**************************************************************************** File name: 8qrm.pdb no. of DNA/RNA chains: 1 [A=955] no. of nucleotides: 957 no. of atoms: 68726 no. of waters: 0 no. of metals: 81 [Mg=59,K=17,Fe=4,Zn=1] **************************************************************************** List of 6 types of 7 modified nucleotides nt count list 1 5MC-c 1 A.5MC1488 2 5MU-t 1 A.5MU1076 3 ATP-a 1 X.ATP402 4 B8T-c 1 A.B8T1486 5 GNP-g 1 X.GNP403 6 MA6-a 2 A.MA6/1583,A.MA6/1584 **************************************************************************** List of 417 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.A649 A.U668 A-U WC 20-XX cWW cW-W 2 A.A651 A.U667 A-U WC 20-XX cWW cW-W 3 A.G652 A.C666 G-C WC 19-XIX cWW cW-W 4 A.G653 A.C665 G-C WC 19-XIX cWW cW-W 5 A.U654 A.G664 U-G Wobble 28-XXVIII cWW cW-W 6 A.U655 A.U662 U-U Calcutta -- tHW tM-W 7 A.U655 A.A1168 U+A Hoogsteen 23-XXIII cWH cW+M 8 A.G657 A.C1173 G-C WC 19-XIX cWW cW-W 9 A.G658 A.C1172 G-C WC 19-XIX cWW cW-W 10 A.G658 A.A1286 G-A -- -- cSS cm-m 11 A.U659 A.A1171 U-A WC 20-XX cWW cW-W 12 A.U659 A.G1285 U-G -- -- cSS cm-m 13 A.C660 A.G1170 C-G WC 19-XIX cWW cW-W 14 A.C661 A.G1169 C-G WC 19-XIX cWW cW-W 15 A.U662 A.A1168 U-A -- -- .WH .W-M 16 A.A663 A.A1167 A-A ~Sheared -- tSH tm-M 17 A.G664 A.A1166 G+A Linker -- tSS tm+m 18 A.U669 A.A928 U-A WC 20-XX cWW cW-W 19 A.C670 A.G927 C-G WC 19-XIX cWW cW-W 20 A.U671 A.A926 U-A WC 20-XX cWW cW-W 21 A.A672 A.U925 A-U WC 20-XX cWW cW-W 22 A.U673 A.A924 U-A WC 20-XX cWW cW-W 23 A.U674 A.A923 U-A WC 20-XX cWW cW-W 24 A.A675 A.C922 A-C -- -- cWW cW-W 25 A.G676 A.U921 G-U Wobble 28-XXVIII cWW cW-W 26 A.C677 A.G920 C-G WC 19-XIX cWW cW-W 27 A.U678 A.A860 U+A rWC 21-XXI tWW tW+W 28 A.U680 A.A866 U-A WC 20-XX cWW cW-W 29 A.U681 A.A865 U-A WC 20-XX cWW cW-W 30 A.A682 A.U864 A-U WC 20-XX cWW cW-W 31 A.G683 A.C863 G-C WC 19-XIX cWW cW-W 32 A.U684 A.A862 U-A WC 20-XX cWW cW-W 33 A.A685 A.U861 A-U WC 20-XX cWW cW-W 34 A.A686 A.U859 A-U WC 20-XX cWW cW-W 35 A.G687 A.C858 G-C WC 19-XIX cWW cW-W 36 A.A688 A.U821 A+U -- -- cWH cW+M 37 A.A688 A.G822 A+G -- -- cWH cW+M 38 A.U689 A.U824 U-U -- 16-XVI cWW cW-W 39 A.U690 A.A823 U-A WC 20-XX cWW cW-W 40 A.A691 A.U716 A+U -- -- cHS cM+m 41 A.A691 A.C800 A-C -- -- cWS cW-m 42 A.C692 A.G822 C-G WC 19-XIX cWW cW-W 43 A.A693 A.U821 A-U WC 20-XX cWW cW-W 44 A.C694 A.G820 C-G WC 19-XIX cWW cW-W 45 A.A695 A.G820 A-G Sheared 11-XI tHS tM-m 46 A.A695 A.U831 A+U rWC 21-XXI tWW tW+W 47 A.U696 A.C815 U-C -- -- tHW tM-W 48 A.U696 A.A819 U-A WC 20-XX cWW cW-W 49 A.G697 A.C818 G-C WC 19-XIX cWW cW-W 50 A.C698 A.G817 C-G WC 19-XIX cWW cW-W 51 A.G701 A.C708 G-C WC 19-XIX cWW cW-W 52 A.C702 A.C707 C-C Metal -- cWW cW-W 53 A.U704 A.C705 U+C Platform -- cSH cm+M 54 A.A714 A.A801 A-A -- -- cWW cW-W 55 A.G715 A.C800 G-C WC 19-XIX cWW cW-W 56 A.G715 A.A816 G-A -- -- cSS cm-m 57 A.U716 A.A799 U-A WC 20-XX cWW cW-W 58 A.G717 A.A718 G+A Platform -- cSH cm+M 59 A.G717 A.C798 G-C WC 19-XIX cWW cW-W 60 A.A718 A.A799 A-A -- -- .WS .W-m 61 A.C724 A.G750 C-G WC 19-XIX cWW cW-W 62 A.C725 A.G749 C-G WC 19-XIX cWW cW-W 63 A.C726 A.G748 C-G WC 19-XIX cWW cW-W 64 A.U727 A.A747 U-A WC 20-XX cWW cW-W 65 A.C728 A.A746 C-A -- -- cWW cW-W 66 A.U729 A.A744 U-A WC 20-XX cWW cW-W 67 A.U729 A.A745 U-A -- -- t.H t.-M 68 A.A730 A.A744 A-A ~Sheared -- tHS tM-m 69 A.A731 A.C743 A-C -- -- cWW cW-W 70 A.A732 A.U742 A-U WC 20-XX cWW cW-W 71 A.U733 A.A741 U-A WC 20-XX cWW cW-W 72 A.C734 A.G740 C-G WC 19-XIX cWW cW-W 73 A.A753 A.U789 A-U WC 20-XX cWW cW-W 74 A.A754 A.U788 A-U WC 20-XX cWW cW-W 75 A.G755 A.C787 G-C WC 19-XIX cWW cW-W 76 A.C756 A.G786 C-G WC 19-XIX cWW cW-W 77 A.A757 A.A784 A-A -- 05-V tWH tW-M 78 A.U758 A.C1146 U-C -- 18-XVIII cWW cW-W 79 A.C759 A.C785 C-C -- -- cWW cW-W 80 A.A760 A.A783 A-A ~Sheared -- tHS tM-m 81 A.A761 A.U779 A-U WC 20-XX cWW cW-W 82 A.G762 A.C778 G-C WC 19-XIX cWW cW-W 83 A.C763 A.C765 C+C -- -- cSH cm+M 84 A.C765 A.G777 C-G WC 19-XIX cWW cW-W 85 A.G766 A.C775 G-C WC 19-XIX cWW cW-W 86 A.C767 A.G774 C-G WC 19-XIX cWW cW-W 87 A.A768 A.U773 A-U WC 20-XX cWW cW-W 88 A.G769 A.A772 G-A Sheared 11-XI tSH tm-M 89 A.G791 A.C797 G-C WC 19-XIX cWW cW-W 90 A.C792 A.G796 C-G WC 19-XIX cWW cW-W 91 A.C802 A.G811 C-G WC 19-XIX cWW cW-W 92 A.C803 A.G810 C-G WC 19-XIX cWW cW-W 93 A.C804 A.G809 C-G WC 19-XIX cWW cW-W 94 A.A807 A.C808 A+C Platform -- cSH cm+M 95 A.A812 A.A814 A-A -- -- cSW cm-W 96 A.C815 A.A819 C+A -- -- cWH cW+M 97 A.C829 A.G857 C-G -- -- c.W c.-W 98 A.U830 A.A856 U-A WC 20-XX cWW cW-W 99 A.U832 A.A855 U-A WC 20-XX cWW cW-W 100 A.A833 A.U854 A-U WC 20-XX cWW cW-W 101 A.G834 A.A836 G+A -- -- cSH cm+M 102 A.G834 A.C853 G-C WC 19-XIX cWW cW-W 103 A.C835 A.A852 C-A ~rHoogsteen 25-XXV tWH tW-M 104 A.A836 A.U854 A-U -- -- cWS cW-m 105 A.A837 A.C853 A-C -- -- cWS cW-m 106 A.U838 A.A852 U-A WC 20-XX cWW cW-W 107 A.A839 A.U850 A-U WC 20-XX cWW cW-W 108 A.A840 A.U849 A-U WC 20-XX cWW cW-W 109 A.A841 A.U848 A-U WC 20-XX cWW cW-W 110 A.C842 A.G847 C-G WC 19-XIX cWW cW-W 111 A.G843 A.A846 G-A -- -- tWH tW-M 112 A.A860 A.A919 A+A -- -- cHS cM+m 113 A.G872 A.C917 G-C WC 19-XIX cWW cW-W 114 A.G873 A.C916 G-C WC 19-XIX cWW cW-W 115 A.G874 A.C915 G-C WC 19-XIX cWW cW-W 116 A.U875 A.A914 U-A WC 20-XX cWW cW-W 117 A.U876 A.A913 U-A WC 20-XX cWW cW-W 118 A.G877 A.C898 G-C WC 19-XIX cWW cW-W 119 A.G878 A.C897 G-C WC 19-XIX cWW cW-W 120 A.U879 A.A896 U-A WC 20-XX cWW cW-W 121 A.C880 A.A881 C+A Platform -- cSH cm+M 122 A.C880 A.A882 C+A -- -- cSH cm+M 123 A.U883 A.U912 U-U -- 16-XVI cWW cW-W 124 A.U884 A.U911 U-U -- 16-XVI cWW cW-W 125 A.U885 A.A910 U-A WC 20-XX cWW cW-W 126 A.C886 A.G909 C-G WC 19-XIX cWW cW-W 127 A.G887 A.C908 G-C WC 19-XIX cWW cW-W 128 A.U888 A.C891 U-C -- -- cSW cm-W 129 A.U888 A.A905 U-A rHoogsteen 24-XXIV tWH tW-M 130 A.A892 A.G901 A-G Sheared 11-XI tHS tM-m 131 A.A892 A.A905 A+A -- -- tW. tW+. 132 A.A892 A.C908 A+C -- -- .WS .W+m 133 A.G893 A.C900 G-C WC 19-XIX cWW cW-W 134 A.C894 A.G899 C-G WC 19-XIX cWW cW-W 135 A.C895 A.C898 C-C -- -- tWH tW-M 136 A.G899 A.A907 G+A -- -- tSW tm+W 137 A.G933 A.C1136 G-C WC 19-XIX cWW cW-W 138 A.G934 A.A940 G+A Linker -- tS. tm+. 139 A.G934 A.C1135 G-C WC 19-XIX cWW cW-W 140 A.C935 A.G1134 C-G WC 19-XIX cWW cW-W 141 A.G936 A.C1123 G-C WC 19-XIX cWW cW-W 142 A.U937 A.A1122 U-A WC 20-XX cWW cW-W 143 A.A938 A.A939 A-A Platform -- cHH cM-M 144 A.A938 A.A940 A-A -- -- cHH cM-M 145 A.A938 A.G1169 A-G -- -- cSS cm-m 146 A.A939 A.C1136 A-C -- -- cWS cW-m 147 A.A940 A.C1136 A-C -- -- cSS cm-m 148 A.G941 A.C1133 G-C WC 19-XIX cWW cW-W 149 A.G943 A.A1026 G-A -- -- cSS cm-m 150 A.G943 A.C1052 G-C WC 19-XIX cWW cW-W 151 A.U944 A.A1051 U-A WC 20-XX cWW cW-W 152 A.G945 A.C1050 G-C WC 19-XIX cWW cW-W 153 A.U946 A.A1049 U-A WC 20-XX cWW cW-W 154 A.U947 A.A1046 U-A rHoogsteen 24-XXIV tWH tW-M 155 A.U949 A.G1045 U-G ~Sheared -- tHS tM-m 156 A.A950 A.U1044 A-U WC 20-XX cWW cW-W 157 A.G951 A.C1043 G-C WC 19-XIX cWW cW-W 158 A.A952 A.U1042 A-U WC 20-XX cWW cW-W 159 A.U953 A.A955 U+A Hoogsteen 23-XXIII cWH cW+M 160 A.C954 A.C1043 C-C -- -- cWS cW-m 161 A.A966 A.U1021 A+U -- -- tHW tM+W 162 A.A967 A.A1037 A-A ~Sheared -- tHS tM-m 163 A.U968 A.A1036 U-A WC 20-XX cWW cW-W 164 A.A969 A.U1035 A-U WC 20-XX cWW cW-W 165 A.A970 A.U1034 A-U WC 20-XX cWW cW-W 166 A.A971 A.U1033 A-U WC 20-XX cWW cW-W 167 A.G972 A.C1032 G-C WC 19-XIX cWW cW-W 168 A.C973 A.G1031 C-G WC 19-XIX cWW cW-W 169 A.U974 A.A1014 U-A WC 20-XX cWW cW-W 170 A.A975 A.A1013 A-A -- -- cWW cW-W 171 A.A976 A.A1012 A-A -- -- cWW cW-W 172 A.A977 A.A1010 A-A -- 05-V tWH tW-M 173 A.C979 A.C1009 C-C -- -- cWW cW-W 174 A.U980 A.A1008 U-A WC 20-XX cWW cW-W 175 A.C981 A.G1007 C-G WC 19-XIX cWW cW-W 176 A.A982 A.U1006 A-U WC 20-XX cWW cW-W 177 A.C983 A.U1005 C-U -- -- cWW cW-W 178 A.C984 A.G1004 C-G WC 19-XIX cWW cW-W 179 A.U985 A.A1003 U-A WC 20-XX cWW cW-W 180 A.G986 A.C1002 G-C WC 19-XIX cWW cW-W 181 A.G988 A.C999 G-C WC 19-XIX cWW cW-W 182 A.U989 A.A998 U-A WC 20-XX cWW cW-W 183 A.U990 A.A997 U-A -- -- cWH cW-M 184 A.G991 A.A996 G-A Sheared 11-XI tSH tm-M 185 A.A995 A.G1074 A-G -- -- cWS cW-m 186 A.C1011 A.G1062 C+G -- -- tWS tW+m 187 A.C1020 A.G1030 C-G WC 19-XIX cWW cW-W 188 A.A1022 A.U1029 A-U WC 20-XX cWW cW-W 189 A.C1023 A.G1028 C-G WC 19-XIX cWW cW-W 190 A.G1024 A.A1027 G-A Sheared 11-XI tSH tm-M 191 A.A1054 A.U1101 A-U rHoogsteen 24-XXIV tHW tM-W 192 A.U1055 A.G1576 U+G -- -- tWS tW+m 193 A.A1056 A.C1099 A-C -- -- cWW cW-W 194 A.G1057 A.C1098 G-C WC 19-XIX cWW cW-W 195 A.C1058 A.G1097 C-G WC 19-XIX cWW cW-W 196 A.U1059 A.A1096 U-A WC 20-XX cWW cW-W 197 A.A1060 A.U1095 A-U WC 20-XX cWW cW-W 198 A.A1061 A.U1094 A-U WC 20-XX cWW cW-W 199 A.G1062 A.C1093 G-C WC 19-XIX cWW cW-W 200 A.C1064 A.C1066 C+C -- -- cSH cm+M 201 A.C1066 A.G1092 C-G WC 19-XIX cWW cW-W 202 A.A1067 A.U1091 A-U WC 20-XX cWW cW-W 203 A.A1068 A.A1090 A-A ~Sheared -- tSH tm-M 204 A.A1069 A.U1089 A-U rHoogsteen 24-XXIV tHW tM-W 205 A.C1070 A.C1088 C-C -- -- .WW .W-W 206 A.U1071 A.A1087 U-A WC 20-XX cWW cW-W 207 A.G1072 A.C1086 G-C WC 19-XIX cWW cW-W 208 A.G1073 A.C1085 G-C WC 19-XIX cWW cW-W 209 A.G1074 A.C1084 G-C WC 19-XIX cWW cW-W 210 A.A1075 A.C1083 A-C -- -- .WH .W-M 211 A.5MU1076 A.A1082 t-A -- -- tWH tW-M 212 A.5MU1076 A.C1083 t-C -- -- tW. tW-. 213 A.C1105 A.G1594 C-G WC 19-XIX cWW cW-W 214 A.A1109 A.U1132 A-U WC 20-XX cWW cW-W 215 A.A1110 A.C1131 A-C ~Wobble -- cWW cW-W 216 A.C1111 A.G1130 C-G WC 19-XIX cWW cW-W 217 A.A1112 A.U1129 A-U WC 20-XX cWW cW-W 218 A.G1113 A.C1128 G-C WC 19-XIX cWW cW-W 219 A.U1114 A.A1116 U-A -- -- cSW cm-W 220 A.U1114 A.A1127 U-A WC 20-XX cWW cW-W 221 A.U1115 A.A1126 U-A WC 20-XX cWW cW-W 222 A.A1121 A.G1170 A+G -- -- tW. tW+. 223 A.G1138 A.C1165 G-C WC 19-XIX cWW cW-W 224 A.A1139 A.U1164 A-U WC 20-XX cWW cW-W 225 A.C1141 A.A1162 C-A -- -- t.H t.-M 226 A.A1142 A.A1161 A+A -- 02-II tHH tM+M 227 A.U1144 A.A1160 U-A rHoogsteen 24-XXIV tWH tW-M 228 A.A1145 A.A1159 A-A ~Sheared -- tHS tM-m 229 A.G1147 A.U1158 G-U Wobble 28-XXVIII cWW cW-W 230 A.A1148 A.U1157 A-U WC 20-XX cWW cW-W 231 A.G1149 A.C1156 G-C WC 19-XIX cWW cW-W 232 A.C1150 A.G1155 C-G WC 19-XIX cWW cW-W 233 A.A1162 A.C1497 A-C -- -- cWS cW-m 234 A.C1172 A.A1286 C+A -- -- tSW tm+W 235 A.U1174 A.A1480 U-A WC 20-XX cWW cW-W 236 A.G1175 A.C1479 G-C WC 19-XIX cWW cW-W 237 A.G1175 A.A1482 G+A Linker -- tSW tm+W 238 A.G1176 A.U1477 G-U Wobble 28-XXVIII cWW cW-W 239 A.C1177 A.G1476 C-G WC 19-XIX cWW cW-W 240 A.G1178 A.C1475 G-C WC 19-XIX cWW cW-W 241 A.U1180 A.G1474 U-G Wobble 28-XXVIII cWW cW-W 242 A.G1181 A.C1473 G-C WC 19-XIX cWW cW-W 243 A.C1182 A.G1472 C-G WC 19-XIX cWW cW-W 244 A.U1183 A.A1471 U-A WC 20-XX cWW cW-W 245 A.U1184 A.A1470 U-A WC 20-XX cWW cW-W 246 A.C1185 A.G1469 C-G WC 19-XIX cWW cW-W 247 A.A1186 A.C1465 A-C ~rHoogsteen 25-XXV tHW tM-W 248 A.A1186 A.U1468 A-U -- -- cWW cW-W 249 A.A1188 A.A1459 A-A -- -- tHW tM-W 250 A.U1189 A.C1191 U+C -- -- cWH cW+M 251 A.C1190 A.G1464 C-G WC 19-XIX cWW cW-W 252 A.C1191 A.G1463 C-G WC 19-XIX cWW cW-W 253 A.C1192 A.G1462 C-G WC 19-XIX cWW cW-W 254 A.C1194 A.G1428 C-G WC 19-XIX cWW cW-W 255 A.C1194 A.A1459 C-A -- -- cSW cm-W 256 A.U1195 A.A1427 U-A WC 20-XX cWW cW-W 257 A.A1196 A.U1426 A-U WC 20-XX cWW cW-W 258 A.G1197 A.U1425 G-U Wobble 28-XXVIII cWW cW-W 259 A.A1198 A.U1424 A-U WC 20-XX cWW cW-W 260 A.G1199 A.A1423 G-A Sheared 11-XI tSH tm-M 261 A.G1200 A.A1365 G-A Imino 08-VIII cWW cW-W 262 A.A1201 A.U1364 A-U WC 20-XX cWW cW-W 263 A.A1201 A.A1417 A-A -- -- cSW cm-W 264 A.G1202 A.C1363 G-C WC 19-XIX cWW cW-W 265 A.C1203 A.G1362 C-G WC 19-XIX cWW cW-W 266 A.C1204 A.G1361 C-G WC 19-XIX cWW cW-W 267 A.U1205 A.G1360 U-G Wobble 28-XXVIII cWW cW-W 268 A.G1206 A.C1224 G-C -- -- cSS cm-m 269 A.G1206 A.U1359 G-U Wobble 28-XXVIII cWW cW-W 270 A.U1207 A.A1358 U-A WC 20-XX cWW cW-W 271 A.U1208 A.A1357 U-A WC 20-XX cWW cW-W 272 A.C1209 A.G1355 C-G WC 19-XIX cWW cW-W 273 A.C1209 A.A1356 C-A -- -- tWH tW-M 274 A.U1210 A.A1354 U-A WC 20-XX cWW cW-W 275 A.A1213 A.C1239 A-C -- -- cWS cW-m 276 A.A1214 A.G1351 A+G Linker -- tWS tW+m 277 A.U1215 A.A1331 U+A rWC 21-XXI tWW tW+W 278 A.C1216 A.G1227 C-G WC 19-XIX cWW cW-W 279 A.G1217 A.C1226 G-C WC 19-XIX cWW cW-W 280 A.C1225 A.G1447 C+G -- -- tWS tW+m 281 A.A1231 A.C1236 A+C -- -- tSH tm+M 282 A.A1232 A.G1401 A+G -- 10-X tWS tW+m 283 A.A1232 A.A1444 A-A -- 05-V tHW tM-W 284 A.C1233 A.A1402 C-A -- -- .SH .m-M 285 A.C1238 A.G1351 C-G WC 19-XIX cWW cW-W 286 A.C1239 A.G1350 C-G WC 19-XIX cWW cW-W 287 A.A1240 A.U1349 A-U WC 20-XX cWW cW-W 288 A.C1241 A.G1348 C-G WC 19-XIX cWW cW-W 289 A.C1242 A.G1347 C-G WC 19-XIX cWW cW-W 290 A.U1243 A.A1346 U-A WC 20-XX cWW cW-W 291 A.C1244 A.G1345 C-G WC 19-XIX cWW cW-W 292 A.U1245 A.A1343 U-A rHoogsteen 24-XXIV tWH tW-M 293 A.A1251 A.C1341 A-C -- -- tHW tM-W 294 A.A1251 A.A1343 A+A -- 01-I tWW tW+W 295 A.G1252 A.C1340 G-C WC 19-XIX cWW cW-W 296 A.C1253 A.G1339 C-G WC 19-XIX cWW cW-W 297 A.U1255 A.A1338 U-A WC 20-XX cWW cW-W 298 A.A1256 A.U1337 A-U WC 20-XX cWW cW-W 299 A.U1257 A.G1336 U-G Wobble 28-XXVIII cWW cW-W 300 A.A1258 A.C1262 A+C -- -- cWH cW+M 301 A.A1258 A.G1333 A-G -- -- -- -- 302 A.A1260 A.C1330 A-C ~rHoogsteen 25-XXV tHW tM-W 303 A.A1260 A.U1335 A-U -- -- cWW cW-W 304 A.C1261 A.G1334 C-G WC 19-XIX cWW cW-W 305 A.C1262 A.G1333 C-G WC 19-XIX cWW cW-W 306 A.G1263 A.U1329 G-U Wobble 28-XXVIII cWW cW-W 307 A.G1263 A.A1332 G-A Sheared 11-XI tSH tm-M 308 A.C1264 A.G1328 C-G WC 19-XIX cWW cW-W 309 A.C1265 A.G1327 C-G WC 19-XIX cWW cW-W 310 A.A1266 A.U1325 A-U WC 20-XX cWW cW-W 311 A.U1267 A.U1324 U-U -- 16-XVI cWW cW-W 312 A.C1268 A.G1323 C-G WC 19-XIX cWW cW-W 313 A.U1269 A.C1322 U+C -- -- .W. .W+. 314 A.C1271 A.A1321 C-A ~rHoogsteen 25-XXV tWH tW-M 315 A.G1273 A.C1302 G-C WC 19-XIX cWW cW-W 316 A.G1273 A.A1321 G+A Linker -- tSS tm+m 317 A.C1274 A.G1301 C-G WC 19-XIX cWW cW-W 318 A.A1275 A.A1300 A-A ~Sheared -- tSH tm-M 319 A.A1276 A.A1299 A-A ~Sheared -- tHS tM-m 320 A.A1277 A.U1298 A-U WC 20-XX cWW cW-W 321 A.C1278 A.G1297 C-G WC 19-XIX cWW cW-W 322 A.C1279 A.G1289 C-G WC 19-XIX cWW cW-W 323 A.C1280 A.G1288 C-G WC 19-XIX cWW cW-W 324 A.U1281 A.A1287 U-A WC 20-XX cWW cW-W 325 A.G1282 A.A1286 G-A -- -- tWH tW-M 326 A.G1289 A.A1296 G-A -- -- cSS cm-m 327 A.U1308 A.A1317 U-A WC 20-XX cWW cW-W 328 A.A1309 A.U1316 A-U WC 20-XX cWW cW-W 329 A.C1310 A.G1315 C-G WC 19-XIX cWW cW-W 330 A.C1330 A.U1335 C+U -- -- tWW tW+W 331 A.G1339 A.U1344 G+U -- -- tSW tm+W 332 A.G1355 A.A1356 G+A Platform -- cSH cm+M 333 A.G1362 A.U1448 G-U -- -- cSS cm-m 334 A.C1366 A.G1421 C-G WC 19-XIX cWW cW-W 335 A.A1367 A.A1384 A+A -- 02-II tHH tM+M 336 A.A1367 A.A1387 A-A ~Sheared -- tHS tM-m 337 A.U1368 A.A1383 U+A -- -- tWS tW+m 338 A.U1370 A.A1382 U-A WC 20-XX cWW cW-W 339 A.U1371 A.A1381 U-A WC 20-XX cWW cW-W 340 A.C1372 A.G1380 C-G WC 19-XIX cWW cW-W 341 A.U1373 A.A1379 U-A WC 20-XX cWW cW-W 342 A.A1387 A.G1419 A-G -- -- cWW cW-W 343 A.C1388 A.G1418 C-G WC 19-XIX cWW cW-W 344 A.G1389 A.A1417 G-A Sheared 11-XI tSH tm-M 345 A.A1392 A.C1414 A-C -- -- cWW cW-W 346 A.G1393 A.U1413 G-U Wobble 28-XXVIII cWW cW-W 347 A.C1394 A.G1412 C-G WC 19-XIX cWW cW-W 348 A.C1395 A.G1411 C-G WC 19-XIX cWW cW-W 349 A.C1396 A.G1410 C-G WC 19-XIX cWW cW-W 350 A.U1397 A.A1409 U-A WC 20-XX cWW cW-W 351 A.U1398 A.A1408 U-A WC 20-XX cWW cW-W 352 A.A1399 A.U1407 A-U WC 20-XX cWW cW-W 353 A.U1400 A.A1404 U-A rHoogsteen 24-XXIV tWH tW-M 354 A.A1404 A.G1445 A+G -- 10-X tWS tW+m 355 A.C1429 A.C1460 C+C -- 15-XV tWW tW+W 356 A.A1430 A.A1459 A+A -- 02-II tHH tM+M 357 A.G1431 A.U1432 G+U Platform -- cSH cm+M 358 A.U1432 A.A1458 U-A rHoogsteen 24-XXIV tWH tW-M 359 A.A1433 A.G1457 A-G Sheared 11-XI tHS tM-m 360 A.A1434 A.U1456 A-U WC 20-XX cWW cW-W 361 A.A1435 A.U1455 A-U WC 20-XX cWW cW-W 362 A.C1436 A.G1454 C-G WC 19-XIX cWW cW-W 363 A.U1437 A.A1453 U-A WC 20-XX cWW cW-W 364 A.G1438 A.U1452 G-U Wobble 28-XXVIII cWW cW-W 365 A.A1439 A.U1451 A-U WC 20-XX cWW cW-W 366 A.G1440 A.C1450 G-C WC 19-XIX cWW cW-W 367 A.A1441 A.G1449 A-G Imino 08-VIII cWW cW-W 368 A.G1442 A.G1447 G-G -- -- tWH tW-M 369 A.U1443 A.A1446 U-A -- -- tSH tm-M 370 A.G1476 A.A1567 G-A -- -- cSS cm-m 371 A.C1483 A.G1569 C-G WC 19-XIX cWW cW-W 372 A.G1485 A.C1566 G-C WC 19-XIX cWW cW-W 373 A.B8T1486 A.A1565 c-A ~Wobble -- cWW cW-W 374 A.C1487 A.A1564 C-A -- -- c.W c.-W 375 A.5MC1488 A.G1562 c-G WC 19-XIX cWW cW-W 376 A.G1489 A.C1561 G-C WC 19-XIX cWW cW-W 377 A.G1489 A.MA6/1583 G-a -- -- cSS cm-m 378 A.U1490 A.U1560 U-U Metal -- cWW cW-W 379 A.U1490 A.G1582 U-G -- -- cWW cW-W 380 A.C1491 A.G1559 C-G WC 19-XIX cWW cW-W 381 A.C1493 A.C1556 C-C -- -- c.W c.-W 382 A.C1494 A.A1555 C-A -- -- cWW cW-W 383 A.C1495 A.G1554 C-G WC 19-XIX cWW cW-W 384 A.U1496 A.A1553 U-A WC 20-XX cWW cW-W 385 A.C1497 A.G1552 C-G WC 19-XIX cWW cW-W 386 A.C1498 A.G1551 C-G WC 19-XIX cWW cW-W 387 A.U1499 A.A1550 U-A WC 20-XX cWW cW-W 388 A.C1500 A.G1549 C-G WC 19-XIX cWW cW-W 389 A.A1501 A.A1548 A-A ~Sheared -- tSH tm-M 390 A.G1503 A.U1547 G-U Wobble 28-XXVIII cWW cW-W 391 A.U1504 A.A1546 U-A WC 20-XX cWW cW-W 392 A.A1505 A.U1545 A-U WC 20-XX cWW cW-W 393 A.U1506 A.A1544 U-A WC 20-XX cWW cW-W 394 A.A1507 A.U1543 A-U WC 20-XX cWW cW-W 395 A.C1508 A.U1542 C-U -- 18-XVIII cWW cW-W 396 A.U1509 A.U1541 U-U -- 16-XVI cWW cW-W 397 A.U1510 A.A1540 U-A WC 20-XX cWW cW-W 398 A.C1511 A.G1538 C-G WC 19-XIX cWW cW-W 399 A.A1514 A.U1535 A-U WC 20-XX cWW cW-W 400 A.G1515 A.C1534 G-C WC 19-XIX cWW cW-W 401 A.G1516 A.C1533 G-C WC 19-XIX cWW cW-W 402 A.U1521 A.A1529 U-A WC 20-XX cWW cW-W 403 A.U1522 A.A1528 U-A WC 20-XX cWW cW-W 404 A.A1523 A.A1527 A-A -- -- cSW cm-W 405 A.C1561 A.G1582 C+G -- -- .SW .m+W 406 A.U1563 A.A1564 U+A Platform -- cSH cm+M 407 A.A1567 A.G1570 A+G -- -- cHW cM+W 408 A.U1568 A.G1598 U+G -- -- ..W ..+W 409 A.A1572 A.U1593 A-U WC 20-XX cWW cW-W 410 A.A1573 A.U1592 A-U WC 20-XX cWW cW-W 411 A.G1574 A.C1591 G-C WC 19-XIX cWW cW-W 412 A.U1575 A.A1590 U-A WC 20-XX cWW cW-W 413 A.G1576 A.C1589 G-C WC 19-XIX cWW cW-W 414 A.U1577 A.G1588 U-G Wobble 28-XXVIII cWW cW-W 415 A.A1578 A.U1587 A-U WC 20-XX cWW cW-W 416 A.C1579 A.G1586 C-G WC 19-XIX cWW cW-W 417 A.U1580 A.A1585 U-A WC 20-XX cWW cW-W **************************************************************************** List of 53 multiplets 1 nts=3 UGA A.U654,A.G664,A.A1166 2 nts=3 UUA A.U655,A.U662,A.A1168 3 nts=3 UAG A.U659,A.A1171,A.G1285 4 nts=3 CAG A.C660,A.A1121,A.G1170 5 nts=3 UAA A.U678,A.A860,A.A919 6 nts=3 ACG A.A688,A.C692,A.G822 7 nts=3 AAU A.A688,A.A693,A.U821 8 nts=3 AUA A.A691,A.U716,A.A799 9 nts=3 UCA A.U696,A.C815,A.A819 10 nts=3 GCA A.G715,A.C800,A.A816 11 nts=3 GAC A.G717,A.A718,A.C798 12 nts=3 UAA A.U729,A.A744,A.A745 13 nts=3 CCG A.C763,A.C765,A.G777 14 nts=3 AAU A.A833,A.A836,A.U854 15 nts=3 GAC A.G834,A.A837,A.C853 16 nts=3 CUA A.C835,A.U838,A.A852 17 nts=3 GCC A.G877,A.C895,A.C898 18 nts=3 UCA A.U888,A.C891,A.A905 19 nts=3 CGA A.C894,A.G899,A.A907 20 nts=3 GAC A.G934,A.A940,A.C1135 21 nts=3 GAC A.G943,A.A1026,A.C1052 22 nts=3 GCC A.G951,A.C954,A.C1043 23 nts=3 CGC A.C1011,A.G1062,A.C1093 24 nts=3 UGC A.U1055,A.G1576,A.C1589 25 nts=3 UAA A.U1114,A.A1116,A.A1127 26 nts=3 GCA A.G1175,A.C1479,A.A1482 27 nts=3 ACU A.A1186,A.C1465,A.U1468 28 nts=3 UCG A.U1189,A.C1191,A.G1463 29 nts=3 GCU A.G1206,A.C1224,A.U1359 30 nts=3 CGA A.C1209,A.G1355,A.A1356 31 nts=3 ACG A.A1213,A.C1239,A.G1350 32 nts=3 ACG A.A1214,A.C1238,A.G1351 33 nts=3 CGG A.C1225,A.G1442,A.G1447 34 nts=3 AGA A.A1232,A.G1401,A.A1444 35 nts=3 CGU A.C1253,A.G1339,A.U1344 36 nts=3 ACG A.A1258,A.C1262,A.G1333 37 nts=3 ACU A.A1260,A.C1330,A.U1335 38 nts=3 GUA A.G1263,A.U1329,A.A1332 39 nts=3 AAG A.A1367,A.A1387,A.G1419 40 nts=3 GUA A.G1431,A.U1432,A.A1458 41 nts=3 CUA A.C1487,A.U1563,A.A1564 42 nts=3 GCa A.G1489,A.C1561,A.MA6/1583 43 nts=3 UUG A.U1490,A.U1560,A.G1582 44 nts=4 GCGA A.G658,A.C1172,A.G1282,A.A1286 45 nts=4 CAGU A.C694,A.A695,A.G820,A.U831 46 nts=4 GAGC A.G887,A.A892,A.G901,A.C908 47 nts=4 CACG A.C1141,A.A1162,A.C1497,A.G1552 48 nts=4 CGAG A.C1177,A.G1476,A.A1567,A.G1570 49 nts=4 CGAA A.C1194,A.G1428,A.A1430,A.A1459 50 nts=4 AUGA A.A1201,A.U1364,A.G1389,A.A1417 51 nts=4 UACA A.U1245,A.A1251,A.C1341,A.A1343 52 nts=4 CGCA A.C1271,A.G1273,A.C1302,A.A1321 53 nts=6 CGAACG A.C661,A.G933,A.A938,A.A939,A.C1136,A.G1169 **************************************************************************** List of 34 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[4] bps=19 strand-1 5'-UUAGUAAGCUUAGUAAACG-3' bp-type ||||||||.|||||||||. strand-2 3'-AAUCAUUCGAAUCAUUUGA-5' helix-form AAAAAxAx.xAAxxAAA. 1 A.U680 A.A866 U-A WC 20-XX cWW cW-W 2 A.U681 A.A865 U-A WC 20-XX cWW cW-W 3 A.A682 A.U864 A-U WC 20-XX cWW cW-W 4 A.G683 A.C863 G-C WC 19-XIX cWW cW-W 5 A.U684 A.A862 U-A WC 20-XX cWW cW-W 6 A.A685 A.U861 A-U WC 20-XX cWW cW-W 7 A.A686 A.U859 A-U WC 20-XX cWW cW-W 8 A.G687 A.C858 G-C WC 19-XIX cWW cW-W 9 A.C829 A.G857 C-G -- -- c.W c.-W 10 A.U830 A.A856 U-A WC 20-XX cWW cW-W 11 A.U832 A.A855 U-A WC 20-XX cWW cW-W 12 A.A833 A.U854 A-U WC 20-XX cWW cW-W 13 A.G834 A.C853 G-C WC 19-XIX cWW cW-W 14 A.U838 A.A852 U-A WC 20-XX cWW cW-W 15 A.A839 A.U850 A-U WC 20-XX cWW cW-W 16 A.A840 A.U849 A-U WC 20-XX cWW cW-W 17 A.A841 A.U848 A-U WC 20-XX cWW cW-W 18 A.C842 A.G847 C-G WC 19-XIX cWW cW-W 19 A.G843 A.A846 G-A -- -- tWH tW-M -------------------------------------------------------------------------- helix#2[1] bps=5 strand-1 5'-UUCAC-3' bp-type .|||| strand-2 3'-UAGUG-5' helix-form .xA. 1 A.U689 A.U824 U-U -- 16-XVI cWW cW-W 2 A.U690 A.A823 U-A WC 20-XX cWW cW-W 3 A.C692 A.G822 C-G WC 19-XIX cWW cW-W 4 A.A693 A.U821 A-U WC 20-XX cWW cW-W 5 A.C694 A.G820 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=4 strand-1 5'-AUGC-3' bp-type .||| strand-2 3'-UACG-5' helix-form xAA 1 A.A695 A.U831 A+U rWC 21-XXI tWW tW+W 2 A.U696 A.A819 U-A WC 20-XX cWW cW-W 3 A.G697 A.C818 G-C WC 19-XIX cWW cW-W 4 A.C698 A.G817 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[0] bps=2 strand-1 5'-GC-3' bp-type |. strand-2 3'-CC-5' helix-form . 1 A.G701 A.C708 G-C WC 19-XIX cWW cW-W 2 A.C702 A.C707 C-C Metal -- cWW cW-W -------------------------------------------------------------------------- helix#5[2] bps=6 strand-1 5'-AGUGGC-3' bp-type .||||| strand-2 3'-ACACCG-5' helix-form .A.xA 1 A.A714 A.A801 A-A -- -- cWW cW-W 2 A.G715 A.C800 G-C WC 19-XIX cWW cW-W 3 A.U716 A.A799 U-A WC 20-XX cWW cW-W 4 A.G717 A.C798 G-C WC 19-XIX cWW cW-W 5 A.G791 A.C797 G-C WC 19-XIX cWW cW-W 6 A.C792 A.G796 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#6[2] bps=10 strand-1 5'-CCCUCUAAUC-3' bp-type ||||.|.