1 HL_4WF9_019 4WF9 0.5286 2 Other HL X LSU rRNA C 654 A 655 G 656 U 657 A 659 U 661 G 662 cWW
2 HL_6CZR_100 6CZR 0.6050 3 T-loop with 3 stacked bulged bases 1a SSU rRNA C 1296 U 1297 G 1298 C 1299 A 1300 A 1301 G 1305 cWW ntWH
3 HL_4LFB_029 4LFB 0.6106 3 T-loop with 3 stacked bulged bases A SSU rRNA C 1314 U 1315 G 1316 C 1317 A 1318 A 1319 G 1323 cWW tWH
4 HL_5J7L_028 5J7L 0.6142 3 T-loop with 3 stacked bulged bases AA SSU rRNA C 1314 U 1315 G 1316 C 1317 A 1318 A 1319 G 1323 cWW tWH
5 HL_2A64_002 2A64 0.3986 1 T-loop with 2 stacked bulged bases A RNase P class B C 69 U 70 G 71 A 72 G 73 A 74 G 76 cWW tWH
6 HL_4WF9_010 4WF9 0.2951 1 T-loop with 2 stacked bulged bases X LSU rRNA C 348 U 349 G 350 G 351 A 352 A 353 G 355 cWW tWH
7 HL_7RQB_010 7RQB 0.2453 1 T-loop with 1 bulged base (H) 1A LSU rRNA U 305 U 306 G 307 G 308 G 309 A 310 G 312 cWW tWH
8 HL_5T5A_001 5T5A 0.3421 2 T-loop with 2 stacked bulged bases A DNA/RNA (71-MER) G 21 U 22 G 23 C 24 A 25 A 26 C 29 cWW tWH
9 HL_7A0S_010 7A0S 0.2078 1 T-loop with 1 bulged base X LSU rRNA C 316 U 317 G 318 G 319 A 320 A 321 G 323 cWW tWH
10 HL_5J7L_142 5J7L 0.2134 1 T-loop with 2 stacked bulged bases DA LSU rRNA C 305 U 306 G 307 G 308 A 309 A 310 G 312 cWW tWH
11 HL_5DH6_002 5DH6 0.2408 1 T-loop with 2 stacked bulged bases A Hammerhead ribozyme (type III) C 27 U 28 G 29 G 30 G 31 A 32 G 34 cWW tWH
12 HL_5Y85_003 5Y85 0.2852 2 T-loop with 2 stacked bulged bases D DNA/RNA (50-MER) G 11 U 12 G 13 C 14 A 15 A 16 C 19 cWW tWH
13 HL_4FRN_005 4FRN 0.1913 2 T-loop with 2 bulged bases not stacked B Cobalamin riboswitch G 28 U 29 G 30 U 31 A 32 A 33 C 36 cWW tWH
14 HL_4V9F_034 4V9F 0.4147 2 T-loop with 2 stacked bulged bases 0 LSU rRNA G 1387 U 1388 G 1389 A 1390 G 1391 A 1392 C 1395 cWW tWH
15 HL_7A0S_032 7A0S 0.3564 2 T-loop with 2 stacked bulged bases X LSU rRNA G 1294 U 1295 G 1296 A 1297 G 1298 A 1299 C 1302 cWW tWH
16 HL_7RQB_033 7RQB 0.3337 2 T-loop with 2 stacked bulged bases (H) 1A LSU rRNA G 1281 U 1282 G 1283 A 1284 G 1285 A 1286 C 1289 cWW tWH
17 HL_4WF9_032 4WF9 0.3669 2 T-loop with 2 stacked bulged bases X LSU rRNA G 1318 U 1319 G 1320 A 1321 G 1322 A 1323 C 1326 cWW tWH
18 HL_8C3A_031 8C3A 0.3508 2 T-loop with 2 stacked bulged bases 1 LSU rRNA A 1458 U 1459 G 1460 A 1461 G 1462 A 1463 U 1466 cWW tWH
19 HL_5TBW_031 5TBW 0.3369 2 T-loop with 2 stacked bulged bases 1 LSU rRNA A 1462 U 1463 G 1464 A 1465 G 1466 A 1467 U 1470 cWW tWH
20 HL_5J7L_165 5J7L 0.2923 2 T-loop with 2 stacked bulged bases DA LSU rRNA G 1281 U 1282 G 1283 A 1284 A 1285 A 1286 C 1289 cWW tWH
21 HL_6UFG_008 6UFG 0.2075 2 T-loop with 2 stacked bulged bases B tRNA G 54 U 55 U 56 C 57 A 58 A 59 C 62 cWW tWH
22 HL_3ICQ_005 3ICQ 0.2025 2 T-loop with 2 stacked bulged bases E RNA (62-MER) G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW tWH
23 HL_4V8Q_110 4V8Q 0.2182 2 T-loop with 2 stacked bulged bases BY tmRNA G 66 U 67 U 68 C 69 G 70 A 71 C 74 cWW ntWH
