1 IL_3IWN_003 3IWN 0.5533 1 Major groove intercalation A Cyclic di-GMP-I riboswitch G 81 G 82 * C 42 C 44 cWW cWW
2 IL_1U9S_006 1U9S 0.5617 1 Major groove intercalation A RNase P class A G 140 G 141 * U 158 C 160 cWW ncWW
3 IL_3UCZ_002 3UCZ 0.5034 1 R Cyclic di-GMP-I riboswitch G 86 G 87 * C 52 C 54 cWW cWW
4 IL_5AJ3_002 5AJ3 0.3480 1 Single bulged A (H) A SSU rRNA A 39 A 40 * U 215 U 217 cWW cWW
5 IL_3J9M_063 3J9M 0.3143 1 Single bulged A (H) AA SSU rRNA A 685 A 686 * U 859 U 861 cWW cWW
6 IL_5A2Q_010 5A2Q 0.3705 2 2 SSU rRNA A 348 A 349 * U 112 U 115 cWW cWW
7 IL_4V88_392 4V88 0.3394 2 Multiple bulged bases A6 SSU rRNA A 300 A 301 * U 113 U 116 cWW cWW
8 IL_4V4Q_219 4V4Q 0.3402 1 Single bulged A (H) CA SSU rRNA G 922 A 923 * U 1393 C 1395 cWW cWW
9 IL_3J79_027 3J79 0.2966 1 A LSU rRNA A 880 A 881 * U 892 U 894 cWW cWW
10 IL_4V4Q_185 4V4Q 0.3023 1 Single bulged G (H) CA SSU rRNA G 75 G 76 * U 93 C 95 cWW cWW
11 IL_3Q1Q_004 3Q1Q 0.3060 2 B RNase P class A G 108 G 109 * C 205 C 208 cWW cWW
12 IL_4V9F_098 4V9F 0.3854 1 Single bulged A 0 LSU rRNA G 2860 G 2861 * C 2895 C 2897 cWW cWW
13 IL_5J7L_271 5J7L 0.3514 1 Single bulged G DA LSU rRNA G 862 A 863 * U 913 C 915 cWW cWW
14 IL_4V4Q_203 4V4Q 0.2445 1 CA SSU rRNA C 470 U 471 * A 460 G 462 cWW cWW
15 IL_5AJ3_028 5AJ3 0.2145 1 Single bulged U (H) A SSU rRNA A 693 G 694 * C 608 U 610 cWW cWW
16 IL_4V4Q_179 4V4Q 0.2177 1 Single bulged A (H) CA SSU rRNA A 44 G 45 * C 396 U 398 cWW cWW
17 IL_4C7O_004 4C7O 0.2121 1 Single bulged G E SRP RNA A 15 A 16 * U 27 U 29 cWW cWW
18 IL_5AJ0_087 5AJ0 0.2712 1 A2 LSU rRNA C 2016 C 2017 * G 1927 G 1929 cWW cWW
19 IL_5FJC_001 5FJC 0.2417 1 Single bulged A A SAM-I riboswitch C 40 C 41 * G 13 G 15 cWW cWW
20 IL_4V8P_361 4V8P 0.2054 1 Single bulged U (H) F1 LSU rRNA C 1323 C 1324 * G 1234 G 1236 cWW cWW
21 IL_4V88_299 4V88 0.2080 1 Single bulged U (H) A5 LSU rRNA C 1296 C 1297 * G 1207 G 1209 cWW cWW
22 IL_5AN9_011 5AN9 0.2054 1 Single bulged U (H) N LSU rRNA C 1531 C 1532 * G 1442 G 1444 cWW cWW
23 IL_3J79_053 3J79 0.1956 1 Single bulged U (H) A LSU rRNA C 1424 C 1425 * G 1335 G 1337 cWW cWW
24 IL_4V91_058 4V91 0.2390 1 Single bulged U (H) 1 LSU rRNA C 1296 C 1297 * G 1207 G 1209 cWW cWW
25 IL_4BTS_287 4BTS 0.3395 1 Single bulged A (H) DA SSU rRNA A 473 G 474 * C 498 U 500 cWW cWW
26 IL_4V91_002 4V91 0.2530 1 Single bulged C (H) 1+4 LSU rRNA + 5.8S rRNA C 7 C 8 * G 150 G 152 cWW cWW
27 IL_4IOA_057 4IOA 0.2549 1 Single bulged C X LSU rRNA A 1534 C 1535 * G 1488 U 1490 cWW cWW
28 IL_2A64_003 2A64 0.1814 1 Single bulged U A RNase P class B C 77 C 78 * G 66 G 68 cWW cWW
29 IL_3DHS_003 3DHS 0.2225 1 A RNase P class B C 77 C 78 * G 66 G 68 cWW cWW
30 IL_5GAN_007 5GAN 0.2070 1 V U4 snRNA U 48 U 49 * A 24 A 26 cWW cWW
31 IL_5GAP_002 5GAP 0.1895 1 V U4 snRNA U 48 U 49 * A 24 A 26 cWW cWW
32 IL_3J9W_069 3J9W 0.2106 1 Single bulged A (H) BA LSU rRNA C 152 C 153 * G 175 G 177 cWW cWW
33 IL_4BTS_313 4BTS 0.1640 1 DA SSU rRNA U 1100 C 1101 * G 1091 A 1093 cWW cWW
34 IL_4RZD_001 4RZD 0.1596 1 Single bulged C A PreQ1-III riboswitch C 56 C 57 * G 78 G 80 cWW cWW
35 IL_4V4Q_225 4V4Q 0.1548 1 Single bulged U (H) CA SSU rRNA C 1208 C 1209 * G 1048 G 1050 cWW cWW
36 IL_4V91_075 4V91 0.1991 1 1 LSU rRNA C 1669 C 1670 * G 1778 G 1780 cWW cWW
37 IL_3JAM_061 3JAM 0.1650 1 Single bulged U (H) 2 SSU rRNA C 1438 C 1439 * G 1267 G 1269 cWW cWW
38 IL_4V8P_295 4V8P 0.1960 1 F1+E2 LSU rRNA C 6 C 7 * G 147 G 149 cWW cWW
39 IL_4V88_243 4V88 0.2160 1 Single bulged C (H) A5+A8 LSU rRNA + 5.8S rRNA C 7 C 8 * G 150 G 152 cWW cWW
40 IL_3J7P_001 3J7P 0.2369 1 Single bulged C (H) 5+8 LSU rRNA + 5.8S rRNA C 6 C 7 * G 149 G 151 cWW cWW
41 IL_3J7P_100 3J7P 0.2040 1 Single bulged A (H) 5 LSU rRNA C 3632 C 3633 * G 3827 G 3829 cWW cWW
42 IL_3J7P_067 3J7P 0.2590 1 5 LSU rRNA G 2063 G 2064 * U 1918 C 1920 cWW cWW
43 IL_3J79_020 3J79 0.2206 1 A LSU rRNA A 605 A 606 * U 584 U 586 cWW cWW
44 IL_4V8P_433 4V8P 0.1664 1 F1 LSU rRNA C 3320 U 3321 * A 3297 G 3299 cWW cWW
45 IL_3J9W_156 3J9W 0.1917 1 BA LSU rRNA G 2249 G 2250 * C 2231 C 2233 cWW cWW
46 IL_4V88_344 4V88 0.1883 1 Single bulged A (H) A5 LSU rRNA G 2614 G 2615 * C 2625 C 2627 cWW cWW
47 IL_5AN9_029 5AN9 0.2097 1 Single bulged A (H) N LSU rRNA G 2947 G 2948 * C 2958 C 2960 cWW cWW
48 IL_3J7P_112 3J7P 0.3212 1 Single bulged A (H) 5 LSU rRNA G 4191 A 4192 * U 4202 C 4204 ncWW cWW
49 IL_3J79_093 3J79 0.2730 1 A LSU rRNA U 2738 U 2739 * A 2809 A 2811 cWW cWW
50 IL_3DHS_002 3DHS 0.2537 1 A RNase P class B G 395 C 396 * G 51 C 53 cWW cWW
51 IL_4V88_267 4V88 0.2312 1 Single bulged U (H) A5 LSU rRNA A 755 U 756 * A 775 U 777 cWW cWW
52 IL_3J9M_064 3J9M 0.2509 1 AA SSU rRNA G 822 A 823 * U 690 C 692 cWW cWW
