7MPJ Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/A1/38:45 | geometric HL_5TBW_001 | NA HL_23481.5* | ||
| 1/A1/69:74 | geometric HL_5TBW_002 | NA HL_96776.3* | ||
| 1/A1/90:96 | geometric HL_7RQB_008 | NA HL_67216.5* | ||
| 1/A1/132:136 | geometric HL_5TBW_004 | NA HL_36982.3* | ||
| 1/A1/194:201 | T-loop with 1 bulged base geometric HL_4V9F_010 | NA HL_68493.6* | ||
| 1/A1/208:212 | geometric HL_5TBW_006 | NA HL_98557.5* | ||
| 1/A1/216:224 | geometric HL_5TBW_007 | NA HL_08002.6* | ||
| 1/A1/278:287 | geometric HL_5TBW_008 | NA HL_54035.7* | ||
| 1/A1/303:312 | geometric HL_5TBW_009 | NA HL_46142.8* | ||
| 1/A1/357:362 | GNRA geometric HL_5J7L_196 | NA HL_43074.18* | ||
| 1/A1/382:387 | GNRA geometric HL_5J7L_010 | NA HL_43074.18* | ||
| 1/A1/540:551 | NA | NA | ||
| 1/A1/599:604 | GNRA geometric HL_5J7L_004 | NA HL_43074.18* | ||
| 1/A1/638:651 | geometric HL_4V9F_011 | NA HL_98557.5* | ||
| 1/A1/686:694 | geometric HL_5TBW_015 | NA HL_80105.3* | ||
| 1/A1/707:712 | GNRA geometric HL_5TBW_016 | NA HL_43074.18* | ||
| 1/A1/732:737 | GNRA geometric HL_5B2P_001 | NA HL_43074.18* | ||
| 1/A1/763:768 | geometric HL_5TBW_018 | NA HL_00996.1* | ||
| 1/A1/844:849 | geometric HL_6LAX_002 | NA HL_62604.1* | ||
| 1/A1/875:886 | NA | NA | ||
| 1/A1/910:918 | geometric HL_5TBW_021 | NA HL_05832.1* | ||
| 1/A1/958:963 | geometric HL_2Y8W_001 | NA HL_69459.1* | ||
| 1/A1/1013:1037 | NA | NA | ||
| 1/A1/1076:1083 | geometric HL_5TBW_024 | NA HL_54035.7* | ||
| 1/A1/1126:1132 | GNRA geometric HL_5TBW_025 | NA HL_43074.18* | ||
| 1/A1/1148:1155 | geometric HL_5TBW_026 | NA HL_72451.5* | ||
| 1/A1/1239:1249 | NA | NA | ||
| 1/A1/1266:1275 | NA | NA | ||
| 1/A1/1347:1357 | geometric HL_4OOG_001 | NA HL_68529.2* | ||
| 1/A1/1403:1408 | geometric HL_7RQB_032 | NA HL_43074.18* | ||
| 1/A1/1462:1470 | T-loop with 2 stacked bulged bases geometric HL_5TBW_031 | NA HL_33239.17* | ||
| 1/A1/1506:1512 | geometric HL_5TBW_032 | NA HL_86880.5* | ||
| 1/A1/1544:1549 | Other HL geometric HL_5TBW_033 | NA HL_43074.18* | ||
| 1/A1/1566:1572 | NA | NA | ||
| 1/A1/1599:1608 | geometric HL_5TBW_035 | NA HL_78457.4* | ||
| 1/A1/1634:1639 | GNRA geometric HL_5TBW_036 | NA HL_43074.18* | ||
| 1/A1/1680:1688 | geometric HL_5TBW_037 | NA HL_73793.2* | ||
| 1/A1/1719:1725 | geometric HL_5TBW_038 | NA HL_00923.1* | ||
| 1/A1/1759:1766 | NA | NA | ||
| 1/A1/1792:1796 | geometric HL_5TBW_040 | NA HL_69353.7* | ||
| 1/A1/1844:1851 | geometric HL_5TBW_041 | NA HL_66171.3* | ||
| 1/A1/1862:1868 | GNRA with one bulged base geometric HL_5TBW_042 | NA HL_02361.6* | ||
| 1/A1/1923:1928 | UNCG geometric HL_4V9F_044 | NA HL_79299.11* | ||
| 1/A1/1953:2094 | NA | NA | ||
| 1/A1/2110:2114 | geometric HL_5TBW_045 | NA HL_99223.1* | ||
| 1/A1/2135:2145 | geometric HL_5J7L_178 | NA HL_43613.4* | ||
| 1/A1/2164:2170 | GNRA geometric HL_5TBW_047 | NA HL_43074.18* | ||
| 1/A1/2219:2226 | geometric HL_6CF2_001 | NA HL_80105.3* | ||
| 1/A1/2251:2265 | NA | NA | ||
| 1/A1/2292:2300 | geometric HL_5TBW_050 | NA HL_53760.4* | ||
| 1/A1/2369:2378 | geometric HL_5TBW_051 | NA HL_90642.5* | ||
| 1/A1/2439:2508 | geometric HL_2Y8W_001 | NA HL_69459.1* | ||
