1 HL_3Q1Q_002 3Q1Q 0.5527 1 B RNase P RNA G 77 U 78 A 79 A 80 C 81 C 83 cWW
2 HL_4V9F_036 4V9F 0.4774 1 GNRA variation 0 LSU rRNA G 1468 C 1469 A 1470 A 1471 C 1472 C 1474 cWW tSHa
3 HL_4V9F_022 4V9F 0.6034 0 Other HL 0 LSU rRNA U 733 U 734 C 735 A 736 A 737 G 738 cWW
4 HL_2OIU_005 2OIU 0.4188 0 Q L1 Ribozyme RNA Ligase C 28 G 29 A 30 A 31 A 32 G 33 cWW
5 HL_4V5O_040 4V5O 0.5102 0 BA SSU rRNA A 226 G 227 C 228 A 229 A 230 U 231 cWW
6 HL_4V9F_040 4V9F 0.2409 0 GNRA 0 LSU rRNA G 1628 G 1629 A 1630 A 1631 A 1632 C 1633 cWW ntSH
7 HL_4LFB_003 4LFB 0.2815 0 GNRA A SSU rRNA G 158 G 159 A 160 A 161 A 162 C 163 cWW ntSH
8 HL_5J7L_003 5J7L 0.2553 0 GNRA AA SSU rRNA G 158 G 159 A 160 A 161 A 162 C 163 cWW ntSH
9 HL_3IAB_001 3IAB 0.2812 0 R P3 domain of the RNA component of RNase MRP G 78 G 79 A 80 A 81 A 82 C 83 cWW ntSH
10 HL_3IAB_002 3IAB 0.2812 0 R P3 domain of the RNA component of RNase MRP G 78||||7_556 G 79||||7_556 A 80||||7_556 A 81||||7_556 A 82||||7_556 C 83||||7_556 cWW ntSH
11 HL_4V9F_020 4V9F 0.2506 0 GNRA 0 LSU rRNA G 690 G 691 A 692 A 693 A 694 C 695 cWW ntSH
12 HL_5DDP_001 5DDP 0.2323 0 GNRA A glnA G 11 G 12 A 13 A 14 A 15 C 16 cWW ntSH
13 HL_4V8P_083 4V8P 0.2287 0 C3 5S rRNA G 86 G 87 G 88 G 89 A 90 C 91 cWW ntSH
14 HL_3E5C_001 3E5C 0.2589 0 GNRA A SMK box (SAM-III) Riboswitch G 18 G 19 A 20 A 21 A 22 C 23 cWW tSH
15 HL_4V9F_070 4V9F 0.2753 0 GNRA 0 LSU rRNA G 2876 G 2877 U 2878 A 2879 A 2880 C 2881 cWW ntSH
16 HL_5FJC_002 5FJC 0.2041 0 GNRA A SAM-I riboswitch A 49 G 50 A 51 A 52 A 53 U 54 cWW ntSH
17 HL_5FJC_003 5FJC 0.2173 0 GNRA A SAM-I riboswitch G 73 G 74 A 75 A 76 A 77 C 78 cWW ntSH
18 HL_4OQU_003 4OQU 0.2302 0 GNRA A SAM-I/IV riboswitch G 57 G 58 A 59 G 60 A 61 C 62 cWW ntSH
19 HL_4Y1J_001 4Y1J 0.2236 0 A yybP-ykoY riboswitch G 20 G 21 A 22 A 23 A 24 C 25 cWW ntSH
20 HL_1MFQ_002 1MFQ 0.2708 0 GNRA A SRP RNA G 197 G 198 A 199 A 200 A 201 C 202 cWW tSH
21 HL_4V8P_103 4V8P 0.2503 0 D1 LSU rRNA G 869 G 870 A 871 A 872 A 873 C 874 cWW ntSH
22 HL_4ZT0_004 4ZT0 0.2390 0 GNRA D single-guide RNA A 32 G 33 A 34 A 35 A 36 U 37 cWW ntSH
23 HL_3Q1Q_004 3Q1Q 0.2081 0 B RNase P RNA G 135 G 136 A 137 A 138 A 139 C 140 cWW ntSH
24 HL_4AOB_003 4AOB 0.2149 0 GNRA A SAM-I riboswitch G 73 G 74 A 75 A 76 A 77 C 78 cWW ntSH
25 HL_4AOB_006 4AOB 0.2149 0 GNRA A SAM-I riboswitch G 73||||7_555 G 74||||7_555 A 75||||7_555 A 76||||7_555 A 77||||7_555 C 78||||7_555 cWW ntSH
26 HL_5F9R_003 5F9R 0.1792 0 GNRA A RNA (116-MER) U 90 G 91 A 92 A 93 A 94 A 95 cWW ntSH
27 HL_2XXA_001 2XXA 0.1766 0 F SSRP RNA C 47 G 48 G 49 A 50 A 51 G 52 cWW
28 HL_3RW6_001 3RW6 0.2816 0 GNRA H constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA G 27 G 28 A 29 A 30 A 31 C 32 cWW tSH
29 HL_3MOJ_001 3MOJ 0.2604 0 GNRA A LSU rRNA G 2529 G 2530 A 2531 A 2532 A 2533 C 2534 cWW ntSH
30 HL_2R8S_001 2R8S 0.2443 0 GNRA R P4-P6 RNA RIBOZYME DOMAIN G 149 G 150 A 151 A 152 A 153 C 154 cWW ntSH
31 HL_3IGI_006 3IGI 0.2313 0 GNRA A Group IIC intron G 274 G 275 A 276 A 277 A 278 C 279 cWW ntSH
32 HL_1U6B_001 1U6B 0.2376 0 GNRA B 197-MER G 23 G 24 A 25 A 26 A 27 C 28 cWW ntSH
33 HL_3V7E_003 3V7E 0.2414 0 GNRA C SAM-I riboswitch G 105 G 106 A 107 A 108 A 109 C 110 cWW ntSH
34 HL_1NBS_007 1NBS 0.2680 0 GNRA B RNase P class B A 204 G 205 A 206 A 207 A 208 U 209 cWW ntSH
35 HL_5CZZ_001 5CZZ 0.2355 0 GNRA B RNA (73-MER) G 34 G 35 A 36 A 37 A 38 C 39 cWW ntSH
