Hairpin Loop Motif Atlas Release 3.78

#	Motif	Num Nts	Instances
1	HL_79546.1 View exemplar Basepair signature: cWW-tSH-F-F History status: Exact match GNRA (261) GNRA with GA tSW pair (4) GNRA related (3)	6	269
2	HL_22280.1 View exemplar Basepair signature: cWW-tWH-F-F-F History status: Exact match T-loop with 2 stacked bulged bases (59) T-loop with 2 bulged bases not stacked (1) Other HL (1)	7	61
3	HL_03562.1 View exemplar Basepair signature: cWW-tSW-F History status: Exact match UNCG (46) UNCG variation (2)	5	53
4	HL_87030.1 View exemplar Basepair signature: cWW-F-F History status: Exact match GNRA (21) GNRA variation (7) UNCG variation (1)	4	35
5	HL_89380.1 View exemplar Basepair signature: cWW-tWH-F-F-F History status: Exact match T-loop with 2 stacked bulged bases (19) T-loop with 2 bulged bases not stacked (8) T-loop with 3 stacked bulged bases (3) T-loop with 1 bulged base (1)	7	34
6	HL_53597.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match tRNA anticodon loop (21) Anticodon loop related (6)	8	29
7	HL_98984.1 View exemplar Basepair signature: cWW-F History status: Exact match U1 small nuclear ribonucleoprotein A binding hairpin (19) tRNA D-loop (1)	3	28
8	HL_53640.1 View exemplar Basepair signature: cWW-F-F-F-F History status: Exact match Pseudoknot geometry (21) Ribsomal LSU H95 (5)	6	28
9	HL_38927.1 View exemplar Basepair signature: cWW-F History status: Exact match Mini UNCG (26)	3	27
10	HL_71309.1 View exemplar Basepair signature: cWW-tWH-F-F-F-F-F History status: Exact match T-loop with 2 stacked bulged bases (25)	9	25
11	HL_12078.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match Pseudoknot geometry (24)	7	24
12	HL_25462.1 View exemplar Basepair signature: cWW-cWS History status: Exact match tRNA D-loop (18) D-loop related (2)	4	20
13	HL_84085.1 View exemplar Basepair signature: cWW-tSH-F-F-F-F History status: Exact match GNRA wlth tandem sheared (10) GNRA related (2) GNRA with extra cWW (1)	8	19
14	HL_76539.1 View exemplar Basepair signature: cWW-F History status: Exact match GNRA variation (4) GNRA related (1) GNRA (1)	3	17
15	HL_53171.1 View exemplar Basepair signature: cWW-F-F-F-F History status: Exact match Other HL (1)	6	17
16	HL_08002.7 View exemplar Basepair signature: cWW-tWH-F-F History status: Exact match T-loop with unstacked turn (17)	6	17
17	HL_82739.1 View exemplar Basepair signature: cWW-F History status: Exact match	3	15
18	HL_89098.1 View exemplar Basepair signature: cWW-F History status: Exact match Mini UNCG (7) Mini UNCG related (1)	0	15
19	HL_73067.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match T-loop related (2)	8	14
20	HL_86152.1 View exemplar Basepair signature: cWW-cSW-F History status: Exact match T-loop with 1 bulged base (1) Other HL (1)	5	13
21	HL_79921.1 View exemplar Basepair signature: cWW-tSW-F History status: Exact match Fab BL3-6 binding hairpin with tSW (11) Other HL (1)	5	13
22	HL_69023.1 View exemplar Basepair signature: cWW-tWH-tSH-F-F History status: Exact match GNRA related (4)	8	13
23	HL_06192.1 View exemplar Basepair signature: cWW-tSH-F-F History status: Exact match	6	12
24	HL_30784.1 View exemplar Basepair signature: cWW-tSH-F History status: Exact match GNRA (4)	5	12
25	HL_97041.1 View exemplar Basepair signature: cWW-F-F History status: Exact match T-loop related (3) GNRA with extra cWW (1)	4	12
26	HL_14843.1 View exemplar Basepair signature: cWW-cWS History status: Exact match tRNA D-loop (8)	0	11
27	HL_20698.1 View exemplar Basepair signature: cWW-F-F History status: Exact match	4	11
28	HL_73266.5 View exemplar Basepair signature: cWW-R-cSW-R-cSH History status: Exact match	9	11