| 1/A1/2534:2545 | NA | NA | ||
| 1/A1/2568:2573 | geometric HL_6CZR_089 | NA HL_18722.3* | ||
| 1/A1/2616:2624 | geometric HL_4WF9_049 | NA HL_46891.3* | ||
| 1/A1/2633:2645 | geometric HL_5TBW_055 | NA HL_19870.5* | ||
| 1/A1/2672:2682 | geometric HL_5J7L_188 | NA HL_11805.3* | ||
| 1/A1/2693:2700 | geometric HL_5TBW_057 | NA HL_46142.8* | ||
| 1/A1/2723:2733 | NA | NA | ||
| 1/A1/2744:2749 | GNRA geometric HL_5TBW_059 | NA HL_43074.18* | ||
| 1/A1/2776:2784 | geometric HL_5TBW_060 | NA HL_46142.8* | ||
| 1/A1/2840:2848 | geometric HL_4V9F_062 | NA HL_36421.5* | ||
| 1/A1/2897:2904 | geometric HL_5TBW_062 | NA HL_92681.5* | ||
| 1/A1/2920:2926 | geometric HL_2ZNI_001 | NA HL_40469.1* | ||
| 1/A1/2963:2968 | GNRA geometric HL_5J7L_196 | NA HL_43074.18* | ||
| 1/A1/3025:3030 | geometric HL_7A0S_063 | NA HL_43074.18* | ||
| 1/A1/3068:3073 | Ribsomal LSU H95 geometric HL_5TBW_066 | NA HL_67719.1* | ||
| 1/A1/3110:3124 | geometric HL_5TBW_067 | NA HL_56677.5* | ||
| 1/A1/3194:3197 | geometric HL_4V88_192 | NA HL_69353.7* | ||
| 1/A1/3240:3247 | geometric HL_2Y9H_003 | NA HL_98557.5* | ||
| 1/A1/3303:3311 | geometric HL_5TBW_070 | NA HL_05018.6* | ||
| 1/A1/3350:3353 | geometric HL_5F9R_002 | NA HL_69353.7* | ||
| 1/A3/36:41 | geometric HL_5TBW_185 | NA HL_02733.5* | ||
| 1/A3/88:93 | GNRA geometric HL_5J7L_010 | NA HL_43074.18* | ||
| 1/A4/69:89 | NA | NA | ||
| 1/A4/108:114 | geometric HL_5TBW_075 | NA HL_06569.2* | ||
| 1/A4/124:129 | geometric HL_5TBW_076 | NA HL_60357.1* | ||
| 1/B5/7:17 | geometric HL_4V88_186 | NA HL_67265.4* | ||
| 1/B5/70:81 | geometric HL_4V9F_011 | NA HL_98557.5* | ||
| 1/B5/154:160 | Other HL geometric HL_4V88_188 | NA HL_43074.18* | ||
| 1/B5/186:199 | NA | NA | ||
| 1/B5/228:237 | NA | NA | ||
| 1/B5/243:250 | T-loop with 1 bulged base geometric HL_4V88_191 | NA HL_68493.6* | ||
| 1/B5/276:279 | geometric HL_6U8D_003 | NA HL_18722.3* | ||
| 1/B5/330:338 | geometric HL_4V88_193 | NA HL_93727.5* | ||
| 1/B5/368:373 | geometric HL_4V88_194 | NA HL_18785.1* | ||
| 1/B5/393:404 | geometric HL_4V88_195 | NA HL_22443.1* | ||
| 1/B5/411:422 | NA | NA | ||
| 1/B5/450:456 | geometric HL_5NFV_001 | NA HL_58912.1* | ||
| 1/B5/490:497 | NA | NA | ||
| 1/B5/520:532 | geometric HL_4V88_199 | NA HL_17086.2* | ||
| 1/B5/569:574 | Other HL geometric HL_4V88_200 | NA HL_43074.18* | ||
| 1/B5/717:723 | NA | NA | ||
| 1/B5/764:772 | geometric HL_4V88_203 | NA HL_72066.1* | ||
| 1/B5/777:783 | NA | NA | ||
| 1/B5/827:845 | NA | NA | ||
| 1/B5/900:909 | geometric HL_4V88_206 | NA HL_87219.4* | ||
| 1/B5/937:942 | Other HL geometric HL_4V88_207 | NA HL_43074.18* | ||
| 1/B5/995:1009 | geometric HL_2ZZM_002 | NA HL_18218.2* | ||
| 1/B5/1055:1064 | NA | NA | ||
| 1/B5/1084:1089 | Other HL geometric HL_4V88_210 | NA HL_43074.18* | ||
| 1/B5/1120:1127 | geometric HL_7A0S_056 | NA HL_93727.5* | ||
| 1/B5/1188:1197 | NA | NA | ||
| 1/B5/1238:1247 | geometric HL_4V88_213 | NA HL_30819.1* | ||
| 1/B5/1296:1301 | GNRA geometric HL_4V9F_065 | NA HL_43074.18* | ||
| 1/B5/1309:1316 | geometric HL_4V88_215 | NA HL_54035.7* | ||
| 1/B5/1360:1363 | NA | NA | ||