||| strand-2 3'-GGGAAACUAG-5' helix-form AAA.xx.AA 1 A.C724 A.G750 C-G WC 19-XIX cWW cW-W 2 A.C725 A.G749 C-G WC 19-XIX cWW cW-W 3 A.C726 A.G748 C-G WC 19-XIX cWW cW-W 4 A.U727 A.A747 U-A WC 20-XX cWW cW-W 5 A.C728 A.A746 C-A -- -- cWW cW-W 6 A.U729 A.A744 U-A WC 20-XX cWW cW-W 7 A.A731 A.C743 A-C -- -- cWW cW-W 8 A.A732 A.U742 A-U WC 20-XX cWW cW-W 9 A.U733 A.A741 U-A WC 20-XX cWW cW-W 10 A.C734 A.G740 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#7[1] bps=7 strand-1 5'-AAGCCAA-3' bp-type ||||... strand-2 3'-UUCGCAA-5' helix-form AAAxxx 1 A.A753 A.U789 A-U WC 20-XX cWW cW-W 2 A.A754 A.U788 A-U WC 20-XX cWW cW-W 3 A.G755 A.C787 G-C WC 19-XIX cWW cW-W 4 A.C756 A.G786 C-G WC 19-XIX cWW cW-W 5 A.C759 A.C785 C-C -- -- cWW cW-W 6 A.A757 A.A784 A-A -- 05-V tWH tW-M 7 A.A760 A.A783 A-A ~Sheared -- tHS tM-m -------------------------------------------------------------------------- helix#8[1] bps=3 strand-1 5'-AGC-3' bp-type ||| strand-2 3'-UCG-5' helix-form Ax 1 A.A761 A.U779 A-U WC 20-XX cWW cW-W 2 A.G762 A.C778 G-C WC 19-XIX cWW cW-W 3 A.C765 A.G777 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#9[1] bps=4 strand-1 5'-GCAG-3' bp-type |||. strand-2 3'-CGUA-5' helix-form AA. 1 A.G766 A.C775 G-C WC 19-XIX cWW cW-W 2 A.C767 A.G774 C-G WC 19-XIX cWW cW-W 3 A.A768 A.U773 A-U WC 20-XX cWW cW-W 4 A.G769 A.A772 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#10[1] bps=5 strand-1 5'-CGGGA-3' bp-type .|||. strand-2 3'-ACCCA-5' helix-form xAAx 1 A.C808 A.A807 C+A Platform -- cHS cM+m 2 A.G809 A.C804 G-C WC 19-XIX cWW cW-W 3 A.G810 A.C803 G-C WC 19-XIX cWW cW-W 4 A.G811 A.C802 G-C WC 19-XIX cWW cW-W 5 A.A812 A.A814 A-A -- -- cSW cm-W -------------------------------------------------------------------------- helix#11[8] bps=37 strand-1 5'-AGUCAAUAGAAAGGUAAGGACCUGGCGUGCUUCACCC-3' bp-type .||.|||||||||||..||||||||||||||||.||| strand-2 3'-UCGAUUAUCUUUCCGAUCCUGGACUGCGCGAAGCGGG-5' helix-form xA..AAAAAxxAA.xxxAAAAx.x.Ax.A.A.xx.A 1 A.A860 A.U678 A+U rWC 21-XXI tWW tW+W 2 A.G920 A.C677 G-C WC 19-XIX cWW cW-W 3 A.U921 A.G676 U-G Wobble 28-XXVIII cWW cW-W 4 A.C922 A.A675 C-A -- -- cWW cW-W 5 A.A923 A.U674 A-U WC 20-XX cWW cW-W 6 A.A924 A.U673 A-U WC 20-XX cWW cW-W 7 A.U925 A.A672 U-A WC 20-XX cWW cW-W 8 A.A926 A.U671 A-U WC 20-XX cWW cW-W 9 A.G927 A.C670 G-C WC 19-XIX cWW cW-W 10 A.A928 A.U669 A-U WC 20-XX cWW cW-W 11 A.A649 A.U668 A-U WC 20-XX cWW cW-W 12 A.A651 A.U667 A-U WC 20-XX cWW cW-W 13 A.G652 A.C666 G-C WC 19-XIX cWW cW-W 14 A.G653 A.C665 G-C WC 19-XIX cWW cW-W 15 A.U654 A.G664 U-G Wobble 28-XXVIII cWW cW-W 16 A.A1167 A.A663 A-A ~Sheared -- tHS tM-m 17 A.A1168 A.U655 A+U Hoogsteen 23-XXIII cHW cM+W 18 A.G1169 A.C661 G-C WC 19-XIX cWW cW-W 19 A.G1170 A.C660 G-C WC 19-XIX cWW cW-W 20 A.A1171 A.U659 A-U WC 20-XX cWW cW-W 21 A.C1172 A.G658 C-G WC 19-XIX cWW cW-W 22 A.C1173 A.G657 C-G WC 19-XIX cWW cW-W 23 A.U1174 A.A1480 U-A WC 20-XX cWW cW-W 24 A.G1175 A.C1479 G-C WC 19-XIX cWW cW-W 25 A.G1176 A.U1477 G-U Wobble 28-XXVIII cWW cW-W 26 A.C1177 A.G1476 C-G WC 19-XIX cWW cW-W 27 A.G1178 A.C1475 G-C WC 19-XIX cWW cW-W 28 A.U1180 A.G1474 U-G Wobble 28-XXVIII cWW cW-W 29 A.G1181 A.C1473 G-C WC 19-XIX cWW cW-W 30 A.C1182 A.G1472 C-G WC 19-XIX cWW cW-W 31 A.U1183 A.A1471 U-A WC 20-XX cWW cW-W 32 A.U1184 A.A1470 U-A WC 20-XX cWW cW-W 33 A.C1185 A.G1469 C-G WC 19-XIX cWW cW-W 34 A.A1186 A.C1465 A-C ~rHoogsteen 25-XXV tHW tM-W 35 A.C1190 A.G1464 C-G WC 19-XIX cWW cW-W 36 A.C1191 A.G1463 C-G WC 19-XIX cWW cW-W 37 A.C1192 A.G1462 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#12[2] bps=11 strand-1 5'-GGGUUUUUCGU-3' bp-type |||||..|||. strand-2 3'-CCCAAUUAGCA-5' helix-form AAAAx..AAx 1 A.G872 A.C917 G-C WC 19-XIX cWW cW-W 2 A.G873 A.C916 G-C WC 19-XIX cWW cW-W 3 A.G874 A.C915 G-C WC 19-XIX cWW cW-W 4 A.U875 A.A914 U-A WC 20-XX cWW cW-W 5 A.U876 A.A913 U-A WC 20-XX cWW cW-W 6 A.U883 A.U912 U-U -- 16-XVI cWW cW-W 7 A.U884 A.U911 U-U -- 16-XVI cWW cW-W 8 A.U885 A.A910 U-A WC 20-XX cWW cW-W 9 A.C886 A.G909 C-G WC 19-XIX cWW cW-W 10 A.G887 A.C908 G-C WC 19-XIX cWW cW-W 11 A.U888 A.A905 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#13[2] bps=7 strand-1 5'-AACCGCG-3' bp-type .|||||. strand-2 3'-CUGGCGA-5' helix-form xAAx.. 1 A.A882 A.C880 A+C -- -- cHS cM+m 2 A.A896 A.U879 A-U WC 20-XX cWW cW-W 3 A.C897 A.G878 C-G WC 19-XIX cWW cW-W 4 A.C898 A.G877 C-G WC 19-XIX cWW cW-W 5 A.G899 A.C894 G-C WC 19-XIX cWW cW-W 6 A.C900 A.G893 C-G WC 19-XIX cWW cW-W 7 A.G901 A.A892 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#14[2] bps=11 strand-1 5'-GGCGAACAGUU-3' bp-type |||||.||||| strand-2 3'-CCGCUCGUCAA-5' helix-form .Axx..AA.A 1 A.G933 A.C1136 G-C WC 19-XIX cWW cW-W 2 A.G934 A.C1135 G-C WC 19-XIX cWW cW-W 3 A.C935 A.G1134 C-G WC 19-XIX cWW cW-W 4 A.G941 A.C1133 G-C WC 19-XIX cWW cW-W 5 A.A1109 A.U1132 A-U WC 20-XX cWW cW-W 6 A.A1110 A.C1131 A-C ~Wobble -- cWW cW-W 7 A.C1111 A.G1130 C-G WC 19-XIX cWW cW-W 8 A.A1112 A.U1129 A-U WC 20-XX cWW cW-W 9 A.G1113 A.C1128 G-C WC 19-XIX cWW cW-W 10 A.U1114 A.A1127 U-A WC 20-XX cWW cW-W 11 A.U1115 A.A1126 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#15[1] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form A 1 A.G936 A.C1123 G-C WC 19-XIX cWW cW-W 2 A.U937 A.A1122 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#16[2] bps=10 strand-1 5'-GUGUUUAGAU-3' bp-type ||||..|||. strand-2 3'-CACAAGUCUA-5' helix-form AAAxx.AAx 1 A.G943 A.C1052 G-C WC 19-XIX cWW cW-W 2 A.U944 A.A1051 U-A WC 20-XX cWW cW-W 3 A.G945 A.C1050 G-C WC 19-XIX cWW cW-W 4 A.U946 A.A1049 U-A WC 20-XX cWW cW-W 5 A.U947 A.A1046 U-A rHoogsteen 24-XXIV tWH tW-M 6 A.U949 A.G1045 U-G ~Sheared -- tHS tM-m 7 A.A950 A.U1044 A-U WC 20-XX cWW cW-W 8 A.G951 A.C1043 G-C WC 19-XIX cWW cW-W 9 A.A952 A.U1042 A-U WC 20-XX cWW cW-W 10 A.U953 A.A955 U+A Hoogsteen 23-XXIII cWH cW+M -------------------------------------------------------------------------- helix#17[3] bps=19 strand-1 5'-AUAAAGCUAAACUCACCUG-3' bp-type .|||||||....|||.||| strand-2 3'-AAUUUCGAAAACAGUUGAC-5' helix-form .AAAAAx..xx.AAAAAA 1 A.A967 A.A1037 A-A ~Sheared -- tHS tM-m 2 A.U968 A.A1036 U-A WC 20-XX cWW cW-W 3 A.A969 A.U1035 A-U WC 20-XX cWW cW-W 4 A.A970 A.U1034 A-U WC 20-XX cWW cW-W 5 A.A971 A.U1033 A-U WC 20-XX cWW cW-W 6 A.G972 A.C1032 G-C WC 19-XIX cWW cW-W 7 A.C973 A.G1031 C-G WC 19-XIX cWW cW-W 8 A.U974 A.A1014 U-A WC 20-XX cWW cW-W 9 A.A975 A.A1013 A-A -- -- cWW cW-W 10 A.A976 A.A1012 A-A -- -- cWW cW-W 11 A.A977 A.A1010 A-A -- 05-V tWH tW-M 12 A.C979 A.C1009 C-C -- -- cWW cW-W 13 A.U980 A.A1008 U-A WC 20-XX cWW cW-W 14 A.C981 A.G1007 C-G WC 19-XIX cWW cW-W 15 A.A982 A.U1006 A-U WC 20-XX cWW cW-W 16 A.C983 A.U1005 C-U -- -- cWW cW-W 17 A.C984 A.G1004 C-G WC 19-XIX cWW cW-W 18 A.U985 A.A1003 U-A WC 20-XX cWW cW-W 19 A.G986 A.C1002 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#18[1] bps=4 strand-1 5'-GUUG-3' bp-type ||.. strand-2 3'-CAAA-5' helix-form A.. 1 A.G988 A.C999 G-C WC 19-XIX cWW cW-W 2 A.U989 A.A998 U-A WC 20-XX cWW cW-W 3 A.U990 A.A997 U-A -- -- cWH cW-M 4 A.G991 A.A996 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#19[1] bps=5 strand-1 5'-CUACG-3' bp-type |.||. strand-2 3'-GAUGA-5' helix-form xxA. 1 A.C1020 A.G1030 C-G WC 19-XIX cWW cW-W 2 A.U1021 A.A966 U+A -- -- tWH tW+M 3 A.A1022 A.U1029 A-U WC 20-XX cWW cW-W 4 A.C1023 A.G1028 C-G WC 19-XIX cWW cW-W 5 A.G1024 A.A1027 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#20[3] bps=18 strand-1 5'-AGCUAAGCAAACUGGGAt-3' bp-type .||||||||...||||.. strand-2 3'-CCGAUUCGUAUCACCCCA-5' helix-form ..AAAAxA....AAA.. 1 A.A1056 A.C1099 A-C -- -- cWW cW-W 2 A.G1057 A.C1098 G-C WC 19-XIX cWW cW-W 3 A.C1058 A.G1097 C-G WC 19-XIX cWW cW-W 4 A.U1059 A.A1096 U-A WC 20-XX cWW cW-W 5 A.A1060 A.U1095 A-U WC 20-XX cWW cW-W 6 A.A1061 A.U1094 A-U WC 20-XX cWW cW-W 7 A.G1062 A.C1093 G-C WC 19-XIX cWW cW-W 8 A.C1066 A.G1092 C-G WC 19-XIX cWW cW-W 9 A.A1067 A.U1091 A-U WC 20-XX cWW cW-W 10 A.A1068 A.A1090 A-A ~Sheared -- tSH tm-M 11 A.A1069 A.U1089 A-U rHoogsteen 24-XXIV tHW tM-W 12 A.C1070 A.C1088 C-C -- -- .WW .W-W 13 A.U1071 A.A1087 U-A WC 20-XX cWW cW-W 14 A.G1072 A.C1086 G-C WC 19-XIX cWW cW-W 15 A.G1073 A.C1085 G-C WC 19-XIX cWW cW-W 16 A.G1074 A.C1084 G-C WC 19-XIX cWW cW-W 17 A.A1075 A.C1083 A-C -- -- .WH .W-M 18 A.5MU1076 A.A1082 t-A -- -- tWH tW-M -------------------------------------------------------------------------- helix#21[2] bps=11 strand-1 5'-GACAUACGAGC-3' bp-type ||.....|||| strand-2 3'-CUAAAAUUUCG-5' helix-form Ax.x.xx.AA 1 A.G1138 A.C1165 G-C WC 19-XIX cWW cW-W 2 A.A1139 A.U1164 A-U WC 20-XX cWW cW-W 3 A.C1141 A.A1162 C-A -- -- t.H t.-M 4 A.A1142 A.A1161 A+A -- 02-II tHH tM+M 5 A.U1144 A.A1160 U-A rHoogsteen 24-XXIV tWH tW-M 6 A.A1145 A.A1159 A-A ~Sheared -- tHS tM-m 7 A.C1146 A.U758 C-U -- 18-XVIII cWW cW-W 8 A.G1147 A.U1158 G-U Wobble 28-XXVIII cWW cW-W 9 A.A1148 A.U1157 A-U WC 20-XX cWW cW-W 10 A.G1149 A.C1156 G-C WC 19-XIX cWW cW-W 11 A.C1150 A.G1155 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#22[1] bps=3 strand-1 5'-UCG-3' bp-type .|| strand-2 3'-AGC-5' helix-form x. 1 A.U1215 A.A1331 U+A rWC 21-XXI tWW tW+W 2 A.C1216 A.G1227 C-G WC 19-XIX cWW cW-W 3 A.G1217 A.C1226 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#23[2] bps=19 strand-1 5'-AAUAAGGGUCAGGAUUUCU-3' bp-type ..|||||||..|...|||| strand-2 3'-AUAUUCCCGAGCAAAAAGA-5' helix-form xxAAAAA..x..x.x.AA 1 A.A1232 A.A1444 A-A -- 05-V tHW tM-W 2 A.A1404 A.U1400 A-U rHoogsteen 24-XXIV tHW tM-W 3 A.U1407 A.A1399 U-A WC 20-XX cWW cW-W 4 A.A1408 A.U1398 A-U WC 20-XX cWW cW-W 5 A.A1409 A.U1397 A-U WC 20-XX cWW cW-W 6 A.G1410 A.C1396 G-C WC 19-XIX cWW cW-W 7 A.G1411 A.C1395 G-C WC 19-XIX cWW cW-W 8 A.G1412 A.C1394 G-C WC 19-XIX cWW cW-W 9 A.U1413 A.G1393 U-G Wobble 28-XXVIII cWW cW-W 10 A.C1414 A.A1392 C-A -- -- cWW cW-W 11 A.A1417 A.G1389 A-G Sheared 11-XI tHS tM-m 12 A.G1418 A.C1388 G-C WC 19-XIX cWW cW-W 13 A.G1419 A.A1387 G-A -- -- cWW cW-W 14 A.A1367 A.A1384 A+A -- 02-II tHH tM+M 15 A.U1368 A.A1383 U+A -- -- tWS tW+m 16 A.U1370 A.A1382 U-A WC 20-XX cWW cW-W 17 A.U1371 A.A1381 U-A WC 20-XX cWW cW-W 18 A.C1372 A.G1380 C-G WC 19-XIX cWW cW-W 19 A.U1373 A.A1379 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#24[1] bps=8 strand-1 5'-CCACCUCU-3' bp-type |||||||. strand-2 3'-GGUGGAGA-5' helix-form AAAAAAx 1 A.C1238 A.G1351 C-G WC 19-XIX cWW cW-W 2 A.C1239 A.G1350 C-G WC 19-XIX cWW cW-W 3 A.A1240 A.U1349 A-U WC 20-XX cWW cW-W 4 A.C1241 A.G1348 C-G WC 19-XIX cWW cW-W 5 A.C1242 A.G1347 C-G WC 19-XIX cWW cW-W 6 A.U1243 A.A1346 U-A WC 20-XX cWW cW-W 7 A.C1244 A.G1345 C-G WC 19-XIX cWW cW-W 8 A.U1245 A.A1343 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#25[4] bps=17 strand-1 5'-AGCUAUACCGCCAUCUC-3' bp-type .|||||.||||||.|.. strand-2 3'-CCGAUGCGGUGGUUGCA-5' helix-form .AxAAxxAxA.x...x 1 A.A1251 A.C1341 A-C -- -- tHW tM-W 2 A.G1252 A.C1340 G-C WC 19-XIX cWW cW-W 3 A.C1253 A.G1339 C-G WC 19-XIX cWW cW-W 4 A.U1255 A.A1338 U-A WC 20-XX cWW cW-W 5 A.A1256 A.U1337 A-U WC 20-XX cWW cW-W 6 A.U1257 A.G1336 U-G Wobble 28-XXVIII cWW cW-W 7 A.A1260 A.C1330 A-C ~rHoogsteen 25-XXV tHW tM-W 8 A.C1261 A.G1334 C-G WC 19-XIX cWW cW-W 9 A.C1262 A.G1333 C-G WC 19-XIX cWW cW-W 10 A.G1263 A.U1329 G-U Wobble 28-XXVIII cWW cW-W 11 A.C1264 A.G1328 C-G WC 19-XIX cWW cW-W 12 A.C1265 A.G1327 C-G WC 19-XIX cWW cW-W 13 A.A1266 A.U1325 A-U WC 20-XX cWW cW-W 14 A.U1267 A.U1324 U-U -- 16-XVI cWW cW-W 15 A.C1268 A.G1323 C-G WC 19-XIX cWW cW-W 16 A.U1269 A.C1322 U+C -- -- .W. .W+. 17 A.C1271 A.A1321 C-A ~rHoogsteen 25-XXV tWH tW-M -------------------------------------------------------------------------- helix#26[3] bps=10 strand-1 5'-GCAAACCCUG-3' bp-type ||..|||||. strand-2 3'-CGAAUGGGAA-5' helix-form ....AxAA. 1 A.G1273 A.C1302 G-C WC 19-XIX cWW cW-W 2 A.C1274 A.G1301 C-G WC 19-XIX cWW cW-W 3 A.A1275 A.A1300 A-A ~Sheared -- tSH tm-M 4 A.A1276 A.A1299 A-A ~Sheared -- tHS tM-m 5 A.A1277 A.U1298 A-U WC 20-XX cWW cW-W 6 A.C1278 A.G1297 C-G WC 19-XIX cWW cW-W 7 A.C1279 A.G1289 C-G WC 19-XIX cWW cW-W 8 A.C1280 A.G1288 C-G WC 19-XIX cWW cW-W 9 A.U1281 A.A1287 U-A WC 20-XX cWW cW-W 10 A.G1282 A.A1286 G-A -- -- tWH tW-M -------------------------------------------------------------------------- helix#27[1] bps=3 strand-1 5'-UAC-3' bp-type ||| strand-2 3'-AUG-5' helix-form .A 1 A.U1308 A.A1317 U-A WC 20-XX cWW cW-W 2 A.A1309 A.U1316 A-U WC 20-XX cWW cW-W 3 A.C1310 A.G1315 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#28[2] bps=12 strand-1 5'-AGAAUGGGCUAC-3' bp-type ||||||||||.| strand-2 3'-UCUUGUCCGAGG-5' helix-form AxAA..AAA.x 1 A.A1354 A.U1210 A-U WC 20-XX cWW cW-W 2 A.G1355 A.C1209 G-C WC 19-XIX cWW cW-W 3 A.A1357 A.U1208 A-U WC 20-XX cWW cW-W 4 A.A1358 A.U1207 A-U WC 20-XX cWW cW-W 5 A.U1359 A.G1206 U-G Wobble 28-XXVIII cWW cW-W 6 A.G1360 A.U1205 G-U Wobble 28-XXVIII cWW cW-W 7 A.G1361 A.C1204 G-C WC 19-XIX cWW cW-W 8 A.G1362 A.C1203 G-C WC 19-XIX cWW cW-W 9 A.C1363 A.G1202 C-G WC 19-XIX cWW cW-W 10 A.U1364 A.A1201 U-A WC 20-XX cWW cW-W 11 A.A1365 A.G1200 A-G Imino 08-VIII cWW cW-W 12 A.C1366 A.G1421 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#29[1] bps=8 strand-1 5'-AUUUAGAC-3' bp-type .|||||.. strand-2 3'-GAGAUCAC-5' helix-form ...AAxx 1 A.A1423 A.G1199 A-G Sheared 11-XI tHS tM-m 2 A.U1424 A.A1198 U-A WC 20-XX cWW cW-W 3 A.U1425 A.G1197 U-G Wobble 28-XXVIII cWW cW-W 4 A.U1426 A.A1196 U-A WC 20-XX cWW cW-W 5 A.A1427 A.U1195 A-U WC 20-XX cWW cW-W 6 A.G1428 A.C1194 G-C WC 19-XIX cWW cW-W 7 A.A1459 A.A1188 A-A -- -- tWH tW-M 8 A.C1460 A.C1429 C+C -- 15-XV tWW tW+W -------------------------------------------------------------------------- helix#30[1] bps=12 strand-1 5'-UAAACUGAGAGU-3' bp-type ..|||||||... strand-2 3'-AGUUGAUUCGGA-5' helix-form ..AAA.AA.x. 1 A.U1432 A.A1458 U-A rHoogsteen 24-XXIV tWH tW-M 2 A.A1433 A.G1457 A-G Sheared 11-XI tHS tM-m 3 A.A1434 A.U1456 A-U WC 20-XX cWW cW-W 4 A.A1435 A.U1455 A-U WC 20-XX cWW cW-W 5 A.C1436 A.G1454 C-G WC 19-XIX cWW cW-W 6 A.U1437 A.A1453 U-A WC 20-XX cWW cW-W 7 A.G1438 A.U1452 G-U Wobble 28-XXVIII cWW cW-W 8 A.A1439 A.U1451 A-U WC 20-XX cWW cW-W 9 A.G1440 A.C1450 G-C WC 19-XIX cWW cW-W 10 A.A1441 A.G1449 A-G Imino 08-VIII cWW cW-W 11 A.G1442 A.G1447 G-G -- -- tWH tW-M 12 A.U1443 A.A1446 U-A -- -- tSH tm-M -------------------------------------------------------------------------- helix#31[1] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form A. 1 A.A1514 A.U1535 A-U WC 20-XX cWW cW-W 2 A.G1515 A.C1534 G-C WC 19-XIX cWW cW-W 3 A.G1516 A.C1533 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#32[1] bps=3 strand-1 5'-UUA-3' bp-type ||. strand-2 3'-AAA-5' helix-form .. 1 A.U1521 A.A1529 U-A WC 20-XX cWW cW-W 2 A.U1522 A.A1528 U-A WC 20-XX cWW cW-W 3 A.A1523 A.A1527 A-A -- -- cSW cm-W -------------------------------------------------------------------------- helix#33[3] bps=27 strand-1 5'-GAUUUAUAUAGAGGAGACGUCGAACGG-3' bp-type ||..|||||.||||||..|.||..||. strand-2 3'-CUUCAUAUGACUCCUCCCCUGcCcGCA-5' helix-form x....AA.x.AAAAA..x..Ax..xx 1 A.G1538 A.C1511 G-C WC 19-XIX cWW cW-W 2 A.A1540 A.U1510 A-U WC 20-XX cWW cW-W 3 A.U1541 A.U1509 U-U -- 16-XVI cWW cW-W 4 A.U1542 A.C1508 U-C -- 18-XVIII cWW cW-W 5 A.U1543 A.A1507 U-A WC 20-XX cWW cW-W 6 A.A1544 A.U1506 A-U WC 20-XX cWW cW-W 7 A.U1545 A.A1505 U-A WC 20-XX cWW cW-W 8 A.A1546 A.U1504 A-U WC 20-XX cWW cW-W 9 A.U1547 A.G1503 U-G Wobble 28-XXVIII cWW cW-W 10 A.A1548 A.A1501 A-A ~Sheared -- tHS tM-m 11 A.G1549 A.C1500 G-C WC 19-XIX cWW cW-W 12 A.A1550 A.U1499 A-U WC 20-XX cWW cW-W 13 A.G1551 A.C1498 G-C WC 19-XIX cWW cW-W 14 A.G1552 A.C1497 G-C WC 19-XIX cWW cW-W 15 A.A1553 A.U1496 A-U WC 20-XX cWW cW-W 16 A.G1554 A.C1495 G-C WC 19-XIX cWW cW-W 17 A.A1555 A.C1494 A-C -- -- cWW cW-W 18 A.C1556 A.C1493 C-C -- -- cW. cW-. 19 A.G1559 A.C1491 G-C WC 19-XIX cWW cW-W 20 A.U1560 A.U1490 U-U Metal -- cWW cW-W 21 A.C1561 A.G1489 C-G WC 19-XIX cWW cW-W 22 A.G1562 A.5MC1488 G-c WC 19-XIX cWW cW-W 23 A.A1564 A.C1487 A-C -- -- cW. cW-. 24 A.A1565 A.B8T1486 A-c ~Wobble -- cWW cW-W 25 A.C1566 A.G1485 C-G WC 19-XIX cWW cW-W 26 A.G1569 A.C1483 G-C WC 19-XIX cWW cW-W 27 A.G1570 A.A1567 G+A -- -- cWH cW+M -------------------------------------------------------------------------- helix#34[1] bps=9 strand-1 5'-AAGUGUACU-3' bp-type ||||||||| strand-2 3'-UUCACGUGA-5' helix-form AAAA.AAA 1 A.A1572 A.U1593 A-U WC 20-XX cWW cW-W 2 A.A1573 A.U1592 A-U WC 20-XX cWW cW-W 3 A.G1574 A.C1591 G-C WC 19-XIX cWW cW-W 4 A.U1575 A.A1590 U-A WC 20-XX cWW cW-W 5 A.G1576 A.C1589 G-C WC 19-XIX cWW cW-W 6 A.U1577 A.G1588 U-G Wobble 28-XXVIII cWW cW-W 7 A.A1578 A.U1587 A-U WC 20-XX cWW cW-W 8 A.C1579 A.G1586 C-G WC 19-XIX cWW cW-W 9 A.U1580 A.A1585 U-A WC 20-XX cWW cW-W **************************************************************************** List of 63 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[#11] bps=4 strand-1 5'-AGGU-3' bp-type |||| strand-2 3'-UCCG-5' helix-form AA. 1 A.A651 A.U667 A-U WC 20-XX cWW cW-W 2 A.G652 A.C666 G-C WC 19-XIX cWW cW-W 3 A.G653 A.C665 G-C WC 19-XIX cWW cW-W 4 A.U654 A.G664 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#2[#11] bps=5 strand-1 5'-GGUCC-3' bp-type ||||| strand-2 3'-CCAGG-5' helix-form AAAA 1 A.G657 A.C1173 G-C WC 19-XIX cWW cW-W 2 A.G658 A.C1172 G-C WC 19-XIX cWW cW-W 3 A.U659 A.A1171 U-A WC 20-XX cWW cW-W 4 A.C660 A.G1170 C-G WC 19-XIX cWW cW-W 5 A.C661 A.G1169 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#11] bps=6 strand-1 5'-UCUAUU-3' bp-type |||||| strand-2 3'-AGAUAA-5' helix-form AAAAA 1 A.U669 A.A928 U-A WC 20-XX cWW cW-W 2 A.C670 A.G927 C-G WC 19-XIX cWW cW-W 3 A.U671 A.A926 U-A WC 20-XX cWW cW-W 4 A.A672 A.U925 A-U WC 20-XX cWW cW-W 5 A.U673 A.A924 U-A WC 20-XX cWW cW-W 6 A.U674 A.A923 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#4[#11] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.G676 A.U921 G-U Wobble 28-XXVIII cWW cW-W 2 A.C677 A.G920 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#1] bps=6 strand-1 5'-UUAGUA-3' bp-type |||||| strand-2 3'-AAUCAU-5' helix-form AAAAA 1 A.U680 A.A866 U-A WC 20-XX cWW cW-W 2 A.U681 A.A865 U-A WC 20-XX cWW cW-W 3 A.A682 A.U864 A-U WC 20-XX cWW cW-W 4 A.G683 A.C863 G-C WC 19-XIX cWW cW-W 5 A.U684 A.A862 U-A WC 20-XX cWW cW-W 6 A.A685 A.U861 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#1] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form A 1 A.A686 A.U859 A-U WC 20-XX cWW cW-W 2 A.G687 A.C858 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#2] bps=3 strand-1 5'-CAC-3' bp-type ||| strand-2 3'-GUG-5' helix-form A. 1 A.C692 A.G822 C-G WC 19-XIX cWW cW-W 2 A.A693 A.U821 A-U WC 20-XX cWW cW-W 3 A.C694 A.G820 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#3] bps=3 strand-1 5'-UGC-3' bp-type ||| strand-2 3'-ACG-5' helix-form AA 1 A.U696 A.A819 U-A WC 20-XX cWW cW-W 2 A.G697 A.C818 G-C WC 19-XIX cWW cW-W 3 A.C698 A.G817 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#5] bps=3 strand-1 5'-GUG-3' bp-type ||| strand-2 3'-CAC-5' helix-form A. 1 A.G715 A.C800 G-C WC 19-XIX cWW cW-W 2 A.U716 A.A799 U-A WC 20-XX cWW cW-W 3 A.G717 A.C798 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#10[#6] bps=4 strand-1 5'-CCCU-3' bp-type |||| strand-2 3'-GGGA-5' helix-form AAA 1 A.C724 A.G750 C-G WC 19-XIX cWW cW-W 2 A.C725 A.G749 C-G WC 19-XIX cWW cW-W 3 A.C726 A.G748 C-G WC 19-XIX cWW cW-W 4 A.U727 A.A747 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#11[#6] bps=3 strand-1 5'-AUC-3' bp-type ||| strand-2 3'-UAG-5' helix-form AA 1 A.A732 A.U742 A-U WC 20-XX cWW cW-W 2 A.U733 A.A741 U-A WC 20-XX cWW cW-W 3 A.C734 A.G740 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#12[#7] bps=4 strand-1 5'-AAGC-3' bp-type |||| strand-2 3'-UUCG-5' helix-form AAA 1 A.A753 A.U789 A-U WC 20-XX cWW cW-W 2 A.A754 A.U788 A-U WC 20-XX cWW cW-W 3 A.G755 A.C787 G-C WC 19-XIX cWW cW-W 4 A.C756 A.G786 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#13[#8] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form A 1 A.A761 A.U779 A-U WC 20-XX cWW cW-W 2 A.G762 A.C778 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#14[#9] bps=3 strand-1 5'-GCA-3' bp-type ||| strand-2 3'-CGU-5' helix-form AA 1 A.G766 A.C775 G-C WC 19-XIX cWW cW-W 2 A.C767 A.G774 C-G WC 19-XIX cWW cW-W 3 A.A768 A.U773 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#15[#5] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G791 A.C797 G-C WC 19-XIX cWW cW-W 2 A.C792 A.G796 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#16[#10] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form AA 1 A.C802 A.G811 C-G WC 19-XIX cWW cW-W 2 A.C803 A.G810 C-G WC 19-XIX cWW cW-W 3 A.C804 A.G809 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#17[#1] bps=3 strand-1 5'-UAG-3' bp-type ||| strand-2 3'-AUC-5' helix-form AA 1 A.U832 A.A855 U-A WC 20-XX cWW cW-W 2 A.A833 A.U854 A-U WC 20-XX cWW cW-W 3 A.G834 A.C853 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#18[#1] bps=4 strand-1 5'-AAAC-3' bp-type |||| strand-2 3'-UUUG-5' helix-form AAA 1 A.A839 A.U850 A-U WC 20-XX cWW cW-W 2 A.A840 A.U849 A-U WC 20-XX cWW cW-W 3 A.A841 A.U848 A-U WC 20-XX cWW cW-W 4 A.C842 A.G847 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#19[#12] bps=5 strand-1 5'-GGGUU-3' bp-type ||||| strand-2 3'-CCCAA-5' helix-form AAAA 1 A.G872 A.C917 G-C WC 19-XIX cWW cW-W 2 A.G873 A.C916 G-C WC 19-XIX cWW cW-W 3 A.G874 A.C915 G-C WC 19-XIX cWW cW-W 4 A.U875 A.A914 U-A WC 20-XX cWW cW-W 5 A.U876 A.A913 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#20[#13] bps=3 strand-1 5'-GGU-3' bp-type ||| strand-2 3'-CCA-5' helix-form AA 1 A.G877 A.C898 G-C WC 19-XIX cWW cW-W 2 A.G878 A.C897 G-C WC 19-XIX cWW cW-W 3 A.U879 A.A896 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#21[#12] bps=3 strand-1 5'-UCG-3' bp-type ||| strand-2 3'-AGC-5' helix-form AA 1 A.U885 A.A910 U-A WC 20-XX cWW cW-W 2 A.C886 A.G909 C-G WC 19-XIX cWW cW-W 3 A.G887 A.C908 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#22[#13] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G893 A.C900 G-C WC 19-XIX cWW cW-W 2 A.C894 A.G899 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#23[#14] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form .A 1 A.G933 A.C1136 G-C WC 19-XIX cWW cW-W 2 A.G934 A.C1135 G-C WC 19-XIX cWW cW-W 3 A.C935 A.G1134 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#24[#15] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form A 1 A.G936 A.C1123 G-C WC 19-XIX cWW cW-W 2 A.U937 A.A1122 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#25[#16] bps=4 strand-1 5'-GUGU-3' bp-type |||| strand-2 3'-CACA-5' helix-form AAA 1 A.G943 A.C1052 G-C WC 19-XIX cWW cW-W 2 A.U944 A.A1051 U-A WC 20-XX cWW cW-W 3 A.G945 A.C1050 G-C WC 19-XIX cWW cW-W 4 A.U946 A.A1049 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#26[#16] bps=3 strand-1 5'-AGA-3' bp-type ||| strand-2 3'-UCU-5' helix-form AA 1 A.A950 A.U1044 A-U WC 20-XX cWW cW-W 2 A.G951 A.C1043 G-C WC 19-XIX cWW cW-W 3 A.A952 A.U1042 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#27[#17] bps=6 strand-1 5'-UAAAGC-3' bp-type |||||| strand-2 3'-AUUUCG-5' helix-form AAAAA 1 A.U968 A.A1036 U-A WC 20-XX cWW cW-W 2 A.A969 A.U1035 A-U WC 20-XX cWW cW-W 3 A.A970 A.U1034 A-U WC 20-XX cWW cW-W 4 A.A971 A.U1033 A-U WC 20-XX cWW cW-W 5 A.G972 A.C1032 G-C WC 19-XIX cWW cW-W 6 A.C973 A.G1031 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#28[#17] bps=3 strand-1 5'-UCA-3' bp-type ||| strand-2 3'-AGU-5' helix-form AA 1 A.U980 A.A1008 U-A WC 20-XX cWW cW-W 2 A.C981 A.G1007 C-G WC 19-XIX cWW cW-W 3 A.A982 A.U1006 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#29[#17] bps=3 strand-1 5'-CUG-3' bp-type ||| strand-2 3'-GAC-5' helix-form AA 1 A.C984 A.G1004 C-G WC 19-XIX cWW cW-W 2 A.U985 A.A1003 U-A WC 20-XX cWW cW-W 3 A.G986 A.C1002 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#30[#18] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form A 1 A.G988 A.C999 G-C WC 19-XIX cWW cW-W 2 A.U989 A.A998 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#31[#19] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A1022 A.U1029 A-U WC 20-XX cWW cW-W 2 A.C1023 A.G1028 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#32[#20] bps=6 strand-1 5'-GCUAAG-3' bp-type |||||| strand-2 3'-CGAUUC-5' helix-form .AAAA 1 A.G1057 A.C1098 G-C WC 19-XIX cWW cW-W 2 A.C1058 A.G1097 C-G WC 19-XIX cWW cW-W 3 A.U1059 A.A1096 U-A WC 20-XX cWW cW-W 4 A.A1060 A.U1095 A-U WC 20-XX cWW cW-W 5 A.A1061 A.U1094 A-U WC 20-XX cWW cW-W 6 A.G1062 A.C1093 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#33[#20] bps=2 strand-1 5'-CA-3' bp-type || strand-2 3'-GU-5' helix-form A 1 A.C1066 A.G1092 C-G WC 19-XIX cWW cW-W 2 A.A1067 A.U1091 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#34[#20] bps=4 strand-1 5'-UGGG-3' bp-type |||| strand-2 3'-ACCC-5' helix-form AAA 1 A.U1071 A.A1087 U-A WC 20-XX cWW cW-W 2 A.G1072 A.C1086 G-C WC 19-XIX cWW cW-W 3 A.G1073 A.C1085 G-C WC 19-XIX cWW cW-W 4 A.G1074 A.C1084 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#35[#14] bps=5 strand-1 5'-CAGUU-3' bp-type ||||| strand-2 3'-GUCAA-5' helix-form AA.A 1 A.C1111 A.G1130 C-G WC 19-XIX cWW cW-W 2 A.A1112 A.U1129 A-U WC 20-XX cWW cW-W 3 A.G1113 A.C1128 G-C WC 19-XIX cWW cW-W 4 A.U1114 A.A1127 U-A WC 20-XX cWW cW-W 5 A.U1115 A.A1126 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#36[#21] bps=2 strand-1 5'-GA-3' bp-type || strand-2 3'-CU-5' helix-form A 1 A.G1138 A.C1165 G-C WC 19-XIX cWW cW-W 2 A.A1139 A.U1164 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#37[#21] bps=4 strand-1 5'-GAGC-3' bp-type |||| strand-2 3'-UUCG-5' helix-form .AA 1 A.G1147 A.U1158 G-U Wobble 28-XXVIII cWW cW-W 2 A.A1148 A.U1157 A-U WC 20-XX cWW cW-W 3 A.G1149 A.C1156 G-C WC 19-XIX cWW cW-W 4 A.C1150 A.G1155 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#38[#11] bps=2 strand-1 5'-UG-3' bp-type || strand-2 3'-AC-5' helix-form . 