36 HL_5DCV_002 5DCV 0.2855 0 GNRA D RNA (47-MER) G 26 G 27 A 28 A 29 A 30 C 31 cWW ntSH
37 HL_5F9R_001 5F9R 0.2367 0 A RNA (116-MER) U 41 G 42 A 43 A 44 A 45 A 46 cWW ntSH
38 HL_3T4B_001 3T4B 0.2465 0 A HCV IRES pseudoknot domain plus crystallization module G 9 G 10 A 11 A 12 A 13 C 14 cWW ntSH
39 HL_5FQ5_003 5FQ5 0.2751 0 GNRA A SGRNA U 72 G 73 A 74 A 75 A 76 A 77 ncWW ntSH
40 HL_4AOB_005 4AOB 0.2104 0 GNRA A SAM-I riboswitch A 49||||7_555 A 50||||7_555 A 51||||7_555 A 52||||7_555 A 53||||7_555 U 54||||7_555 cWW tSH
41 HL_4AOB_002 4AOB 0.2104 0 GNRA A SAM-I riboswitch A 49 A 50 A 51 A 52 A 53 U 54 cWW tSH
42 HL_4R0D_008 4R0D 0.3618 0 A Group II catalytic intron G 369 G 370 A 371 A 372 A 373 C 374 cWW tSH
43 HL_5DDO_001 5DDO 0.2290 0 GNRA A L-glutamine riboswitch (58-MER) G 11 G 12 A 13 A 14 A 15 C 16 cWW
44 HL_4V9F_028 4V9F 0.2351 1 GNRA 0 LSU rRNA G 1054 G 1055 U 1056 A 1057 A 1058 C 1060 cWW ntSH
45 HL_4IOA_026 4IOA 0.2748 2 GNRA X LSU rRNA A 966 G 967 C 968 A 970 A 971 U 973 cWW ntSH
46 HL_4V8P_109 4V8P 0.3318 1 D1 LSU rRNA G 1153 G 1154 U 1155 A 1156 A 1157 C 1159 cWW
47 HL_4R0D_005 4R0D 0.2507 0 A Group II catalytic intron C 173 G 174 A 175 A 176 A 177 G 178 cWW ntSH
48 HL_4V8P_096 4V8P 0.2892 0 D1 LSU rRNA A 582 G 583 C 584 A 585 A 586 U 587 cWW ntSH
49 HL_4IOA_005 4IOA 0.3624 0 Other HL X LSU rRNA C 146 G 147 C 148 A 149 A 150 G 151 cWW
50 HL_4V5O_069 4V5O 0.5776 0 BA SSU rRNA A 1660 G 1661 C 1662 A 1663 A 1664 U 1665 cWW
51 HL_3Q1Q_010 3Q1Q 0.5998 0 C TRNA (PHE) G 37 C 38 A 39 C 40 C 41 C 42 cWW ntWH
52 HL_4WF9_027 4WF9 0.2768 2 GNRA X LSU rRNA U 999 G 1000 A 1001 A 1003 A 1004 G 1006 cWW ntSH
53 HL_4Y4O_129 4Y4O 0.2211 2 GNRA 2A LSU rRNA C 955 G 956 A 957 A 959 A 960 G 962 cWW ntSH
54 HL_4V9F_009 4V9F 0.2069 0 GNRA 0 LSU rRNA C 252 U 253 C 254 A 255 C 256 G 257 cWW ntSH
55 HL_3RG5_011 3RG5 0.2903 0 GNRA B Selenocysteine transfer RNA U 47|||C|1_556 U 47|||D|1_556 A 47|||E|1_556 G 47|||F|1_556 C 47|||G|1_556 G 47|||H|1_556 cWW ntSHa
56 HL_3RG5_007 3RG5 0.2903 0 GNRA B Selenocysteine transfer RNA U 47|||C U 47|||D A 47|||E G 47|||F C 47|||G G 47|||H cWW ntSHa
57 HL_4LFB_007 4LFB 0.2636 0 GNRA A SSU rRNA U 296 G 297 A 298 G 299 A 300 G 301 cWW ntSH
58 HL_5J7L_007 5J7L 0.2545 0 GNRA AA SSU rRNA U 296 G 297 A 298 G 299 A 300 G 301 cWW ntSH
59 HL_4R0D_012 4R0D 0.3286 0 A Group II catalytic intron U 481 G 482 A 483 A 484 A 485 G 486 cWW tSH
60 HL_1KXK_001 1KXK 0.2087 0 GNRA A ai5g group II Self-splicing intron U 33 G 34 A 35 A 36 A 37 G 38 cWW ntSH
61 HL_4K50_001 4K50 0.1750 0 GNRA B RNA (33-MER) U 587 G 588 A 589 A 590 A 591 G 592 cWW ntSH
62 HL_4K27_001 4K27 0.2127 0 GNRA U Myotonic Dystrophy Type 2 RNA U 26 G 27 A 28 A 29 A 30 G 31 cWW ntSH
63 HL_4PCJ_001 4PCJ 0.2106 0 GNRA A trCUG-3('5) U 16 G 17 A 18 A 19 A 20 G 21 cWW ntSH
64 HL_5BTM_001 5BTM 0.2198 0 GNRA A RNA (55-mer) U 26 G 27 A 28 A 29 A 30 G 31 cWW ntSH
65 HL_5M0H_001 5M0H 0.2355 0 GNRA A ASH1 E3 (42 nt-TL/TLR) U 21 G 22 A 23 A 24 A 25 G 26 cWW ntSH
66 HL_4R0D_014 4R0D 0.2507 0 A Group II catalytic intron U 563 G 564 A 565 A 566 A 567 G 568 cWW ntSH
67 HL_4LFB_022 4LFB 0.3280 0 GNRA A SSU rRNA U 1012 G 1013 A 1014 A 1015 A 1016 G 1017 cWW ntSH
68 HL_5J7L_019 5J7L 0.2204 0 GNRA AA SSU rRNA C 862 U 863 A 864 A 865 C 866 G 867 cWW ntSH
69 HL_4LFB_019 4LFB 0.2030 0 GNRA A SSU rRNA C 862 U 863 A 864 A 865 C 866 G 867 cWW ntSH