| 1/B5/1396:1402 | GNRA geometric HL_6CZR_090 | NA HL_43074.18* | ||
| 1/B5/1501:1506 | GNRA geometric HL_4V88_218 | NA HL_43074.18* | ||
| 1/B5/1550:1561 | geometric HL_4V88_219 | NA HL_32458.3* | ||
| 1/B5/1594:1602 | geometric HL_4V88_220 | NA HL_01181.4* | ||
| 1/B5/1778:1783 | Other HL geometric HL_4V88_222 | NA HL_43074.18* |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7MPJ_112 | NA |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/A1/7:8, 1/A4/150:152 | Single bulged C geometric IL_5TBW_002 | NA IL_61258.10* | ||
| 1/A1/13:15, 1/A4/144:145 | Single bulged U geometric IL_5TBW_003 | NA IL_83039.11* | ||
| 1/A1/27:28, 1/A1/56:58 | Single stack bend geometric IL_5TBW_004 | NA IL_04038.4* | ||
| 1/A1/31:38, 1/A1/45:53 | tSH-tHW-tHH-tHS geometric IL_5TBW_005 | NA IL_22863.1* | ||
| 1/A1/82:89, 1/A1/97:103 | geometric IL_5TBW_006 | NA IL_29509.1* | ||
| 1/A1/123:124, 1/A1/144:149 | geometric IL_5TBW_007 | NA IL_19724.1* | ||
| 1/A1/125:127, 1/A1/141:143 | geometric IL_5TBW_008 | NA IL_01312.13* | ||
| 1/A1/163:166, 1/A1/256:258 | NA | NA | ||
| 1/A1/168:171, 1/A1/246:254 | NA | NA | ||
| 1/A1/171:175, 1/A1/243:246 | NA | NA | ||
| 1/A1/176:179, 1/A1/237:242 | NA | NA | ||
| 1/A1/189:191, 1/A1/204:205 | Single bulged U geometric IL_5TBW_012 | NA IL_83039.11* | ||
| 1/A1/337:339, 1/A4/25:26 | Single bulged A geometric IL_5TBW_013 | NA IL_80007.16* | ||
| 1/A1/376:379, 1/A1/390:403 | geometric IL_5TBW_014 | NA IL_60992.5* | ||
| 1/A1/404:410, 1/A4/13:19 | Triple sheared with non-canonical cWW geometric IL_5TBW_015 | NA IL_66414.5* | ||
| 1/A1/417:419, 1/A4/4:6 | geometric IL_3LA5_001 | NA IL_01312.13* | ||
| 1/A1/429:431, 1/A1/628:630 | geometric IL_5TBW_016 | NA IL_01312.13* | ||
| 1/A1/435:495, 1/A1/618:624 | NA | NA | ||
| 1/A1/512:513, 1/A1/577:579 | Single bulged A geometric IL_5TBW_018 | NA IL_40508.4* | ||
| 1/A1/517:525, 1/A1/567:573 | geometric IL_5TBW_019 | NA IL_41593.1* | ||
| 1/A1/531:538, 1/A1/553:561 | geometric IL_5TBW_020 | NA IL_94501.1* | ||
| 1/A1/668:670, 1/A1/792:794 | geometric IL_5TBW_021 | NA IL_01312.13* | ||
| 1/A1/680:684, 1/A1/696:700 | geometric IL_5TBW_022 | NA IL_92343.1* | ||
| 1/A1/725:728, 1/A1/741:745 | UAA/GAN geometric IL_5TBW_023 | NA IL_53523.5* | ||
| 1/A1/752:753, 1/A1/779:781 | Single bulged A geometric IL_5TBW_024 | NA IL_80007.16* | ||
| 1/A1/758:763, 1/A1/768:773 | geometric IL_5TBW_026 | NA IL_19954.1* | ||
| 1/A1/803:809, 1/A1/931:940 | NA | NA | ||
| 1/A1/826:828, 1/A1/897:899 | geometric IL_5TBW_110 | NA IL_01312.13* | ||
| 1/A1/828:829, 1/A1/895:897 | Single bulged A geometric IL_4V9F_025 | NA IL_80007.16* | ||
| 1/A1/833:834, 1/A1/859:861 | Single bulged G geometric IL_5TBW_029 | NA IL_99645.1* | ||
| 1/A1/834:838, 1/A1/855:859 | Triple sheared geometric IL_5J7L_263 | NA IL_56467.6* | ||
| 1/A1/869:872, 1/A1/888:890 | Major groove platform with extra cWW geometric IL_5TBW_031 | NA IL_95485.6* | ||
| 1/A1/873:875, 1/A1/886:887 | Single bulged U geometric IL_5TBW_032 | NA IL_83039.11* | ||
| 1/A1/907:909, 1/A1/919:923 | Multiple bulged bases geometric IL_5TBW_033 | NA IL_90991.5* | ||
| 1/A1/969:970, 1/A1/1111:1113 | Single stack bend geometric IL_5TBW_035 | NA IL_04038.4* | ||