1 A.U1174 A.A1480 U-A WC 20-XX cWW cW-W 2 A.G1175 A.C1479 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#39[#11] bps=3 strand-1 5'-GCG-3' bp-type ||| strand-2 3'-UGC-5' helix-form .A 1 A.G1176 A.U1477 G-U Wobble 28-XXVIII cWW cW-W 2 A.C1177 A.G1476 C-G WC 19-XIX cWW cW-W 3 A.G1178 A.C1475 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#40[#11] bps=6 strand-1 5'-UGCUUC-3' bp-type |||||| strand-2 3'-GCGAAG-5' helix-form .A.A. 1 A.U1180 A.G1474 U-G Wobble 28-XXVIII cWW cW-W 2 A.G1181 A.C1473 G-C WC 19-XIX cWW cW-W 3 A.C1182 A.G1472 C-G WC 19-XIX cWW cW-W 4 A.U1183 A.A1471 U-A WC 20-XX cWW cW-W 5 A.U1184 A.A1470 U-A WC 20-XX cWW cW-W 6 A.C1185 A.G1469 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#41[#11] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form .A 1 A.C1190 A.G1464 C-G WC 19-XIX cWW cW-W 2 A.C1191 A.G1463 C-G WC 19-XIX cWW cW-W 3 A.C1192 A.G1462 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#42[#29] bps=5 strand-1 5'-CUAGA-3' bp-type ||||| strand-2 3'-GAUUU-5' helix-form AA.. 1 A.C1194 A.G1428 C-G WC 19-XIX cWW cW-W 2 A.U1195 A.A1427 U-A WC 20-XX cWW cW-W 3 A.A1196 A.U1426 A-U WC 20-XX cWW cW-W 4 A.G1197 A.U1425 G-U Wobble 28-XXVIII cWW cW-W 5 A.A1198 A.U1424 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#43[#28] bps=8 strand-1 5'-AGCCUGUU-3' bp-type |||||||| strand-2 3'-UCGGGUAA-5' helix-form AAA..AA 1 A.A1201 A.U1364 A-U WC 20-XX cWW cW-W 2 A.G1202 A.C1363 G-C WC 19-XIX cWW cW-W 3 A.C1203 A.G1362 C-G WC 19-XIX cWW cW-W 4 A.C1204 A.G1361 C-G WC 19-XIX cWW cW-W 5 A.U1205 A.G1360 U-G Wobble 28-XXVIII cWW cW-W 6 A.G1206 A.U1359 G-U Wobble 28-XXVIII cWW cW-W 7 A.U1207 A.A1358 U-A WC 20-XX cWW cW-W 8 A.U1208 A.A1357 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#44[#28] bps=2 strand-1 5'-CU-3' bp-type || strand-2 3'-GA-5' helix-form A 1 A.C1209 A.G1355 C-G WC 19-XIX cWW cW-W 2 A.U1210 A.A1354 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#45[#22] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form . 1 A.C1216 A.G1227 C-G WC 19-XIX cWW cW-W 2 A.G1217 A.C1226 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#46[#24] bps=7 strand-1 5'-CCACCUC-3' bp-type ||||||| strand-2 3'-GGUGGAG-5' helix-form AAAAAA 1 A.C1238 A.G1351 C-G WC 19-XIX cWW cW-W 2 A.C1239 A.G1350 C-G WC 19-XIX cWW cW-W 3 A.A1240 A.U1349 A-U WC 20-XX cWW cW-W 4 A.C1241 A.G1348 C-G WC 19-XIX cWW cW-W 5 A.C1242 A.G1347 C-G WC 19-XIX cWW cW-W 6 A.U1243 A.A1346 U-A WC 20-XX cWW cW-W 7 A.C1244 A.G1345 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#47[#25] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G1252 A.C1340 G-C WC 19-XIX cWW cW-W 2 A.C1253 A.G1339 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#48[#25] bps=3 strand-1 5'-UAU-3' bp-type ||| strand-2 3'-AUG-5' helix-form AA 1 A.U1255 A.A1338 U-A WC 20-XX cWW cW-W 2 A.A1256 A.U1337 A-U WC 20-XX cWW cW-W 3 A.U1257 A.G1336 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#49[#25] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C1261 A.G1334 C-G WC 19-XIX cWW cW-W 2 A.C1262 A.G1333 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#50[#25] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-UGG-5' helix-form A. 1 A.G1263 A.U1329 G-U Wobble 28-XXVIII cWW cW-W 2 A.C1264 A.G1328 C-G WC 19-XIX cWW cW-W 3 A.C1265 A.G1327 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#51[#26] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G1273 A.C1302 G-C WC 19-XIX cWW cW-W 2 A.C1274 A.G1301 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#52[#26] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A1277 A.U1298 A-U WC 20-XX cWW cW-W 2 A.C1278 A.G1297 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#53[#26] bps=3 strand-1 5'-CCU-3' bp-type ||| strand-2 3'-GGA-5' helix-form AA 1 A.C1279 A.G1289 C-G WC 19-XIX cWW cW-W 2 A.C1280 A.G1288 C-G WC 19-XIX cWW cW-W 3 A.U1281 A.A1287 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#54[#27] bps=3 strand-1 5'-UAC-3' bp-type ||| strand-2 3'-AUG-5' helix-form .A 1 A.U1308 A.A1317 U-A WC 20-XX cWW cW-W 2 A.A1309 A.U1316 A-U WC 20-XX cWW cW-W 3 A.C1310 A.G1315 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#55[#23] bps=4 strand-1 5'-UUCU-3' bp-type |||| strand-2 3'-AAGA-5' helix-form .AA 1 A.U1370 A.A1382 U-A WC 20-XX cWW cW-W 2 A.U1371 A.A1381 U-A WC 20-XX cWW cW-W 3 A.C1372 A.G1380 C-G WC 19-XIX cWW cW-W 4 A.U1373 A.A1379 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#56[#23] bps=7 strand-1 5'-GCCCUUA-3' bp-type ||||||| strand-2 3'-UGGGAAU-5' helix-form .AAAAA 1 A.G1393 A.U1413 G-U Wobble 28-XXVIII cWW cW-W 2 A.C1394 A.G1412 C-G WC 19-XIX cWW cW-W 3 A.C1395 A.G1411 C-G WC 19-XIX cWW cW-W 4 A.C1396 A.G1410 C-G WC 19-XIX cWW cW-W 5 A.U1397 A.A1409 U-A WC 20-XX cWW cW-W 6 A.U1398 A.A1408 U-A WC 20-XX cWW cW-W 7 A.A1399 A.U1407 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#57[#30] bps=7 strand-1 5'-AACUGAG-3' bp-type ||||||| strand-2 3'-UUGAUUC-5' helix-form AAA.AA 1 A.A1434 A.U1456 A-U WC 20-XX cWW cW-W 2 A.A1435 A.U1455 A-U WC 20-XX cWW cW-W 3 A.C1436 A.G1454 C-G WC 19-XIX cWW cW-W 4 A.U1437 A.A1453 U-A WC 20-XX cWW cW-W 5 A.G1438 A.U1452 G-U Wobble 28-XXVIII cWW cW-W 6 A.A1439 A.U1451 A-U WC 20-XX cWW cW-W 7 A.G1440 A.C1450 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#58[#33] bps=2 strand-1 5'-cG-3' bp-type || strand-2 3'-GC-5' helix-form A 1 A.5MC1488 A.G1562 c-G WC 19-XIX cWW cW-W 2 A.G1489 A.C1561 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#59[#33] bps=6 strand-1 5'-CUCCUC-3' bp-type |||||| strand-2 3'-GAGGAG-5' helix-form AAAAA 1 A.C1495 A.G1554 C-G WC 19-XIX cWW cW-W 2 A.U1496 A.A1553 U-A WC 20-XX cWW cW-W 3 A.C1497 A.G1552 C-G WC 19-XIX cWW cW-W 4 A.C1498 A.G1551 C-G WC 19-XIX cWW cW-W 5 A.U1499 A.A1550 U-A WC 20-XX cWW cW-W 6 A.C1500 A.G1549 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#60[#33] bps=5 strand-1 5'-GUAUA-3' bp-type ||||| strand-2 3'-UAUAU-5' helix-form .AA. 1 A.G1503 A.U1547 G-U Wobble 28-XXVIII cWW cW-W 2 A.U1504 A.A1546 U-A WC 20-XX cWW cW-W 3 A.A1505 A.U1545 A-U WC 20-XX cWW cW-W 4 A.U1506 A.A1544 U-A WC 20-XX cWW cW-W 5 A.A1507 A.U1543 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#61[#31] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form A. 1 A.A1514 A.U1535 A-U WC 20-XX cWW cW-W 2 A.G1515 A.C1534 G-C WC 19-XIX cWW cW-W 3 A.G1516 A.C1533 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#62[#32] bps=2 strand-1 5'-UU-3' bp-type || strand-2 3'-AA-5' helix-form . 1 A.U1521 A.A1529 U-A WC 20-XX cWW cW-W 2 A.U1522 A.A1528 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#63[#34] bps=9 strand-1 5'-AAGUGUACU-3' bp-type ||||||||| strand-2 3'-UUCACGUGA-5' helix-form AAAA.AAA 1 A.A1572 A.U1593 A-U WC 20-XX cWW cW-W 2 A.A1573 A.U1592 A-U WC 20-XX cWW cW-W 3 A.G1574 A.C1591 G-C WC 19-XIX cWW cW-W 4 A.U1575 A.A1590 U-A WC 20-XX cWW cW-W 5 A.G1576 A.C1589 G-C WC 19-XIX cWW cW-W 6 A.U1577 A.G1588 U-G Wobble 28-XXVIII cWW cW-W 7 A.A1578 A.U1587 A-U WC 20-XX cWW cW-W 8 A.C1579 A.G1586 C-G WC 19-XIX cWW cW-W 9 A.U1580 A.A1585 U-A WC 20-XX cWW cW-W **************************************************************************** List of 21 isolated WC/wobble pairs Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#11] -1 A.A649 A.U668 A-U WC 20-XX cWW cW-W [#2] -2 A.U690 A.A823 U-A WC 20-XX cWW cW-W [#4] -3 A.G701 A.C708 G-C WC 19-XIX cWW cW-W [#6] -4 A.U729 A.A744 U-A WC 20-XX cWW cW-W [#8] -5 A.C765 A.G777 C-G WC 19-XIX cWW cW-W [#1] -6 A.U830 A.A856 U-A WC 20-XX cWW cW-W [#1] -7 A.U838 A.A852 U-A WC 20-XX cWW cW-W [#14] -8 A.G941 A.C1133 G-C WC 19-XIX cWW cW-W [#17] -9 A.U974 A.A1014 U-A WC 20-XX cWW cW-W [#19] -10 A.C1020 A.G1030 C-G WC 19-XIX cWW cW-W -- -11 A.C1105 A.G1594 C-G WC 19-XIX cWW cW-W [#14] -12 A.A1109 A.U1132 A-U WC 20-XX cWW cW-W [#25] -13 A.A1266 A.U1325 A-U WC 20-XX cWW cW-W [#25] -14 A.C1268 A.G1323 C-G WC 19-XIX cWW cW-W [#28] -15 A.C1366 A.G1421 C-G WC 19-XIX cWW cW-W [#23] -16 A.C1388 A.G1418 C-G WC 19-XIX cWW cW-W [#33] -17 A.C1483 A.G1569 C-G WC 19-XIX cWW cW-W [#33] -18 A.G1485 A.C1566 G-C WC 19-XIX cWW cW-W [#33] -19 A.C1491 A.G1559 C-G WC 19-XIX cWW cW-W [#33] -20 A.U1510 A.A1540 U-A WC 20-XX cWW cW-W [#33] -21 A.C1511 A.G1538 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 16 coaxial stacks 1 Helix#1 contains 4 stems: [#5,#6,#17,#18] 2 Helix#5 contains 2 stems: [#9,#15] 3 Helix#6 contains 2 stems: [#10,#11] 4 Helix#11 contains 8 stems: [#4,#3,#1,#2,#38,#39,#40,#41] 5 Helix#12 contains 2 stems: [#19,#21] 6 Helix#13 contains 2 stems: [#20,#22] 7 Helix#14 contains 2 stems: [#23,#35] 8 Helix#16 contains 2 stems: [#25,#26] 9 Helix#17 contains 3 stems: [#27,#28,#29] 10 Helix#20 contains 3 stems: [#32,#33,#34] 11 Helix#21 contains 2 stems: [#36,#37] 12 Helix#23 contains 2 stems: [#56,#55] 13 Helix#25 contains 4 stems: [#47,#48,#49,#50] 14 Helix#26 contains 3 stems: [#51,#52,#53] 15 Helix#28 contains 2 stems: [#44,#43] 16 Helix#33 contains 3 stems: [#60,#59,#58] **************************************************************************** List of 228 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 UR A.U650,D.ARG427 2 nts=2 GA A.G657,A.A1480 3 nts=2 UU A.U667,A.U668 4 nts=2 CU A.C677,A.U678 5 nts=2 AA A.A685,A.A686 6 nts=2 GC A.G687,A.C829 7 nts=2 CC A.C694,A.C815 8 nts=2 AU A.A695,A.U696 9 nts=2 AG A.A699,A.G817 10 nts=2 AR A.A700,U.ARG27 11 nts=2 CY A.C705,0.TYR136 12 nts=2 UR A.U711,M.ARG13 13 nts=2 GG A.G717,A.G791 14 nts=2 AC A.A735,A.C736 15 nts=2 UG A.U758,A.G1147 16 nts=2 AR A.A761,L.ARG197 17 nts=2 GC A.G762,A.C763 18 nts=2 AG A.A768,A.G769 19 nts=2 CA A.C775,A.A776 20 nts=2 AR A.A782,N.ARG46 21 nts=2 UG A.U794,A.G796 22 nts=2 AY A.A795,T.TYR134 23 nts=2 CC A.C797,A.C798 24 nts=2 CA A.C800,A.A801 25 nts=2 CA A.C802,A.A814 26 nts=2 CG A.C808,A.G809 27 nts=2 AG A.A819,A.G820 28 nts=2 AA A.A826,A.A827 29 nts=2 GG A.G843,A.G847 30 nts=2 AA A.A855,A.A856 31 nts=2 AC A.A866,A.C867 32 nts=2 AA A.A871,A.A919 33 nts=2 UU A.U876,A.U883 34 nts=2 GA A.G877,A.A907 35 nts=2 UC A.U879,A.C880 36 nts=2 AA A.A881,A.A882 37 nts=2 UU A.U884,A.U885 38 nts=2 AC A.A905,A.C908 39 nts=2 CR A.C906,G.ARG50 40 nts=2 UC A.U921,A.C922 41 nts=2 CY A.C931,N.TYR38 42 nts=2 CW A.C932,D.TRP408 43 nts=2 GA A.G933,A.A1137 44 nts=2 AU A.A952,A.U953 45 nts=2 AU A.A955,A.U1042 46 nts=2 CU A.C973,A.U974 47 nts=2 GA A.G986,A.A987 48 nts=2 GR A.G988,8.ARG140 49 nts=2 CU A.C999,A.U1000 50 nts=2 AC A.A1008,A.C1009 51 nts=2 GG A.G1024,A.G1028 52 nts=2 AA A.A1036,A.A1037 53 nts=2 AU A.A1039,A.U1040 54 nts=2 AR A.A1041,L.ARG123 55 nts=2 AA A.A1046,A.A1049 56 nts=2 AC A.A1047,A.C1048 57 nts=2 CC A.C1065,A.C1066 58 nts=2 AG A.A1103,A.G1594 59 nts=2 CU A.C1105,A.U1107 60 nts=2 AA A.A1116,A.A1117 61 nts=2 AA A.A1121,A.A1122 62 nts=2 CA A.C1123,A.A1124 63 nts=2 AY A.A1126,S.TYR53 64 nts=2 CH A.C1143,3.HIS140 65 nts=2 CA A.C1150,A.A1152 66 nts=2 CR A.C1153,3.ARG197 67 nts=2 UA A.U1158,A.A1159 68 nts=2 CA A.C1165,A.A1166 69 nts=2 CU A.C1173,A.U1174 70 nts=2 GG A.G1175,A.G1176 71 nts=2 GU A.G1178,A.U1180 72 nts=2 GG A.G1179,A.G1570 73 nts=2 UU A.U1187,A.U1189 74 nts=2 CU A.C1192,A.U1193 75 nts=2 AG A.A1198,A.G1199 76 nts=2 UC A.U1208,A.C1209 77 nts=2 AA A.A1213,A.A1214 78 nts=2 CC A.C1223,A.C1224 79 nts=2 CQ A.C1250,Z.GLN63 80 nts=2 CG A.C1262,A.G1263 81 nts=2 CC A.C1278,A.C1279 82 nts=2 GA A.G1282,A.A1287 83 nts=2 UF A.U1284,D.PHE256 84 nts=2 GA A.G1285,A.A1286 85 nts=2 GG A.G1289,A.G1297 86 nts=2 AG A.A1332,A.G1333 87 nts=2 GU A.G1334,A.U1335 88 nts=2 AG A.A1338,A.G1339 89 nts=2 CC A.C1340,A.C1341 90 nts=2 AG A.A1343,A.G1345 91 nts=2 AA A.A1356,A.A1357 92 nts=2 UU A.U1368,A.U1370 93 nts=2 CU A.C1405,A.U1406 94 nts=2 AU A.A1430,A.U1432 95 nts=2 GC A.G1464,A.C1465 96 nts=2 GC A.G1474,A.C1475 97 nts=2 CA A.C1500,A.A1501 98 nts=2 AC A.A1507,A.C1508 99 nts=2 UU A.U1520,A.U1521 100 nts=2 CR A.C1525,V.ARG105 101 nts=2 UW A.U1526,V.TRP102 102 nts=2 AA A.A1527,A.A1528 103 nts=2 GU A.G1562,A.U1563 104 nts=2 GA A.G1581,A.A1585 105 nts=2 AY A.A1599,Q.TYR64 106 nts=2 Yg X.TYR173,X.GNP403 107 nts=3 GAA A.G676,A.A675,A.A923 108 nts=3 CAG A.C679,A.A860,A.G920 109 nts=3 UUU A.U690,A.U689,A.U825 110 nts=3 CCC A.C706,A.C707,A.C708 111 nts=3 UCU A.U727,A.C728,A.U729 112 nts=3 UCA A.U742,A.C743,A.A744 113 nts=3 ACG A.A757,A.C759,A.G786 114 nts=3 UCY A.U779,A.C780,L.TYR195 115 nts=3 GAA A.G811,A.A812,A.A813 116 nts=3 GAU A.G822,A.A823,A.U824 117 nts=3 UGC A.U830,A.G857,A.C858 118 nts=3 GCU A.G834,A.C835,A.U850 119 nts=3 AAU A.A836,A.A837,A.U838 120 nts=3 AAC A.A839,A.A852,A.C853 121 nts=3 CCR A.C869,A.C870,O.ARG97 122 nts=3 CAG A.C891,A.A892,A.G893 123 nts=3 GCQ A.G899,A.C895,J.GLN116 124 nts=3 CAR A.C917,A.A918,O.ARG96 125 nts=3 CAA A.C935,A.A940,A.A939 126 nts=3 GCA A.G936,A.C1108,A.A1125 127 nts=3 GAU A.G943,A.A1104,A.U1101 128 nts=3 UUA A.U948,A.U949,A.A950 129 nts=3 CCC A.C956,A.C957,A.C958 130 nts=3 CCC A.C962,A.C963,A.C964 131 nts=3 UAC A.U968,A.A967,A.C1038 132 nts=3 ACC A.A982,A.C983,A.C984 133 nts=3 GUU A.G1004,A.U1005,A.U1006 134 nts=3 AAG A.A1022,A.A966,A.G1030 135 nts=3 GAC A.G1062,A.A1063,A.C1064 136 nts=3 AAU A.A1069,A.A1090,A.U1091 137 nts=3 UCU A.U1071,A.C1070,A.U1089 138 nts=3 AAG A.A1167,A.A1168,A.G1169 139 nts=3 CAG A.C1190,A.A1186,A.G1469 140 nts=3 AGG A.A1201,A.G1200,A.G1421 141 nts=3 UGA A.U1212,A.G1211,A.A1354 142 nts=3 GAU A.G1217,A.A1218,A.U1219 143 nts=3 AAA A.A1220,A.A1221,A.A1222 144 nts=3 GAR A.G1227,A.A1228,K.ARG98 145 nts=3 CUC A.C1244,A.U1245,A.C1342 146 nts=3 GAG A.G1247,A.A1251,A.G1252 147 nts=3 UCW A.U1249,A.C1248,K.TRP35 148 nts=3 UAR A.U1259,A.A1326,D.ARG114 149 nts=3 CAG A.C1261,A.A1260,A.G1336 150 nts=3 CUA A.C1290,A.U1291,A.A1295 151 nts=3 AAY A.A1292,A.A1294,B.TYR170 152 nts=3 CCG A.C1312,A.C1314,A.G1315 153 nts=3 ACR A.A1331,A.C1254,K.ARG33 154 nts=3 GCA A.G1351,A.C1352,A.A1353 155 nts=3 AAR A.A1382,A.A1383,F.ARG198 156 nts=3 AUG A.A1399,A.U1400,A.G1401 157 nts=3 UCG A.U1413,A.C1414,A.G1415 158 nts=3 GAU A.G1422,A.A1423,A.U1424 159 nts=3 CCU A.C1466,A.C1467,A.U1468 160 nts=3 GUC A.G1489,A.U1490,A.C1491 161 nts=3 AAA A.A1514,A.A1512,A.A1536 162 nts=3 GAC A.G1516,A.A1517,A.C1518 163 nts=3 AAC A.A1529,A.A1530,A.C1531 164 nts=3 GAU A.G1538,A.A1540,A.U1541 165 nts=3 Gaa A.G1582,A.MA6/1583,A.MA6/1584 166 nts=3 ACC A.A1600,A.C1601,A.C1602 167 nts=3 HAR P.HIS95,A.A1019,Q.ARG62 168 nts=3 DCR Q.ASP82,A.C1293,2.ARG110 169 nts=4 AAWU A.A651,A.A649,D.TRP422,A.U669 170 nts=4 CUAG A.C661,A.U662,A.A663,A.G664 171 nts=4 CCAG A.C712,A.C713,A.A714,A.G715 172 nts=4 UCAG A.U721,A.C752,A.A751,A.G750 173 nts=4 CACG A.C737,A.A738,A.C739,A.G740 174 nts=4 CAAU A.C770,A.A771,A.A772,A.U773 175 nts=4 CGAF A.C778,A.G777,A.A764,L.PHE214 176 nts=4 AAAC A.A781,A.A760,A.A784,A.C785 177 nts=4 AAAW A.A846,A.A845,A.A844,0.TRP201 178 nts=4 GUGU A.G887,A.U888,A.G889,A.U903 179 nts=4 CGCG A.C900,A.G901,A.C890,A.G902 180 nts=4 AUUA A.A910,A.U911,A.U912,A.A913 181 nts=4 AAAG A.A928,A.A929,A.A648,A.G930 182 nts=4 UUGU A.U946,A.U947,A.G1045,A.U1044 183 nts=4 UUGU A.U989,A.U990,A.G991,A.U992 184 nts=4 AAAR A.A1027,A.A1026,A.A1025,L.ARG154 185 nts=4 AACA A.A1067,A.A1068,A.C1088,A.A1087 186 nts=4 GAtU A.G1074,A.A1075,A.5MU1076,A.U1077 187 nts=4 GCUC A.G1130,A.C1131,A.U1132,A.C1133 188 nts=4 UCAU A.U1257,A.C1330,A.A1258,A.U1329 189 nts=4 CAAU A.C1274,A.A1275,A.A1299,A.U1298 190 nts=4 AAAG A.A1277,A.A1276,A.A1300,A.G1301 191 nts=4 AAAG A.A1317,A.A1318,A.A1319,A.G1320 192 nts=4 UACU A.U1364,A.A1365,A.C1366,A.U1420 193 nts=4 CCAA A.C1376,A.C1375,A.A1374,A.A1379 194 nts=4 AACG A.A1384,A.A1387,A.C1388,A.G1389 195 nts=4 GACA A.G1428,A.A1188,A.C1429,A.A1461 196 nts=4 GAGU A.G1440,A.A1441,A.G1442,A.U1443 197 nts=4 UGGR A.U1456,A.G1457,A.G1431,G.ARG375 198 nts=4 CGcC A.C1483,A.G1485,A.B8T1486,A.C1487 199 nts=4 GAAG A.G1503,A.A1502,A.A1548,A.G1549 200 nts=4 UAAR A.U1522,A.A1523,A.A1524,V.ARG392 201 nts=4 GACA A.G1554,A.A1555,A.C1556,A.A1557 202 nts=5 CACCR A.C804,A.A807,A.C806,A.C805,0.ARG7 203 nts=5 AAAAG A.A1010,A.A1012,A.A1013,A.A1014,A.G1031 204 nts=5 CACCC A.C1052,A.A1053,A.C1100,A.C1099,A.C1098 205 nts=5 GAUAA A.G1057,A.A1056,A.U1055,A.A1054,A.A1102 206 nts=5 CAAGG A.C1111,A.A1110,A.A1109,A.G941,A.G1134 207 nts=5 AACAU A.A1139,A.A1140,A.C1141,A.A1142,A.U1144 208 nts=5 ACGUU A.A1321,A.C1322,A.G1323,A.U1324,A.U1325 209 nts=5 AAAAU A.A1402,A.A1403,A.A1232,A.A1404,A.U1407 210 nts=5 AAAAC A.A1434,A.A1433,A.A1458,A.A1459,A.C1460 211 nts=5 AGACY A.A1572,A.G1595,A.A1596,A.C1597,Q.TYR57 212 nts=5 FACUR D.PHE298,A.A1283,A.C1120,A.U1119,S.ARG48 213 nts=6 ACGGUR A.A703,A.C702,A.G701,A.G709,A.U710,U.ARG30 214 nts=6 AAAAAA A.A732,A.A731,A.A730,A.A745,A.A746,A.A747 215 nts=6 AAAACU A.A975,A.A976,A.A977,A.A978,A.C979,A.U980 216 nts=6 AAAAAA A.A993,A.A994,A.A995,A.A996,A.A997,A.A998 217 nts=6 AGAACC A.A1078,A.G1079,A.A1080,A.A1082,A.C1083,A.C1084 218 nts=6 cAACGA A.5MC1488,A.A1564,A.A1565,A.C1566,A.G1569,A.A1567 219 nts=6 CCUUUU A.C1537,A.C1511,A.U1510,A.U1509,A.U1542,A.U1543 220 nts=7 AAUGAAA A.A753,A.A790,A.U720,A.G719,A.A718,A.A691,A.A816 221 nts=7 UCGAUAH A.U1021,A.C1020,A.G1018,A.A1017,A.U1016,A.A1015,I.HIS183 222 nts=7 CAAAACU A.C1146,A.A1145,A.A1160,A.A1161,A.A1162,A.C1163,A.U1164 223 nts=7 CUACUCC A.C1216,A.U1215,A.A1237,A.C1236,A.U1235,A.C1234,A.C1233 224 nts=7 ACUCUAG A.A1272,A.C1271,A.U1269,A.C1268,A.U1267,A.A1266,A.G1327 225 nts=7 GGCAAGU A.G1273,A.G1303,A.C1304,A.A1305,A.A1306,A.G1307,A.U1308 226 nts=7 GAAAAGG A.G1393,A.A1392,A.A1390,A.A1416,A.A1417,A.G1418,A.G1419 227 nts=7 AGACGGC A.A1444,A.G1445,A.A1446,A.C1230,A.G1447,A.G1449,A.C1450 228 nts=8 CCCAAGUC A.C1495,A.C1494,A.C1493,A.A1492,A.A1558,A.G1559,A.U1560,A.C1561 **************************************************************************** Nucleotides not involved in stacking interactions nts=58 UACCACACCUAUCCAACCCUCCCUCCACCCUACUUUCAUUCCUUUACCACACCCUUGa A.U656,A.A688,A.C692,A.C722,A.A723,A.C724,A.A783,A.C793,A.C828,A.U831,A.A851,A.U861,A.C868,A.C904,A.A938,A.A942,A.C954,A.C959,A.C960,A.U961,A.C965,A.C1001,A.C1011,A.U1081,A.C1093,A.C1106,A.A1118,A.C1151,A.C1225,A.C1226,A.U1229,A.A1231,A.C1238,A.U1246,A.U1255,A.U1270,A.C1311,A.A1313,A.U1344,A.U1369,A.C1377,A.C1385,A.U1386,A.U1391,A.U1448,A.A1478,A.C1479,A.C1481,A.A1482,A.C1484,A.A1519,A.C1532,A.C1533,A.C1539,A.U1568,A.U1571,A.G1598,X.ATP402 **************************************************************************** List of 55 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.G658 A.U656 3.11 2 sugar O4'@A.U710 A.A700 3.47 3 sugar O4'@A.A764 A.C765 3.16 4 phosphate OP2@A.A771 A.G769 3.03 5 sugar O4'@A.U773 A.A772 3.40 6 sugar O4'@A.A781 A.A783 3.21 7 sugar O4'@A.U794 A.G796 3.30 8 sugar O2'@A.C806 A.A807 3.22 9 sugar O4'@A.A812 A.G811 3.41 10 phosphate OP2@A.A827 A.U825 2.95 11 sugar O4'@A.U689 A.A827 3.42 12 phosphate OP2@A.A845 A.G843 2.87 13 phosphate O5'@A.A845 A.G843 3.43 14 phosphate OP2@A.A846 A.G847 3.46 15 sugar O4'@A.C853 A.A852 3.10 16 sugar O4'@A.U876 A.A882 3.24 17 sugar O4'@A.U903 A.G889 3.28 18 sugar O4'@A.C900 A.A907 3.20 19 sugar O4'@A.C679 A.A919 3.43 20 sugar O4'@A.C935 A.A940 3.14 21 sugar O4'@A.G1018 A.C1020 2.97 22 phosphate OP2@A.A1026 A.G1024 2.89 23 sugar O4'@A.G1028 A.A1027 3.34 24 other N6A@A.NAD1701 A.A1046 3.49 25 phosphate OP2@A.G1079 A.U1077 3.09 26 sugar O2'@A.G1581 A.U1081 3.36 27 sugar O4'@A.A1104 A.A1102 3.05 28 sugar O4'@A.G936 A.C1108 3.11 29 phosphate OP1@A.C1120 A.A1118 2.72 30 phosphate OP2@A.A1214 A.U1212 2.87 31 sugar O2'@A.U1219 A.C1223 3.01 32 sugar O2'@A.U1205 A.C1225 3.39 33 sugar O4'@A.G1449 A.C1225 3.31 34 sugar O4'@A.C1236 A.A1237 3.45 35 sugar O4'@A.U1246 A.G1247 3.21 36 sugar O4'@A.G1252 A.A1251 3.19 37 sugar O4'@A.A1331 A.C1254 3.24 38 sugar O2'@A.A1272 A.G1273 3.03 39 phosphate OP1@A.G1285 A.G1282 3.49 40 phosphate OP2@A.A1286 A.A1287 3.32 41 sugar O4'@A.G1301 A.A1300 3.29 42 phosphate OP2@A.C1312 A.C1310 3.27 43 sugar O4'@A.U1259 A.A1326 3.09 44 sugar O4'@A.C1388 A.A1367 3.33 45 sugar O4'@A.A1384 A.A1387 3.20 46 phosphate OP2@A.A1403 A.G1401 3.02 47 phosphate OP2@A.G1445 A.U1443 2.92 48 sugar O4'@A.C1566 A.A1478 3.33 49 sugar O4'@A.A1512 A.A1514 3.36 50 sugar O4'@A.C1537 A.G1538 3.33 51 sugar O4'@A.G1178 A.A1567 3.16 52 sugar O2'@A.G1178 A.A1567 3.49 53 sugar O4'@A.G1569 A.G1570 3.49 54 sugar O2'@A.G1181 A.G1598 3.45 55 other NZ@2.LYS25 A.A1599 2.60 **************************************************************************** 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 22 hairpin loops 1 hairpin loop: nts=11; [9]; linked by [#1] summary: [1] 9 [A.654 A.664] 4 nts=11 UUUGGUCCUAG A.U654,A.U655,A.U656,A.G657,A.G658,A.U659,A.C660,A.C661,A.U662,A.A663,A.G664 nts=9 UUGGUCCUA A.U655,A.U656,A.G657,A.G658,A.U659,A.C660,A.C661,A.U662,A.A663 2 hairpin loop: nts=8; [6]; linked by [#-3] summary: [1] 6 [A.701 A.708] 1 nts=8 GCAUCCCC A.G701,A.C702,A.A703,A.U704,A.C705,A.C706,A.C707,A.C708 nts=6 CAUCCC A.C702,A.A703,A.U704,A.C705,A.C706,A.C707 3 hairpin loop: nts=7; [5]; linked by [#11] summary: [1] 5 [A.734 A.740] 3 nts=7 CACCACG A.C734,A.A735,A.C736,A.C737,A.A738,A.C739,A.G740 nts=5 ACCAC A.A735,A.C736,A.C737,A.A738,A.C739 4 hairpin loop: nts=6; [4]; linked by [#14] summary: [1] 4 [A.768 A.773] 3 nts=6 AGCAAU A.A768,A.G769,A.C770,A.A771,A.A772,A.U773 nts=4 GCAA A.G769,A.C770,A.A771,A.A772 5 hairpin loop: nts=5; [3]; linked by [#15] summary: [1] 3 [A.792 A.796] 2 nts=5 CCUAG