70 HL_4P95_004 4P95 0.2020 0 GNRA A RNA (192-MER) C 317 U 318 A 319 A 320 C 321 G 322 cWW ntSH
71 HL_4P8Z_003 4P8Z 0.1853 0 A Lariat capping ribozyme C 99 U 100 A 101 A 102 C 103 G 104 cWW ntSH
72 HL_3PDR_001 3PDR 0.1879 0 GNRA X M-box riboswitch (ykoK leader) C 68 C 69 A 70 A 71 A 72 G 73 cWW ntSH
73 HL_2IL9_003 2IL9 0.1815 0 GNRA A Ribosomal Binding Domain of the IRES RNA C 6119 G 6119|||A A 6119|||B A 6119|||C A 6119|||D G 6119|||E ncWW tSH
74 HL_4GMA_004 4GMA 0.1451 0 Z Adenosylcobalamin riboswitch C 119 G 120 A 121 A 122 A 123 G 124 cWW ntSH
75 HL_5D5L_001 5D5L 0.1450 0 GNRA A PreQ1-II riboswitch C 8 G 9 A 10 A 11 A 12 G 13 cWW ntSH
76 HL_4JF2_001 4JF2 0.1487 0 GNRA A PreQ1-II Riboswitch C 8 G 9 A 10 A 11 A 12 G 13 cWW ntSH
77 HL_4FRG_002 4FRG 0.1621 0 GNRA B cobalamin riboswitch aptamer domain C 46 G 47 A 48 A 49 A 50 G 51 cWW ntSH
78 HL_2OIU_001 2OIU 0.1357 0 GNRA P L1 Ribozyme RNA Ligase C 10 G 11 A 12 A 13 A 14 G 15 cWW ntSH
79 HL_2OIU_004 2OIU 0.1479 0 Q L1 Ribozyme RNA Ligase C 10 G 11 A 12 A 13 A 14 G 15 cWW ntSH
80 HL_3P22_001 3P22 0.2239 0 GNRA A Core ENE hairpin from KSHV PAN RNA C 17 G 18 A 19 A 20 A 21 G 22 cWW ntSH
81 HL_4BW0_001 4BW0 0.2004 0 GNRA A HMKT-7 C 9 G 10 A 11 A 12 A 13 G 14 cWW ntSH
82 HL_4RUM_002 4RUM 0.1373 0 GNRA A NiCo riboswitch RNA C 51 G 52 A 53 A 54 A 55 G 56 cWW ntSH
83 HL_4QK8_001 4QK8 0.1614 0 A C-di-AMP riboswitch C 13 G 14 A 15 A 16 A 17 G 18 cWW ntSH
84 HL_4LFB_027 4LFB 0.1398 0 GNRA A SSU rRNA C 1165 G 1166 A 1167 A 1168 A 1169 G 1171 cWW ntSH
85 HL_4PLX_001 4PLX 0.1357 0 GNRA A Core ENE hairpin and A-rich tract from MALAT1 C 24 G 25 A 26 A 27 A 28 G 29 cWW ntSH
86 HL_4W90_003 4W90 0.1579 0 GNRA C cyclic di-AMP riboswitch C 82 G 83 A 84 A 85 A 86 G 87 cWW ntSH
87 HL_3CUL_001 3CUL 0.2251 0 GNRA C RNA (92-MER) C 7 G 8 A 9 A 10 A 11 G 12 cWW ntSH
88 HL_1MZP_001 1MZP 0.1691 0 GNRA B fragment of 23S rRNA C 25 G 26 C 27 A 28 A 29 G 30 cWW ntSH
89 HL_2EZ6_002 2EZ6 0.1709 0 GNRA D 28-MER C 11 G 12 C 13 A 14 A 15 G 16 cWW ntSH
90 HL_4Y4O_148 4Y4O 0.1476 0 GNRA 2A LSU rRNA C 1806 G 1807 U 1808 A 1809 A 1810 G 1811 cWW ntSH
91 HL_4V8P_101 4V8P 0.2267 0 D1 LSU rRNA C 757 G 758 C 759 A 760 A 761 G 762 cWW ntSH
92 HL_4WF9_060 4WF9 0.1882 0 GNRA X LSU rRNA C 2685 G 2686 A 2687 G 2688 A 2689 G 2690 cWW ntSH
93 HL_5B2T_003 5B2T 0.1408 0 GNRA A Guide RNA U 72 G 73 A 74 A 75 A 76 A 77 cWW ntSH
94 HL_4V8P_148 4V8P 0.1693 0 D1 LSU rRNA C 3014 G 3015 A 3016 G 3017 A 3018 G 3019 cWW ntSH
95 HL_4Y4O_167 4Y4O 0.1406 0 GNRA 2A LSU rRNA C 2658 G 2659 A 2660 G 2661 A 2662 G 2663 cWW ntSH
96 HL_5J7L_197 5J7L 0.1384 0 GNRA DA LSU rRNA C 2658 G 2659 A 2660 G 2661 A 2662 G 2663 cWW ntSH
97 HL_4IOA_063 4IOA 0.1621 0 GNRA X LSU rRNA C 2637 G 2638 A 2639 G 2640 A 2641 G 2642 cWW tSH
98 HL_3KTW_002 3KTW 0.1961 0 GNRA C SRP RNA C 209 G 210 G 211 A 212 A 213 G 214 cWW ntSH
99 HL_4V9F_066 4V9F 0.1620 0 GNRA 0 LSU rRNA C 2695 G 2696 A 2697 G 2698 A 2699 G 2700 cWW ntSH
100 HL_3NDB_002 3NDB 0.1438 0 GNRA M SRP RNA C 208 G 209 G 210 A 211 A 212 G 213 cWW tSH
101 HL_2OIU_002 2OIU 0.1711 0 P L1 Ribozyme RNA Ligase C 28 G 29 A 30 A 31 A 32 G 33 cWW ntSH
102 HL_4Y4O_118 4Y4O 0.1951 0 GNRA 2A LSU rRNA C 487 G 488 G 489 G 491 A 492 G 493 cWW ntSH
103 HL_4WF9_016 4WF9 0.2013 0 GNRA X LSU rRNA C 533 G 534 G 535 A 536 A 537 G 538 cWW ntSH