24 HL_8SP9_004 8SP9 0.2544 2 T-loop with 2 stacked bulged bases C Enterovirus 5' cloverleaf cis-acting replication element G 130 U 131 U 132 C 133 A 134 A 135 C 138 cWW ntWH
25 HL_3AKZ_012 3AKZ 0.2022 2 T-loop with 2 stacked bulged bases E tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW tWH
26 HL_3EPH_003 3EPH 0.1720 2 T-loop with 2 stacked bulged bases E tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW tWH
27 HL_1N78_003 1N78 0.1573 2 T-loop with 2 stacked bulged bases C tRNA G 553 U 554 U 555 C 556 G 557 A 558 C 561 cWW tWH
28 HL_3TUP_003 3TUP 0.1568 2 T-loop with 2 stacked bulged bases T tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW ntWH
29 HL_4QEI_003 4QEI 0.1908 2 T-loop with 2 stacked bulged bases C tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW
30 HL_5E6M_003 5E6M 0.1741 2 T-loop with 2 stacked bulged bases C tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW
31 HL_3AM1_004 3AM1 0.1613 2 T-loop with 2 stacked bulged bases B ASL-truncated tRNA G 59 U 60 U 61 C 62 G 63 A 64 C 67 cWW tWH
32 HL_3FOZ_006 3FOZ 0.1309 2 T-loop with 2 stacked bulged bases D tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW tWH
33 HL_2DER_006 2DER 0.1424 2 T-loop with 2 stacked bulged bases D tRNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW tWH
34 HL_2DU3_003 2DU3 0.1007 2 T-loop with 2 stacked bulged bases D tRNA G 952 U 953 U 954 C 955 G 956 A 957 C 960 cWW tWH
35 HL_4X4V_001 4X4V 0.1153 2 T-loop with 2 stacked bulged bases B Human MenBeta minihelix ending in CCACC G 12 U 13 U 14 C 15 G 16 A 17 C 20 cWW tWH
36 HL_4MGN_004 4MGN 0.0907 2 T-loop with 2 stacked bulged bases B tRNA G 52 U 53 U 54 C 55 G 56 A 57 C 60 cWW tWH
37 HL_3ADD_004 3ADD 0.0947 2 T-loop with 2 stacked bulged bases C Selenocysteine transfer RNA G 53 U 54 U 55 C 56 A 57 A 58 C 61 cWW tWH
38 HL_3W3S_004 3W3S 0.0903 2 T-loop with 2 stacked bulged bases B Selenocysteine transfer RNA G 53 U 54 U 55 C 56 G 57 A 58 C 61 cWW tWH
39 HL_3RG5_008 3RG5 0.0934 2 T-loop with 2 stacked bulged bases B Selenocysteine transfer RNA G 53 U 54 U 55 C 56 A 57 A 58 C 61 cWW tWH
40 HL_6JXM_003 6JXM 0.1004 2 T-loop with 2 stacked bulged bases B tRNA G 74 U 75 U 76 C 77 G 78 A 79 C 82 cWW tWH
41 HL_8G9Z_004 8G9Z 0.1036 2 T-loop with 2 stacked bulged bases E Selenocysteine transfer RNA G 53||A U 54||A U 55||A C 56||A A 57||A A 58||A C 61||A cWW tWH
42 HL_4LCK_003 4LCK 0.0000 2 T-loop with 2 stacked bulged bases B tRNA G 52 U 53 U 54 C 55 G 56 A 57 C 60 cWW tWH
43 HL_3ZGZ_003 3ZGZ 0.0761 2 T-loop with 2 stacked bulged bases B tRNA G 53 U 54 U 55 C 56 A 57 A 58 C 61 cWW tWH
44 HL_4P5J_003 4P5J 0.1270 2 T-loop with 2 stacked bulged bases A tRNA-like 3' UTR element G 46 U 47 G 48 C 49 A 50 A 51 C 54 cWW tWH
45 HL_5WT1_003 5WT1 0.1341 2 T-loop with 2 stacked bulged bases C tRNA G 53 U 54 U 55 C 56 A 57 A 58 C 61 cWW tWH
46 HL_8V1I_006 8V1I 0.0946 2 T-loop with 2 stacked bulged bases B MALAT1-associated small cytoplasmic RNA/MEN beta RNA G 38 U 39 U 40 C 41 A 42 A 43 C 46 cWW tWH
