 A.C2494 G-C WC 19-XIX cWW cW-W -- -13 A.A1962 A.U3096 A-U WC 20-XX cWW cW-W [#17] -14 A.G1985 A.C2001 G-C WC 19-XIX cWW cW-W [#22] -15 A.A2153 A.U2248 A-U WC 20-XX cWW cW-W [#24] -16 A.A2306 A.U2680 A-U WC 20-XX cWW cW-W [#28] -17 A.G2343 A.C2423 G-C WC 19-XIX cWW cW-W [#14] -18 A.C2400 A.G2403 C-G WC 19-XIX cWW cW-W [#33] -19 A.A2473 A.U2656 A-U WC 20-XX cWW cW-W [#33] -20 A.G2478 A.C2653 G-C WC 19-XIX cWW cW-W [#33] -21 A.G2542 A.C2637 G-C WC 19-XIX cWW cW-W [#9] -22 A.C2683 A.G2697 C-G WC 19-XIX cWW cW-W [#41] -23 A.G2846 A.C2915 G-C WC 19-XIX cWW cW-W -- -24 A.C2867 A.G2916 C-G WC 19-XIX cWW cW-W [#46] -25 A.C2999 A.G3061 C-G WC 19-XIX cWW cW-W [#49] -26 A.C3126 A.G3131 C-G WC 19-XIX cWW cW-W [#53] -27 B.G1606 B.C1665 G-C WC 19-XIX cWW cW-W [#55] -28 B.C1627 B.G1641 C-G WC 19-XIX cWW cW-W [#56] -29 B.C1649 B.G1660 C-G WC 19-XIX cWW cW-W [#56] -30 B.A1651 B.U1658 A-U WC 20-XX cWW cW-W **************************************************************************** List of 18 coaxial stacks 1 Helix#2 contains 2 stems: [#2,#3] 2 Helix#10 contains 2 stems: [#12,#13] 3 Helix#11 contains 2 stems: [#9,#10] 4 Helix#13 contains 2 stems: [#14,#15] 5 Helix#15 contains 3 stems: [#16,#17,#18] 6 Helix#19 contains 3 stems: [#21,#22,#23] 7 Helix#20 contains 2 stems: [#24,#25] 8 Helix#22 contains 2 stems: [#28,#29] 9 Helix#23 contains 2 stems: [#20,#30] 10 Helix#25 contains 3 stems: [#31,#39,#40] 11 Helix#26 contains 2 stems: [#32,#33] 12 Helix#33 contains 3 stems: [#41,#42,#43] 13 Helix#37 contains 2 stems: [#48,#49] 14 Helix#39 contains 5 stems: [#51,#52,#53,#54,#55] 15 Helix#42 contains 2 stems: [#58,#59] 16 Helix#46 contains 5 stems: [#62,#63,#64,#65,#66] 17 Helix#48 contains 2 stems: [#68,#69] 18 Helix#50 contains 4 stems: [#71,#70,#72,#73] **************************************************************************** List of 302 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 HC D.HIS87,A.C2523 2 nts=2 QA D.GLN205,A.A2521 3 nts=2 WA D.TRP265,A.A2401 4 nts=2 RU E.ARG156,A.U3227 5 nts=2 RC F.ARG108,A.C1769 6 nts=2 HC K.HIS80,A.C2234 7 nts=2 YU K.TYR83,A.U3109 8 nts=2 RC M.ARG59,A.C2016 9 nts=2 QG M.GLN71,A.G2916 10 nts=2 RC Q.ARG84,A.C3157 11 nts=2 YA R.TYR58,A.A2251 12 nts=2 RC S.ARG173,A.C2262 13 nts=2 YU U.TYR96,A.U2372 14 nts=2 RG Z.ARG76,A.G2140 15 nts=2 RA 2.ARG49,A.A2500 16 nts=2 DA 3.ASP182,A.A1892 17 nts=2 YU 5.TYR31,A.U2522 18 nts=2 FC 5.PHE87,A.C1707 19 nts=2 FU 9.PHE30,A.U1701 20 nts=2 HA a.HIS102,A.A3209 21 nts=2 EC a.GLU104,A.C3208 22 nts=2 HU a.HIS121,A.U1824 23 nts=2 YA f.TYR48,A.A2064 24 nts=2 HG i.HIS69,A.G1886 25 nts=2 YG i.TYR116,A.G2011 26 nts=2 FU o.PHE71,A.U2055 27 nts=2 WC r.TRP154,A.C3189 28 nts=2 WA r.TRP192,A.A2241 29 nts=2 WA s.TRP66,A.A2446 30 nts=2 FA s.PHE98,A.A2374 31 nts=2 CU A.C1678,A.U1679 32 nts=2 UU A.U1700,A.U1704 33 nts=2 AC A.A1713,A.C1714 34 nts=2 AG A.A1724,A.G2015 35 nts=2 UU A.U1728,A.U1729 36 nts=2 GG A.G1768,A.G1770 37 nts=2 CA A.C1771,A.A1772 38 nts=2 AG A.A1775,A.G1776 39 nts=2 AA A.A1777,A.A1779 40 nts=2 AU A.A1781,A.U1783 41 nts=2 GG A.G1787,A.G1791 42 nts=2 AG A.A1825,A.G1826 43 nts=2 UA A.U1834,A.A1835 44 nts=2 UA A.U1841,A.A1842 45 nts=2 AU A.A1856,A.U1857 46 nts=2 AA A.A1867,A.A2298 47 nts=2 GC A.G1868,A.C1903 48 nts=2 GU A.G1879,A.U1896 49 nts=2 AA A.A1882,A.A1893 50 nts=2 GA A.G1883,A.A1891 51 nts=2 GA A.G1884,A.A1885 52 nts=2 AA A.A1925,A.A1926 53 nts=2 AC A.A1929,A.C1930 54 nts=2 AA A.A1938,A.A1940 55 nts=2 CG A.C1948,A.G1949 56 nts=2 UC A.U1950,A.C1951 57 nts=2 CA A.C1959,A.A2434 58 nts=2 AA A.A1961,A.A1999 59 nts=2 GU A.G1966,A.U1967 60 nts=2 GG A.G1985,A.G1987 61 nts=2 AA A.A1986,A.A2003 62 nts=2 GU A.G2009,A.U2010 63 nts=2 GU A.G2019,A.U2020 64 nts=2 UG A.U2030,A.G2098 65 nts=2 AC A.A2031,A.C2865 66 nts=2 UU A.U2035,A.U2037 67 nts=2 CC A.C2076,A.C2077 68 nts=2 AC A.A2091,A.C2092 69 nts=2 UG A.U2093,A.G2094 70 nts=2 GG A.G2107,A.G2108 71 nts=2 AA A.A2109,A.A2110 72 nts=2 UA A.U2126,A.A2127 73 nts=2 AA A.A2134,A.A2135 74 nts=2 UU A.U2138,A.U2139 75 nts=2 UA A.U2141,A.A2142 76 nts=2 GG A.G2145,A.G2147 77 nts=2 CC A.C2235,A.C2236 78 nts=2 CC A.C2254,A.C2255 79 nts=2 CC A.C2271,A.C2272 80 nts=2 UA A.U2285,A.A2286 81 nts=2 UA A.U2296,A.A2297 82 nts=2 CA A.C2314,A.A2315 83 nts=2 GA A.G2317,A.A2450 84 nts=2 GU A.G2333,A.U2442 85 nts=2 UC A.U2342,A.C2423 86 nts=2 CA A.C2344,A.A2425 87 nts=2 GC A.G2377,A.C2378 88 nts=2 GU A.G2421,A.U2422 89 nts=2 GC A.G2436,A.C2437 90 nts=2 AA A.A2451,A.A2452 91 nts=2 CU A.C2474,A.U2475 92 nts=2 CG A.C2476,A.G2477 93 nts=2 UU A.U2485,A.U2486 94 nts=2 CC A.C2490,A.C2491 95 nts=2 CC A.C2493,A.C2540 96 nts=2 AA A.A2505,A.A2507 97 nts=2 GC A.G2542,A.C2543 98 nts=2 CU A.C2544,A.U2545 99 nts=2 AA A.A2615,A.A2616 100 nts=2 UC A.U2638,A.C2639 101 nts=2 GG A.G2643,A.G2645 102 nts=2 UC A.U2658,A.C2659 103 nts=2 GA A.G2719,A.A3064 104 nts=2 AG A.A2730,A.G2732 105 nts=2 GA A.G2733,A.A2734 106 nts=2 UU A.U2737,A.U2738 107 nts=2 AA A.A2740,A.A2922 108 nts=2 GA A.G2810,A.A2914 109 nts=2 UU A.U2812,A.U2813 110 nts=2 UC A.U2823,A.C2915 111 nts=2 CU A.C2862,A.U2863 112 nts=2 CC A.C2899,A.C2900 113 nts=2 CU A.C2929,A.U2930 114 nts=2 CU A.C2954,A.U2955 115 nts=2 AU A.A2963,A.U2964 116 nts=2 AG A.A2965,A.G3016 117 nts=2 CA A.C2967,A.A2968 118 nts=2 CG A.C3007,A.G3054 119 nts=2 CC A.C3008,A.C3009 120 nts=2 UC A.U3015,A.C3017 121 nts=2 CC A.C3020,A.C3021 122 nts=2 CU A.C3023,A.U3024 123 nts=2 AG A.A3030,A.G3031 124 nts=2 GU A.G3032,A.U3033 125 nts=2 CA A.C3043,A.A3044 126 nts=2 GG A.G3079,A.G3090 127 nts=2 AG A.A3081,A.G3082 128 nts=2 AA A.A3113,A.A3144 129 nts=2 CC A.C3148,A.C3149 130 nts=2 AA A.A3158,A.A3159 131 nts=2 GG A.G3161,A.G3163 132 nts=2 CR A.C3187,4.ARG84 133 nts=2 CU A.C3192,A.U3193 134 nts=2 CC A.C3205,A.C3206 135 nts=2 CC A.C3210,A.C3211 136 nts=2 CA A.C3212,A.A3213 137 nts=2 GU B.G1606,B.U1607 138 nts=2 AC B.A1625,B.C1626 139 nts=2 AC B.A1630,B.C1631 140 nts=2 CU B.C1637,B.U1638 141 nts=2 UC B.U1666,B.C1667 142 nts=3 HAR E.HIS292,A.A3217,Q.ARG86 143 nts=3 RAU O.ARG17,A.A2457,A.U2456 144 nts=3 RCA R.ARG32,A.C2684,A.A1828 145 nts=3 FUW R.PHE128,A.U2244,S.TRP61 146 nts=3 RCA S.ARG184,A.C2261,A.A2260 147 nts=3 WAC 2.TRP66,A.A1702,A.C1703 148 nts=3 FAC 5.PHE66,A.A1712,A.C1711 149 nts=3 QCA 5.GLN305,A.C2389,A.A2388 150 nts=3 RAC 6.ARG52,B.A1636,B.C1635 151 nts=3 WCC 9.TRP48,A.C2379,A.C2380 152 nts=3 FAC 9.PHE50,A.A2418,A.C2419 153 nts=3 YAG g.TYR97,A.A1881,A.G1894 154 nts=3 YAC i.TYR118,A.A1731,A.C1732 155 nts=3 RAA r.ARG168,A.A2131,A.A2132 156 nts=3 FAC s.PHE274,A.A2373,A.C2375 157 nts=3 CCC A.C1689,A.C1690,A.C1691 158 nts=3 GGA A.G1742,A.G1754,A.A1753 159 nts=3 AGC A.A1746,A.G1747,A.C1749 160 nts=3 AAG A.A1814,A.A1815,A.G1816 161 nts=3 AUA A.A1821,A.U1822,A.A1823 162 nts=3 CGG A.C1827,A.G2698,A.G2697 163 nts=3 GAC A.G1831,A.A1832,A.C1833 164 nts=3 ACC A.A1836,A.C1837,A.C1838 165 nts=3 AAC A.A1853,A.A2696,A.C2699 166 nts=3 GAC A.G1899,A.A1900,A.C1901 167 nts=3 GAC A.G1913,A.A1914,A.C1915 168 nts=3 GAU A.G1927,A.A1978,A.U1979 169 nts=3 UAA A.U1934,A.A1935,A.A1936 170 nts=3 GUG A.G1939,A.U2495,A.G2496 171 nts=3 UGU A.U1954,A.G1955,A.U1956 172 nts=3 GAA A.G1958,A.A1960,A.A1963 173 nts=3 AGU A.A1972,A.G1973,A.U1975 174 nts=3 AAC A.A1993,A.A1995,A.C1996 175 nts=3 GAA A.G2032,A.A2044,A.A2045 176 nts=3 CCC A.C2058,A.C2059,A.C2078 177 nts=3 AAG A.A2073,A.A2072,A.G2831 178 nts=3 UAA A.U2075,A.A2074,A.A2832 179 nts=3 GAA A.G2129,A.A2130,A.A2133 180 nts=3 GAC A.G2143,A.A2258,A.C2259 181 nts=3 AGA A.A2232,A.G2231,A.A3005 182 nts=3 AAC A.A2245,A.A2246,A.C2247 183 nts=3 UCA A.U2279,A.C2280,A.A2281 184 nts=3 GGU A.G2310,A.G2675,A.U2674 185 nts=3 AAC A.A2319,A.A2320,A.C2322 186 nts=3 GAC A.G2343,A.A2424,A.C2426 187 nts=3 UAC A.U2351,A.A2350,A.C2364 188 nts=3 GAG A.G2453,A.A2672,A.G2673 189 nts=3 AAC A.A2469,A.A2468,A.C3162 190 nts=3 UUA A.U2497,A.U2498,A.A2504 191 nts=3 CAC A.C2511,A.A2512,A.C2513 192 nts=3 AAG A.A2518,A.A2530,A.G2519 193 nts=3 CUU A.C2612,A.U2613,A.U2614 194 nts=3 AAG A.A2617,A.A2619,A.G2620 195 nts=3 CAC A.C2640,A.A2641,A.C2642 196 nts=3 UUA A.U2666,A.U2667,A.A2668 197 nts=3 GUG A.G2690,A.U2691,A.G2692 198 nts=3 CAU A.C2703,A.A2704,A.U2705 199 nts=3 ACA A.A2709,A.C2710,A.A2711 200 nts=3 AUU A.A2745,A.U2746,A.U2747 201 nts=3 AAA A.A2753,A.A2754,A.A2755 202 nts=3 CCU A.C2793,A.C2794,A.U2795 203 nts=3 AAA A.A2801,A.A2802,A.A2803 204 nts=3 AAC A.A2837,A.A2838,A.C2840 205 nts=3 AGA A.A2845,A.G2846,A.A2913 206 nts=3 UAG A.U2898,A.A2897,A.G2917 207 nts=3 AAC A.A2904,A.A2905,A.C2906 208 nts=3 AUC A.A2946,A.U2947,A.C2948 209 nts=3 GCC A.G2959,A.C2962,A.C2961 210 nts=3 AUC A.A2997,A.U2998,A.C2999 211 nts=3 GGA A.G3014,A.G3013,A.A3025 212 nts=3 UUG A.U3038,A.U3039,A.G3040 213 nts=3 AUU A.A3048,A.U3049,A.U3050 214 nts=3 GGG A.G3075,A.G3094,A.G3095 215 nts=3 UAA A.U3083,A.A3084,A.A3085 216 nts=3 UAC A.U3104,A.A3105,A.C3106 217 nts=3 UCC A.U3115,A.C3116,A.C3117 218 nts=3 GAA A.G3139,A.A3140,A.A3141 219 nts=3 UAC A.U3150,A.A3151,A.C3152 220 nts=3 CAG A.C3216,A.A3218,A.G3219 221 nts=3 AAA B.A1616,B.A1615,B.A1622 222 nts=3 CCA B.C1627,B.C1628,B.A1629 223 nts=4 RAAA M.ARG39,A.A2293,A.A2291,A.A2290 224 nts=4 RACU Q.ARG83,A.A3156,A.C3155,A.U3154 225 nts=4 QAAG U.GLN73,A.A2370,A.A2369,A.G2345 226 nts=4 RACC W.ARG74,A.A2065,A.C2066,A.C2067 227 nts=4 YAAC a.TYR124,A.A2706,A.A2707,A.C2708 228 nts=4 CCAC A.C1695,A.C1696,A.A1697,A.C1698 229 nts=4 AGCC A.A1718,A.G1719,A.C1720,A.C1721 230 nts=4 GGAU A.G1748,A.G1750,A.A1751,A.U1752 231 nts=4 UGGG A.U1778,A.G1782,A.G1793,A.G1792 232 nts=4 UCGA A.U1847,A.C1846,A.G1858,A.A1859 233 nts=4 UGCA A.U1850,A.G1851,A.C1852,A.A1855 234 nts=4 CAAU A.C1910,A.A1909,A.A2012,A.U2013 235 nts=4 CAAG A.C1942,A.A1943,A.A1971,A.G1970 236 nts=4 GCGC A.G1988,A.C1989,A.G1990,A.C1992 237 nts=4 AGCC A.A1994,A.G2002,A.C2927,A.C2928 238 nts=4 AGCC A.A2027,A.G2028,A.C2263,A.C2125 239 nts=4 GUGU A.G2149,A.U2150,A.G2249,A.U2248 240 nts=4 AAAC A.A2237,A.A2238,A.A2239,A.C2240 241 nts=4 AUCU A.A2384,A.U2385,A.C2386,A.U2387 242 nts=4 CCAG A.C2431,A.C2433,A.A2429,A.G2435 243 nts=4 CAUA A.C2443,A.A2444,A.U2445,A.A2447 244 nts=4 UAAC A.U2499,A.A2503,A.A3074,A.C3073 245 nts=4 GCAA A.G2712,A.C2713,A.A2714,A.A3101 246 nts=4 AGAC A.A2723,A.G2724,A.A2725,A.C2726 247 nts=4 GGAA A.G2855,A.G2878,A.A2879,A.A2880 248 nts=4 UAAA A.U3034,A.A3053,A.A3052,A.A3051 249 nts=4 GAGU A.G3068,A.A3069,A.G3070,A.U3071 250 nts=4 UCCG A.U3122,A.C3121,A.C3120,A.G3137 251 nts=4 AUAC A.A3201,A.U3202,A.A3203,A.C3204 252 nts=4 GAGA B.G1604,B.A1603,B.G1669,B.A1670 253 nts=4 AGGA B.A1640,B.G1641,B.G1642,B.A1643 254 nts=4 UGGC B.U1648,B.G1608,B.G1664,B.C1665 255 nts=4 AGAC B.A1650,B.G1660,B.A1661,B.C1663 256 nts=5 RUCUG M.ARG41,A.U2021,A.C2295,A.U1866,A.G2300 257 nts=5 RAUAG a.ARG128,A.A1820,A.U1819,A.A1818,A.G1671 258 nts=5 FAAUY o.PHE26,A.A2155,A.A2156,A.U2157,r.TYR195 259 nts=5 AAACG A.A1688,A.A1687,A.A1686,A.C1685,A.G1767 260 nts=5 GACAC A.G1932,A.A1931,A.C1944,A.A1945,A.C1946 261 nts=5 GAAAU A.G2022,A.A2294,A.A2273,A.A2274,A.U2275 262 nts=5 CAAGU A.C2111,A.A2112,A.A2945,A.G2977,A.U2978 263 nts=5 AACRC A.A2381,A.A2412,A.C2413,s.ARG162,A.C2414 264 nts=5 AUAAG A.A2394,A.U2392,A.A2391,A.A2390,A.G2403 265 nts=5 CUAAC A.C2856,A.U2857,A.A2858,A.A2873,A.C2872 266 nts=5 GAAAG A.G2860,A.A2859,A.A2874,A.A2875,A.G2876 267 nts=5 ACCAG A.A2866,A.C2867,A.C2868,A.A2869,A.G2870 268 nts=5 GAACA A.G2957,A.A2956,A.A2969,A.C2970,A.A2971 269 nts=5 AGUCG A.A3000,A.G3061,A.U3062,A.C3060,A.G3063 270 nts=5 CAUAU A.C3004,A.A3029,A.U3006,A.A3028,A.U3027 271 nts=5 AUAAA A.A3182,A.U3181,A.A3180,A.A3190,A.A3191 272 nts=5 GAAAU B.G1644,B.A1610,B.A1645,B.A1621,B.U1646 273 nts=6 RACCGU D.ARG92,A.A2524,A.C2525,A.C2526,A.G2528,A.U2529 274 nts=6 AUAAAU A.A1737,A.U1738,A.A1739,A.A1740,A.A1741,A.U1743 275 nts=6 UAAAAC A.U1780,A.A1796,A.A1795,A.A1794,A.A1784,A.C1785 276 nts=6 AACUCU A.A1790,A.A1789,A.C1788,A.U1998,A.C1919,A.U1920 277 nts=6 CAGACU A.C1845,A.A1844,A.G2681,A.A2682,A.C2683,A.U2685 278 nts=6 AAUAAU A.A1860,A.A2306,A.U2307,A.A2308,A.A2309,A.U2311 279 nts=6 AAAGUG A.A1908,A.A1907,A.A2014,A.G1906,A.U2017,A.G2018 280 nts=6 AAAGGC A.A1921,A.A1917,A.A1984,A.G1916,A.G2004,A.C2005 281 nts=6 CAAAAU A.C2123,A.A2124,A.A2029,A.A2264,A.A2265,A.U2266 282 nts=6 CCGAAA A.C2341,A.C2340,A.G2339,A.A2338,A.A2337,A.A2438 283 nts=6 GAUCGU A.G2478,A.A2472,A.U2656,A.C2657,A.G2655,A.U2660 284 nts=6 CAUACG A.C2508,A.A2509,A.U2510,A.A2539,A.C2538,A.G2537 285 nts=6 CUAACA A.C2809,A.U2808,A.A2921,A.A1727,A.C2920,A.A2919 286 nts=6 GGGAAA A.G3123,A.G3132,A.G3131,A.A3130,A.A3129,A.A3128 287 nts=7 HCAAAUC E.HIS231,A.C2479,A.A2480,A.A2481,A.A2482,A.U2483,A.C2484 288 nts=7 UAACCAC A.U1730,A.A1722,A.A1723,A.C1726,A.C1725,A.A2918,A.C2036 289 nts=7 ARAAAAC A.A2154,o.ARG30,A.A2153,A.A2152,A.A2151,A.A2250,A.C2252 290 nts=7 AAAAAUU A.A2313,A.A2312,A.A2676,A.A2677,A.A2678,A.U2679,A.U2680 291 nts=7 GGUCGAC A.G2470,A.G2471,A.U2654,A.C2653,A.G2652,A.A2651,A.C2650 292 nts=7 AGCGGGU A.A2820,A.G2819,A.C2818,A.G2817,A.G2814,A.G2815,A.U2980 293 nts=7 GCACCCA A.G2828,A.C2829,A.A2830,A.C2836,A.C2835,A.C2834,A.A2833 294 nts=7 GCAACAA A.G3127,A.C3126,A.A3125,A.A3133,A.C3134,A.A3135,A.A3136 295 nts=7 AAUGUAC A.A3176,A.A3177,A.U3178,A.G3179,A.U3186,A.A3185,A.C3184 296 nts=8 FACAUAAC i.PHE121,A.A1870,A.C1902,A.A1871,A.U1872,A.A1873,A.A1874,A.C1875 297 nts=8 GACACUUG A.G2063,A.A2062,A.C2061,A.A2060,A.C2079,A.U2080,A.U2081,A.G2082 298 nts=8 GCCAGAAU A.G2896,A.C2912,A.C2911,A.A2910,A.G2909,A.A2901,A.A2902,A.U2903 299 nts=9 YACAACCAH D.TYR131,A.A2402,A.C2400,A.A2399,A.A2398,A.C2397,A.C2396,A.A2395,5.HIS385 300 nts=9 AAAAAACAG A.A2461,A.A2460,A.A2459,A.A2458,A.A3220,A.A3221,A.C3222,A.A3223,A.G3224 301 nts=10 WAGUUAAAAU q.TRP50,A.A1761,A.G1760,A.U1759,A.U1758,A.A1757,A.A1756,A.A1755,A.A1744,A.U1745 302 nts=11 CUAAACAGAAG A.C1672,A.U1673,A.A1674,A.A1675,A.A1676,A.C1677,A.A1798,A.G1797,A.A1773,A.A1680,A.G1681 **************************************************************************** Nucleotides not involved in stacking interactions nts=105 CACAUUCUUCUUAGAAAAACCUAUUUUAGCCAUUUAUUUCCUUCUCCAACCACUCCUAUUCUUACCCUUUACUUACUAGUUUACUUUUCUUAAUAUUUUAUAUUU A.C1699,A.A1705,A.C1706,A.A1708,A.U1717,A.U1774,A.C1813,A.U1843,A.U1848,A.C1849,A.U1854,A.U1878,A.A1887,A.G1888,A.A1937,A.A1957,A.A1962,A.A1974,A.A1991,A.C2000,A.C2001,A.U2038,A.A2039,A.U2047,A.U2048,A.U2049,A.U2096,A.A2097,A.G2113,A.C2114,A.C2136,A.A2146,A.U2233,A.U2299,A.U2316,A.A2323,A.U2324,A.U2325,A.U2330,A.C2331,A.C2393,A.U2407,A.U2408,A.C2415,A.U2416,A.C2417,A.C2427,A.A2430,A.A2473,A.C2494,A.C2501,A.A2506,A.C2516,A.U2531,A.C2541,A.C2611,A.U2618,A.A2644,A.U2649,A.U2661,A.C2718,A.U2731,A.U2739,A.A2792,A.C2824,A.C2839,A.C2842,A.U2864,A.U2907,A.U2908,A.A2926,A.C2944,A.U2953,A.U2960,A.A2981,A.C2982,A.U2994,A.A3018,A.G3019,A.U3041,A.U3042,A.U3072,A.A3089,A.C3093,A.U3096,A.U3097,A.U3100,A.U3108,A.C3168,A.U3174,A.U3194,A.A3195,A.A3207,A.U3228,B.A1605,B.U1609,B.U1614,B.U1632,B.U1633,B.A1634,B.U1639,B.A1651,B.U1658,B.U1659,B.U1668 **************************************************************************** List of 66 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.A1789 A.G1787 2.72 2 sugar O4'@A.A1825 A.G1826 3.10 3 sugar O4'@A.A1844 A.C1827 3.44 4 sugar O4'@A.C1827 A.A1828 3.49 5 phosphate OP2@A.A1835 A.C1833 2.96 6 sugar O2'@A.A1853 A.U1843 3.18 7 sugar O4'@A.C1852 A.G1851 3.28 8 other P@A.A1855 A.A1853 3.49 9 sugar O4'@A.G2681 A.A1859 3.13 10 sugar O4'@A.C1903 A.G1868 3.44 11 sugar O2'@A.A1887 A.G1888 2.82 12 sugar O2'@A.C1997 A.A1917 3.26 13 sugar O4'@A.C1946 A.A1945 3.46 14 sugar O4'@A.C2501 A.A1962 3.25 15 sugar O4'@A.A1972 A.G1973 3.17 16 sugar O4'@A.U2497 A.A1991 3.40 17 sugar O4'@A.C1992 A.A1993 2.87 18 sugar O4'@A.A1995 A.A1993 2.87 19 sugar O4'@A.A2012 A.U2010 2.79 20 phosphate OP1@A.U2731 A.G2015 3.36 21 phosphate OP2@A.A2097 A.A2097 2.81 22 phosphate O3'@A.A2109 A.G2108 3.28 23 sugar O2'@A.A2131 A.A2132 2.78 24 sugar O4'@A.U2141 A.A2142 2.94 25 sugar O4'@A.C1846 A.A2297 2.90 26 sugar O4'@A.U2324 A.A2323 3.31 27 sugar O4'@A.U2342 A.G2343 2.80 28 sugar O4'@A.C2423 A.U2371 2.97 29 sugar O4'@A.A2402 A.G2403 3.13 30 phosphate OP2@A.U2416 A.U2416 2.71 31 sugar O4'@A.C2443 A.A2444 2.96 32 sugar O4'@A.A3220 A.A2458 3.19 33 sugar O4'@A.A2472 A.A2473 3.46 34 phosphate OP2@A.G2477 A.U2475 2.96 35 sugar O4'@A.A2530 A.U2532 3.08 36 phosphate OP2@A.A2616 A.U2614 2.87 37 sugar O4'@A.U3037 A.A2616 2.81 38 sugar O4'@A.U1950 A.A2644 3.16 39 sugar O4'@A.G1969 A.A2644 3.30 40 sugar O4'@A.A1860 A.U2680 3.36 41 phosphate O3'@A.C2036 A.U2731 3.48 42 sugar O4'@A.G2817 A.G2816 3.05 43 sugar O4'@A.C2076 A.A2833 3.19 44 sugar O4'@A.U2117 A.A2837 2.76 45 sugar O4'@A.U2903 A.A2902 3.41 46 phosphate OP2@A.A2905 A.U2903 3.02 47 sugar O4'@A.U2823 A.C2915 3.29 48 sugar O4'@A.G2916 A.G2917 3.27 49 sugar O4'@A.A2968 A.C2967 3.23 50 sugar O2'@A.U2980 A.A2981 2.96 51 sugar O4'@A.A3000 A.C2999 3.49 52 sugar O4'@A.G3054 A.C3007 3.48 53 phosphate O3'@A.G3127 A.A3018 3.42 54 sugar O2'@A.G3127 A.A3018 2.80 55 phosphate OP2@A.A3052 A.U3050 2.71 56 sugar O4'@A.G3061 A.U3058 3.19 57 sugar O2'@A.U3071 A.G3070 3.32 58 phosphate OP2@A.A3084 A.G3082 3.23 59 sugar O4'@A.U3086 A.A3085 3.42 60 sugar O4'@A.C2502 A.U3096 3.12 61 sugar O2'@A.A3064 A.C3099 3.37 62 other P@A.A3129 A.G3127 3.42 63 phosphate OP1@A.A3129 A.G3127 2.65 64 sugar O4'@A.A3130 A.A3129 3.05 65 sugar O4'@B.U1607 B.G1606 3.49 66 phosphate OP2@B.A1625 B.A1625 2.91 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 29 hairpin loops 1 hairpin loop: nts=8; [6]; linked by [#-2] summary: [1] 6 [A.1722 A.1729] 1 nts=8 AAACCAUU A.A1722,A.A1723,A.A1724,A.C1725,A.C1726,A.A1727,A.U1728,A.U1729 nts=6 AACCAU A.A1723,A.A1724,A.C1725,A.C1726,A.A1727,A.U1728 2 hairpin loop: nts=7; [5]; linked by [#4] summary: [1] 5 [A.1746 A.1752] 2 nts=7 AGGCGAU A.A1746,A.G1747,A.G1748,A.C1749,A.G1750,A.A1751,A.U1752 nts=5 GGCGA A.G1747,A.G1748,A.C1749,A.G1750,A.A1751 3 hairpin loop: nts=6; [4]; linked by [#5] summary: [1] 4 [A.1786 A.1791] 2 nts=6 CGCAAG A.C1786,A.G1787,A.C1788,A.A1789,A.A1790,A.G1791 nts=4 GCAA A.G1787,A.C1788,A.A1789,A.A1790 4 hairpin loop: nts=9; [7]; linked by [#6] summary: [1] 7 [A.1831 A.1839] 3 nts=9 GACUAACCC A.G1831,A.A1832,A.C1833,A.U1834,A.A1835,A.A1836,A.C1837,A.C1838,A.C1839 nts=7 ACUAACC A.A1832,A.C1833,A.U1834,A.A1835,A.A1836,A.C1837,A.C1838 5 hairpin loop: nts=8; [6]; linked by [#7] summary: [1] 6 [A.1848 A.1855] 2 nts=8 UCUGCAUA A.U1848,A.C1849,A.U1850,A.G1851,A.C1852,A.A1853,A.U1854,A.A1855 nts=6 CUGCAU A.C1849,A.U1850,A.G1851,A.C1852,A.A1853,A.U1854 6 hairpin loop: nts=6; [4]; linked by [#11] summary: [1] 4 [A.1884 A.1889] 2 nts=6 GAGAGC A.G1884,A.A1885,A.G1886,A.A1887,A.G1888,A.C1889 nts=4 AGAG A.A1885,A.G1886,A.A1887,A.G1888 7 hairpin loop: nts=7; [5]; linked by [#16] summary: [1] 5 [A.1934 A.1940] 3 nts=7 UAAAAGA A.U1934,A.A1935,A.A1936,A.A1937,A.A1938,A.G1939,A.A1940 nts=5 AAAAG A.A1935,A.A1936,A.A1937,A.A1938,A.G1939 8 hairpin loop: nts=10; [8]; linked by [#18] summary: [1] 8 [A.1954 A.1963] 4 nts=10 UGUAGCAAAA A.U1954,A.G1955,A.U1956,A.A1957,A.G1958,A.C1959,A.A1960,A.A1961,A.A1962,A.A1963 nts=8 GUAGCAAA A.G1955,A.U1956,A.A1957,A.G1958,A.C1959,A.A1960,A.A1961,A.A1962 9 hairpin loop: nts=9; [7]; linked by [#19] summary: [1] 7 [A.1988 A.1996] 2 nts=9 GCGACAAAC A.G1988,A.C1989,A.G1990,A.A1991,A.C1992,A.A1993,A.A1994,A.A1995,A.C1996 nts=7 CGACAAA A.C1989,A.G1990,A.A1991,A.C1992,A.A1993,A.A1994,A.A1995 10 hairpin loop: nts=6; [4]; linked by [#21] summary: [1] 4 [A.2035 A.2040] 4 nts=6 UCUUAG A.U2035,A.C2036,A.U2037,A.U2038,A.A2039,A.G2040 nts=4 CUUA A.C2036,A.U2037,A.U2038,A.A2039 11 hairpin loop: nts=8; [6]; linked by [#26] summary: [1] 6 [A.2107 A.2114] 10 nts=8 GGAACAGC A.G2107,A.G2108,A.A2109,A.A2110,A.C2111,A.A2112,A.G2113,A.C2114 nts=6 GAACAG A.G2108,A.A2109,A.A2110,A.C2111,A.A2112,A.G2113 12 hairpin loop: nts=8; [6]; linked by [#27] summary: [1] 6 [A.2129 A.2136] 3 nts=8 GAAAAAAC A.G2129,A.A2130,A.A2131,A.A2132,A.A2133,A.A2134,A.A2135,A.C2136 nts=6 AAAAAA A.A2130,A.A2131,A.A2132,A.A2133,A.A2134,A.A2135 13 hairpin loop: nts=6; [4]; linked by [#32] summary: [1] 4 [A.2319 A.2324] 3 nts=6 AAACAU A.A2319,A.A2320,A.A2321,A.C2322,A.A2323,A.U2324 nts=4 AACA A.A2320,A.A2321,A.C2322,A.A2323 14 hairpin loop: nts=4; [2]; linked by [#-18] summary: [1] 2 [A.2400 A.2403] 1 nts=4 CAAG A.C2400,A.A2401,A.A2402,A.G2403 nts=2 AA A.A2401,A.A2402 15 hairpin loop: nts=11; [9]; linked by [#44] summary: [1] 9 [A.2497 A.2507] 2 nts=11 UUUACCAAAAA A.U2497,A.U2498,A.U2499,A.A2500,A.C2501,A.C2502,A.A2503,A.A2504,A.A2505,A.A2506,A.A2507 nts=9 UUACCAAAA A.U2498,A.U2499,A.A2500,A.C2501,A.C2502,A.A2503,A.A2504,A.A2505,A.A2506 16 hairpin loop: nts=15; [13]; linked by [#45] summary: [1] 13 [A.2518 A.2532] 6 nts=15 AGCAUCACCAGUAUU A.A2518,A.G2519,A.C2520,A.A2521,A.U2522,A.C2523,A.A2524,A.C2525,A.C2526,A.A2527,A.G2528,A.U2529,A.A2530,A.U2531,A.U2532 nts=13 GCAUCACCAGUAU A.G2519,A.C2520,A.A2521,A.U2522,A.C2523,A.A2524,A.C2525,A.C2526,A.A2527,A.G2528,A.U2529,A.A2530,A.U2531 17 hairpin loop: nts=9; [7]; linked by [#46] summary: [1] 7 [A.2612 A.2620] 2 nts=9 CUUAAAUAG A.C2612,A.U2613,A.U2614,A.A2615,A.A2616,A.A2617,A.U2618,A.A2619,A.G2620 nts=7 UUAAAUA A.U2613,A.U2614,A.A2615,A.A2616,A.A2617,A.U2618,A.A2619 18 hairpin loop: nts=9; [7]; linked by [#56] summary: [1] 7 [A.2812 A.2820] 3 nts=9 UUGGGGCGA A.U2812,A.U2813,A.G2814,A.G2815,A.G2816,A.G2817,A.C2818,A.G2819,A.A2820 nts=7 UGGGGCG A.U2813,A.G2814,A.G2815,A.G2816,A.G2817,A.C2818,A.G2819 19 hairpin loop: nts=13; [11]; linked by [#57] summary: [1] 11 [A.2828 A.2840] 6 nts=13 GCAGAACCCAACC A.G2828,A.C2829,A.A2830,A.G2831,A.A2832,A.A2833,A.C2834,A.C2835,A.C2836,A.A2837,A.A2838,A.C2839,A.C2840 nts=11 CAGAACCCAAC A.C2829,A.A2830,A.G2831,A.A2832,A.A2833,A.C2834,A.C2835,A.C2836,A.A2837,A.A2838,A.C2839 20 hairpin loop: nts=9; [7]; linked by [#59] summary: [1] 7 [A.2862 A.2870] 3 