29	HL_91948.1 View exemplar Basepair signature: cWW-F History status: Exact match Mini UNCG (4)	3	11
30	HL_64430.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	11
31	HL_64970.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match Pseudoknot geometry with 3' bulge (6) Pseudoknot geometry (1)	5	10
32	HL_65572.1 View exemplar Basepair signature: cWW-F History status: Exact match Mini UNCG (5)	3	9
33	HL_49288.1 View exemplar Basepair signature: cWW-cWW-F-F-F History status: Exact match tRNA anticodon loop (5) Anticodon loop related (1) GNRA with extra tWH (1)	7	9
34	HL_34168.1 View exemplar Basepair signature: cWW-cWW-F History status: Exact match Other HL (1)	5	9
35	HL_08678.1 View exemplar Basepair signature: cWW-cSW-F-F-F-F History status: Exact match Anticodon loop related (1)	8	9
36	HL_26881.1 View exemplar Basepair signature: cWW-tWH-F-F History status: Exact match	6	9
37	HL_80489.1 View exemplar Basepair signature: cWW-tSH History status: Exact match GNRA (4) UNCG variation (1) GNRA variation (1)	4	9
38	HL_88526.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match tRNA anticodon loop (2)	7	9
39	HL_82201.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F-F History status: Exact match	10	9
40	HL_71554.1 View exemplar Basepair signature: cWW-cWW-F-F-F History status: Exact match T-loop related (4)	7	9
41	HL_97896.1 View exemplar Basepair signature: cWW-F History status: Exact match	3	9
42	HL_66853.1 View exemplar Basepair signature: cWW-cWS-F-cSH History status: Exact match	7	8
43	HL_32617.4 View exemplar Basepair signature: cWW-F-cSH History status: Exact match tRNA D-loop (4) D-loop related (3)	5	7
44	HL_56677.6 View exemplar Basepair signature: cWW-tWH-tSH-tSH-tHW-tHW-F-F-cWH History status: Exact match	13	7
45	HL_93374.1 View exemplar Basepair signature: cWW-cWH History status: Exact match	4	7
46	HL_56691.1 View exemplar Basepair signature: cWW-F History status: Exact match Mini UNCG (2) GNRA related (1)	3	7
47	HL_05241.1 View exemplar Basepair signature: cWW-F History status: Exact match Mini UNCG (5) Mini UNCG with extended bulge (2)	3	7
48	HL_67216.6 View exemplar Basepair signature: cWW-tSH-F-F History status: Exact match	6	7
49	HL_02733.5 View exemplar Basepair signature: cWW-R-R-R History status: Exact match	6	7
50	HL_36684.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F-F-F History status: Exact match	0	7
51	HL_43656.1 View exemplar Basepair signature: cWW-F-F History status: Exact match GNRA (2)	4	7
52	HL_84503.1 View exemplar Basepair signature: cWW-cWS-F-F History status: Exact match	6	7
53	HL_10895.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F-F History status: Exact match	10	7
54	HL_04171.5 View exemplar Basepair signature: cWW-cWW-F-F-cSS-F-F History status: Exact match	0	7
55	HL_19870.5 View exemplar Basepair signature: cWW-tSH-tHH-tWW-R-R-R History status: Exact match	11	6
56	HL_52841.1 View exemplar Basepair signature: cWW-F History status: Exact match	0	6
57	HL_86769.3 View exemplar Basepair signature: cWW-F-cSS-cSH History status: Exact match	0	6
58	HL_20743.3 View exemplar Basepair signature: cWW-F-F-cSS-F History status: Exact match	7	6
59	HL_84193.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F History status: Exact match	9	6
60	HL_32369.1 View exemplar Basepair signature: cWW-tSW-F History status: Exact match UNCG (3) UNCG variation (1)	5	6
61	HL_24068.1 View exemplar Basepair signature: cWW-cWW-F-F-F History status: Exact match	7	5
62	HL_01057.1 View exemplar Basepair signature: cWW History status: Exact match Pseudoknot geometry with 3' bulge (3)	0	5
63	HL_35015.1 View exemplar Basepair signature: cWW-cWW-F-F History status: Exact match	6	5
