**************************************************************************** File name: 6ytf.pdb no. of DNA/RNA chains: 3 [3=453,7=20,9=4] no. of nucleotides: 477 no. of atoms: 16906 no. of waters: 0 no. of metals: 24 [Mg=24] **************************************************************************** List of 239 base pairs nt1 nt2 bp name Saenger LW DSSR 1 3.C927 3.G1384 C-G WC 19-XIX cWW cW-W 2 3.C928 3.G1383 C-G WC 19-XIX cWW cW-W 3 3.C929 3.G1382 C-G WC 19-XIX cWW cW-W 4 3.G930 3.C1381 G-C WC 19-XIX cWW cW-W 5 3.C931 3.A935 C+A ~rWobble 26-XXVI tWW tW+W 6 3.A932 3.U1377 A-U WC 20-XX cWW cW-W 7 3.A932 3.C1380 A-C -- -- cSW cm-W 8 3.C933 3.G1376 C-G WC 19-XIX cWW cW-W 9 3.A934 3.U1342 A-U -- -- tW. tW-. 10 3.A934 3.C1375 A-C ~Sheared -- tSH tm-M 11 3.A935 3.U1373 A-U -- -- cSS cm-m 12 3.G936 3.C1341 G-C WC 19-XIX cWW cW-W 13 3.C937 3.G1340 C-G WC 19-XIX cWW cW-W 14 3.G938 3.C1339 G-C WC 19-XIX cWW cW-W 15 3.G939 3.U1338 G-U Wobble 28-XXVIII cWW cW-W 16 3.U940 3.A1337 U-A WC 20-XX cWW cW-W 17 3.G941 3.A1336 G-A Sheared 11-XI tSH tm-M 18 3.G942 3.A1233 G-A Imino 08-VIII cWW cW-W 19 3.A943 3.U1232 A-U WC 20-XX cWW cW-W 20 3.A943 3.A1330 A-A -- -- cSS cm-m 21 3.G944 3.C1231 G-C WC 19-XIX cWW cW-W 22 3.C945 3.G1230 C-G WC 19-XIX cWW cW-W 23 3.A946 3.G968 A-G Sheared 11-XI tSH tm-M 24 3.A946 3.U1229 A-U WC 20-XX cWW cW-W 25 3.U947 3.G1228 U-G Wobble 28-XXVIII cWW cW-W 26 3.G948 3.C967 G-C -- -- cSS cm-m 27 3.G948 3.C1227 G-C WC 19-XIX cWW cW-W 28 3.U949 3.A1226 U-A WC 20-XX cWW cW-W 29 3.G950 3.C1225 G-C WC 19-XIX cWW cW-W 30 3.G951 3.C1223 G-C WC 19-XIX cWW cW-W 31 3.G951 3.A1224 G+A -- -- t.W t.+W 32 3.U952 3.A1222 U-A WC 20-XX cWW cW-W 33 3.U953 3.U957 U+U -- 13-XIII tWW tW+W 34 3.U954 3.A956 U-A -- -- tSH tm-M 35 3.A955 3.C982 A-C -- -- cSS cm-m 36 3.A956 3.G1218 A+G -- -- tSS tm+m 37 3.U958 3.A1198 U+A -- -- tWW tW+W 38 3.C959 3.G970 C-G WC 19-XIX cWW cW-W 39 3.G960 3.C969 G-C WC 19-XIX cWW cW-W 40 3.A975 3.G1313 A+G -- 10-X tWS tW+m 41 3.A975 3.A1357 A-A -- 05-V tHW tM-W 42 3.C976 3.C1314 C-C -- -- cSW cm-W 43 3.C981 3.G1218 C-G WC 19-XIX cWW cW-W 44 3.C982 3.G1217 C-G WC 19-XIX cWW cW-W 45 3.U983 3.A1216 U-A WC 20-XX cWW cW-W 46 3.G984 3.A1011 G+A -- -- tSW tm+W 47 3.G984 3.C1215 G-C WC 19-XIX cWW cW-W 48 3.G985 3.G1012 G+G -- -- tSW tm+W 49 3.G985 3.C1214 G-C WC 19-XIX cWW cW-W 50 3.C986 3.G1213 C-G WC 19-XIX cWW cW-W 51 3.C987 3.G1212 C-G WC 19-XIX cWW cW-W 52 3.U988 3.A1210 U-A rHoogsteen 24-XXIV tWH tW-M 53 3.U989 3.A1041 U-A rHoogsteen 24-XXIV tWH tW-M 54 3.G990 3.C1042 G-C WC 19-XIX cWW cW-W 55 3.G990 3.A1210 G-A -- -- tHW tM-W 56 3.U994 3.A1041 U-A WC 20-XX cWW cW-W 57 3.A995 3.U1040 A-U WC 20-XX cWW cW-W 58 3.C996 3.G1038 C-G WC 19-XIX cWW cW-W 59 3.C996 3.A1039 C-A -- -- cWW cW-W 60 3.U997 3.A1037 U-A WC 20-XX cWW cW-W 61 3.A998 3.U1036 A-U WC 20-XX cWW cW-W 62 3.G999 3.U1036 G-U -- -- cWW cW-W 63 3.A1000 3.C1035 A-C ~Wobble -- cWW cW-W 64 3.C1003 3.G1020 C-G WC 19-XIX cWW cW-W 65 3.U1004 3.U1019 U-U -- 16-XVI cWW cW-W 66 3.U1005 3.U1018 U-U -- 16-XVI cWW cW-W 67 3.U1006 3.A1017 U-A WC 20-XX cWW cW-W 68 3.C1007 3.G1016 C-G WC 19-XIX cWW cW-W 69 3.C1008 3.G1015 C-G WC 19-XIX cWW cW-W 70 3.A1009 3.U1014 A-U WC 20-XX cWW cW-W 71 3.G1010 3.A1013 G-A Sheared 11-XI tSH tm-M 72 3.C1042 3.U1208 C-U -- -- tHW tM-W 73 3.A1043 3.U1208 A-U -- -- tHW tM-W 74 3.G1044 3.C1207 G-C WC 19-XIX cWW cW-W 75 3.G1045 3.C1206 G-C WC 19-XIX cWW cW-W 76 3.G1047 3.C1205 G-C WC 19-XIX cWW cW-W 77 3.C1048 3.G1204 C-G WC 19-XIX cWW cW-W 78 3.U1049 3.G1203 U-G Wobble 28-XXVIII cWW cW-W 79 3.G1050 3.G1054 G+G -- 06-VI cWH cW+M 80 3.G1050 3.C1200 G-C -- -- -- -- 81 3.A1052 3.C1197 A-C ~rHoogsteen 25-XXV tHW tM-W 82 3.A1052 3.U1202 A-U -- -- cWW cW-W 83 3.U1053 3.A1201 U-A WC 20-XX cWW cW-W 84 3.G1054 3.C1200 G-C WC 19-XIX cWW cW-W 85 3.G1055 3.U1196 G-U Wobble 28-XXVIII cWW cW-W 86 3.G1055 3.U1199 G-U -- -- tSW tm-W 87 3.C1056 3.G1195 C-G WC 19-XIX cWW cW-W 88 3.U1057 3.A1194 U-A WC 20-XX cWW cW-W 89 3.G1058 3.C1192 G-C WC 19-XIX cWW cW-W 90 3.U1059 3.U1191 U-U -- 16-XVI cWW cW-W 91 3.C1060 3.G1190 C-G WC 19-XIX cWW cW-W 92 3.G1061 3.G1187 G+G -- 04-IV tSS tm+m 93 3.G1061 3.C1189 G+C -- -- c.H c.+M 94 3.C1063 3.A1188 C-A ~rHoogsteen 25-XXV tWH tW-M 95 3.G1065 3.C1104 G-C WC 19-XIX cWW cW-W 96 3.C1066 3.G1103 C-G WC 19-XIX cWW cW-W 97 3.U1067 3.G1091 U-G -- -- .HW .M-W 98 3.U1067 3.A1102 U-A WC 20-XX cWW cW-W 99 3.C1068 3.U1082 C+U -- -- .HH .M+M 100 3.C1068 3.G1101 C-G WC 19-XIX cWW cW-W 101 3.G1069 3.G1081 G-G -- -- tHS tM-m 102 3.G1069 3.C1100 G-C WC 19-XIX cWW cW-W 103 3.U1070 3.A1099 U-A WC 20-XX cWW cW-W 104 3.G1071 3.A1079 G-A -- -- cWW cW-W 105 3.G1071 3.U1080 G-U Wobble 28-XXVIII cWW cW-W 106 3.G1071 3.A1098 G+A Linker -- tS. tm+. 107 3.U1072 3.A1079 U-A WC 20-XX cWW cW-W 108 3.C1073 3.G1078 C-G WC 19-XIX cWW cW-W 109 3.G1074 3.A1077 G-A Sheared 11-XI tSH tm-M 110 3.U1080 3.A1099 U+A -- -- cWH cW+M 111 3.U1083 3.G1096 U-G -- -- cWW cW-W 112 3.G1084 3.C1095 G-C WC 19-XIX cWW cW-W 113 3.G1085 3.C1094 G-C WC 19-XIX cWW cW-W 114 3.G1085 3.A1164 G+A -- 10-X tSW tm+W 115 3.G1086 3.C1093 G-C WC 19-XIX cWW cW-W 116 3.G1086 3.A1167 G+A Linker -- tSS tm+m 117 3.U1087 3.U1092 U-U -- 16-XVI cWW cW-W 118 3.C1110 3.G1184 C-G WC 19-XIX cWW cW-W 119 3.C1111 3.G1183 C-G WC 19-XIX cWW cW-W 120 3.U1112 3.G1182 U-G Wobble 28-XXVIII cWW cW-W 121 3.U1113 3.G1181 U-G Wobble 28-XXVIII cWW cW-W 122 3.U1115 3.A1152 U-A WC 20-XX cWW cW-W 123 3.C1116 3.G1151 C-G WC 19-XIX cWW cW-W 124 3.C1117 3.G1150 C-G WC 19-XIX cWW cW-W 125 3.U1118 3.A1149 U-A WC 20-XX cWW cW-W 126 3.U1119 3.A1148 U-A WC 20-XX cWW cW-W 127 3.A1120 3.U1147 A-U WC 20-XX cWW cW-W 128 3.C1121 3.G1124 C+G -- -- tSW tm+W 129 3.U1122 3.A1277 U+A Hoogsteen 23-XXIII cWH cW+M 130 3.G1124 3.A1142 G-A -- -- cWW cW-W 131 3.G1124 3.U1145 G-U -- -- cSW cm-W 132 3.C1125 3.G1141 C-G WC 19-XIX cWW cW-W 133 3.C1125 3.A1143 C-A -- -- ..H ..-M 134 3.C1126 3.A1127 C+A Platform -- cSH cm+M 135 3.C1126 3.G1140 C-G WC 19-XIX cWW cW-W 136 3.A1127 3.G1140 A-G -- -- cWW cW-W 137 3.A1127 3.G1141 A-G -- -- cWS cW-m 138 3.G1128 3.G1136 G-G -- -- -- -- 139 3.G1128 3.G1140 G-G -- -- cWS cW-m 140 3.C1129 3.G1136 C-G -- -- -- -- 141 3.C1129 3.G1139 C-G WC 19-XIX cWW cW-W 142 3.A1130 3.U1138 A-U WC 20-XX cWW cW-W 143 3.U1131 3.A1137 U-A WC 20-XX cWW cW-W 144 3.U1132 3.G1135 U+G -- -- tSW tm+W 145 3.G1136 3.G1139 G+G -- 06-VI cWH cW+M 146 3.G1141 3.A1143 G+A -- -- cSH cm+M 147 3.A1142 3.C1144 A+C -- -- cSH cm+M 148 3.U1146 3.A1277 U-A -- -- cSW cm-W 149 3.U1153 3.A1176 U+A -- -- t.W t.+W 150 3.A1154 3.G1175 A+G -- 10-X tWS tW+m 151 3.C1155 3.G1178 C-G WC 19-XIX cWW cW-W 152 3.G1157 3.A1173 G-A -- -- cWW cW-W 153 3.G1157 3.G1179 G+G -- 06-VI cHW cM+W 154 3.C1158 3.G1172 C-G WC 19-XIX cWW cW-W 155 3.C1158 3.G1179 C+G -- -- c.W c.+W 156 3.C1159 3.G1171 C-G WC 19-XIX cWW cW-W 157 3.A1160 3.U1170 A-U WC 20-XX cWW cW-W 158 3.G1161 3.C1169 G-C WC 19-XIX cWW cW-W 159 3.U1162 3.A1168 U-A WC 20-XX cWW cW-W 160 3.G1163 3.A1167 G-A Sheared 11-XI tSH tm-M 161 3.A1173 3.G1179 A-G -- -- tH. tM-. 162 3.G1174 3.G1178 G-G -- 07-VII tWH tW-M 163 3.C1197 3.U1202 C+U -- -- tWW tW+W 164 3.C1223 3.A1224 C-A Platform -- cSW cm-W 165 3.C1234 3.G1334 C-G WC 19-XIX cWW cW-W 166 3.A1235 3.G1238 A-G -- -- cWS cW-m 167 3.A1235 3.U1298 A-U rHoogsteen 24-XXIV tHW tM-W 168 3.A1236 3.A1296 A+A -- -- .HW .M+W 169 3.G1238 3.C1293 G-C WC 19-XIX cWW cW-W 170 3.G1239 3.U1292 G-U Wobble 28-XXVIII cWW cW-W 171 3.G1239 3.C1299 G-C -- -- cWS cW-m 172 3.U1240 3.A1291 U-A WC 20-XX cWW cW-W 173 3.C1241 3.G1290 C-G WC 19-XIX cWW cW-W 174 3.G1242 3.C1289 G-C WC 19-XIX cWW cW-W 175 3.G1243 3.C1288 G-C WC 19-XIX cWW cW-W 176 3.U1244 3.G1287 U-G Wobble 28-XXVIII cWW cW-W 177 3.A1245 3.A1286 A-A -- 05-V tWH tW-M 178 3.C1246 3.A1285 C-A ~rHoogsteen 25-XXV tWH tW-M 179 3.A1247 3.G1350 A+G -- -- tWS tW+m 180 3.A1249 3.A1282 A+A -- -- tWW tW+W 181 3.G1250 3.C1281 G-C WC 19-XIX cWW cW-W 182 3.G1251 3.U1280 G-U Wobble 28-XXVIII cWW cW-W 183 3.G1252 3.C1256 G-C -- -- cSS cm-m 184 3.G1252 3.C1274 G+C -- -- tWS tW+m 185 3.G1252 3.C1279 G-C WC 19-XIX cWW cW-W 186 3.G1255 3.C1274 G-C WC 19-XIX cWW cW-W 187 3.G1255 3.A1276 G+A -- -- t.W t.+W 188 3.C1256 3.G1273 C-G WC 19-XIX cWW cW-W 189 3.U1257 3.U1272 U-U -- 16-XVI cWW cW-W 190 3.A1258 3.A1271 A+A -- -- tWS tW+m 191 3.C1259 3.G1270 C-G WC 19-XIX cWW cW-W 192 3.A1260 3.U1269 A-U WC 20-XX cWW cW-W 193 3.C1261 3.G1268 C-G WC 19-XIX cWW cW-W 194 3.A1262 3.U1267 A-U WC 20-XX cWW cW-W 195 3.G1263 3.A1266 G-A Sheared 11-XI tSH tm-M 196 3.A1266 3.G1309 A+G Linker -- tSS tm+m 197 3.A1284 3.G1367 A+G -- 10-X tWS tW+m 198 3.G1297 3.U1298 G+U Platform -- cSH cm+M 199 3.C1300 3.G1331 C-G WC 19-XIX cWW cW-W 200 3.G1301 3.A1330 G-A Sheared 11-XI tSH tm-M 201 3.G1302 3.A1329 G+A -- -- tSW tm+W 202 3.A1303 3.G1328 A-G Sheared 11-XI tHS tM-m 203 3.U1304 3.U1327 U-U -- -- cWW cW-W 204 3.U1305 3.A1326 U-A WC 20-XX cWW cW-W 205 3.G1306 3.C1325 G-C WC 19-XIX cWW cW-W 206 3.G1307 3.C1324 G-C WC 19-XIX cWW cW-W 207 3.A1308 3.U1323 A-U WC 20-XX cWW cW-W 208 3.G1309 3.C1322 G-C WC 19-XIX cWW cW-W 209 3.U1310 3.A1321 U-A WC 20-XX cWW cW-W 210 3.C1311 3.G1320 C-G WC 19-XIX cWW cW-W 211 3.U1312 3.A1316 U-A rHoogsteen 24-XXIV tWH tW-M 212 3.U1312 3.A1357 U-A -- -- cSW cm-W 213 3.A1316 3.G1358 A+G -- 10-X tWS tW+m 214 3.G1335 7.C41 G-C -- -- cSS cm-m 215 3.A1336 7.G30 A+G Linker -- tSS tm+m 216 3.U1342 3.U1373 U+U -- 13-XIII tWW tW+W 217 3.A1343 3.A1372 A+A -- 02-II tHH tM+M 218 3.G1344 3.U1345 G+U Platform -- cSH cm+M 219 3.U1345 3.A1371 U-A rHoogsteen 24-XXIV tWH tW-M 220 3.A1346 3.G1370 A-G Sheared 11-XI tHS tM-m 221 3.A1347 3.U1369 A-U WC 20-XX cWW cW-W 222 3.U1348 3.G1368 U-G Wobble 28-XXVIII cWW cW-W 223 3.C1349 3.G1367 C-G WC 19-XIX cWW cW-W 224 3.G1350 3.C1366 G-C WC 19-XIX cWW cW-W 225 3.C1351 3.G1365 C-G WC 19-XIX cWW cW-W 226 3.G1352 3.C1364 G-C WC 19-XIX cWW cW-W 227 3.G1353 3.C1363 G-C WC 19-XIX cWW cW-W 228 3.A1354 3.G1362 A-G Imino 08-VIII cWW cW-W 229 3.U1355 3.A1360 U+A rWC 21-XXI tWW tW+W 230 3.U1377 3.C1379 U+C -- -- c.H c.+M 231 7.G26 7.A44 G-A -- -- cWW cW-W 232 7.U27 7.A43 U-A WC 20-XX cWW cW-W 233 7.C28 7.G42 C-G WC 19-XIX cWW cW-W 234 7.G29 7.C41 G-C WC 19-XIX cWW cW-W 235 7.G30 7.C40 G-C WC 19-XIX cWW cW-W 236 7.G31 7.C39 G-C WC 19-XIX cWW cW-W 237 7.C34 9.U3 C-U -- -- cWW cW-W 238 7.A35 9.U2 A-U WC 20-XX cWW cW-W 239 7.A37 9.U1 A-U WC 20-XX cWW cW-W **************************************************************************** List of 41 multiplets 1 nts=3 CAU 3.C931,3.A935,3.U1373 2 nts=3 AUC 3.A932,3.U1377,3.C1380 3 nts=3 AGU 3.A946,3.G968,3.U1229 4 nts=3 GCC 3.G948,3.C967,3.C1227 5 nts=3 GCA 3.G951,3.C1223,3.A1224 6 nts=3 ACG 3.A955,3.C982,3.G1217 7 nts=3 AGA 3.A975,3.G1313,3.A1357 8 nts=3 GGC 3.G985,3.G1012,3.C1214 9 nts=3 UUA 3.U989,3.U994,3.A1041 10 nts=3 GGC 3.G1050,3.G1054,3.C1200 11 nts=3 ACU 3.A1052,3.C1197,3.U1202 12 nts=3 GUU 3.G1055,3.U1196,3.U1199 13 nts=3 GGC 3.G1061,3.G1187,3.C1189 14 nts=3 UGA 3.U1067,3.G1091,3.A1102 15 nts=3 CUG 3.C1068,3.U1082,3.G1101 16 nts=3 GGC 3.G1069,3.G1081,3.C1100 17 nts=3 UUA 3.U1070,3.U1080,3.A1099 18 nts=3 GUA 3.G1071,3.U1080,3.A1098 19 nts=3 UUA 3.U1122,3.U1146,3.A1277 20 nts=3 GAU 3.G1124,3.A1142,3.U1145 21 nts=3 CGA 3.C1125,3.G1141,3.A1143 22 nts=3 CAG 3.C1126,3.A1127,3.G1140 23 nts=3 CGG 3.C1126,3.G1128,3.G1140 24 nts=3 CGG 3.C1129,3.G1136,3.G1139 25 nts=3 CGG 3.C1155,3.G1174,3.G1178 26 nts=3 GAG 3.G1157,3.A1173,3.G1179 27 nts=3 GUC 3.G1239,3.U1292,3.C1299 28 nts=3 AGC 3.A1247,3.G1350,3.C1366 29 nts=3 ACG 3.A1284,3.C1349,3.G1367 30 nts=3 UAG 3.U1312,3.A1316,3.G1358 31 nts=3 GGC 3.G1335,7.G29,7.C41 32 nts=3 GUA 3.G1344,3.U1345,3.A1371 33 nts=4 AUUC 3.A934,3.U1342,3.U1373,3.C1375 34 nts=4 GAGC 3.G941,3.A1336,7.G30,7.C40 35 nts=4 AUGA 3.A943,3.U1232,3.G1301,3.A1330 36 nts=4 UACG 3.U954,3.A956,3.C981,3.G1218 37 nts=4 UGCA 3.U988,3.G990,3.C1042,3.A1210 38 nts=4 GCGA 3.G1086,3.C1093,3.G1163,3.A1167 39 nts=4 GCGC 3.G1252,3.C1256,3.G1273,3.C1279 40 nts=4 GAGC 3.G1263,3.A1266,3.G1309,3.C1322 41 nts=5 AGCGU 3.A1235,3.G1238,3.C1293,3.G1297,3.U1298 **************************************************************************** List of 19 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[3] bps=14 strand-1 5'-CCCGACAAGCGGUG-3' bp-type ||||||..