A.C792,A.C793,A.U794,A.A795,A.G796 nts=3 CUA A.C793,A.U794,A.A795 6 hairpin loop: nts=6; [4]; linked by [#16] summary: [1] 4 [A.804 A.809] 3 nts=6 CCCACG A.C804,A.C805,A.C806,A.A807,A.C808,A.G809 nts=4 CCAC A.C805,A.C806,A.A807,A.C808 7 hairpin loop: nts=6; [4]; linked by [#18] summary: [1] 4 [A.842 A.847] 4 nts=6 CGAAAG A.C842,A.G843,A.A844,A.A845,A.A846,A.G847 nts=4 GAAA A.G843,A.A844,A.A845,A.A846 8 hairpin loop: nts=18; [16]; linked by [#20] summary: [1] 16 [A.879 A.896] 3 nts=18 UCAAUUUCGUGCCAGCCA A.U879,A.C880,A.A881,A.A882,A.U883,A.U884,A.U885,A.C886,A.G887,A.U888,A.G889,A.C890,A.C891,A.A892,A.G893,A.C894,A.C895,A.A896 nts=16 CAAUUUCGUGCCAGCC A.C880,A.A881,A.A882,A.U883,A.U884,A.U885,A.C886,A.G887,A.U888,A.G889,A.C890,A.C891,A.A892,A.G893,A.C894,A.C895 9 hairpin loop: nts=6; [4]; linked by [#22] summary: [1] 4 [A.894 A.899] 2 nts=6 CCACCG A.C894,A.C895,A.A896,A.C897,A.C898,A.G899 nts=4 CACC A.C895,A.A896,A.C897,A.C898 10 hairpin loop: nts=10; [8]; linked by [#30] summary: [1] 8 [A.989 A.998] 2 nts=10 UUGUAAAAAA A.U989,A.U990,A.G991,A.U992,A.A993,A.A994,A.A995,A.A996,A.A997,A.A998 nts=8 UGUAAAAA A.U990,A.G991,A.U992,A.A993,A.A994,A.A995,A.A996,A.A997 11 hairpin loop: nts=6; [4]; linked by [#31] summary: [1] 4 [A.1023 A.1028] 2 nts=6 CGAAAG A.C1023,A.G1024,A.A1025,A.A1026,A.A1027,A.G1028 nts=4 GAAA A.G1024,A.A1025,A.A1026,A.A1027 12 hairpin loop: nts=11; [9]; linked by [#34] summary: [1] 9 [A.1074 A.1084] 4 nts=11 GAtUAGAUACC A.G1074,A.A1075,A.5MU1076,A.U1077,A.A1078,A.G1079,A.A1080,A.U1081,A.A1082,A.C1083,A.C1084 nts=9 AtUAGAUAC A.A1075,A.5MU1076,A.U1077,A.A1078,A.G1079,A.A1080,A.U1081,A.A1082,A.C1083 13 hairpin loop: nts=12; [10]; linked by [#35] summary: [1] 10 [A.1115 A.1126] 5 nts=12 UAAAUCAACAAA A.U1115,A.A1116,A.A1117,A.A1118,A.U1119,A.C1120,A.A1121,A.A1122,A.C1123,A.A1124,A.A1125,A.A1126 nts=10 AAAUCAACAA A.A1116,A.A1117,A.A1118,A.U1119,A.C1120,A.A1121,A.A1122,A.C1123,A.A1124,A.A1125 14 hairpin loop: nts=6; [4]; linked by [#37] summary: [1] 4 [A.1150 A.1155] 4 nts=6 CCACAG A.C1150,A.C1151,A.A1152,A.C1153,A.A1154,A.G1155 nts=4 CACA A.C1151,A.A1152,A.C1153,A.A1154 15 hairpin loop: nts=10; [8]; linked by [#45] summary: [1] 8 [A.1217 A.1226] 2 nts=10 GAUAAACCCC A.G1217,A.A1218,A.U1219,A.A1220,A.A1221,A.A1222,A.C1223,A.C1224,A.C1225,A.C1226 nts=8 AUAAACCC A.A1218,A.U1219,A.A1220,A.A1221,A.A1222,A.C1223,A.C1224,A.C1225 16 hairpin loop: nts=7; [5]; linked by [#53] summary: [1] 5 [A.1281 A.1287] 3 nts=7 UGAUGAA A.U1281,A.G1282,A.A1283,A.U1284,A.G1285,A.A1286,A.A1287 nts=5 GAUGA A.G1282,A.A1283,A.U1284,A.G1285,A.A1286 17 hairpin loop: nts=6; [4]; linked by [#54] summary: [1] 4 [A.1310 A.1315] 3 nts=6 CCCACG A.C1310,A.C1311,A.C1312,A.A1313,A.C1314,A.G1315 nts=4 CCAC A.C1311,A.C1312,A.A1313,A.C1314 18 hairpin loop: nts=7; [5]; linked by [#55] summary: [1] 5 [A.1373 A.1379] 4 nts=7 UACCCCA A.U1373,A.A1374,A.C1375,A.C1376,A.C1377,A.C1378,A.A1379 nts=5 ACCCC A.A1374,A.C1375,A.C1376,A.C1377,A.C1378 19 hairpin loop: nts=9; [7]; linked by [#56] summary: [1] 7 [A.1399 A.1407] 7 nts=9 AUGAAACUU A.A1399,A.U1400,A.G1401,A.A1402,A.A1403,A.A1404,A.C1405,A.U1406,A.U1407 nts=7 UGAAACU A.U1400,A.G1401,A.A1402,A.A1403,A.A1404,A.C1405,A.U1406 20 hairpin loop: nts=11; [9]; linked by [#57] summary: [1] 9 [A.1440 A.1450] 7 nts=11 GAGUAGAGUGC A.G1440,A.A1441,A.G1442,A.U1443,A.A1444,A.G1445,A.A1446,A.G1447,A.U1448,A.G1449,A.C1450 nts=9 AGUAGAGUG A.A1441,A.G1442,A.U1443,A.A1444,A.G1445,A.A1446,A.G1447,A.U1448,A.G1449 21 hairpin loop: nts=7; [5]; linked by [#62] summary: [1] 5 [A.1522 A.1528] 2 nts=7 UAACUAA A.U1522,A.A1523,A.A1524,A.C1525,A.U1526,A.A1527,A.A1528 nts=5 AACUA A.A1523,A.A1524,A.C1525,A.U1526,A.A1527 22 hairpin loop: nts=6; [4]; linked by [#63] summary: [1] 4 [A.1580 A.1585] 9 nts=6 UGGaaA A.U1580,A.G1581,A.G1582,A.MA6/1583,A.MA6/1584,A.A1585 nts=4 GGaa A.G1581,A.G1582,A.MA6/1583,A.MA6/1584 **************************************************************************** List of 19 bulges 1 bulge: nts=5; [1,0]; linked by [#-1,#1] summary: [2] 1 0 [A.649 A.668 A.651 A.667] 1 4 nts=5 AUAUU A.A649,A.U650,A.A651,A.U667,A.U668 nts=1 U A.U650 nts=0 2 bulge: nts=5; [0,1]; linked by [#5,#6] summary: [2] 0 1 [A.685 A.861 A.686 A.859] 6 2 nts=5 AAUAU A.A685,A.A686,A.U859,A.A860,A.U861 nts=0 nts=1 A A.A860 3 bulge: nts=5; [1,0]; linked by [#-2,#7] summary: [2] 1 0 [A.690 A.823 A.692 A.822] 1 3 nts=5 UACGA A.U690,A.A691,A.C692,A.G822,A.A823 nts=1 A A.A691 nts=0 4 bulge: nts=5; [1,0]; linked by [#7,#8] summary: [2] 1 0 [A.694 A.820 A.696 A.819] 3 3 nts=5 CAUAG A.C694,A.A695,A.U696,A.A819,A.G820 nts=1 A A.A695 nts=0 5 bulge: nts=5; [0,1]; linked by [#-5,#14] summary: [2] 0 1 [A.765 A.777 A.766 A.775] 1 3 nts=5 CGCAG A.C765,A.G766,A.C775,A.A776,A.G777 nts=0 nts=1 A A.A776 6 bulge: nts=5; [1,0]; linked by [#-6,#17] summary: [2] 1 0 [A.830 A.856 A.832 A.855] 1 3 nts=5 UUUAA A.U830,A.U831,A.U832,A.A855,A.A856 nts=1 U A.U831 nts=0 7 bulge: nts=5; [0,1]; linked by [#-7,#18] summary: [2] 0 1 [A.838 A.852 A.839 A.850] 1 4 nts=5 UAUAA A.U838,A.A839,A.U850,A.A851,A.A852 nts=0 nts=1 A A.A851 8 bulge: nts=5; [1,0]; linked by [#-10,#31] summary: [2] 1 0 [A.1020 A.1030 A.1022 A.1029] 1 2 nts=5 CUAUG A.C1020,A.U1021,A.A1022,A.U1029,A.G1030 nts=1 U A.U1021 nts=0 9 bulge: nts=5; [0,1]; linked by [#38,#39] summary: [2] 0 1 [A.1175 A.1479 A.1176 A.1477] 2 3 nts=5 GGUAC A.G1175,A.G1176,A.U1477,A.A1478,A.C1479 nts=0 nts=1 A A.A1478 10 bulge: nts=5; [1,0]; linked by [#39,#40] summary: [2] 1 0 [A.1178 A.1475 A.1180 A.1474] 3 6 nts=5 GGUGC A.G1178,A.G1179,A.U1180,A.G1474,A.C1475 nts=1 G A.G1179 nts=0 11 bulge: nts=5; [0,1]; linked by [#43,#44] summary: [2] 0 1 [A.1208 A.1357 A.1209 A.1355] 8 2 nts=5 UCGAA A.U1208,A.C1209,A.G1355,A.A1356,A.A1357 nts=0 nts=1 A A.A1356 12 bulge: nts=5; [1,0]; linked by [#47,#48] summary: [2] 1 0 [A.1253 A.1339 A.1255 A.1338] 2 3 nts=5 CCUAG A.C1253,A.C1254,A.U1255,A.A1338,A.G1339 nts=1 C A.C1254 nts=0 13 bulge: nts=5; [0,1]; linked by [#50,#-13] summary: [2] 0 1 [A.1265 A.1327 A.1266 A.1325] 3 1 nts=5 CAUAG A.C1265,A.A1266,A.U1325,A.A1326,A.G1327 nts=0 nts=1 A A.A1326 14 bulge: nts=5; [0,1]; linked by [#-20,#-21] summary: [2] 0 1 [A.1510 A.1540 A.1511 A.1538] 1 1 nts=5 UCGCA A.U1510,A.C1511,A.G1538,A.C1539,A.A1540 nts=0 nts=1 C A.C1539 15 bulge: nts=6; [2,0]; linked by [#13,#-5] summary: [2] 2 0 [A.762 A.778 A.765 A.777] 2 1 nts=6 GCACGC A.G762,A.C763,A.A764,A.C765,A.G777,A.C778 nts=2 CA A.C763,A.A764 nts=0 16 bulge: nts=7; [3,0]; linked by [#17,#-7] summary: [2] 3 0 [A.834 A.853 A.838 A.852] 3 1 nts=7 GCAAUAC A.G834,A.C835,A.A836,A.A837,A.U838,A.A852,A.C853 nts=3 CAA A.C835,A.A836,A.A837 nts=0 17 bulge: nts=7; [3,0]; linked by [#32,#33] summary: [2] 3 0 [A.1062 A.1093 A.1066 A.1092] 6 2 nts=7 GACCCGC A.G1062,A.A1063,A.C1064,A.C1065,A.C1066,A.G1092,A.C1093 nts=3 ACC A.A1063,A.C1064,A.C1065 nts=0 18 bulge: nts=7; [0,3]; linked by [#49,#50] summary: [2] 0 3 [A.1262 A.1333 A.1263 A.1329] 2 3 nts=7 CGUCAAG A.C1262,A.G1263,A.U1329,A.C1330,A.A1331,A.A1332,A.G1333 nts=0 nts=3 CAA A.C1330,A.A1331,A.A1332 19 bulge: nts=11; [0,7]; linked by [#52,#53] summary: [2] 0 7 [A.1278 A.1297 A.1279 A.1289] 2 3 nts=11 CCGCUACAAAG A.C1278,A.C1279,A.G1289,A.C1290,A.U1291,A.A1292,A.C1293,A.A1294,A.A1295,A.A1296,A.G1297 nts=0 nts=7 CUACAAA A.C1290,A.U1291,A.A1292,A.C1293,A.A1294,A.A1295,A.A1296 **************************************************************************** List of 27 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#3,#4] summary: [2] 1 1 [A.674 A.923 A.676 A.921] 6 2 nts=6 UAGUCA A.U674,A.A675,A.G676,A.U921,A.C922,A.A923 nts=1 A A.A675 nts=1 C A.C922 2 symmetric internal loop: nts=6; [1,1]; linked by [#28,#29] summary: [2] 1 1 [A.982 A.1006 A.984 A.1004] 3 3 nts=6 ACCGUU A.A982,A.C983,A.C984,A.G1004,A.U1005,A.U1006 nts=1 C A.C983 nts=1 U A.U1005 3 symmetric internal loop: nts=6; [1,1]; linked by [#-12,#35] summary: [2] 1 1 [A.1109 A.1132 A.1111 A.1130] 1 5 nts=6 AACGCU A.A1109,A.A1110,A.C1111,A.G1130,A.C1131,A.U1132 nts=1 A A.A1110 nts=1 C A.C1131 4 symmetric internal loop: nts=6; [1,1]; linked by [#-13,#-14] summary: [2] 1 1 [A.1266 A.1325 A.1268 A.1323] 1 1 nts=6 AUCGUU A.A1266,A.U1267,A.C1268,A.G1323,A.U1324,A.U1325 nts=1 U A.U1267 nts=1 U A.U1324 5 symmetric internal loop: nts=6; [1,1]; linked by [#58,#-19] summary: [2] 1 1 [A.1489 A.1561 A.1491 A.1559] 2 1 nts=6 GUCGUC A.G1489,A.U1490,A.C1491,A.G1559,A.U1560,A.C1561 nts=1 U A.U1490 nts=1 U A.U1560 6 asymmetric internal loop: nts=7; [1,2]; linked by [#10,#-4] summary: [2] 1 2 [A.727 A.747 A.729 A.744] 4 1 nts=7 UCUAAAA A.U727,A.C728,A.U729,A.A744,A.A745,A.A746,A.A747 nts=1 C A.C728 nts=2 AA A.A745,A.A746 7 asymmetric internal loop: nts=7; [2,1]; linked by [#-4,#11] summary: [2] 2 1 [A.729 A.744 A.732 A.742] 1 3 nts=7 UAAAUCA A.U729,A.A730,A.A731,A.A732,A.U742,A.C743,A.A744 nts=2 AA A.A730,A.A731 nts=1 C A.C743 8 asymmetric internal loop: nts=7; [1,2]; linked by [#29,#30] summary: [2] 1 2 [A.986 A.1002 A.988 A.999] 3 2 nts=7 GAGCUCC A.G986,A.A987,A.G988,A.C999,A.U1000,A.C1001,A.C1002 nts=1 A A.A987 nts=2 UC A.U1000,A.C1001 9 asymmetric internal loop: nts=7; [1,2]; linked by [#-17,#-18] summary: [2] 1 2 [A.1483 A.1569 A.1485 A.1566] 1 1 nts=7 CCGCAUG A.C1483,A.C1484,A.G1485,A.C1566,A.A1567,A.U1568,A.G1569 nts=1 C A.C1484 nts=2 AU A.A1567,A.U1568 10 asymmetric internal loop: nts=7; [2,1]; linked by [#59,#60] summary: [2] 2 1 [A.1500 A.1549 A.1503 A.1547] 6 5 nts=7 CAAGUAG A.C1500,A.A1501,A.A1502,A.G1503,A.U1547,A.A1548,A.G1549 nts=2 AA A.A1501,A.A1502 nts=1 A A.A1548 11 asymmetric internal loop: nts=8; [3,1]; linked by [#48,#49] summary: [2] 3 1 [A.1257 A.1336 A.1261 A.1334] 3 2 nts=8 UAUACGUG A.U1257,A.A1258,A.U1259,A.A1260,A.C1261,A.G1334,A.U1335,A.G1336 nts=3 AUA A.A1258,A.U1259,A.A1260 nts=1 U A.U1335 12 symmetric internal loop: nts=8; [2,2]; linked by [#51,#52] summary: [2] 2 2 [A.1274 A.1301 A.1277 A.1298] 2 2 nts=8 CAAAUAAG A.C1274,A.A1275,A.A1276,A.A1277,A.U1298,A.A1299,A.A1300,A.G1301 nts=2 AA A.A1275,A.A1276 nts=2 AA A.A1299,A.A1300 13 symmetric internal loop: nts=8; [2,2]; linked by [#60,#-20] summary: [2] 2 2 [A.1507 A.1543 A.1510 A.1540] 5 1 nts=8 ACUUAUUU A.A1507,A.C1508,A.U1509,A.U1510,A.A1540,A.U1541,A.U1542,A.U1543 nts=2 CU A.C1508,A.U1509 nts=2 UU A.U1541,A.U1542 14 symmetric internal loop: nts=8; [2,2]; linked by [#-21,#61] summary: [2] 2 2 [A.1511 A.1538 A.1514 A.1535] 1 3 nts=8 CAAAUACG A.C1511,A.A1512,A.A1513,A.A1514,A.U1535,A.A1536,A.C1537,A.G1538 nts=2 AA A.A1512,A.A1513 nts=2 AC A.A1536,A.C1537 15 asymmetric internal loop: nts=9; [2,3]; linked by [#-18,#58] summary: [2] 2 3 [A.1485 A.1566 A.1488 A.1562] 1 2 nts=9 GcCcGUAAC A.G1485,A.B8T1486,A.C1487,A.5MC1488,A.G1562,A.U1563,A.A1564,A.A1565,A.C1566 nts=2 cC A.B8T1486,A.C1487 nts=3 UAA A.U1563,A.A1564,A.A1565 16 symmetric internal loop: nts=10; [3,3]; linked by [#33,#34] summary: [2] 3 3 [A.1067 A.1091 A.1071 A.1087] 2 4 nts=10 AAACUACUAU A.A1067,A.A1068,A.A1069,A.C1070,A.U1071,A.A1087,A.C1088,A.U1089,A.A1090,A.U1091 nts=3 AAC A.A1068,A.A1069,A.C1070 nts=3 CUA A.C1088,A.U1089,A.A1090 17 asymmetric internal loop: nts=11; [3,4]; linked by [#25,#26] summary: [2] 3 4 [A.946 A.1049 A.950 A.1044] 4 3 nts=11 UUUUAUGAACA A.U946,A.U947,A.U948,A.U949,A.A950,A.U1044,A.G1045,A.A1046,A.A1047,A.C1048,A.A1049 nts=3 UUU A.U947,A.U948,A.U949 nts=4 GAAC A.G1045,A.A1046,A.A1047,A.C1048 18 asymmetric internal loop: nts=11; [3,4]; linked by [#-19,#59] summary: [2] 3 4 [A.1491 A.1559 A.1495 A.1554] 1 6 nts=11 CACCCGACAAG A.C1491,A.A1492,A.C1493,A.C1494,A.C1495,A.G1554,A.A1555,A.C1556,A.A1557,A.A1558,A.G1559 nts=3 ACC A.A1492,A.C1493,A.C1494 nts=4 ACAA A.A1555,A.C1556,A.A1557,A.A1558 19 asymmetric internal loop: nts=11; [4,3]; linked by [#61,#62] summary: [2] 4 3 [A.1516 A.1533 A.1521 A.1529] 3 2 nts=11 GACAUUAACCC A.G1516,A.A1517,A.C1518,A.A1519,A.U1520,A.U1521,A.A1529,A.A1530,A.C1531,A.C1532,A.C1533 nts=4 ACAU A.A1517,A.C1518,A.A1519,A.U1520 nts=3 ACC A.A1530,A.C1531,A.C1532 20 symmetric internal loop: nts=12; [4,4]; linked by [#40,#41] summary: [2] 4 4 [A.1185 A.1469 A.1190 A.1464] 6 3 nts=12 CAUAUCGCCCUG A.C1185,A.A1186,A.U1187,A.A1188,A.U1189,A.C1190,A.G1464,A.C1465,A.C1466,A.C1467,A.U1468,A.G1469 nts=4 AUAU A.A1186,A.U1187,A.A1188,A.U1189 nts=4 CCCU A.C1465,A.C1466,A.C1467,A.U1468 21 symmetric internal loop: nts=12; [4,4]; linked by [#-16,#56] summary: [2] 4 4 [A.1388 A.1418 A.1393 A.1413] 1 7 nts=12 CGAUAGUCGAAG A.C1388,A.G1389,A.A1390,A.U1391,A.A1392,A.G1393,A.U1413,A.C1414,A.G1415,A.A1416,A.A1417,A.G1418 nts=4 GAUA A.G1389,A.A1390,A.U1391,A.A1392 nts=4 CGAA A.C1414,A.G1415,A.A1416,A.A1417 22 asymmetric internal loop: nts=14; [4,6]; linked by [#12,#13] summary: [2] 4 6 [A.756 A.786 A.761 A.779] 4 2 nts=14 CAUCAAUCAAAACG A.C756,A.A757,A.U758,A.C759,A.A760,A.A761,A.U779,A.C780,A.A781,A.A782,A.A783,A.A784,A.C785,A.G786 nts=4 AUCA A.A757,A.U758,A.C759,A.A760 nts=6 CAAAAC A.C780,A.A781,A.A782,A.A783,A.A784,A.C785 23 symmetric internal loop: nts=14; [5,5]; linked by [#-9,#28] summary: [2] 5 5 [A.974 A.1014 A.980 A.1008] 1 3 nts=14 UAAAACUACACAAA A.U974,A.A975,A.A976,A.A977,A.A978,A.C979,A.U980,A.A1008,A.C1009,A.A1010,A.C1011,A.A1012,A.A1013,A.A1014 nts=5 AAAAC A.A975,A.A976,A.A977,A.A978,A.C979 nts=5 CACAA A.C1009,A.A1010,A.C1011,A.A1012,A.A1013 24 asymmetric internal loop: nts=15; [7,4]; linked by [#46,#47] summary: [2] 7 4 [A.1244 A.1345 A.1252 A.1340] 7 2 nts=15 CUUGCUCAGCCCAUG A.C1244,A.U1245,A.U1246,A.G1247,A.C1248,A.U1249,A.C1250,A.A1251,A.G1252,A.C1340,A.C1341,A.C1342,A.A1343,A.U1344,A.G1345 nts=7 UUGCUCA A.U1245,A.U1246,A.G1247,A.C1248,A.U1249,A.C1250,A.A1251 nts=4 CCAU A.C1341,A.C1342,A.A1343,A.U1344 25 asymmetric internal loop: nts=16; [5,7]; linked by [#21,#22] summary: [2] 5 7 [A.887 A.908 A.893 A.900] 3 2 nts=16 GUGCCAGCGGUCACAC A.G887,A.U888,A.G889,A.C890,A.C891,A.A892,A.G893,A.C900,A.G901,A.G902,A.U903,A.C904,A.A905,A.C906,A.A907,A.C908 nts=5 UGCCA A.U888,A.G889,A.C890,A.C891,A.A892 nts=7 GGUCACA A.G901,A.G902,A.U903,A.C904,A.A905,A.C906,A.A907 26 asymmetric internal loop: nts=16; [7,5]; linked by [#36,#37] summary: [2] 7 5 [A.1139 A.1164 A.1147 A.1158] 2 4 nts=16 AACACUACGUAAAACU A.A1139,A.A1140,A.C1141,A.A1142,A.C1143,A.U1144,A.A1145,A.C1146,A.G1147,A.U1158,A.A1159,A.A1160,A.A1161,A.A1162,A.C1163,A.U1164 nts=7 ACACUAC A.A1140,A.C1141,A.A1142,A.C1143,A.U1144,A.A1145,A.C1146 nts=5 AAAAC A.A1159,A.A1160,A.A1161,A.A1162,A.C1163 27 asymmetric internal loop: nts=24; [15,5]; linked by [#26,#27] summary: [2] 15 5 [A.952 A.1042 A.968 A.1036] 3 6 nts=24 AUCACCCCCUCCCCAAUAACAUAU A.A952,A.U953,A.C954,A.A955,A.C956,A.C957,A.C958,A.C959,A.C960,A.U961,A.C962,A.C963,A.C964,A.C965,A.A966,A.A967,A.U968,A.A1036,A.A1037,A.C1038,A.A1039,A.U1040,A.A1041,A.U1042 nts=15 UCACCCCCUCCCCAA A.U953,A.C954,A.A955,A.C956,A.C957,A.C958,A.C959,A.C960,A.U961,A.C962,A.C963,A.C964,A.C965,A.A966,A.A967 nts=5 ACAUA A.A1037,A.C1038,A.A1039,A.U1040,A.A1041 **************************************************************************** List of 13 junctions 1 3-way junction: nts=11; [0,5,0]; linked by [#27,#-9,#-10] summary: [3] 0 5 0 [A.973 A.1031 A.974 A.1014 A.1020 A.1030] 6 1 1 nts=11 CUAAUAGACGG A.C973,A.U974,A.A1014,A.A1015,A.U1016,A.A1017,A.G1018,A.A1019,A.C1020,A.G1030,A.G1031 nts=0 nts=5 AUAGA A.A1015,A.U1016,A.A1017,A.G1018,A.A1019 nts=0 2 3-way junction: nts=11; [2,1,2]; linked by [#42,#43,#-15] summary: [3] 2 1 2 [A.1198 A.1424 A.1201 A.1364 A.1366 A.1421] 5 8 1 nts=11 AGGAUACGGAU A.A1198,A.G1199,A.G1200,A.A1201,A.U1364,A.A1365,A.C1366,A.G1421,A.G1422,A.A1423,A.U1424 nts=2 GG A.G1199,A.G1200 nts=1 A A.A1365 nts=2 GA A.G1422,A.A1423 3 3-way junction: nts=15; [2,5,2]; linked by [#4,#5,#19] summary: [3] 2 5 2 [A.677 A.920 A.680 A.866 A.872 A.917] 2 6 5 nts=15 CUCUACCCCAGCAAG A.C677,A.U678,A.C679,A.U680,A.A866,A.C867,A.C868,A.C869,A.C870,A.A871,A.G872,A.C917,A.A918,A.A919,A.G920 nts=2 UC A.U678,A.C679 nts=5 CCCCA A.C867,A.C868,A.C869,A.C870,A.A871 nts=2 AA A.A918,A.A919 4 3-way junction: nts=15; [2,6,1]; linked by [#6,#-2,#-6] summary: [3] 2 6 1 [A.687 A.858 A.690 A.823 A.830 A.856] 2 1 1 nts=15 GAUUAUUAACCUAGC A.G687,A.A688,A.U689,A.U690,A.A823,A.U824,A.U825,A.A826,A.A827,A.C828,A.C829,A.U830,A.A856,A.G857,A.C858 nts=2 AU A.A688,A.U689 nts=6 UUAACC A.U824,A.U825,A.A826,A.A827,A.C828,A.C829 nts=1 G A.G857 5 3-way junction: nts=16; [3,5,2]; linked by [#-15,#55,#-16] summary: [3] 3 5 2 [A.1366 A.1421 A.1370 A.1382 A.1388 A.1418] 1 4 1 nts=16 CAUUUAAACUACGGUG A.C1366,A.A1367,A.U1368,A.U1369,A.U1370,A.A1382,A.A1383,A.A1384,A.C1385,A.U1386,A.A1387,A.C1388,A.G1418,A.G1419,A.U1420,A.G1421 nts=3 AUU A.A1367,A.U1368,A.U1369 nts=5 AACUA A.A1383,A.A1384,A.C1385,A.U1386,A.A1387 nts=2 GU A.G1419,A.U1420 6 3-way junction: nts=17; [1,5,5]; linked by [#41,#42,#57] summary: [3] 1 5 5 [A.1192 A.1462 A.1194 A.1428 A.1434 A.1456] 3 5 7 nts=17 CUCGCAGUAAUGAACAG A.C1192,A.U1193,A.C1194,A.G1428,A.C1429,A.A1430,A.G1431,A.U1432,A.A1433,A.A1434,A.U1456,A.G1457,A.A1458,A.A1459,A.C1460,A.A1461,A.G1462 nts=1 U A.U1193 nts=5 CAGUA A.C1429,A.A1430,A.G1431,A.U1432,A.A1433 nts=5 GAACA A.G1457,A.A1458,A.A1459,A.C1460,A.A1461 7 3-way junction: nts=20; [4,5,5]; linked by [#-14,#51,#54] summary: [3] 4 5 5 [A.1268 A.1323 A.1273 A.1302 A.1308 A.1317] 1 2 3 nts=20 CUUCAGCGCAAGUAAAGACG A.C1268,A.U1269,A.U1270,A.C1271,A.A1272,A.G1273,A.C1302,A.G1303,A.C1304,A.A1305,A.A1306,A.G1307,A.U1308,A.A1317,A.A1318,A.A1319,A.G1320,A.A1321,A.C1322,A.G1323 nts=4 UUCA A.U1269,A.U1270,A.C1271,A.A1272 nts=5 GCAAG A.G1303,A.C1304,A.A1305,A.A1306,A.G1307 nts=5 AAGAC A.A1318,A.A1319,A.G1320,A.A1321,A.C1322 8 3-way junction: nts=23; [5,10,2]; linked by [#44,#45,#46] summary: [3] 5 10 2 [A.1210 A.1354 A.1216 A.1227 A.1238 A.1351] 2 2 7 nts=23 UGUAAUCGAUCAACCUCACGCAA A.U1210,A.G1211,A.U1212,A.A1213,A.A1214,A.U1215,A.C1216,A.G1227,A.A1228,A.U1229,A.C1230,A.A1231,A.A1232,A.C1233,A.C1234,A.U1235,A.C1236,A.A1237,A.C1238,A.G1351,A.C1352,A.A1353,A.A1354 nts=5 GUAAU A.G1211,A.U1212,A.A1213,A.A1214,A.U1215 nts=10 AUCAACCUCA A.A1228,A.U1229,A.C1230,A.A1231,A.A1232,A.C1233,A.C1234,A.U1235,A.C1236,A.A1237 nts=2 CA A.C1352,A.A1353 9 4-way junction: nts=17; [6,2,1,0]; linked by [#9,#10,#12,#15] summary: [4] 6 2 1 0 [A.717 A.798 A.724 A.750 A.753 A.789 A.791 A.797] 3 4 4 2 nts=17 GAGUUCACGACAUAGCC A.G717,A.A718,A.G719,A.U720,A.U721,A.C722,A.A723,A.C724,A.G750,A.A751,A.C752,A.A753,A.U789,A.A790,A.G791,A.C797,A.C798 nts=6 AGUUCA A.A718,A.G719,A.U720,A.U721,A.C722,A.A723 nts=2 AC A.A751,A.C752 nts=1 A A.A790 nts=0 10 4-way junction: nts=22; [2,6,1,5]; linked by [#8,#-3,#9,#16] summary: [4] 2 6 1 5 [A.698 A.817 A.701 A.708 A.715 A.800 A.802 A.811] 3 1 3 3 nts=22 CAAGCGUUCCAGCACGAAACAG A.C698,A.A699,A.A700,A.G701,A.C708,A.G709,A.U710,A.U711,A.C712,A.C713,A.A714,A.G715,A.C800,A.A801,A.C802,A.G811,A.A812,A.A813,A.A814,A.C815,A.A816,A.G817 nts=2 AA A.A699,A.A700 nts=6 GUUCCA A.G709,A.U710,A.U711,A.C712,A.C713,A.A714 nts=1 A A.A801 nts=5 AAACA A.A812,A.A813,A.A814,A.C815,A.A816 11 4-way junction: nts=23; [1,4,10,0]; linked by [#-8,#25,#32,#-12] summary: [4] 1 4 10 0 [A.941 A.1133 A.943 A.1052 A.1057 A.1098 A.1109 A.1132] 1 4 6 1 nts=23 GAGCAAUAGCCCUAAACCUCAUC A.G941,A.A942,A.G943,A.C1052,A.A1053,A.A1054,A.U1055,A.A1056,A.G1057,A.C1098,A.C1099,A.C1100,A.U1101,A.A1102,A.A1103,A.A1104,A.C1105,A.C1106,A.U1107,A.C1108,A.A1109,A.U1132,A.C1133 nts=1 A A.A942 nts=4 AAUA A.A1053,A.A1054,A.U1055,A.A1056 nts=10 CCUAAACCUC A.C1099,A.C1100,A.U1101,A.A1102,A.A1103,A.A1104,A.C1105,A.C1106,A.U1107,A.C1108 nts=0 12* 5-way junction: nts=18; [0,0,1,5,2]; linked by [#19,#20,#22,#20,#21] summary: [5] 0 0 1 5 2 [A.876 A.913 A.877 A.898 A.899 A.894 A.896 A.879 A.885 A.910] 5 3 2 3 3 nts=18 UGCGCCAUCAAUUUAUUA A.U876,A.G877,A.C898,A.G899,A.C894,A.C895,A.A896,A.U879,A.C880,A.A881,A.A882,A.U883,A.U884,A.U885,A.A910,A.U911,A.U912,A.A913 nts=0 nts=0 nts=1 C A.C895 nts=5 CAAUU A.C880,A.A881,A.A882,A.U883,A.U884 nts=2 UU A.U911,A.U912 13* 5-way junction: nts=21; [0,2,6,3,0]; linked by [#23,#24,#35,#24,#-8] summary: [5] 0 2 6 3 0 [A.935 A.1134 A.936 A.1123 A.1126 A.1115 A.1122 A.937 A.941 A.1133] 3 2 5 2 1 nts=21 CGCAAAUAAAUCAAUAAAGCG A.C935,A.G936,A.C1123,A.A1124,A.A1125,A.A1126,A.U1115,A.A1116,A.A1117,A.A1118,A.U1119,A.C1120,A.A1121,A.A1122,A.U937,A.A938,A.A939,A.A940,A.G941,A.C1133,A.G1134 nts=0 nts=2 AA A.A1124,A.A1125 nts=6 AAAUCA A.A1116,A.A1117,A.A1118,A.U1119,A.C1120,A.A1121 nts=3 AAA A.A938,A.A939,A.A940 nts=0 **************************************************************************** List of 8 non-loop single-stranded segments 1 nts=1 A A.A648 2 nts=4 AGCC A.A929,A.G930,A.C931,A.C932 3 nts=1 A A.A1137 4 nts=3 AAA A.A1166,A.A1167,A.A1168 5 nts=2 CA A.C1481,A.A1482 6 nts=2 GU A.G1570,A.U1571 7 nts=8 GACGAACC A.G1595,A.A1596,A.C1597,A.G1598,A.A1599,A.A1600,A.C1601,A.C1602 8 nts=2* ag X.ATP402,X.GNP403 **************************************************************************** List of 41 A-minor motifs (types I, II, or X) 1 type=X A|G-C A.A691|A.G715,A.C800 WC +A.G715 H-bonds[0]: "" -A.C800 H-bonds[2]: "N6(amino)-O2(carbonyl)[3.10],N1-O2'(hydroxyl)[3.19]" 2 type=X A|U-A A.A691|A.U716,A.A799 WC +A.U716 H-bonds[2]: "N7-O2'(hydroxyl)[2.62],N6(amino)-O2(carbonyl)[2.53]" -A.A799 H-bonds[0]: "" 3 type=X A|C-G A.A695|A.C694,A.G820 WC +A.C694 H-bonds[0]: "" -A.G820 H-bonds[2]: "N7-N2(amino)[3.21],N6(amino)-N3[3.43]" 4 type=X A|U-A A.A718|A.U716,A.A799 WC +A.U716 H-bonds[0]: "" -A.A799 H-bonds[2]: "N6(amino)-N3[2.88],N1-O2'(hydroxyl)[3.27]" 5 type=X A|G-C A.A723|A.G791,A.C797 WC +A.G791 H-bonds[1]: "N1-N2(amino)[3.59]" -A.C797 H-bonds[1]: "N3-O2'(hydroxyl)[3.18]" 6 type=X A|U-A A.A730|A.U729,A.A744 WC +A.U729 H-bonds[1]: "O4'-O2'(hydroxyl)[3.34]" -A.A744 H-bonds[1]: "N6(amino)-N3[3.24]" 7 type=X A|U-A A.A745|A.U729,A.A744 WC -A.U729 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.36]" +A.A744 H-bonds[1]: "O4'-O2'(hydroxyl)[3.13]" 8 type=I A|A-U A.A784|A.A761,A.U779 WC +A.A761 H-bonds[1]: "N1-O2'(hydroxyl)[2.69]" -A.U779 H-bonds[1]: "O2'(hydroxyl)-O2(carbonyl)[3.25]" 9 type=I A|G-C A.A816|A.G715,A.C800 WC -A.G715 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[3.00],O2'(hydroxyl)-N3[2.90],N3-N2(amino)[3.34]" +A.C800 H-bonds[0]: "" 10 type=X A|A-U A.A836|A.A833,A.U854 WC +A.A833 H-bonds[0]: "" -A.U854 H-bonds[2]: "N6(amino)-O2(carbonyl)[2.66],N1-O2'(hydroxyl)[3.08]" 11 type=X A|G-C A.A836|A.G834,A.C853 WC +A.G834 H-bonds[2]: "N7-O2'(hydroxyl)[3.29],N6(amino)-N3[3.29]" -A.C853 H-bonds[0]: "" 12 type=X A|G-C A.A837|A.G834,A.C853 WC +A.G834 H-bonds[0]: "" -A.C853 H-bonds[2]: "N6(amino)-O2(carbonyl)[2.86],N1-O2'(hydroxyl)[2.91]" 13 type=II A|G-C A.A881|A.G874,A.C915 WC +A.G874 H-bonds[0]: "" -A.C915 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.65],N3-O2'(hydroxyl)[2.86]" 14 type=I A|U-A A.A882|A.U875,A.A914 WC +A.U875 H-bonds[1]: "N1-O2'(hydroxyl)[3.08]" -A.A914 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.09],O2'(hydroxyl)-N3[3.36]" 15 type=I A|C-G A.A907|A.C894,A.G899 WC -A.C894 H-bonds[0]: "" +A.G899 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.32],N1-O2'(hydroxyl)[2.56]" 16 type=I A|C-G A.A938|A.C661,A.G1169 WC +A.C661 H-bonds[1]: "N1-O2'(hydroxyl)[2.97]" -A.G1169 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.06],N3-N2(amino)[3.46]" 