| 1/A1/970:972, 1/A1/1109:1111 | Stack and bulge geometric IL_2O3X_001 | NA IL_04038.4* | ||
| 1/A1/977:982, 1/A1/1101:1104 | NA | NA | ||
| 1/A1/983:985, 1/A1/1099:1100 | Single bulged G geometric IL_5TBW_037 | NA IL_59137.10* | ||
| 1/A1/989:991, 1/A1/1058:1060 | geometric IL_1NBS_006 | NA IL_01312.13* | ||
| 1/A1/991:998, 1/A1/1050:1058 | NA | NA | ||
| 1/A1/999:1005, 1/A1/1045:1049 | geometric IL_4V9F_035 | NA IL_21121.1* | ||
| 1/A1/1006:1009, 1/A1/1041:1044 | Tandem non-canonical cWW pairs geometric IL_6JDV_001 | NA IL_85877.10* | ||
| 1/A1/1009:1011, 1/A1/1039:1041 | geometric IL_5TBW_042 | NA IL_01312.13* | ||
| 1/A1/1069:1071, 1/A1/1087:1089 | geometric IL_5CCB_001 | NA IL_01312.13* | ||
| 1/A1/1074:1076, 1/A1/1083:1084 | Single bulged A geometric IL_5TBW_045 | NA IL_80007.16* | ||
| 1/A1/1120:1122, 1/A1/1136:1138 | geometric IL_5TBW_046 | NA IL_01312.13* | ||
| 1/A1/1167:1171, 1/A1/1328:1332 | UAA/GAN geometric IL_5TBW_048 | NA IL_53523.5* | ||
| 1/A1/1173:1180, 1/A1/1325:1326 | SSU/LSU pseudoknot geometric IL_5TBW_049 | NA IL_15861.6* | ||
| 1/A1/1180:1182, 1/A1/1324:1325 | Single bulged U geometric IL_5TBW_050 | NA IL_83039.11* | ||
| 1/A1/1187:1194, 1/A1/1314:1319 | geometric IL_5TBW_051 | NA IL_17971.1* | ||
| 1/A1/1194:1205, 1/A1/1299:1314 | geometric IL_5TBW_052 | NA IL_94878.1* | ||
| 1/A1/1207:1209, 1/A1/1296:1297 | Single bulged U geometric IL_4V9F_107 | NA IL_83039.11* | ||
| 1/A1/1218:1226, 1/A1/1283:1287 | Kink-turn geometric IL_4V9F_042 | NA IL_90538.3* | ||
| 1/A1/1262:1266, 1/A1/1275:1277 | NA | NA | ||
| 1/A1/1376:1378, 1/A1/1428:1431 | Isolated cWS basepair geometric IL_5TBW_057 | NA IL_01312.13* | ||
| 1/A1/1385:1387, 1/A1/1420:1421 | Single bulged A geometric IL_5TBW_058 | NA IL_80007.16* | ||
| 1/A1/1388:1395, 1/A1/1415:1419 | Kink-turn geometric IL_5TBW_059 | NA IL_29549.9* | ||
| 1/A1/1398:1400, 1/A1/1411:1412 | Single bulged A geometric IL_5TBW_060 | NA IL_80007.16* | ||
| 1/A1/1444:1451, 1/A1/2353:2359 | 8x7 Sarcin-Ricin with CC bifurcated pair; G-bulge geometric IL_4V9F_012 | NA IL_59724.1* | ||
| 1/A1/1500:1505, 1/A1/1513:1516 | geometric IL_5TBW_062 | NA IL_47743.1* | ||
| 1/A1/1532:1536, 1/A1/1585:1590 | UAA/GAN geometric IL_5TBW_063 | NA IL_53523.5* | ||
| 1/A1/1561:1562, 1/A1/1577:1579 | Single stack bend geometric IL_7KGA_003 | NA IL_04038.4* | ||
| 1/A1/1562:1566, 1/A1/1572:1577 | NA | NA | ||
| 1/A1/1618:1621, 1/A1/1824:1826 | Other IL geometric IL_5TBW_064 | NA IL_87630.5* | ||
| 1/A1/1623:1625, 1/A1/1818:1822 | Isolated non-canonical cWW with bulges geometric IL_5ML7_010 | NA IL_01312.13* | ||
| 1/A1/1627:1631, 1/A1/1811:1816 | NA | NA | ||
| 1/A1/1645:1649, 1/A1/1806:1810 | Triple sheared geometric IL_5TBW_067 | NA IL_56467.6* | ||
| 1/A1/1661:1663, 1/A1/1786:1788 | geometric IL_5TBW_068 | NA IL_01312.13* | ||
| 1/A1/1669:1670, 1/A1/1778:1780 | Single bulged C geometric IL_5TBW_069 | NA IL_61258.10* | ||
| 1/A1/1670:1671, 1/A1/1776:1778 | Single stack bend geometric IL_5TBW_070 | NA IL_72766.2* | ||
| 1/A1/1702:1707, 1/A1/1737:1743 | geometric IL_5TBW_072 | NA IL_98876.1* | ||
