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5WYK Internal, Hairpin and 3-way Junction Loop Motifs

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Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/5A/120:125NANA
1/5A/196:201NANA
1/5A/360:365NANA
1/5A/515:522NANA
1/SA/154:160
geometric
HL_4WF9_003		NA

HL_62869.3*
1/SA/190:195NANA
1/SA/276:279
geometric
HL_5TBW_071		NA

HL_69353.7*
1/SA/330:338
homologous
HL_4V88_193		NA

HL_93727.5*
1/SA/368:373NANA
1/SA/393:404
homologous
HL_4V88_195		NA

HL_22443.1*
1/SA/414:419UNCG
homologous
HL_4V88_196		NA

HL_79299.11*
1/SA/450:456
homologous
HL_4V88_197		NA

HL_50374.1*
1/SA/491:496
geometric
HL_5U3G_001		NA

HL_40469.1*
1/SA/520:532
homologous
HL_4V88_199		NA

HL_17086.2*
1/SA/569:574NANA
1/SA/900:909
homologous
HL_4V88_206		NA

HL_87219.4*
1/SA/937:942Other HL
homologous
HL_4V88_207		NA

HL_43074.18*
1/SA/1055:1064
geometric
HL_2ZZM_002		NA

HL_18218.2*
1/SA/1501:1506GNRA
homologous
HL_4V88_218		NA

HL_43074.18*
1/SA/1594:1602NANA
1/SA/1802:1807Other HL
geometric
HL_5J7L_180		NA

HL_43074.18*

Problematic loops

#loop idProblemSequence
HL_5WYK_001NA
HL_5WYK_002NA
HL_5WYK_003NA
HL_5WYK_006NA
HL_5WYK_008NA
HL_5WYK_010NA
HL_5WYK_013
geometric
HL_361D_002
HL_5WYK_023NA
HL_5WYK_027NA
HL_5WYK_030NA

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/3A/1:4,
1/SA/1120:1123		Tandem non-canonical cWW pairs
geometric
IL_1MFQ_004		NA

IL_85877.10*
1/3A/4:6,
1/SA/1118:1120
geometric
IL_1YZ9_002		NA

IL_01312.13*
1/3A/48:50,
1/5A/468:470		NANA
1/3A/50:52,
1/5A/466:468		NANA
1/3A/78:85,
1/3A/325:329		NANA
1/3A/97:98,
1/3A/317:319		NANA
1/5A/11:15,
1/5A/66:71		NANA
1/5A/16:18,
1/5A/62:65		NANA
1/5A/94:95,
1/5A/149:156		NANA
1/5A/97:99,
1/5A/145:147		NANA
1/5A/100:104,
1/5A/140:144		NANA
1/5A/107:111,
1/5A/135:137		NANA
1/5A/115:120,
1/5A/125:131		NANA
1/5A/167:172,
1/5A/224:228		NANA
1/5A/175:178,
1/5A/219:221		NANA
1/5A/181:183,
1/5A/214:216		NANA
1/5A/187:189,
1/5A/208:210		NANA
1/5A/246:247,
1/5A/265:267		NANA
1/5A/336:341,
1/5A/384:387		NANA
1/5A/342:343,
1/5A/381:383		NANA
1/5A/346:349,
1/5A/375:378		NANA
1/5A/352:356,
1/5A/369:372		NANA
1/5A/395:397,
1/5A/460:462		NANA
1/5A/400:406,
1/5A/450:457		NANA
1/5A/413:414,
1/5A/440:443		NANA
1/5A/501:503,
1/5A/533:537		NANA
1/5A/505:507,
1/5A/529:531		NANA
1/5A/513:515,
1/5A/522:523		NANA
1/5A/550:552,
1/5A/585:587		NANA
1/5A/555:558,
1/5A/579:582		NANA
1/5A/559:561,
1/5A/576:578		NANA
1/SA/24:26,
1/SA/600:601		NANA
1/SA/50:52,
1/SA/428:429		Minor groove platform
homologous
IL_4V88_388		NA

IL_06437.11*
1/SA/109:112,
1/SA/302:305		Tandem non-canonical cWW pairs
homologous
IL_4V88_391		NA

IL_85877.10*
1/SA/113:116,
1/SA/300:301		Multiple bulged bases
homologous
IL_4V88_392		NA

IL_13730.12*
1/SA/117:122,
1/SA/295:299
homologous
IL_4V88_393		NA

IL_76386.1*
1/SA/144:149,
1/SA/165:171		tWH-tWH-tHW-tHW
geometric
IL_4LFB_009		NA