nts=9 CUUCACCAG A.C2862,A.U2863,A.U2864,A.C2865,A.A2866,A.C2867,A.C2868,A.A2869,A.G2870 nts=7 UUCACCA A.U2863,A.U2864,A.C2865,A.A2866,A.C2867,A.C2868,A.A2869 21 hairpin loop: nts=9; [7]; linked by [#61] summary: [1] 7 [A.2958 A.2966] 2 nts=9 AGUCCAUAU A.A2958,A.G2959,A.U2960,A.C2961,A.C2962,A.A2963,A.U2964,A.A2965,A.U2966 nts=7 GUCCAUA A.G2959,A.U2960,A.C2961,A.C2962,A.A2963,A.U2964,A.A2965 22 hairpin loop: nts=8; [6]; linked by [#66] summary: [1] 6 [A.3015 A.3022] 2 nts=8 UGCAGCCG A.U3015,A.G3016,A.C3017,A.A3018,A.G3019,A.C3020,A.C3021,A.G3022 nts=6 GCAGCC A.G3016,A.C3017,A.A3018,A.G3019,A.C3020,A.C3021 23 hairpin loop: nts=7; [5]; linked by [#67] summary: [1] 5 [A.3038 A.3044] 5 nts=7 UUGUUCA A.U3038,A.U3039,A.G3040,A.U3041,A.U3042,A.C3043,A.A3044 nts=5 UGUUC A.U3039,A.G3040,A.U3041,A.U3042,A.C3043 24 hairpin loop: nts=6; [4]; linked by [#69] summary: [1] 4 [A.3081 A.3086] 3 nts=6 AGUAAU A.A3081,A.G3082,A.U3083,A.A3084,A.A3085,A.U3086 nts=4 GUAA A.G3082,A.U3083,A.A3084,A.A3085 25 hairpin loop: nts=6; [4]; linked by [#-26] summary: [1] 4 [A.3126 A.3131] 1 nts=6 CGAAAG A.C3126,A.G3127,A.A3128,A.A3129,A.A3130,A.G3131 nts=4 GAAA A.G3127,A.A3128,A.A3129,A.A3130 26 hairpin loop: nts=6; [4]; linked by [#73] summary: [1] 4 [A.3154 A.3159] 3 nts=6 UCACAA A.U3154,A.C3155,A.A3156,A.C3157,A.A3158,A.A3159 nts=4 CACA A.C3155,A.A3156,A.C3157,A.A3158 27 hairpin loop: nts=18; [16]; linked by [#74] summary: [1] 16 [A.3176 A.3193] 3 nts=18 AAUGAUAUCAUCUCAACU A.A3176,A.A3177,A.U3178,A.G3179,A.A3180,A.U3181,A.A3182,A.U3183,A.C3184,A.A3185,A.U3186,A.C3187,A.U3188,A.C3189,A.A3190,A.A3191,A.C3192,A.U3193 nts=16 AUGAUAUCAUCUCAAC A.A3177,A.U3178,A.G3179,A.A3180,A.U3181,A.A3182,A.U3183,A.C3184,A.A3185,A.U3186,A.C3187,A.U3188,A.C3189,A.A3190,A.A3191,A.C3192 28 hairpin loop: nts=9; [7]; linked by [#75] summary: [1] 7 [A.3216 A.3224] 4 nts=9 CAAGAACAG A.C3216,A.A3217,A.A3218,A.G3219,A.A3220,A.A3221,A.C3222,A.A3223,A.G3224 nts=7 AAGAACA A.A3217,A.A3218,A.G3219,A.A3220,A.A3221,A.C3222,A.A3223 29 hairpin loop: nts=15; [13]; linked by [#-28] summary: [1] 13 [B.1627 B.1641] 1 nts=15 CCAACUUACACUUAG B.C1627,B.C1628,B.A1629,B.A1630,B.C1631,B.U1632,B.U1633,B.A1634,B.C1635,B.A1636,B.C1637,B.U1638,B.U1639,B.A1640,B.G1641 nts=13 CAACUUACACUUA B.C1628,B.A1629,B.A1630,B.C1631,B.U1632,B.U1633,B.A1634,B.C1635,B.A1636,B.C1637,B.U1638,B.U1639,B.A1640 **************************************************************************** List of 8 bulges 1 bulge: nts=5; [0,1]; linked by [#2,#3] summary: [2] 0 1 [A.1682 A.1770 A.1683 A.1768] 2 2 nts=5 CCGCG A.C1682,A.C1683,A.G1768,A.C1769,A.G1770 nts=0 nts=1 C A.C1769 2 bulge: nts=5; [0,1]; linked by [#15,#-10] summary: [2] 0 1 [A.1929 A.1975 A.1930 A.1973] 3 1 nts=5 ACGAU A.A1929,A.C1930,A.G1973,A.A1974,A.U1975 nts=0 nts=1 A A.A1974 3 bulge: nts=5; [1,0]; linked by [#28,#29] summary: [2] 1 0 [A.2145 A.2255 A.2147 A.2254] 3 3 nts=5 GAGCC A.G2145,A.A2146,A.G2147,A.C2254,A.C2255 nts=1 A A.A2146 nts=0 4 bulge: nts=5; [0,1]; linked by [#42,#43] summary: [2] 0 1 [A.2490 A.2645 A.2491 A.2643] 4 2 nts=5 CCGAG A.C2490,A.C2491,A.G2643,A.A2644,A.G2645 nts=0 nts=1 A A.A2644 5 bulge: nts=5; [1,0]; linked by [#51,#52] summary: [2] 1 0 [A.2730 A.2930 A.2732 A.2929] 5 2 nts=5 AUGCU A.A2730,A.U2731,A.G2732,A.C2929,A.U2930 nts=1 U A.U2731 nts=0 6 bulge: nts=5; [0,1]; linked by [#68,#69] summary: [2] 0 1 [A.3078 A.3090 A.3079 A.3088] 4 3 nts=5 CGCAG A.C3078,A.G3079,A.C3088,A.A3089,A.G3090 nts=0 nts=1 A A.A3089 7 bulge: nts=6; [2,0]; linked by [#41,#-19] summary: [2] 2 0 [A.2470 A.2657 A.2473 A.2656] 2 1 nts=6 GGAAUC A.G2470,A.G2471,A.A2472,A.A2473,A.U2656,A.C2657 nts=2 GA A.G2471,A.A2472 nts=0 8 bulge: nts=6; [0,2]; linked by [#52,#53] summary: [2] 0 2 [A.2733 A.2928 A.2734 A.2925] 2 4 nts=6 GAUACC A.G2733,A.A2734,A.U2925,A.A2926,A.C2927,A.C2928 nts=0 nts=2 AC A.A2926,A.C2927 **************************************************************************** List of 32 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#-7,#7] summary: [2] 1 1 [A.1845 A.1858 A.1847 A.1856] 1 2 nts=6 CCUAUG A.C1845,A.C1846,A.U1847,A.A1856,A.U1857,A.G1858 nts=1 C A.C1846 nts=1 U A.U1857 2 symmetric internal loop: nts=6; [1,1]; linked by [#9,#10] summary: [2] 1 1 [A.1877 A.1897 A.1879 A.1895] 3 2 nts=6 UUGCUA A.U1877,A.U1878,A.G1879,A.C1895,A.U1896,A.A1897 nts=1 U A.U1878 nts=1 U A.U1896 3 symmetric internal loop: nts=6; [1,1]; linked by [#12,#-8] summary: [2] 1 1 [A.1904 A.2018 A.1906 A.2016] 2 1 nts=6 CCGCUG A.C1904,A.C1905,A.G1906,A.C2016,A.U2017,A.G2018 nts=1 C A.C1905 nts=1 U A.U2017 4 symmetric internal loop: nts=6; [1,1]; linked by [#13,#-9] summary: [2] 1 1 [A.1913 A.2006 A.1915 A.2004] 4 1 nts=6 GACGCC A.G1913,A.A1914,A.C1915,A.G2004,A.C2005,A.C2006 nts=1 A A.A1914 nts=1 C A.C2005 5 symmetric internal loop: nts=6; [1,1]; linked by [#14,#15] summary: [2] 1 1 [A.1925 A.1979 A.1927 A.1977] 5 3 nts=6 AAGUAU A.A1925,A.A1926,A.G1927,A.U1977,A.A1978,A.U1979 nts=1 A A.A1926 nts=1 A A.A1978 6 symmetric internal loop: nts=6; [1,1]; linked by [#40,#41] summary: [2] 1 1 [A.2467 A.2660 A.2469 A.2658] 7 2 nts=6 AAAUCU A.A2467,A.A2468,A.A2469,A.U2658,A.C2659,A.U2660 nts=1 A A.A2468 nts=1 C A.C2659 7 symmetric internal loop: nts=6; [1,1]; linked by [#65,#66] summary: [2] 1 1 [A.3012 A.3025 A.3014 A.3023] 3 2 nts=6 UGGCUA A.U3012,A.G3013,A.G3014,A.C3023,A.U3024,A.A3025 nts=1 G A.G3013 nts=1 U A.U3024 8 symmetric internal loop: nts=6; [1,1]; linked by [#70,#71] summary: [2] 1 1 [A.3115 A.3141 A.3117 A.3139] 3 3 nts=6 UCCGAA A.U3115,A.C3116,A.C3117,A.G3139,A.A3140,A.A3141 nts=1 C A.C3116 nts=1 A A.A3140 9 symmetric internal loop: nts=6; [1,1]; linked by [#-29,#-30] summary: [2] 1 1 [B.1649 B.1660 B.1651 B.1658] 1 1 nts=6 CAAUUG B.C1649,B.A1650,B.A1651,B.U1658,B.U1659,B.G1660 nts=1 A B.A1650 nts=1 U B.U1659 10 asymmetric internal loop: nts=7; [2,1]; linked by [#17,#18] summary: [2] 2 1 [A.1948 A.1968 A.1951 A.1966] 3 4 nts=7 CGUCGUG A.C1948,A.G1949,A.U1950,A.C1951,A.G1966,A.U1967,A.G1968 nts=2 GU A.G1949,A.U1950 nts=1 U A.U1967 11 asymmetric internal loop: nts=7; [1,2]; linked by [#22,#23] summary: [2] 1 2 [A.2046 A.2094 A.2048 A.2091] 2 7 nts=7 CUUACUG A.C2046,A.U2047,A.U2048,A.A2091,A.C2092,A.U2093,A.G2094 nts=1 U A.U2047 nts=2 CU A.C2092,A.U2093 12 asymmetric internal loop: nts=7; [2,1]; linked by [#48,#49] summary: [2] 2 1 [A.2712 A.3106 A.2715 A.3104] 2 3 nts=7 GCAAUAC A.G2712,A.C2713,A.A2714,A.A2715,A.U3104,A.A3105,A.C3106 nts=2 CA A.C2713,A.A2714 nts=1 A A.A3105 13 asymmetric internal loop: nts=7; [1,2]; linked by [#49,#50] summary: [2] 1 2 [A.2717 A.3102 A.2719 A.3099] 3 2 nts=7 ACGCUAU A.A2717,A.C2718,A.G2719,A.C3099,A.U3100,A.A3101,A.U3102 nts=1 C A.C2718 nts=2 UA A.U3100,A.A3101 14 asymmetric internal loop: nts=7; [2,1]; linked by [#54,#55] summary: [2] 2 1 [A.2744 A.2803 A.2747 A.2801] 5 7 nts=7 UAUUAAA A.U2744,A.A2745,A.U2746,A.U2747,A.A2801,A.A2802,A.A2803 nts=2 AU A.A2745,A.U2746 nts=1 A A.A2802 15 asymmetric internal loop: nts=8; [1,3]; linked by [#-14,#19] summary: [2] 1 3 [A.1985 A.2001 A.1987 A.1997] 1 2 nts=8 GAGCUACC A.G1985,A.A1986,A.G1987,A.C1997,A.U1998,A.A1999,A.C2000,A.C2001 nts=1 A A.A1986 nts=3 UAC A.U1998,A.A1999,A.C2000 16 asymmetric internal loop: nts=8; [1,3]; linked by [#62,#-25] summary: [2] 1 3 [A.2997 A.3065 A.2999 A.3061] 4 1 nts=8 AUCGUGAU A.A2997,A.U2998,A.C2999,A.G3061,A.U3062,A.G3063,A.A3064,A.U3065 nts=1 U A.U2998 nts=3 UGA A.U3062,A.G3063,A.A3064 17 asymmetric internal loop: nts=8; [1,3]; linked by [#64,#65] summary: [2] 1 3 [A.3008 A.3031 A.3010 A.3027] 2 3 nts=8 CCGUAAAG A.C3008,A.C3009,A.G3010,A.U3027,A.A3028,A.A3029,A.A3030,A.G3031 nts=1 C A.C3009 nts=3 AAA A.A3028,A.A3029,A.A3030 18 asymmetric internal loop: nts=8; [3,1]; linked by [#72,#73] summary: [2] 3 1 [A.3148 A.3163 A.3152 A.3161] 5 3 nts=8 CCUACGCG A.C3148,A.C3149,A.U3150,A.A3151,A.C3152,A.G3161,A.C3162,A.G3163 nts=3 CUA A.C3149,A.U3150,A.A3151 nts=1 C A.C3162 19 asymmetric internal loop: nts=9; [2,3]; linked by [#10,#11] summary: [2] 2 3 [A.1880 A.1894 A.1883 A.1890] 2 2 nts=9 CAAGCAAAG A.C1880,A.A1881,A.A1882,A.G1883,A.C1890,A.A1891,A.A1892,A.A1893,A.G1894 nts=2 AA A.A1881,A.A1882 nts=3 AAA A.A1891,A.A1892,A.A1893 20 asymmetric internal loop: nts=9; [4,1]; linked by [#39,#40] summary: [2] 4 1 [A.2456 A.2668 A.2461 A.2666] 4 7 nts=9 UAAAAAUUA A.U2456,A.A2457,A.A2458,A.A2459,A.A2460,A.A2461,A.U2666,A.U2667,A.A2668 nts=4 AAAA A.A2457,A.A2458,A.A2459,A.A2460 nts=1 U A.U2667 21 symmetric internal loop: nts=10; [3,3]; linked by [#29,#-15] summary: [2] 3 3 [A.2149 A.2252 A.2153 A.2248] 3 1 nts=10 GUAAAUGAAC A.G2149,A.U2150,A.A2151,A.A2152,A.A2153,A.U2248,A.G2249,A.A2250,A.A2251,A.C2252 nts=3 UAA A.U2150,A.A2151,A.A2152 nts=3 GAA A.G2249,A.A2250,A.A2251 22 asymmetric internal loop: nts=10; [4,2]; linked by [#-19,#-20] summary: [2] 4 2 [A.2473 A.2656 A.2478 A.2653] 1 1 nts=10 ACUCGGCUGU A.A2473,A.C2474,A.U2475,A.C2476,A.G2477,A.G2478,A.C2653,A.U2654,A.G2655,A.U2656 nts=4 CUCG A.C2474,A.U2475,A.C2476,A.G2477 nts=2 UG A.U2654,A.G2655 23 symmetric internal loop: nts=10; [3,3]; linked by [#58,#59] summary: [2] 3 3 [A.2856 A.2876 A.2860 A.2872] 2 3 nts=10 CUAAGCAAAG A.C2856,A.U2857,A.A2858,A.A2859,A.G2860,A.C2872,A.A2873,A.A2874,A.A2875,A.G2876 nts=3 UAA A.U2857,A.A2858,A.A2859 nts=3 AAA A.A2873,A.A2874,A.A2875 24 symmetric internal loop: nts=10; [3,3]; linked by [#60,#61] summary: [2] 3 3 [A.2953 A.2971 A.2957 A.2967] 6 2 nts=10 UCUAGCAACA A.U2953,A.C2954,A.U2955,A.A2956,A.G2957,A.C2967,A.A2968,A.A2969,A.C2970,A.A2971 nts=3 CUA A.C2954,A.U2955,A.A2956 nts=3 AAC A.A2968,A.A2969,A.C2970 25 asymmetric internal loop: nts=11; [2,5]; linked by [#33,#34] summary: [2] 2 5 [A.2330 A.2447 A.2333 A.2441] 4 4 nts=11 UCCGCUCAUAA A.U2330,A.C2331,A.C2332,A.G2333,A.C2441,A.U2442,A.C2443,A.A2444,A.U2445,A.A2446,A.A2447 nts=2 CC A.C2331,A.C2332 nts=5 UCAUA A.U2442,A.C2443,A.A2444,A.U2445,A.A2446 26 asymmetric internal loop: nts=13; [5,4]; linked by [#-4,#4] summary: [2] 5 4 [A.1739 A.1758 A.1745 A.1753] 1 2 nts=13 AAAGUAUAGAAAU A.A1739,A.A1740,A.A1741,A.G1742,A.U1743,A.A1744,A.U1745,A.A1753,A.G1754,A.A1755,A.A1756,A.A1757,A.U1758 nts=5 AAGUA A.A1740,A.A1741,A.G1742,A.U1743,A.A1744 nts=4 GAAA A.G1754,A.A1755,A.A1756,A.A1757 27 asymmetric internal loop: nts=13; [3,6]; linked by [#-8,#13] summary: [2] 3 6 [A.1906 A.2016 A.1910 A.2009] 1 4 nts=13 GAAACGUGAUAGC A.G1906,A.A1907,A.A1908,A.A1909,A.C1910,A.G2009,A.U2010,A.G2011,A.A2012,A.U2013,A.A2014,A.G2015,A.C2016 nts=3 AAA A.A1907,A.A1908,A.A1909 nts=6 UGAUAG A.U2010,A.G2011,A.A2012,A.U2013,A.A2014,A.G2015 28 symmetric internal loop: nts=14; [5,5]; linked by [#24,#25] summary: [2] 5 5 [A.2057 A.2082 A.2063 A.2076] 3 2 nts=14 CCCACAGCCCCUUG A.C2057,A.C2058,A.C2059,A.A2060,A.C2061,A.A2062,A.G2063,A.C2076,A.C2077,A.C2078,A.C2079,A.U2080,A.U2081,A.G2082 nts=5 CCACA A.C2058,A.C2059,A.A2060,A.C2061,A.A2062 nts=5 CCCUU A.C2077,A.C2078,A.C2079,A.U2080,A.U2081 29 asymmetric internal loop: nts=14; [3,7]; linked by [#36,#37] summary: [2] 3 7 [A.2377 A.2419 A.2381 A.2411] 3 4 nts=14 GCCCAUACCCUCAC A.G2377,A.C2378,A.C2379,A.C2380,A.A2381,A.U2411,A.A2412,A.C2413,A.C2414,A.C2415,A.U2416,A.C2417,A.A2418,A.C2419 nts=3 CCC A.C2378,A.C2379,A.C2380 nts=7 ACCCUCA A.A2412,A.C2413,A.C2414,A.C2415,A.U2416,A.C2417,A.A2418 30 asymmetric internal loop: nts=15; [6,5]; linked by [#-16,#31] summary: [2] 6 5 [A.2306 A.2680 A.2313 A.2674] 1 2 nts=15 AUAAGUAAUGAAAUU A.A2306,A.U2307,A.A2308,A.A2309,A.G2310,A.U2311,A.A2312,A.A2313,A.U2674,A.G2675,A.A2676,A.A2677,A.A2678,A.U2679,A.U2680 nts=6 UAAGUA A.U2307,A.A2308,A.A2309,A.G2310,A.U2311,A.A2312 nts=5 GAAAU A.G2675,A.A2676,A.A2677,A.A2678,A.U2679 31 asymmetric internal loop: nts=15; [6,5]; linked by [#71,#-26] summary: [2] 6 5 [A.3119 A.3137 A.3126 A.3131] 3 1 nts=15 CCCUGUACGGACAAG A.C3119,A.C3120,A.C3121,A.U3122,A.G3123,A.U3124,A.A3125,A.C3126,A.G3131,A.G3132,A.A3133,A.C3134,A.A3135,A.A3136,A.G3137 nts=6 CCUGUA A.C3120,A.C3121,A.U3122,A.G3123,A.U3124,A.A3125 nts=5 GACAA A.G3132,A.A3133,A.C3134,A.A3135,A.A3136 32 asymmetric internal loop: nts=16; [8,4]; linked by [#-20,#42] summary: [2] 8 4 [A.2478 A.2653 A.2487 A.2648] 1 4 nts=16 GCAAAUCUUAUUCAGC A.G2478,A.C2479,A.A2480,A.A2481,A.A2482,A.U2483,A.C2484,A.U2485,A.U2486,A.A2487,A.U2648,A.U2649,A.C2650,A.A2651,A.G2652,A.C2653 nts=8 CAAAUCUU A.C2479,A.A2480,A.A2481,A.A2482,A.U2483,A.C2484,A.U2485,A.U2486 nts=4 UCAG A.U2649,A.C2650,A.A2651,A.G2652 **************************************************************************** List of 10 junctions 1 3-way junction: nts=12; [1,3,2]; linked by [#-10,#16,#17] summary: [3] 1 3 2 [A.1930 A.1973 A.1932 A.1942 A.1946 A.1970] 1 3 3 nts=12 CAGCACACGAAG A.C1930,A.A1931,A.G1932,A.C1942,A.A1943,A.C1944,A.A1945,A.C1946,A.G1970,A.A1971,A.A1972,A.G1973 nts=1 A A.A1931 nts=3 ACA A.A1943,A.C1944,A.A1945 nts=2 AA A.A1971,A.A1972 2 3-way junction: nts=14; [5,1,2]; linked by [#-9,#14,#-14] summary: [3] 5 1 2 [A.1915 A.2004 A.1921 A.1983 A.1985 A.2001] 1 5 1 nts=14 CGAGCUAUAGCGAG A.C1915,A.G1916,A.A1917,A.G1918,A.C1919,A.U1920,A.A1921,A.U1983,A.A1984,A.G1985,A.C2001,A.G2002,A.A2003,A.G2004 nts=5 GAGCU A.G1916,A.A1917,A.G1918,A.C1919,A.U1920 nts=1 A A.A1984 nts=2 GA A.G2002,A.A2003 3 3-way junction: nts=14; [1,6,1]; linked by [#-17,#35,#36] summary: [3] 1 6 1 [A.2343 A.2423 A.2345 A.2368 A.2375 A.2421] 1 5 3 nts=14 GCGCAAUUAACGUC A.G2343,A.C2344,A.G2345,A.C2368,A.A2369,A.A2370,A.U2371,A.U2372,A.A2373,A.A2374,A.C2375,A.G2421,A.U2422,A.C2423 nts=1 C A.C2344 nts=6 AAUUAA A.A2369,A.A2370,A.U2371,A.U2372,A.A2373,A.A2374 nts=1 U A.U2422 4 3-way junction: nts=14; [2,1,5]; linked by [#63,#64,#67] summary: [3] 2 1 5 [A.3004 A.3054 A.3007 A.3032 A.3034 A.3048] 5 2 5 nts=14 CAUCGUUAUUAAAG A.C3004,A.A3005,A.U3006,A.C3007,A.G3032,A.U3033,A.U3034,A.A3048,A.U3049,A.U3050,A.A3051,A.A3052,A.A3053,A.G3054 nts=2 AU A.A3005,A.U3006 nts=1 U A.U3033 nts=5 UUAAA A.U3049,A.U3050,A.A3051,A.A3052,A.A3053 5 3-way junction: nts=16; [6,3,1]; linked by [#34,#-17,#38] summary: [3] 6 3 1 [A.2336 A.2438 A.2343 A.2423 A.2427 A.2436] 4 1 2 nts=16 UAAGCCUGCAACCGCA A.U2336,A.A2337,A.A2338,A.G2339,A.C2340,A.C2341,A.U2342,A.G2343,A.C2423,A.A2424,A.A2425,A.C2426,A.C2427,A.G2436,A.C2437,A.A2438 nts=6 AAGCCU A.A2337,A.A2338,A.G2339,A.C2340,A.C2341,A.U2342 nts=3 AAC A.A2424,A.A2425,A.C2426 nts=1 C A.C2437 6 3-way junction: nts=25; [2,13,4]; linked by [#-1,#2,#5] summary: [3] 2 13 4 [A.1678 A.1797 A.1681 A.1771 A.1785 A.1792] 1 2 2 nts=25 CUAGCAAUAGAUAUAGUACGGAAAG A.C1678,A.U1679,A.A1680,A.G1681,A.C1771,A.A1772,A.A1773,A.U1774,A.A1775,A.G1776,A.A1777,A.U1778,A.A1779,A.U1780,A.A1781,A.G1782,A.U1783,A.A1784,A.C1785,A.G1792,A.G1793,A.A1794,A.A1795,A.A1796,A.G1797 nts=2 UA A.U1679,A.A1680 nts=13 AAUAGAUAUAGUA A.A1772,A.A1773,A.U1774,A.A1775,A.G1776,A.A1777,A.U1778,A.A1779,A.U1780,A.A1781,A.G1782,A.U1783,A.A1784 nts=4 GAAA A.G1793,A.A1794,A.A1795,A.A1796 7 4-way junction: nts=13; [2,0,2,1]; linked by [#31,#32,#33,#39] summary: [4] 2 0 2 1 [A.2314 A.2673 A.2317 A.2326 A.2327 A.2450 A.2453 A.2671] 2 3 4 4 nts=13 CAUGCUAAAGCAG A.C2314,A.A2315,A.U2316,A.G2317,A.C2326,A.U2327,A.A2450,A.A2451,A.A2452,A.G2453,A.C2671,A.A2672,A.G2673 nts=2 AU A.A2315,A.U2316 nts=0 nts=2 AA A.A2451,A.A2452 nts=1 A A.A2672 8 4-way junction: nts=23; [3,4,4,4]; linked by [#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 nts=23 GCCUGCAUCACGCACCGCUCCAC A.G2492,A.C2493,A.C2494,A.U2495,A.G2496,A.C2508,A.A2509,A.U2510,A.C2511,A.A2512,A.C2513,A.G2537,A.C2538,A.A2539,A.C2540,A.C2541,A.G2542,A.C2637,A.U2638,A.C2639,A.C2640,A.A2641,A.C2642 nts=3 CCU A.C2493,A.C2494,A.U2495 nts=4 AUCA A.A2509,A.U2510,A.C2511,A.A2512 nts=4 CACC A.C2538,A.A2539,A.C2540,A.C2541 nts=4 UCCA A.U2638,A.C2639,A.C2640,A.A2641 9 5-way junction: nts=36; [9,3,2,3,9]; linked by [#8,#9,#12,#20,#30] summary: [5] 9 3 2 3 9 [A.1865 A.2300 A.1875 A.1899 A.1903 A.2019 A.2022 A.2271 A.2275 A.2290] 6 3 2 6 5 nts=36 CUAGAAAUAACGACCCGUUGCCAAUAAGAACUAAUG A.C1865,A.U1866,A.A1867,A.G1868,A.A1869,A.A1870,A.A1871,A.U1872,A.A1873,A.A1874,A.C1875,A.G1899,A.A1900,A.C1901,A.C1902,A.C1903,A.G2019,A.U2020,A.U2021,A.G2022,A.C2271,A.C2272,A.A2273,A.A2274,A.U2275,A.A2290,A.A2291,A.G2292,A.A2293,A.A2294,A.C2295,A.U2296,A.A2297,A.A2298,A.U2299,A.G2300 nts=9 UAGAAAUAA A.U1866,A.A1867,A.G1868,A.A1869,A.A1870,A.A1871,A.U1872,A.A1873,A.A1874 nts=3 ACC A.A1900,A.C1901,A.C1902 nts=2 UU A.U2020,A.U2021 nts=3 CAA A.C2272,A.A2273,A.A2274 nts=9 AGAACUAAU A.A2291,A.G2292,A.A2293,A.A2294,A.C2295,A.U2296,A.A2297,A.A2298,A.U2299 10 6-way junction: nts=34; [4,1,2,3,4,8]; linked by [#20,#21,#22,#26,#27,#28] summary: [6] 4 1 2 3 4 8 [A.2027 A.2266 A.2032 A.2043 A.2045 A.2095 A.2098 A.2123 A.2127 A.2138 A.2143 A.2257] 6 4 2 10 3 3 nts=34 AGAUAGCAAUUAGCACUAUUGUAGCACACCCAAU A.A2027,A.G2028,A.A2029,A.U2030,A.A2031,A.G2032,A.C2043,A.A2044,A.A2045,A.U2095,A.U2096,A.A2097,A.G2098,A.C2123,A.A2124,A.C2125,A.U2126,A.A2127,A.U2138,A.U2139,A.G2140,A.U2141,A.A2142,A.G2143,A.C2257,A.A2258,A.C2259,A.A2260,A.C2261,A.C2262,A.C2263,A.A2264,A.A2265,A.U2266 nts=4 GAUA A.G2028,A.A2029,A.U2030,A.A2031 nts=1 A A.A2044 nts=2 UA A.U2096,A.A2097 nts=3 ACU A.A2124,A.C2125,A.U2126 nts=4 UGUA A.U2139,A.G2140,A.U2141,A.A2142 nts=8 ACACCCAA A.A2258,A.C2259,A.A2260,A.C2261,A.C2262,A.C2263,A.A2264,A.A2265 **************************************************************************** List of 47 non-loop single-stranded segments 1 nts=5 UAAAC A.U1673,A.A1674,A.A1675,A.A1676,A.C1677 2 nts=31* CAAACCCCCACCUUACUACCACAACUUAGCC A.C1685,A.A1686,A.A1687,A.A1688,A.C1689,A.C1690,A.C1691,A.C1695,A.C1696,A.A1697,A.C1698,A.C1699,A.U1700,A.U1701,A.A1702,A.C1703,A.U1704,A.A1705,A.C1706,A.C1707,A.A1708,A.C1711,A.A1712,A.A1713,A.C1714,A.U1716,A.U1717,A.A1718,A.G1719,A.C1720,A.C1721 3 nts=5* UACAU A.U1730,A.A1731,A.C1732,A.A1737,A.U1738 4 nts=4* UGAU A.U1759,A.G1760,A.A1761,A.U1766 5 nts=4* ACAA A.A1798,A.C1813,A.A1814,A.A1815 6 nts=9 AUAAUAUAG A.A1818,A.U1819,A.A1820,A.A1821,A.U1822,A.A1823,A.U1824,A.A1825,A.G1826 7 nts=1 A A.A1828 8 nts=1 A A.A1842 9 nts=1 A A.A1844 10 nts=1 A A.A1859 11 nts=6* ACCAAA A.A2065,A.C2066,A.C2067,A.A2072,A.A2073,A.A2074 12 nts=21* AAAUGAUCCCAAACAUAUAAC A.A2154,A.A2155,A.A2156,A.U2157,A.G2231,A.A2232,A.U2233,A.C2234,A.C2235,A.C2236,A.A2237,A.A2238,A.A2239,A.C2240,A.A2241,A.U2242,A.A2243,A.U2244,A.A2245,A.A2246,A.C2247 13 nts=3* CAU A.C2280,A.A2281,A.U2285 14 nts=2 AU A.A2350,A.U2351 15 nts=7 UCUACAA A.U2385,A.C2386,A.U2387,A.A2388,A.C2389,A.A2390,A.A2391 16 nts=7 CAACCAA A.C2393,A.A2394,A.A2395,A.C2396,A.C2397,A.A2398,A.A2399 17 nts=1 U A.U2407 18 nts=5* AACCA A.A2429,A.A2430,A.C2431,A.C2433,A.A2434 19 nts=3 CCU A.C2543,A.C2544,A.U2545 20 nts=1 A A.A2682 21 nts=2 CU A.C2684,A.U2685 22 nts=2 UG A.U2691,A.G2692 23 nts=1 G A.G2698 24 nts=7 AUAACAC A.A2704,A.U2705,A.A2706,A.A2707,A.C2708,A.A2709,A.C2710 25 nts=3 AGA A.A2723,A.G2724,A.A2725 26 nts=2 UU A.U2738,A.U2739 27 nts=5* AAACC A.A2754,A.A2755,A.A2792,A.C2793,A.C2794 28 nts=2 UC A.U2808,A.C2809 29 nts=22* GAAGAUCCAAUAACUUGACCAA A.G2878,A.A2879,A.A2880,A.G2896,A.A2897,A.U2898,A.C2899,A.C2900,A.A2901,A.A2902,A.U2903,A.A2904,A.A2905,A.C2906,A.U2907,A.U2908,A.G2909,A.A2910,A.C2911,A.C2912,A.A2913,A.A2914 30 nts=5 GAACA A.G2917,A.A2918,A.A2919,A.C2920,A.A2921 31 nts=4 CAAU A.C2944,A.A2945,A.A2946,A.U2947 32 nts=6 GUUUAC A.G2977,A.U2978,A.U2979,A.U2980,A.A2981,A.C2982 33 nts=1 C A.C3060 34 nts=6 AGUUCA A.A3069,A.G3070,A.U3071,A.U3072,A.C3073,A.A3074 35 nts=2 GG A.G3094,A.G3095 36 nts=1 U A.U3097 37 nts=2 UU A.U3108,A.U3109 38 nts=1 C A.C3168 39 nts=12 AUACCCACACCC A.A3201,A.U3202,A.A3203,A.C3204,A.C3205,A.C3206,A.A3207,A.C3208,A.A3209,A.C3210,A.C3211,A.C3212 40 nts=1 U A.U3228 41 nts=3 AGA B.A1603,B.G1604,B.A1605 42 nts=4 UGUA B.U1607,B.G1608,B.U1609,B.A1610 43 nts=4* UAAA B.U1614,B.A1615,B.A1616,B.A1621 44 nts=2 AC B.A1625,B.C1626 45 nts=6* GAGAUU B.G1642,B.A1643,B.G1644,B.A1645,B.U1646,B.U1648 46 nts=3* ACG B.A1661,B.C1663,B.G1664 47 nts=5 UCUGA B.U1666,B.C1667,B.U1668,B.G1669,B.A1670 **************************************************************************** List of 1 kissing loop interaction 1 isolated-pair #-3 between hairpin loops #1 and #2 **************************************************************************** List of 45 A-minor motifs (types I, II, or X) 1 type=X A|C-G A.A1718|A.C1911,A.G2008 WC -A.C1911 H-bonds[1]: "N3-O2'(hydroxyl)[2.13]" +A.G2008 H-bonds[0]: "" 2 type=X A|U-G A.A1724|A.U2035,A.G2040 Wobble -A.U2035 H-bonds[0]: "" +A.G2040 H-bonds[3]: "N6(amino)-O2'(hydroxyl)[3.31],N6(amino)-N3[3.18],N1-N2(amino)[2.97]" 3 type=X A|A-U A.A1727|A.A2741,A.U2806 WC +A.A2741 H-bonds[1]: "N1-O2'(hydroxyl)[3.57]" -A.U2806 H-bonds[0]: "" 4 type=X A|A-U A.A1751|A.A1722,A.U1729 WC -A.A1722 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.17]" +A.U1729 H-bonds[1]: "N1-O2'(hydroxyl)[3.03]" 5 type=II A|G-C A.A1775|A.G1681,A.C1771 WC +A.G1681 H-bonds[0]: "" -A.C1771 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.77],N3-O2'(hydroxyl)[2.75]" 6 type=II A|C-G A.A1789|A.C1915,A.G2004 WC -A.C1915 H-bonds[3]: "O2'(hydroxyl)-O3'[3.13],O2'(hydroxyl)-O2'(hydroxyl)[2.80],N3-O2'(hydroxyl)[2.66]" +A.G2004 H-bonds[0]: "" 7 type=X A|A-C A.A1790|A.A1914,A.C2005 ~Wobble -A.A1914 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.56]" +A.C2005 H-bonds[1]: "N1-O2'(hydroxyl)[2.64]" 8 type=II A|U-A A.A1814|A.U1862,A.A2303 WC -A.U1862 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.34],N3-O2'(hydroxyl)[2.86]" +A.A2303 H-bonds[0]: "" 9 type=I A|U-G A.A1815|A.U1861,A.G2304 Wobble -A.U1861 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.08]" +A.G2304 H-bonds[1]: "N3-N2(amino)[2.99]" 10 type=X A|A-G A.A1828|A.A2682,A.G2698 Imino -A.A2682 H-bonds[0]: "" +A.G2698 H-bonds[1]: "N1-N2(amino)[2.92]" 11 type=X A|C-G A.A1828|A.C2683,A.G2697 WC -A.C2683 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.16]" +A.G2697 