104 HL_4IOA_015 4IOA 0.2714 0 GNRA X LSU rRNA C 498 G 499 G 500 G 501 A 502 G 503 cWW tSH
105 HL_3D0U_004 3D0U 0.2256 0 GNRA A Lysine Riboswitch RNA C 142 G 143 A 144 A 145 A 146 G 147 cWW ntSH
106 HL_2OIU_006 2OIU 0.1564 0 Q L1 Ribozyme RNA Ligase C 59 G 60 A 61 A 62 A 63 G 64 cWW ntSH
107 HL_1KH6_002 1KH6 0.1503 0 GNRA A JIIIabc C 28 G 29 A 30 A 31 A 32 G 33 cWW ntSH
108 HL_3NVI_002 3NVI 0.1402 0 GNRA F RNA (24-mer) C 9 G 10 A 11 A 12 A 13 G 14 cWW ntSH
109 HL_3MXH_001 3MXH 0.1219 0 GNRA R c-di-GMP riboswitch C 31 G 32 A 33 A 34 A 35 G 36 cWW ntSH
110 HL_5TPY_003 5TPY 0.1110 0 GNRA A RNA (71-MER) C 62||||11_655 G 63||||11_655 A 64||||11_655 A 65||||11_655 A 66||||11_655 G 67||||11_655 cWW ntSH
111 HL_5TPY_009 5TPY 0.1110 0 GNRA A RNA (71-MER) C 62||||4_655 G 63||||4_655 A 64||||4_655 A 65||||4_655 A 66||||4_655 G 67||||4_655 cWW ntSH
112 HL_5TPY_006 5TPY 0.1110 0 GNRA A RNA (71-MER) C 62 G 63 A 64 A 65 A 66 G 67 cWW ntSH
113 HL_5TPY_012 5TPY 0.1110 0 GNRA A RNA (71-MER) C 62||||8_555 G 63||||8_555 A 64||||8_555 A 65||||8_555 A 66||||8_555 G 67||||8_555 cWW ntSH
114 HL_3IWN_001 3IWN 0.1303 0 GNRA A C-di-GMP riboswitch C 21 G 22 A 23 A 24 A 25 G 26 cWW ntSH
115 HL_4ENC_002 4ENC 0.1378 0 GNRA A Fluoride riboswitch U 28 G 29 A 30 A 31 A 32 A 33 cWW ntSH
116 HL_4WZJ_013 4WZJ 0.1340 0 XXX U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor. U 12 G 13 A 14 A 15 A 16 A 17 cWW ntSH
117 HL_4V9F_023 4V9F 0.1273 0 GNRA 0 LSU rRNA C 804 G 805 A 806 A 807 A 808 G 809 cWW ntSH
118 HL_1G1X_001 1G1X 0.1411 0 GNRA D 16S RIBOSOMAL RNA C 590 G 591 A 592 A 593 A 594 G 649 cWW ntSH
119 HL_1RLG_002 1RLG 0.1074 0 GNRA D 25-MER C 9 G 10 A 11 A 12 A 13 G 14 cWW ntSH
120 HL_4R4V_008 4R4V 0.1237 0 GNRA A VS ribozyme RNA C 735||||7_556 G 736||||7_556 U 737||||7_556 A 738||||7_556 A 739||||7_556 G 740||||7_556 cWW ntSH
121 HL_4R4V_004 4R4V 0.1237 0 GNRA A VS ribozyme RNA C 735 G 736 U 737 A 738 A 739 G 740 cWW ntSH
122 HL_4V8P_094 4V8P 0.0000 0 D1 LSU rRNA U 381 G 382 A 383 A 384 A 385 A 386 cWW ntSH
123 HL_5X2G_001 5X2G 0.0873 0 GNRA B sgRNA U 32 G 33 A 34 A 35 A 36 A 37 cWW ntSH
124 HL_4Y1M_003 4Y1M 0.1280 0 GNRA B E. coli yybP-ykoY riboswitch U 55 G 56 A 57 A 58 A 59 A 60 cWW ntSH
125 HL_3AM1_003 3AM1 0.1424 0 GNRA B ASL-truncated tRNA C 45 G 46 A 47 G 48 A 49 G 50 cWW ntSH
126 HL_3AM1_007 3AM1 0.1424 0 GNRA B ASL-truncated tRNA C 45||||5_555 G 46||||5_555 A 47||||5_555 G 48||||5_555 A 49||||5_555 G 50||||5_555 cWW ntSH
127 HL_4V9F_054 4V9F 0.1432 0 GNRA 0 LSU rRNA C 2248 G 2249 G 2250 G 2251 A 2252 G 2253 cWW ntSH
128 HL_4Y1M_002 4Y1M 0.1517 0 GNRA B E. coli yybP-ykoY riboswitch C 24 G 25 A 26 A 27 A 28 G 29 cWW ntSH
129 HL_4V9F_072 4V9F 0.1643 0 GNRA 9 5S rRNA C 89 G 90 C 91 G 92 A 93 G 94 cWW ntSH
130 HL_4NLF_001 4NLF 0.1365 0 GNRA A 23S ribosomal RNA Sarcin Ricin Loop C 2658 G 2659 A 2660 G 2661 A 2662 G 2663 cWW ntSH
131 HL_5M0I_001 5M0I 0.1342 0 GNRA E ASH1-E3 element, RNA (28-MER) C 12 G 13 A 14 A 15 A 16 G 17 cWW ntSH
132 HL_5M0I_002 5M0I 0.1292 0 GNRA F ASH1-E3 element, RNA (28-MER) C 12 G 13 A 14 A 15 A 16 G 17 cWW ntSH
133 HL_4Y1J_003 4Y1J 0.1247 0 A yybP-ykoY riboswitch C 76 G 77 A 78 A 79 A 80 G 81 cWW ntSH
134 HL_5M0J_002 5M0J 0.1544 0 GNRA F ASH1 E3 (28 nt-loop) C 12 G 13 A 14 A 15 A 16 G 17 cWW ntSH
135 HL_5M0J_001 5M0J 0.1832 0 GNRA E ASH1 E3 (28 nt-loop) C 12 G 13 A 14 A 15 A 16 G 17 cWW ntSH