47 HL_5WWT_002 5WWT 0.0994 2 T-loop with 2 stacked bulged bases C tRNA G 53 U 54 U 55 C 56 A 57 A 58 C 61 cWW tWH
48 HL_3IGI_001 3IGI 0.1351 2 T-loop with 2 stacked bulged bases A Group II catalytic intron D1-D4-3 G 30 U 31 G 32 A 33 G 34 A 35 C 38 cWW tWH
49 HL_6JQ5_003 6JQ5 0.1785 2 T-loop with 2 stacked bulged bases B Hatchet ribozyme G 6 U 7 G 8 A 9 G 10 A 11 C 14 cWW tWH
50 HL_6JQ5_001 6JQ5 0.1790 2 T-loop with 2 stacked bulged bases A Hatchet ribozyme G 6 U 7 G 8 A 9 G 10 A 11 C 14 cWW tWH
51 HL_6JQ6_003 6JQ6 0.1701 2 T-loop with 2 stacked bulged bases U Hatchet ribozyme G 6 U 7 G 8 A 9 G 10 A 11 C 14 cWW tWH
52 HL_4GXY_002 4GXY 0.2727 2 T-loop with 2 stacked bulged bases A Cobalamin riboswitch G 49 U 50 G 51 C 52 A 53 A 54 C 57 cWW tWH
53 HL_5TBW_005 5TBW 0.2614 1 T-loop with 2 stacked bulged bases 1 LSU rRNA U 194 U 195 G 196 G 197 A 198 A 199 A 201 cWW tWH
54 HL_8C3A_005 8C3A 0.2417 1 T-loop with 2 stacked bulged bases 1 LSU rRNA U 193 U 194 G 195 G 196 A 197 A 198 A 200 cWW tWH
55 HL_4V9F_010 4V9F 0.2072 1 T-loop with 2 stacked bulged bases 0 LSU rRNA U 312 U 313 G 314 G 315 A 316 A 317 A 319 cWW tWH
56 HL_6MJ0_009 6MJ0 0.2023 2 T-loop with 2 stacked bulged bases B tRNA-like 3' UTR element G 66 U 67 G 68 C 69 A 70 A 71 C 74 cWW tWH
57 HL_4FRG_001 4FRG 0.2437 2 T-loop with 2 bulged bases not stacked B Cobalamin riboswitch G 28 U 29 G 30 A 31 A 32 A 33 C 36 cWW tWH
58 HL_3F2X_004 3F2X 0.2331 2 T-loop with 2 bulged bases not stacked X FMN riboswitch (RFN element) G 68 U 69 G 70 A 71 A 72 A 73 C 76 cWW tWH
59 HL_6DN2_003 6DN2 0.2390 2 T-loop with 2 bulged bases not stacked Y RNA (56-MER) G 68 U 69 G 70 A 71 A 72 A 73 C 76 cWW tWH
60 HL_5C45_003 5C45 0.2348 2 T-loop with 2 bulged bases not stacked Y FMN Riboswitch G 68 U 69 G 70 A 71 A 72 A 73 C 76 cWW tWH
61 HL_6DN2_001 6DN2 0.2287 2 T-loop with 2 bulged bases not stacked X RNA RIBOSWITCH G 17 U 18 G 19 A 20 A 21 A 22 C 25 cWW tWH
62 HL_3F2X_001 3F2X 0.2008 2 T-loop with 2 bulged bases not stacked X FMN riboswitch (RFN element) G 17 U 18 G 19 A 20 A 21 A 22 C 25 cWW tWH
63 HL_5C45_001 5C45 0.2266 2 T-loop with 2 bulged bases not stacked X FMN Riboswitch G 17 U 18 G 19 A 20 A 21 A 22 C 25 cWW tWH
64 HL_4WF9_018 4WF9 0.3505 3 T-loop with 2 stacked bulged bases X LSU rRNA U 609 U 610 U 611 U 612 G 613 U 614 A 618 cWW
65 HL_5J7L_150 5J7L 0.3408 3 T-loop with 2 stacked bulged bases DA LSU rRNA U 566 U 567 U 568 U 569 G 570 U 571 A 575 cWW
66 HL_7RQB_018 7RQB 0.3820 3 T-loop with 2 stacked bulged bases (H) 1A LSU rRNA U 566 A 567 U 568 U 569 G 570 A 571 A 575 cWW
67 HL_7A0S_018 7A0S 0.3705 3 T-loop with 2 stacked bulged bases X LSU rRNA U 575 A 576 U 577 U 578 G 579 A 580 A 584 cWW
68 HL_8C3A_014 8C3A 0.3443 3 T-loop with 2 stacked bulged bases 1 LSU rRNA U 638 C 639 U 640 U 641 G 642 A 643 A 647 cWW
69 HL_5TBW_014 5TBW 0.3622 3 T-loop with 2 stacked bulged bases 1 LSU rRNA U 640 C 641 U 642 U 643 G 644 A 645 A 649 cWW