64	HL_78614.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	7	5
65	HL_82832.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	5
66	HL_99167.1 View exemplar Basepair signature: cWW-F-F-F-F-F-cSH-cSH History status: Exact match Pseudoknot with intercalation (4)	10	5
67	HL_90617.1 View exemplar Basepair signature: cWW-tSH History status: Exact match	4	5
68	HL_43613.4 View exemplar Basepair signature: cWW-tWH-tWH-R History status: Exact match	7	5
69	HL_94651.2 View exemplar Basepair signature: cWW-tSS History status: Exact match	4	5
70	HL_90642.5 View exemplar Basepair signature: cWW-R-R-tWH-R History status: Exact match	7	5
71	HL_06285.1 View exemplar Basepair signature: cWW-cWW-F-F-F-F-F-F-F-F-F History status: Exact match	13	5
72	HL_02862.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	5
73	HL_04221.1 View exemplar Basepair signature: cWW-cWS-tSH-cWS-F History status: Exact match tRNA D-loop (5)	0	5
74	HL_39334.5 View exemplar Basepair signature: cWW-tSW-R-R History status: Exact match	7	5
75	HL_76501.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match Pseudoknot geometry (2) G-quadruplex fragment (1)	0	5
76	HL_82231.1 View exemplar Basepair signature: cWW-cWW-F-F-F-F History status: Exact match	0	5
77	HL_85680.1 View exemplar Basepair signature: cWW-tSH-F History status: Exact match	0	5
78	HL_89881.1 View exemplar Basepair signature: cWW-tHW-F-F-F-F-F-F History status: Exact match	10	4
79	HL_50142.1 View exemplar Basepair signature: cWW-F-F-F-F History status: Exact match GNRA variation (2)	6	4
80	HL_14449.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	4
81	HL_83808.1 View exemplar Basepair signature: cWW-tWW-F-F-F History status: Exact match Pseudoknot (4)	0	4
82	HL_67667.1 View exemplar Basepair signature: cWW-F-F History status: Exact match	0	4
83	HL_37658.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match Pseudoknot (2) Anticodon loop related (1)	0	4
84	HL_43667.1 View exemplar Basepair signature: cWW-cWW-F-F History status: Exact match	6	4
85	HL_91503.4 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F History status: Exact match	9	4
86	HL_11410.1 View exemplar Basepair signature: cWW-F History status: Exact match	3	4
87	HL_74322.1 View exemplar Basepair signature: cWW-tSW-F History status: Exact match	5	4
88	HL_86109.1 View exemplar Basepair signature: cWW-F-tWH-F-F-F-F-F-F-F History status: Exact match	0	3
89	HL_40407.1 View exemplar Basepair signature: cWW History status: Exact match Externally structured (1) Mini UNCG (1)	2	3
90	HL_14201.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F History status: Exact match	9	3
91	HL_94352.5 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	3
92	HL_50537.4 View exemplar Basepair signature: cWW-cWW-F-F History status: Exact match	0	3
93	HL_86332.1 View exemplar Basepair signature: cWW-tSH-cWS-F-F-F History status: Exact match	0	3
94	HL_06048.2 View exemplar Basepair signature: cWW-F-F-cSS-cSS-F History status: Exact match	0	3
95	HL_20482.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	3
96	HL_29732.1 View exemplar Basepair signature: cWW-F-F History status: Exact match Pseudoknot geometry (2)	0	3
97	HL_73247.1 View exemplar Basepair signature: cWW-F-tWH-F-F-F-F-F-F-F-F-F-F History status: Exact match Pseudoknot geometry (3)	0	3
98	HL_95902.1 View exemplar Basepair signature: cWW-F History status: Exact match	3	3
99	HL_96366.1 View exemplar Basepair signature: cWW-cWW-tWW-F-F-F-F History status: Exact match	10	3
100	HL_16845.6 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	3