|||||. strand-2 3'-GGGCUGCCCGCUAA-5' helix-form .AAxA.xxAA... 1 3.C927 3.G1384 C-G WC 19-XIX cWW cW-W 2 3.C928 3.G1383 C-G WC 19-XIX cWW cW-W 3 3.C929 3.G1382 C-G WC 19-XIX cWW cW-W 4 3.G930 3.C1381 G-C WC 19-XIX cWW cW-W 5 3.A932 3.U1377 A-U WC 20-XX cWW cW-W 6 3.C933 3.G1376 C-G WC 19-XIX cWW cW-W 7 3.A934 3.C1375 A-C ~Sheared -- tSH tm-M 8 3.A935 3.C931 A+C ~rWobble 26-XXVI tWW tW+W 9 3.G936 3.C1341 G-C WC 19-XIX cWW cW-W 10 3.C937 3.G1340 C-G WC 19-XIX cWW cW-W 11 3.G938 3.C1339 G-C WC 19-XIX cWW cW-W 12 3.G939 3.U1338 G-U Wobble 28-XXVIII cWW cW-W 13 3.U940 3.A1337 U-A WC 20-XX cWW cW-W 14 3.G941 3.A1336 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#2[2] bps=14 strand-1 5'-AUACCACGUGCUAC-3' bp-type ..||||||||||.| strand-2 3'-UUUGGUGUACGAGG-5' helix-form .xBxAA......x 1 3.A956 3.U954 A-U -- -- tHS tM-m 2 3.U957 3.U953 U+U -- 13-XIII tWW tW+W 3 3.A1222 3.U952 A-U WC 20-XX cWW cW-W 4 3.C1223 3.G951 C-G WC 19-XIX cWW cW-W 5 3.C1225 3.G950 C-G WC 19-XIX cWW cW-W 6 3.A1226 3.U949 A-U WC 20-XX cWW cW-W 7 3.C1227 3.G948 C-G WC 19-XIX cWW cW-W 8 3.G1228 3.U947 G-U Wobble 28-XXVIII cWW cW-W 9 3.U1229 3.A946 U-A WC 20-XX cWW cW-W 10 3.G1230 3.C945 G-C WC 19-XIX cWW cW-W 11 3.C1231 3.G944 C-G WC 19-XIX cWW cW-W 12 3.U1232 3.A943 U-A WC 20-XX cWW cW-W 13 3.A1233 3.G942 A-G Imino 08-VIII cWW cW-W 14 3.C1234 3.G1334 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=3 strand-1 5'-UCG-3' bp-type .|| strand-2 3'-AGC-5' helix-form xA 1 3.U958 3.A1198 U+A -- -- tWW tW+W 2 3.C959 3.G970 C-G WC 19-XIX cWW cW-W 3 3.G960 3.C969 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[1] bps=17 strand-1 5'-CAAGACUCCAUGAAGAA-3' bp-type ...|||||||....|.. strand-2 3'-CGUCUGAGGUUAGGCUA-5' helix-form .xxAA.AAA.....xx 1 3.C976 3.C1314 C-C -- -- cSW cm-W 2 3.A975 3.G1313 A+G -- 10-X tWS tW+m 3 3.A1316 3.U1312 A-U rHoogsteen 24-XXIV tHW tM-W 4 3.G1320 3.C1311 G-C WC 19-XIX cWW cW-W 5 3.A1321 3.U1310 A-U WC 20-XX cWW cW-W 6 3.C1322 3.G1309 C-G WC 19-XIX cWW cW-W 7 3.U1323 3.A1308 U-A WC 20-XX cWW cW-W 8 3.C1324 3.G1307 C-G WC 19-XIX cWW cW-W 9 3.C1325 3.G1306 C-G WC 19-XIX cWW cW-W 10 3.A1326 3.U1305 A-U WC 20-XX cWW cW-W 11 3.U1327 3.U1304 U-U -- -- cWW cW-W 12 3.G1328 3.A1303 G-A Sheared 11-XI tSH tm-M 13 3.A1329 3.G1302 A+G -- -- tWS tW+m 14 3.A1330 3.G1301 A-G Sheared 11-XI tHS tM-m 15 3.G1331 3.C1300 G-C WC 19-XIX cWW cW-W 16 3.A1235 3.U1298 A-U rHoogsteen 24-XXIV tHW tM-W 17 3.A1236 3.A1296 A+A -- -- .HW .M+W -------------------------------------------------------------------------- helix#5[1] bps=8 strand-1 5'-CCUGGCCU-3' bp-type |||||||. strand-2 3'-GGACCGGA-5' helix-form AA...Ax 1 3.C981 3.G1218 C-G WC 19-XIX cWW cW-W 2 3.C982 3.G1217 C-G WC 19-XIX cWW cW-W 3 3.U983 3.A1216 U-A WC 20-XX cWW cW-W 4 3.G984 3.C1215 G-C WC 19-XIX cWW cW-W 5 3.G985 3.C1214 G-C WC 19-XIX cWW cW-W 6 3.C986 3.G1213 C-G WC 19-XIX cWW cW-W 7 3.C987 3.G1212 C-G WC 19-XIX cWW cW-W 8 3.U988 3.A1210 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#6[1] bps=8 strand-1 5'-CUUUCCAG-3' bp-type |..||||. strand-2 3'-GUUAGGUA-5' helix-form ....AA. 1 3.C1003 3.G1020 C-G WC 19-XIX cWW cW-W 2 3.U1004 3.U1019 U-U -- 16-XVI cWW cW-W 3 3.U1005 3.U1018 U-U -- 16-XVI cWW cW-W 4 3.U1006 3.A1017 U-A WC 20-XX cWW cW-W 5 3.C1007 3.G1016 C-G WC 19-XIX cWW cW-W 6 3.C1008 3.G1015 C-G WC 19-XIX cWW cW-W 7 3.A1009 3.U1014 A-U WC 20-XX cWW cW-W 8 3.G1010 3.A1013 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#7[6] bps=24 strand-1 5'-CUAGUACAGGGCUAUGGCUGUCGA-3' bp-type .||||||.|||||.||||||.|.. strand-2 3'-AAUCAUGUCCCGGUACUGACUGGC-5' helix-form xAAx.xx.AxA.x.Ax.Ax..xx 1 3.C1035 3.A1000 C-A ~Wobble -- cWW cW-W 2 3.U1036 3.A998 U-A WC 20-XX cWW cW-W 3 3.A1037 3.U997 A-U WC 20-XX cWW cW-W 4 3.G1038 3.C996 G-C WC 19-XIX cWW cW-W 5 3.U1040 3.A995 U-A WC 20-XX cWW cW-W 6 3.A1041 3.U994 A-U WC 20-XX cWW cW-W 7 3.C1042 3.G990 C-G WC 19-XIX cWW cW-W 8 3.A1043 3.U1208 A-U -- -- tHW tM-W 9 3.G1044 3.C1207 G-C WC 19-XIX cWW cW-W 10 3.G1045 3.C1206 G-C WC 19-XIX cWW cW-W 11 3.G1047 3.C1205 G-C WC 19-XIX cWW cW-W 12 3.C1048 3.G1204 C-G WC 19-XIX cWW cW-W 13 3.U1049 3.G1203 U-G Wobble 28-XXVIII cWW cW-W 14 3.A1052 3.U1202 A-U -- -- cWW cW-W 15 3.U1053 3.A1201 U-A WC 20-XX cWW cW-W 16 3.G1054 3.C1200 G-C WC 19-XIX cWW cW-W 17 3.G1055 3.U1196 G-U Wobble 28-XXVIII cWW cW-W 18 3.C1056 3.G1195 C-G WC 19-XIX cWW cW-W 19 3.U1057 3.A1194 U-A WC 20-XX cWW cW-W 20 3.G1058 3.C1192 G-C WC 19-XIX cWW cW-W 21 3.U1059 3.U1191 U-U -- 16-XVI cWW cW-W 22 3.C1060 3.G1190 C-G WC 19-XIX cWW cW-W 23 3.G1187 3.G1061 G+G -- 04-IV tSS tm+m 24 3.A1188 3.C1063 A-C ~rHoogsteen 25-XXV tHW tM-W -------------------------------------------------------------------------- helix#8[2] bps=10 strand-1 5'-GCUCGUGUCG-3' bp-type |||||||||. strand-2 3'-CGAGCAUAGA-5' helix-form A.AA.x.A. 1 3.G1065 3.C1104 G-C WC 19-XIX cWW cW-W 2 3.C1066 3.G1103 C-G WC 19-XIX cWW cW-W 3 3.U1067 3.A1102 U-A WC 20-XX cWW cW-W 4 3.C1068 3.G1101 C-G WC 19-XIX cWW cW-W 5 3.G1069 3.C1100 G-C WC 19-XIX cWW cW-W 6 3.U1070 3.A1099 U-A WC 20-XX cWW cW-W 7 3.G1071 3.U1080 G-U Wobble 28-XXVIII cWW cW-W 8 3.U1072 3.A1079 U-A WC 20-XX cWW cW-W 9 3.C1073 3.G1078 C-G WC 19-XIX cWW cW-W 10 3.G1074 3.A1077 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#9[1] bps=5 strand-1 5'-UGGGU-3' bp-type .|||. strand-2 3'-GCCCU-5' helix-form .AA. 1 3.U1083 3.G1096 U-G -- -- cWW cW-W 2 3.G1084 3.C1095 G-C WC 19-XIX cWW cW-W 3 3.G1085 3.C1094 G-C WC 19-XIX cWW cW-W 4 3.G1086 3.C1093 G-C WC 19-XIX cWW cW-W 5 3.U1087 3.U1092 U-U -- 16-XVI cWW cW-W -------------------------------------------------------------------------- helix#10[1] bps=4 strand-1 5'-CCUU-3' bp-type |||| strand-2 3'-GGGG-5' helix-form A.. 1 3.C1110 3.G1184 C-G WC 19-XIX cWW cW-W 2 3.C1111 3.G1183 C-G WC 19-XIX cWW cW-W 3 3.U1112 3.G1182 U-G Wobble 28-XXVIII cWW cW-W 4 3.U1113 3.G1181 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- helix#11[2] bps=9 strand-1 5'-UGCCGCAUU-3' bp-type ..||.|||. strand-2 3'-AAGGGGUAG-5' helix-form x.Axx..x 1 3.U1122 3.A1277 U+A Hoogsteen 23-XXIII cWH cW+M 2 3.G1124 3.A1142 G-A -- -- cWW cW-W 3 3.C1125 3.G1141 C-G WC 19-XIX cWW cW-W 4 3.C1126 3.G1140 C-G WC 19-XIX cWW cW-W 5 3.G1128 3.G1136 G-G -- -- -- -- 6 3.C1129 3.G1139 C-G WC 19-XIX cWW cW-W 7 3.A1130 3.U1138 A-U WC 20-XX cWW cW-W 8 3.U1131 3.A1137 U-A WC 20-XX cWW cW-W 9 3.U1132 3.G1135 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#12[1] bps=7 strand-1 5'-UAAGGAU-3' bp-type ||||||. strand-2 3'-AUUCCUA-5' helix-form ...AAx 1 3.U1147 3.A1120 U-A WC 20-XX cWW cW-W 2 3.A1148 3.U1119 A-U WC 20-XX cWW cW-W 3 3.A1149 3.U1118 A-U WC 20-XX cWW cW-W 4 3.G1150 3.C1117 G-C WC 19-XIX cWW cW-W 5 3.G1151 3.C1116 G-C WC 19-XIX cWW cW-W 6 3.A1152 3.U1115 A-U WC 20-XX cWW cW-W 7 3.U1153 3.A1176 U+A -- -- t.W t.+W -------------------------------------------------------------------------- helix#13[0] bps=2 strand-1 5'-AC-3' bp-type .| strand-2 5'-GG-3' helix-form x 1 3.A1154 3.G1175 A+G -- 10-X tWS tW+m 2 3.C1155 3.G1178 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#14[1] bps=7 strand-1 5'-GCCAGUG-3' bp-type .|||||. strand-2 3'-AGGUCAA-5' helix-form .AAAA. 1 3.G1157 3.A1173 G-A -- -- cWW cW-W 2 3.C1158 3.G1172 C-G WC 19-XIX cWW cW-W 3 3.C1159 3.G1171 C-G WC 19-XIX cWW cW-W 4 3.A1160 3.U1170 A-U WC 20-XX cWW cW-W 5 3.G1161 3.C1169 G-C WC 19-XIX cWW cW-W 6 3.U1162 3.A1168 U-A WC 20-XX cWW cW-W 7 3.G1163 3.A1167 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#15[1] bps=9 strand-1 5'-GGUCGGUAC-3' bp-type |||||||.. strand-2 3'-CUAGCCGAA-5' helix-form ..AAAA.. 1 3.G1238 3.C1293 G-C WC 19-XIX cWW cW-W 2 3.G1239 3.U1292 G-U Wobble 28-XXVIII cWW cW-W 3 3.U1240 3.A1291 U-A WC 20-XX cWW cW-W 4 3.C1241 3.G1290 C-G WC 19-XIX cWW cW-W 5 3.G1242 3.C1289 G-C WC 19-XIX cWW cW-W 6 3.G1243 3.C1288 G-C WC 19-XIX cWW cW-W 7 3.U1244 3.G1287 U-G Wobble 28-XXVIII cWW cW-W 8 3.A1245 3.A1286 A-A -- 05-V tWH tW-M 9 3.C1246 3.A1285 C-A ~rHoogsteen 25-XXV tWH tW-M -------------------------------------------------------------------------- helix#16[1] bps=4 strand-1 5'-AGGG-3' bp-type .||| strand-2 3'-ACUC-5' helix-form ... 1 3.A1249 3.A1282 A+A -- -- tWW tW+W 2 3.G1250 3.C1281 G-C WC 19-XIX cWW cW-W 3 3.G1251 3.U1280 G-U Wobble 28-XXVIII cWW cW-W 4 3.G1252 3.C1279 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#17[2] bps=9 strand-1 5'-GCUACACAG-3' bp-type ||..||||. strand-2 3'-CGUAGUGUA-5' helix-form ....AAA. 1 3.G1255 3.C1274 G-C WC 19-XIX cWW cW-W 2 3.C1256 3.G1273 C-G WC 19-XIX cWW cW-W 3 3.U1257 3.U1272 U-U -- 16-XVI cWW cW-W 4 3.A1258 3.A1271 A+A -- -- tWS tW+m 5 3.C1259 3.G1270 C-G WC 19-XIX cWW cW-W 6 3.A1260 3.U1269 A-U WC 20-XX cWW cW-W 7 3.C1261 3.G1268 C-G WC 19-XIX cWW cW-W 8 3.A1262 3.U1267 A-U WC 20-XX cWW cW-W 9 3.G1263 3.A1266 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#18[1] bps=13 strand-1 5'-UAUAAUCGCGGAU-3' bp-type ....|||||||.. strand-2 3'-UAAGUGGCGCCGA-5' helix-form .x....A....x 1 3.U1342 3.U1373 U+U -- 13-XIII tWW tW+W 2 3.A1343 3.A1372 A+A -- 02-II tHH tM+M 3 3.U1345 3.A1371 U-A rHoogsteen 24-XXIV tWH tW-M 4 3.A1346 3.G1370 A-G Sheared 11-XI tHS tM-m 5 3.A1347 3.U1369 A-U WC 20-XX cWW cW-W 6 3.U1348 3.G1368 U-G Wobble 28-XXVIII cWW cW-W 7 3.C1349 3.G1367 C-G WC 19-XIX cWW cW-W 8 3.G1350 3.C1366 G-C WC 19-XIX cWW cW-W 9 3.C1351 3.G1365 C-G WC 19-XIX cWW cW-W 10 3.G1352 3.C1364 G-C WC 19-XIX cWW cW-W 11 3.G1353 3.C1363 G-C WC 19-XIX cWW cW-W 12 3.A1354 3.G1362 A-G Imino 08-VIII cWW cW-W 13 3.U1355 3.A1360 U+A rWC 21-XXI tWW tW+W -------------------------------------------------------------------------- helix#19[1] bps=9 strand-1 5'-GUCGGGUUU-3' bp-type .|||||||. strand-2 3'-AAGCCCAAC-5' helix-form ..AAAxx. 1 7.G26 7.A44 G-A -- -- cWW cW-W 2 7.U27 7.A43 U-A WC 20-XX cWW cW-W 3 7.C28 7.G42 C-G WC 19-XIX cWW cW-W 4 7.G29 7.C41 G-C WC 19-XIX cWW cW-W 5 7.G30 7.C40 G-C WC 19-XIX cWW cW-W 6 7.G31 7.C39 G-C WC 19-XIX cWW cW-W 7 9.U1 7.A37 U-A WC 20-XX cWW cW-W 8 9.U2 7.A35 U-A WC 20-XX cWW cW-W 9 9.U3 7.C34 U-C -- -- cWW cW-W **************************************************************************** List of 29 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=4 strand-1 5'-CCCG-3' bp-type |||| strand-2 3'-GGGC-5' helix-form .AA 1 3.C927 3.G1384 C-G WC 19-XIX cWW cW-W 2 3.C928 3.G1383 C-G WC 19-XIX cWW cW-W 3 3.C929 3.G1382 C-G WC 19-XIX cWW cW-W 4 3.G930 3.C1381 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 3.A932 3.U1377 A-U WC 20-XX cWW cW-W 2 3.C933 3.G1376 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=5 strand-1 5'-GCGGU-3' bp-type ||||| strand-2 3'-CGCUA-5' helix-form AA.. 1 3.G936 3.C1341 G-C WC 19-XIX cWW cW-W 2 3.C937 3.G1340 C-G WC 19-XIX cWW cW-W 3 3.G938 3.C1339 G-C WC 19-XIX cWW cW-W 4 3.G939 3.U1338 G-U Wobble 28-XXVIII cWW cW-W 5 3.U940 3.A1337 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#4[#2] bps=8 strand-1 5'-AGCAUGUG-3' bp-type |||||||| strand-2 3'-UCGUGCAC-5' helix-form .....AA 1 3.A943 3.U1232 A-U WC 20-XX cWW cW-W 2 3.G944 3.C1231 G-C WC 19-XIX cWW cW-W 3 3.C945 3.G1230 C-G WC 19-XIX cWW cW-W 4 3.A946 3.U1229 A-U WC 20-XX cWW cW-W 5 3.U947 3.G1228 U-G Wobble 28-XXVIII cWW cW-W 6 3.G948 3.C1227 G-C WC 19-XIX cWW cW-W 7 3.U949 3.A1226 U-A WC 20-XX cWW cW-W 8 3.G950 3.C1225 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#2] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form . 