H-bonds[0]: "" 12 type=I A|C-G A.A1867|A.C1903,A.G2019 WC -A.C1903 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.52],O2'(hydroxyl)-O2(carbonyl)[2.67]" +A.G2019 H-bonds[2]: "N1-O2'(hydroxyl)[2.37],N3-N2(amino)[2.87]" 13 type=II A|A-U A.A1907|A.A2730,A.U2930 WC +A.A2730 H-bonds[0]: "" -A.U2930 H-bonds[3]: "O2'(hydroxyl)-O3'[3.07],O2'(hydroxyl)-O2'(hydroxyl)[2.41],N3-O2'(hydroxyl)[2.75]" 14 type=I A|G-C A.A1908|A.G2732,A.C2929 WC +A.G2732 H-bonds[2]: "N1-O2'(hydroxyl)[2.92],N3-N2(amino)[2.98]" -A.C2929 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.72],O2'(hydroxyl)-O2(carbonyl)[3.16]" 15 type=X A|G-C A.A1917|A.G1988,A.C1996 WC +A.G1988 H-bonds[2]: "N6(amino)-N3[2.88],N1-N2(amino)[2.99]" -A.C1996 H-bonds[0]: "" 16 type=I A|G-C A.A1984|A.G1987,A.C1997 WC -A.G1987 H-bonds[1]: "N3-N2(amino)[3.06]" +A.C1997 H-bonds[1]: "N1-O2'(hydroxyl)[2.87]" 17 type=I A|G-C A.A1991|A.G2496,A.C2508 WC +A.G2496 H-bonds[2]: "N1-O2'(hydroxyl)[3.31],N3-N2(amino)[3.11]" -A.C2508 H-bonds[3]: "O3'-O2'(hydroxyl)[2.95],O2'(hydroxyl)-O2'(hydroxyl)[2.69],O2'(hydroxyl)-O2(carbonyl)[2.57]" 18 type=X A|C-G A.A2039|A.C2728,A.G2932 WC +A.C2728 H-bonds[0]: "" -A.G2932 H-bonds[2]: "N6(amino)-N3[3.35],N1-O2'(hydroxyl)[2.90]" 19 type=X A|C-G A.A2131|A.C2689,A.G2700 WC +A.C2689 H-bonds[0]: "" -A.G2700 H-bonds[1]: "N3-O2'(hydroxyl)[3.05]" 20 type=I A|G-C A.A2132|A.G2690,A.C2699 WC +A.G2690 H-bonds[2]: "N1-O2'(hydroxyl)[3.25],N3-N2(amino)[3.17]" -A.C2699 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.85],O2'(hydroxyl)-O2(carbonyl)[2.94]" 21 type=II A|G-C A.A2134|A.G2098,A.C2123 WC +A.G2098 H-bonds[0]: "" -A.C2123 H-bonds[1]: "N3-O2'(hydroxyl)[2.73]" 22 type=II A|A-U A.A2151|A.A2127,A.U2138 WC +A.A2127 H-bonds[0]: "" -A.U2138 H-bonds[3]: "O2'(hydroxyl)-O3'[3.09],O2'(hydroxyl)-O2'(hydroxyl)[3.05],N3-O2'(hydroxyl)[2.63]" 23 type=I A|G-C A.A2152|A.G2128,A.C2137 WC +A.G2128 H-bonds[2]: "N1-O2'(hydroxyl)[3.17],N3-N2(amino)[3.20]" -A.C2137 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.17],O2'(hydroxyl)-O2(carbonyl)[3.29]" 24 type=I A|G-C A.A2232|A.G3002,A.C3056 WC -A.G3002 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.49],O2'(hydroxyl)-N3[3.00],N3-N2(amino)[3.20]" +A.C3056 H-bonds[1]: "N1-O2'(hydroxyl)[3.26]" 25 type=X A|A-U A.A2250|A.A2127,A.U2138 WC -A.A2127 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.86]" +A.U2138 H-bonds[0]: "" 26 type=X A|C-G A.A2265|A.C2046,A.G2094 WC +A.C2046 H-bonds[0]: "" -A.G2094 H-bonds[3]: "O2'(hydroxyl)-O3'[3.12],O2'(hydroxyl)-O2'(hydroxyl)[2.79],N3-O2'(hydroxyl)[2.67]" 27 type=I A|C-G A.A2297|A.C1845,A.G1858 WC +A.C1845 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.23],N1-O2'(hydroxyl)[2.47]" -A.G1858 H-bonds[1]: "N3-N2(amino)[3.51]" 28 type=I A|C-G A.A2298|A.C1904,A.G2018 WC +A.C1904 H-bonds[0]: "" -A.G2018 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.88],N3-N2(amino)[3.11]" 29 type=X A|U-A A.A2451|A.U2327,A.A2450 WC -A.U2327 H-bonds[0]: "" +A.A2450 H-bonds[1]: "N6(amino)-N3[3.06]" 30 type=X A|C-G A.A2451|A.C2328,A.G2449 WC -A.C2328 H-bonds[1]: "N1-O2'(hydroxyl)[2.81]" +A.G2449 H-bonds[0]: "" 31 type=X A|G-C A.A2481|A.G2478,A.C2653 WC +A.G2478 H-bonds[1]: "N1-N2(amino)[2.91]" -A.C2653 H-bonds[0]: "" 32 type=II A|G-C A.A2482|A.G2478,A.C2653 WC +A.G2478 H-bonds[0]: "" -A.C2653 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.77],N3-O2'(hydroxyl)[3.29]" 33 type=I A|G-C A.A2505|A.G3075,A.C3093 WC +A.G3075 H-bonds[1]: "N1-O2'(hydroxyl)[2.99]" -A.C3093 H-bonds[0]: "" 34 type=X A|C-G A.A2615|A.C3035,A.G3047 WC +A.C3035 H-bonds[0]: "" -A.G3047 H-bonds[1]: "N3-O2'(hydroxyl)[3.49]" 35 type=I A|G-C A.A2616|A.G3036,A.C3046 WC +A.G3036 H-bonds[2]: "N1-O2'(hydroxyl)[3.11],N3-N2(amino)[3.38]" -A.C3046 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.27],O2'(hydroxyl)-O2(carbonyl)[3.17]" 36 type=X A|C-G A.A2644|A.C1948,A.G1968 WC +A.C1948 H-bonds[0]: "" -A.G1968 H-bonds[2]: "N1-N2(amino)[3.14],N3-O2'(hydroxyl)[2.60]" 37 type=X A|U-A A.A2745|A.U2744,A.A2803 WC +A.U2744 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.96]" -A.A2803 H-bonds[0]: "" 38 type=II A|G-C A.A2837|A.G2105,A.C2116 WC +A.G2105 H-bonds[1]: "N1-N2(amino)[3.00]" -A.C2116 H-bonds[1]: "N3-O2'(hydroxyl)[2.31]" 39 type=X A|C-G A.A2919|A.C1726,A.G1748 WC -A.C1726 H-bonds[0]: "" +A.G1748 H-bonds[1]: "N6(amino)-N3[3.41]" 40 type=II A|C-G A.A3051|A.C3008,A.G3031 WC -A.C3008 H-bonds[1]: "N3-O2'(hydroxyl)[2.97]" +A.G3031 H-bonds[0]: "" 41 type=I A|C-G A.A3052|A.C3007,A.G3032 WC -A.C3007 H-bonds[0]: "" +A.G3032 H-bonds[2]: "N1-O2'(hydroxyl)[2.65],N3-N2(amino)[3.14]" 42 type=II A|U-A A.A3084|A.U2737,A.A2922 WC -A.U2737 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.00],N3-O2'(hydroxyl)[2.63]" +A.A2922 H-bonds[0]: "" 43 type=I A|C-G A.A3085|A.C2736,A.G2923 WC -A.C2736 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.54],O2'(hydroxyl)-O2(carbonyl)[3.07]" +A.G2923 H-bonds[2]: "N1-O2'(hydroxyl)[3.36],N3-N2(amino)[2.80]" 44 type=X A|C-G A.A3151|A.C3148,A.G3163 WC +A.C3148 H-bonds[0]: "" -A.G3163 H-bonds[2]: "N6(amino)-N3[2.77],N1-O2'(hydroxyl)[2.99]" 45 type=X A|C-G A.A3151|A.C3149,A.G3163 -- +A.C3149 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.56]" -A.G3163 H-bonds[2]: "N6(amino)-N3[2.77],N1-O2'(hydroxyl)[2.99]" **************************************************************************** List of 8 ribose zippers 1 nts=4 ACAC A.A1697,A.C1698,A.A1702,A.C1703 2 nts=4 AAAC A.A1789,A.A1790,A.A1914,A.C1915 3 nts=4 AAUU A.A1814,A.A1815,A.U1861,A.U1862 4 nts=4 AACU A.A1907,A.A1908,A.C2929,A.U2930 5 nts=4 CUAA A.C2137,A.U2138,A.A2151,A.A2152 6 nts=4 GAGA A.G2231,A.A2232,A.G3002,A.A3003 7 nts=4 CAGG A.C2502,A.A2503,A.G3094,A.G3095 8 nts=4 CUAA A.C2736,A.U2737,A.A3084,A.A3085 **************************************************************************** List of 206 splayed-apart dinucleotides 1 A.C1698 A.C1699 angle=89 distance=12.9 ratio=0.70 2 A.C1699 A.U1700 angle=117 distance=16.0 ratio=0.85 3 A.U1701 A.A1702 angle=107 distance=16.3 ratio=0.80 4 A.C1703 A.U1704 angle=105 distance=15.7 ratio=0.79 5 A.U1704 A.A1705 angle=125 distance=18.2 ratio=0.89 6 A.U1716 A.U1717 angle=113 distance=16.5 ratio=0.83 7 A.A1723 A.A1724 angle=126 distance=16.5 ratio=0.89 8 A.A1724 A.C1725 angle=116 distance=16.1 ratio=0.85 9 A.A1727 A.U1728 angle=92 distance=13.7 ratio=0.72 10 A.U1730 A.A1731 angle=92 distance=11.9 ratio=0.72 11 A.G1747 A.G1748 angle=92 distance=14.6 ratio=0.72 12 A.G1748 A.C1749 angle=130 distance=19.2 ratio=0.91 13 A.C1749 A.G1750 angle=89 distance=14.2 ratio=0.70 14 A.G1768 A.C1769 angle=148 distance=18.1 ratio=0.96 15 A.C1769 A.G1770 angle=149 distance=20.2 ratio=0.96 16 A.A1773 A.U1774 angle=162 distance=18.3 ratio=0.99 17 A.U1774 A.A1775 angle=117 distance=16.1 ratio=0.85 18 A.A1779 A.U1780 angle=152 distance=17.3 ratio=0.97 19 A.A1796 A.G1797 angle=85 distance=13.1 ratio=0.68 20 A.C1813 A.A1814 angle=109 distance=14.5 ratio=0.81 21 A.A1820 A.A1821 angle=141 distance=17.8 ratio=0.94 22 A.A1823 A.U1824 angle=125 distance=17.6 ratio=0.89 23 A.G1826 A.C1827 angle=123 distance=18.7 ratio=0.88 24 A.A1842 A.U1843 angle=103 distance=15.1 ratio=0.78 25 A.U1843 A.A1844 angle=97 distance=15.9 ratio=0.75 26 A.A1859 A.A1860 angle=137 distance=16.8 ratio=0.93 27 A.A1885 A.G1886 angle=123 distance=16.0 ratio=0.88 28 A.G1886 A.A1887 angle=103 distance=15.4 ratio=0.79 29 A.G1888 A.C1889 angle=88 distance=13.7 ratio=0.70 30 A.A1891 A.A1892 angle=108 distance=14.4 ratio=0.81 31 A.A1892 A.A1893 angle=129 distance=17.5 ratio=0.90 32 A.C1902 A.C1903 angle=137 distance=18.2 ratio=0.93 33 A.A1917 A.G1918 angle=119 distance=16.2 ratio=0.86 34 A.C1930 A.A1931 angle=136 distance=17.1 ratio=0.93 35 A.A1938 A.G1939 angle=146 distance=17.0 ratio=0.96 36 A.G1939 A.A1940 angle=151 distance=18.0 ratio=0.97 37 A.U1956 A.A1957 angle=151 distance=17.6 ratio=0.97 38 A.A1957 A.G1958 angle=85 distance=13.3 ratio=0.68 39 A.A1960 A.A1961 angle=127 distance=15.8 ratio=0.89 40 A.A1961 A.A1962 angle=111 distance=15.0 ratio=0.82 41 A.A1971 A.A1972 angle=131 distance=16.8 ratio=0.91 42 A.G1973 A.A1974 angle=135 distance=18.3 ratio=0.92 43 A.A1974 A.U1975 angle=161 distance=18.6 ratio=0.99 44 A.G1990 A.A1991 angle=154 distance=18.4 ratio=0.97 45 A.A1991 A.C1992 angle=154 distance=19.2 ratio=0.97 46 A.C1997 A.U1998 angle=144 distance=17.8 ratio=0.95 47 A.U1998 A.A1999 angle=93 distance=13.8 ratio=0.73 48 A.C2000 A.C2001 angle=91 distance=12.3 ratio=0.71 49 A.C2001 A.G2002 angle=120 distance=17.1 ratio=0.87 50 A.A2003 A.G2004 angle=98 distance=14.3 ratio=0.75 51 A.U2010 A.G2011 angle=116 distance=16.9 ratio=0.85 52 A.G2011 A.A2012 angle=146 distance=18.3 ratio=0.96 53 A.A2014 A.G2015 angle=125 distance=17.6 ratio=0.89 54 A.G2015 A.C2016 angle=108 distance=15.8 ratio=0.81 55 A.U2020 A.U2021 angle=111 distance=14.9 ratio=0.83 56 A.U2021 A.G2022 angle=85 distance=14.0 ratio=0.68 57 A.U2030 A.A2031 angle=123 distance=17.9 ratio=0.88 58 A.U2035 A.C2036 angle=141 distance=17.2 ratio=0.94 59 A.U2038 A.A2039 angle=173 distance=19.3 ratio=1.00 60 A.A2039 A.G2040 angle=120 distance=16.6 ratio=0.87 61 A.A2064 A.A2065 angle=105 distance=14.8 ratio=0.79 62 A.A2097 A.G2098 angle=135 distance=18.1 ratio=0.93 63 A.A2112 A.G2113 angle=123 distance=16.5 ratio=0.88 64 A.A2124 A.C2125 angle=87 distance=13.3 ratio=0.69 65 A.A2130 A.A2131 angle=114 distance=14.5 ratio=0.84 66 A.A2133 A.A2134 angle=128 distance=17.5 ratio=0.90 67 A.A2142 A.G2143 angle=124 distance=16.6 ratio=0.89 68 A.G2145 A.A2146 angle=140 distance=17.9 ratio=0.94 69 A.A2146 A.G2147 angle=156 distance=19.4 ratio=0.98 70 A.A2154 A.A2155 angle=139 distance=18.4 ratio=0.94 71 A.A2232 A.U2233 angle=163 distance=19.2 ratio=0.99 72 A.C2236 A.A2237 angle=93 distance=14.8 ratio=0.73 73 A.C2240 A.A2241 angle=113 distance=16.2 ratio=0.84 74 A.U2242 A.A2243 angle=107 distance=15.8 ratio=0.81 75 A.U2244 A.A2245 angle=115 distance=13.3 ratio=0.85 76 A.A2250 A.A2251 angle=103 distance=12.5 ratio=0.79 77 A.A2251 A.C2252 angle=89 distance=13.0 ratio=0.70 78 A.C2259 A.A2260 angle=139 distance=15.8 ratio=0.94 79 A.C2261 A.C2262 angle=146 distance=18.3 ratio=0.96 80 A.C2262 A.C2263 angle=108 distance=16.8 ratio=0.81 81 A.A2291 A.G2292 angle=123 distance=16.9 ratio=0.88 82 A.G2292 A.A2293 angle=141 distance=18.2 ratio=0.94 83 A.A2294 A.C2295 angle=115 distance=16.4 ratio=0.85 84 A.C2295 A.U2296 angle=109 distance=16.1 ratio=0.82 85 A.A2297 A.A2298 angle=118 distance=17.0 ratio=0.86 86 A.A2298 A.U2299 angle=159 distance=17.9 ratio=0.98 87 A.U2299 A.G2300 angle=147 distance=19.6 ratio=0.96 88 A.U2316 A.G2317 angle=115 distance=16.3 ratio=0.85 89 A.A2320 A.A2321 angle=91 distance=12.7 ratio=0.72 90 A.A2321 A.C2322 angle=100 distance=14.8 ratio=0.77 91 A.U2330 A.C2331 angle=123 distance=15.6 ratio=0.88 92 A.G2343 A.C2344 angle=152 distance=16.1 ratio=0.97 93 A.C2344 A.G2345 angle=138 distance=17.6 ratio=0.93 94 A.U2371 A.U2372 angle=98 distance=12.1 ratio=0.77 95 A.A2374 A.C2375 angle=93 distance=13.8 ratio=0.73 96 A.C2380 A.A2381 angle=109 distance=15.1 ratio=0.82 97 A.U2387 A.A2388 angle=151 distance=17.9 ratio=0.97 98 A.C2389 A.A2390 angle=172 distance=18.9 ratio=1.00 99 A.U2392 A.C2393 angle=114 distance=15.5 ratio=0.84 100 A.A2401 A.A2402 angle=100 distance=14.6 ratio=0.77 101 A.C2414 A.C2415 angle=106 distance=14.5 ratio=0.80 102 A.U2422 A.C2423 angle=134 distance=17.7 ratio=0.92 103 A.A2424 A.A2425 angle=124 distance=14.7 ratio=0.88 104 A.A2425 A.C2426 angle=103 distance=15.4 ratio=0.78 105 A.C2426 A.C2427 angle=97 distance=13.8 ratio=0.75 106 A.A2429 A.A2430 angle=112 distance=13.8 ratio=0.83 107 A.C2433 A.A2434 angle=118 distance=14.5 ratio=0.86 108 A.A2434 A.G2435 angle=113 distance=15.7 ratio=0.83 109 A.U2445 A.A2446 angle=104 distance=14.6 ratio=0.79 110 A.A2446 A.A2447 angle=96 distance=14.4 ratio=0.74 111 A.A2452 A.G2453 angle=136 distance=17.6 ratio=0.93 112 A.G2477 A.G2478 angle=103 distance=15.4 ratio=0.78 113 A.U2499 A.A2500 angle=128 distance=17.6 ratio=0.90 114 A.C2501 A.C2502 angle=120 distance=16.6 ratio=0.86 115 A.A2505 A.A2506 angle=87 distance=13.7 ratio=0.69 116 A.A2506 A.A2507 angle=121 distance=15.8 ratio=0.87 117 A.C2520 A.A2521 angle=91 distance=12.6 ratio=0.72 118 A.U2522 A.C2523 angle=161 distance=18.3 ratio=0.99 119 A.C2523 A.A2524 angle=116 distance=15.6 ratio=0.85 120 A.A2527 A.G2528 angle=110 distance=15.1 ratio=0.82 121 A.A2530 A.U2531 angle=154 distance=18.3 ratio=0.97 122 A.U2531 A.U2532 angle=118 distance=16.4 ratio=0.86 123 A.U2614 A.A2615 angle=86 distance=12.4 ratio=0.68 124 A.A2617 A.U2618 angle=98 distance=15.6 ratio=0.75 125 A.U2618 A.A2619 angle=114 distance=15.6 ratio=0.84 126 A.G2643 A.A2644 angle=152 distance=17.4 ratio=0.97 127 A.A2644 A.G2645 angle=148 distance=18.0 ratio=0.96 128 A.U2654 A.G2655 angle=106 distance=13.3 ratio=0.80 129 A.U2680 A.G2681 angle=129 distance=17.4 ratio=0.90 130 A.C2683 A.C2684 angle=101 distance=13.8 ratio=0.77 131 A.C2684 A.U2685 angle=108 distance=16.0 ratio=0.81 132 A.U2685 A.G2686 angle=157 distance=18.8 ratio=0.98 133 A.A2696 A.G2697 angle=89 distance=13.7 ratio=0.70 134 A.G2698 A.C2699 angle=109 distance=15.7 ratio=0.81 135 A.U2705 A.A2706 angle=132 distance=17.8 ratio=0.91 136 A.A2717 A.C2718 angle=126 distance=18.2 ratio=0.89 137 A.C2718 A.G2719 angle=142 distance=16.6 ratio=0.94 138 A.A2730 A.U2731 angle=123 distance=18.6 ratio=0.88 139 A.U2731 A.G2732 angle=147 distance=19.0 ratio=0.96 140 A.U2738 A.U2739 angle=120 distance=16.1 ratio=0.87 141 A.U2739 A.A2740 angle=165 distance=18.4 ratio=0.99 142 A.C2809 A.G2810 angle=123 distance=17.7 ratio=0.88 143 A.C2822 A.U2823 angle=110 distance=15.8 ratio=0.82 144 A.A2830 A.G2831 angle=140 distance=19.6 ratio=0.94 145 A.A2832 A.A2833 angle=110 distance=17.6 ratio=0.82 146 A.A2838 A.C2839 angle=139 distance=18.6 ratio=0.94 147 A.C2839 A.C2840 angle=145 distance=19.6 ratio=0.95 148 A.U2863 A.U2864 angle=100 distance=14.1 ratio=0.77 149 A.U2864 A.C2865 angle=100 distance=16.3 ratio=0.77 150 A.C2865 A.A2866 angle=133 distance=18.2 ratio=0.92 151 A.A2913 A.A2914 angle=155 distance=18.5 ratio=0.98 152 A.A2914 A.C2915 angle=125 distance=17.6 ratio=0.89 153 A.C2915 A.G2916 angle=137 distance=17.5 ratio=0.93 154 A.G2917 A.A2918 angle=138 distance=16.8 ratio=0.93 155 A.A2918 A.A2919 angle=95 distance=14.4 ratio=0.74 156 A.A2921 A.A2922 angle=95 distance=14.0 ratio=0.74 157 A.U2925 A.A2926 angle=156 distance=18.2 ratio=0.98 158 A.A2926 A.C2927 angle=158 distance=18.5 ratio=0.98 159 A.C2944 A.A2945 angle=167 distance=18.6 ratio=0.99 160 A.G2959 A.U2960 angle=104 distance=13.5 ratio=0.79 161 A.C2962 A.A2963 angle=89 distance=14.7 ratio=0.71 162 A.U2964 A.A2965 angle=135 distance=17.2 ratio=0.92 163 A.A2968 A.A2969 angle=88 distance=12.3 ratio=0.69 164 A.U2978 A.U2979 angle=161 distance=18.5 ratio=0.99 165 A.A3005 A.U3006 angle=111 distance=16.4 ratio=0.82 166 A.U3015 A.G3016 angle=130 distance=16.2 ratio=0.91 167 A.G3016 A.C3017 angle=110 distance=16.9 ratio=0.82 168 A.C3017 A.A3018 angle=97 distance=10.9 ratio=0.76 169 A.U3033 A.U3034 angle=136 distance=18.0 ratio=0.93 170 A.G3040 A.U3041 angle=142 distance=18.6 ratio=0.94 171 A.U3042 A.C3043 angle=109 distance=15.1 ratio=0.81 172 A.A3053 A.G3054 angle=112 distance=17.1 ratio=0.83 173 A.G3063 A.A3064 angle=133 distance=17.4 ratio=0.92 174 A.A3064 A.U3065 angle=112 distance=16.8 ratio=0.83 175 A.U3072 A.C3073 angle=141 distance=18.4 ratio=0.94 176 A.G3082 A.U3083 angle=93 distance=12.7 ratio=0.73 177 A.C3088 A.A3089 angle=150 distance=19.7 ratio=0.97 178 A.A3089 A.G3090 angle=170 distance=19.5 ratio=1.00 179 A.G3095 A.U3096 angle=114 distance=16.7 ratio=0.84 180 A.U3096 A.U3097 angle=99 distance=16.6 ratio=0.76 181 A.C3099 A.U3100 angle=110 distance=16.6 ratio=0.82 182 A.U3100 A.A3101 angle=129 distance=17.5 ratio=0.90 183 A.U3107 A.U3108 angle=114 distance=14.1 ratio=0.84 184 A.U3108 A.U3109 angle=171 distance=19.3 ratio=1.00 185 A.G3127 A.A3128 angle=88 distance=12.1 ratio=0.70 186 A.G3132 A.A3133 angle=86 distance=12.4 ratio=0.68 187 A.A3156 A.C3157 angle=138 distance=17.6 ratio=0.93 188 A.C3157 A.A3158 angle=105 distance=15.2 ratio=0.79 189 A.U3167 A.C3168 angle=102 distance=14.5 ratio=0.78 190 A.A3182 A.U3183 angle=131 distance=18.2 ratio=0.91 191 A.U3183 A.C3184 angle=128 distance=17.5 ratio=0.90 192 A.U3186 A.C3187 angle=121 distance=16.1 ratio=0.87 193 A.C3187 A.U3188 angle=118 distance=15.4 ratio=0.86 194 A.U3188 A.C3189 angle=146 distance=19.8 ratio=0.96 195 A.C3189 A.A3190 angle=161 distance=21.0 ratio=0.99 196 A.C3206 A.A3207 angle=100 distance=15.8 ratio=0.77 197 A.A3207 A.C3208 angle=127 distance=19.1 ratio=0.89 198 A.A3209 A.C3210 angle=142 distance=18.3 ratio=0.95 199 A.C3216 A.A3217 angle=94 distance=13.2 ratio=0.73 200 A.A3217 A.A3218 angle=87 distance=13.0 ratio=0.69 201 A.G3219 A.A3220 angle=116 distance=14.6 ratio=0.85 202 A.U3227 A.U3228 angle=147 distance=17.3 ratio=0.96 203 B.G1608 B.U1609 angle=163 distance=18.7 ratio=0.99 204 B.U1614 B.A1615 angle=123 distance=16.3 ratio=0.88 205 B.C1631 B.U1632 angle=137 distance=19.3 ratio=0.93 206 B.U1633 B.A1634 angle=125 distance=15.4 ratio=0.89 ---------------------------------------------------------------- Summary of 141 splayed-apart units 1 nts=3 CCU A.C1698,A.C1699,A.U1700 2 nts=2 UA A.U1701,A.A1702 3 nts=3 CUA A.C1703,A.U1704,A.A1705 4 nts=2 UU A.U1716,A.U1717 5 nts=3 AAC A.A1723,A.A1724,A.C1725 6 nts=2 AU A.A1727,A.U1728 7 nts=2 UA A.U1730,A.A1731 8 nts=4 GGCG A.G1747,A.G1748,A.C1749,A.G1750 9 nts=3 GCG A.G1768,A.C1769,A.G1770 10 nts=3 AUA A.A1773,A.U1774,A.A1775 11 nts=2 AU A.A1779,A.U1780 12 nts=2 AG A.A1796,A.G1797 13 nts=2 CA A.C1813,A.A1814 14 nts=2 AA A.A1820,A.A1821 15 nts=2 AU A.A1823,A.U1824 16 nts=2 GC A.G1826,A.C1827 17 nts=3 AUA A.A1842,A.U1843,A.A1844 18 nts=2 AA A.A1859,A.A1860 19 nts=3 AGA A.A1885,A.G1886,A.A1887 20 nts=2 GC A.G1888,A.C1889 21 nts=3 AAA A.A1891,A.A1892,A.A1893 22 nts=2 CC A.C1902,A.C1903 23 nts=2 AG A.A1917,A.G1918 24 nts=2 CA A.C1930,A.A1931 25 nts=3 AGA A.A1938,A.G1939,A.A1940 26 nts=3 UAG A.U1956,A.A1957,A.G1958 27 nts=3 AAA A.A1960,A.A1961,A.A1962 28 nts=2 AA A.A1971,A.A1972 29 nts=3 GAU A.G1973,A.A1974,A.U1975 30 nts=3 GAC A.G1990,A.A1991,A.C1992 31 nts=3 CUA A.C1997,A.U1998,A.A1999 32 nts=3 CCG A.C2000,A.C2001,A.G2002 33 nts=2 AG A.A2003,A.G2004 34 nts=3 UGA A.U2010,A.G2011,A.A2012 35 nts=3 AGC A.A2014,A.G2015,A.C2016 36 nts=3 UUG A.U2020,A.U2021,A.G2022 37 nts=2 UA A.U2030,A.A2031 38 nts=2 UC A.U2035,A.C2036 39 nts=3 UAG A.U2038,A.A2039,A.G2040 40 nts=2 AA A.A2064,A.A2065 41 nts=2 AG A.A2097,A.G2098 42 nts=2 AG A.A2112,A.G2113 43 nts=2 AC A.A2124,A.C2125 44 nts=2 AA A.A2130,A.A2131 45 nts=2 AA A.A2133,A.A2134 46 nts=2 AG A.A2142,A.G2143 47 nts=3 GAG A.G2145,A.A2146,A.G2147 48 nts=2 AA A.A2154,A.A2155 49 nts=2 AU A.A2232,A.U2233 50 nts=2 CA A.C2236,A.A2237 51 nts=2 CA A.C2240,A.A2241 52 nts=2 UA A.U2242,A.A2243 53 nts=2 UA A.U2244,A.A2245 54 nts=3 AAC A.A2250,A.A2251,A.C2252 55 nts=2 CA A.C2259,A.A2260 56 nts=3 CCC A.C2261,A.C2262,A.C2263 57 nts=3 AGA A.A2291,A.G2292,A.A2293 58 nts=3 ACU A.A2294,A.C2295,A.U2296 59 nts=4 AAUG A.A2297,A.A2298,A.U2299,A.G2300 60 nts=2 UG A.U2316,A.G2317 61 nts=3 AAC A.A2320,A.A2321,A.C2322 62 nts=2 UC A.U2330,A.C2331 63 nts=3 GCG A.G2343,A.C2344,A.G2345 64 nts=2 UU A.U2371,A.U2372 65 nts=2 AC A.A2374,A.C2375 66 nts=2 CA A.C2380,A.A2381 67 nts=2 UA A.U2387,A.A2388 68 nts=2 CA A.C2389,A.A2390 69 nts=2 UC A.U2392,A.C2393 70 nts=2 AA A.A2401,A.A2402 71 nts=2 CC A.C2414,A.C2415 72 nts=2 UC A.U2422,A.C2423 73 nts=4 AACC A.A2424,A.A2425,A.C2426,A.C2427 74 nts=2 AA A.A2429,A.A2430 75 nts=3 CAG A.C2433,A.A2434,A.G2435 76 nts=3 UAA A.U2445,A.A2446,A.A2447 77 nts=2 AG A.A2452,A.G2453 78 nts=2 GG A.G2477,A.G2478 79 nts=2 UA A.U2499,A.A2500 80 nts=2 CC A.C2501,A.C2502 81 nts=3 AAA A.A2505,A.A2506,A.A2507 82 nts=2 CA A.C2520,A.A2521 83 nts=3 UCA A.U2522,A.C2523,A.A2524 84 nts=2 AG A.A2527,A.G2528 85 nts=3 AUU A.A2530,A.U2531,A.U2532 86 nts=2 UA A.U2614,A.A2615 87 nts=3 AUA A.A2617,A.U2618,A.A2619 88 nts=3 GAG A.G2643,A.A2644,A.G2645 89 nts=2 UG A.U2654,A.G2655 90 nts=2 UG A.U2680,A.G2681 91 nts=4 CCUG A.C2683,A.C2684,A.U2685,A.G2686 92 nts=2 AG A.A2696,A.G2697 93 nts=2 GC A.G2698,A.C2699 94 nts=2 UA A.U2705,A.A2706 95 nts=3 ACG A.A2717,A.C2718,A.G2719 96 nts=3 AUG A.A2730,A.U2731,A.G2732 97 nts=3 UUA A.U2738,A.U2739,A.A2740 98 nts=2 CG A.C2809,A.G2810 99 nts=2 CU A.C2822,A.U2823 100 nts=2 AG A.A2830,A.G2831 101 nts=2 AA A.A2832,A.A2833 102 nts=3 ACC A.A2838,A.C2839,A.C2840 103 nts=4 UUCA A.U2863,A.U2864,A.C2865,A.A2866 104 nts=4 AACG A.A2913,A.A2914,A.C2915,A.G2916 105 nts=3 GAA A.G2917,A.A2918,A.A2919 106 nts=2 AA A.A2921,A.A2922 107 nts=3 UAC A.U2925,A.A2926,A.C2927 108 nts=2 CA A.C2944,A.A2945 109 nts=2 GU A.G2959,A.U2960 110 nts=2 CA A.C2962,A.A2963 111 nts=2 UA A.U2964,A.A2965 112 nts=2 AA A.A2968,A.A2969 113 nts=2 UU A.U2978,A.U2979 114 nts=2 AU A.A3005,A.U3006 115 nts=4 UGCA A.U3015,A.G3016,A.C3017,A.A3018 116 nts=2 UU A.U3033,A.U3034 117 nts=2 GU A.G3040,A.U3041 118 nts=2 UC A.U3042,A.C3043 119 nts=2 AG A.A3053,A.G3054 120 nts=3 GAU A.G3063,A.A3064,A.U3065 121 nts=2 UC A.U3072,A.C3073 122 nts=2 GU A.G3082,A.U3083 123 nts=3 CAG A.C3088,A.A3089,A.G3090 124 nts=3 GUU A.G3095,A.U3096,A.U3097 125 nts=3 CUA A.C3099,A.U3100,A.A3101 126 nts=3 UUU A.U3107,A.U3108,A.U3109 127 nts=2 GA A.G3127,A.A3128 128 nts=2 GA A.G3132,A.A3133 129 nts=3 ACA A.A3156,A.C3157,A.A3158 130 nts=2 UC A.U3167,A.C3168 131 nts=3 AUC A.A3182,A.U3183,A.C3184 132 nts=5 UCUCA A.U3186,A.C3187,A.U3188,A.C3189,A.A3190 133 nts=3 CAC A.C3206,A.A3207,A.C3208 134 nts=2 AC A.A3209,A.C3210 135 nts=3 CAA A.C3216,A.A3217,A.A3218 136 nts=2 GA A.G3219,A.A3220 137 nts=2 UU A.U3227,A.U3228 138 nts=2 GU B.G1608,B.U1609 139 nts=2 UA B.U1614,B.A1615 140 nts=2 CU B.C1631,B.U1632 141 nts=2 UA B.U1633,B.A1634 **************************************************************************** This structure contains 3-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7qh7 nts=1312 [whole] GCUAAACCUAGCCCCAAACCC&CCACCUUACUACCA&CAAC&UUAGCCAAACCAUUUAC&AUAAAGUAUAGGCGAUAGAAAUUGA&UGGCGCAAUAGAUAUAGUACCGCAAGGGAAAGA&CAAGCAUAAUAUAGCAAGGACUAACCCCUAUACCUUCUGCAUAAUGAAUUAACUAGAAAUAACUUUGCAAGGAGAGCCAAAGCUAAGACCCCCGAAACCAGACGAGCUACCUAAGAACAGCUAAAAGAGCACACCCGUCUAUGUAGCAAAAUAGUGGGAAGAUUUAUAGGUAGAGGCGACAAACCUACCGAGCCUGGUGAUAGCUGGUUGUCCAAGAUAGAAUCUUAGUUCAACUUUAAAUUUGCCCACAGAACC&AAAUCCCCUUGUAAAUUUAACUGUUAGUCCAAAGAGGAACAGCUCUUUGGACACUAGGAAAAAACCUUGUAGAGAGAGUAAAAAAU&GAUCCCAAACAUAUAACUGAACUCCUCACACCCAAUUGGACCAAUCUAUCA&UAUAGAAGAACUAAUGUUAGUAUAAGUAACAUGAAAACAUUCUCCUCCGCAUAAGCCUGCGUCAGAU&CUGACAAUUAACAGCCCAAUAUCUACAAUCAACCAACAAG&UUAUUACCCUCACUGUCAACCCAAC&CAGGCAUGCUCAUAAGGAAAGGUUAAAAAAAGUAAAAGGAACUCGGCAAAUCUUACCCCGCCUGUUUACCAAAAACAUCACCUCUAGCAUCACCAGUAUUAGAGGCACCGCCU&CCUUAAAUAGG&CUCCACGAGGGUUCAGCUGUCUCUUACUUUUAACCAGUGAAAUUGACCUGCCCGUG&AGGCGGGCAUAACACAGCAAGACGA&AGACCCUAUGGAGCUUUAAUUUAUUAAUGCAAA&ACCUGCAUUAAAAAUUUCGGUUGGGGCGACCUCGGAGCAGAACCCAACCUCCGAG&GCUAAGACUUCACCAGUCAAAGCGAA&GAUCCAAUAACUUGACCAACGGAACAAGUUACCCUAGGG&CAAUCCUAUUCUAGAGUCCAUAUCAACAAUAGGGUUUAC&UGGAUCAGGACAUCCCGAUGGUGCAGCCGCUAUUAAAGGUUCGUUUGUUCAACGAUUAAAGUCCU&CGUGAUCUGAGUUCAGACCGGAGUAAUCCAGGUCGGUUUCUAUCUACUUU&AUUCCUCCCUGUACGAAAGGACAAGAGAAAUAAGGCCUACUUCACAAAGCGCCUUC&UAAAUGAUAUCAUCUCAACUUA&AUACCCACACCCACCCAAGAACAGGGUU&AGAGUGUAGCUUAA&AAGCACCCAACUUACACUUAGGAGAU&UCAA&UUGA&CGCUCUGA ((.....