53 IL_4V88_370 4V88 0.3088 1 A5 LSU rRNA A 3210 C 3211 * G 3177 U 3179 cWW cWW
54 IL_5AJ3_003 5AJ3 0.2830 1 A SSU rRNA G 178 A 179 * U 44 C 46 cWW cWW
55 IL_3J7P_002 3J7P 0.3342 1 Single bulged U (H) 8+5 5.8S rRNA G 143 U 144 * A 12 C 14 cWW
56 IL_4V91_133 4V91 0.3056 1 Single bulged A (H) 1 LSU rRNA A 3210 C 3211 * G 3177 U 3179 cWW cWW
57 IL_4V8P_313 4V8P 0.3365 1 Single bulged U (H) F1 LSU rRNA A 204 C 205 * G 189 U 191 cWW cWW
58 IL_5AJ3_025 5AJ3 0.3710 1 Single bulged G (H) A SSU rRNA A 834 C 835 * G 529 U 531 cWW cWW
59 IL_5AN9_015 5AN9 0.3041 1 Single bulged A (H) N LSU rRNA C 2395 C 2396 * G 2589 G 2591 cWW cWW
60 IL_4V19_031 4V19 0.2558 1 Single bulged A (H) A LSU rRNA C 820 C 821 * G 973 G 975 cWW cWW
61 IL_3J7Y_033 3J7Y 0.2607 1 Single bulged A (H) A LSU rRNA C 2490 C 2491 * G 2643 G 2645 cWW cWW
62 IL_3J79_080 3J79 0.2115 1 Single bulged A (H) A LSU rRNA C 2421 C 2422 * G 2616 G 2618 cWW cWW
63 IL_5A2Q_066 5A2Q 0.2599 1 Single bulged U (H) 2 SSU rRNA C 1502 C 1503 * G 1325 G 1327 cWW cWW
64 IL_3J79_058 3J79 0.2231 1 A LSU rRNA U 1557 U 1558 * A 1548 A 1550 cWW cWW
65 IL_4V91_003 4V91 0.2632 1 Single bulged U (H) 1+4 LSU rRNA + 5.8S rRNA A 13 C 15 * G 144 U 145 ncWW cWW
66 IL_4V88_330 4V88 0.3450 1 Single bulged A (H) A5 LSU rRNA C 2128 U 2129 * G 2323 G 2325 cWW cWW
67 IL_4BTS_315 4BTS 0.3504 1 Single bulged G (H) DA SSU rRNA U 1599 U 1600 * G 1122 A 1124 cWW cWW
68 IL_5A2Q_058 5A2Q 0.3733 1 Single bulged G (H) 2 SSU rRNA U 1691 U 1692 * G 1206 A 1208 cWW cWW
69 IL_4AOB_006 4AOB 0.2062 1 Single bulged A A SAM-I riboswitch C 40||||7_555 C 41||||7_555 * G 13||||7_555 G 15||||7_555 cWW cWW
70 IL_4AOB_001 4AOB 0.2062 1 Single bulged A A SAM-I riboswitch C 40 C 41 * G 13 G 15 cWW cWW
71 IL_2ZY6_002 2ZY6 0.1873 1 Single bulged U A phenylalanyl transfer RNA C 24 C 25 * G 10 G 12 cWW cWW
72 IL_4BTS_323 4BTS 0.1729 1 Single bulged U (H) DA SSU rRNA C 1411 C 1412 * G 1240 G 1242 cWW cWW
73 IL_5AOX_002 5AOX 0.1465 1 Single bulged A C ALU JO CONSENSUS RNA C 108 C 109 * G 56 G 58 cWW cWW
74 IL_4V88_449 4V88 0.1785 1 Single bulged U A6 SSU rRNA C 1440 C 1441 * G 1268 G 1270 cWW cWW
75 IL_5A2Q_090 5A2Q 0.1788 1 2 SSU rRNA C 1750 C 1751 * G 1782 G 1784 cWW cWW
76 IL_4P3U_011 4P3U 0.1091 1 Single bulged A D+C RNA (23-mer) C 30 U 31 * A 17 G 19 cWW cWW
77 IL_4BTS_334 4BTS 0.1220 1 DA SSU rRNA C 1374 C 1375 * G 1364 G 1366 cWW cWW
78 IL_1S72_104 1S72 0.1222 1 Single bulged U (H) 9 5S rRNA C 95 C 96 * G 86 G 88 cWW cWW
79 IL_1S03_006 1S03 0.0979 1 Single bulged C B 47-MER C 39 C 40 * G 9 G 11 cWW cWW
80 IL_3JAM_025 3JAM 0.0984 1 2 SSU rRNA U 462 A 463 * U 438 A 440 cWW cWW
81 IL_1DQH_001 1DQH 0.0000 1 Single bulged C A+B RNA (9-mer) + RNA (10-mer) C 3 A 4 * U 15 G 17 cWW cWW
82 IL_4V4Q_178 4V4Q 0.0794 1 Single bulged G (H) CA SSU rRNA U 552 A 553 * U 30 A 32 cWW cWW
83 IL_3J9M_091 3J9M 0.1090 1 Single bulged U (H) AA SSU rRNA A 1338 G 1339 * C 1253 U 1255 cWW cWW
84 IL_4V9F_079 4V9F 0.1594 1 Single bulged A 0 LSU rRNA G 2279 A 2280 * U 2290 C 2292 cWW cWW
85 IL_3GX5_001 3GX5 0.1495 1 A SAM-I riboswitch C 40 C 41 * G 13 G 15 cWW cWW
86 IL_1FJG_040 1FJG 0.1529 1 Single bulged U (H) A SSU rRNA C 1208 C 1209 * G 1048 G 1050 cWW cWW
87 IL_4BTS_275 4BTS 0.0977 1 DA SSU rRNA C 192 C 193 * G 181 G 183 cWW cWW
88 IL_4V88_407 4V88 0.1003 1 Single bulged U A6 SSU rRNA U 463 A 464 * U 439 A 441 cWW cWW
89 IL_4BTS_284 4BTS 0.1291 1 DA SSU rRNA C 455 A 456 * U 431 G 433 cWW cWW
90 IL_1U63_004 1U63 0.2024 1 Single bulged A D 49 NT FRAGMENT OF MRNA FOR L1 U 16 C 17 * G 28 A 30 cWW cWW
91 IL_3J7A_001 3J7A 0.1755 1 Single bulged C (H) A SSU rRNA U 607 A 608 * U 24 A 26 cWW cWW
92 IL_3JAM_001 3JAM 0.1530 1 Single bulged C (H) 2 SSU rRNA U 599 A 600 * U 24 A 26 cWW cWW
93 IL_3J79_026 3J79 0.1909 1 Single bulged A (H) A LSU rRNA G 898 G 900 * C 875 C 876 cWW cWW
94 IL_3J7A_059 3J7A 0.1901 1 Single bulged A (H) A SSU rRNA C 1381 G 1382 * C 1672 G 1674 cWW cWW
95 IL_4V8P_333 4V8P 0.1501 1 Single bulged A (H) F1 LSU rRNA G 804 G 806 * C 776 C 777 cWW cWW
96 IL_4V19_003 4V19 0.1554 1 Single bulged A (H) A LSU rRNA C 12 U 13 * A 103 G 105 cWW cWW
97 IL_4V88_381 4V88 0.1610 1 Single bulged U (H) A5 LSU rRNA U 3363 C 3364 * G 3340 A 3342 cWW cWW
98 IL_1I9X_001 1I9X 0.1507 1 Single bulged A B+A RNA (13-mer) U 9 A 10 * U 4 A 6 cWW cWW
99 IL_5AJ0_180 5AJ0 0.2056 1 Single bulged U (H) A2 LSU rRNA U 4993 C 4994 * G 4970 A 4972 cWW cWW
100 IL_1DQF_001 1DQF 0.1404 1 Single bulged C A+B RNA (9-mer) + RNA (10-mer) C 3 A 4 * U 15 G 17 cWW cWW
101 IL_4V4Q_194 4V4Q 0.1813 1 Single bulged U (H) CA SSU rRNA C 392 A 393 * U 367 G 369 cWW cWW
102 IL_3J7Y_019 3J7Y 0.1453 1 Single bulged C (H) A LSU rRNA C 2254 C 2255 * G 2145 G 2147 cWW cWW