101	HL_31581.5 View exemplar Basepair signature: cWW-F-F-F-cSH-F-F-F-F History status: Exact match U1 small nuclear ribonucleoprotein A binding hairpin (1)	0	3
102	HL_73530.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	3
103	HL_81205.2 View exemplar Basepair signature: cWW-cWW-tWH-F-tWH-F-F-F-F-F History status: Exact match	0	3
104	HL_92229.1 View exemplar Basepair signature: cWW-cWW-F-F-F History status: Exact match GNRA with extra cWW (1)	7	3
105	HL_07579.2 View exemplar Basepair signature: cWW-cWW-F-F-F-F-F-F-F-F-F-F History status: Exact match	14	3
106	HL_11805.3 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F-F-F History status: Exact match	11	3
107	HL_19162.3 View exemplar Basepair signature: cWW-tSH-F-F-F-F-F-F-F History status: Exact match	11	3
108	HL_22629.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F History status: Exact match	9	3
109	HL_85445.1 View exemplar Basepair signature: cWW-cWW-F-F-F-F-F History status: Exact match	0	3
110	HL_92747.1 View exemplar Basepair signature: cWW-F-F-F-F History status: Exact match	6	3
111	HL_23083.1 View exemplar Basepair signature: cWW-F History status: Exact match	3	3
112	HL_71924.1 View exemplar Basepair signature: cWW-tSH-F-F-F-F-F-F History status: Exact match	10	3
113	HL_12758.1 View exemplar Basepair signature: cWW-tSH-F-F-F-cWH-cHW-cWH-cHW-cHW-cWH-F-cWH-F-cWH-cHW-tSH-cWH-cWH-cHW History status: Exact match G-quadruplex (2)	22	2
114	HL_04775.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F-F-F-F-F-F-F History status: Exact match	0	2
115	HL_40310.1 View exemplar Basepair signature: cWW-tSH-F-F-F History status: Exact match	0	2
116	HL_08510.1 View exemplar Basepair signature: cWW-F-F-cSH-F-F History status: Exact match	0	2
117	HL_72714.3 View exemplar Basepair signature: cWW-cWW-cWH-F-F-F-F-F History status: Exact match	0	2
118	HL_98870.1 View exemplar Basepair signature: cWW-tSH-tWW-F-F-F-F-F History status: Exact match	0	2
119	HL_77805.1 View exemplar Basepair signature: cWW-F-F-F-F History status: Exact match	6	2
120	HL_89914.1 View exemplar Basepair signature: cWW-tSH-F-F-F-F History status: Exact match T-loop related (1)	8	2
121	HL_90574.1 View exemplar Basepair signature: cWW-F History status: Exact match	0	2
122	HL_05727.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	0	2
123	HL_20146.1 View exemplar Basepair signature: cWW-tSH-F-F History status: Exact match	0	2
124	HL_73183.1 View exemplar Basepair signature: cWW-tSH-tHW-F-F-F-F-F-F-F-F-F History status: Exact match Pseudoknot geometry with G-bulge (2)	0	2
125	HL_79531.1 View exemplar Basepair signature: cWW-F-F History status: Exact match	0	2
126	HL_09785.1 View exemplar Basepair signature: cWW-cWW-F-F-F-F-F-F History status: Exact match	10	2
127	HL_86373.1 View exemplar Basepair signature: cWW-cWW History status: Exact match	4	2
128	HL_90620.1 View exemplar Basepair signature: cWW-F-F-F-F-cSW-cSH-F History status: Exact match	0	2
129	HL_09829.1 View exemplar Basepair signature: cWW-F History status: Exact match	0	2
130	HL_30239.1 View exemplar Basepair signature: cWW-F-F History status: Exact match	0	2
131	HL_73255.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match	0	2
132	HL_15708.1 View exemplar Basepair signature: cWW-F-F-cSH History status: Exact match	6	2
133	HL_68830.1 View exemplar Basepair signature: cWW-F History status: Exact match	3	2
134	HL_10775.1 View exemplar Basepair signature: cWW-cSH-F-F History status: Exact match	5	2
135	HL_38243.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	7	2
136	HL_60293.1 View exemplar Basepair signature: cWW-cWH-F-cWH-cHW-cHW-cWH-cHW-cWH-F-cWH-cWH-cWH-F History status: Exact match G-quadruplex (2)	0	2