| 1/A1/1711:1717, 1/A1/1727:1733 | Kink-turn geometric IL_5TBW_073 | NA IL_76900.1* | ||
| 1/A1/1880:1882, 1/A1/2350:2352 | Not an internal loop geometric IL_5VCI_005 | NA IL_04038.4* | ||
| 1/A1/1882:1889, 1/A1/2346:2350 | NA | NA | ||
| 1/A1/1894:1897, 1/A1/2338:2341 | NA | NA | ||
| 1/A1/1897:1901, 1/A1/2336:2338 | Major groove platform with extra pair geometric IL_7RQB_093 | NA IL_87630.5* | ||
| 1/A1/1901:1906, 1/A1/2333:2336 | Intercalated tWH geometric IL_4V9F_062 | NA IL_01312.13* | ||
| 1/A1/1918:1923, 1/A1/1928:1934 | tSH-tSH-tHH-tHS geometric IL_4V9F_063 | NA IL_66584.5* | ||
| 1/A1/1940:1942, 1/A1/2106:2108 | geometric IL_1U9S_007 | NA IL_01312.13* | ||
| 1/A1/1947:1948, 1/A1/2098:2101 | geometric IL_5TBW_080 | NA IL_76195.1* | ||
| 1/A1/1949:1953, 1/A1/2094:2097 | NA | NA | ||
| 1/A1/2128:2130, 1/A1/2322:2325 | Intercalated cWW geometric IL_7A0S_044 | NA IL_04038.4* | ||
| 1/A1/2156:2161, 1/A1/2173:2180 | Kink-turn related geometric IL_5TBW_083 | NA IL_95993.1* | ||
| 1/A1/2190:2192, 1/A1/2315:2317 | Stack and bulge geometric IL_2ET8_001 | NA IL_04038.4* | ||
| 1/A1/2196:2199, 1/A1/2245:2246 | Major groove outside cWW, minor groove, intercalation pocket geometric IL_5J7L_314 | NA IL_06437.11* | ||
| 1/A1/2200:2201, 1/A1/2241:2244 | Major groove outside cWW, minor groove, intercalation pocket geometric IL_5J7L_315 | NA IL_13730.12* | ||
| 1/A1/2204:2206, 1/A1/2237:2238 | Single bulged U geometric IL_5TBW_025 | NA IL_83039.11* | ||
| 1/A1/2206:2210, 1/A1/2235:2237 | NA | NA | ||
| 1/A1/2211:2217, 1/A1/2228:2234 | geometric IL_5TBW_088 | NA IL_36973.5* | ||
| 1/A1/2249:2251, 1/A1/2265:2267 | Stack and bulge geometric IL_2O3X_001 | NA IL_04038.4* | ||
| 1/A1/2276:2277, 1/A1/2307:2310 | Multiple bulged bases geometric IL_5TBW_089 | NA IL_69632.1* | ||
| 1/A1/2277:2289, 1/A1/2303:2307 | NA | NA | ||
| 1/A1/2391:2394, 1/A1/2986:2988 | Major groove platform with extra pair geometric IL_5TBW_091 | NA IL_87630.5* | ||
| 1/A1/2396:2398, 1/A1/2981:2984 | Minor groove platform with intercalation geometric IL_5TBW_092 | NA IL_86964.1* | ||
| 1/A1/2409:2411, 1/A1/2811:2812 | Single bulged U geometric IL_5TBW_093 | NA IL_83039.11* | ||
| 1/A1/2412:2413, 1/A1/2807:2810 | Minor groove platform geometric IL_5TBW_094 | NA IL_06437.11* | ||
| 1/A1/2420:2422, 1/A1/2608:2610 | geometric IL_4WF9_042 | NA IL_01312.13* | ||
| 1/A1/2423:2425, 1/A1/2604:2607 | Isolated tHS basepair with bulges geometric IL_5TBW_095 | NA IL_38958.6* | ||
| 1/A1/2520:2526, 1/A1/2584:2587 | geometric IL_5TBW_096 | NA IL_98353.1* | ||
| 1/A1/2614:2615, 1/A1/2625:2627 | Single bulged A geometric IL_4WF9_098 | NA IL_71960.4* | ||
| 1/A1/2666:2668, 1/A1/2686:2690 | Isolated tHS basepair with bulges geometric IL_5TBW_099 | NA IL_38958.6* | ||
| 1/A1/2718:2722, 1/A1/2734:2738 | geometric IL_5TBW_121 | NA IL_05867.1* | ||
| 1/A1/2766:2768, 1/A1/2790:2792 | UU cWW geometric IL_3SZX_003 | NA IL_01312.13* | ||
| 1/A1/2770:2773, 1/A1/2787:2788 | Single stack bend with bulge geometric IL_5TBW_101 | NA IL_31836.1* | ||
| 1/A1/2823:2828, 1/A1/2862:2867 | NA | NA | ||
| 1/A1/2828:2830, 1/A1/2858:2862 | geometric IL_5TBW_105 | NA IL_07931.5* | ||