17 type=II A|G-C A.A939|A.G933,A.C1136 WC +A.G933 H-bonds[0]: "" -A.C1136 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.99],N3-O2'(hydroxyl)[2.96]" 18 type=I A|G-C A.A940|A.G934,A.C1135 WC +A.G934 H-bonds[2]: "N1-O2'(hydroxyl)[2.61],N3-N2(amino)[3.34]" -A.C1135 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.52],O2'(hydroxyl)-O2(carbonyl)[2.86]" 19 type=X A|G-C A.A996|A.G1073,A.C1085 WC -A.G1073 H-bonds[0]: "" +A.C1085 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.07],N1*O2(carbonyl)[3.31]" 20 type=II A|U-A A.A1025|A.U944,A.A1051 WC -A.U944 H-bonds[3]: "O2'(hydroxyl)-O3'[3.19],O2'(hydroxyl)-O2'(hydroxyl)[2.67],N3-O2'(hydroxyl)[3.15]" +A.A1051 H-bonds[0]: "" 21 type=I A|G-C A.A1026|A.G943,A.C1052 WC -A.G943 H-bonds[1]: "N3-N2(amino)[3.50]" +A.C1052 H-bonds[1]: "N1-O2'(hydroxyl)[3.10]" 22 type=X A|U-A A.A1054|A.U1575,A.A1590 WC +A.U1575 H-bonds[0]: "" -A.A1590 H-bonds[1]: "N3-O2'(hydroxyl)[3.49]" 23 type=I A|U-A A.A1102|A.U1575,A.A1590 WC -A.U1575 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.99]" +A.A1590 H-bonds[0]: "" 24 type=X A|U-A A.A1116|A.U1114,A.A1127 WC -A.U1114 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.93]" +A.A1127 H-bonds[0]: "" 25 type=X A|C-G A.A1121|A.C660,A.G1170 WC -A.C660 H-bonds[1]: "N3-O2'(hydroxyl)[3.15]" +A.G1170 H-bonds[1]: "N1-N2(amino)[2.91]" 26 type=X A|C-G A.A1162|A.C1497,A.G1552 WC -A.C1497 H-bonds[1]: "N3-O2'(hydroxyl)[2.68]" +A.G1552 H-bonds[0]: "" 27 type=I A|U-G A.A1166|A.U654,A.G664 Wobble -A.U654 H-bonds[0]: "" +A.G664 H-bonds[2]: "N1-O2'(hydroxyl)[2.80],N3-N2(amino)[3.40]" 28 type=II A|C-G A.A1213|A.C1239,A.G1350 WC -A.C1239 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.89],N3-O2'(hydroxyl)[2.72]" +A.G1350 H-bonds[0]: "" 29 type=I A|C-G A.A1214|A.C1238,A.G1351 WC -A.C1238 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.00],O2'(hydroxyl)-O2(carbonyl)[3.01]" +A.G1351 H-bonds[2]: "N1-O2'(hydroxyl)[3.04],N3-N2(amino)[3.26]" 30 type=I A|G-C A.A1286|A.G658,A.C1172 WC -A.G658 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.87]" +A.C1172 H-bonds[1]: "N1-O2'(hydroxyl)[3.15]" 31 type=I A|C-G A.A1296|A.C1279,A.G1289 WC +A.C1279 H-bonds[1]: "N1-O2'(hydroxyl)[2.85]" -A.G1289 H-bonds[1]: "O3'-O2'(hydroxyl)[3.51]" 32 type=X A|G-U A.A1332|A.G1263,A.U1329 Wobble -A.G1263 H-bonds[2]: "N7-N2(amino)[3.35],N6(amino)-N3[3.51]" +A.U1329 H-bonds[1]: "OP1-O2'(hydroxyl)[3.12]" 33 type=X A|C-G A.A1356|A.C1209,A.G1355 WC -A.C1209 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.24]" +A.G1355 H-bonds[1]: "N7-N2(amino)[3.24]" 34 type=II A|U-A A.A1367|A.U1370,A.A1382 WC -A.U1370 H-bonds[1]: "N3-O2'(hydroxyl)[2.61]" +A.A1382 H-bonds[0]: "" 35 type=X A|A-U A.A1417|A.A1201,A.U1364 WC -A.A1201 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.15],N3-O2'(hydroxyl)[2.50]" +A.U1364 H-bonds[0]: "" 36 type=II A|C-G A.A1459|A.C1194,A.G1428 WC -A.C1194 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.57],N3-O2'(hydroxyl)[3.12]" +A.G1428 H-bonds[0]: "" 37 type=X A|c-A A.A1478|A.B8T1486,A.A1565 ~Wobble -A.B8T1486 H-bonds[0]: "" +A.A1565 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.02],N1-O2'(hydroxyl)[2.87]" 38 type=I A|G-C A.A1482|A.G1175,A.C1479 WC +A.G1175 H-bonds[2]: "N1-O2'(hydroxyl)[3.10],N3-N2(amino)[3.20]" -A.C1479 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.65],O2'(hydroxyl)-O2(carbonyl)[3.01]" 39 type=I A|C-G A.A1567|A.C1177,A.G1476 WC +A.C1177 H-bonds[1]: "N1-O2'(hydroxyl)[2.91]" -A.G1476 H-bonds[2]: "O5'-O2'(hydroxyl)[3.11],N3-N2(amino)[3.60]" 40 type=I a|c-G A.MA6/1583|A.5MC1488,A.G1562 WC -A.5MC1488 H-bonds[0]: "" +A.G1562 H-bonds[1]: "N1-O2'(hydroxyl)[2.92]" 41 type=I a|c-G A.MA6/1584|A.5MC1488,A.G1562 WC -A.5MC1488 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.63],O2'(hydroxyl)-O2(carbonyl)[2.20]" +A.G1562 H-bonds[1]: "N3-N2(amino)[3.06]" **************************************************************************** List of 9 ribose zippers 1 nts=4 GUGA A.G658,A.U659,A.G1285,A.A1286 2 nts=4 AGAG A.A714,A.G715,A.A816,A.G817 3 nts=4 AAAC A.A881,A.A882,A.A914,A.C915 4 nts=4 AACC A.A939,A.A940,A.C1135,A.C1136 5 nts=4 UAUG A.U1101,A.A1102,A.U1575,A.G1576 6 nts=4 ACUC A.A1162,A.C1163,A.U1496,A.C1497 7 nts=4 AACC A.A1213,A.A1214,A.C1238,A.C1239 8 nts=4 CGGA A.C1302,A.G1303,A.G1320,A.A1321 9 nts=4 cGaa A.5MC1488,A.G1489,A.MA6/1583,A.MA6/1584 **************************************************************************** List of 158 splayed-apart dinucleotides 1 A.U655 A.U656 angle=94 distance=14.3 ratio=0.73 2 A.C679 A.U680 angle=85 distance=13.4 ratio=0.68 3 A.G687 A.A688 angle=105 distance=16.0 ratio=0.80 4 A.U690 A.A691 angle=133 distance=17.5 ratio=0.92 5 A.A691 A.C692 angle=111 distance=17.6 ratio=0.83 6 A.A699 A.A700 angle=114 distance=14.0 ratio=0.84 7 A.A703 A.U704 angle=96 distance=14.9 ratio=0.74 8 A.C705 A.C706 angle=90 distance=13.9 ratio=0.71 9 A.U711 A.C712 angle=112 distance=16.2 ratio=0.83 10 A.U720 A.U721 angle=94 distance=13.9 ratio=0.74 11 A.U721 A.C722 angle=156 distance=18.6 ratio=0.98 12 A.A723 A.C724 angle=92 distance=13.8 ratio=0.72 13 A.C734 A.A735 angle=103 distance=13.7 ratio=0.78 14 A.A757 A.U758 angle=133 distance=18.0 ratio=0.92 15 A.U758 A.C759 angle=155 distance=18.8 ratio=0.98 16 A.A781 A.A782 angle=134 distance=17.1 ratio=0.92 17 A.A782 A.A783 angle=100 distance=14.9 ratio=0.76 18 A.C793 A.U794 angle=119 distance=16.6 ratio=0.86 19 A.U794 A.A795 angle=134 distance=17.9 ratio=0.92 20 A.A795 A.G796 angle=119 distance=16.8 ratio=0.86 21 A.A801 A.C802 angle=166 distance=18.5 ratio=0.99 22 A.C804 A.C805 angle=104 distance=14.2 ratio=0.79 23 A.A814 A.C815 angle=149 distance=18.5 ratio=0.96 24 A.C815 A.A816 angle=157 distance=17.6 ratio=0.98 25 A.A816 A.G817 angle=149 distance=17.2 ratio=0.96 26 A.A827 A.C828 angle=88 distance=13.1 ratio=0.69 27 A.C828 A.C829 angle=160 distance=18.9 ratio=0.99 28 A.U830 A.U831 angle=122 distance=18.1 ratio=0.88 29 A.U831 A.U832 angle=144 distance=20.2 ratio=0.95 30 A.U850 A.A851 angle=152 distance=17.5 ratio=0.97 31 A.A851 A.A852 angle=110 distance=16.9 ratio=0.82 32 A.U859 A.A860 angle=125 distance=15.4 ratio=0.89 33 A.A860 A.U861 angle=122 distance=14.9 ratio=0.87 34 A.U876 A.G877 angle=156 distance=17.7 ratio=0.98 35 A.G889 A.C890 angle=86 distance=14.4 ratio=0.68 36 A.C890 A.C891 angle=88 distance=14.4 ratio=0.70 37 A.G902 A.U903 angle=148 distance=18.7 ratio=0.96 38 A.U903 A.C904 angle=147 distance=17.7 ratio=0.96 39 A.C904 A.A905 angle=110 distance=14.2 ratio=0.82 40 A.A905 A.C906 angle=112 distance=16.1 ratio=0.83 41 A.A907 A.C908 angle=109 distance=15.2 ratio=0.81 42 A.G930 A.C931 angle=119 distance=17.0 ratio=0.86 43 A.C932 A.G933 angle=108 distance=15.4 ratio=0.81 44 A.C935 A.G936 angle=166 distance=17.7 ratio=0.99 45 A.A942 A.G943 angle=110 distance=14.9 ratio=0.82 46 A.U961 A.C962 angle=106 distance=15.4 ratio=0.80 47 A.A966 A.A967 angle=133 distance=18.1 ratio=0.92 48 A.U1000 A.C1001 angle=169 distance=18.4 ratio=1.00 49 A.C1001 A.C1002 angle=125 distance=15.6 ratio=0.89 50 A.A1010 A.C1011 angle=89 distance=14.4 ratio=0.70 51 A.C1011 A.A1012 angle=142 distance=17.2 ratio=0.95 52 A.A1014 A.A1015 angle=96 distance=15.9 ratio=0.75 53 A.G1018 A.A1019 angle=143 distance=18.3 ratio=0.95 54 A.A1019 A.C1020 angle=119 distance=17.0 ratio=0.86 55 A.G1030 A.G1031 angle=168 distance=19.1 ratio=0.99 56 A.C1038 A.A1039 angle=131 distance=17.1 ratio=0.91 57 A.U1040 A.A1041 angle=111 distance=15.0 ratio=0.83 58 A.A1041 A.U1042 angle=142 distance=18.8 ratio=0.95 59 A.A1046 A.A1047 angle=94 distance=13.6 ratio=0.73 60 A.C1048 A.A1049 angle=101 distance=14.9 ratio=0.77 61 A.A1053 A.A1054 angle=85 distance=12.6 ratio=0.68 62 A.A1080 A.U1081 angle=94 distance=14.9 ratio=0.73 63 A.U1081 A.A1082 angle=105 distance=17.1 ratio=0.79 64 A.A1102 A.A1103 angle=93 distance=15.1 ratio=0.73 65 A.A1103 A.A1104 angle=146 distance=19.6 ratio=0.96 66 A.A1104 A.C1105 angle=113 distance=16.1 ratio=0.83 67 A.C1105 A.C1106 angle=127 distance=17.6 ratio=0.90 68 A.C1106 A.U1107 angle=123 distance=18.8 ratio=0.88 69 A.U1107 A.C1108 angle=95 distance=14.5 ratio=0.74 70 A.C1108 A.A1109 angle=145 distance=17.8 ratio=0.95 71 A.A1118 A.U1119 angle=94 distance=13.7 ratio=0.73 72 A.C1120 A.A1121 angle=98 distance=14.7 ratio=0.76 73 A.A1125 A.A1126 angle=100 distance=14.8 ratio=0.77 74 A.A1137 A.G1138 angle=158 distance=18.9 ratio=0.98 75 A.A1142 A.C1143 angle=143 distance=17.8 ratio=0.95 76 A.C1143 A.U1144 angle=144 distance=17.1 ratio=0.95 77 A.C1150 A.C1151 angle=121 distance=16.6 ratio=0.87 78 A.C1151 A.A1152 angle=141 distance=15.0 ratio=0.95 79 A.C1153 A.A1154 angle=174 distance=19.4 ratio=1.00 80 A.A1154 A.G1155 angle=140 distance=17.7 ratio=0.94 81 A.G1178 A.G1179 angle=127 distance=16.7 ratio=0.89 82 A.G1179 A.U1180 angle=129 distance=18.6 ratio=0.90 83 A.A1186 A.U1187 angle=85 distance=13.5 ratio=0.68 84 A.A1214 A.U1215 angle=120 distance=18.0 ratio=0.86 85 A.U1219 A.A1220 angle=170 distance=19.4 ratio=1.00 86 A.A1222 A.C1223 angle=110 distance=17.5 ratio=0.82 87 A.C1224 A.C1225 angle=144 distance=18.9 ratio=0.95 88 A.C1225 A.C1226 angle=98 distance=15.8 ratio=0.75 89 A.A1228 A.U1229 angle=131 distance=17.9 ratio=0.91 90 A.U1229 A.C1230 angle=117 distance=17.5 ratio=0.85 91 A.A1231 A.A1232 angle=136 distance=17.8 ratio=0.93 92 A.U1245 A.U1246 angle=98 distance=14.9 ratio=0.75 93 A.G1247 A.C1248 angle=90 distance=15.4 ratio=0.71 94 A.U1249 A.C1250 angle=141 distance=18.1 ratio=0.94 95 A.C1250 A.A1251 angle=140 distance=19.8 ratio=0.94 96 A.C1253 A.C1254 angle=156 distance=18.0 ratio=0.98 97 A.C1254 A.U1255 angle=116 distance=17.9 ratio=0.85 98 A.A1258 A.U1259 angle=150 distance=19.0 ratio=0.97 99 A.U1259 A.A1260 angle=154 distance=18.5 ratio=0.98 100 A.U1269 A.U1270 angle=152 distance=19.0 ratio=0.97 101 A.U1270 A.C1271 angle=127 distance=18.8 ratio=0.90 102 A.G1282 A.A1283 angle=114 distance=15.1 ratio=0.84 103 A.A1283 A.U1284 angle=128 distance=17.1 ratio=0.90 104 A.U1284 A.G1285 angle=170 distance=18.9 ratio=1.00 105 A.G1289 A.C1290 angle=115 distance=15.3 ratio=0.84 106 A.U1291 A.A1292 angle=123 distance=17.0 ratio=0.88 107 A.A1292 A.C1293 angle=157 distance=18.8 ratio=0.98 108 A.C1293 A.A1294 angle=144 distance=18.1 ratio=0.95 109 A.A1294 A.A1295 angle=105 distance=14.7 ratio=0.80 110 A.A1295 A.A1296 angle=148 distance=18.6 ratio=0.96 111 A.A1313 A.C1314 angle=90 distance=13.5 ratio=0.71 112 A.G1320 A.A1321 angle=107 distance=13.6 ratio=0.81 113 A.U1325 A.A1326 angle=102 distance=16.5 ratio=0.78 114 A.A1326 A.G1327 angle=124 distance=15.6 ratio=0.88 115 A.C1330 A.A1331 angle=150 distance=18.8 ratio=0.97 116 A.A1331 A.A1332 angle=153 distance=18.8 ratio=0.97 117 A.C1341 A.C1342 angle=150 distance=18.9 ratio=0.97 118 A.U1344 A.G1345 angle=119 distance=16.0 ratio=0.86 119 A.A1353 A.A1354 angle=117 distance=15.4 ratio=0.85 120 A.C1366 A.A1367 angle=139 distance=16.8 ratio=0.94 121 A.U1368 A.U1369 angle=163 distance=18.8 ratio=0.99 122 A.U1369 A.U1370 angle=124 distance=17.0 ratio=0.88 123 A.C1377 A.C1378 angle=151 distance=18.2 ratio=0.97 124 A.C1378 A.A1379 angle=133 distance=17.6 ratio=0.92 125 A.A1383 A.A1384 angle=101 distance=14.1 ratio=0.77 126 A.A1384 A.C1385 angle=87 distance=13.4 ratio=0.69 127 A.C1385 A.U1386 angle=177 distance=18.8 ratio=1.00 128 A.U1386 A.A1387 angle=136 distance=17.2 ratio=0.93 129 A.A1390 A.U1391 angle=123 distance=16.9 ratio=0.88 130 A.U1391 A.A1392 angle=124 distance=16.8 ratio=0.88 131 A.G1415 A.A1416 angle=93 distance=14.2 ratio=0.73 132 A.G1419 A.U1420 angle=89 distance=14.0 ratio=0.70 133 A.G1421 A.G1422 angle=104 distance=15.1 ratio=0.79 134 A.G1447 A.U1448 angle=121 distance=16.8 ratio=0.87 135 A.U1448 A.G1449 angle=120 distance=16.7 ratio=0.87 136 A.A1461 A.G1462 angle=94 distance=12.8 ratio=0.73 137 A.U1477 A.A1478 angle=131 distance=16.2 ratio=0.91 138 A.A1478 A.C1479 angle=115 distance=16.1 ratio=0.85 139 A.A1480 A.C1481 angle=132 distance=16.7 ratio=0.91 140 A.C1481 A.A1482 angle=109 distance=16.1 ratio=0.81 141 A.A1482 A.C1483 angle=116 distance=15.0 ratio=0.85 142 A.C1483 A.C1484 angle=144 distance=18.5 ratio=0.95 143 A.C1484 A.G1485 angle=140 distance=17.5 ratio=0.94 144 A.A1512 A.A1513 angle=162 distance=18.9 ratio=0.99 145 A.A1513 A.A1514 angle=131 distance=17.4 ratio=0.91 146 A.A1524 A.C1525 angle=179 distance=19.9 ratio=1.00 147 A.C1531 A.C1532 angle=110 distance=15.0 ratio=0.82 148 A.C1532 A.C1533 angle=169 distance=18.1 ratio=1.00 149 A.G1538 A.C1539 angle=108 distance=14.9 ratio=0.81 150 A.C1539 A.A1540 angle=125 distance=15.2 ratio=0.89 151 A.A1567 A.U1568 angle=117 distance=16.6 ratio=0.85 152 A.U1568 A.G1569 angle=115 distance=17.3 ratio=0.84 153 A.G1570 A.U1571 angle=131 distance=17.6 ratio=0.91 154 A.U1571 A.A1572 angle=97 distance=15.2 ratio=0.75 155 A.G1594 A.G1595 angle=103 distance=16.9 ratio=0.79 156 A.C1597 A.G1598 angle=87 distance=11.6 ratio=0.69 157 A.G1598 A.A1599 angle=94 distance=15.1 ratio=0.73 158 A.A1599 A.A1600 angle=158 distance=18.4 ratio=0.98 ---------------------------------------------------------------- Summary of 94 splayed-apart units 1 nts=2 UU A.U655,A.U656 2 nts=2 CU A.C679,A.U680 3 nts=2 GA A.G687,A.A688 4 nts=3 UAC A.U690,A.A691,A.C692 5 nts=2 AA A.A699,A.A700 6 nts=2 AU A.A703,A.U704 7 nts=2 CC A.C705,A.C706 8 nts=2 UC A.U711,A.C712 9 nts=3 UUC A.U720,A.U721,A.C722 10 nts=2 AC A.A723,A.C724 11 nts=2 CA A.C734,A.A735 12 nts=3 AUC A.A757,A.U758,A.C759 13 nts=3 AAA A.A781,A.A782,A.A783 14 nts=4 CUAG A.C793,A.U794,A.A795,A.G796 15 nts=2 AC A.A801,A.C802 16 nts=2 CC A.C804,A.C805 17 nts=4 ACAG A.A814,A.C815,A.A816,A.G817 18 nts=3 ACC A.A827,A.C828,A.C829 19 nts=3 UUU A.U830,A.U831,A.U832 20 nts=3 UAA A.U850,A.A851,A.A852 21 nts=3 UAU A.U859,A.A860,A.U861 22 nts=2 UG A.U876,A.G877 23 nts=3 GCC A.G889,A.C890,A.C891 24 nts=5 GUCAC A.G902,A.U903,A.C904,A.A905,A.C906 25 nts=2 AC A.A907,A.C908 26 nts=2 GC A.G930,A.C931 27 nts=2 CG A.C932,A.G933 28 nts=2 CG A.C935,A.G936 29 nts=2 AG A.A942,A.G943 30 nts=2 UC A.U961,A.C962 31 nts=2 AA A.A966,A.A967 32 nts=3 UCC A.U1000,A.C1001,A.C1002 33 nts=3 ACA A.A1010,A.C1011,A.A1012 34 nts=2 AA A.A1014,A.A1015 35 nts=3 GAC A.G1018,A.A1019,A.C1020 36 nts=2 GG A.G1030,A.G1031 37 nts=2 CA A.C1038,A.A1039 38 nts=3 UAU A.U1040,A.A1041,A.U1042 39 nts=2 AA A.A1046,A.A1047 40 nts=2 CA A.C1048,A.A1049 41 nts=2 AA A.A1053,A.A1054 42 nts=3 AUA A.A1080,A.U1081,A.A1082 43 nts=8 AAACCUCA A.A1102,A.A1103,A.A1104,A.C1105,A.C1106,A.U1107,A.C1108,A.A1109 44 nts=2 AU A.A1118,A.U1119 45 nts=2 CA A.C1120,A.A1121 46 nts=2 AA A.A1125,A.A1126 47 nts=2 AG A.A1137,A.G1138 48 nts=3 ACU A.A1142,A.C1143,A.U1144 49 nts=3 CCA A.C1150,A.C1151,A.A1152 50 nts=3 CAG A.C1153,A.A1154,A.G1155 51 nts=3 GGU A.G1178,A.G1179,A.U1180 52 nts=2 AU A.A1186,A.U1187 53 nts=2 AU A.A1214,A.U1215 54 nts=2 UA A.U1219,A.A1220 55 nts=2 AC A.A1222,A.C1223 56 nts=3 CCC A.C1224,A.C1225,A.C1226 57 nts=3 AUC A.A1228,A.U1229,A.C1230 58 nts=2 AA A.A1231,A.A1232 59 nts=2 UU A.U1245,A.U1246 60 nts=2 GC A.G1247,A.C1248 61 nts=3 UCA A.U1249,A.C1250,A.A1251 62 nts=3 CCU A.C1253,A.C1254,A.U1255 63 nts=3 AUA A.A1258,A.U1259,A.A1260 64 nts=3 UUC A.U1269,A.U1270,A.C1271 65 nts=4 GAUG A.G1282,A.A1283,A.U1284,A.G1285 66 nts=2 GC A.G1289,A.C1290 67 nts=6 UACAAA A.U1291,A.A1292,A.C1293,A.A1294,A.A1295,A.A1296 68 nts=2 AC A.A1313,A.C1314 69 nts=2 GA A.G1320,A.A1321 70 nts=3 UAG A.U1325,A.A1326,A.G1327 71 nts=3 CAA A.C1330,A.A1331,A.A1332 72 nts=2 CC A.C1341,A.C1342 73 nts=2 UG A.U1344,A.G1345 74 nts=2 AA A.A1353,A.A1354 75 nts=2 CA A.C1366,A.A1367 76 nts=3 UUU A.U1368,A.U1369,A.U1370 77 nts=3 CCA A.C1377,A.C1378,A.A1379 78 nts=5 AACUA A.A1383,A.A1384,A.C1385,A.U1386,A.A1387 79 nts=3 AUA A.A1390,A.U1391,A.A1392 80 nts=2 GA A.G1415,A.A1416 81 nts=2 GU A.G1419,A.U1420 82 nts=2 GG A.G1421,A.G1422 83 nts=3 GUG A.G1447,A.U1448,A.G1449 84 nts=2 AG A.A1461,A.G1462 85 nts=3 UAC A.U1477,A.A1478,A.C1479 86 nts=6 ACACCG A.A1480,A.C1481,A.A1482,A.C1483,A.C1484,A.G1485 87 nts=3 AAA A.A1512,A.A1513,A.A1514 88 nts=2 AC A.A1524,A.C1525 89 nts=3 CCC A.C1531,A.C1532,A.C1533 90 nts=3 GCA A.G1538,A.C1539,A.A1540 91 nts=3 AUG A.A1567,A.U1568,A.G1569 92 nts=3 GUA A.G1570,A.U1571,A.A1572 93 nts=2 GG A.G1594,A.G1595 94 nts=4 CGAA A.C1597,A.G1598,A.A1599,A.A1600 **************************************************************************** This structure contains 2-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >8qrm nts=957 [whole] AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAtUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGcCcGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGaaAGUGCACUUGGACGAACC&a&g .[.[[[[..(((((..]]]]]((((((.((..((((((((..(.(((.(((..(......)......(((......((((.(..(((.....))).)..))))..((((....((..((((....))).)))......)))).((...))))).(((....))).....)))))))......(.(((...(((((....)))).))))).)).)))))).....((((([[[.....(((.....((.]]])).......)))..)))))..)).))))))....((([[...(.((((...(((...............(((((((.....(((.(((.((........))..))).))).....).....(.((....))))))))).....)))....))))....((((((...((...((((.........))))...))))))))......{...(.(((((......]]..))))).))))).((.......((((....)))).....))...)))))(((((.((((((....(((.(((((..((((((((((.....((........))..........(((((((.......((.(((...((((((.(....((..(((((.....))).......))..)).....(((....))).....).).)))...)).)))))....)))))))..)).)))))))).(...((((.....)))).....(....(((((((.......)))))))....)..)..))))).....(((((((.........))))))).....)))....))))))))).))..(.(..((.(...((((((..(((((..((..(((....((.....))...)))..).)..))))).))))))....).))...)..)..(((((((((....)))))))))}........&.&. >8qrm-A #1 nts=955 0.02(3.47) [chain] RNA AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAtUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGcCcGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGaaAGUGCACUUGGACGAACC .[.[[[[..(((((..]]]]]((((((.((..((((((((..(.(((.(((..(......)......(((......((((.(..(((.....))).)..))))..((((....((..((((....))).)))......)))).((...))))).(((....))).....)))))))......(.(((...(((((....)))).))))).)).)))))).....((((([[[.....(((.....((.]]])).......)))..)))))..)).))))))....((([[...(.((((...(((...............(((((((.....(((.(((.((........))..))).))).....).....(.((....))))))))).....)))....))))....((((((...((...((((.........))))...))))))))......{...(.(((((......]]..))))).))))).((.......((((....)))).....))...)))))(((((.((((((....(((.(((((..((((((((((.....((........))..........(((((((.......((.(((...((((((.(....((..(((((.....))).......))..)).....(((....))).....).).)))...)).)))))....)))))))..)).)))))))).(...((((.....)))).....(....(((((((.......)))))))....)..)..))))).....(((((((.........))))))).....)))....))))))))).))..(.(..((.(...((((((..(((((..((..(((....((.....))...)))..).)..))))).))))))....).))...)..)..(((((((((....)))))))))}........ **************************************************************************** Summary of structural features of 957 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 A . A.A648 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop 2 A [ A.A649 0.014 pseudoknotted,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,bulge,phosphate 3 U . A.U650 0.010 turn,anti,~C2'-endo,BII,non-pair-contact,bulge,phosphate 4 A [ A.A651 0.013 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 5 G [ A.G652 0.015 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 6 G [ A.G653 0.020 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 U [ A.U654 0.010 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 8 U . A.U655 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,splayed-apart 9 U . A.U656 0.009 u-turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 10 G ( A.G657 0.015 turn,u-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 11 G ( A.G658 0.018 u-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 12 U ( A.U659 0.011 u-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,ribose-zipper,phosphate 13 C ( A.C660 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor 14 C ( A.C661 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,phosphate 15 U . A.U662 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop 16 A . A.A663 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 17 G ] A.G664 0.018 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 18 C ] A.C665 0.011 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 C ] A.C666 0.012 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 U ] A.U667 0.012 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 21 U ] A.U668 0.009 pseudoknotted,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge 22 U ( A.U669 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 23 C ( A.C670 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 24 U ( A.U671 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 25 A ( A.A672 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 U ( A.U673 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 27 U ( A.U674 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 28 A . A.A675 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 29 G ( A.G676 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 30 C ( A.C677 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 31 U . A.U678 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 32 C . A.C679 0.008 anti,~C3'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 33 U ( A.U680 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 34 U ( A.U681 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 A ( A.A682 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 G ( A.G683 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 37 U ( A.U684 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 A ( A.A685 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 39 A ( A.A686 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 40 G ( A.G687 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 41 A . A.A688 0.006 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 42 U . A.U689 0.007 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,phosphate 43 U ( A.U690 0.009 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate,splayed-apart 44 A . A.A691 0.013 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor,splayed-apart 45 C ( A.C692 0.008 anti,~C3'-endo,non-stack,canonical,helix,stem-end,multiplet,bulge,splayed-apart 46 A ( A.A693 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet 47 C ( A.C694 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,multiplet,bulge,A-minor 48 A . A.A695 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,bulge,A-minor,phosphate 49 U ( A.U696 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge 50 G ( A.G697 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 51 C ( A.C698 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop,phosphate 52 A . A.A699 0.011 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 53 A . A.A700 0.010 anti,~C2'-endo,non-pair-contact,junction-loop,cap-acceptor,phosphate,splayed-apart 54 G ( A.G701 0.012 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop 55 C . A.C702 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 56 A . A.A703 0.008 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 