136 HL_1Q96_001 1Q96 0.1576 0 GNRA A sarcin/ricin 28S rRNA U 13 G 14 A 15 G 16 A 17 A 18 cWW ntSH
137 HL_3LQX_001 3LQX 0.1659 0 GNRA B SRP RNA C 153 G 154 A 155 A 156 A 157 G 158 cWW tSH
138 HL_5TPY_007 5TPY 0.1468 0 GNRA A RNA (71-MER) C 13||||4_655 G 14||||4_655 A 15||||4_655 A 16||||4_655 A 17||||4_655 G 18||||4_655 cWW ntSH
139 HL_5TPY_010 5TPY 0.1468 0 GNRA A RNA (71-MER) C 13||||8_555 G 14||||8_555 A 15||||8_555 A 16||||8_555 A 17||||8_555 G 18||||8_555 cWW ntSH
140 HL_5TPY_001 5TPY 0.1468 0 GNRA A RNA (71-MER) C 13||||11_655 G 14||||11_655 A 15||||11_655 A 16||||11_655 A 17||||11_655 G 18||||11_655 cWW ntSH
141 HL_5TPY_004 5TPY 0.1468 0 GNRA A RNA (71-MER) C 13 G 14 A 15 A 16 A 17 G 18 cWW ntSH
142 HL_4Y4O_161 4Y4O 0.1790 0 GNRA 2A LSU rRNA C 2374 G 2375 A 2376 A 2377 A 2378 G 2379 cWW ntSH
143 HL_5J7L_010 5J7L 0.1269 0 GNRA AA SSU rRNA C 379 G 380 C 381 A 382 A 383 G 384 cWW ntSH
144 HL_4LFB_010 4LFB 0.1760 0 GNRA A SSU rRNA C 379 G 380 C 381 A 382 A 383 G 384 cWW ntSH
145 HL_3NMU_002 3NMU 0.1380 0 GNRA E RNA (34-MER) C 18 G 19 A 20 A 21 A 22 G 23 cWW ntSH
146 HL_5J7L_004 5J7L 0.1346 0 GNRA AA SSU rRNA C 186 G 187 C 188 A 189 A 190 G 191 cWW ntSH
147 HL_4LFB_023 4LFB 0.2204 0 A SSU rRNA C 1030 G 1030|||A C 1030|||B G 1030|||C A 1030|||D G 1031 cWW
148 HL_4V88_211 4V88 0.1722 0 GNRA A6 SSU rRNA C 1121 G 1122 C 1123 A 1124 A 1125 G 1126 cWW ntSH
149 HL_4LFB_020 4LFB 0.1809 0 GNRA A SSU rRNA C 897 G 898 C 899 A 900 A 901 G 902 cWW ntSH
150 HL_5J7L_020 5J7L 0.1978 0 GNRA AA SSU rRNA C 897 G 898 C 899 A 900 A 901 G 902 cWW ntSH
151 HL_4V9F_048 4V9F 0.2116 0 GNRA 0 LSU rRNA C 1862 G 1863 C 1864 A 1865 A 1866 G 1867 cWW ntSH
152 HL_3SUX_002 3SUX 0.2211 0 GNRA X THF riboswitch C 65 G 66 A 67 A 68 A 69 G 70 cWW
153 HL_3SUX_004 3SUX 0.2211 0 GNRA X THF riboswitch C 65||||17_555 G 66||||17_555 A 67||||17_555 A 68||||17_555 A 69||||17_555 G 70||||17_555 cWW
154 HL_1Y0Q_004 1Y0Q 0.3267 0 A Group I catalytic intron C 130 G 131 A 132 U 133 A 134 G 135 cWW
155 HL_4V88_188 4V88 0.5333 1 Other HL A6 SSU rRNA G 154 U 155 A 156 A 157 U 158 C 160 cWW
156 HL_1U6B_004 1U6B 0.4457 0 GNRA related B 197-MER C 153 A 154 A 155 A 156 C 157 G 158 cWW
157 HL_4QK9_001 4QK9 0.4493 0 Other HL A C-di-AMP riboswitch C 14 U 15 G 16 A 17 A 18 G 19 cWW
158 HL_4Y4O_149 4Y4O 0.3692 0 GNRA 2A LSU rRNA U 1864 G 1865 C 1866 A 1876 A 1877 G 1878 cWW
159 HL_4IOA_046 4IOA 0.3582 0 GNRA X LSU rRNA U 1856 G 1857 C 1858 A 1859 A 1860 G 1861 cWW
160 HL_2ZZM_003 2ZZM 0.3028 0 GNRA B RNA (84-MER) C 47 G 47|||A U 47|||B A 47|||C G 47|||D G 47|||E cWW
161 HL_4P95_006 4P95 0.2816 0 GNRA A RNA (192-MER) C 567 G 568 A 569 A 570 A 571 G 572 cWW
162 HL_4P8Z_005 4P8Z 0.2542 0 A Lariat capping ribozyme C 157 G 158 A 159 A 160 A 161 G 162 cWW
163 HL_4WF9_054 4WF9 0.2140 0 GNRA X LSU rRNA C 2401 G 2402 A 2403 A 2404 A 2405 G 2406 cWW
164 HL_4IOA_070 4IOA 0.3685 0 GNRA Y 5S rRNA C 88 G 89 C 90 A 91 G 92 G 93 cWW
165 HL_5FDV_070 5FDV 0.3090 0 GNRA 1B 5S rRNA G 86 G 87 C 88 G 89 A 90 C 91 cWW
166 HL_4R0D_015 4R0D 0.3316 0 A Group II catalytic intron A 600 G 601 A 602 G 603 A 604 U 605 ncWW
167 HL_4WF9_020 4WF9 0.2497 0 GNRA X LSU rRNA C 674 G 675 A 676 A 677 A 678 G 679 cWW
168 HL_5J7L_191 5J7L 0.2478 0 GNRA DA LSU rRNA C 2374 G 2375 A 2376 A 2377 A 2378 G 2379 cWW
169 HL_4V8P_100 4V8P 0.2396 0 D1 LSU rRNA C 732 G 733 A 734 A 735 A 736 G 737 cWW