103 IL_4V91_145 4V91 0.1594 1 1 LSU rRNA U 3363 C 3364 * G 3340 A 3342 cWW cWW
104 IL_3J7P_024 3J7P 0.1916 1 5 LSU rRNA G 497 G 499 * C 655 C 656 cWW cWW
105 IL_3J7P_086 3J7P 0.2431 1 Single bulged C (H) 5 LSU rRNA C 2613 C 2614 * G 2724 G 2726 cWW cWW
106 IL_4V8P_352 4V8P 0.4366 1 F1 LSU rRNA G 1094 G 1096 * U 1117 C 1118 cWW cWW
107 IL_4V88_452 4V88 0.2995 1 Single bulged A A6 SSU rRNA C 1426 G 1428 * C 1280 G 1281 cWW cWW
108 IL_5A2Q_068 5A2Q 0.3190 1 Single bulged A (H) 2 SSU rRNA C 1488 G 1490 * C 1337 G 1338 cWW cWW
109 IL_3J7P_214 3J7P 0.2372 1 Single bulged A (H) S2 SSU rRNA C 1337 G 1338 * C 1488 G 1490 cWW cWW
110 IL_3J7P_040 3J7P 0.1890 1 5 LSU rRNA C 1086 A 1087 * U 1209 G 1211 cWW cWW
111 IL_3J7Y_056 3J7Y 0.1418 1 Single bulged A (H) A LSU rRNA C 3078 G 3079 * C 3088 G 3090 cWW cWW
112 IL_4V19_053 4V19 0.2228 1 Single bulged A (H) A LSU rRNA C 1412 G 1413 * C 1422 G 1424 cWW cWW
113 IL_3JAM_064 3JAM 0.2059 1 Single bulged A (H) 2 SSU rRNA C 1279 G 1280 * C 1424 G 1426 cWW cWW
114 IL_3MEI_001 3MEI 0.1784 1 Single bulged U A+B RNA (23-mer) C 7 G 8 * C 15 G 17 cWW cWW
115 IL_3J79_109 3J79 0.2041 1 Single bulged A (H) A LSU rRNA C 3319 G 3320 * C 3329 G 3331 cWW cWW
116 IL_3JCS_109 3JCS 0.2541 1 Single bulged A (H) 2 LSU rRNA C 1399 G 1400 * C 1409 G 1411 cWW cWW
117 IL_2QUX_006 2QUX 0.2851 1 R RNA (25-MER) C 20 G 21 * C 5 G 7 cWW cWW
118 IL_3J7P_089 3J7P 0.2385 1 5 LSU rRNA G 2681 G 2682 * C 2651 C 2653 cWW cWW
119 IL_3NDB_004 3NDB 0.1722 1 Single bulged G M SRP RNA G 137 G 138 * C 239 C 241 cWW ncWW
120 IL_4P3U_008 4P3U 0.1488 1 Single bulged A D+C RNA (23-mer) A 40 G 42 * C 7 U 8 cWW cWW
121 IL_4ANG_003 4ANG 0.1849 1 R RNA (20-mer) A 5||A||P_P G 7||A||P_P * C 15||A||P_P U 16||A||P_P
122 IL_4ANG_001 4ANG 0.1849 1 R RNA (20-mer) A 5||A||P_1 G 7||A||P_1 * C 15||A||P_1 U 16||A||P_1 cWW cWW
123 IL_4PHY_004 4PHY 0.3373 1 Single bulged A A+B RNA (26-MER) + RNA (20-mer) C 20 C 22 * G 30 G 31 ncWW cWW
124 IL_4V91_093 4V91 0.3286 1 1 LSU rRNA C 2237 G 2238 * C 2204 G 2206 cWW
125 IL_4PHY_002 4PHY 0.3192 1 Single bulged A A+B RNA (26-MER) + RNA (20-mer) C 12 C 13 * G 38 G 40 cWW cWW
126 IL_4P43_003 4P43 0.2197 1 Single bulged A B+A RNA (23-mer) C 30 U 31 * A 17 G 19 cWW cWW
127 IL_4P43_002 4P43 0.2093 1 Single bulged A A+B RNA (23-mer) C 7 U 8 * A 40 G 42 cWW cWW
128 IL_5AJ0_001 5AJ0 0.2158 1 Single bulged C (H) A2+A3 LSU rRNA + 5.8S rRNA C 6 C 7 * G 149 G 151 cWW cWW
129 IL_3J9M_073 3J9M 0.1832 1 Single bulged G (H) AA SSU rRNA U 838 A 839 * U 850 A 852 cWW cWW
130 IL_3J79_124 3J79 0.1584 1 A LSU rRNA C 3716 A 3717 * U 3773 G 3775 cWW cWW
131 IL_4X4O_002 4X4O 0.1293 3 D G70A tRNA minihelix C 3 C 4 * G 28 G 32 cWW cWW
132 IL_4V8P_418 4V8P 0.1688 1 Single bulged A (H) F1 LSU rRNA C 2948 G 2949 * C 2958 G 2960 cWW cWW
133 IL_4V9F_090 4V9F 0.1612 1 Single bulged A 0 LSU rRNA C 2626 G 2627 * C 2636 G 2638 cWW cWW
134 IL_4V88_360 4V88 0.1858 1 Single bulged A (H) A5 LSU rRNA C 2960 G 2961 * C 2970 G 2972 cWW cWW
135 IL_5AJ0_157 5AJ0 0.1884 1 A2 LSU rRNA C 4499 G 4500 * C 4509 G 4511 cWW cWW
136 IL_5AN9_045 5AN9 0.2044 1 Single bulged A (H) N LSU rRNA C 3293 G 3294 * C 3303 G 3305 cWW cWW
137 IL_3J9W_169 3J9W 0.2000 1 Single bulged A (H) BA LSU rRNA C 2620 G 2621 * C 2630 G 2632 cWW cWW
138 IL_5J7L_344 5J7L 0.1861 1 Single bulged A DA LSU rRNA C 2591 G 2592 * C 2601 G 2603 cWW cWW
139 IL_4V91_122 4V91 0.1801 1 Single bulged A (H) 1 LSU rRNA C 2960 G 2961 * C 2970 G 2972 cWW cWW
140 IL_4R0D_005 4R0D 0.2534 1 A Group II catalytic intron G 148 G 149 * U 121 C 123 ncWW
141 IL_5J7L_275 5J7L 0.2479 1 Single bulged A (H) DA LSU rRNA G 880 G 881 * U 895 C 897 cWW cWW
142 IL_4V8P_308 4V8P 0.3230 1 F1 LSU rRNA G 158 G 159 * U 260 C 262 cWW cWW
143 IL_4BTS_271 4BTS 0.3242 2 Multiple bulged bases (H) DA SSU rRNA A 291 G 292 * U 109 U 112 cWW cWW
144 IL_3J7A_009 3J7A 0.3902 2 Multiple bulged bases (H) A SSU rRNA A 306 G 307 * U 115 U 118 cWW cWW
145 IL_5AJ3_012 5AJ3 0.3820 1 Single bulged G (H) A SSU rRNA U 194 G 195 * U 206 A 208 cWW cWW
146 IL_3J9W_015 3J9W 0.3216 1 Single bulged G (H) AA SSU rRNA U 383 G 384 * U 395 A 397 cWW cWW
147 IL_3DIR_005 3DIR 0.4045 1 A Lysine riboswitch G 84 G 85 * U 109 C 111 cWW cWW
148 IL_3J9W_159 3J9W 0.3244 1 Single bulged U (H) BA LSU rRNA G 2443 G 2444 * U 2430 C 2432 cWW cWW
149 IL_4V9F_010 4V9F 0.3517 1 Single bulged G 0 LSU rRNA G 274 G 275 * U 374 C 376 cWW cWW
150 IL_3IWN_004 3IWN 0.3587 2 Major groove intercalation A Cyclic di-GMP-I riboswitch G 46 G 47 * U 76 C 79 cWW cWW
151 IL_1FJG_007 1FJG 0.2985 2 Multiple bulged bases (H) A SSU rRNA G 231 G 232 * U 129 C 131 cWW cWW