1 3.G951 3.C1223 G-C WC 19-XIX cWW cW-W 2 3.U952 3.A1222 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#3] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form A 1 3.C959 3.G970 C-G WC 19-XIX cWW cW-W 2 3.G960 3.C969 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#5] bps=7 strand-1 5'-CCUGGCC-3' bp-type ||||||| strand-2 3'-GGACCGG-5' helix-form AA...A 1 3.C981 3.G1218 C-G WC 19-XIX cWW cW-W 2 3.C982 3.G1217 C-G WC 19-XIX cWW cW-W 3 3.U983 3.A1216 U-A WC 20-XX cWW cW-W 4 3.G984 3.C1215 G-C WC 19-XIX cWW cW-W 5 3.G985 3.C1214 G-C WC 19-XIX cWW cW-W 6 3.C986 3.G1213 C-G WC 19-XIX cWW cW-W 7 3.C987 3.G1212 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#7] bps=2 strand-1 5'-UA-3' bp-type || strand-2 3'-AU-5' helix-form . 1 3.U994 3.A1041 U-A WC 20-XX cWW cW-W 2 3.A995 3.U1040 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#9[#7] bps=3 strand-1 5'-CUA-3' bp-type ||| strand-2 3'-GAU-5' helix-form AA 1 3.C996 3.G1038 C-G WC 19-XIX cWW cW-W 2 3.U997 3.A1037 U-A WC 20-XX cWW cW-W 3 3.A998 3.U1036 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#10[#6] bps=4 strand-1 5'-UCCA-3' bp-type |||| strand-2 3'-AGGU-5' helix-form .AA 1 3.U1006 3.A1017 U-A WC 20-XX cWW cW-W 2 3.C1007 3.G1016 C-G WC 19-XIX cWW cW-W 3 3.C1008 3.G1015 C-G WC 19-XIX cWW cW-W 4 3.A1009 3.U1014 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#11[#7] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 3.G1044 3.C1207 G-C WC 19-XIX cWW cW-W 2 3.G1045 3.C1206 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#12[#7] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-CGG-5' helix-form A. 1 3.G1047 3.C1205 G-C WC 19-XIX cWW cW-W 2 3.C1048 3.G1204 C-G WC 19-XIX cWW cW-W 3 3.U1049 3.G1203 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#13[#7] bps=2 strand-1 5'-UG-3' bp-type || strand-2 3'-AC-5' helix-form A 1 3.U1053 3.A1201 U-A WC 20-XX cWW cW-W 2 3.G1054 3.C1200 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#14[#7] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-UGA-5' helix-form .A 1 3.G1055 3.U1196 G-U Wobble 28-XXVIII cWW cW-W 2 3.C1056 3.G1195 C-G WC 19-XIX cWW cW-W 3 3.U1057 3.A1194 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#15[#8] bps=6 strand-1 5'-GCUCGU-3' bp-type |||||| strand-2 3'-CGAGCA-5' helix-form A.AA. 1 3.G1065 3.C1104 G-C WC 19-XIX cWW cW-W 2 3.C1066 3.G1103 C-G WC 19-XIX cWW cW-W 3 3.U1067 3.A1102 U-A WC 20-XX cWW cW-W 4 3.C1068 3.G1101 C-G WC 19-XIX cWW cW-W 5 3.G1069 3.C1100 G-C WC 19-XIX cWW cW-W 6 3.U1070 3.A1099 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#16[#8] bps=3 strand-1 5'-GUC-3' bp-type ||| strand-2 3'-UAG-5' helix-form .A 1 3.G1071 3.U1080 G-U Wobble 28-XXVIII cWW cW-W 2 3.U1072 3.A1079 U-A WC 20-XX cWW cW-W 3 3.C1073 3.G1078 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#17[#9] bps=3 strand-1 5'-GGG-3' bp-type ||| strand-2 3'-CCC-5' helix-form AA 1 3.G1084 3.C1095 G-C WC 19-XIX cWW cW-W 2 3.G1085 3.C1094 G-C WC 19-XIX cWW cW-W 3 3.G1086 3.C1093 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#18[#10] bps=4 strand-1 5'-CCUU-3' bp-type |||| strand-2 3'-GGGG-5' helix-form A.. 1 3.C1110 3.G1184 C-G WC 19-XIX cWW cW-W 2 3.C1111 3.G1183 C-G WC 19-XIX cWW cW-W 3 3.U1112 3.G1182 U-G Wobble 28-XXVIII cWW cW-W 4 3.U1113 3.G1181 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#19[#12] bps=6 strand-1 5'-UCCUUA-3' bp-type |||||| strand-2 3'-AGGAAU-5' helix-form .A... 1 3.U1115 3.A1152 U-A WC 20-XX cWW cW-W 2 3.C1116 3.G1151 C-G WC 19-XIX cWW cW-W 3 3.C1117 3.G1150 C-G WC 19-XIX cWW cW-W 4 3.U1118 3.A1149 U-A WC 20-XX cWW cW-W 5 3.U1119 3.A1148 U-A WC 20-XX cWW cW-W 6 3.A1120 3.U1147 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#20[#11] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 3.C1125 3.G1141 C-G WC 19-XIX cWW cW-W 2 3.C1126 3.G1140 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#21[#11] bps=3 strand-1 5'-CAU-3' bp-type ||| strand-2 3'-GUA-5' helix-form .. 1 3.C1129 3.G1139 C-G WC 19-XIX cWW cW-W 2 3.A1130 3.U1138 A-U WC 20-XX cWW cW-W 3 3.U1131 3.A1137 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#22[#14] bps=5 strand-1 5'-CCAGU-3' bp-type ||||| strand-2 3'-GGUCA-5' helix-form AAAA 1 3.C1158 3.G1172 C-G WC 19-XIX cWW cW-W 2 3.C1159 3.G1171 C-G WC 19-XIX cWW cW-W 3 3.A1160 3.U1170 A-U WC 20-XX cWW cW-W 4 3.G1161 3.C1169 G-C WC 19-XIX cWW cW-W 5 3.U1162 3.A1168 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#23[#15] bps=7 strand-1 5'-GGUCGGU-3' bp-type ||||||| strand-2 3'-CUAGCCG-5' helix-form ..AAAA 1 3.G1238 3.C1293 G-C WC 19-XIX cWW cW-W 2 3.G1239 3.U1292 G-U Wobble 28-XXVIII cWW cW-W 3 3.U1240 3.A1291 U-A WC 20-XX cWW cW-W 4 3.C1241 3.G1290 C-G WC 19-XIX cWW cW-W 5 3.G1242 3.C1289 G-C WC 19-XIX cWW cW-W 6 3.G1243 3.C1288 G-C WC 19-XIX cWW cW-W 7 3.U1244 3.G1287 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#24[#16] bps=3 strand-1 5'-GGG-3' bp-type ||| strand-2 3'-CUC-5' helix-form .. 1 3.G1250 3.C1281 G-C WC 19-XIX cWW cW-W 2 3.G1251 3.U1280 G-U Wobble 28-XXVIII cWW cW-W 3 3.G1252 3.C1279 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#25[#17] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 3.G1255 3.C1274 G-C WC 19-XIX cWW cW-W 2 3.C1256 3.G1273 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#26[#17] bps=4 strand-1 5'-CACA-3' bp-type |||| strand-2 3'-GUGU-5' helix-form AAA 1 3.C1259 3.G1270 C-G WC 19-XIX cWW cW-W 2 3.A1260 3.U1269 A-U WC 20-XX cWW cW-W 3 3.C1261 3.G1268 C-G WC 19-XIX cWW cW-W 4 3.A1262 3.U1267 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#27[#4] bps=7 strand-1 5'-UGGAGUC-3' bp-type ||||||| strand-2 3'-ACCUCAG-5' helix-form AAA.AA 1 3.U1305 3.A1326 U-A WC 20-XX cWW cW-W 2 3.G1306 3.C1325 G-C WC 19-XIX cWW cW-W 3 3.G1307 3.C1324 G-C WC 19-XIX cWW cW-W 4 3.A1308 3.U1323 A-U WC 20-XX cWW cW-W 5 3.G1309 3.C1322 G-C WC 19-XIX cWW cW-W 6 3.U1310 3.A1321 U-A WC 20-XX cWW cW-W 7 3.C1311 3.G1320 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#28[#18] bps=7 strand-1 5'-AUCGCGG-3' bp-type ||||||| strand-2 3'-UGGCGCC-5' helix-form ..A... 1 3.A1347 3.U1369 A-U WC 20-XX cWW cW-W 2 3.U1348 3.G1368 U-G Wobble 28-XXVIII cWW cW-W 3 3.C1349 3.G1367 C-G WC 19-XIX cWW cW-W 4 3.G1350 3.C1366 G-C WC 19-XIX cWW cW-W 5 3.C1351 3.G1365 C-G WC 19-XIX cWW cW-W 6 3.G1352 3.C1364 G-C WC 19-XIX cWW cW-W 7 3.G1353 3.C1363 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#29[#19] bps=5 strand-1 5'-UCGGG-3' bp-type ||||| strand-2 3'-AGCCC-5' helix-form .AAA 1 7.U27 7.A43 U-A WC 20-XX cWW cW-W 2 7.C28 7.G42 C-G WC 19-XIX cWW cW-W 3 7.G29 7.C41 G-C WC 19-XIX cWW cW-W 4 7.G30 7.C40 G-C WC 19-XIX cWW cW-W 5 7.G31 7.C39 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 9 isolated WC/wobble pairs Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#7] -1 3.G990 3.C1042 G-C WC 19-XIX cWW cW-W [#6] -2 3.C1003 3.G1020 C-G WC 19-XIX cWW cW-W [#7] -3 3.G1058 3.C1192 G-C WC 19-XIX cWW cW-W [#7] -4 3.C1060 3.G1190 C-G WC 19-XIX cWW cW-W [#13] -5 3.C1155 3.G1178 C-G WC 19-XIX cWW cW-W [#2] -6 3.C1234 3.G1334 C-G WC 19-XIX cWW cW-W [#4] -7 3.C1300 3.G1331 C-G WC 19-XIX cWW cW-W [#19] -8 7.A35 9.U2 A-U WC 20-XX cWW cW-W [#19] -9 7.A37 9.U1 A-U WC 20-XX cWW cW-W **************************************************************************** List of 6 coaxial stacks 1 Helix#1 contains 3 stems: [#1,#2,#3] 2 Helix#2 contains 2 stems: [#5,#4] 3 Helix#7 contains 6 stems: [#9,#8,#11,#12,#13,#14] 4 Helix#8 contains 2 stems: [#15,#16] 5 Helix#11 contains 2 stems: [#20,#21] 6 Helix#17 contains 2 stems: [#25,#26] **************************************************************************** List of 99 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 GA 3.G930,3.A932 2 nts=2 GA 3.G941,3.A1337 3 nts=2 GG 3.G942,3.G1334 4 nts=2 GG 3.G950,3.G951 5 nts=2 GA 3.G960,3.A961 6 nts=2 AC 3.A991,3.C992 7 nts=2 AU 3.A993,3.U994 8 nts=2 AC 3.A995,3.C996 9 nts=2 AA 3.A1001,3.A1002 10 nts=2 CU 3.C1003,3.U1004 11 nts=2 UU 3.U1005,3.U1006 12 nts=2 AG 3.A1009,3.G1010 13 nts=2 AA 3.A1032,3.A1033 14 nts=2 UC 3.U1034,3.C1035 15 nts=2 AC 3.A1041,3.C1042 16 nts=2 GG 3.G1045,3.G1047 17 nts=2 UA 3.U1046,3.A1198 18 nts=2 UC 3.U1049,3.C1197 19 nts=2 CA 3.C1051,3.A1193 20 nts=2 GG 3.G1054,3.G1055 21 nts=2 GA 3.G1071,3.A1099 22 nts=2 GG 3.G1074,3.G1078 23 nts=2 UG 3.U1114,3.G1181 24 nts=2 UU 3.U1123,3.U1278 25 nts=2 CG 3.C1126,3.G1136 26 nts=2 UC 3.U1132,3.C1134 27 nts=2 GA 3.G1135,3.A1137 28 nts=2 GG 3.G1139,3.G1140 29 nts=2 AU 3.A1152,3.U1153 30 nts=2 UG 3.U1162,3.G1163 31 nts=2 AU 3.A1201,3.U1202 32 nts=2 CC 3.C1205,3.C1206 33 nts=2 CU 3.C1207,3.U1208 34 nts=2 AG 3.A1210,3.G1212 35 nts=2 UQ 3.U1237,h.GLN32 36 nts=2 GA 3.G1252,3.A1276 37 nts=2 CU 3.C1256,3.U1257 38 nts=2 AC 3.A1258,3.C1259 39 nts=2 AG 3.A1262,3.G1263 40 nts=2 CA 3.C1281,3.A1282 41 nts=2 GA 3.G1335,3.A1336 42 nts=2 CG 3.C1375,3.G1376 43 nts=2 GU 7.G26,7.U27 44 nts=2 GC 7.G31,7.C32 45 nts=3 UUU 3.U952,3.U953,3.U954 46 nts=3 UAC 3.U962,3.A966,3.C967 47 nts=3 GCA 3.G963,3.C964,3.A965 48 nts=3 GAH 3.G970,3.A971,o.HIS71 49 nts=3 CUU 3.C987,3.U988,3.U1209 50 nts=3 AGA 3.A998,3.G999,3.A1000 51 nts=3 AUU 3.A1017,3.U1018,3.U1019 52 nts=3 GGU 3.G1020,3.G1021,3.U1022 53 nts=3 GAU 3.G1038,3.A1039,3.U1040 54 nts=3 UGA 3.U1075,3.G1076,3.A1077 55 nts=3 GGC 3.G1084,3.G1096,3.C1097 56 nts=3 GUU 3.G1086,3.U1087,3.U1088 57 nts=3 UGC 3.U1122,3.G1124,3.C1125 58 nts=3 CGC 3.C1155,3.G1157,3.C1158 59 nts=3 CUN 3.C1200,3.U1199,o.ASN82 60 nts=3 CAH 3.C1225,3.A1224,t.HIS83 61 nts=3 GAU 3.G1238,3.A1236,3.U1295 62 nts=3 CAG 3.C1246,3.A1245,3.G1287 63 nts=3 GUU 3.G1255,3.U1253,3.U1275 64 nts=3 CGA 3.C1264,3.G1265,3.A1266 65 nts=3 CUG 3.C1311,3.U1312,3.G1313 66 nts=3 UAR 3.U1345,3.A1343,h.ARG10 67 nts=3 CCC 3.C1379,3.C1380,3.C1381 68 nts=3 AAG 7.A43,7.A44,7.G45 69 nts=4 GGGC 3.G924,3.G925,3.G926,3.C927 70 nts=4 CAAG 3.C933,3.A934,3.A935,3.G936 71 nts=4 AACC 3.A943,3.A1233,3.C1234,3.C1333 72 nts=4 ACGG 3.A974,3.C1220,3.G1219,3.G1218 73 nts=4 UGAG 3.U989,3.G990,3.A1043,3.G1044 74 nts=4 UCAG 3.U1062,3.C1186,3.A1185,3.G1184 75 nts=4 ACAG 3.A1120,3.C1121,3.A1142,3.G1141 76 nts=4 AAAA 3.A1164,3.A1166,3.A1167,3.A1168 77 nts=4 GAGG 3.G1172,3.A1173,3.G1174,3.G1175 78 nts=4 UCUC 3.U1221,3.C1319,3.U1318,3.C1317 79 nts=4 GAUG 3.G1270,3.A1271,3.U1272,3.G1273 80 nts=4 CCUA 3.C1341,3.C931,3.U1342,3.A1374 81 nts=4 GAUC 3.G1353,3.A1354,3.U1355,3.C1356 82 nts=4 UGGR 3.U1369,3.G1370,3.G1344,j.ARG107 83 nts=5 UAGAW 3.U1014,3.A1013,3.G1012,3.A1011,t.TRP34 84 nts=5 CUAAC 3.C1093,3.U1092,3.A1090,3.A1089,3.C1180 85 nts=5 ACGUC 3.A1188,3.C1189,3.G1190,3.U1191,3.C1192 86 nts=5 UGUAG 3.U1196,3.G1050,3.U1053,3.A1052,3.G1203 87 nts=5 AUAAR 3.A1222,3.U957,3.A956,3.A955,t.ARG55 88 nts=5 CAAAG 3.C1314,3.A1315,3.A975,3.A1316,3.G1320 89 nts=5 AAAAU 3.A1347,3.A1346,3.A1371,3.A1372,3.U1373 90 nts=5 AUAAC 7.A35,7.U36,7.A37,7.A38,7.C39 91 nts=7 CUAUUCC 3.C959,3.U958,3.A980,3.U979,3.U978,3.C977,3.C976 92 nts=7 ACGCUGA 3.A1064,3.C1063,3.G1061,3.C1060,3.U1059,3.G1058,3.A1194 93 nts=7 UAAAGGU 3.U1115,3.A1176,3.A1177,3.A1154,3.G1178,3.G1179,3.U1156 94 nts=7 GAAAAAA 3.G1250,3.A1249,3.A1248,3.A1247,3.A1284,3.A1285,3.A1286 95 nts=7 AGAGAGC 3.A1357,3.G1358,3.A1359,3.G973,3.A1360,3.G1362,3.C1363 96 nts=8 CGAACUUU 3.C1129,3.G1128,3.A1127,3.A1143,3.C1144,3.U1145,3.U1146,3.U1147 97 nts=8 AUCGGGUA 3.A1296,3.U1298,3.C1300,3.G1301,3.G1302,3.G1328,3.U1327,3.A1326 