(..((((.......&..............&....&......(...[..)...&..(.....((.]...))....)...&.)).)).............((....))....).&...)).........(.(((.......))).[.(.((......)).).((((((.........(((.((..((....))...)).)))...((.(...((((.(.....(((((.((((.(((..<.[)))...(((..((((.......{)))).)))..).))).))))).(.((.......))...)..).))))......).))..((((((....((((....)))).((.((((((((((.....((...&...)).....))))))))))..))..((((((((((......))))))))))...(((......)))....(((.(((...(....&.................)...))))))........))))))...(((((..&.))))).........))))))(......((..(((....)))((((..((((......(.(((((..&)))))......(((...((((.......>.......(..)&.)))).......))).)...((...&..)).)))).....))))..((((....(((((((.((..(....(........((((((.].((.........))....((((((.............))))))....(...&((.......))&)....)).))))....)..))).))))))).)))).)).....)).{..(((((..&]}.))))).......((..(((.((&...(((((.((((((..(((((..(((((((..&...))))))).)))))..(((.......)))((((((...........))))))(&((...(((....[..)))...))...&...................)].....))))..)))))))&....((((((...((.......))...))))))......&((((.((((((..((.(((.((......)).)))...)).(((((.....))))).....)))))&.)...))))......(((((((....))).))))..}.))..))).))..&(((.(((......(....).....))).)))(((((...(((....))).))))).&(((................)))&............((((.......)))).&...(....(((...&.)))..(.............).....&.(.(&).).&..)..... >7qh7-A #1 nts=1256 0.02(3.74) [chain] RNA* GCUAAACCUAGCCCCAAACCC&CCACCUUACUACCA&CAAC&UUAGCCAAACCAUUUAC&AUAAAGUAUAGGCGAUAGAAAUUGA&UGGCGCAAUAGAUAUAGUACCGCAAGGGAAAGA&CAAGCAUAAUAUAGCAAGGACUAACCCCUAUACCUUCUGCAUAAUGAAUUAACUAGAAAUAACUUUGCAAGGAGAGCCAAAGCUAAGACCCCCGAAACCAGACGAGCUACCUAAGAACAGCUAAAAGAGCACACCCGUCUAUGUAGCAAAAUAGUGGGAAGAUUUAUAGGUAGAGGCGACAAACCUACCGAGCCUGGUGAUAGCUGGUUGUCCAAGAUAGAAUCUUAGUUCAACUUUAAAUUUGCCCACAGAACC&AAAUCCCCUUGUAAAUUUAACUGUUAGUCCAAAGAGGAACAGCUCUUUGGACACUAGGAAAAAACCUUGUAGAGAGAGUAAAAAAU&GAUCCCAAACAUAUAACUGAACUCCUCACACCCAAUUGGACCAAUCUAUCA&UAUAGAAGAACUAAUGUUAGUAUAAGUAACAUGAAAACAUUCUCCUCCGCAUAAGCCUGCGUCAGAU&CUGACAAUUAACAGCCCAAUAUCUACAAUCAACCAACAAG&UUAUUACCCUCACUGUCAACCCAAC&CAGGCAUGCUCAUAAGGAAAGGUUAAAAAAAGUAAAAGGAACUCGGCAAAUCUUACCCCGCCUGUUUACCAAAAACAUCACCUCUAGCAUCACCAGUAUUAGAGGCACCGCCU&CCUUAAAUAGG&CUCCACGAGGGUUCAGCUGUCUCUUACUUUUAACCAGUGAAAUUGACCUGCCCGUG&AGGCGGGCAUAACACAGCAAGACGA&AGACCCUAUGGAGCUUUAAUUUAUUAAUGCAAA&ACCUGCAUUAAAAAUUUCGGUUGGGGCGACCUCGGAGCAGAACCCAACCUCCGAG&GCUAAGACUUCACCAGUCAAAGCGAA&GAUCCAAUAACUUGACCAACGGAACAAGUUACCCUAGGG&CAAUCCUAUUCUAGAGUCCAUAUCAACAAUAGGGUUUAC&UGGAUCAGGACAUCCCGAUGGUGCAGCCGCUAUUAAAGGUUCGUUUGUUCAACGAUUAAAGUCCU&CGUGAUCUGAGUUCAGACCGGAGUAAUCCAGGUCGGUUUCUAUCUACUUU&AUUCCUCCCUGUACGAAAGGACAAGAGAAAUAAGGCCUACUUCACAAAGCGCCUUC&UAAAUGAUAUCAUCUCAACUUA&AUACCCACACCCACCCAAGAACAGGGUU ((.....(..((((.......&..............&....&......(...[..)...&..(.....((.]...))....)...&.)).)).............((....))....).&...)).........(.(((.......))).[.(.((......)).).((((((.........(((.((..((....))...)).)))...((.(...((((.(.....(((((.((((.(((..<.[)))...(((..((((.......{)))).)))..).))).))))).(.((.......))...)..).))))......).))..((((((....((((....)))).((.((((((((((.....((...&...)).....))))))))))..))..((((((((((......))))))))))...(((......)))....(((.(((...(....&.................)...))))))........))))))...(((((..&.))))).........))))))(......((..(((....)))((((..((((......(.(((((..&)))))......(((...((((.......>.......(..)&.)))).......))).)...((...&..)).)))).....))))..((((....(((((((.((..(....(........((((((.].((.........))....((((((.............))))))....(...&((.......))&)....)).))))....)..))).))))))).)))).)).....)).{..(((((..&]}.))))).......((..(((.((&...(((((.((((((..(((((..(((((((..&...))))))).)))))..(((.......)))((((((...........))))))(&((...(((....[..)))...))...&...................)].....))))..)))))))&....((((((...((.......))...))))))......&((((.((((((..((.(((.((......)).)))...)).(((((.....))))).....)))))&.)...))))......(((((((....))).))))..}.))..))).))..&(((.(((......(....).....))).)))(((((...(((....))).))))).&(((................)))&............((((.......)))). >7qh7-B #2 nts=56 0.15(3.27) [chain] RNA* AGAGUGUAGCUUAA&AAGCACCCAACUUACACUUAGGAGAU&UCAA&UUGA&CGCUCUGA ...(....(((...&.)))..(.............).....&.(.(&).).&..)..... **************************************************************************** Summary of structural features of 1312 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G ( A.G1671 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( A.C1672 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 3 U . A.U1673 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,phosphate 4 A . A.A1674 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 5 A . A.A1675 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 6 A . A.A1676 0.010 anti,~C3'-endo,non-pair-contact,ss-non-loop 7 C . A.C1677 0.008 anti,~C2'-endo,non-pair-contact,ss-non-loop 8 C ( A.C1678 0.014 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,junction-loop,phosphate 9 U . A.U1679 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 10 A . A.A1680 0.021 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate 11 G ( A.G1681 0.019 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 12 C ( A.C1682 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 13 C ( A.C1683 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 14 C ( A.C1684 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 15 C . A.C1685 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 16 A . A.A1686 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 17 A . A.A1687 0.016 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 18 A . A.A1688 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 19 C . A.C1689 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 20 C . A.C1690 0.005 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop 21 C . A.C1691 0.002 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 22 C . A.C1695 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 23 C . A.C1696 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 24 A . A.A1697 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,ribose-zipper,phosphate 25 C . A.C1698 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,ribose-zipper,phosphate,splayed-apart 26 C . A.C1699 0.014 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 27 U . A.U1700 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 28 U . A.U1701 0.011 turn,anti,~C2'-endo,ss-non-loop,splayed-apart 29 A . A.A1702 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,ribose-zipper,phosphate,splayed-apart 30 C . A.C1703 0.010 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,ribose-zipper,splayed-apart 31 U . A.U1704 0.014 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 32 A . A.A1705 0.017 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 33 C . A.C1706 0.008 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate 34 C . A.C1707 0.007 anti,~C2'-endo,BII,ss-non-loop,phosphate 35 A . A.A1708 0.010 break,anti,~C2'-endo,non-stack,ss-non-loop 36 C . A.C1711 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 37 A . A.A1712 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 38 A . A.A1713 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 39 C . A.C1714 0.004 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 40 U . A.U1716 0.016 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 41 U . A.U1717 0.004 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,ss-non-loop,phosphate,splayed-apart 42 A . A.A1718 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop,A-minor 43 G . A.G1719 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 44 C . A.C1720 0.008 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 45 C . A.C1721 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 46 A ( A.A1722 0.016 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,hairpin-loop,A-minor,kissing-loop 47 A . A.A1723 0.018 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,kissing-loop,splayed-apart 48 A . A.A1724 0.022 turn,syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,kissing-loop,phosphate,splayed-apart 49 C . A.C1725 0.011 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 50 C [ A.C1726 0.014 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,kissing-loop,phosphate 51 A . A.A1727 0.017 anti,~C2'-endo,non-pair-contact,hairpin-loop,A-minor,kissing-loop,phosphate,splayed-apart 52 U . A.U1728 0.014 anti,~C3'-endo,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 53 U ) A.U1729 0.015 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,A-minor,kissing-loop,phosphate 54 U . A.U1730 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 55 A . A.A1731 0.020 ~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 56 C . A.C1732 0.014 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 57 A . A.A1737 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 58 U . A.U1738 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 59 A ( A.A1739 0.023 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 60 A . A.A1740 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 61 A . A.A1741 0.020 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop,phosphate 62 G . A.G1742 0.020 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 63 U . A.U1743 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 64 A . A.A1744 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 65 U ( A.U1745 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 66 A ( A.A1746 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,kissing-loop 67 G . A.G1747 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,phosphate,splayed-apart 68 G ] A.G1748 0.016 pseudoknotted,turn,anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,kissing-loop,phosphate,splayed-apart 69 C . A.C1749 0.011 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 70 G . A.G1750 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,kissing-loop,phosphate,splayed-apart 71 A . A.A1751 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,A-minor,kissing-loop,phosphate 72 U ) A.U1752 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,kissing-loop 73 A ) A.A1753 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 74 G . A.G1754 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 75 A . A.A1755 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 76 A . A.A1756 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 77 A . A.A1757 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 78 U ) A.U1758 0.014 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 79 U . A.U1759 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 80 G . A.G1760 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 81 A . A.A1761 0.008 break,anti,~C2'-endo,non-pair-contact,ss-non-loop 82 U . A.U1766 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 83 G ) A.G1767 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 84 G ) A.G1768 0.019 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 85 C . A.C1769 0.012 turn,anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge,splayed-apart 86 G ) A.G1770 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 87 C ) A.C1771 0.021 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 88 A . A.A1772 0.020 anti,~C2'-endo,BII,non-pair-contact,junction-loop,phosphate 89 A . A.A1773 0.016 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 90 U . A.U1774 0.015 turn,anti,~C2'-endo,non-stack,non-canonical,multiplet,junction-loop,splayed-apart 91 A . A.A1775 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,phosphate,splayed-apart 92 G . A.G1776 0.022 anti,~C3'-endo,non-canonical,non-pair-contact,junction-loop,phosphate 93 A . A.A1777 0.016 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 94 U . A.U1778 0.017 turn,anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 95 A . A.A1779 0.016 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate,splayed-apart 96 U . A.U1780 0.010 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 97 A . A.A1781 0.016 anti,~C2'-endo,non-canonical,non-pair-contact,junction-loop,phosphate 98 G . A.G1782 0.021 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 99 U . A.U1783 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 100 A . A.A1784 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 101 C ( A.C1785 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 102 C ( A.C1786 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 103 G . A.G1787 0.021 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor 104 C . A.C1788 0.017 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 105 A . A.A1789 0.025 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 106 A . A.A1790 0.023 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 107 G ) A.G1791 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 108 G ) A.G1792 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 109 G . A.G1793 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 110 A . A.A1794 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 111 A . A.A1795 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,phosphate 112 A . A.A1796 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 113 G ) A.G1797 0.011 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 114 A . A.A1798 0.018 break,anti,~C2'-endo,non-pair-contact,ss-non-loop 115 C . A.C1813 0.006 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 116 A . A.A1814 0.016 anti,~C3'-endo,non-pair-contact,ss-non-loop,A-minor,ribose-zipper,splayed-apart 117 A . A.A1815 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,A-minor,ribose-zipper,phosphate 118 G ) A.G1816 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 119 C ) A.C1817 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 120 A . A.A1818 0.016 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 121 U . A.U1819 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 122 A . A.A1820 0.013 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 123 A . A.A1821 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 124 U . A.U1822 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 125 A . A.A1823 0.016 syn,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 126 U . A.U1824 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 127 A . A.A1825 0.017 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,cap-donor 128 G . A.G1826 0.013 ~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop,cap-acceptor,splayed-apart 129 C ( A.C1827 0.013 turn,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,cap-donor,cap-acceptor,splayed-apart 130 A . A.A1828 0.018 turn,syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,cap-acceptor 131 A ( A.A1829 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 132 G ( A.G1830 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 133 G ( A.G1831 0.023 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate 134 A . A.A1832 0.017 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 135 C . A.C1833 0.014 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 136 U . A.U1834 0.015 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 137 A . A.A1835 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,hairpin-loop,cap-donor,phosphate 138 A . A.A1836 0.015 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 139 C . A.C1837 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,phosphate 140 C . A.C1838 0.013 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 141 C ) A.C1839 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate 142 C ) A.C1840 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 143 U ) A.U1841 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 144 A . A.A1842 0.016 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 145 U [ A.U1843 0.016 pseudoknotted,turn,anti,~C2'-endo,non-stack,isolated-canonical,non-pair-contact,helix,multiplet,cap-acceptor,splayed-apart 146 A . A.A1844 0.022 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,cap-donor,phosphate,splayed-apart 147 C ( A.C1845 0.016 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 148 C . A.C1846 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate 149 U ( A.U1847 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 150 U ( A.U1848 0.010 anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end,hairpin-loop,phosphate 151 C . A.C1849 0.007 anti,~C3'-endo,non-stack,hairpin-loop 152 U . A.U1850 0.007 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop 153 G . A.G1851 0.009 anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 154 C . A.C1852 0.007 anti,~C2'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 155 A . A.A1853 0.009 turn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,cap-acceptor 156 U . A.U1854 0.004 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop 157 A ) A.A1855 0.018 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,cap-donor 158 A ) A.A1856 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 159 U . A.U1857 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 160 G ) A.G1858 0.020 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 161 A . A.A1859 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,cap-acceptor,phosphate,splayed-apart 162 A ( A.A1860 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,cap-donor,splayed-apart 163 U ( A.U1861 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 164 U ( A.U1862 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,ribose-zipper,phosphate 165 A ( A.A1863 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet 166 A ( A.A1864 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 167 C ( A.C1865 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 168 U . A.U1866 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 169 A . A.A1867 0.022 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor 170 G . A.G1868 0.019 syn,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,phosphate 171 A . A.A1869 0.018 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate 172 A . A.A1870 0.016 anti,~C2'-endo,BII,non-pair-contact,junction-loop 173 A . A.A1871 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 174 U . A.U1872 0.013 anti,~C3'-endo,non-pair-contact,junction-loop 175 A . A.A1873 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 176 A . A.A1874 0.015 anti,~C3'-endo,BI,non-pair-contact,junction-loop 177 C ( A.C1875 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 178 U ( A.U1876 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 179 U ( A.U1877 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 180 U . A.U1878 0.017 anti,~C3'-endo,BI,non-stack,non-canonical,helix,internal-loop,phosphate 181 G ( A.G1879 0.034 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 182 C ( A.C1880 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,phosphate 183 A . A.A1881 0.020 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 184 A . A.A1882 0.015 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate 185 G ( A.G1883 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 186 G ( A.G1884 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate 187 A . A.A1885 0.016 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 188 G . A.G1886 0.027 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 189 A . A.A1887 0.015 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 190 G . A.G1888 0.009 ~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 191 C ) A.C1889 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,splayed-apart 192 C ) A.C1890 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 193 A . A.A1891 0.016 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 194 A . A.A1892 0.012 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 195 A . A.A1893 0.019 anti,~C2'-endo,BII,non-pair-contact,internal-loop,phosphate,splayed-apart 196 G ) A.G1894 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 197 C ) A.C1895 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 198 U . A.U1896 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 199 A ) A.A1897 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 200 A ) A.A1898 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 201 G ) A.G1899 