| 1/A1/2835:2839, 1/A1/2849:2853 | Triple sheared geometric IL_5J7L_338 | NA IL_56467.6* | ||
| 1/A1/2876:2877, 1/A1/2949:2951 | Major groove platform geometric IL_5TBW_107 | NA IL_80663.10* | ||
| 1/A1/2877:2879, 1/A1/2947:2949 | geometric IL_2ZNI_001 | NA IL_01312.13* | ||
| 1/A1/2879:2881, 1/A1/2943:2947 | NA | NA | ||
| 1/A1/2881:2882, 1/A1/2940:2943 | Multiple bulged bases geometric IL_5TBW_109 | NA IL_13730.12* | ||
| 1/A1/2889:2891, 1/A1/2912:2914 | geometric IL_5TBW_110 | NA IL_01312.13* | ||
| 1/A1/2891:2892, 1/A1/2909:2912 | Minor groove platform with intercalation geometric IL_5TBW_111 | NA IL_95601.1* | ||
| 1/A1/2918:2920, 1/A1/2926:2928 | geometric IL_5TBW_112 | NA IL_01312.13* | ||
| 1/A1/2958:2960, 1/A1/2972:2974 | Isolated cWH basepair geometric IL_4J50_003 | NA IL_01312.13* | ||
| 1/A1/2960:2961, 1/A1/2970:2972 | Single bulged A geometric IL_1U9S_001 | NA IL_80007.16* | ||
| 1/A1/3004:3007, 1/A1/3139:3144 | Double sheared geometric IL_5TBW_114 | NA IL_09705.7* | ||
| 1/A1/3012:3014, 1/A1/3040:3042 | geometric IL_5TBW_115 | NA IL_01312.13* | ||
| 1/A1/3016:3018, 1/A1/3036:3038 | UG cWW geometric IL_4LFB_061 | NA IL_01312.13* | ||
| 1/A1/3018:3025, 1/A1/3030:3036 | 8x7 Sarcin-Ricin; G-bulge geometric IL_5TBW_116 | NA IL_04346.5* | ||
| 1/A1/3047:3051, 1/A1/3091:3094 | Major groove minor groove platform with tHH geometric IL_5TBW_117 | NA IL_28060.3* | ||
| 1/A1/3054:3059, 1/A1/3084:3088 | UAA/GAN related geometric IL_5TBW_118 | NA IL_53523.5* | ||
| 1/A1/3063:3064, 1/A1/3077:3080 | Multiple bulged bases geometric IL_5TBW_119 | NA IL_13730.12* | ||
| 1/A1/3103:3107, 1/A1/3127:3131 | UAA/GAN geometric IL_5TBW_120 | NA IL_53523.5* | ||
| 1/A1/3164:3166, 1/A1/3284:3286 | geometric IL_1YZ9_002 | NA IL_01312.13* | ||
| 1/A1/3168:3170, 1/A1/3280:3282 | CC cWW geometric IL_4KNQ_002 | NA IL_01312.13* | ||
| 1/A1/3177:3179, 1/A1/3210:3211 | Single bulged A geometric IL_5TBW_123 | NA IL_80007.16* | ||
| 1/A1/3179:3188, 1/A1/3204:3210 | geometric IL_5TBW_124 | NA IL_56867.1* | ||
| 1/A1/3193:3194, 1/A1/3197:3199 | Single bulged U geometric IL_5J7L_298 | NA IL_83039.11* | ||
| 1/A1/3225:3229, 1/A1/3258:3260 | geometric IL_5TBW_126 | NA IL_50789.1* | ||
| 1/A1/3233:3235, 1/A1/3252:3254 | AA cWW geometric IL_5ED1_002 | NA IL_01312.13* | ||
| 1/A1/3235:3238, 1/A1/3249:3252 | Tandem non-canonical cWW pairs geometric IL_4UYK_003 | NA IL_85877.10* | ||
| 1/A1/3300:3303, 1/A1/3311:3314 | Tandem non-canonical cWW pairs geometric IL_5TBW_129 | NA IL_85877.10* | ||
| 1/A1/3318:3320, 1/A1/3387:3388 | Single bulged U geometric IL_5J7L_279 | NA IL_83039.11* | ||
| 1/A1/3324:3325, 1/A1/3381:3383 | Single bulged U geometric IL_2A64_002 | NA IL_83039.11* | ||
| 1/A1/3328:3330, 1/A1/3373:3378 | Isolated non-canonical cWW with bulges geometric IL_5TBW_132 | NA IL_55456.1* | ||
| 1/A1/3332:3337, 1/A1/3367:3371 | geometric IL_5TBW_133 | NA IL_47002.1* | ||
| 1/A1/3340:3342, 1/A1/3363:3364 | Single bulged U geometric IL_3WBM_001 | NA IL_83039.11* | ||
| 1/A1/3342:3345, 1/A1/3360:3363 | Double sheared geometric IL_4V9F_100 | NA IL_09705.7* | ||