98 nts=8 UUAAAGGU 3.U1305,3.U1304,3.A1303,3.A1329,3.A1330,3.G1331,3.G1297,3.U1332 99 nts=10 UGUGGGCAAC 3.U1080,3.G1081,3.U1082,3.G1091,3.G1065,3.G1105,3.C1106,3.A1107,3.A1108,3.C1109 **************************************************************************** Nucleotides not involved in stacking interactions nts=27 GCACGUCCUACUCGCUUAACCUUCUUU 3.G968,3.C969,3.A972,3.C981,3.G1031,3.U1036,3.C1068,3.C1073,3.U1083,3.A1098,3.C1110,3.U1133,3.C1165,3.G1187,3.C1211,3.U1254,3.U1267,3.A1277,3.A1283,3.C1299,3.C1324,3.U1361,3.U1378,7.C34,9.U1,9.U3,9.U4 **************************************************************************** List of 31 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O2'@3.U947 3.G968 3.46 2 sugar O4'@3.G1362 3.G968 3.19 3 sugar O4'@3.U979 3.A980 3.09 4 sugar O4'@3.C1003 3.A1002 3.45 5 sugar O2'@3.C1003 3.A1002 2.89 6 phosphate OP2@3.G1012 3.G1010 3.16 7 phosphate O5'@3.G1012 3.G1010 3.46 8 sugar O4'@3.U1014 3.A1013 3.25 9 sugar O2'@3.C1042 3.A1041 2.88 10 sugar O4'@3.G1044 3.A1043 3.33 11 other O10@3.T1C1624 3.C1051 3.20 12 phosphate OP2@3.G1076 3.G1074 3.17 13 phosphate OP1@3.G1081 3.U1083 2.96 14 phosphate OP2@3.A1090 3.U1088 3.21 15 sugar O4'@3.U1092 3.A1090 2.96 16 sugar O4'@3.U1082 3.G1091 3.09 17 sugar O4'@3.U1072 3.A1098 3.31 18 sugar O2'@3.U1072 3.A1098 3.35 19 sugar O4'@3.C1106 3.G1105 3.48 20 sugar O4'@3.C1134 3.G1135 3.27 21 sugar O4'@3.A1137 3.G1135 3.18 22 sugar O2'@3.C1121 3.A1142 2.89 23 phosphate OP2@3.A1177 3.G1175 3.08 24 sugar O4'@3.C1225 3.A1224 3.50 25 sugar O4'@3.U1253 3.G1255 2.85 26 sugar O4'@3.C1259 3.A1258 3.35 27 phosphate OP2@3.G1265 3.G1263 2.88 28 sugar O4'@3.U1295 3.A1296 2.86 29 phosphate OP2@3.A1315 3.G1313 3.25 30 sugar O4'@3.C1333 3.G1334 2.91 31 phosphate OP2@7.A35 7.U33 2.97 **************************************************************************** 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 10 hairpin loops 1 hairpin loop: nts=10; [8]; linked by [#6] summary: [1] 8 [3.960 3.969] 2 nts=10 GAUGCAACGC 3.G960,3.A961,3.U962,3.G963,3.C964,3.A965,3.A966,3.C967,3.G968,3.C969 nts=8 AUGCAACG 3.A961,3.U962,3.G963,3.C964,3.A965,3.A966,3.C967,3.G968 2 hairpin loop: nts=6; [4]; linked by [#10] summary: [1] 4 [3.1009 3.1014] 4 nts=6 AGAGAU 3.A1009,3.G1010,3.A1011,3.G1012,3.A1013,3.U1014 nts=4 GAGA 3.G1010,3.A1011,3.G1012,3.A1013 3 hairpin loop: nts=6; [4]; linked by [#16] summary: [1] 4 [3.1073 3.1078] 3 nts=6 CGUGAG 3.C1073,3.G1074,3.U1075,3.G1076,3.A1077,3.G1078 nts=4 GUGA 3.G1074,3.U1075,3.G1076,3.A1077 4 hairpin loop: nts=8; [6]; linked by [#17] summary: [1] 6 [3.1086 3.1093] 3 nts=8 GUUAAGUC 3.G1086,3.U1087,3.U1088,3.A1089,3.A1090,3.G1091,3.U1092,3.C1093 nts=6 UUAAGU 3.U1087,3.U1088,3.A1089,3.A1090,3.G1091,3.U1092 5 hairpin loop: nts=7; [5]; linked by [#21] summary: [1] 5 [3.1131 3.1137] 3 nts=7 UUUCGGA 3.U1131,3.U1132,3.U1133,3.C1134,3.G1135,3.G1136,3.A1137 nts=5 UUCGG 3.U1132,3.U1133,3.C1134,3.G1135,3.G1136 6 hairpin loop: nts=7; [5]; linked by [#22] summary: [1] 5 [3.1162 3.1168] 5 nts=7 UGACAAA 3.U1162,3.G1163,3.A1164,3.C1165,3.A1166,3.A1167,3.A1168 nts=5 GACAA 3.G1163,3.A1164,3.C1165,3.A1166,3.A1167 7 hairpin loop: nts=6; [4]; linked by [#26] summary: [1] 4 [3.1262 3.1267] 4 nts=6 AGCGAU 3.A1262,3.G1263,3.C1264,3.G1265,3.A1266,3.U1267 nts=4 GCGA 3.G1263,3.C1264,3.G1265,3.A1266 8 hairpin loop: nts=10; [8]; linked by [#27] summary: [1] 8 [3.1311 3.1320] 7 nts=10 CUGCAACUCG 3.C1311,3.U1312,3.G1313,3.C1314,3.A1315,3.A1316,3.C1317,3.U1318,3.C1319,3.G1320 nts=8 UGCAACUC 3.U1312,3.G1313,3.C1314,3.A1315,3.A1316,3.C1317,3.U1318,3.C1319 9 hairpin loop: nts=11; [9]; linked by [#28] summary: [1] 9 [3.1353 3.1363] 7 nts=11 GAUCAGAAUGC 3.G1353,3.A1354,3.U1355,3.C1356,3.A1357,3.G1358,3.A1359,3.A1360,3.U1361,3.G1362,3.C1363 nts=9 AUCAGAAUG 3.A1354,3.U1355,3.C1356,3.A1357,3.G1358,3.A1359,3.A1360,3.U1361,3.G1362 10 hairpin loop: nts=9; [7]; linked by [#29] summary: [1] 7 [7.31 7.39] 5 nts=9 GCUCAUAAC 7.G31,7.C32,7.U33,7.C34,7.A35,7.U36,7.A37,7.A38,7.C39 nts=7 CUCAUAA 7.C32,7.U33,7.C34,7.A35,7.U36,7.A37,7.A38 **************************************************************************** List of 8 bulges 1 bulge: nts=5; [0,1]; linked by [#4,#5] summary: [2] 0 1 [3.950 3.1225 3.951 3.1223] 8 2 nts=5 GGCAC 3.G950,3.G951,3.C1223,3.A1224,3.C1225 nts=0 nts=1 A 3.A1224 2 bulge: nts=5; [0,1]; linked by [#8,#9] summary: [2] 0 1 [3.995 3.1040 3.996 3.1038] 2 3 nts=5 ACGAU 3.A995,3.C996,3.G1038,3.A1039,3.U1040 nts=0 nts=1 A 3.A1039 3 bulge: nts=5; [1,0]; linked by [#11,#12] summary: [2] 1 0 [3.1045 3.1206 3.1047 3.1205] 2 3 nts=5 GUGCC 3.G1045,3.U1046,3.G1047,3.C1205,3.C1206 nts=1 U 3.U1046 nts=0 4 bulge: nts=5; [0,1]; linked by [#14,#-3] summary: [2] 0 1 [3.1057 3.1194 3.1058 3.1192] 3 1 nts=5 UGCAA 3.U1057,3.G1058,3.C1192,3.A1193,3.A1194 nts=0 nts=1 A 3.A1193 5 bulge: nts=5; [1,0]; linked by [#-8,#-9] summary: [2] 1 0 [7.35 9.2 7.37 9.1] 1 1 nts=5 AUAUU 7.A35,7.U36,7.A37,9.U1,9.U2 nts=1 U 7.U36 nts=0 6 bulge: nts=6; [2,0]; linked by [#20,#21] summary: [2] 2 0 [3.1126 3.1140 3.1129 3.1139] 2 3 nts=6 CAGCGG 3.C1126,3.A1127,3.G1128,3.C1129,3.G1139,3.G1140 nts=2 AG 3.A1127,3.G1128 nts=0 7 bulge: nts=7; [3,0]; linked by [#-1,#8] summary: [2] 3 0 [3.990 3.1042 3.994 3.1041] 1 2 nts=7 GACAUAC 3.G990,3.A991,3.C992,3.A993,3.U994,3.A1041,3.C1042 nts=3 ACA 3.A991,3.C992,3.A993 nts=0 8 bulge: nts=7; [0,3]; linked by [#13,#14] summary: [2] 0 3 [3.1054 3.1200 3.1055 3.1196] 2 3 nts=7 GGUCAUC 3.G1054,3.G1055,3.U1196,3.C1197,3.A1198,3.U1199,3.C1200 nts=0 nts=3 CAU 3.C1197,3.A1198,3.U1199 **************************************************************************** List of 10 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#-3,#-4] summary: [2] 1 1 [3.1058 3.1192 3.1060 3.1190] 1 1 nts=6 GUCGUC 3.G1058,3.U1059,3.C1060,3.G1190,3.U1191,3.C1192 nts=1 U 3.U1059 nts=1 U 3.U1191 2 asymmetric internal loop: nts=8; [1,3]; linked by [#1,#2] summary: [2] 1 3 [3.930 3.1381 3.932 3.1377] 4 2 nts=8 GCAUUCCC 3.G930,3.C931,3.A932,3.U1377,3.U1378,3.C1379,3.C1380,3.C1381 nts=1 C 3.C931 nts=3 UCC 3.U1378,3.C1379,3.C1380 3 symmetric internal loop: nts=8; [2,2]; linked by [#-2,#10] summary: [2] 2 2 [3.1003 3.1020 3.1006 3.1017] 1 4 nts=8 CUUUAUUG 3.C1003,3.U1004,3.U1005,3.U1006,3.A1017,3.U1018,3.U1019,3.G1020 nts=2 UU 3.U1004,3.U1005 nts=2 UU 3.U1018,3.U1019 4 asymmetric internal loop: nts=8; [3,1]; linked by [#12,#13] summary: [2] 3 1 [3.1049 3.1203 3.1053 3.1201] 3 2 nts=8 UGCAUAUG 3.U1049,3.G1050,3.C1051,3.A1052,3.U1053,3.A1201,3.U1202,3.G1203 nts=3 GCA 3.G1050,3.C1051,3.A1052 nts=1 U 3.U1202 5 symmetric internal loop: nts=8; [2,2]; linked by [#25,#26] summary: [2] 2 2 [3.1256 3.1273 3.1259 3.1270] 2 4 nts=8 CUACGAUG 3.C1256,3.U1257,3.A1258,3.C1259,3.G1270,3.A1271,3.U1272,3.G1273 nts=2 UA 3.U1257,3.A1258 nts=2 AU 3.A1271,3.U1272 6 asymmetric internal loop: nts=10; [2,4]; linked by [#24,#25] summary: [2] 2 4 [3.1252 3.1279 3.1255 3.1274] 3 2 nts=10 GUUGCUAAUC 3.G1252,3.U1253,3.U1254,3.G1255,3.C1274,3.U1275,3.A1276,3.A1277,3.U1278,3.C1279 nts=2 UU 3.U1253,3.U1254 nts=4 UAAU 3.U1275,3.A1276,3.A1277,3.U1278 7 asymmetric internal loop: nts=11; [2,5]; linked by [#-5,#22] summary: [2] 2 5 [3.1155 3.1178 3.1158 3.1172] 1 5 nts=11 CUGCGAGGAAG 3.C1155,3.U1156,3.G1157,3.C1158,3.G1172,3.A1173,3.G1174,3.G1175,3.A1176,3.A1177,3.G1178 nts=2 UG 3.U1156,3.G1157 nts=5 AGGAA 3.A1173,3.G1174,3.G1175,3.A1176,3.A1177 8 symmetric internal loop: nts=12; [4,4]; linked by [#-7,#27] summary: [2] 4 4 [3.1300 3.1331 3.1305 3.1326] 1 7 nts=12 CGGAUUAUGAAG 3.C1300,3.G1301,3.G1302,3.A1303,3.U1304,3.U1305,3.A1326,3.U1327,3.G1328,3.A1329,3.A1330,3.G1331 nts=4 GGAU 3.G1301,3.G1302,3.A1303,3.U1304 nts=4 UGAA 3.U1327,3.G1328,3.A1329,3.A1330 9 asymmetric internal loop: nts=13; [4,5]; linked by [#19,#20] summary: [2] 4 5 [3.1120 3.1147 3.1125 3.1141] 6 2 nts=13 ACUUGCGAACUUU 3.A1120,3.C1121,3.U1122,3.U1123,3.G1124,3.C1125,3.G1141,3.A1142,3.A1143,3.C1144,3.U1145,3.U1146,3.U1147 nts=4 CUUG 3.C1121,3.U1122,3.U1123,3.G1124 nts=5 AACUU 3.A1142,3.A1143,3.C1144,3.U1145,3.U1146 10 symmetric internal loop: nts=14; [5,5]; linked by [#23,#24] summary: [2] 5 5 [3.1244 3.1287 3.1250 3.1281] 7 3 nts=14 UACAAAGCAAAAAG 3.U1244,3.A1245,3.C1246,3.A1247,3.A1248,3.A1249,3.G1250,3.C1281,3.A1282,3.A1283,3.A1284,3.A1285,3.A1286,3.G1287 nts=5 ACAAA 3.A1245,3.C1246,3.A1247,3.A1248,3.A1249 nts=5 AAAAA 3.A1282,3.A1283,3.A1284,3.A1285,3.A1286 **************************************************************************** List of 8 junctions 1 3-way junction: nts=11; [2,1,2]; linked by [#3,#4,#-6] summary: [3] 2 1 2 [3.940 3.1337 3.943 3.1232 3.1234 3.1334] 5 8 1 nts=11 UGGAUACGGAA 3.U940,3.G941,3.G942,3.A943,3.U1232,3.A1233,3.C1234,3.G1334,3.G1335,3.A1336,3.A1337 nts=2 GG 3.G941,3.G942 nts=1 A 3.A1233 nts=2 GA 3.G1335,3.A1336 2 3-way junction: nts=11; [1,2,2]; linked by [#18,#19,#-5] summary: [3] 1 2 2 [3.1113 3.1181 3.1115 3.1152 3.1155 3.1178] 4 6 1 nts=11 UUUAUACGGCG 3.U1113,3.U1114,3.U1115,3.A1152,3.U1153,3.A1154,3.C1155,3.G1178,3.G1179,3.C1180,3.G1181 nts=1 U 3.U1114 nts=2 UA 3.U1153,3.A1154 nts=2 GC 3.G1179,3.C1180 3 3-way junction: nts=12; [0,3,3]; linked by [#15,#16,#17] summary: [3] 0 3 3 [3.1070 3.1099 3.1071 3.1080 3.1084 3.1095] 6 3 3 nts=12 UGUGUUGCGCAA 3.U1070,3.G1071,3.U1080,3.G1081,3.U1082,3.U1083,3.G1084,3.C1095,3.G1096,3.C1097,3.A1098,3.A1099 nts=0 nts=3 GUU 3.G1081,3.U1082,3.U1083 nts=3 GCA 3.G1096,3.C1097,3.A1098 4 3-way junction: nts=13; [2,1,4]; linked by [#7,#-1,#11] summary: [3] 2 1 4 [3.987 3.1212 3.990 3.1042 3.1044 3.1207] 7 1 2 nts=13 CUUGCAGCUUACG 3.C987,3.U988,3.U989,3.G990,3.C1042,3.A1043,3.G1044,3.C1207,3.U1208,3.U1209,3.A1210,3.C1211,3.G1212 nts=2 UU 3.U988,3.U989 nts=1 A 3.A1043 nts=4 UUAC 3.U1208,3.U1209,3.A1210,3.C1211 5 3-way junction: nts=17; [3,6,2]; linked by [#-6,#23,#-7] summary: [3] 3 6 2 [3.1234 3.1334 3.1238 3.1293 3.1300 3.1331] 1 7 1 nts=17 CAAUGCGUAGUCCGUCG 3.C1234,3.A1235,3.A1236,3.U1237,3.G1238,3.C1293,3.G1294,3.U1295,3.A1296,3.G1297,3.U1298,3.C1299,3.C1300,3.G1331,3.U1332,3.C1333,3.G1334 nts=3 AAU 3.A1235,3.A1236,3.U1237 nts=6 GUAGUC 3.G1294,3.U1295,3.A1296,3.G1297,3.U1298,3.C1299 nts=2 UC 3.U1332,3.C1333 6 3-way junction: nts=19; [2,5,6]; linked by [#2,#3,#28] summary: [3] 2 5 6 [3.933 3.1376 3.936 3.1341 3.1347 3.1369] 2 5 7 nts=19 CAAGCUAGUAAUGAAUACG 3.C933,3.A934,3.A935,3.G936,3.C1341,3.U1342,3.A1343,3.G1344,3.U1345,3.A1346,3.A1347,3.U1369,3.G1370,3.A1371,3.A1372,3.U1373,3.A1374,3.C1375,3.G1376 nts=2 AA 3.A934,3.A935 nts=5 UAGUA 3.U1342,3.A1343,3.G1344,3.U1345,3.A1346 nts=6 GAAUAC 3.G1370,3.A1371,3.A1372,3.U1373,3.A1374,3.C1375 7 3-way junction: nts=20; [4,5,5]; linked by [#-4,#15,#18] summary: [3] 4 5 5 [3.1060 3.1190 3.1065 3.1104 3.1110 3.1184] 1 6 4 nts=20 CGUCAGCGCAACCGACGACG 3.C1060,3.G1061,3.U1062,3.C1063,3.A1064,3.G1065,3.C1104,3.G1105,3.C1106,3.A1107,3.A1108,3.C1109,3.C1110,3.G1184,3.A1185,3.C1186,3.G1187,3.A1188,3.C1189,3.G1190 nts=4 GUCA 3.G1061,3.U1062,3.C1063,3.A1064 nts=5 GCAAC 3.G1105,3.C1106,3.A1107,3.A1108,3.C1109 nts=5 ACGAC 3.A1185,3.C1186,3.G1187,3.A1188,3.C1189 8 3-way junction: nts=25; [6,10,3]; linked by [#5,#6,#7] summary: [3] 6 10 3 [3.952 3.1222 3.959 3.970 3.981 3.1218] 2 2 7 nts=25 UUUAAUUCGAAGAACCUUACGGCUA 3.U952,3.U953,3.U954,3.A955,3.A956,3.U957,3.U958,3.C959,3.G970,3.A971,3.A972,3.G973,3.A974,3.A975,3.C976,3.C977,3.U978,3.U979,3.A980,3.C981,3.G1218,3.G1219,3.C1220,3.U1221,3.A1222 nts=6 UUAAUU 3.U953,3.U954,3.A955,3.A956,3.U957,3.U958 nts=10 AAGAACCUUA 3.A971,3.A972,3.G973,3.A974,3.A975,3.C976,3.C977,3.U978,3.U979,3.A980 nts=3 GCU 3.G1219,3.C1220,3.U1221 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=3 