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 202 A . A.A1900 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop 203 C . A.C1901 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 204 C . A.C1902 0.015 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 205 C ( A.C1903 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,cap-donor,phosphate,splayed-apart 206 C ( A.C1904 0.020 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,phosphate 207 C . A.C1905 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 208 G ( A.G1906 0.020 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate 209 A . A.A1907 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper,phosphate 210 A . A.A1908 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper 211 A . A.A1909 0.019 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 212 C ( A.C1910 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 213 C ( A.C1911 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 214 A ( A.A1912 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 215 G ( A.G1913 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 216 A . A.A1914 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper 217 C ( A.C1915 0.017 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,junction-loop,A-minor,ribose-zipper 218 G . A.G1916 0.022 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 219 A . A.A1917 0.026 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 220 G . A.G1918 0.028 turn,syn,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 221 C . A.C1919 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 222 U . A.U1920 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop 223 A ( A.A1921 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 224 C ( A.C1922 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 225 C ( A.C1923 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 226 U ( A.U1924 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 227 A ( A.A1925 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 228 A . A.A1926 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 229 G ( A.G1927 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 230 A ( A.A1928 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 231 A ( A.A1929 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 232 C ( A.C1930 0.012 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,junction-loop,splayed-apart 233 A . A.A1931 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 234 G ( A.G1932 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 235 C ( A.C1933 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 236 U ( A.U1934 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 237 A . A.A1935 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 238 A . A.A1936 0.005 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop 239 A < A.A1937 0.006 pseudoknotted,turn,anti,~C2'-endo,non-stack,isolated-canonical,helix-end,multiplet,hairpin-loop 240 A . A.A1938 0.010 ~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 241 G [ A.G1939 0.018 pseudoknotted,turn,syn,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 242 A ) A.A1940 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate,splayed-apart 243 G ) A.G1941 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 244 C ) A.C1942 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 245 A . A.A1943 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 246 C . A.C1944 0.009 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 247 A . A.A1945 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor,phosphate 248 C ( A.C1946 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor 249 C ( A.C1947 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 250 C ( A.C1948 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 251 G . A.G1949 0.015 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,internal-loop 252 U . A.U1950 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,cap-donor,phosphate 253 C ( A.C1951 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 254 U ( A.U1952 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 255 A ( A.A1953 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 256 U ( A.U1954 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop 257 G . A.G1955 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 258 U . A.U1956 0.008 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 259 A . A.A1957 0.004 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 260 G . A.G1958 0.013 anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 261 C . A.C1959 0.013 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop 262 A . A.A1960 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 263 A . A.A1961 0.019 turn,anti,~C3'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 264 A { A.A1962 0.015 pseudoknotted,anti,~C2'-endo,non-stack,isolated-canonical,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 265 A ) A.A1963 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,phosphate 266 U ) A.U1964 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 267 A ) A.A1965 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 268 G ) A.G1966 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 269 U . A.U1967 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 270 G ) A.G1968 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 271 G ) A.G1969 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 272 G ) A.G1970 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 273 A . A.A1971 0.019 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 274 A . A.A1972 0.009 turn,anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 275 G ) A.G1973 0.018 ~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,bulge,junction-loop,cap-acceptor,phosphate,splayed-apart 276 A . A.A1974 0.018 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,helix,multiplet,bulge,phosphate,splayed-apart 277 U ) A.U1975 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 278 U ) A.U1976 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 279 U ) A.U1977 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 280 A . A.A1978 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 281 U ) A.U1979 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 282 A ) A.A1980 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 283 G ) A.G1981 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 284 G ) A.G1982 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 285 U ) A.U1983 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 286 A . A.A1984 0.025 ~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 287 G ( A.G1985 0.015 anti,~C2'-endo,BII,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,junction-loop,phosphate 288 A . A.A1986 0.011 turn,anti,~C2'-endo,non-pair-contact,internal-loop 289 G ( A.G1987 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,phosphate 290 G ( A.G1988 0.023 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,hairpin-loop,A-minor,phosphate 291 C . A.C1989 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 292 G . A.G1990 0.016 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 293 A . A.A1991 0.016 turn,anti,~C3'-endo,BII,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-acceptor,phosphate,splayed-apart 294 C . A.C1992 0.010 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 295 A . A.A1993 0.022 turn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 296 A . A.A1994 0.005 turn,anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,phosphate 297 A . A.A1995 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate 298 C ) A.C1996 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,hairpin-loop,A-minor 299 C ) A.C1997 0.015 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,cap-donor,phosphate,splayed-apart 300 U . A.U1998 0.015 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 301 A . A.A1999 0.012 anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 302 C . A.C2000 0.004 anti,~C3'-endo,non-stack,internal-loop,splayed-apart 303 C ) A.C2001 0.017 anti,~C2'-endo,non-stack,isolated-canonical,non-pair-contact,helix-end,multiplet,internal-loop,junction-loop,splayed-apart 304 G . A.G2002 0.010 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 305 A . A.A2003 0.011 anti,~C2'-endo,BII,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 306 G ) A.G2004 0.019 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,multiplet,internal-loop,junction-loop,A-minor,splayed-apart 307 C . A.C2005 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 308 C ) A.C2006 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 309 U ) A.U2007 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 310 G ) A.G2008 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 311 G ) A.G2009 0.020 turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 312 U . A.U2010 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,phosphate,splayed-apart 313 G . A.G2011 0.015 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 314 A . A.A2012 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,cap-donor,splayed-apart 315 U . A.U2013 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 316 A . A.A2014 0.020 anti,~C3'-endo,BII,non-pair-contact,internal-loop,splayed-apart 317 G . A.G2015 0.018 turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-acceptor,phosphate,splayed-apart 318 C ) A.C2016 0.018 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 319 U . A.U2017 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 320 G ) A.G2018 0.019 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 321 G ) A.G2019 0.020 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 322 U . A.U2020 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 323 U . A.U2021 0.021 anti,~C2'-endo,BI,non-pair-contact,junction-loop,splayed-apart 324 G ( A.G2022 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 325 U ( A.U2023 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 326 C ( A.C2024 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 327 C ( A.C2025 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 328 A ( A.A2026 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 329 A ( A.A2027 0.021 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 330 G . A.G2028 0.013 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop 331 A . A.A2029 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,phosphate 332 U . A.U2030 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 333 A . A.A2031 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 334 G ( A.G2032 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 335 A ( A.A2033 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 336 A ( A.A2034 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 337 U ( A.U2035 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,phosphate,splayed-apart 338 C . A.C2036 0.011 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 339 U . A.U2037 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,phosphate 340 U . A.U2038 0.007 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,hairpin-loop,phosphate,splayed-apart 341 A . A.A2039 0.016 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,splayed-apart 342 G ) A.G2040 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,splayed-apart 343 U ) A.U2041 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 344 U ) A.U2042 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 345 C ) A.C2043 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 346 A . A.A2044 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 347 A ( A.A2045 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 348 C ( A.C2046 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor 349 U . A.U2047 0.012 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix,internal-loop 350 U ( A.U2048 0.011 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 351 U ( A.U2049 0.014 anti,~C3'-endo,BI,non-stack,canonical,helix,stem,coaxial-stack 352 A ( A.A2050 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 353 A ( A.A2051 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 354 A ( A.A2052 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 355 U ( A.U2053 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 356 U ( A.U2054 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 357 U ( A.U2055 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 358 G ( A.G2056 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 359 C ( A.C2057 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 360 C . A.C2058 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 361 C . A.C2059 0.010 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 362 A . A.A2060 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,internal-loop 363 C . A.C2061 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 364 A . A.A2062 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 365 G ( A.G2063 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 366 A ( A.A2064 0.016 anti,~C3'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate,splayed-apart 367 A . A.A2065 0.009 ~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 368 C . A.C2066 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 369 C . A.C2067 0.002 break,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 370 A . A.A2072 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 371 A . A.A2073 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,ss-non-loop,phosphate 372 A . A.A2074 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 373 U ) A.U2075 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 374 C ) A.C2076 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 375 C . A.C2077 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 376 C . A.C2078 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 377 C . A.C2079 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 378 U . A.U2080 0.009 anti,~C3'-endo,BI,non-pair-contact,internal-loop 379 U . A.U2081 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 380 G ) A.G2082 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 381 U ) A.U2083 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 382 A ) A.A2084 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 383 A ) A.A2085 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 384 A ) A.A2086 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 385 U ) A.U2087 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 386 U ) A.U2088 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 387 U ) A.U2089 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 388 A ) A.A2090 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 389 A ) A.A2091 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 390 C . A.C2092 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 391 U . A.U2093 0.015 anti,~C3'-endo,BI,non-pair-contact,internal-loop 392 G ) A.G2094 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor 393 U ) A.U2095 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 394 U . A.U2096 0.007 anti,~C3'-endo,BII,non-stack,non-canonical,non-pair-contact,helix,multiplet,junction-loop 395 A . A.A2097 0.009 turn,~C3'-endo,non-stack,non-pair-contact,junction-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 396 G ( A.G2098 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,A-minor,splayed-apart 397 U ( A.U2099 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 398 C ( A.C2100 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 399 C ( A.C2101 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 400 A ( A.A2102 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 401 A ( A.A2103 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 402 A ( A.A2104 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 403 G ( A.G2105 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,phosphate 404 A ( A.A2106 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 405 G ( A.G2107 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate 406 G . A.G2108 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,cap-acceptor 407 A . A.A2109 0.008 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor 408 A . A.A2110 0.006 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 409 C . A.C2111 0.007 anti,~C3'-endo,non-pair-contact,hairpin-loop 410 A . A.A2112 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 411 G . A.G2113 0.003 turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 412 C ) A.C2114 0.005 anti,~C3'-endo,BII,non-stack,canonical,non-canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 413 U ) A.U2115 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 414 C ) A.C2116 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 415 U ) A.U2117 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-donor 416 U ) A.U2118 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 417 U ) A.U2119 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 418 G ) A.G2120 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 419 G ) A.G2121 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 420 A ) A.A2122 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 421 C ) A.C2123 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,A-minor 422 A . A.A2124 0.013 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 423 C . A.C2125 0.006 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 424 U . A.U2126 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 425 A ( A.A2127 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,A-minor 426 G ( A.G2128 0.019 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 427 G ( A.G2129 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 428 A . A.A2130 0.012 anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 429 A . A.A2131 0.018 anti,~C2'-endo,non-pair-contact,hairpin-loop,A-minor,cap-donor,phosphate,splayed-apart 430 A . A.A2132 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-acceptor 431 A . A.A2133 0.007 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 432 A . A.A2134 0.008 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,A-minor,splayed-apart 433 A . A.A2135 0.011 ~C2'-endo,non-pair-contact,hairpin-loop,phosphate 434 C ) A.C2136 0.014 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate 435 C ) A.C2137 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 436 U ) A.U2138 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,A-minor,ribose-zipper 437 U . A.U2139 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 438 G . A.G2140 0.004 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 439 U . A.U2141 0.007 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor 440 A . A.A2142 0.008 ~C2'-endo,non-pair-contact,junction-loop,cap-acceptor,splayed-apart 441 G ( A.G2143 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 442 A ( A.A2144 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 443 G ( A.G2145 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 444 A . A.A2146 0.022 turn,anti,~C2'-endo,non-stack,bulge,phosphate,splayed-apart 445 G ( A.G2147 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 446 A ( A.A2148 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 447 G ( A.G2149 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 448 U . A.U2150 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 449 A . A.A2151 0.018 anti,~C3'-endo,non-pair-contact,internal-loop,A-minor,ribose-zipper,phosphate 450 A . A.A2152 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper,phosphate 451 A ( A.A2153 0.020 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate 452 A . A.A2154 0.007 ~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 453 A . A.A2155 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 454 A . A.A2156 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop 455 U . A.U2157 0.005 break,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 456 G . A.G2231 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,ribose-zipper 457 A . A.A2232 0.015 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,ribose-zipper,splayed-apart 458 U . A.U2233 0.017 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 459 C . A.C2234 0.016 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 460 C . A.C2235 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 461 C . A.C2236 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 462 A . A.A2237 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 463 A . A.A2238 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 464 A . A.A2239 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 465 C . A.C2240 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 466 A . A.A2241 0.021 syn,~C3'-endo,ss-non-loop,phosphate,splayed-apart 467 U . A.U2242 0.012 anti,~C2'-endo,BII,ss-non-loop,splayed-apart 468 A . A.A2243 0.007 anti,~C2'-endo,ss-non-loop,splayed-apart 469 U . A.U2244 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 470 A . A.A2245 0.014 ~C2'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 471 A . A.A2246 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 472 C . A.C2247 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 473 U ) A.U2248 0.010 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate 474 G . A.G2249 0.018 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 475 A . A.A2250 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor,phosphate,splayed-apart 476 A . A.A2251 0.013 turn,syn,~C2'-endo,non-canonical,non-pair-contact,internal-loop,phosphate,splayed-apart 477 C ) A.C2252 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 478 U ) A.U2253 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 479 C ) A.C2254 