57 U . A.U704 0.007 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,hairpin-loop,phosphate,splayed-apart 58 C . A.C705 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,hairpin-loop,phosphate,splayed-apart 59 C . A.C706 0.010 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 60 C . A.C707 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 61 C ) A.C708 0.008 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop 62 G . A.G709 0.010 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 63 U . A.U710 0.007 turn,anti,~C3'-endo,non-pair-contact,junction-loop,cap-donor,phosphate 64 U . A.U711 0.006 turn,anti,~C2'-endo,junction-loop,phosphate,splayed-apart 65 C . A.C712 0.011 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 66 C . A.C713 0.010 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 67 A . A.A714 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,ribose-zipper 68 G ( A.G715 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,ribose-zipper 69 U ( A.U716 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 70 G ( A.G717 0.013 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 71 A . A.A718 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 72 G . A.G719 0.012 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 73 U . A.U720 0.008 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 74 U . A.U721 0.006 turn,anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 75 C . A.C722 0.004 turn,anti,~C2'-endo,BI,non-stack,non-pair-contact,junction-loop,splayed-apart 76 A . A.A723 0.008 anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,A-minor,splayed-apart 77 C ( A.C724 0.008 anti,~C3'-endo,non-stack,canonical,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 78 C ( A.C725 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 79 C ( A.C726 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 80 U ( A.U727 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 81 C . A.C728 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 82 U ( A.U729 0.006 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 83 A . A.A730 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop,A-minor 84 A . A.A731 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 85 A ( A.A732 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 86 U ( A.U733 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 87 C ( A.C734 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,splayed-apart 88 A . A.A735 0.004 ~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 89 C . A.C736 0.002 anti,~C3'-endo,non-pair-contact,hairpin-loop 90 C . A.C737 0.003 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 91 A . A.A738 0.006 anti,~C3'-endo,non-pair-contact,hairpin-loop 92 C . A.C739 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop 93 G ) A.G740 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 94 A ) A.A741 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 95 U ) A.U742 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 96 C . A.C743 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 97 A ) A.A744 0.008 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 98 A . A.A745 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor 99 A . A.A746 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 100 A ) A.A747 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 101 G ) A.G748 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 102 G ) A.G749 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 103 G ) A.G750 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 104 A . A.A751 0.008 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 105 C . A.C752 0.007 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 106 A ( A.A753 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,junction-loop 107 A ( A.A754 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 108 G ( A.G755 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 109 C ( A.C756 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 110 A . A.A757 0.011 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 111 U . A.U758 0.010 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 112 C . A.C759 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 113 A . A.A760 0.013 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop 114 A ( A.A761 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,A-minor,phosphate 115 G ( A.G762 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,bulge,phosphate 116 C . A.C763 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,phosphate 117 A . A.A764 0.008 turn,anti,~C2'-endo,non-pair-contact,bulge,cap-donor,phosphate 118 C ( A.C765 0.009 turn,syn,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,bulge,cap-acceptor 119 G ( A.G766 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,bulge,phosphate 120 C ( A.C767 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 121 A ( A.A768 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 122 G . A.G769 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 123 C . A.C770 0.003 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 124 A . A.A771 0.003 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 125 A . A.A772 0.004 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 126 U ) A.U773 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 127 G ) A.G774 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 128 C ) A.C775 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,bulge 129 A . A.A776 0.007 anti,~C2'-endo,non-pair-contact,bulge 130 G ) A.G777 0.010 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,multiplet,bulge,phosphate 131 C ) A.C778 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,bulge,phosphate 132 U ) A.U779 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,A-minor,phosphate 133 C . A.C780 0.011 anti,~C3'-endo,non-pair-contact,internal-loop 134 A . A.A781 0.012 turn,syn,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 135 A . A.A782 0.012 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 136 A . A.A783 0.012 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,splayed-apart 137 A . A.A784 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,A-minor,phosphate 138 C . A.C785 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 139 G ) A.G786 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 140 C ) A.C787 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 141 U ) A.U788 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 142 U ) A.U789 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 143 A . A.A790 0.008 anti,~C3'-endo,BI,non-pair-contact,junction-loop 144 G ( A.G791 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,A-minor,phosphate 145 C ( A.C792 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,phosphate 146 C . A.C793 0.004 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 147 U . A.U794 0.006 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 148 A . A.A795 0.007 turn,anti,~C2'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 149 G ) A.G796 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,cap-acceptor,splayed-apart 150 C ) A.C797 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,A-minor,phosphate 151 C ) A.C798 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 152 A ) A.A799 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 153 C ) A.C800 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 154 A . A.A801 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 155 C ( A.C802 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 156 C ( A.C803 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 157 C ( A.C804 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop,splayed-apart 158 C . A.C805 0.005 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 159 C . A.C806 0.007 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 160 A . A.A807 0.008 ~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 161 C . A.C808 0.005 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 162 G ) A.G809 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 163 G ) A.G810 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 164 G ) A.G811 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,cap-acceptor 165 A . A.A812 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor 166 A . A.A813 0.004 anti,~C2'-endo,non-pair-contact,junction-loop 167 A . A.A814 0.008 ~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 168 C . A.C815 0.010 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 169 A . A.A816 0.011 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,phosphate,splayed-apart 170 G ) A.G817 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,junction-loop,ribose-zipper,phosphate,splayed-apart 171 C ) A.C818 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 172 A ) A.A819 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge 173 G ) A.G820 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,bulge,A-minor,phosphate 174 U ) A.U821 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 175 G ) A.G822 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge,phosphate 176 A ) A.A823 0.012 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,junction-loop 177 U . A.U824 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 178 U . A.U825 0.009 anti,~C3'-endo,BI,non-pair-contact,junction-loop,cap-acceptor 179 A . A.A826 0.011 turn,anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 180 A . A.A827 0.012 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 181 C . A.C828 0.004 anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 182 C . A.C829 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 183 U ( A.U830 0.008 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate,splayed-apart 184 U . A.U831 0.007 turn,anti,~C3'-endo,BII,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,bulge,splayed-apart 185 U ( A.U832 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 186 A ( A.A833 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 187 G ( A.G834 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 188 C . A.C835 0.009 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge 189 A . A.A836 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor 190 A . A.A837 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor 191 U ( A.U838 0.009 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,multiplet,bulge 192 A ( A.A839 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 193 A ( A.A840 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 194 A ( A.A841 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 195 C ( A.C842 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 196 G . A.G843 0.014 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 197 A . A.A844 0.009 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 198 A . A.A845 0.009 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 199 A . A.A846 0.008 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,phosphate 200 G ) A.G847 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-acceptor,phosphate 201 U ) A.U848 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 202 U ) A.U849 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 203 U ) A.U850 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 204 A . A.A851 0.009 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,phosphate,splayed-apart 205 A ) A.A852 0.009 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,cap-acceptor,phosphate,splayed-apart 206 C ) A.C853 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,cap-donor 207 U ) A.U854 0.011 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 208 A ) A.A855 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 209 A ) A.A856 0.011 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate 210 G . A.G857 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 211 C ) A.C858 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 212 U ) A.U859 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 213 A . A.A860 0.010 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,bulge,splayed-apart 214 U ) A.U861 0.009 turn,anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 215 A ) A.A862 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 216 C ) A.C863 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 217 U ) A.U864 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 218 A ) A.A865 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 219 A ) A.A866 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 220 C . A.C867 0.004 anti,~C3'-endo,non-pair-contact,junction-loop 221 C . A.C868 0.003 turn,anti,~C3'-endo,non-stack,junction-loop 222 C . A.C869 0.002 anti,~C3'-endo,non-pair-contact,junction-loop 223 C . A.C870 0.004 anti,~C3'-endo,BII,non-pair-contact,junction-loop 224 A . A.A871 0.011 anti,~C2'-endo,BII,non-pair-contact,junction-loop,phosphate 225 G ( A.G872 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 226 G ( A.G873 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 227 G ( A.G874 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 228 U ( A.U875 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 229 U ( A.U876 0.009 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 230 G [ A.G877 0.017 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate,splayed-apart 231 G [ A.G878 0.016 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 232 U [ A.U879 0.010 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate 233 C . A.C880 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop,phosphate 234 A . A.A881 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,hairpin-loop,junction-loop,A-minor,ribose-zipper,phosphate 235 A . A.A882 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 236 U . A.U883 0.009 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop 237 U . A.U884 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop 238 U ( A.U885 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 239 C ( A.C886 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 240 G ( A.G887 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,internal-loop 241 U . A.U888 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,internal-loop 242 G . A.G889 0.011 anti,~C2'-endo,non-pair-contact,hairpin-loop,internal-loop,cap-acceptor,splayed-apart 243 C . A.C890 0.008 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,internal-loop,phosphate,splayed-apart 244 C . A.C891 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,internal-loop,splayed-apart 245 A . A.A892 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,internal-loop,phosphate 246 G ( A.G893 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop,phosphate 247 C ( A.C894 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor,phosphate 248 C . A.C895 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop 249 A ] A.A896 0.011 pseudoknotted,turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 250 C ] A.C897 0.012 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 251 C ] A.C898 0.011 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,phosphate 252 G ) A.G899 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor,phosphate 253 C ) A.C900 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 254 G . A.G901 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 255 G . A.G902 0.010 turn,anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 256 U . A.U903 0.005 anti,~C2'-endo,BII,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 257 C . A.C904 0.005 turn,~C3'-endo,BI,non-stack,internal-loop,splayed-apart 258 A . A.A905 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate,splayed-apart 259 C . A.C906 0.006 turn,anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 260 A . A.A907 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,cap-acceptor,phosphate,splayed-apart 261 C ) A.C908 0.006 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate,splayed-apart 262 G ) A.G909 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 263 A ) A.A910 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 264 U . A.U911 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 265 U . A.U912 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 266 A ) A.A913 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 267 A ) A.A914 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper 268 C ) A.C915 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper 269 C ) A.C916 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 270 C ) A.C917 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 271 A . A.A918 0.011 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 272 A . A.A919 0.011 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-acceptor,phosphate 273 G ) A.G920 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 274 U ) A.U921 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 275 C . A.C922 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 276 A ) A.A923 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 277 A ) A.A924 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 278 U ) A.U925 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 279 A ) A.A926 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 280 G ) A.G927 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 281 A ) A.A928 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 282 A . A.A929 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop 283 G . A.G930 0.002 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 284 C . A.C931 0.002 anti,~C3'-endo,ss-non-loop,phosphate,splayed-apart 285 C . A.C932 0.009 turn,anti,~C2'-endo,ss-non-loop,phosphate,splayed-apart 286 G ( A.G933 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,A-minor,phosphate,splayed-apart 287 G ( A.G934 0.013 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 288 C ( A.C935 0.011 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 289 G [ A.G936 0.016 pseudoknotted,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,junction-loop,cap-donor,splayed-apart 290 U [ A.U937 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 291 A . A.A938 0.010 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 292 A . A.A939 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,phosphate 293 A . A.A940 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 294 G ( A.G941 0.023 turn,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,junction-loop 295 A . A.A942 0.008 anti,~C3'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 296 G ( A.G943 0.018 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate,splayed-apart 297 U ( A.U944 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 298 G ( A.G945 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 299 U ( A.U946 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 300 U . A.U947 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 301 U . A.U948 0.009 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate 302 U . A.U949 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 303 A ( A.A950 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 304 G ( A.G951 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 305 A ( A.A952 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 306 U . A.U953 0.008 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop 307 C . A.C954 0.006 turn,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,internal-loop 308 A . A.A955 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 309 C . A.C956 0.004 anti,~C3'-endo,non-pair-contact,internal-loop 310 C . A.C957 0.005 anti,~C3'-endo,non-pair-contact,internal-loop 311 C . A.C958 0.003 anti,~C2'-endo,non-pair-contact,internal-loop 312 C . A.C959 0.007 ~C3'-endo,non-stack,internal-loop 313 C . A.C960 0.003 anti,~C3'-endo,non-stack,internal-loop 314 U . A.U961 0.004 anti,~C2'-endo,non-stack,internal-loop,splayed-apart 315 C . A.C962 0.005 anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 316 C . A.C963 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop 317 C . A.C964 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop 318 C . A.C965 0.006 anti,~C2'-endo,non-stack,non-pair-contact,internal-loop 319 A . A.A966 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 320 A . A.A967 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,splayed-apart 321 U ( A.U968 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 322 A ( A.A969 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 323 A ( A.A970 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 324 A ( A.A971 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 325 G ( A.G972 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 326 C ( A.C973 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 327 U ( A.U974 0.009 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 328 A . A.A975 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 329 A . A.A976 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 330 A . A.A977 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 331 A . A.A978 0.008 anti,~C3'-endo,BI,non-pair-contact,internal-loop 332 C . A.C979 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 333 U ( A.U980 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 334 C ( A.C981 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 335 A ( A.A982 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 336 C . A.C983 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 337 C ( A.C984 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 338 U ( A.U985 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 339 G ( A.G986 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 340 A . A.A987 0.005 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate 341 G ( A.G988 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 342 U ( A.U989 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 343 U . A.U990 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 344 G . A.G991 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 345 U . A.U992 0.008 u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate 346 A . A.A993 0.005 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 347 A . A.A994 0.006 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 348 A . A.A995 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,phosphate 349 A . A.A996 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,A-minor,phosphate 350 A . A.A997 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 351 A ) A.A998 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 352 C ) A.C999 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 353 U . A.U1000 0.003 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 354 C . A.C1001 0.005 turn,anti,~C3'-endo,non-stack,internal-loop,splayed-apart 355 C ) A.C1002 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,splayed-apart 356 A ) A.A1003 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 357 G ) A.G1004 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 358 U . A.U1005 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 359 U ) A.U1006 