152 IL_5FDU_033 5FDU 0.3876 1 Single bulged A (H) 1A LSU rRNA G 927 G 928 * U 941 C 943 cWW cWW
153 IL_4V4Q_196 4V4Q 0.3175 1 Single bulged G (H) CA SSU rRNA U 375 G 376 * U 387 A 389 cWW cWW
154 IL_1FJG_016 1FJG 0.2749 1 A SSU rRNA U 375 G 376 * U 387 A 389 cWW cWW
155 IL_1FUF_002 1FUF 0.3710 2 Multiple bulged bases B+A RNA (14-mer) G 23 G 24 * U 5 C 8 cWW cWW
156 IL_1FUF_003 1FUF 0.3784 2 Multiple bulged bases A+B RNA (14-mer) G 9 G 10 * U 19 C 22 cWW cWW
157 IL_5J7L_334 5J7L 0.3451 1 Single bulged U DA LSU rRNA G 2414 G 2415 * U 2401 C 2403 cWW cWW
158 IL_3UCZ_003 3UCZ 0.3299 2 R Cyclic di-GMP-I riboswitch G 56 G 57 * U 81 C 84 cWW cWW
159 IL_5AN9_018 5AN9 0.3503 2 Multiple bulged bases (H) N LSU rRNA U 2466 G 2467 * U 2507 A 2510 cWW cWW
160 IL_3J7Y_035 3J7Y 0.3622 2 Major groove intercalation (H) A LSU rRNA U 2552 G 2553 * U 2562 A 2565 cWW cWW
161 IL_3J79_083 3J79 0.3535 2 Multiple bulged bases (H) A LSU rRNA U 2493 G 2494 * U 2534 A 2537 cWW cWW
162 IL_5J7L_315 5J7L 0.3852 2 Major groove intercalation DA LSU rRNA U 1841 G 1842 * U 1898 A 1901 cWW cWW
163 IL_3J9W_139 3J9W 0.3770 2 Major groove intercalation (H) BA LSU rRNA U 1870 G 1871 * U 1927 A 1930 cWW cWW
164 IL_4V19_033 4V19 0.4003 2 Major groove intercalation (H) A LSU rRNA U 882 G 883 * U 892 A 895 cWW cWW
165 IL_4V88_333 4V88 0.4032 2 Multiple bulged bases (H) A5 LSU rRNA U 2200 G 2201 * U 2241 A 2244 cWW cWW
166 IL_3J7P_103 3J7P 0.3671 2 Multiple bulged bases (H) 5 LSU rRNA U 3704 G 3705 * U 3745 A 3748 cWW cWW
167 IL_5LJ3_006 5LJ3 0.2122 1 V U6 snRNA G 81 A 82 * U 65 C 67 cWW cWW
168 IL_3J7A_041 3J7A 0.2031 1 A SSU rRNA A 936 G 937 * C 1027 U 1029 cWW cWW
169 IL_4IOA_031 4IOA 0.2333 1 Single bulged C X LSU rRNA U 1170 A 1171 * U 1005 A 1007 cWW cWW
170 IL_5FDU_035 5FDU 0.2179 1 Single bulged C (H) 1A LSU rRNA U 1205 G 1206 * C 1040 A 1042 cWW cWW
171 IL_4V9F_064 4V9F 0.2110 1 Single bulged A 0 LSU rRNA C 1826 G 1827 * C 2021 G 2023 cWW cWW
172 IL_3B31_001 3B31 0.2346 1 Single bulged A A RNA (29-MER) C 6194 G 6195 * C 6181 G 6183 cWW cWW
173 IL_4V8P_390 4V8P 0.2813 1 F1 LSU rRNA C 2232 G 2233 * C 2199 G 2201 cWW cWW
174 IL_5J7L_276 5J7L 0.2799 1 Single bulged C DA LSU rRNA U 1159 G 1160 * C 994 A 996 cWW cWW
175 IL_1U9S_003 1U9S 0.2898 2 Major groove intercalation A RNase P class A U 116 G 117 * C 224 A 227 cWW cWW
176 IL_4KZD_001 4KZD 0.2369 1 Single bulged U R RNA (84-MER) C 10 G 11 * C 74 G 76 cWW cWW
177 IL_4R4V_004 4R4V 0.2775 1 Single bulged A A VS ribozyme RNA C 660 A 661 * U 712 G 714 cWW cWW
178 IL_4R4V_010 4R4V 0.2775 1 Single bulged A A VS ribozyme RNA C 660||||7_556 A 661||||7_556 * U 712||||7_556 G 714||||7_556 cWW cWW
179 IL_4V8P_407 4V8P 0.3700 1 F1 LSU rRNA A 2774 G 2775 * C 2760 U 2762 cWW cWW
180 IL_1NBS_009 1NBS 0.3735 2 Major groove intercalation B RNase P class B U 181 G 182 * U 228 A 231 cWW cWW
181 IL_4V88_334 4V88 0.3879 1 Single bulged U (H) A5 LSU rRNA C 2237 G 2238 * C 2204 G 2206 cWW cWW
182 IL_5AN9_019 5AN9 0.3514 1 N LSU rRNA C 2503 G 2504 * C 2470 G 2472 cWW cWW
183 IL_3JB9_001 3JB9 0.4264 1 C U5 snRNA C 7 G 8 * C 89 G 91 cWW cWW
184 IL_3JAM_081 3JAM 0.4172 1 2 SSU rRNA U 1654 G 1656 * U 1741 A 1742 cWW cWW
185 IL_4V91_022 4V91 0.3164 1 Single bulged A (H) 1 LSU rRNA C 577 G 579 * U 512 G 513 cWW ncWW
186 IL_4BTS_326 4BTS 0.2964 1 Single bulged A (H) DA SSU rRNA C 1397 G 1399 * C 1252 G 1253 cWW cWW
187 IL_5DEA_002 5DEA 0.2351 1 Single bulged G C sc1 C 30 G 31 * C 5 G 7 cWW cWW
188 IL_5DEA_001 5DEA 0.2167 1 A sc1 C 30 G 31 * C 5 G 7 cWW cWW
189 IL_5A2Q_074 5A2Q 0.2724 1 2 SSU rRNA C 1412 G 1413 * C 1427 G 1429 cWW cWW
190 IL_3J9M_094 3J9M 0.3268 1 AA SSU rRNA U 1325 G 1327 * C 1265 A 1266 cWW cWW
191 IL_4V88_275 4V88 0.2289 1 Single bulged U (H) A5 LSU rRNA C 873 G 875 * C 886 G 887 cWW cWW
192 IL_4V8P_341 4V8P 0.2561 1 Single bulged U (H) F1 LSU rRNA C 898 G 900 * C 911 G 912 cWW cWW
193 IL_1FJG_043 1FJG 0.3051 1 A SSU rRNA C 1195 G 1197 * C 1060 G 1061 cWW cWW
194 IL_4R4V_003 4R4V 0.3050 1 Single bulged A A VS ribozyme RNA C 766 G 767 * C 651 G 653 cWW cWW
195 IL_4R4V_009 4R4V 0.3050 1 Single bulged A A VS ribozyme RNA C 766||||7_556 G 767||||7_556 * C 651||||7_556 G 653||||7_556 cWW cWW
196 IL_5AJ3_031 5AJ3 0.3547 1 Single bulged A (H) A SSU rRNA C 620 A 621 * U 680 G 682 cWW cWW
197 IL_3J9W_099 3J9W 0.3830 1 Single bulged C (H) BA LSU rRNA U 1205 G 1206 * C 1040 A 1042 cWW cWW
198 IL_4BTS_283 4BTS 0.4246 1 DA SSU rRNA U 412 G 414 * C 402 A 403 cWW cWW
199 IL_4R0D_019 4R0D 0.4285 2 Multiple bulged bases (H) A Group II catalytic intron C 572 G 575 * U 558 G 559 cWW cWW
200 IL_4V8P_425 4V8P 0.4140 1 F1 LSU rRNA G 3144 G 3146 * U 3247 C 3248 cWW cWW