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 480 C ) A.C2255 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 481 U ) A.U2256 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 482 C ) A.C2257 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 483 A . A.A2258 0.018 anti,~C3'-endo,BI,non-pair-contact,junction-loop 484 C . A.C2259 0.010 anti,~C3'-endo,BI,non-pair-contact,junction-loop,splayed-apart 485 A . A.A2260 0.012 turn,anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 486 C . A.C2261 0.012 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 487 C . A.C2262 0.011 anti,~C2'-endo,BII,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 488 C . A.C2263 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 489 A . A.A2264 0.013 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 490 A . A.A2265 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,A-minor,phosphate 491 U ) A.U2266 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 492 U ) A.U2267 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 493 G ) A.G2268 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 494 G ) A.G2269 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 495 A ) A.A2270 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 496 C ) A.C2271 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 497 C . A.C2272 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 498 A . A.A2273 0.018 ~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop 499 A . A.A2274 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 500 U ( A.U2275 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 501 C ( A.C2276 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 502 U ( A.U2277 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 503 A ( A.A2278 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 504 U ( A.U2279 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 505 C . A.C2280 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 506 A . A.A2281 0.006 break,anti,~C2'-endo,non-pair-contact,ss-non-loop 507 U . A.U2285 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 508 A ) A.A2286 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 509 U ) A.U2287 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 510 A ) A.A2288 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 511 G ) A.G2289 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 512 A ) A.A2290 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 513 A . A.A2291 0.018 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 514 G . A.G2292 0.023 turn,anti,~C2'-endo,non-pair-contact,junction-loop,splayed-apart 515 A . A.A2293 0.014 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 516 A . A.A2294 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 517 C . A.C2295 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate,splayed-apart 518 U . A.U2296 0.012 turn,anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 519 A . A.A2297 0.019 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 520 A . A.A2298 0.021 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,phosphate,splayed-apart 521 U . A.U2299 0.007 turn,anti,~C3'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 522 G ) A.G2300 0.020 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 523 U ) A.U2301 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 524 U ) A.U2302 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,phosphate 525 A ) A.A2303 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 526 G ) A.G2304 0.019 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 527 U ) A.U2305 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 528 A ( A.A2306 0.022 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate 529 U . A.U2307 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 530 A . A.A2308 0.027 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 531 A . A.A2309 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 532 G . A.G2310 0.020 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 533 U . A.U2311 0.024 ~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 534 A . A.A2312 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 535 A ( A.A2313 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 536 C ( A.C2314 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 537 A . A.A2315 0.022 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop 538 U . A.U2316 0.007 anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 539 G ( A.G2317 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 540 A ( A.A2318 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 541 A ( A.A2319 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 542 A . A.A2320 0.013 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 543 A . A.A2321 0.018 turn,anti,~C2'-endo,hairpin-loop,phosphate,splayed-apart 544 C . A.C2322 0.007 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 545 A . A.A2323 0.005 turn,anti,~C3'-endo,non-stack,hairpin-loop,cap-acceptor 546 U ) A.U2324 0.013 anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 547 U ) A.U2325 0.012 anti,~C3'-endo,BI,non-stack,canonical,helix,stem,coaxial-stack,phosphate 548 C ) A.C2326 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 549 U ( A.U2327 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 550 C ( A.C2328 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 551 C ( A.C2329 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 552 U ( A.U2330 0.011 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,splayed-apart 553 C . A.C2331 0.008 turn,~C2'-endo,non-stack,internal-loop,splayed-apart 554 C . A.C2332 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 555 G ( A.G2333 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 556 C ( A.C2334 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 557 A ( A.A2335 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 558 U ( A.U2336 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 559 A . A.A2337 0.014 anti,~C3'-endo,BI,non-pair-contact,junction-loop 560 A . A.A2338 0.011 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 561 G . A.G2339 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,phosphate 562 C . A.C2340 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 563 C . A.C2341 0.009 anti,~C2'-endo,BII,non-pair-contact,junction-loop 564 U . A.U2342 0.012 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,phosphate 565 G ( A.G2343 0.013 syn,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,splayed-apart 566 C . A.C2344 0.009 turn,anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 567 G ( A.G2345 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop,phosphate,splayed-apart 568 U ( A.U2346 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 569 C ( A.C2347 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 570 A ( A.A2348 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 571 G ( A.G2349 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 572 A . A.A2350 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 573 U . A.U2351 0.003 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 574 C ) A.C2364 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 575 U ) A.U2365 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 576 G ) A.G2366 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 577 A ) A.A2367 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 578 C ) A.C2368 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 579 A . A.A2369 0.015 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 580 A . A.A2370 0.018 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate 581 U . A.U2371 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,splayed-apart 582 U . A.U2372 0.013 syn,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 583 A . A.A2373 0.016 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 584 A . A.A2374 0.014 turn,~C2'-endo,BI,non-pair-contact,junction-loop,phosphate,splayed-apart 585 C ( A.C2375 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 586 A ( A.A2376 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 587 G ( A.G2377 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 588 C . A.C2378 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 589 C . A.C2379 0.009 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 590 C . A.C2380 0.005 anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 591 A ( A.A2381 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,splayed-apart 592 A ( A.A2382 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 593 U ( A.U2383 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 594 A ( A.A2384 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 595 U . A.U2385 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,ss-non-loop,phosphate 596 C . A.C2386 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 597 U . A.U2387 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 598 A . A.A2388 0.013 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 599 C . A.C2389 0.006 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 600 A . A.A2390 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate,splayed-apart 601 A . A.A2391 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 602 U > A.U2392 0.006 pseudoknotted,anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,splayed-apart 603 C . A.C2393 0.007 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 604 A . A.A2394 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,ss-non-loop 605 A . A.A2395 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 606 C . A.C2396 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,ss-non-loop 607 C . A.C2397 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop 608 A . A.A2398 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop 609 A . A.A2399 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 610 C ( A.C2400 0.010 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop 611 A . A.A2401 0.011 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 612 A . A.A2402 0.011 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 613 G ) A.G2403 0.032 break,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 614 U . A.U2407 0.002 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix-end,ss-non-loop 615 U ) A.U2408 0.007 anti,~C3'-endo,non-stack,canonical,non-canonical,non-pair-contact,helix,stem-end 616 A ) A.A2409 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 617 U ) A.U2410 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 618 U ) A.U2411 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 619 A . A.A2412 0.010 anti,~C3'-endo,BI,non-pair-contact,internal-loop 620 C . A.C2413 0.005 anti,~C3'-endo,non-pair-contact,internal-loop 621 C . A.C2414 0.002 turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,splayed-apart 622 C . A.C2415 0.007 anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 623 U . A.U2416 0.007 ~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,cap-donor,cap-acceptor,phosphate 624 C . A.C2417 0.005 anti,~C3'-endo,non-stack,non-pair-contact,internal-loop 625 A . A.A2418 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 626 C ) A.C2419 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 627 U ) A.U2420 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 628 G ) A.G2421 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 629 U . A.U2422 0.014 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 630 C ) A.C2423 0.012 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-donor,phosphate,splayed-apart 631 A . A.A2424 0.014 anti,~C3'-endo,BI,non-pair-contact,junction-loop,splayed-apart 632 A . A.A2425 0.015 turn,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 633 C . A.C2426 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,junction-loop,splayed-apart 634 C ( A.C2427 0.014 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,junction-loop,splayed-apart 635 C ( A.C2428 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 636 A . A.A2429 0.016 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 637 A . A.A2430 0.009 turn,anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 638 C . A.C2431 0.011 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 639 C . A.C2433 0.008 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 640 A . A.A2434 0.013 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 641 G ) A.G2435 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 642 G ) A.G2436 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 643 C . A.C2437 0.007 anti,~C3'-endo,non-pair-contact,junction-loop 644 A ) A.A2438 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 645 U ) A.U2439 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 646 G ) A.G2440 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 647 C ) A.C2441 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 648 U . A.U2442 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 649 C . A.C2443 0.006 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate 650 A . A.A2444 0.016 ~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,cap-acceptor 651 U . A.U2445 0.012 anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 652 A . A.A2446 0.015 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 653 A ) A.A2447 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 654 G ) A.G2448 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 655 G ) A.G2449 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,phosphate 656 A ) A.A2450 0.012 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 657 A . A.A2451 0.020 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 658 A . A.A2452 0.014 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 659 G ( A.G2453 0.020 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 660 G ( A.G2454 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 661 U ( A.U2455 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 662 U ( A.U2456 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 663 A . A.A2457 0.017 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate 664 A . A.A2458 0.019 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-acceptor,phosphate 665 A . A.A2459 0.017 anti,~C3'-endo,BI,non-pair-contact,internal-loop 666 A . A.A2460 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 667 A ( A.A2461 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 668 A ( A.A2462 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 669 A ( A.A2463 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 670 G ( A.G2464 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 671 U ( A.U2465 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 672 A ( A.A2466 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 673 A ( A.A2467 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 674 A . A.A2468 0.021 ~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 675 A ( A.A2469 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 676 G ( A.G2470 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 677 G . A.G2471 0.023 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge,phosphate 678 A . A.A2472 0.018 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,bulge,cap-donor,phosphate 679 A ( A.A2473 0.024 turn,~C3'-endo,non-stack,isolated-canonical,non-pair-contact,helix,multiplet,bulge,internal-loop,cap-acceptor 680 C . A.C2474 0.014 syn,~C3'-endo,BI,non-pair-contact,internal-loop 681 U . A.U2475 0.012 u-turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-acceptor 682 C . A.C2476 0.013 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop 683 G . A.G2477 0.015 u-turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 684 G ( A.G2478 0.019 turn,u-turn,anti,~C2'-endo,BII,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,phosphate,splayed-apart 685 C . A.C2479 0.013 turn,anti,~C3'-endo,non-pair-contact,internal-loop 686 A . A.A2480 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 687 A . A.A2481 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop,A-minor 688 A . A.A2482 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor 689 U . A.U2483 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 690 C . A.C2484 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 691 U . A.U2485 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 692 U . A.U2486 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop 693 A ( A.A2487 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 694 C ( A.C2488 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 695 C ( A.C2489 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 696 C ( A.C2490 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 697 C ( A.C2491 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 698 G ( A.G2492 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 699 C . A.C2493 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 700 C ] A.C2494 0.013 pseudoknotted,anti,~C3'-endo,non-stack,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 701 U . A.U2495 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 702 G ( A.G2496 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,junction-loop,A-minor,phosphate 703 U ( A.U2497 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 704 U . A.U2498 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 705 U . A.U2499 0.019 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 706 A . A.A2500 0.014 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 707 C . A.C2501 0.011 anti,~C2'-endo,BII,non-stack,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 708 C . A.C2502 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,ribose-zipper,cap-donor,splayed-apart 709 A . A.A2503 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,ribose-zipper 710 A . A.A2504 0.013 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 711 A . A.A2505 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,A-minor,phosphate,splayed-apart 712 A . A.A2506 0.008 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 713 A ) A.A2507 0.018 ~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,splayed-apart 714 C ) A.C2508 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,junction-loop,A-minor 715 A . A.A2509 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop 716 U . A.U2510 0.010 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop 717 C . A.C2511 0.007 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 718 A . A.A2512 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 719 C ( A.C2513 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 720 C ( A.C2514 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 721 U ( A.U2515 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 722 C ( A.C2516 0.006 anti,~C3'-endo,BI,non-stack,canonical,helix,stem 723 U ( A.U2517 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 724 A ( A.A2518 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 725 G . A.G2519 0.012 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 726 C . A.C2520 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 727 A . A.A2521 0.020 ~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 728 U . A.U2522 0.009 syn,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 729 C . A.C2523 0.008 ~C2'-endo,BII,hairpin-loop,phosphate,splayed-apart 730 A . A.A2524 0.012 ~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 731 C . A.C2525 0.009 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 732 C . A.C2526 0.007 anti,~C2'-endo,non-pair-contact,hairpin-loop 733 A . A.A2527 0.021 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 734 G . A.G2528 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,phosphate,splayed-apart 735 U . A.U2529 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 736 A . A.A2530 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-donor,phosphate,splayed-apart 737 U . A.U2531 0.009 turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 738 U ) A.U2532 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,cap-acceptor,splayed-apart 739 A ) A.A2533 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 740 G ) A.G2534 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 741 A ) A.A2535 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 742 G ) A.G2536 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 743 G ) A.G2537 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 744 C . A.C2538 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 745 A . A.A2539 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 746 C . A.C2540 0.003 anti,~C2'-endo,BI,non-pair-contact,junction-loop 747 C . A.C2541 0.004 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix,junction-loop,phosphate 748 G ( A.G2542 0.010 ~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,multiplet,junction-loop 749 C . A.C2543 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 750 C . A.C2544 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 751 U . A.U2545 0.002 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 752 C ( A.C2611 0.004 anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end 753 C ( A.C2612 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 754 U . A.U2613 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 755 U . A.U2614 0.007 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 756 A . A.A2615 0.011 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,A-minor,splayed-apart 757 A . A.A2616 0.007 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,cap-acceptor,phosphate 758 A . A.A2617 0.006 u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 759 U . A.U2618 0.006 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 760 A . A.A2619 