170 HL_4IOA_019 4IOA 0.2935 0 GNRA X LSU rRNA C 640 G 641 A 642 A 643 A 644 G 645 cWW
171 HL_4V9F_060 4V9F 0.2483 0 GNRA 0 LSU rRNA C 2411 G 2412 A 2413 A 2414 A 2415 G 2416 cWW
172 HL_4V5O_066 4V5O 0.2641 0 BA SSU rRNA U 1472 G 1473 G 1474 G 1475 A 1476 A 1477 cWW
173 HL_4LVW_002 4LVW 0.3650 0 GNRA A THF riboswitch C 58 G 59 A 60 G 61 A 62 G 63 cWW
174 HL_4WF9_015 4WF9 0.2934 0 GNRA X LSU rRNA C 508 G 509 U 510 G 511 A 512 G 513 cWW
175 HL_4Y4O_117 4Y4O 0.2765 0 GNRA 2A LSU rRNA C 462 G 463 U 464 G 465 A 466 G 467 cWW
176 HL_5J7L_147 5J7L 0.2772 0 GNRA DA LSU rRNA C 462 G 463 U 464 G 465 A 466 G 467 cWW
177 HL_4IOA_014 4IOA 0.3137 0 GNRA X LSU rRNA C 473 G 474 U 475 G 476 A 477 G 478 cWW
178 HL_4QK9_002 4QK9 0.2992 0 GNRA A C-di-AMP riboswitch C 56 G 57 U 58 A 59 A 60 G 61 cWW
179 HL_3NKB_002 3NKB 0.3078 0 GNRA B The hepatitis delta virus ribozyme C 49 G 50 A 51 A 52 A 53 G 54 cWW
180 HL_3E5C_002 3E5C 0.3092 0 GNRA A SMK box (SAM-III) Riboswitch C 41 G 42 A 43 A 44 A 45 G 46 cWW
181 HL_2OIU_003 2OIU 0.2787 0 GNRA P L1 Ribozyme RNA Ligase C 59 G 60 A 61 A 62 A 63 G 64 cWW
182 HL_3NPQ_001 3NPQ 0.3213 0 GNRA A S-ADENOSYLHOMOCYSTEINE RIBOSWITCH C 20 G 21 A 22 G 23 A 24 G 25 cWW
183 HL_4PQV_001 4PQV 0.3564 0 GNRA A Flavivirus 3' UTR stem loop IV C 13 G 14 A 15 A 16 A 17 G 18 cWW
184 HL_1G1X_004 1G1X 0.3964 0 Other HL I 16S RIBOSOMAL RNA C 590 G 591 A 592 A 593 A 594 G 649 cWW
185 HL_5J7L_190 5J7L 0.3101 0 Other HL DA LSU rRNA U 2356 G 2357 A 2358 C 2359 G 2360 G 2361 cWW
186 HL_4C7O_001 4C7O 0.3447 0 Other HL E SRP RNA C 19 G 20 G 21 A 22 A 23 G 24 cWW
187 HL_2BTE_003 2BTE 0.4112 0 GNRA B tRNA C 46 G 47 C 47|||A A 47|||B A 47|||C G 47|||D cWW
188 HL_4V9F_033 4V9F 0.4333 0 GNRA 0 LSU rRNA C 1326 G 1327 A 1328 G 1329 A 1330 G 1331 cWW
189 HL_4V8P_112 4V8P 0.4616 0 D1 LSU rRNA C 1429 G 1430 U 1431 G 1432 A 1433 G 1434 cWW
190 HL_5J7L_023 5J7L 0.3873 0 GNRA AA SSU rRNA U 1076 G 1077 U 1078 G 1079 A 1080 A 1081 cWW
191 HL_4LFB_024 4LFB 0.3812 0 GNRA A SSU rRNA C 1076 G 1077 U 1078 G 1079 A 1080 G 1081 cWW
192 HL_5J7L_027 5J7L 0.3841 0 GNRA AA SSU rRNA C 1265 G 1266 C 1267 G 1268 A 1269 G 1270 cWW
193 HL_3W3S_007 3W3S 0.3279 0 GNRA B Selenocysteine transfer RNA C 47|||F|43_455 G 47|||G|43_455 C 47|||H|43_455 A 47|||I|43_455 A 47|||J|43_455 G 47|||K|43_455 cWW
194 HL_3W3S_003 3W3S 0.3279 0 GNRA B Selenocysteine transfer RNA C 47|||F G 47|||G C 47|||H A 47|||I A 47|||J G 47|||K cWW
195 HL_4Y4O_172 4Y4O 0.3463 0 GNRA 2A LSU rRNA C 2856 G 2857 C 2858 G 2859 A 2860 G 2861 cWW
196 HL_4V9F_065 4V9F 0.3206 0 GNRA 0 LSU rRNA C 2629 G 2630 U 2631 G 2632 A 2633 G 2634 cWW
197 HL_5J7L_196 5J7L 0.2988 0 GNRA DA LSU rRNA C 2594 G 2595 U 2596 G 2597 A 2598 G 2599 cWW
198 HL_4V9F_017 4V9F 0.3329 0 GNRA 0 LSU rRNA C 576 G 577 C 578 G 579 A 580 G 581 cWW
199 HL_4YAZ_003 4YAZ 0.3260 0 GNRA R Cyclic di-GMP-I riboswitch C 25 G 26 C 27 G 28 A 29 G 30 cWW
200 HL_4Y4O_133 4Y4O 0.3489 0 GNRA 2A LSU rRNA C 1222 G 1223 C 1224 G 1225 A 1226 G 1227 cWW
201 HL_5U3G_002 5U3G 0.2602 0 GNRA B Guanidine-I riboswitch C 47 G 48 A 49 A 50 A 51 G 52 cWW ntSH
202 HL_4IOA_062 4IOA 0.3343 0 GNRA X LSU rRNA C 2573 G 2574 U 2575 G 2576 A 2577 G 2578 cWW ntSH
203 HL_4V8P_147 4V8P 0.3331 0 D1 LSU rRNA C 2951 G 2952 U 2953 G 2954 A 2955 G 2956 cWW
204 HL_4Y4O_166 4Y4O 0.3302 0 GNRA 2A LSU rRNA C 2594 G 2595 U 2596 G 2597 A 2598 G 2599 cWW ntSH