GGG 3.G924,3.G925,3.G926 2 nts=4 GAAA 3.G999,3.A1000,3.A1001,3.A1002 3 nts=7* GUGAAUC 3.G1021,3.U1022,3.G1031,3.A1032,3.A1033,3.U1034,3.C1035 4 nts=1 G 7.G26 5 nts=2 AG 7.A44,7.G45 6 nts=2 UU 9.U3,9.U4 **************************************************************************** List of 19 A-minor motifs (types I, II, or X) 1 type=II A|C-G 3.A955|3.C982,3.G1217 WC -3.C982 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.34],N3-O2'(hydroxyl)[3.20]" +3.G1217 H-bonds[0]: "" 2 type=X A|G-C 3.A993|3.G990,3.C1042 WC +3.G990 H-bonds[0]: "" -3.C1042 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[2.87],N1-O2'(hydroxyl)[2.32]" 3 type=I A|G-C 3.A1013|3.G985,3.C1214 WC +3.G985 H-bonds[0]: "" -3.C1214 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.47]" 4 type=I A|G-U 3.A1098|3.G1071,3.U1080 Wobble +3.G1071 H-bonds[3]: "N6(amino)-O2'(hydroxyl)[3.14],N1-O2'(hydroxyl)[2.23],N3-N2(amino)[3.20]" -3.U1080 H-bonds[0]: "" 5 type=X A|C-G 3.A1127|3.C1125,3.G1141 WC +3.C1125 H-bonds[0]: "" -3.G1141 H-bonds[1]: "N6(amino)-N3[3.17]" 6 type=X A|C-G 3.A1127|3.C1126,3.G1140 WC +3.C1126 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.60]" -3.G1140 H-bonds[1]: "N6(amino)*N2(amino)[2.83]" 7 type=X A|C-G 3.A1143|3.C1125,3.G1141 WC -3.C1125 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.80]" +3.G1141 H-bonds[2]: "N7-N2(amino)[3.02],N6(amino)*N2(amino)[2.91]" 8 type=II A|G-C 3.A1166|3.G1085,3.C1094 WC +3.G1085 H-bonds[0]: "" -3.C1094 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.31]" 9 type=I A|G-C 3.A1167|3.G1086,3.C1093 WC +3.G1086 H-bonds[1]: "N1-O2'(hydroxyl)[3.50]" -3.C1093 H-bonds[1]: "O2'(hydroxyl)-O2(carbonyl)[3.10]" 10 type=X A|G-C 3.A1224|3.G951,3.C1223 WC +3.G951 H-bonds[1]: "N1-N2(amino)[2.39]" -3.C1223 H-bonds[0]: "" 11 type=X A|G-C 3.A1235|3.G1238,3.C1293 WC -3.G1238 H-bonds[2]: "N1-N2(amino)[3.06],N3-O2'(hydroxyl)[3.38]" +3.C1293 H-bonds[0]: "" 12 type=X A|G-C 3.A1247|3.G1350,3.C1366 WC +3.G1350 H-bonds[1]: "N1-N2(amino)[3.07]" -3.C1366 H-bonds[0]: "" 13 type=II A|G-C 3.A1248|3.G1350,3.C1366 WC +3.G1350 H-bonds[0]: "" -3.C1366 H-bonds[2]: "O2'(hydroxyl)-O3'[2.96],N3-O2'(hydroxyl)[2.50]" 14 type=I A|G-C 3.A1266|3.G1309,3.C1322 WC +3.G1309 H-bonds[2]: "N1-O2'(hydroxyl)[3.46],N3-N2(amino)[3.58]" -3.C1322 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.94]" 15 type=X A|C-G 3.A1284|3.C1349,3.G1367 WC -3.C1349 H-bonds[0]: "" +3.G1367 H-bonds[1]: "N1-N2(amino)[3.01]" 16 type=II A|C-G 3.A1285|3.C1349,3.G1367 WC -3.C1349 H-bonds[3]: "O2'(hydroxyl)-O3'[3.05],O2'(hydroxyl)-O2'(hydroxyl)[2.85],N3-O2'(hydroxyl)[2.74]" +3.G1367 H-bonds[0]: "" 17 type=I A|U-G 3.A1286|3.U1348,3.G1368 Wobble -3.U1348 H-bonds[0]: "" +3.G1368 H-bonds[1]: "N1-O2'(hydroxyl)[3.12]" 18 type=II A|A-U 3.A1330|3.A943,3.U1232 WC -3.A943 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.99],N3-O2'(hydroxyl)[2.80]" +3.U1232 H-bonds[0]: "" 19 type=I A|G-C 3.A1336|7.G30,7.C40 WC +7.G30 H-bonds[2]: "N1-O2'(hydroxyl)[3.53],N3-N2(amino)[3.16]" -7.C40 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.89],O2'(hydroxyl)-O2(carbonyl)[2.82]" **************************************************************************** List of 7 ribose zippers 1 nts=4 AGAU 3.A935,3.G936,3.A1372,3.U1373 2 nts=4 AACC 3.A955,3.A956,3.C981,3.C982 3 nts=4 GACC 3.G1012,3.A1013,3.C1214,3.C1215 4 nts=4 CCAA 3.C1093,3.C1094,3.A1166,3.A1167 5 nts=4 AACG 3.A1247,3.A1248,3.C1366,3.G1367 6 nts=4 GACU 3.G1265,3.A1266,3.C1322,3.U1323 7 nts=4 AACG 3.A1284,3.A1285,3.C1349,3.G1350 **************************************************************************** List of 53 splayed-apart dinucleotides 1 3.G930 3.C931 angle=97 distance=14.3 ratio=0.75 2 3.U954 3.A955 angle=100 distance=13.5 ratio=0.77 3 3.U957 3.U958 angle=161 distance=18.1 ratio=0.99 4 3.U962 3.G963 angle=144 distance=17.9 ratio=0.95 5 3.A965 3.A966 angle=108 distance=17.2 ratio=0.81 6 3.C967 3.G968 angle=126 distance=17.7 ratio=0.89 7 3.G968 3.C969 angle=97 distance=16.1 ratio=0.75 8 3.A971 3.A972 angle=149 distance=17.0 ratio=0.96 9 3.G973 3.A974 angle=91 distance=14.0 ratio=0.71 10 3.A974 3.A975 angle=124 distance=15.2 ratio=0.89 11 3.U988 3.U989 angle=93 distance=15.1 ratio=0.72 12 3.A1000 3.A1001 angle=87 distance=13.8 ratio=0.69 13 3.G1010 3.A1011 angle=88 distance=12.0 ratio=0.70 14 3.G1045 3.U1046 angle=169 distance=17.8 ratio=1.00 15 3.U1046 3.G1047 angle=110 distance=17.6 ratio=0.82 16 3.G1050 3.C1051 angle=152 distance=18.7 ratio=0.97 17 3.C1051 3.A1052 angle=154 distance=17.6 ratio=0.97 18 3.G1074 3.U1075 angle=90 distance=12.6 ratio=0.71 19 3.U1082 3.U1083 angle=110 distance=15.3 ratio=0.82 20 3.A1090 3.G1091 angle=100 distance=16.6 ratio=0.77 21 3.G1091 3.U1092 angle=116 distance=16.1 ratio=0.85 22 3.U1123 3.G1124 angle=88 distance=13.0 ratio=0.69 23 3.U1132 3.U1133 angle=124 distance=13.5 ratio=0.89 24 3.G1163 3.A1164 angle=86 distance=12.3 ratio=0.68 25 3.A1164 3.C1165 angle=116 distance=18.1 ratio=0.85 26 3.C1165 3.A1166 angle=134 distance=18.0 ratio=0.92 27 3.G1179 3.C1180 angle=166 distance=18.4 ratio=0.99 28 3.C1180 3.G1181 angle=120 distance=16.1 ratio=0.87 29 3.G1187 3.A1188 angle=96 distance=13.1 ratio=0.74 30 3.C1192 3.A1193 angle=98 distance=16.4 ratio=0.75 31 3.A1193 3.A1194 angle=133 distance=16.4 ratio=0.92 32 3.C1197 3.A1198 angle=151 distance=19.6 ratio=0.97 33 3.A1198 3.U1199 angle=164 distance=18.7 ratio=0.99 34 3.U1208 3.U1209 angle=147 distance=18.0 ratio=0.96 35 3.C1211 3.G1212 angle=108 distance=14.7 ratio=0.81 36 3.U1221 3.A1222 angle=128 distance=16.8 ratio=0.90 37 3.C1234 3.A1235 angle=136 distance=16.6 ratio=0.93 38 3.A1236 3.U1237 angle=170 distance=19.1 ratio=1.00 39 3.U1237 3.G1238 angle=123 distance=16.9 ratio=0.88 40 3.U1253 3.U1254 angle=157 distance=17.7 ratio=0.98 41 3.U1254 3.G1255 angle=121 distance=16.3 ratio=0.87 42 3.G1263 3.C1264 angle=89 distance=12.6 ratio=0.70 43 3.A1276 3.A1277 angle=139 distance=19.7 ratio=0.94 44 3.A1277 3.U1278 angle=100 distance=15.2 ratio=0.77 45 3.U1298 3.C1299 angle=104 distance=14.1 ratio=0.79 46 3.C1299 3.C1300 angle=141 distance=18.5 ratio=0.94 47 3.A1316 3.C1317 angle=102 distance=15.2 ratio=0.78 48 3.C1319 3.G1320 angle=118 distance=17.2 ratio=0.86 49 3.U1332 3.C1333 angle=102 distance=15.2 ratio=0.78 50 3.G1334 3.G1335 angle=103 distance=15.1 ratio=0.78 51 3.C1356 3.A1357 angle=108 distance=14.6 ratio=0.81 52 3.A1360 3.U1361 angle=99 distance=12.6 ratio=0.78 53 3.A1374 3.C1375 angle=116 distance=14.9 ratio=0.85 ---------------------------------------------------------------- Summary of 39 splayed-apart units 1 nts=2 GC 3.G930,3.C931 2 nts=2 UA 3.U954,3.A955 3 nts=2 UU 3.U957,3.U958 4 nts=2 UG 3.U962,3.G963 5 nts=2 AA 3.A965,3.A966 6 nts=3 CGC 3.C967,3.G968,3.C969 7 nts=2 AA 3.A971,3.A972 8 nts=3 GAA 3.G973,3.A974,3.A975 9 nts=2 UU 3.U988,3.U989 10 nts=2 AA 3.A1000,3.A1001 11 nts=2 GA 3.G1010,3.A1011 12 nts=3 GUG 3.G1045,3.U1046,3.G1047 13 nts=3 GCA 3.G1050,3.C1051,3.A1052 14 nts=2 GU 3.G1074,3.U1075 15 nts=2 UU 3.U1082,3.U1083 16 nts=3 AGU 3.A1090,3.G1091,3.U1092 17 nts=2 UG 3.U1123,3.G1124 18 nts=2 UU 3.U1132,3.U1133 19 nts=4 GACA 3.G1163,3.A1164,3.C1165,3.A1166 20 nts=3 GCG 3.G1179,3.C1180,3.G1181 21 nts=2 GA 3.G1187,3.A1188 22 nts=3 CAA 3.C1192,3.A1193,3.A1194 23 nts=3 CAU 3.C1197,3.A1198,3.U1199 24 nts=2 UU 3.U1208,3.U1209 25 nts=2 CG 3.C1211,3.G1212 26 nts=2 UA 3.U1221,3.A1222 27 nts=2 CA 3.C1234,3.A1235 28 nts=3 AUG 3.A1236,3.U1237,3.G1238 29 nts=3 UUG 3.U1253,3.U1254,3.G1255 30 nts=2 GC 3.G1263,3.C1264 31 nts=3 AAU 3.A1276,3.A1277,3.U1278 32 nts=3 UCC 3.U1298,3.C1299,3.C1300 33 nts=2 AC 3.A1316,3.C1317 34 nts=2 CG 3.C1319,3.G1320 35 nts=2 UC 3.U1332,3.C1333 36 nts=2 GG 3.G1334,3.G1335 37 nts=2 CA 3.C1356,3.A1357 38 nts=2 AU 3.A1360,3.U1361 39 nts=2 AC 3.A1374,3.C1375 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *1-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. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6ytf nts=477 [whole] GGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGCCUUGACAUACUAGAAACUUUCCAGAGAUGGAUUGGU&GAAUCUAGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUCCUUACUUGCCAGCAUUUCGGAUGGGAACUUUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGCCAGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCUACACAGCGAUGUGAUGCUAAUCUCAAAAAGCCGAUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGG&GUCGGGCUCAUAACCCGAAG&UUUU ...((((.((..(((((..((((((((((......((........))..........(((((((..(...(((((....(..((((....))))..)..&.....))).))).((.(((...((((((.(....(((((((((....)))...(((......)))...)))))).....((((.((((((....((..(((.....))))).....))))))..(..(((((.....))))).....)..)))).....).).)))...)).)))))....)))))))...)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((.........)))))))......))...))))&.(((((...[.[.)))))..&]].. >6ytf-3 #1 nts=453 0.03(3.27) [chain] RNA* GGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGCCUUGACAUACUAGAAACUUUCCAGAGAUGGAUUGGU&GAAUCUAGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUCCUUACUUGCCAGCAUUUCGGAUGGGAACUUUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGCCAGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCUACACAGCGAUGUGAUGCUAAUCUCAAAAAGCCGAUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGG ...((((.((..(((((..((((((((((......((........))..........(((((((..(...(((((....(..((((....))))..)..&.....))).))).((.(((...((((((.(....(((((((((....)))...(((......)))...)))))).....((((.((((((....((..(((.....))))).....))))))..(..(((((.....))))).....)..)))).....).).)))...)).)))))....)))))))...)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((.........)))))))......))...)))) >6ytf-7 #2 nts=20 0.01(2.51) [chain] RNA GUCGGGCUCAUAACCCGAAG .(((((...[.[.))))).. >6ytf-9 #3 nts=4 2.57(0.09) [chain] RNA UUUU ]].. **************************************************************************** Summary of structural features of 477 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 . 3.G924 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 2 G . 3.G925 0.013 anti,~C3'-endo,non-pair-contact,ss-non-loop 3 G . 3.G926 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 4 C ( 3.C927 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 5 C ( 3.C928 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 C ( 3.C929 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( 3.G930 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,splayed-apart 8 C . 3.C931 0.016 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 9 A ( 3.A932 0.013 turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 10 C ( 3.C933 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 11 A . 3.A934 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 12 A . 3.A935 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,ribose-zipper 13 G ( 3.G936 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,ribose-zipper 14 C ( 3.C937 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 G ( 3.G938 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 16 G ( 3.G939 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 U ( 3.U940 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 18 G . 3.G941 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 19 G . 3.G942 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 20 A ( 3.A943 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 21 G ( 3.G944 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 C ( 3.C945 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 23 A ( 3.A946 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 24 U ( 3.U947 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor,phosphate 25 G ( 3.G948 0.027 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 26 U ( 3.U949 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 27 G ( 3.G950 0.027 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 28 G ( 3.G951 0.017 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 29 U ( 3.U952 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 30 U . 