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 360 G ) A.G1007 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 361 A ) A.A1008 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 362 C . A.C1009 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 363 A . A.A1010 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 364 C . A.C1011 0.004 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 365 A . A.A1012 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 366 A . A.A1013 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 367 A ) A.A1014 0.011 anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,splayed-apart 368 A . A.A1015 0.008 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 369 U . A.U1016 0.011 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 370 A . A.A1017 0.012 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 371 G . A.G1018 0.015 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,phosphate,splayed-apart 372 A . A.A1019 0.009 turn,anti,~C2'-endo,junction-loop,phosphate,splayed-apart 373 C ( A.C1020 0.009 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,junction-loop,cap-acceptor,splayed-apart 374 U . A.U1021 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix,bulge 375 A ( A.A1022 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,bulge 376 C ( A.C1023 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 377 G . A.G1024 0.014 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 378 A . A.A1025 0.013 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,A-minor,phosphate 379 A . A.A1026 0.014 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,phosphate 380 A . A.A1027 0.014 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 381 G ) A.G1028 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 382 U ) A.U1029 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,bulge 383 G ) A.G1030 0.017 anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix-end,bulge,junction-loop,splayed-apart 384 G ) A.G1031 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 385 C ) A.C1032 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 386 U ) A.U1033 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 387 U ) A.U1034 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 388 U ) A.U1035 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 389 A ) A.A1036 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 390 A . A.A1037 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 391 C . A.C1038 0.007 anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 392 A . A.A1039 0.009 anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 393 U . A.U1040 0.006 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 394 A . A.A1041 0.005 turn,anti,~C2'-endo,BII,internal-loop,phosphate,splayed-apart 395 U ) A.U1042 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 396 C ) A.C1043 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 397 U ) A.U1044 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 398 G . A.G1045 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 399 A . A.A1046 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,splayed-apart 400 A . A.A1047 0.008 turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate,splayed-apart 401 C . A.C1048 0.008 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 402 A ) A.A1049 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,splayed-apart 403 C ) A.C1050 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 404 A ) A.A1051 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 405 C ) A.C1052 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 406 A . A.A1053 0.014 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 407 A . A.A1054 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,A-minor,phosphate,splayed-apart 408 U . A.U1055 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop 409 A . A.A1056 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 410 G ( A.G1057 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 411 C ( A.C1058 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 412 U ( A.U1059 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 413 A ( A.A1060 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 414 A ( A.A1061 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 415 G ( A.G1062 0.011 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 416 A . A.A1063 0.007 anti,~C3'-endo,non-pair-contact,bulge 417 C . A.C1064 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,bulge 418 C . A.C1065 0.008 anti,~C3'-endo,non-pair-contact,bulge 419 C ( A.C1066 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 420 A ( A.A1067 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 421 A . A.A1068 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 422 A . A.A1069 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 423 C . A.C1070 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 424 U ( A.U1071 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 425 G ( A.G1072 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 426 G ( A.G1073 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 427 G ( A.G1074 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 428 A . A.A1075 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 429 t . A.5MU1076 0.051 modified,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 430 U . A.U1077 0.009 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor 431 A . A.A1078 0.007 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 432 G . A.G1079 0.013 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 433 A . A.A1080 0.014 u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 434 U . A.U1081 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 435 A . A.A1082 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 436 C . A.C1083 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop 437 C ) A.C1084 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 438 C ) A.C1085 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,phosphate 439 C ) A.C1086 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 440 A ) A.A1087 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 441 C . A.C1088 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 442 U . A.U1089 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 443 A . A.A1090 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 444 U ) A.U1091 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 445 G ) A.G1092 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 446 C ) A.C1093 0.007 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 447 U ) A.U1094 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 448 U ) A.U1095 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 449 A ) A.A1096 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 450 G ) A.G1097 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 451 C ) A.C1098 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 452 C . A.C1099 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 453 C . A.C1100 0.009 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate 454 U . A.U1101 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,ribose-zipper,phosphate 455 A . A.A1102 0.011 anti,~C3'-endo,non-pair-contact,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate,splayed-apart 456 A . A.A1103 0.011 turn,anti,~C2'-endo,non-pair-contact,junction-loop,splayed-apart 457 A . A.A1104 0.012 turn,anti,~C3'-endo,non-pair-contact,junction-loop,cap-donor,phosphate,splayed-apart 458 C { A.C1105 0.011 pseudoknotted,anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,junction-loop,splayed-apart 459 C . A.C1106 0.008 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 460 U . A.U1107 0.008 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 461 C . A.C1108 0.009 anti,~C2'-endo,non-pair-contact,junction-loop,cap-acceptor,phosphate,splayed-apart 462 A ( A.A1109 0.012 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate,splayed-apart 463 A . A.A1110 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 464 C ( A.C1111 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 465 A ( A.A1112 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 466 G ( A.G1113 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 467 U ( A.U1114 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 468 U ( A.U1115 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate 469 A . A.A1116 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,phosphate 470 A . A.A1117 0.003 anti,~C3'-endo,non-pair-contact,hairpin-loop,junction-loop 471 A . A.A1118 0.008 turn,anti,~C3'-endo,non-stack,hairpin-loop,junction-loop,cap-acceptor,splayed-apart 472 U . A.U1119 0.002 anti,~C3'-endo,non-pair-contact,hairpin-loop,junction-loop,phosphate,splayed-apart 473 C . A.C1120 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop,junction-loop,cap-donor,phosphate,splayed-apart 474 A . A.A1121 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,phosphate,splayed-apart 475 A ] A.A1122 0.014 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,junction-loop 476 C ] A.C1123 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,junction-loop 477 A . A.A1124 0.012 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,phosphate 478 A . A.A1125 0.009 anti,~C2'-endo,non-pair-contact,hairpin-loop,junction-loop,splayed-apart 479 A ) A.A1126 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate,splayed-apart 480 A ) A.A1127 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 481 C ) A.C1128 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 482 U ) A.U1129 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 483 G ) A.G1130 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 484 C . A.C1131 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 485 U ) A.U1132 0.010 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 486 C ) A.C1133 0.012 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,junction-loop,phosphate 487 G ) A.G1134 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 488 C ) A.C1135 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 489 C ) A.C1136 0.010 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,A-minor,ribose-zipper 490 A . A.A1137 0.008 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 491 G ( A.G1138 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,splayed-apart 492 A ( A.A1139 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 493 A . A.A1140 0.013 anti,~C3'-endo,BI,non-pair-contact,internal-loop 494 C . A.C1141 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 495 A . A.A1142 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 496 C . A.C1143 0.009 turn,anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 497 U . A.U1144 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 498 A . A.A1145 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 499 C . A.C1146 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 500 G ( A.G1147 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 501 A ( A.A1148 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 502 G ( A.G1149 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 503 C ( A.C1150 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,phosphate,splayed-apart 504 C . A.C1151 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 505 A . A.A1152 0.013 ~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 506 C . A.C1153 0.006 anti,~C2'-endo,BII,hairpin-loop,phosphate,splayed-apart 507 A . A.A1154 0.005 turn,anti,~C2'-endo,hairpin-loop,phosphate,splayed-apart 508 G ) A.G1155 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,phosphate,splayed-apart 509 C ) A.C1156 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 510 U ) A.U1157 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 511 U ) A.U1158 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 512 A . A.A1159 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 513 A . A.A1160 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 514 A . A.A1161 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 515 A . A.A1162 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper 516 C . A.C1163 0.008 anti,~C3'-endo,non-pair-contact,internal-loop,ribose-zipper 517 U ) A.U1164 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 518 C ) A.C1165 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 519 A . A.A1166 0.012 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,phosphate 520 A . A.A1167 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 521 A . A.A1168 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop 522 G ) A.G1169 0.016 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor 523 G ) A.G1170 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 524 A ) A.A1171 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 525 C ) A.C1172 0.011 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 526 C ) A.C1173 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 527 U ( A.U1174 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 528 G ( A.G1175 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 529 G ( A.G1176 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 530 C ( A.C1177 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 531 G ( A.G1178 0.015 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,cap-donor,splayed-apart 532 G . A.G1179 0.010 turn,anti,~C3'-endo,non-pair-contact,bulge,splayed-apart 533 U ( A.U1180 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 534 G ( A.G1181 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 535 C ( A.C1182 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 536 U ( A.U1183 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 537 U ( A.U1184 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 538 C ( A.C1185 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 539 A . A.A1186 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 540 U . A.U1187 0.004 anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 541 A . A.A1188 0.014 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop,phosphate 542 U . A.U1189 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 543 C ( A.C1190 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 544 C ( A.C1191 0.008 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 545 C ( A.C1192 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 546 U . A.U1193 0.007 anti,~C3'-endo,BI,non-pair-contact,junction-loop 547 C ( A.C1194 0.009 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,junction-loop,A-minor,phosphate 548 U ( A.U1195 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 549 A ( A.A1196 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 550 G ( A.G1197 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 551 A ( A.A1198 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop 552 G . A.G1199 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 553 G . A.G1200 0.011 ~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 554 A ( A.A1201 0.008 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 555 G ( A.G1202 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 556 C ( A.C1203 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 557 C ( A.C1204 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 558 U ( A.U1205 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 559 G ( A.G1206 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 560 U ( A.U1207 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 561 U ( A.U1208 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 562 C ( A.C1209 0.008 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 563 U ( A.U1210 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 564 G . A.G1211 0.010 anti,~C3'-endo,BI,non-pair-contact,junction-loop 565 U . A.U1212 0.005 anti,~C3'-endo,non-pair-contact,junction-loop,cap-acceptor 566 A . A.A1213 0.005 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper 567 A . A.A1214 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,cap-donor,phosphate,splayed-apart 568 U . A.U1215 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 569 C ( A.C1216 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 570 G ( A.G1217 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 571 A . A.A1218 0.011 anti,~C3'-endo,non-pair-contact,hairpin-loop 572 U . A.U1219 0.006 anti,~C3'-endo,BII,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 573 A . A.A1220 0.005 anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 574 A . A.A1221 0.006 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 575 A . A.A1222 0.008 anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 576 C . A.C1223 0.008 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 577 C . A.C1224 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 578 C . A.C1225 0.008 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor,phosphate,splayed-apart 579 C ) A.C1226 0.008 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate,splayed-apart 580 G ) A.G1227 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 581 A . A.A1228 0.011 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 582 U . A.U1229 0.008 turn,anti,~C3'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 583 C . A.C1230 0.010 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 584 A . A.A1231 0.008 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 585 A . A.A1232 0.010 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate,splayed-apart 586 C . A.C1233 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop,phosphate 587 C . A.C1234 0.011 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 588 U . A.U1235 0.010 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 589 C . A.C1236 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,junction-loop,cap-donor,phosphate 590 A . A.A1237 0.013 turn,~C3'-endo,non-pair-contact,junction-loop,cap-acceptor,phosphate 591 C ( A.C1238 0.009 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,A-minor,ribose-zipper 592 C ( A.C1239 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 593 A ( A.A1240 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 594 C ( A.C1241 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 595 C ( A.C1242 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 596 U ( A.U1243 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 597 C ( A.C1244 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop 598 U . A.U1245 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,splayed-apart 599 U . A.U1246 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 600 G . A.G1247 0.009 syn,~C2'-endo,non-pair-contact,internal-loop,cap-acceptor,splayed-apart 601 C . A.C1248 0.009 turn,anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 602 U . A.U1249 0.007 anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 603 C . A.C1250 0.004 turn,anti,~C2'-endo,internal-loop,phosphate,splayed-apart 604 A . A.A1251 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,cap-acceptor,splayed-apart 605 G ( A.G1252 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 606 C ( A.C1253 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,splayed-apart 607 C . A.C1254 0.008 turn,anti,~C2'-endo,non-pair-contact,bulge,cap-acceptor,splayed-apart 608 U ( A.U1255 0.009 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 609 A ( A.A1256 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 610 U ( A.U1257 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 611 A . A.A1258 0.011 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 612 U . A.U1259 0.006 turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 613 A . A.A1260 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate,splayed-apart 614 C ( A.C1261 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 615 C ( A.C1262 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 616 G ( A.G1263 0.014 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 617 C ( A.C1264 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 618 C ( A.C1265 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 619 A ( A.A1266 0.013 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,internal-loop,phosphate 620 U . A.U1267 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 621 C ( A.C1268 0.009 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate 622 U . A.U1269 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 623 U . A.U1270 0.003 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 624 C . A.C1271 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,splayed-apart 625 A . A.A1272 0.007 anti,~C2'-endo,BII,non-pair-contact,junction-loop,cap-donor 626 G ( A.G1273 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,cap-acceptor 627 C ( A.C1274 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 628 A . A.A1275 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 629 A . A.A1276 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 630 A ( A.A1277 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 631 C ( A.C1278 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 632 C ( A.C1279 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,A-minor 633 C ( A.C1280 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 634 U ( A.U1281 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 635 G . A.G1282 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor,splayed-apart 636 A . A.A1283 0.008 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 637 U . A.U1284 0.010 turn,anti,~C2'-endo,BII,hairpin-loop,splayed-apart 638 G . A.G1285 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,ribose-zipper,cap-donor,phosphate,splayed-apart 639 A . A.A1286 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 640 A ) A.A1287 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-acceptor,phosphate 641 G ) A.G1288 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 642 G ) A.G1289 0.011 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,A-minor,splayed-apart 643 C . A.C1290 0.006 anti,~C2'-endo,non-pair-contact,bulge,splayed-apart 644 U . A.U1291 0.009 anti,~C2'-endo,non-pair-contact,bulge,phosphate,splayed-apart 645 A . A.A1292 0.008 turn,anti,~C2'-endo,non-pair-contact,bulge,splayed-apart 646 C . A.C1293 0.006 turn,anti,~C2'-endo,bulge,phosphate,splayed-apart 647 A . A.A1294 0.010 anti,~C3'-endo,non-pair-contact,bulge,phosphate,splayed-apart 648 A . A.A1295 0.009 anti,~C2'-endo,non-pair-contact,bulge,phosphate,splayed-apart 649 A . A.A1296 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,bulge,A-minor,splayed-apart 650 G ) A.G1297 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 651 U ) A.U1298 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 652 A . A.A1299 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 653 A . A.A1300 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor 654 G ) A.G1301 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 655 C ) A.C1302 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,ribose-zipper,phosphate 656 G . A.G1303 0.006 anti,~C3'-endo,BI,non-pair-contact,junction-loop,ribose-zipper 657 C . A.C1304 0.007 