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 761 G ) A.G2620 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 762 G ) A.G2621 0.004 break,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 763 C ) A.C2637 0.006 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 764 U . A.U2638 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 765 C . A.C2639 0.004 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,phosphate 766 C . A.C2640 0.007 anti,~C3'-endo,non-pair-contact,junction-loop 767 A . A.A2641 0.013 anti,~C3'-endo,BI,non-pair-contact,junction-loop 768 C ) A.C2642 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 769 G ) A.G2643 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 770 A . A.A2644 0.015 turn,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,bulge,A-minor,cap-acceptor,splayed-apart 771 G ) A.G2645 0.015 ~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 772 G ) A.G2646 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 773 G ) A.G2647 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 774 U ) A.U2648 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 775 U . A.U2649 0.007 anti,~C3'-endo,BI,non-stack,internal-loop 776 C . A.C2650 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 777 A . A.A2651 0.010 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 778 G . A.G2652 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 779 C ) A.C2653 0.014 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 780 U . A.U2654 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 781 G . A.G2655 0.022 turn,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 782 U ) A.U2656 0.014 turn,anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,internal-loop 783 C ) A.C2657 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 784 U ) A.U2658 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 785 C . A.C2659 0.011 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 786 U ) A.U2660 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 787 U ) A.U2661 0.013 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 788 A ) A.A2662 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 789 C ) A.C2663 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 790 U ) A.U2664 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 791 U ) A.U2665 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 792 U ) A.U2666 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 793 U . A.U2667 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 794 A ) A.A2668 0.024 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 795 A ) A.A2669 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 796 C ) A.C2670 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 797 C ) A.C2671 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 798 A . A.A2672 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 799 G ) A.G2673 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 800 U ) A.U2674 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 801 G . A.G2675 0.024 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 802 A . A.A2676 0.024 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 803 A . A.A2677 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 804 A . A.A2678 0.019 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 805 U . A.U2679 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 806 U ) A.U2680 0.017 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,splayed-apart 807 G ) A.G2681 0.015 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,cap-donor,splayed-apart 808 A . A.A2682 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,A-minor,phosphate 809 C { A.C2683 0.020 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,A-minor,phosphate,splayed-apart 810 C . A.C2684 0.011 turn,syn,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 811 U . A.U2685 0.014 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 812 G ( A.G2686 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,splayed-apart 813 C ( A.C2687 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 814 C ( A.C2688 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 815 C ( A.C2689 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,phosphate 816 G ( A.G2690 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,A-minor 817 U . A.U2691 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop 818 G . A.G2692 0.013 break,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 819 A ] A.A2696 0.014 pseudoknotted,anti,~C2'-endo,BII,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,splayed-apart 820 G } A.G2697 0.023 pseudoknotted,turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,multiplet,A-minor,splayed-apart 821 G . A.G2698 0.023 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,A-minor,phosphate,splayed-apart 822 C ) A.C2699 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,A-minor,splayed-apart 823 G ) A.G2700 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 824 G ) A.G2701 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 825 G ) A.G2702 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 826 C ) A.C2703 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 827 A . A.A2704 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 828 U . A.U2705 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 829 A . A.A2706 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 830 A . A.A2707 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 831 C . A.C2708 0.011 anti,~C3'-endo,non-pair-contact,ss-non-loop 832 A . A.A2709 0.016 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 833 C . A.C2710 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 834 A ( A.A2711 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 835 G ( A.G2712 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 836 C . A.C2713 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 837 A . A.A2714 0.022 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 838 A ( A.A2715 0.026 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 839 G ( A.G2716 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 840 A ( A.A2717 0.019 turn,anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,internal-loop,splayed-apart 841 C . A.C2718 0.004 turn,anti,~C2'-endo,non-stack,internal-loop,phosphate,splayed-apart 842 G ( A.G2719 0.020 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,splayed-apart 843 A ( A.A2720 0.019 break,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 844 A . A.A2723 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 845 G . A.G2724 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 846 A . A.A2725 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop 847 C ( A.C2726 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 848 C ( A.C2727 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 849 C ( A.C2728 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 850 U ( A.U2729 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 851 A ( A.A2730 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,splayed-apart 852 U . A.U2731 0.013 turn,anti,~C3'-endo,BII,non-stack,non-canonical,non-pair-contact,bulge,cap-donor,cap-acceptor,phosphate,splayed-apart 853 G ( A.G2732 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate,splayed-apart 854 G ( A.G2733 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 855 A ( A.A2734 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 856 G ( A.G2735 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 857 C ( A.C2736 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 858 U ( A.U2737 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,ribose-zipper 859 U . A.U2738 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,splayed-apart 860 U . A.U2739 0.004 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 861 A ( A.A2740 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,phosphate,splayed-apart 862 A ( A.A2741 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 863 U ( A.U2742 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 864 U ( A.U2743 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 865 U ( A.U2744 0.007 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 866 A . A.A2745 0.008 turn,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor 867 U . A.U2746 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 868 U ( A.U2747 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 869 A ( A.A2748 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 870 A ( A.A2749 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 871 U ( A.U2750 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 872 G ( A.G2751 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 873 C ( A.C2752 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 874 A ( A.A2753 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 875 A . A.A2754 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 876 A . A.A2755 0.008 break,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 877 A . A.A2792 0.004 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop 878 C . A.C2793 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 879 C . A.C2794 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 880 U ) A.U2795 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 881 G ) A.G2796 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 882 C ) A.C2797 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 883 A ) A.A2798 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 884 U ) A.U2799 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 885 U ) A.U2800 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 886 A ) A.A2801 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 887 A . A.A2802 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 888 A ) A.A2803 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 889 A ) A.A2804 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 890 A ) A.A2805 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 891 U ) A.U2806 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 892 U ) A.U2807 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet 893 U . A.U2808 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,ss-non-loop 894 C . A.C2809 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate,splayed-apart 895 G ( A.G2810 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 896 G ( A.G2811 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 897 U ( A.U2812 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 898 U . A.U2813 0.006 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 899 G . A.G2814 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 900 G . A.G2815 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop 901 G . A.G2816 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 902 G . A.G2817 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate 903 C . A.C2818 0.005 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 904 G . A.G2819 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 905 A ) A.A2820 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 906 C ) A.C2821 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 907 C ) A.C2822 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 908 U ( A.U2823 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,cap-donor,splayed-apart 909 C ( A.C2824 0.007 anti,~C3'-endo,BI,non-stack,canonical,helix,stem 910 G ( A.G2825 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 911 G ( A.G2826 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 912 A ( A.A2827 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 913 G ( A.G2828 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 914 C . A.C2829 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 915 A . A.A2830 0.003 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 916 G . A.G2831 0.004 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 917 A . A.A2832 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,hairpin-loop,phosphate,splayed-apart 918 A . A.A2833 0.007 anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 919 C . A.C2834 0.005 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 920 C . A.C2835 0.008 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 921 C . A.C2836 0.004 anti,~C3'-endo,BII,non-pair-contact,hairpin-loop 922 A . A.A2837 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,cap-acceptor,phosphate 923 A . A.A2838 0.006 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,splayed-apart 924 C . A.C2839 0.004 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 925 C ) A.C2840 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate,splayed-apart 926 U ) A.U2841 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 927 C ) A.C2842 0.004 anti,~C3'-endo,BI,non-stack,canonical,helix,stem 928 C ) A.C2843 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 929 G ) A.G2844 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 930 A ) A.A2845 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 931 G ( A.G2846 0.015 break,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end 932 G ( A.G2855 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 933 C ( A.C2856 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 934 U . A.U2857 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 935 A . A.A2858 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 936 A . A.A2859 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 937 G ( A.G2860 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 938 A ( A.A2861 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 939 C ( A.C2862 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 940 U . A.U2863 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 941 U . A.U2864 0.006 turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 942 C . A.C2865 0.004 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 943 A . A.A2866 0.017 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 944 C [ A.C2867 0.014 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,hairpin-loop 945 C . A.C2868 0.012 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 946 A . A.A2869 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 947 G ) A.G2870 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 948 U ) A.U2871 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 949 C ) A.C2872 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 950 A . A.A2873 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 951 A . A.A2874 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 952 A . A.A2875 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 953 G ) A.G2876 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 954 C ) A.C2877 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 955 G . A.G2878 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 956 A . A.A2879 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 957 A . A.A2880 0.003 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 958 G . A.G2896 0.018 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,phosphate 959 A . A.A2897 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 960 U . A.U2898 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 961 C . A.C2899 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 962 C . A.C2900 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 963 A . A.A2901 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 964 A . A.A2902 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor 965 U . A.U2903 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-donor,cap-acceptor 966 A . A.A2904 0.002 turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 967 A . A.A2905 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate 968 C . A.C2906 0.007 turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 969 U . A.U2907 0.008 anti,~C3'-endo,BI,non-stack,ss-non-loop 970 U . A.U2908 0.006 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix-end,ss-non-loop 971 G . A.G2909 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 972 A . A.A2910 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 973 C . A.C2911 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop 974 C . A.C2912 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 975 A . A.A2913 0.013 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate,splayed-apart 976 A . A.A2914 0.008 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 977 C ) A.C2915 0.016 turn,anti,~C3'-endo,BII,isolated-canonical,non-pair-contact,helix-end,cap-acceptor,phosphate,splayed-apart 978 G ] A.G2916 0.022 pseudoknotted,turn,anti,~C3'-endo,isolated-canonical,cap-donor,splayed-apart 979 G . A.G2917 0.015 ~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,cap-acceptor,splayed-apart 980 A . A.A2918 0.013 turn,~C2'-endo,non-canonical,non-pair-contact,ss-non-loop,splayed-apart 981 A . A.A2919 0.016 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,splayed-apart 982 C . A.C2920 0.011 anti,~C3'-endo,non-pair-contact,ss-non-loop 983 A . A.A2921 0.014 syn,~C3'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 984 A ) A.A2922 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,splayed-apart 985 G ) A.G2923 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 986 U ) A.U2924 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 987 U ) A.U2925 0.008 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 988 A . A.A2926 0.004 turn,syn,~C2'-endo,non-stack,non-pair-contact,bulge,splayed-apart 989 C . A.C2927 0.006 anti,~C3'-endo,non-pair-contact,bulge,phosphate,splayed-apart 990 C ) A.C2928 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 991 C ) A.C2929 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,ribose-zipper 992 U ) A.U2930 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,ribose-zipper 993 A ) A.A2931 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 994 G ) A.G2932 0.021 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 995 G ) A.G2933 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 996 G ) A.G2934 0.006 break,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 997 C . A.C2944 0.003 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 998 A . A.A2945 0.004 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 999 A . A.A2946 0.009 turn,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 1000 U . A.U2947 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 1001 C ( A.C2948 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 1002 C ( A.C2949 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 1003 U ( A.U2950 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 1004 A ( A.A2951 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1005 U ( A.U2952 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1006 U ( A.U2953 0.006 anti,~C3'-endo,non-stack,canonical,non-canonical,helix-end,stem-end,multiplet,internal-loop 1007 C . A.C2954 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 1008 U . A.U2955 0.005 anti,~C2'-endo,BII,non-pair-contact,internal-loop 1009 A . A.A2956 0.006 anti,~C2'-endo,non-pair-contact,internal-loop 1010 G ( A.G2957 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 1011 A ( A.A2958 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 1012 G . A.G2959 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 1013 U . A.U2960 0.003 turn,anti,~C3'-endo,non-stack,hairpin-loop,splayed-apart 1014 C . A.C2961 0.005 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1015 C . A.C2962 0.002 anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 1016 A . A.A2963 0.002 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 1017 U . A.U2964 0.006 anti,~C3'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 1018 A . A.A2965 0.002 turn,anti,~C2'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1019 U ) A.U2966 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate 1020 C ) A.C2967 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,cap-acceptor 1021 A . A.A2968 0.003 anti,~C3'-endo,BII,non-canonical,non-pair-contact,internal-loop,cap-donor,splayed-apart 1022 A . A.A2969 0.005 ~C3'-endo,non-pair-contact,internal-loop,splayed-apart 1023 C . A.C2970 0.003 anti,~C3'-endo,non-pair-contact,internal-loop 1024 A ) A.A2971 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop 1025 A ) A.A2972 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1026 U ) A.U2973 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1027 A ) A.A2974 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 1028 G ) A.G2975 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1029 G ) A.G2976 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 1030 G . A.G2977 0.005 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 1031 U . A.U2978 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 1032 U . A.U2979 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 1033 U . A.U2980 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate 1034 A . A.A2981 0.003 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop,cap-acceptor,phosphate 1035 C . A.C2982 0.003 break,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 1036 U ( A.U2994 0.005 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 1037 G ( A.G2995 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1038 G ( A.G2996 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 1039 A ( A.A2997 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1040 U . A.U2998 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1041 C ( A.C2999 0.015 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,phosphate 1042 A ( A.A3000 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor 1043 G ( A.G3001 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1044 