3.U953 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop 31 U . 3.U954 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,splayed-apart 32 A . 3.A955 0.022 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,phosphate,splayed-apart 33 A . 3.A956 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,ribose-zipper 34 U . 3.U957 0.012 turn,syn,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 35 U . 3.U958 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 36 C ( 3.C959 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 37 G ( 3.G960 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 38 A . 3.A961 0.017 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 39 U . 3.U962 0.007 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 40 G . 3.G963 0.011 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 41 C . 3.C964 0.012 syn,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 42 A . 3.A965 0.013 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 43 A . 3.A966 0.017 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 44 C . 3.C967 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 45 G . 3.G968 0.013 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor,phosphate,splayed-apart 46 C ) 3.C969 0.019 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate,splayed-apart 47 G ) 3.G970 0.016 turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 48 A . 3.A971 0.017 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 49 A . 3.A972 0.014 turn,syn,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 50 G . 3.G973 0.019 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 51 A . 3.A974 0.021 ~C3'-endo,non-pair-contact,junction-loop,splayed-apart 52 A . 3.A975 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate,splayed-apart 53 C . 3.C976 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 54 C . 3.C977 0.012 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 55 U . 3.U978 0.016 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 56 U . 3.U979 0.011 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,phosphate 57 A . 3.A980 0.019 turn,syn,~C3'-endo,non-pair-contact,junction-loop,cap-acceptor,phosphate 58 C ( 3.C981 0.024 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,ribose-zipper 59 C ( 3.C982 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 60 U ( 3.U983 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 61 G ( 3.G984 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 62 G ( 3.G985 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 63 C ( 3.C986 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 64 C ( 3.C987 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 65 U . 3.U988 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,splayed-apart 66 U . 3.U989 0.010 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 67 G ( 3.G990 0.027 syn,~C2'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,A-minor 68 A . 3.A991 0.013 turn,~C3'-endo,non-pair-contact,bulge 69 C . 3.C992 0.008 anti,~C3'-endo,BI,non-pair-contact,bulge 70 A . 3.A993 0.010 anti,~C3'-endo,non-pair-contact,bulge,A-minor 71 U ( 3.U994 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 72 A ( 3.A995 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 73 C ( 3.C996 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 74 U ( 3.U997 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 75 A ( 3.A998 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 76 G . 3.G999 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 77 A . 3.A1000 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 78 A . 3.A1001 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 79 A . 3.A1002 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor,phosphate 80 C ( 3.C1003 0.011 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,cap-donor 81 U . 3.U1004 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 82 U . 3.U1005 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 83 U ( 3.U1006 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 84 C ( 3.C1007 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 85 C ( 3.C1008 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 86 A ( 3.A1009 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 87 G . 3.G1010 0.014 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,splayed-apart 88 A . 3.A1011 0.015 turn,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,hairpin-loop,phosphate,splayed-apart 89 G . 3.G1012 0.013 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,ribose-zipper,cap-donor,phosphate 90 A . 3.A1013 0.015 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 91 U ) 3.U1014 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 92 G ) 3.G1015 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 93 G ) 3.G1016 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 94 A ) 3.A1017 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 95 U . 3.U1018 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 96 U . 3.U1019 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 97 G ) 3.G1020 0.006 ~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,internal-loop 98 G . 3.G1021 0.011 anti,~C3'-endo,non-pair-contact,ss-non-loop 99 U . 3.U1022 0.004 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 100 G . 3.G1031 0.004 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop 101 A . 3.A1032 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop 102 A . 3.A1033 0.008 anti,~C3'-endo,non-pair-contact,ss-non-loop 103 U . 3.U1034 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 104 C . 3.C1035 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 105 U ) 3.U1036 0.010 anti,~C3'-endo,BI,non-stack,canonical,non-canonical,helix,stem-end,coaxial-stack 106 A ) 3.A1037 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 107 G ) 3.G1038 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 108 A . 3.A1039 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,bulge 109 U ) 3.U1040 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 110 A ) 3.A1041 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,cap-acceptor 111 C ) 3.C1042 0.006 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,A-minor,cap-donor 112 A . 3.A1043 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor 113 G ( 3.G1044 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor 114 G ( 3.G1045 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 115 U . 3.U1046 0.009 turn,anti,~C2'-endo,non-pair-contact,bulge,splayed-apart 116 G ( 3.G1047 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 117 C ( 3.C1048 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 118 U ( 3.U1049 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 119 G . 3.G1050 0.003 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,splayed-apart 120 C . 3.C1051 0.004 turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-acceptor,phosphate,splayed-apart 121 A . 3.A1052 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate,splayed-apart 122 U ( 3.U1053 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 123 G ( 3.G1054 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 124 G ( 3.G1055 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 125 C ( 3.C1056 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 126 U ( 3.U1057 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 127 G ( 3.G1058 0.022 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,internal-loop 128 U . 3.U1059 0.024 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 129 C ( 3.C1060 0.017 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate 130 G . 3.G1061 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 131 U . 3.U1062 0.008 turn,anti,~C2'-endo,non-pair-contact,junction-loop 132 C . 3.C1063 0.019 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 133 A . 3.A1064 0.017 anti,~C2'-endo,non-pair-contact,junction-loop 134 G ( 3.G1065 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 135 C ( 3.C1066 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 136 U ( 3.U1067 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 137 C ( 3.C1068 0.013 anti,~C3'-endo,BI,non-stack,canonical,non-canonical,helix,stem,coaxial-stack,multiplet 138 G ( 3.G1069 0.019 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 139 U ( 3.U1070 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 140 G ( 3.G1071 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 141 U ( 3.U1072 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 142 C ( 3.C1073 0.008 anti,~C3'-endo,BI,non-stack,canonical,helix,stem-end,coaxial-stack,hairpin-loop 143 G . 3.G1074 0.006 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,splayed-apart 144 U . 3.U1075 0.001 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 145 G . 3.G1076 0.003 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 146 A . 3.A1077 0.008 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 147 G ) 3.G1078 0.024 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 148 A ) 3.A1079 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 149 U ) 3.U1080 0.019 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 150 G . 3.G1081 0.022 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,phosphate 151 U . 3.U1082 0.016 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,splayed-apart 152 U . 3.U1083 0.011 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,splayed-apart 153 G ( 3.G1084 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 154 G ( 3.G1085 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,A-minor 155 G ( 3.G1086 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,hairpin-loop,A-minor 156 U . 3.U1087 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 157 U . 3.U1088 0.012 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor 158 A . 3.A1089 0.015 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 159 A . 3.A1090 0.017 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 160 G . 3.G1091 0.022 turn,u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor,phosphate,splayed-apart 161 U . 3.U1092 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,phosphate,splayed-apart 162 C ) 3.C1093 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,hairpin-loop,A-minor,ribose-zipper 163 C ) 3.C1094 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,ribose-zipper 164 C ) 3.C1095 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 165 G . 3.G1096 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 166 C . 3.C1097 0.007 anti,~C3'-endo,non-pair-contact,junction-loop 167 A . 3.A1098 0.013 turn,anti,~C2'-endo,non-stack,non-canonical,multiplet,junction-loop,A-minor,cap-acceptor 168 A ) 3.A1099 0.023 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 169 C ) 3.C1100 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 170 G ) 3.G1101 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 171 A ) 3.A1102 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 172 G ) 3.G1103 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 173 C ) 3.C1104 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 174 G . 3.G1105 0.017 anti,~C3'-endo,BI,non-pair-contact,junction-loop,cap-acceptor,phosphate 175 C . 3.C1106 0.018 anti,~C3'-endo,BI,non-pair-contact,junction-loop,cap-donor,phosphate 176 A . 