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 658 A . A.A1305 0.006 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 659 A . A.A1306 0.010 anti,~C3'-endo,BI,non-pair-contact,junction-loop 660 G . A.G1307 0.013 anti,~C3'-endo,non-pair-contact,junction-loop 661 U ( A.U1308 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,junction-loop 662 A ( A.A1309 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 663 C ( A.C1310 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,cap-acceptor 664 C . A.C1311 0.009 anti,~C3'-endo,non-stack,hairpin-loop,phosphate 665 C . A.C1312 0.008 anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 666 A . A.A1313 0.003 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 667 C . A.C1314 0.010 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 668 G ) A.G1315 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 669 U ) A.U1316 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 670 A ) A.A1317 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,junction-loop 671 A . A.A1318 0.012 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 672 A . A.A1319 0.007 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 673 G . A.G1320 0.006 anti,~C3'-endo,non-pair-contact,junction-loop,ribose-zipper,phosphate,splayed-apart 674 A . A.A1321 0.007 ~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,ribose-zipper,splayed-apart 675 C . A.C1322 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 676 G ) A.G1323 0.012 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 677 U . A.U1324 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 678 U ) A.U1325 0.007 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,internal-loop,phosphate,splayed-apart 679 A . A.A1326 0.004 turn,anti,~C2'-endo,non-pair-contact,bulge,cap-acceptor,splayed-apart 680 G ) A.G1327 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 681 G ) A.G1328 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 682 U ) A.U1329 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 683 C . A.C1330 0.008 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,bulge,phosphate,splayed-apart 684 A . A.A1331 0.010 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,bulge,cap-donor,phosphate,splayed-apart 685 A . A.A1332 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor,phosphate,splayed-apart 686 G ) A.G1333 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 687 G ) A.G1334 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 688 U . A.U1335 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 689 G ) A.G1336 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 690 U ) A.U1337 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 691 A ) A.A1338 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 692 G ) A.G1339 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 693 C ) A.C1340 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 694 C . A.C1341 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate,splayed-apart 695 C . A.C1342 0.002 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 696 A . A.A1343 0.008 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 697 U . A.U1344 0.006 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 698 G ) A.G1345 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate,splayed-apart 699 A ) A.A1346 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 700 G ) A.G1347 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 701 G ) A.G1348 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 702 U ) A.U1349 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 703 G ) A.G1350 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,phosphate 704 G ) A.G1351 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,A-minor 705 C . A.C1352 0.006 anti,~C3'-endo,BI,non-pair-contact,junction-loop 706 A . A.A1353 0.008 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 707 A ) A.A1354 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 708 G ) A.G1355 0.010 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 709 A . A.A1356 0.003 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor 710 A ) A.A1357 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 711 A ) A.A1358 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 712 U ) A.U1359 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 713 G ) A.G1360 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 714 G ) A.G1361 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 715 G ) A.G1362 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 716 C ) A.C1363 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 717 U ) A.U1364 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 718 A . A.A1365 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop 719 C ( A.C1366 0.008 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 720 A . A.A1367 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 721 U . A.U1368 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 722 U . A.U1369 0.006 turn,anti,~C2'-endo,non-stack,junction-loop,phosphate,splayed-apart 723 U ( A.U1370 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,A-minor,splayed-apart 724 U ( A.U1371 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 725 C ( A.C1372 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 726 U ( A.U1373 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 727 A . A.A1374 0.009 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 728 C . A.C1375 0.007 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 729 C . A.C1376 0.004 anti,~C2'-endo,non-pair-contact,hairpin-loop 730 C . A.C1377 0.006 anti,~C2'-endo,BII,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 731 C . A.C1378 0.007 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 732 A ) A.A1379 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,splayed-apart 733 G ) A.G1380 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 734 A ) A.A1381 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 735 A ) A.A1382 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,A-minor 736 A . A.A1383 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 737 A . A.A1384 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-donor,phosphate,splayed-apart 738 C . A.C1385 0.004 turn,anti,~C2'-endo,non-stack,junction-loop,splayed-apart 739 U . A.U1386 0.003 turn,~C2'-endo,non-stack,junction-loop,splayed-apart 740 A . A.A1387 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,cap-acceptor,splayed-apart 741 C ( A.C1388 0.007 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,cap-donor 742 G . A.G1389 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 743 A . A.A1390 0.006 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 744 U . A.U1391 0.006 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 745 A . A.A1392 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 746 G ( A.G1393 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 747 C ( A.C1394 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 748 C ( A.C1395 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 749 C ( A.C1396 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 750 U ( A.U1397 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 751 U ( A.U1398 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 752 A ( A.A1399 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 753 U . A.U1400 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 754 G . A.G1401 0.015 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor 755 A . A.A1402 0.010 turn,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,hairpin-loop,phosphate 756 A . A.A1403 0.012 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 757 A . A.A1404 0.012 u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 758 C . A.C1405 0.005 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 759 U . A.U1406 0.003 anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate 760 U ) A.U1407 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 761 A ) A.A1408 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 762 A ) A.A1409 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 763 G ) A.G1410 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 764 G ) A.G1411 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 765 G ) A.G1412 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 766 U ) A.U1413 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 767 C . A.C1414 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 768 G . A.G1415 0.008 syn,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 769 A . A.A1416 0.011 anti,~C3'-endo,BI,non-pair-contact,internal-loop,splayed-apart 770 A . A.A1417 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 771 G ) A.G1418 0.010 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 772 G . A.G1419 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,splayed-apart 773 U . A.U1420 0.006 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 774 G ) A.G1421 0.013 ~C3'-endo,isolated-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 775 G . A.G1422 0.005 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate,splayed-apart 776 A . A.A1423 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 777 U ) A.U1424 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 778 U ) A.U1425 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 779 U ) A.U1426 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 780 A ) A.A1427 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 781 G ) A.G1428 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,multiplet,junction-loop,A-minor,phosphate 782 C . A.C1429 0.009 ~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 783 A . A.A1430 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 784 G . A.G1431 0.021 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 785 U . A.U1432 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 786 A . A.A1433 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 787 A ( A.A1434 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 788 A ( A.A1435 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 789 C ( A.C1436 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 790 U ( A.U1437 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 791 G ( A.G1438 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 792 A ( A.A1439 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 793 G ( A.G1440 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 794 A . A.A1441 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop 795 G . A.G1442 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate 796 U . A.U1443 0.008 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 797 A . A.A1444 0.011 turn,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,phosphate 798 G . A.G1445 0.016 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,cap-donor,phosphate 799 A . A.A1446 0.010 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 800 G . A.G1447 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,splayed-apart 801 U . A.U1448 0.009 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,hairpin-loop,splayed-apart 802 G . A.G1449 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate,splayed-apart 803 C ) A.C1450 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 804 U ) A.U1451 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 805 U ) A.U1452 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 806 A ) A.A1453 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 807 G ) A.G1454 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 808 U ) A.U1455 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 809 U ) A.U1456 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 810 G . A.G1457 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 811 A . A.A1458 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 812 A . A.A1459 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,phosphate 813 C . A.C1460 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 814 A . A.A1461 0.008 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 815 G ) A.G1462 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 816 G ) A.G1463 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 817 G ) A.G1464 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 818 C . A.C1465 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop 819 C . A.C1466 0.008 turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 820 C . A.C1467 0.004 anti,~C3'-endo,non-pair-contact,internal-loop 821 U . A.U1468 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 822 G ) A.G1469 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 823 A ) A.A1470 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 824 A ) A.A1471 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 825 G ) A.G1472 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 826 C ) A.C1473 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 827 G ) A.G1474 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 828 C ) A.C1475 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 829 G ) A.G1476 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 830 U ) A.U1477 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 831 A . A.A1478 0.013 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,A-minor,cap-acceptor,splayed-apart 832 C ) A.C1479 0.008 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,splayed-apart 833 A ) A.A1480 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,splayed-apart 834 C . A.C1481 0.003 turn,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 835 A . A.A1482 0.007 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,phosphate,splayed-apart 836 C ( A.C1483 0.009 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 837 C . A.C1484 0.003 turn,anti,~C2'-endo,non-stack,internal-loop,splayed-apart 838 G ( A.G1485 0.013 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,splayed-apart 839 c . A.B8T1486 0.030 modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 840 C . A.C1487 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 841 c ( A.5MC1488 0.031 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor,ribose-zipper 842 G ( A.G1489 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,ribose-zipper 843 U . A.U1490 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 844 C ( A.C1491 0.010 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 845 A . A.A1492 0.009 anti,~C3'-endo,BI,non-pair-contact,internal-loop 846 C . A.C1493 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 847 C . A.C1494 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 848 C ( A.C1495 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 849 U ( A.U1496 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,ribose-zipper,phosphate 850 C ( A.C1497 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 851 C ( A.C1498 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 852 U ( A.U1499 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 853 C ( A.C1500 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 854 A . A.A1501 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 855 A . A.A1502 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 856 G ( A.G1503 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 857 U ( A.U1504 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 858 A ( A.A1505 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 859 U ( A.U1506 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 860 A ( A.A1507 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 861 C . A.C1508 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 862 U . A.U1509 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 863 U ( A.U1510 0.006 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,internal-loop 864 C ( A.C1511 0.004 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,internal-loop,phosphate 865 A . A.A1512 0.004 turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,splayed-apart 866 A . A.A1513 0.004 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 867 A ( A.A1514 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,cap-acceptor,splayed-apart 868 G ( A.G1515 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 869 G ( A.G1516 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 870 A . A.A1517 0.002 anti,~C3'-endo,BI,non-pair-contact,internal-loop 871 C . A.C1518 0.002 anti,~C3'-endo,non-pair-contact,internal-loop 872 A . A.A1519 0.002 anti,~C3'-endo,non-stack,internal-loop 873 U . A.U1520 0.003 ~C2'-endo,non-pair-contact,internal-loop 874 U ( A.U1521 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop 875 U ( A.U1522 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 876 A . A.A1523 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 877 A . A.A1524 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 878 C . A.C1525 0.005 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 879 U . A.U1526 0.004 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 880 A . A.A1527 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 881 A ) A.A1528 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 882 A ) A.A1529 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 883 A . A.A1530 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 884 C . A.C1531 0.003 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 885 C . A.C1532 0.004 anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 886 C ) A.C1533 0.002 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 887 C ) A.C1534 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 888 U ) A.U1535 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop 889 A . A.A1536 0.004 anti,~C2'-endo,non-pair-contact,internal-loop 890 C . A.C1537 0.003 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor 891 G ) A.G1538 0.008 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,internal-loop,cap-acceptor,splayed-apart 892 C . A.C1539 0.006 turn,~C3'-endo,non-stack,bulge,splayed-apart 893 A ) A.A1540 0.004 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,internal-loop,splayed-apart 894 U . A.U1541 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 895 U . A.U1542 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 896 U ) A.U1543 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 897 A ) A.A1544 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 898 U ) A.U1545 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 899 A ) A.A1546 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 900 U ) A.U1547 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 901 A . A.A1548 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 902 G ) A.G1549 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 903 A ) A.A1550 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 904 G ) A.G1551 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 905 G ) A.G1552 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 906 A ) A.A1553 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 907 G ) A.G1554 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 908 A . A.A1555 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 909 C . A.C1556 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 910 A . A.A1557 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 911 A . A.A1558 0.004 anti,~C3'-endo,non-pair-contact,internal-loop 912 G ) A.G1559 0.011 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 913 U . A.U1560 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 914 C ) A.C1561 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 915 G ) A.G1562 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor,phosphate 916 U . A.U1563 0.007 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 917 A . A.A1564 0.010 ~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 918 A . A.A1565 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor,phosphate 919 C ) A.C1566 0.010 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate 920 A . A.A1567 0.014 ~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,A-minor,cap-acceptor,splayed-apart 921 U . A.U1568 0.005 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,internal-loop,phosphate,splayed-apart 922 G ) A.G1569 0.017 turn,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate,splayed-apart 923 G . A.G1570 0.019 ~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,cap-acceptor,phosphate,splayed-apart 924 U . A.U1571 0.009 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 925 A ( A.A1572 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 926 A ( A.A1573 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 927 G ( A.G1574 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 928 U ( A.U1575 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,A-minor,ribose-zipper,phosphate 929 G ( A.G1576 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,ribose-zipper,phosphate 930 U ( A.U1577 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 931 A ( A.A1578 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 932 C ( A.C1579 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 933 U ( A.U1580 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 934 G . A.G1581 0.013 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor 935 G . A.G1582 0.011 turn,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop 936 a . A.MA6/1583 0.051 modified,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 937 a . A.MA6/1584 0.053 modified,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,phosphate 938 A ) A.A1585 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 939 G ) A.G1586 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 940 U ) A.U1587 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 941 G ) A.G1588 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 942 C ) A.C1589 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet,phosphate 943 A ) A.A1590 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,phosphate 944 C ) A.C1591 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 945 U ) A.U1592 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 946 U ) A.U1593 0.011 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,phosphate 947 G } A.G1594 0.015 pseudoknotted,turn,syn,~C2'-endo,isolated-canonical,non-pair-contact,phosphate,splayed-apart 948 G . A.G1595 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 949 A . A.A1596 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 950 C . A.C1597 0.007 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 951 G . A.G1598 0.007 turn,~C2'-endo,non-stack,non-canonical,non-pair-contact,ss-non-loop,cap-acceptor,phosphate,splayed-apart 952 A . A.A1599 0.010 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor,phosphate,splayed-apart 953 A . A.A1600 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 954 C . A.C1601 0.007 anti,~C3'-endo,non-pair-contact,ss-non-loop 955 C . A.C1602 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop 956 a . X.ATP402 0.059 modified,break,anti,~C3'-endo,non-stack,ss-non-loop 957 g . X.GNP403 0.012 modified,anti,~C3'-endo,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