201 IL_5AJ0_165 5AJ0 0.4020 2 Multiple bulged bases (H) A2 LSU rRNA A 4617 G 4620 * U 4603 U 4604 ncWW cWW
202 IL_3J79_116 3J79 0.3434 2 Multiple bulged bases (H) A LSU rRNA A 3462 G 3465 * U 3448 U 3449 cWW cWW
203 IL_5J7L_349 5J7L 0.3681 2 Multiple bulged bases DA LSU rRNA A 2711 G 2714 * U 2695 U 2696 cWW cWW
204 IL_5AN9_050 5AN9 0.3929 2 Multiple bulged bases (H) N LSU rRNA A 3413 G 3416 * U 3399 U 3400 cWW cWW
205 IL_4V8P_423 4V8P 0.4080 2 Multiple bulged bases (H) F1 LSU rRNA A 3066 G 3069 * U 3052 U 3053 cWW cWW
206 IL_3J9W_174 3J9W 0.4567 2 Multiple bulged bases (H) BA LSU rRNA A 2740 G 2743 * U 2724 U 2725 cWW cWW
207 IL_3J7P_136 3J7P 0.4664 2 Multiple bulged bases (H) 5 LSU rRNA A 4655 G 4658 * U 4641 U 4642 cWW ncWW
208 IL_3J7P_075 3J7P 0.4068 1 5 LSU rRNA C 2083 G 2085 * C 2272 G 2273 cWW
209 IL_4V91_064 4V91 0.4130 1 Single bulged A (H) 1 LSU rRNA C 1385 G 1387 * C 1420 G 1421 cWW cWW
210 IL_3J9W_043 3J9W 0.3138 1 Single bulged A (H) AA SSU rRNA C 1204 A 1206 * U 1070 G 1071 cWW cWW
211 IL_5AJ0_065 5AJ0 0.2310 1 Single bulged U (H) A2 LSU rRNA C 1572 G 1574 * C 1585 G 1586 cWW cWW
212 IL_4V4Q_228 4V4Q 0.2472 1 Single bulged A (H) CA SSU rRNA C 1195 A 1197 * U 1060 G 1061 cWW cWW
213 IL_4LGT_004 4LGT 0.2725 1 F stem-loop of 23S rRNA C 2601 G 2603 * C 2591 G 2592 cWW cWW
214 IL_3J7P_052 3J7P 0.2035 1 Single bulged U (H) 5 LSU rRNA C 1590 G 1592 * C 1603 G 1604 cWW cWW
215 IL_3J9M_071 3J9M 0.2636 1 AA SSU rRNA A 855 A 856 * U 830 U 832 cWW cWW
216 IL_1JZV_005 1JZV 0.2149 1 C+D RNA (8-mer) + RNA (9-mer) G 24 A 25 * U 32 C 34 cWW cWW
217 IL_4FRN_004 4FRN 0.2865 1 B Cobalamin riboswitch C 39 C 40 * G 23 G 25 cWW cWW
218 IL_5AJ0_094 5AJ0 0.3789 1 Single bulged A (H) A2 LSU rRNA G 2278 G 2280 * C 2313 C 2314 cWW cWW
219 IL_1S03_001 1S03 0.4253 1 Single bulged U A 47-MER A 6 G 8 * C 41 U 42 cWW cWW
220 IL_3JCS_105 3JCS 0.4208 2 Multiple bulged bases (H) 2 LSU rRNA A 1379 G 1382 * C 1320 U 1321 cWW cWW
221 IL_4V88_366 4V88 0.3419 2 Multiple bulged bases (H) A5 LSU rRNA A 3077 G 3080 * C 3063 U 3064 cWW cWW
222 IL_4V91_129 4V91 0.3298 2 Multiple bulged bases (H) 1 LSU rRNA A 3077 G 3080 * C 3063 U 3064 cWW cWW
223 IL_3J7P_142 3J7P 0.4119 1 5 LSU rRNA G 4899 G 4901 * C 4920 C 4921 cWW cWW
224 IL_5AN9_042 5AN9 0.4444 2 Multiple bulged bases (H) N LSU rRNA A 3273 G 3276 * C 3214 U 3215 cWW cWW
225 IL_3J79_106 3J79 0.4859 2 Multiple bulged bases (H) A LSU rRNA A 3299 G 3302 * C 3240 U 3241 cWW cWW
226 IL_3J7P_125 3J7P 0.5490 2 5 LSU rRNA A 4517 G 4520 * C 4458 U 4459 cWW cWW
227 IL_3J7P_077 3J7P 0.3170 1 Single bulged A (H) 5 LSU rRNA G 2299 G 2301 * C 2334 C 2335 ncWW ncWW
228 IL_3J7P_028 3J7P 0.2451 1 5 LSU rRNA G 708 C 709 * G 1287 C 1289 cWW
229 IL_3J7P_046 3J7P 0.2076 1 Single bulged A (H) 5 LSU rRNA G 1496 G 1498 * C 1467 C 1468 cWW cWW
230 IL_5AJ0_120 5AJ0 0.1455 1 Single bulged A (H) A2 LSU rRNA C 3603 C 3604 * G 3798 G 3800 cWW cWW
231 IL_1I9X_002 1I9X 0.1182 1 Single bulged A A+B RNA (13-mer) U 9 A 10 * U 4 A 6 cWW cWW
232 IL_3J7Q_149 3J7Q 0.1632 1 7 5S rRNA C 15 A 16 * U 62 G 64 cWW ncWW
233 IL_3J7P_147 3J7P 0.1990 1 Single bulged U (H) 5 LSU rRNA U 5035 C 5036 * G 5012 A 5014 cWW ncWW
234 IL_5A2Q_026 5A2Q 0.1565 1 Single bulged U (H) 2 SSU rRNA U 511 A 512 * U 487 A 489 cWW cWW
235 IL_3J7P_177 3J7P 0.1207 1 Single bulged U (H) S2 SSU rRNA U 511 A 512 * U 487 A 489 cWW cWW
236 IL_3J7A_021 3J7A 0.1376 1 Single bulged U (H) A SSU rRNA U 469 A 470 * U 445 A 447 cWW cWW
237 IL_3J79_030 3J79 0.1225 1 A LSU rRNA C 1014 A 1016 * U 947 G 948 cWW cWW
238 IL_1FJG_001 1FJG 0.1334 1 Single bulged G (H) A SSU rRNA U 552 A 553 * U 30 A 32 cWW cWW
239 IL_4V8P_312 4V8P 0.2107 2 F1 LSU rRNA A 240 G 243 * C 177 U 178 cWW cWW
240 IL_4IOA_075 4IOA 0.2373 1 Single bulged U X LSU rRNA G 2050 G 2052 * C 2421 C 2422 cWW cWW
241 IL_3J9W_148 3J9W 0.2479 1 Single bulged U (H) BA LSU rRNA G 2096 G 2098 * C 2471 C 2472 cWW cWW
242 IL_5FDU_081 5FDU 0.2065 1 Single bulged U (H) 1A LSU rRNA G 2089 G 2091 * C 2454 C 2455 cWW cWW
243 IL_1S03_005 1S03 0.2192 1 Single bulged U B 47-MER A 6 G 8 * C 41 U 42 cWW cWW
244 IL_4V9F_039 4V9F 0.2524 1 Single bulged U 0 LSU rRNA G 1108 G 1110 * C 1253 C 1254 cWW cWW
245 IL_3D0U_001 3D0U 0.2319 1 Single bulged C A Lysine riboswitch G 9 G 11 * C 75 C 76 cWW cWW
246 IL_3DIR_001 3DIR 0.2520 1 A Lysine riboswitch G 12 G 14 * C 78 C 79 cWW cWW
247 IL_5AJ0_002 5AJ0 0.2411 1 Single bulged U (H) A3+A2 5.8S rRNA G 143 U 144 * A 12 C 14 cWW cWW
248 IL_1ZDK_003 1ZDK 0.2647 1 S RNA (19-mer) G 7||||P_1 G 9||||P_1 * C 16||||P_1 C 17||||P_1 cWW cWW
249 IL_1ZDK_007 1ZDK 0.2647 1 S RNA (19-mer) G 7||||P_P G 9||||P_P * C 16||||P_P C 17||||P_P
250 IL_3J7P_026 3J7P 0.2169 1 5 LSU rRNA G 508 U 510 * A 649 C 650 cWW cWW