3.A1107 0.016 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 177 A . 3.A1108 0.015 anti,~C3'-endo,BI,non-pair-contact,junction-loop 178 C . 3.C1109 0.016 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 179 C ( 3.C1110 0.014 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,junction-loop 180 C ( 3.C1111 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 181 U ( 3.U1112 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 182 U ( 3.U1113 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 183 U . 3.U1114 0.010 anti,~C3'-endo,non-pair-contact,junction-loop 184 U ( 3.U1115 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 185 C ( 3.C1116 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 186 C ( 3.C1117 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 187 U ( 3.U1118 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 188 U ( 3.U1119 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 189 A ( 3.A1120 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop 190 C . 3.C1121 0.007 anti,~C2'-endo,BII,non-canonical,non-pair-contact,internal-loop,cap-donor 191 U . 3.U1122 0.016 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 192 U . 3.U1123 0.012 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 193 G . 3.G1124 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 194 C ( 3.C1125 0.009 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 195 C ( 3.C1126 0.009 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 196 A . 3.A1127 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor,phosphate 197 G . 3.G1128 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,bulge 198 C ( 3.C1129 0.009 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 199 A ( 3.A1130 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 200 U ( 3.U1131 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 201 U . 3.U1132 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 202 U . 3.U1133 0.009 turn,syn,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 203 C . 3.C1134 0.005 turn,anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,cap-donor 204 G . 3.G1135 0.008 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 205 G . 3.G1136 0.014 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop 206 A ) 3.A1137 0.005 turn,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 207 U ) 3.U1138 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 208 G ) 3.G1139 0.006 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 209 G ) 3.G1140 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 210 G ) 3.G1141 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 211 A . 3.A1142 0.009 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,cap-acceptor 212 A . 3.A1143 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor 213 C . 3.C1144 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop 214 U . 3.U1145 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 215 U . 3.U1146 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 216 U ) 3.U1147 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop 217 A ) 3.A1148 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 218 A ) 3.A1149 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 219 G ) 3.G1150 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 220 G ) 3.G1151 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 221 A ) 3.A1152 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 222 U . 3.U1153 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 223 A . 3.A1154 0.014 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 224 C ( 3.C1155 0.012 syn,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,multiplet,internal-loop,junction-loop 225 U . 3.U1156 0.005 turn,syn,~C2'-endo,non-pair-contact,internal-loop 226 G . 3.G1157 0.011 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 227 C ( 3.C1158 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,internal-loop 228 C ( 3.C1159 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 229 A ( 3.A1160 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 230 G ( 3.G1161 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 231 U ( 3.U1162 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 232 G . 3.G1163 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 233 A . 3.A1164 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,hairpin-loop,splayed-apart 234 C . 3.C1165 0.003 turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 235 A . 3.A1166 0.009 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,splayed-apart 236 A . 3.A1167 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 237 A ) 3.A1168 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 238 C ) 3.C1169 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 239 U ) 3.U1170 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 240 G ) 3.G1171 0.031 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 241 G ) 3.G1172 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 242 A . 3.A1173 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 243 G . 3.G1174 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 244 G . 3.G1175 0.020 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 245 A . 3.A1176 0.008 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 246 A . 3.A1177 0.012 u-turn,anti,~C3'-endo,non-pair-contact,internal-loop,cap-donor,phosphate 247 G ) 3.G1178 0.020 u-turn,~C2'-endo,BII,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,junction-loop,phosphate 248 G . 3.G1179 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 249 C . 3.C1180 0.008 turn,anti,~C2'-endo,BI,non-pair-contact,junction-loop,phosphate,splayed-apart 250 G ) 3.G1181 0.009 turn,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop,splayed-apart 251 G ) 3.G1182 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 252 G ) 3.G1183 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 253 G ) 3.G1184 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 254 A . 3.A1185 0.016 anti,~C3'-endo,BI,non-pair-contact,junction-loop 255 C . 3.C1186 0.011 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 256 G . 3.G1187 0.018 anti,~C2'-endo,non-stack,non-canonical,helix,multiplet,junction-loop,phosphate,splayed-apart 257 A . 3.A1188 0.024 ~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 258 C . 3.C1189 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 259 G ) 3.G1190 0.018 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate 260 U . 3.U1191 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 261 C ) 3.C1192 0.002 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,internal-loop,splayed-apart 262 A . 3.A1193 0.005 turn,anti,~C2'-endo,non-pair-contact,bulge,splayed-apart 263 A ) 3.A1194 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 264 G ) 3.G1195 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 265 U ) 3.U1196 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 266 C . 3.C1197 0.007 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,phosphate,splayed-apart 267 A . 3.A1198 0.012 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,bulge,splayed-apart 268 U . 3.U1199 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,phosphate,splayed-apart 269 C ) 3.C1200 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 270 A ) 3.A1201 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 271 U . 3.U1202 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 272 G ) 3.G1203 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 273 G ) 3.G1204 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 274 C ) 3.C1205 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 275 C ) 3.C1206 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 276 C ) 3.C1207 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 277 U . 3.U1208 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 278 U . 3.U1209 0.004 turn,anti,~C2'-endo,non-pair-contact,junction-loop,splayed-apart 279 A . 3.A1210 0.017 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 280 C . 3.C1211 0.008 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 281 G ) 3.G1212 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 282 G ) 3.G1213 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 283 C ) 3.C1214 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 284 C ) 3.C1215 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,ribose-zipper 285 A ) 3.A1216 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 286 G ) 3.G1217 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,phosphate 287 G ) 3.G1218 0.024 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,phosphate 288 G . 3.G1219 0.023 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 289 C . 3.C1220 0.022 turn,anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 290 U . 3.U1221 0.015 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 291 A ) 3.A1222 0.013 ~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 292 C ) 3.C1223 0.010 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 293 A . 3.A1224 0.008 turn,syn,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor,cap-acceptor 294 C ) 3.C1225 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,cap-donor,phosphate 295 A ) 3.A1226 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 296 C ) 3.C1227 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 297 G ) 3.G1228 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 298 U ) 3.U1229 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 299 G ) 3.G1230 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 300 C ) 3.C1231 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 301 U ) 3.U1232 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 302 A . 3.A1233 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 303 C ( 3.C1234 0.012 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 304 A . 3.A1235 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,phosphate,splayed-apart 305 A . 3.A1236 0.014 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 306 U . 3.U1237 0.005 turn,anti,~C2'-endo,junction-loop,phosphate,splayed-apart 307 G ( 3.G1238 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,A-minor,splayed-apart 308 G ( 3.G1239 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 309 U ( 3.U1240 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 310 C ( 3.C1241 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 311 G ( 3.G1242 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 312 G ( 3.G1243 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 313 U ( 3.U1244 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 314 A . 3.A1245 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 315 C . 3.C1246 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 316 A . 3.A1247 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,ribose-zipper,phosphate 317 A . 3.A1248 0.015 anti,~C3'-endo,BI,non-pair-contact,internal-loop,A-minor,ribose-zipper 318 A . 3.A1249 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 319 G ( 3.G1250 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop 320 G ( 3.G1251 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 321 G ( 3.G1252 0.013 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,phosphate 322 U . 3.U1253 0.012 anti,~C2'-endo,BII,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 323 U . 3.U1254 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 324 G ( 3.G1255 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,cap-acceptor,phosphate,splayed-apart 325 C ( 3.C1256 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 326 U . 