IL_87677.1*
1/SA/150:152,
1/SA/162:164
geometric
IL_1RPU_001		NA

IL_01312.13*
1/SA/186:189,
1/SA/196:199		Double sheared
homologous
IL_4V88_396		NA

IL_09705.7*
1/SA/204:206,
1/SA/259:263		Major groove platform with extra cWW
geometric
IL_1MMS_002		NA

IL_95485.6*
1/SA/206:208,
1/SA/257:259		NANA
1/SA/265:267,
1/SA/288:289		NANA
1/SA/270:273,
1/SA/283:285		NANA
1/SA/275:276,
1/SA/279:281		NANA
1/SA/311:316,
1/SA/348:355		Kink-turn with non-sequential stacking
homologous
IL_4V88_402		NA

IL_29549.9*
1/SA/318:323,
1/SA/345:346		NANA
1/SA/363:365,
1/SA/376:381		NANA
1/SA/389:391,
1/SA/406:408		Isolated cWH basepair
homologous
IL_4V88_405		NA

IL_42589.6*
1/SA/443:447,
1/SA/460:461		C-loop
geometric
IL_5J7L_018		NA

IL_08376.2*
1/SA/447:448,
1/SA/458:460		Single bulged G
geometric
IL_3NDB_004		NA

IL_59137.10*
1/SA/480:485,
1/SA/502:508		NANA
1/SA/517:520,
1/SA/532:535		NANA
1/SA/557:559,
1/SA/586:587		NANA
1/SA/627:631,
1/SA/968:972		tSH-tHW-tHS
homologous
IL_4V88_418		NA

IL_39521.5*
1/SA/865:866,
1/SA/962:965		Major groove platform; stack outside cWW
geometric
IL_6N5P_003		NA

IL_70995.6*
1/SA/867:870,
1/SA/957:961		Tandem non-canonical cWW pairs
homologous
IL_4V88_429		NA

IL_85877.10*
1/SA/871:873,
1/SA/954:956
geometric
IL_2R8S_001		NA

IL_01312.13*
1/SA/874:878,
1/SA/950:953		Tandem non-canonical cWW pairs
homologous
IL_4V88_431		NA

IL_85877.10*
1/SA/885:888,
1/SA/924:927		Tandem non-canonical cWW pairs
homologous
IL_4V88_432		NA

IL_85877.10*
1/SA/893:899,
1/SA/910:919		NANA
1/SA/1041:1044,
1/SA/1074:1077		Tandem non-canonical cWW pairs
homologous
IL_4V88_438		NA

IL_85877.10*
1/SA/1051:1053,
1/SA/1066:1067		NANA
1/SA/1149:1151,
1/SA/1627:1628		Single bulged G
homologous
IL_4V88_442		NA

IL_59137.10*
1/SA/1157:1161,
1/SA/1616:1621		NANA
1/SA/1173:1175,
1/SA/1464:1466
homologous
IL_4V88_444		NA

IL_01312.13*
1/SA/1470:1474,
1/SA/1533:1574		NANA
1/SA/1495:1498,
1/SA/1509:1512		Tandem non-canonical cWW pairs
homologous
IL_4V88_461		NA

IL_85877.10*
1/SA/1642:1644,
1/SA/1757:1759
geometric
IL_4LFB_010		NA

IL_01312.13*
1/SA/1644:1649,
1/SA/1751:1757		NANA
1/SA/1650:1652,
1/SA/1748:1750		AA cWW
homologous
IL_4V88_467		NA

IL_01312.13*
1/SA/1653:1656,
1/SA/1744:1747		Double sheared
geometric
IL_5AOX_003		NA

IL_09705.7*
1/SA/1656:1658,
1/SA/1743:1744		NANA
1/SA/1665:1667,
1/SA/1734:1736
homologous
IL_4V88_470		NA

IL_01312.13*
1/SA/1669:1672,
1/SA/1729:1732		Double sheared
homologous
IL_4V88_471		NA

IL_09705.7*
1/SA/1672:1674,
1/SA/1727:1729
geometric
IL_5UNE_001		NA

IL_01312.13*
1/SA/1675:1678,
1/SA/1723:1726		Tandem non-canonical cWW pairs
homologous
IL_4V88_473		NA

IL_85877.10*

Problematic loops

No problematic loops

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/3A/106:111,
1/3A/259:263,
1/3A/308:309		NANA
1/SA/633:635,
1/SA/861:865,
1/SA/965:966		NANA
1/SA/881:884,
1/SA/928:936,
1/SA/943:947
homologous
J3_4V88_033		NA
1/SA/1168:1171,
1/SA/1468:1470,
1/SA/1574:1577		NANA

Problematic loops

No problematic loops


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