251 IL_3J7Y_040 3J7Y 0.1700 1 Single bulged U (H) A LSU rRNA A 2730 G 2732 * C 2929 U 2930 cWW cWW
252 IL_4V19_038 4V19 0.2185 1 Single bulged U (H) A LSU rRNA A 1060 G 1062 * C 1263 U 1264 cWW cWW
253 IL_4FRG_002 4FRG 0.1993 1 Single bulged U B Cobalamin riboswitch G 23 G 25 * C 39 C 40 cWW cWW
254 IL_2IZN_005 2IZN 0.2095 1 Single bulged G R RNA (19-mer) G 14||||P_P G 15||||P_P * C 5||||P_P C 7||||P_P
255 IL_2IZN_001 2IZN 0.2095 1 Single bulged G R RNA (19-mer) G 14||||P_1 G 15||||P_1 * C 5||||P_1 C 7||||P_1 cWW cWW
256 IL_4V91_028 4V91 0.2658 1 Single bulged A (H) 1 LSU rRNA G 779 G 781 * C 752 C 753 cWW cWW
257 IL_4V8P_378 4V8P 0.2421 1 F1 LSU rRNA U 1758 G 1760 * C 1733 A 1734 ncWW cWW
258 IL_4V91_036 4V91 0.2178 1 Single bulged U (H) 1 LSU rRNA C 873 G 875 * C 886 G 887 cWW cWW
259 IL_3J79_034 3J79 0.1976 1 Single bulged U (H) A LSU rRNA C 992 G 994 * C 1005 G 1006 cWW cWW
260 IL_4V8P_440 4V8P 0.2331 1 Single bulged A (H) G3 5S rRNA U 62 A 64 * U 15 A 16 cWW cWW
261 IL_4V9F_074 4V9F 0.2403 1 Single bulged U 0 LSU rRNA A 2108 G 2110 * C 2477 U 2478 cWW cWW
262 IL_3NDB_005 3NDB 0.2496 1 Single bulged U M SRP RNA G 237 G 238 * C 139 C 141 cWW cWW
263 IL_6MSF_003 6MSF 0.2741 1 Single bulged A R RNA (14-mer) G 12||||P_P G 13||||P_P * C 2||||P_P C 4||||P_P
264 IL_6MSF_001 6MSF 0.2741 1 Single bulged A R RNA (14-mer) G 12||||P_1 G 13||||P_1 * C 2||||P_1 C 4||||P_1 cWW cWW
265 IL_4V88_384 4V88 0.2553 1 Single bulged C A6 SSU rRNA U 24 A 26 * U 600 A 601 cWW cWW
266 IL_3J9W_076 3J9W 0.3229 1 BA LSU rRNA G 344 G 346 * C 359 C 360 cWW cWW
267 IL_5AJ0_057 5AJ0 0.2773 1 Single bulged A (H) A2 LSU rRNA G 1478 G 1480 * C 1449 C 1450 cWW cWW
268 IL_4V88_266 4V88 0.2337 1 Single bulged A (H) A5 LSU rRNA G 779 G 781 * C 752 C 753 cWW cWW
269 IL_4V88_439 4V88 0.2962 1 Single bulged U A6 SSU rRNA G 1051 G 1053 * C 1066 C 1067 cWW cWW
270 IL_3J7Y_001 3J7Y 0.2603 1 Single bulged A (H) A LSU rRNA G 1768 G 1770 * C 1682 C 1683 cWW cWW
271 IL_3SN2_001 3SN2 0.2106 1 Single bulged C B IRE II U 7 G 9 * C 24 A 25 cWW cWW
272 IL_1S03_002 1S03 0.1853 1 Single bulged C A 47-MER G 9 G 11 * C 39 C 40 cWW cWW
273 IL_3J92_171 3J92 0.1572 1 Single bulged A (H) 7 5S rRNA C 15 A 16 * U 62 G 64 cWW cWW
274 IL_3J9W_001 3J9W 0.2102 1 Single bulged G (H) AA SSU rRNA C 32 A 34 * U 561 G 562 cWW cWW
275 IL_2UWM_003 2UWM 0.2282 1 Single bulged U D RNA (23-mer) C 21 G 22 * C 25 G 27 cWW cWW
276 IL_3W3S_005 3W3S 0.2733 1 Single bulged U B Selenocysteine transfer RNA G 43||||43_455 G 44||||43_455 * C 26||||43_455 C 27||||43_455 cWW cWW
277 IL_3W3S_002 3W3S 0.2733 1 Single bulged U B Selenocysteine transfer RNA G 43 G 44 * C 26 C 27 cWW cWW
278 IL_4V88_318 4V88 0.2705 1 Single bulged C (H) A5 LSU rRNA G 1778 G 1780 * C 1669 C 1670 cWW cWW
279 IL_4V8P_386 4V8P 0.2976 1 Single bulged A (H) F1 LSU rRNA G 2318 G 2320 * C 2124 C 2125 cWW cWW
280 IL_4V8P_358 4V8P 0.2343 1 Single bulged U (H) F1 LSU rRNA A 1207 G 1209 * U 1351 U 1352 cWW cWW
281 IL_3J9W_040 3J9W 0.2511 1 Single bulged U (H) AA SSU rRNA G 1058 G 1060 * C 1217 C 1218 cWW cWW
282 IL_3D2V_001 3D2V 0.2383 1 Single bulged U A TPP riboswitch (THI element) G 73 G 75 * C 5 C 6 cWW cWW
283 IL_4U4U_453 4U4U 0.1624 1 Single bulged A (H) 7 5S rRNA A 63 G 65 * C 15 U 16 cWW cWW
284 IL_3J79_127 3J79 0.1703 1 A LSU rRNA A 3731 G 3733 * C 3756 U 3757 cWW cWW
285 IL_1R3E_001 1R3E 0.1810 3 Multiple bulged bases D+E RNA (17-mer) G 408 G 412 * C 415 C 416 cWW cWW
286 IL_3J7P_211 3J7P 0.2665 1 Single bulged U (H) S2 SSU rRNA G 1325 G 1327 * C 1502 C 1503 cWW cWW
287 IL_4V19_017 4V19 0.3311 1 Single bulged C (H) A LSU rRNA G 477 G 479 * C 586 C 587 cWW cWW
288 IL_3J7P_019 3J7P 0.2951 1 5 LSU rRNA G 695 G 697 * C 459 C 460 cWW cWW
289 IL_3J79_119 3J79 0.2822 1 A LSU rRNA G 3580 G 3582 * C 3620 C 3621 cWW cWW
290 IL_3JAM_050 3JAM 0.2734 1 Single bulged U (H) 2 SSU rRNA G 1050 G 1052 * C 1065 C 1066 cWW cWW
291 IL_3JAN_006 3JAN 0.3192 1 4 SRP RNA G 175 G 177 * C 220 C 221 cWW cWW
292 IL_3J9W_035 3J9W 0.3365 1 Single bulged G (H) AA SSU rRNA G 935 G 937 * U 1399 U 1400 cWW cWW
293 IL_1FJG_036 1FJG 0.3571 1 Single bulged G (H) A SSU rRNA G 925 G 927 * U 1390 U 1391 cWW cWW
294 IL_4V4Q_220 4V4Q 0.3350 1 Single bulged G (H) CA SSU rRNA G 925 G 927 * U 1390 U 1391 cWW cWW
295 IL_3TZR_002 3TZR 0.2141 1 Single bulged U B+A RNA (16-mer) G 105 G 107 * U 61 C 62 cWW cWW
296 IL_3J79_012 3J79 0.3323 1 Single bulged U (H) A LSU rRNA G 197 G 199 * U 212 C 213 cWW cWW
297 IL_2PN4_008 2PN4 0.3214 1 D+C RNA (20-mer) G 105 G 107 * U 61 C 62 cWW cWW
298 IL_5A2Q_094 5A2Q 0.2947 1 3 IRES G 105 G 107 * U 61 C 62 cWW cWW
299 IL_5AJ0_108 5AJ0 0.3923 1 Single bulged C (H) A2 LSU rRNA G 2703 G 2705 * C 2592 C 2593 cWW ncWW