3.U1257 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 327 A . 3.A1258 0.013 syn,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,phosphate 328 C ( 3.C1259 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor,phosphate 329 A ( 3.A1260 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 330 C ( 3.C1261 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 331 A ( 3.A1262 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 332 G . 3.G1263 0.012 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor,splayed-apart 333 C . 3.C1264 0.007 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 334 G . 3.G1265 0.010 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,ribose-zipper,cap-donor,phosphate 335 A . 3.A1266 0.008 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 336 U ) 3.U1267 0.008 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 337 G ) 3.G1268 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 338 U ) 3.U1269 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 339 G ) 3.G1270 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 340 A . 3.A1271 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 341 U . 3.U1272 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 342 G ) 3.G1273 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 343 C ) 3.C1274 0.013 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 344 U . 3.U1275 0.004 turn,syn,~C2'-endo,non-pair-contact,internal-loop 345 A . 3.A1276 0.012 ~C3'-endo,non-canonical,non-pair-contact,internal-loop,phosphate,splayed-apart 346 A . 3.A1277 0.011 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate,splayed-apart 347 U . 3.U1278 0.011 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 348 C ) 3.C1279 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop 349 U ) 3.U1280 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 350 C ) 3.C1281 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 351 A . 3.A1282 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 352 A . 3.A1283 0.033 turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop 353 A . 3.A1284 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,ribose-zipper 354 A . 3.A1285 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,ribose-zipper 355 A . 3.A1286 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 356 G ) 3.G1287 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 357 C ) 3.C1288 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 358 C ) 3.C1289 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 359 G ) 3.G1290 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 360 A ) 3.A1291 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 361 U ) 3.U1292 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet 362 C ) 3.C1293 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,A-minor 363 G . 3.G1294 0.006 anti,~C2'-endo,BII,non-pair-contact,junction-loop 364 U . 3.U1295 0.010 syn,~C2'-endo,non-pair-contact,junction-loop,cap-donor 365 A . 3.A1296 0.012 syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor 366 G . 3.G1297 0.014 turn,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 367 U . 3.U1298 0.014 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,splayed-apart 368 C . 3.C1299 0.008 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 369 C ( 3.C1300 0.013 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate,splayed-apart 370 G . 3.G1301 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 371 G . 3.G1302 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 372 A . 3.A1303 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 373 U . 3.U1304 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 374 U ( 3.U1305 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 375 G ( 3.G1306 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 376 G ( 3.G1307 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 377 A ( 3.A1308 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 378 G ( 3.G1309 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 379 U ( 3.U1310 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 380 C ( 3.C1311 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 381 U . 3.U1312 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop 382 G . 3.G1313 0.019 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,cap-acceptor 383 C . 3.C1314 0.011 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 384 A . 3.A1315 0.016 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 385 A . 3.A1316 0.015 u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate,splayed-apart 386 C . 3.C1317 0.017 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 387 U . 3.U1318 0.017 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 388 C . 3.C1319 0.014 syn,~C2'-endo,BII,non-pair-contact,hairpin-loop,phosphate,splayed-apart 389 G ) 3.G1320 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,splayed-apart 390 A ) 3.A1321 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 391 C ) 3.C1322 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 392 U ) 3.U1323 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,ribose-zipper 393 C ) 3.C1324 0.008 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem 394 C ) 3.C1325 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 395 A ) 3.A1326 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 396 U . 3.U1327 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 397 G . 3.G1328 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 398 A . 3.A1329 0.016 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 399 A . 3.A1330 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 400 G ) 3.G1331 0.012 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate 401 U . 3.U1332 0.006 turn,anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 402 C . 3.C1333 0.004 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 403 G ) 3.G1334 0.019 ~C3'-endo,BII,isolated-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,splayed-apart 404 G . 3.G1335 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 405 A . 3.A1336 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor 406 A ) 3.A1337 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 407 U ) 3.U1338 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 408 C ) 3.C1339 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 409 G ) 3.G1340 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 410 C ) 3.C1341 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 411 U . 3.U1342 0.020 ~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 412 A . 3.A1343 0.018 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,phosphate 413 G . 3.G1344 0.018 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 414 U . 3.U1345 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 415 A . 3.A1346 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 416 A ( 3.A1347 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 417 U ( 3.U1348 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 418 C ( 3.C1349 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 419 G ( 3.G1350 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 420 C ( 3.C1351 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 421 G ( 3.G1352 0.029 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 422 G ( 3.G1353 0.033 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 423 A . 3.A1354 0.027 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 424 U . 3.U1355 0.022 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 425 C . 3.C1356 0.011 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 426 A . 3.A1357 0.013 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate,splayed-apart 427 G . 3.G1358 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate 428 A . 3.A1359 0.024 anti,~C3'-endo,non-pair-contact,hairpin-loop 429 A . 3.A1360 0.021 syn,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 430 U . 3.U1361 0.011 turn,syn,~C2'-endo,BI,non-stack,non-pair-contact,hairpin-loop,splayed-apart 431 G . 3.G1362 0.028 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate 432 C ) 3.C1363 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 433 C ) 3.C1364 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 434 G ) 3.G1365 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 435 C ) 3.C1366 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 436 G ) 3.G1367 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 437 G ) 3.G1368 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,phosphate 438 U ) 3.U1369 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 439 G . 3.G1370 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 440 A . 3.A1371 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 441 A . 3.A1372 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,ribose-zipper 442 U . 3.U1373 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,ribose-zipper,phosphate 443 A . 3.A1374 0.014 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 444 C . 3.C1375 0.007 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,splayed-apart 445 G ) 3.G1376 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 446 U ) 3.U1377 0.014 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 447 U . 3.U1378 0.005 turn,anti,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop 448 C . 3.C1379 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop 449 C . 3.C1380 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 450 C ) 3.C1381 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 451 G ) 3.G1382 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 452 G ) 3.G1383 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 453 G ) 3.G1384 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 454 G . 7.G26 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 455 U ( 7.U27 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end 456 C ( 7.C28 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 457 G ( 7.G29 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet 458 G ( 7.G30 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,phosphate 459 G ( 7.G31 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 460 C . 7.C32 0.009 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 461 U . 7.U33 0.007 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 462 C . 7.C34 0.008 turn,u-turn,anti,~C3'-endo,BI,non-stack,non-canonical,helix-end,hairpin-loop,phosphate 463 A [ 7.A35 0.021 pseudoknotted,u-turn,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,hairpin-loop,bulge,cap-donor,phosphate 464 U . 7.U36 0.008 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,bulge,phosphate 465 A [ 7.A37 0.012 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,hairpin-loop,bulge 466 A . 7.A38 0.007 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 467 C ) 7.C39 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 468 C ) 7.C40 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor 469 C ) 7.C41 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 470 G ) 7.G42 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 471 A ) 7.A43 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 472 A . 7.A44 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 473 G . 7.G45 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop 474 U ] 9.U1 0.006 pseudoknotted,anti,~C3'-endo,non-stack,isolated-canonical,helix,bulge 475 U ] 9.U2 0.007 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge 476 U . 9.U3 0.021 anti,~C3'-endo,BI,non-stack,non-canonical,helix-end,ss-non-loop 477 U . 9.U4 0.005 anti,~C3'-endo,non-stack,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