205 HL_4WF9_059 4WF9 0.3698 0 GNRA X LSU rRNA C 2621 G 2622 U 2623 G 2624 A 2625 G 2626 cWW
206 HL_4V9F_015 4V9F 0.3291 0 GNRA 0 LSU rRNA U 468 G 469 U 470 G 471 A 472 A 473 cWW
207 HL_4V8P_093 4V8P 0.3221 0 D1 LSU rRNA U 356 G 357 C 358 G 359 A 360 A 361 cWW
208 HL_4R0D_003 4R0D 0.3288 0 A Group II catalytic intron A 87 G 88 U 89 A 90 A 91 U 92 cWW
209 HL_1Y0Q_007 1Y0Q 0.3176 0 A Group I catalytic intron G 204 G 205 A 206 A 207 A 208 C 209 cWW tSH
210 HL_4R0D_009 4R0D 0.2501 0 A Group II catalytic intron A 390 G 391 C 392 A 393 A 394 U 395 cWW ntSH
211 HL_4V9F_045 4V9F 0.2321 1 GNRA 0 LSU rRNA C 1793 G 1794 G 1795 A 1796 A 1797 G 1799 cWW
212 HL_4V8P_142 4V8P 0.1784 0 D1 LSU rRNA C 2733 G 2734 A 2735 A 2736 A 2737 G 2738 cWW
213 HL_5F9F_003 5F9F 0.2523 0 GNRA F RNA (24-mer) A 10 G 11 U 12 G 13 A 14 U 15 cWW
214 HL_5B2T_001 5B2T 0.1759 0 GNRA A Guide RNA A 32 G 33 A 34 A 35 A 36 U 37 cWW
215 HL_4OQU_001 4OQU 0.2078 0 GNRA A SAM-I/IV riboswitch G 13 G 14 A 15 G 16 A 17 C 18 ncWW
216 HL_1UN6_004 1UN6 0.1872 0 GNRA F 5S RIBOSOMAL RNA G 82 G 83 A 84 A 85 A 86 C 94 cWW ntSH
217 HL_1U9S_002 1U9S 0.2681 0 GNRA A RIBONUCLEASE P G 99 G 100 U 101 A 102 A 103 C 104 cWW ntSH
218 HL_1U9S_004 1U9S 0.2374 0 GNRA A RIBONUCLEASE P G 204 G 205 C 206 A 207 A 208 C 209 cWW ntSH
219 HL_5FQ5_001 5FQ5 0.2755 0 GNRA A SGRNA A 32 G 33 A 34 A 35 A 36 U 37 cWW
220 HL_5J7L_152 5J7L 0.2137 0 GNRA DA LSU rRNA G 629 G 630 A 631 A 632 A 633 C 634 cWW
221 HL_4Y4O_122 4Y4O 0.2304 0 GNRA 2A LSU rRNA G 629 G 630 A 631 A 632 A 633 C 634 cWW
222 HL_4IOA_057 4IOA 0.3268 0 GNRA X LSU rRNA G 2353 G 2354 A 2355 A 2356 A 2357 C 2358 cWW
223 HL_3Q1Q_008 3Q1Q 0.2664 0 B RNase P RNA G 284 G 285 U 286 A 287 A 288 C 289 cWW
224 HL_4Y1M_004 4Y1M 0.2391 0 Other HL B E. coli yybP-ykoY riboswitch A 81 G 82 A 83 A 84 A 85 U 86 cWW ntSH
225 HL_4V88_210 4V88 0.2132 0 GNRA A6 SSU rRNA A 1084 G 1085 A 1086 A 1087 A 1088 U 1089 cWW
226 HL_4V5O_058 4V5O 0.2769 0 BA SSU rRNA A 1056 G 1057 A 1058 A 1059 A 1060 U 1061 cWW
227 HL_1Y0Q_001 1Y0Q 0.3233 0 A Group I catalytic intron A 21 G 22 U 23 A 24 A 25 U 26 cWW ntSH
228 HL_3Q1Q_006 3Q1Q 0.3838 0 B RNase P RNA G 187 G 188 C 189 A 190 A 191 C 192 cWW
229 HL_3Q1Q_003 3Q1Q 0.3056 0 B RNase P RNA G 92 G 93 U 94 G 95 A 96 C 97 cWW
230 HL_4WF9_065 4WF9 0.3114 0 Other HL X LSU rRNA G 2876 G 2877 U 2878 G 2879 A 2880 C 2881 cWW
231 HL_4LFB_028 4LFB 0.2692 0 Other HL A SSU rRNA G 1265 G 1266 C 1267 A 1268 A 1269 C 1270 cWW
232 HL_4IOA_068 4IOA 0.2814 0 Other HL X LSU rRNA A 2831 G 2832 C 2833 A 2834 A 2835 U 2836 cWW
233 HL_5J7L_202 5J7L 0.2558 0 Other HL DA LSU rRNA A 2856 G 2857 C 2858 G 2859 A 2860 U 2861 cWW
234 HL_4WFL_003 4WFL 0.2581 0 GNRA A LSRP RNA G 81 G 82 U 83 A 84 A 85 C 86 cWW
235 HL_3G9C_008 3G9C 0.2582 0 GNRA Q GLMS RIBOZYME G 108 G 109 U 110 G 111 A 112 C 113 cWW
236 HL_3IGI_003 3IGI 0.2870 0 GNRA A Group IIC intron G 89 G 90 C 91 G 92 A 93 C 94 cWW
237 HL_2Z75_004 2Z75 0.3202 0 GNRA B glmS ribozyme G 113 G 114 C 115 G 116 A 117 C 118 cWW
238 HL_1Y0Q_003 1Y0Q 0.2923 0 A Group I catalytic intron A 101 G 102 U 103 A 104 A 105 U 106 cWW ntSH
239 HL_4V8P_118 4V8P 0.3242 0 D1 LSU rRNA G 1658 G 1659 U 1660 A 1661 A 1662 C 1663 cWW
240 HL_4V88_214 4V88 0.3251 0 GNRA A6 SSU rRNA A 1296 G 1297 U 1298 G 1299 A 1300 U 1301 cWW
241 HL_4V5O_062 4V5O 0.3875 0 BA SSU rRNA A 1268 G 1269 U 1270 G 1271 A 1272 U 1273 cWW