300 IL_4V8P_374 4V8P 0.4662 1 F1 LSU rRNA G 1804 G 1806 * U 1693 C 1694 cWW cWW
301 IL_4JGN_006 4JGN 0.3949 0 E RNA (20-mer) U 503 G 504 * C 520||||4_555 U 521||||4_555 cWw cWW
302 IL_3JAM_053 3JAM 0.3735 1 Single bulged G (H) 2 SSU rRNA G 1148 A 1150 * U 1625 U 1626 cWW cWW
303 IL_3J7A_052 3J7A 0.3900 1 Single bulged G (H) A SSU rRNA G 1250 A 1252 * U 1924 U 1925 cWW cWW
304 IL_4V91_088 4V91 0.4669 1 Single bulged A (H) 1 LSU rRNA G 2323 G 2325 * C 2128 U 2129 cWW cWW
305 IL_4V88_442 4V88 0.4324 1 Single bulged G A6 SSU rRNA G 1149 A 1151 * U 1627 U 1628 cWW cWW
306 IL_4V8P_292 4V8P 0.4623 1 Single bulged A (H) F1+E2 LSU rRNA G 336 C 338 * G 28 U 29 cWW cWW
307 IL_5A2Q_033 5A2Q 0.3883 1 2 SSU rRNA G 606 C 608 * G 635 C 636 cWW cWW
308 IL_3J9M_061 3J9M 0.3491 1 AA SSU rRNA A 649 A 651 * U 667 U 668 cWW cWW
309 IL_5AJ0_038 5AJ0 0.3020 1 A2 LSU rRNA G 699 C 700 * G 1270 C 1272 cWW cWW
310 IL_3J79_090 3J79 0.3033 1 Single bulged U (H) A LSU rRNA A 3170 C 3171 * G 2702 U 2704 cWW cWW
311 IL_1NBS_005 1NBS 0.2949 1 Single bulged A B RNase P class B G 113 C 114 * G 129 C 131 cWW cWW
312 IL_5AJ3_001 5AJ3 0.3041 1 A SSU rRNA U 21 U 22 * A 3 A 5 ncWW cWW
313 IL_3J79_050 3J79 0.3267 1 Single bulged U (H) A LSU rRNA A 1308 A 1310 * U 1452 U 1453 cWW cWW
314 IL_4V88_372 4V88 0.2820 1 A5 LSU rRNA C 3193 C 3194 * G 3197 G 3199 cWW cWW
315 IL_1FJG_014 1FJG 0.2141 1 Single bulged U (H) A SSU rRNA G 392 A 393 * U 367 C 369 cWW cWW
316 IL_4V9F_029 4V9F 0.2328 1 Single bulged U 0 LSU rRNA G 834 G 836 * C 847 C 848 cWW cWW
317 IL_4V8P_397 4V8P 0.2387 1 Single bulged U (H) F1 LSU rRNA G 2404 U 2406 * A 2799 C 2800 cWW cWW
318 IL_4V88_339 4V88 0.2251 1 Single bulged U (H) A5 LSU rRNA G 2409 U 2411 * A 2811 C 2812 cWW cWW
319 IL_5AJ0_131 5AJ0 0.2663 1 Single bulged U (H) A2 LSU rRNA G 3884 U 3886 * A 4350 C 4351 cWW cWW
320 IL_4V91_100 4V91 0.2843 1 Single bulged U (H) 1 LSU rRNA A 2811 C 2812 * G 2409 U 2411 cWW cWW
321 IL_3J7P_107 3J7P 0.2980 1 Single bulged U (H) 5 LSU rRNA G 3913 U 3915 * A 4388 C 4389 cWW cWW
322 IL_4IOA_002 4IOA 0.3147 1 Single bulged A X LSU rRNA G 36 C 37 * G 454 C 456 cWW cWW
323 IL_5J7L_246 5J7L 0.2563 1 Single bulged A DA LSU rRNA G 36 C 37 * G 442 C 444 cWW cWW
324 IL_5FDU_002 5FDU 0.3132 1 Single bulged A (H) 1A LSU rRNA G 36 C 37 * G 468 C 470 cWW cWW
325 IL_5AN9_025 5AN9 0.3051 1 Single bulged U (H) N LSU rRNA G 2675 U 2677 * A 3144 C 3145 cWW cWW
326 IL_3JCS_069 3JCS 0.3319 1 2 LSU rRNA A 74 A 76 * U 589 U 590 cWW cWW
327 IL_4V8C_111 4V8C 0.3429 1 AB 5S rRNA G 118 A 119 * U 1 C 2 cWW cWW
328 IL_4R0D_008 4R0D 0.2990 1 A Group II catalytic intron G 312 A 314 * U 161 C 162 cWW ncWW
329 IL_4V8P_426 4V8P 0.2965 1 F1 LSU rRNA G 3158 A 3160 * U 3179 C 3180 cWW cWW
330 IL_3V7E_001 3V7E 0.3263 1 Single bulged A C SAM-I riboswitch G 13 G 15 * C 40 C 41 cWW cWW
331 IL_2VPL_002 2VPL 0.2106 1 Single bulged A B FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE U 16 C 17 * G 28 A 30 cWW cWW
332 IL_3J7A_056 3J7A 0.1557 1 Single bulged U (H) A SSU rRNA C 1686 C 1687 * G 1369 G 1371 cWW cWW
333 IL_3WBM_001 3WBM 0.1955 1 Single bulged U Y+X RNA (25-MER) U 23 C 24 * G 2 A 4 cWW cWW
334 IL_4V88_244 4V88 0.2374 1 Single bulged U (H) A5+A8 LSU rRNA + 5.8S rRNA A 13 C 15 * G 144 U 145 cWW cWW
335 IL_1R3E_002 1R3E 0.1706 3 Multiple bulged bases D+E RNA (17-mer) C 415 C 416 * G 408 G 412 cWW cWW
336 IL_4BTS_293 4BTS 0.2057 1 DA SSU rRNA A 579 G 580 * C 552 U 554 cWW cWW
337 IL_4P3U_005 4P3U 0.1641 1 Single bulged A A+B RNA (23-mer) A 17 G 19 * C 30 U 31 cWW cWW
338 IL_4P3U_002 4P3U 0.2903 1 Single bulged A B+A RNA (23-mer) A 40 G 42 * C 7 U 8 ncWW cWW
339 IL_1SI3_002 1SI3 0.3163 0 B RNA (9-mer) C 401 G 402 * C 406||||4_675 U 407||||4_675 cWW cWW
340 IL_5FDU_060 5FDU 0.3427 1 Single bulged A (H) 1A LSU rRNA G 1506 G 1508 * C 1498 C 1499 cWW cWW
341 IL_4IOA_015 4IOA 0.3174 1 Single bulged A X LSU rRNA G 776 G 778 * C 710 C 711 cWW cWW
342 IL_5FDU_019 5FDU 0.3147 1 Single bulged A (H) 1A LSU rRNA G 810 G 812 * C 744 C 745 cWW cWW
343 IL_4IOA_034 4IOA 0.2934 1 Single bulged U X LSU rRNA A 1022 G 1024 * C 1160 U 1161 cWW cWW
344 IL_3OX0_001 3OX0 0.3649 1 A Glycine riboswitch G 12 A 14 * U 27 C 28 cWW cWW
345 IL_4V88_296 4V88 0.3871 1 A5 LSU rRNA A 1180 A 1182 * U 1324 U 1325 cWW cWW
346 IL_4V91_055 4V91 0.3706 1 1 LSU rRNA A 1180 A 1182 * U 1324 U 1325 cWW cWW
347 IL_3J79_031 3J79 0.3915 1 Single bulged G (H) A LSU rRNA G 978 A 980 * U 952 U 953 cWW cWW
348 IL_4V88_383 4V88 0.3267 2 Multiple bulged bases (H) A5 LSU rRNA G 3353 G 3356 * C 3349 C 3350 cWW cWW
349 IL_5AN9_033 5AN9 0.3406 1 N LSU rRNA G 3104 G 3106 * C 3120 C 3121 cWW cWW