| 1/A1/3349:3350, 1/A1/3353:3356 | Multiple bulged bases geometric IL_5TBW_136 | NA IL_13730.12* | ||
| 1/A3/15:16, 1/A3/63:65 | Single bulged A geometric IL_5TBW_372 | NA IL_80007.16* | ||
| 1/A3/21:27, 1/A3/53:58 | geometric IL_5TBW_373 | NA IL_05523.1* | ||
| 1/A3/28:29, 1/A3/49:52 | Minor groove platform geometric IL_5TBW_374 | NA IL_94431.4* | ||
| 1/A3/29:30, 1/A3/47:49 | Single stack bend geometric IL_5TBW_375 | NA IL_04038.4* | ||
| 1/A3/32:36, 1/A3/41:45 | Symmetric double minor groove platform geometric IL_5TBW_376 | NA IL_58103.5* | ||
| 1/A3/72:80, 1/A3/100:106 | 8x7 Sarcin-Ricin; G-bulge geometric IL_5TBW_377 | NA IL_04346.5* | ||
| 1/A3/84:87, 1/A3/94:96 | geometric IL_5MSF_001 | NA IL_01312.13* | ||
| 1/A4/44:64, 1/A4/96:100 | geometric IL_5TBW_144 | NA IL_23735.1* | ||
| 1/A4/64:66, 1/A4/93:96 | Isolated non-canonical cWW with bulges geometric IL_5TBW_145 | NA IL_55456.1* | ||
| 1/A4/68:69, 1/A4/89:91 | Single bulged U geometric IL_5TBW_146 | NA IL_83039.11* | ||
| 1/B5/24:26, 1/B5/600:601 | Single bulged C geometric IL_7KGA_004 | NA IL_61258.10* | ||
| 1/B5/27:29, 1/B5/597:599 | UU cWW geometric IL_3SZX_003 | NA IL_01312.13* | ||
| 1/B5/35:37, 1/B5/471:473 | UC cWW geometric IL_4V88_385 | NA IL_01312.13* | ||
| 1/B5/42:48, 1/B5/431:433 | geometric IL_4V88_387 | NA IL_34626.4* | ||
| 1/B5/50:52, 1/B5/428:429 | Minor groove platform geometric IL_4V88_388 | NA IL_06437.11* | ||
| 1/B5/58:63, 1/B5/87:89 | geometric IL_4V88_389 | NA IL_96451.1* | ||
| 1/B5/64:69, 1/B5/82:86 | geometric IL_4V88_390 | NA IL_59423.1* | ||
| 1/B5/109:113, 1/B5/301:305 | geometric IL_4V88_422 | NA IL_79670.1* | ||
| 1/B5/113:116, 1/B5/300:301 | Multiple bulged bases geometric IL_4V88_392 | NA IL_13730.12* | ||
| 1/B5/117:122, 1/B5/295:299 | geometric IL_4V88_393 | NA IL_76386.1* | ||
| 1/B5/143:149, 1/B5/165:172 | tWH-tWH-tHW-tHW geometric IL_4V88_394 | NA IL_92440.5* | ||
| 1/B5/150:152, 1/B5/162:164 | Isolated cWH basepair geometric IL_3W3S_003 | NA IL_42589.6* | ||
| 1/B5/204:206, 1/B5/259:263 | Major groove platform with extra cWW geometric IL_4V88_397 | NA IL_95485.6* | ||
| 1/B5/206:208, 1/B5/257:259 | geometric IL_4V88_398 | NA IL_01312.13* | ||
| 1/B5/210:212, 1/B5/253:255 | Not an internal loop geometric IL_5VCI_005 | NA IL_04038.4* | ||
| 1/B5/265:267, 1/B5/288:289 | Single bulged A geometric IL_4V88_399 | NA IL_80007.16* | ||
| 1/B5/270:273, 1/B5/283:285 | geometric IL_4V88_400 | NA IL_05922.1* | ||
| 1/B5/275:276, 1/B5/279:281 | NA | NA | ||
| 1/B5/311:316, 1/B5/348:355 | Kink-turn with non-sequential stacking geometric IL_4V88_402 | NA IL_29549.9* | ||
| 1/B5/318:323, 1/B5/345:346 | geometric IL_5Y58_001 | NA IL_98882.3* | ||
| 1/B5/363:365, 1/B5/376:381 | geometric IL_4V88_404 | NA IL_46732.1* | ||
| 1/B5/389:391, 1/B5/406:408 | Isolated cWH basepair geometric IL_4V88_405 | NA IL_42589.6* | ||
| 1/B5/439:441, 1/B5/463:464 | Single bulged U geometric IL_4V88_407 | NA IL_83039.11* | ||
| 1/B5/443:447, 1/B5/460:461 | C-loop geometric IL_5J7L_018 | NA IL_08376.2* | ||
| 1/B5/447:448, 1/B5/458:460 | Single bulged G geometric IL_5J7L_019 | NA IL_59137.10* | ||
| 1/B5/480:484, 1/B5/503:508 | NA | NA | ||