242 HL_4V5O_059 4V5O 0.5217 0 BA SSU rRNA C 1094 G 1095 C 1096 A 1097 A 1098 G 1099 cWW ntsS
243 HL_4ZT0_006 4ZT0 0.4989 0 GNRA with GA tSW pair D single-guide RNA U 72 G 73 A 74 A 75 A 76 A 77 cWW
244 HL_5DDO_003 5DDO 0.5526 0 GNRA with GA tSW pair B L-glutamine riboswitch (58-MER) G 11 G 12 A 13 A 14 A 15 C 16 cWW
245 HL_4IOA_004 4IOA 0.6537 0 Other HL X LSU rRNA C 133 G 134 U 135 A 136 A 137 G 138 cWW ntSH
246 HL_4V8P_135 4V8P 0.5726 0 Other HL D1 LSU rRNA U 2531 G 2532 C 2533 A 2534 A 2535 A 2536 cWW ntSH
247 HL_3AM1_006 3AM1 0.4698 0 Other HL B ASL-truncated tRNA C 32||||5_555 U 33||||5_555 U 34||||5_555 C 35||||5_555 G 36||||5_555 G 37||||5_555 cWW
248 HL_3AM1_002 3AM1 0.4698 0 Other HL B ASL-truncated tRNA C 32 U 33 U 34 C 35 G 36 G 37 cWW
249 HL_4WZJ_014 4WZJ 0.3799 0 XXX U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor. G 50 G 51 U 52 A 53 A 54 C 55 cWW ntSH
250 HL_1JID_001 1JID 0.4671 0 Other HL B HELIX 6 OF HUMAN SRP RNA G 146 G 147 G 148 A 149 G 150 C 151 cWW
251 HL_1MFQ_001 1MFQ 0.4952 0 Other HL A SRP RNA G 146 G 147 G 148 A 149 G 150 C 151 cWW
252 HL_4OQU_004 4OQU 0.3298 0 Other HL A SAM-I/IV riboswitch C 76 G 77 A 78 G 79 A 80 G 81 cWW
253 HL_4V5O_055 4V5O 0.2983 0 BA SSU rRNA C 915 G 916 A 917 A 918 A 919 G 920 cWW
254 HL_4V88_207 4V88 0.3630 0 Other HL A6 SSU rRNA C 937 G 938 A 939 A 940 A 941 G 942 cWW
255 HL_5J7L_016 5J7L 0.3427 0 GNRA related AA SSU rRNA C 726 G 727 A 728 A 729 G 730 G 731 cWW
256 HL_4LFB_016 4LFB 0.3934 0 Other HL A SSU rRNA C 726 G 727 A 728 A 729 G 730 G 731 cWW
257 HL_1G1X_005 1G1X 0.3758 0 Other HL J 16S RIBOSOMAL RNA C 726 G 727 A 728 A 729 G 730 G 731 cWW
258 HL_1G1X_003 1G1X 0.3807 0 Other HL E 16S RIBOSOMAL RNA C 726 G 727 A 728 A 729 G 730 G 731 cWW
259 HL_5J7L_164 5J7L 0.5599 0 Other HL DA LSU rRNA U 1222 G 1223 U 1224 G 1225 A 1226 G 1227 cWW
260 HL_4WF9_034 4WF9 0.4939 0 GNRA related X LSU rRNA C 1400 G 1401 A 1402 C 1403 A 1404 G 1405 cWW
261 HL_5J7L_167 5J7L 0.4558 0 GNRA DA LSU rRNA C 1363 G 1364 A 1365 A 1366 A 1367 G 1368 cWW
262 HL_4Y4O_136 4Y4O 0.4765 0 Other HL 2A LSU rRNA C 1363 G 1364 A 1365 A 1366 A 1367 G 1368 cWW
263 HL_4IOA_033 4IOA 0.5701 0 Other HL X LSU rRNA C 1376 G 1377 A 1378 A 1379 C 1380 G 1381 cWW
264 HL_4V88_222 4V88 0.5408 0 Other HL A6 SSU rRNA G 1778 U 1779 G 1780 A 1781 A 1782 C 1783 cWW
265 HL_4V5O_070 4V5O 0.5630 0 BA SSU rRNA G 1731 U 1732 G 1733 A 1734 A 1735 C 1736 cWW
266 HL_4V8P_129 4V8P 0.4293 0 D1 LSU rRNA U 2160 C 2161 A 2162 A 2163 C 2164 A 2165 cWW
267 HL_4V5O_044 4V5O 0.4773 0 BA SSU rRNA U 359 U 360 A 361 G 362 G 363 G 364 ncWW
268 HL_3Q1Q_001 3Q1Q 0.6763 0 B RNase P RNA A 29 C 30 A 31 C 32 C 33 U 34 cWW
269 HL_4V5O_050 4V5O 0.5264 0 BA SSU rRNA C 563 A 564 G 565 C 566 C 567 G 568 cWW
270 HL_4V88_200 4V88 0.6058 0 Other HL A6 SSU rRNA C 569 A 570 G 571 C 572 C 573 G 574 cWW
271 HL_4KQY_005 4KQY 0.4023 0 Other HL A SAM-I riboswitch C 60||||4_555 G 61||||4_555 A 62||||4_555 A 63||||4_555 A 64||||4_555 G 65||||4_555 ncWW ntSH
272 HL_4KQY_002 4KQY 0.4023 0 GNRA A SAM-I riboswitch C 60 G 61 A 62 A 63 A 64 G 65 ncWW ntSH
273 HL_1M5K_003 1M5K 0.6234 0 GNRA B RNA HAIRPIN RIBOZYME G 74 G 75 A 76 A 77 A 78 C 79 cWW ntSH
274 HL_4V88_218 4V88 0.5550 0 GNRA A6 SSU rRNA C 1501 G 1502 A 1503 G 1504 A 1505 G 1506 cWW ntSH
275 HL_4QLM_001 4QLM 0.7562 0 GNRA A cyclic di-AMP riboswitch C 54 G 55 A 56 A 57 A 58 G 59 cWW ntSH