350 IL_4V91_135 4V91 0.4998 1 Single bulged U (H) 1 LSU rRNA G 3197 G 3199 * C 3193 C 3194 cWW cWW
351 IL_4V19_034 4V19 0.5995 2 A LSU rRNA G 926 C 927 * G 957 U 960 cWW cWW
352 IL_4V9F_026 4V9F 0.4817 1 Single bulged G 0 LSU rRNA A 819 U 821 * A 793 U 794 cWW cWW
353 IL_4V91_141 4V91 0.4768 1 1 LSU rRNA G 3318 A 3320 * U 3387 C 3388 cWW cWW
354 IL_4V88_401 4V88 0.4977 1 Single bulged U A6 SSU rRNA G 279 G 281 * C 275 C 276 cWW cWW
355 IL_4V88_377 4V88 0.4798 1 Single bulged U (H) A5 LSU rRNA G 3318 A 3320 * U 3387 C 3388 cWW cWW
356 IL_4V91_148 4V91 0.4959 2 Multiple bulged bases (H) 1 LSU rRNA G 3353 G 3356 * C 3349 C 3350 cWW cWW
357 IL_3J9M_105 3J9M 0.4498 1 AA SSU rRNA G 1538 A 1540 * U 1510 C 1511 cWW cWW
358 IL_4V8P_294 4V8P 0.4403 1 E2 5.8S rRNA G 71 C 72 * G 90 C 92 cWW cWW
359 IL_4V91_157 4V91 0.4761 1 Single bulged U (H) 4 5.8S rRNA G 68 U 69 * A 89 C 91 cWW cWW
360 IL_4V88_486 4V88 0.4719 1 Single bulged U (H) A8 5.8S rRNA G 68 U 69 * A 89 C 91 cWW cWW
361 IL_4V8P_403 4V8P 0.4627 1 Single bulged A (H) F1 LSU rRNA G 2603 U 2604 * A 2614 U 2616 cWW cWW
362 IL_4V88_255 4V88 0.4557 1 Single bulged A (H) A8+A5 5.8S rRNA G 25 U 26 * G 337 C 339 cWW cWW
363 IL_4V91_016 4V91 0.4636 1 Single bulged A (H) 4+1 5.8S rRNA G 25 U 26 * G 337 C 339 cWW cWW
364 IL_3J7P_179 3J7P 0.4103 1 S2 SSU rRNA U 495 C 496 * G 506 A 508 cWW ncWW
365 IL_4V9F_013 4V9F 0.3337 1 Single bulged U 0 LSU rRNA G 322 C 323 * G 307 C 309 cWW cWW
366 IL_4V88_414 4V88 0.4092 1 Single bulged U A6 SSU rRNA G 586 C 587 * G 557 C 559 cWW cWW
367 IL_2OIU_001 2OIU 0.3532 1 P L1 Ribozyme RNA Ligase A 41 C 42 * G 18 U 20 cWW cWW
368 IL_4V91_015 4V91 0.4182 1 Single bulged U (H) 1 LSU rRNA A 204 C 205 * G 189 U 191 cWW cWW
369 IL_5AJ0_035 5AJ0 0.4227 1 A2 LSU rRNA A 643 C 644 * G 502 U 504 cWW cWW
370 IL_4V9F_002 4V9F 0.3898 1 Single bulged A 0 LSU rRNA G 33 C 34 * G 448 C 450 cWW cWW
371 IL_5AJ0_017 5AJ0 0.3644 1 Single bulged A (H) A3+A2 5.8S rRNA G 25 C 26 * G 342 C 344 cWW cWW
372 IL_1DUQ_008 1DUQ 0.3282 1 G+H THE REV BINDING ELEMENT G 408 C 409 * G 420 C 422 cWW cWW
373 IL_2PJP_001 2PJP 0.3758 1 Single bulged U B SECIS RNA A 29 C 30 * G 16 U 18 cWW cWW
374 IL_1U9S_001 1U9S 0.4069 1 Single bulged A A RNase P class A G 95 C 96 * G 107 C 109 cWW cWW
375 IL_5A2Q_028 5A2Q 0.4349 1 Single bulged A (H) 2 SSU rRNA A 529 U 530 * A 554 U 556 cWW cWW
376 IL_2OIU_003 2OIU 0.3814 1 Single bulged U Q L1 Ribozyme RNA Ligase A 41 C 42 * G 18 U 20 cWW cWW
377 IL_4BTS_292 4BTS 0.3981 1 DA SSU rRNA G 580 C 581 * G 550 C 552 cWW cWW
378 IL_1CSL_002 1CSL 0.4048 1 Single bulged A A+B RNA (13-mer) + RNA (15-mer) G 50 C 51 * G 67 C 69 cWW cWW
379 IL_5F5H_002 5F5H 0.4044 1 Single bulged C D RNA (21-mer) A 4 C 5 * G 18 U 20 cWW cWW
380 IL_5F5H_001 5F5H 0.3830 1 Single bulged C C RNA (21-mer) A 4 C 5 * G 18 U 20 cWW cWW
381 IL_3JAM_032 3JAM 0.3889 1 Single bulged U (H) 2 SSU rRNA G 585 C 586 * G 556 C 558 cWW cWW
382 IL_3J79_001 3J79 0.3243 1 Single bulged U (H) C+A 5.8S rRNA A 151 C 152 * G 13 U 15 cWW cWW
383 IL_4BTS_331 4BTS 0.3767 1 DA SSU rRNA U 1322 C 1323 * G 1343 A 1345 cWW cWW
384 IL_3J7P_013 3J7P 0.4368 1 Single bulged U (H) 5 LSU rRNA G 214 C 215 * G 199 C 201 cWW cWW
385 IL_4V8P_402 4V8P 0.4211 1 F1 LSU rRNA A 2557 U 2558 * A 2561 U 2563 cWW cWW
386 IL_3HHN_003 3HHN 0.3593 1 Single bulged C E Class I ligase ribozyme, self-ligation product A 112 C 113 * G 46 U 48 cWW cWW
387 IL_4V88_254 4V88 0.3717 1 Single bulged U (H) A5 LSU rRNA A 204 C 205 * G 189 U 191 cWW cWW
388 IL_5AJ0_070 5AJ0 0.3837 1 Single bulged G (H) A2 LSU rRNA A 1819 U 1820 * A 1705 U 1707 cWW cWW
389 IL_4V88_399 4V88 0.3658 1 Single bulged A A6 SSU rRNA A 288 U 289 * A 265 U 267 cWW cWW
390 IL_3JAM_018 3JAM 0.3476 1 Single bulged A (H) 2 SSU rRNA A 287 U 288 * A 264 U 266 cWW cWW
391 IL_3J79_038 3J79 0.4638 1 Single bulged G (H) A LSU rRNA A 1226 U 1227 * A 1105 U 1107 cWW cWW
392 IL_2A64_002 2A64 0.4222 1 Single bulged U A RNase P class B G 395 C 396 * G 51 C 53 cWW cWW
393 IL_3J7A_014 3J7A 0.4295 1 Single bulged A (H) A SSU rRNA G 294 U 295 * A 266 C 268 cWW cWW
394 IL_3JAM_027 3JAM 0.4426 1 2 SSU rRNA U 446 C 447 * G 457 A 459 cWW cWW
395 IL_4O26_001 4O26 0.4843 1 Single bulged U E Telomerase TR G 193 C 194 * G 181 C 183 cWW cWW
396 IL_4V88_409 4V88 0.3965 1 Single bulged A A6 SSU rRNA A 481 U 482 * A 505 U 507 cWW cWW
397 IL_3J9W_002 3J9W 0.3108 1 Single bulged A (H) AA SSU rRNA G 46 U 47 * A 404 C 406 cWW cWW
398 IL_4BTS_286 4BTS 0.3656 1 DA SSU rRNA U 439 C 440 * G 450 A 452 cWW cWW
399 IL_2XXA_010 2XXA 0.4158 1 G SSRP RNA G 17 C 18 * G 82 C 84 cWW cWW ncWw
400 IL_5A2Q_019 5A2Q 0.3816 1 Single bulged A (H) 2 SSU rRNA A 336 C 337 * G 312 U 314 cWW cWW