| 1/B5/516:518, 1/B5/533:536 | Minor groove platform with extra cWW geometric IL_4V88_411 | NA IL_87332.1* | ||
| 1/B5/518:520, 1/B5/532:533 | Minor groove platform geometric IL_4V88_412 | NA IL_06437.11* | ||
| 1/B5/550:557, 1/B5/587:588 | SSU/LSU pseudoknot geometric IL_4V88_413 | NA IL_15861.6* | ||
| 1/B5/557:559, 1/B5/586:587 | Single bulged U geometric IL_4V88_414 | NA IL_83039.11* | ||
| 1/B5/561:568, 1/B5/575:584 | NA | NA | ||
| 1/B5/616:622, 1/B5/1104:1105 | geometric IL_4V88_416 | NA IL_12418.1* | ||
| 1/B5/624:626, 1/B5/973:975 | geometric IL_4V88_417 | NA IL_01312.13* | ||
| 1/B5/627:631, 1/B5/968:972 | tSH-tHW-tHS geometric IL_4V88_418 | NA IL_39521.5* | ||
| 1/B5/631:633, 1/B5/966:968 | Stack and bulge geometric IL_2O3X_001 | NA IL_04038.4* | ||
| 1/B5/646:648, 1/B5/686:688 | Isolated near basepair geometric IL_4V88_406 | NA IL_01312.13* | ||
| 1/B5/651:658, 1/B5/676:683 | NA | NA | ||
| 1/B5/746:747, 1/B5/802:805 | Major groove minor groove platform; mini C-loop geometric IL_4V88_423 | NA IL_09061.4* | ||
| 1/B5/748:750, 1/B5/799:801 | geometric IL_4V88_424 | NA IL_01312.13* | ||
| 1/B5/751:760, 1/B5/790:798 | NA | NA | ||
| 1/B5/817:824, 1/B5/848:854 | NA | NA | ||
| 1/B5/865:866, 1/B5/962:965 | Major groove platform; stack outside cWW geometric IL_4V88_428 | NA IL_70995.6* | ||
| 1/B5/868:869, 1/B5/958:960 | Single bulged U geometric IL_6UFH_004 | NA IL_83039.11* | ||
| 1/B5/871:874, 1/B5/953:956 | Tandem non-canonical cWW pairs geometric IL_4V88_430 | NA IL_85877.10* | ||
| 1/B5/874:878, 1/B5/950:953 | Tandem non-canonical cWW pairs geometric IL_4V88_431 | NA IL_85877.10* | ||
| 1/B5/885:888, 1/B5/924:927 | Tandem non-canonical cWW pairs geometric IL_4V88_432 | NA IL_85877.10* | ||
| 1/B5/893:899, 1/B5/910:919 | NA | NA | ||
| 1/B5/985:990, 1/B5/1014:1016 | Other IL geometric IL_4V88_435 | NA IL_51590.1* | ||
| 1/B5/990:994, 1/B5/1010:1014 | tSH-tHW-tHS geometric IL_4V88_436 | NA IL_39521.5* | ||
| 1/B5/1034:1036, 1/B5/1095:1101 | geometric IL_4V88_437 | NA IL_19557.1* | ||
| 1/B5/1041:1044, 1/B5/1074:1077 | Tandem non-canonical cWW pairs geometric IL_4V88_438 | NA IL_85877.10* | ||
| 1/B5/1051:1053, 1/B5/1066:1067 | Single bulged U geometric IL_5J7L_017 | NA IL_83039.11* | ||
| 1/B5/1111:1118, 1/B5/1129:1134 | 8x6 Sarcin-Ricin with inserted Y; G-bulge geometric IL_4V88_440 | NA IL_24606.1* | ||
| 1/B5/1146:1147, 1/B5/1630:1632 | Single bulged A geometric IL_5J7L_039 | NA IL_80007.16* | ||
| 1/B5/1149:1151, 1/B5/1627:1628 | Single bulged G geometric IL_4V88_442 | NA IL_59137.10* | ||
| 1/B5/1157:1160, 1/B5/1617:1621 | C-loop geometric IL_4V88_443 | NA IL_63596.4* | ||
| 1/B5/1173:1175, 1/B5/1464:1466 | geometric IL_4V88_444 | NA IL_01312.13* | ||
| 1/B5/1178:1179, 1/B5/1459:1461 | Minor groove platform geometric IL_4V88_445 | NA IL_06437.11* | ||
| 1/B5/1213:1215, 1/B5/1448:1450 | geometric IL_4V88_446 | NA IL_01312.13* | ||
| 1/B5/1224:1233, 1/B5/1252:1259 | NA | NA | ||
| 1/B5/1234:1236, 1/B5/1249:1251 | geometric IL_4V88_448 | NA IL_01312.13* | ||
| 1/B5/1270:1272, 1/B5/1438:1440 | geometric IL_5Y7M_007 | NA IL_01312.13* | ||
| 1/B5/1272:1276, 1/B5/1436:1438 | Isolated cWS basepair |