G ( A.G3002 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 1045 A ( A.A3003 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,ribose-zipper 1046 C ( A.C3004 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 1047 A . A.A3005 0.010 turn,syn,~C2'-endo,non-pair-contact,junction-loop,splayed-apart 1048 U . A.U3006 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 1049 C ( A.C3007 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,cap-acceptor 1050 C ( A.C3008 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 1051 C . A.C3009 0.010 syn,~C3'-endo,BI,non-pair-contact,internal-loop 1052 G ( A.G3010 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1053 A ( A.A3011 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1054 U ( A.U3012 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1055 G . A.G3013 0.010 anti,~C3'-endo,BI,non-pair-contact,internal-loop 1056 G ( A.G3014 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1057 U ( A.U3015 0.006 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,splayed-apart 1058 G . A.G3016 0.005 turn,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 1059 C . A.C3017 0.004 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 1060 A . A.A3018 0.013 turn,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 1061 G . A.G3019 0.004 anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop 1062 C . A.C3020 0.004 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 1063 C . A.C3021 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 1064 G ) A.G3022 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 1065 C ) A.C3023 0.011 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1066 U . A.U3024 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,internal-loop 1067 A ) A.A3025 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1068 U ) A.U3026 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1069 U ) A.U3027 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1070 A . A.A3028 0.013 anti,~C3'-endo,non-pair-contact,internal-loop 1071 A . A.A3029 0.015 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 1072 A . A.A3030 0.009 turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop 1073 G ) A.G3031 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 1074 G ) A.G3032 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 1075 U . A.U3033 0.010 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 1076 U ( A.U3034 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 1077 C ( A.C3035 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 1078 G ( A.G3036 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,phosphate 1079 U ( A.U3037 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,cap-donor 1080 U ( A.U3038 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,hairpin-loop 1081 U . A.U3039 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 1082 G . A.G3040 0.002 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 1083 U . A.U3041 0.002 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1084 U . A.U3042 0.005 anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 1085 C . A.C3043 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 1086 A ) A.A3044 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1087 A ) A.A3045 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 1088 C ) A.C3046 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 1089 G ) A.G3047 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 1090 A ) A.A3048 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 1091 U . A.U3049 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 1092 U . A.U3050 0.013 u-turn,anti,~C3'-endo,BI,non-pair-contact,junction-loop,cap-acceptor 1093 A . A.A3051 0.020 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 1094 A . A.A3052 0.015 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,cap-donor,phosphate 1095 A . A.A3053 0.010 turn,u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 1096 G ) A.G3054 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,cap-donor,splayed-apart 1097 U ) A.U3055 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1098 C ) A.C3056 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 1099 C ) A.C3057 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1100 U ) A.U3058 0.012 break,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor 1101 C . A.C3060 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop 1102 G ) A.G3061 0.018 turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate 1103 U . A.U3062 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1104 G . A.G3063 0.010 ~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,splayed-apart 1105 A . A.A3064 0.018 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,cap-donor,splayed-apart 1106 U ) A.U3065 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 1107 C ) A.C3066 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1108 U ) A.U3067 0.010 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1109 G ) A.G3068 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 1110 A . A.A3069 0.010 anti,~C3'-endo,non-pair-contact,ss-non-loop 1111 G . A.G3070 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor 1112 U . A.U3071 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor 1113 U . A.U3072 0.007 ~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 1114 C . A.C3073 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 1115 A . A.A3074 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 1116 G ( A.G3075 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,A-minor 1117 A ( A.A3076 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1118 C ( A.C3077 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1119 C ( A.C3078 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 1120 G ( A.G3079 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 1121 G ( A.G3080 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1122 A ( A.A3081 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 1123 G . A.G3082 0.006 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor,splayed-apart 1124 U . A.U3083 0.008 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 1125 A . A.A3084 0.008 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 1126 A . A.A3085 0.010 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 1127 U ) A.U3086 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 1128 C ) A.C3087 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1129 C ) A.C3088 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 1130 A . A.A3089 0.003 turn,anti,~C3'-endo,non-stack,non-pair-contact,bulge,phosphate,splayed-apart 1131 G ) A.G3090 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 1132 G ) A.G3091 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1133 U ) A.U3092 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 1134 C ) A.C3093 0.010 anti,~C3'-endo,BI,non-stack,canonical,helix,stem-end,coaxial-stack,A-minor 1135 G . A.G3094 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,ribose-zipper 1136 G . A.G3095 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop,ribose-zipper,splayed-apart 1137 U } A.U3096 0.015 pseudoknotted,~C2'-endo,non-stack,isolated-canonical,cap-acceptor,splayed-apart 1138 U . A.U3097 0.006 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 1139 U ) A.U3098 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 1140 C ) A.C3099 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,cap-acceptor,splayed-apart 1141 U . A.U3100 0.013 turn,anti,~C2'-endo,non-stack,non-canonical,helix-end,multiplet,internal-loop,splayed-apart 1142 A . A.A3101 0.022 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,internal-loop,splayed-apart 1143 U ) A.U3102 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 1144 C ) A.C3103 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1145 U ) A.U3104 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 1146 A . A.A3105 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1147 C ) A.C3106 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1148 U ) A.U3107 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate,splayed-apart 1149 U . A.U3108 0.006 ~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 1150 U . A.U3109 0.004 break,anti,~C2'-endo,ss-non-loop,splayed-apart 1151 A ( A.A3113 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 1152 U ( A.U3114 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1153 U ( A.U3115 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 1154 C . A.C3116 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1155 C ( A.C3117 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1156 U ( A.U3118 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1157 C ( A.C3119 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1158 C . A.C3120 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1159 C . A.C3121 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 1160 U . A.U3122 0.006 ~C2'-endo,non-pair-contact,internal-loop 1161 G . A.G3123 0.005 turn,anti,~C3'-endo,non-pair-contact,internal-loop 1162 U . A.U3124 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop 1163 A . A.A3125 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 1164 C ( A.C3126 0.003 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop 1165 G . A.G3127 0.010 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,cap-acceptor,splayed-apart 1166 A . A.A3128 0.005 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 1167 A . A.A3129 0.002 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,cap-acceptor,phosphate 1168 A . A.A3130 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,phosphate 1169 G ) A.G3131 0.003 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop 1170 G . A.G3132 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate,splayed-apart 1171 A . A.A3133 0.004 anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 1172 C . A.C3134 0.013 syn,~C3'-endo,BI,non-pair-contact,internal-loop 1173 A . A.A3135 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 1174 A . A.A3136 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1175 G ) A.G3137 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1176 A ) A.A3138 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1177 G ) A.G3139 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1178 A . A.A3140 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1179 A ) A.A3141 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1180 A ) A.A3142 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1181 U ) A.U3143 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 1182 A ( A.A3144 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 1183 A ( A.A3145 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1184 G ( A.G3146 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1185 G ( A.G3147 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1186 C ( A.C3148 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor,phosphate 1187 C . A.C3149 0.026 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 1188 U . A.U3150 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop 1189 A . A.A3151 0.019 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 1190 C ( A.C3152 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 1191 U ( A.U3153 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1192 U ( A.U3154 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 1193 C . A.C3155 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 1194 A . A.A3156 0.012 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 1195 C . A.C3157 0.010 turn,anti,~C2'-endo,hairpin-loop,splayed-apart 1196 A . A.A3158 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 1197 A ) A.A3159 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 1198 A ) A.A3160 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1199 G ) A.G3161 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1200 C . A.C3162 0.015 turn,anti,~C2'-endo,BI,non-pair-contact,internal-loop,phosphate 1201 G ) A.G3163 0.022 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 1202 C ) A.C3164 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1203 C ) A.C3165 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1204 U ) A.U3166 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1205 U ) A.U3167 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,splayed-apart 1206 C . A.C3168 0.010 break,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 1207 U ( A.U3174 0.006 anti,~C2'-endo,BII,non-stack,canonical,non-pair-contact,helix-end,stem-end,phosphate 1208 A ( A.A3175 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1209 A ( A.A3176 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1210 A . A.A3177 0.012 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1211 U . A.U3178 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop 1212 G . A.G3179 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop 1213 A . A.A3180 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 1214 U . A.U3181 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 1215 A . A.A3182 0.010 anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1216 U . A.U3183 0.006 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 1217 C . A.C3184 0.005 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1218 A . A.A3185 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 1219 U . A.U3186 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,splayed-apart 1220 C . A.C3187 0.008 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 1221 U . A.U3188 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate,splayed-apart 1222 C . A.C3189 0.009 turn,anti,~C3'-endo,BII,hairpin-loop,phosphate,splayed-apart 1223 A . A.A3190 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate,splayed-apart 1224 A . A.A3191 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate 1225 C . A.C3192 0.007 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1226 U ) A.U3193 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1227 U ) A.U3194 0.006 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem,phosphate 1228 A ) A.A3195 0.005 break,anti,~C2'-endo,non-stack,canonical,helix-end,stem-end 1229 A . A.A3201 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop 1230 U . A.U3202 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1231 A . A.A3203 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop 1232 C . A.C3204 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1233 C . A.C3205 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1234 C . A.C3206 0.009 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 1235 A . A.A3207 0.012 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 1236 C . A.C3208 0.008 anti,~C3'-endo,BI,ss-non-loop,splayed-apart 1237 A . A.A3209 0.008 anti,~C2'-endo,ss-non-loop,phosphate,splayed-apart 1238 C . A.C3210 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 1239 C . A.C3211 0.007 anti,~C3'-endo,non-pair-contact,ss-non-loop 1240 C . A.C3212 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 1241 A ( A.A3213 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 1242 C ( A.C3214 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1243 C ( A.C3215 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1244 C ( A.C3216 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop,splayed-apart 1245 A . A.A3217 0.014 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1246 A . A.A3218 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 1247 G . A.G3219 0.019 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1248 A . A.A3220 0.019 turn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,phosphate,splayed-apart 1249 A . A.A3221 0.015 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 1250 C . A.C3222 0.013 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1251 A . A.A3223 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 1252 G ) A.G3224 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 1253 G ) A.G3225 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1254 G ) A.G3226 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1255 U ) A.U3227 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 1256 U . A.U3228 0.010 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 1257 A . B.A1603 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 1258 G . B.G1604 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1259 A . B.A1605 0.002 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix-end,ss-non-loop 1260 G ( B.G1606 0.010 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,cap-acceptor 1261 U . B.U1607 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate 1262 G . B.G1608 0.003 ~C2'-endo,BII,non-canonical,non-pair-contact,ss-non-loop,splayed-apart 1263 U . B.U1609 0.003 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,ss-non-loop,splayed-apart 1264 A . B.A1610 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop 1265 G ( B.G1611 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet 1266 C ( B.C1612 0.008 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 1267 U ( B.U1613 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet 1268 U . B.U1614 0.002 turn,anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 1269 A . B.A1615 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate,splayed-apart 1270 A . B.A1616 0.006 break,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 1271 A . B.A1621 0.002 anti,~C3'-endo,non-pair-contact,ss-non-loop 1272 A ) B.A1622 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,phosphate 1273 G ) B.G1623 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 1274 C ) B.C1624 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,phosphate 1275 A . B.A1625 0.014 ~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop,cap-donor,cap-acceptor,phosphate 1276 C . B.C1626 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop 1277 C ( B.C1627 0.002 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 1278 C . B.C1628 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 1279 A . B.A1629 0.003 anti,~C3'-endo,non-pair-contact,hairpin-loop 1280 A . B.A1630 0.002 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1281 C . B.C1631 0.002 anti,~C3'-endo,BII,non-canonical,non-pair-contact,hairpin-loop,splayed-apart 1282 U . B.U1632 0.002 anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 1283 U . B.U1633 0.003 turn,anti,~C3'-endo,non-stack,hairpin-loop,splayed-apart 1284 A . B.A1634 0.002 anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop,splayed-apart 1285 C . B.C1635 0.001 anti,~C3'-endo,non-pair-contact,hairpin-loop 1286 A . B.A1636 0.003 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 1287 C . B.C1637 0.005 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 1288 U . B.U1638 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,hairpin-loop 1289 U . B.U1639 0.004 anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop 1290 A . B.A1640 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 1291 G ) B.G1641 0.003 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 1292 G . B.G1642 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1293 A . B.A1643 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1294 G . B.G1644 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop 1295 A . B.A1645 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop 1296 U . B.U1646 0.007 break,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 1297 U . B.U1648 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1298 C ( B.C1649 0.005 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,internal-loop 1299 A . B.A1650 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1300 A ( B.A1651 0.002 break,anti,~C3'-endo,non-stack,isolated-canonical,helix-end,internal-loop 1301 U ) B.U1658 0.003 anti,~C3'-endo,non-stack,isolated-canonical,non-pair-contact,helix-end,internal-loop 1302 U . B.U1659 0.003 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix,internal-loop 1303 G ) B.G1660 0.007 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,internal-loop 1304 A . B.A1661 0.006 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 1305 C . B.C1663 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 1306 G . B.G1664 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1307 C ) B.C1665 0.004 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end 1308 U . B.U1666 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1309 C . B.C1667 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 1310 U . B.U1668 0.002 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,ss-non-loop 1311 G . B.G1669 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1312 A . B.A1670 0.001 anti,~C3'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 20 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-bulges.pdb -- an ensemble of bulges 7 dssr-iloops.pdb -- an ensemble of internal loops 8 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 9 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 10 dssr-2ndstrs.ct -- secondary structure in connectivity table format 11 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 12 dssr-torsions.txt -- backbone torsion angles and suite names 13 dssr-splays.pdb -- an ensemble of splayed-apart units 14 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 15 dssr-stacks.pdb -- an ensemble of base stacks 16 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 17 dssr-rotmat.txt -- position vector and rotation matrix 18 dssr-viewV.pdb -- vertical view of the principal moment of inertia 19 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 20 dssr-viewT.pdb -- top view of the principal moment of inertia