137	HL_07518.1 View exemplar Basepair signature: cWW-tSH-F History status: Exact match GNRA related (1)	0	2
138	HL_20751.1 View exemplar Basepair signature: cWW-tHW-F-F-F-F-F-F-F-F-F History status: Exact match	0	2
139	HL_96851.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	2
140	HL_07551.1 View exemplar Basepair signature: cWW-F-F History status: Exact match	4	2
141	HL_45785.1 View exemplar Basepair signature: cWW-F-F-F-F-cSH-F-F History status: Exact match	0	2
142	HL_88982.1 View exemplar Basepair signature: cWW-R-R-R-R-R History status: Exact match	8	2
143	HL_39267.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match tRNA anticodon loop (1)	8	2
144	HL_64163.1 View exemplar Basepair signature: cWW-cWW-F-F-F-F-F-F-F-F History status: Exact match	0	2
145	HL_46465.1 View exemplar Basepair signature: cWW-tSW-cSH-tHH-tWW-cHW-cWH-cHW-cWH-tWW-cWH-cWH-R-cWH-cWH-R History status: Exact match	21	2
146	HL_76406.3 View exemplar Basepair signature: cWW-cWH-R-R-R-R History status: Exact match	9	2
147	HL_46766.1 View exemplar Basepair signature: cWW-tWH-F-F-F History status: Exact match	8	2
148	HL_08127.1 View exemplar Basepair signature: cWW History status: Exact match Pseudoknot geometry (1)	0	2
149	HL_19650.1 View exemplar Basepair signature: cWW-cWH-tWH-F-F-F History status: Exact match	9	1
150	HL_00317.1 View exemplar Basepair signature: cWW-F-cSS-F-F-F-F-F-F-F-F-F-F-F-F-F-F History status: Exact match	0	1
151	HL_12870.1 View exemplar Basepair signature: cWW-tHW-F-F-F-F-F-F-F-F-F History status: Exact match	0	1
152	HL_82782.1 View exemplar Basepair signature: cWW-R-tSH-tHS-R-R-R-R-R-R-R-R-R-R History status: Exact match	18	1
153	HL_94032.1 View exemplar Basepair signature: cWW-cSH-F-F-F-F-F-F History status: Exact match	0	1
154	HL_08602.1 View exemplar Basepair signature: cWW-cSS-F-cSS-F-F-F-F-F History status: Exact match	0	1
155	HL_57204.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match Mini UNCG related (1)	0	1
156	HL_40442.1 View exemplar Basepair signature: cWW-tSW-cWW-cWS-cWW-F-F History status: Exact match	0	1
157	HL_66902.1 View exemplar Basepair signature: cWW-cWS-R-R-R-R-R History status: Exact match tRNA D-loop (1)	8	1
158	HL_02483.1 View exemplar Basepair signature: cWW-tWH-F-cSH-F-F-F History status: Exact match	0	1
159	HL_35888.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	0	1
160	HL_58539.1 View exemplar Basepair signature: cWW-tWS-F-tHW-F-F-F-F-F-F-F-F History status: Exact match	0	1
161	HL_52434.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	5	1
162	HL_59445.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	7	1
163	HL_02811.1 View exemplar Basepair signature: cWW-F-F History status: Exact match	0	1
164	HL_59564.1 View exemplar Basepair signature: cWW-F-cSS-F-cSS-F-F-F-F-F-F-F-F-F-F-F-F History status: Exact match	0	1
165	HL_44294.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	0	1
166	HL_53189.1 View exemplar Basepair signature: cWW-F-F-F History status: Exact match	0	1
167	HL_16991.1 View exemplar Basepair signature: cWW-cWH-cWH-F-cWH-F History status: Exact match G-quadruplex fragment (1)	0	1
168	HL_60914.1 View exemplar Basepair signature: cWW-F History status: Exact match	0	1
169	HL_70682.1 View exemplar Basepair signature: cWW-tWH-F-F-F-F History status: Exact match	0	1
170	HL_84847.1 View exemplar Basepair signature: cWW-F-F-F-F-tWW-F-F-F-F-F-F History status: Exact match	0	1
171	HL_32255.1 View exemplar Basepair signature: cWW-tWW-F-F-cWW-F-F History status: Exact match	0	1
172	HL_18495.1 View exemplar Basepair signature: cWW-cWW-cSH-F-F History status: Exact match	8	1
173	HL_81820.1 View exemplar Basepair signature: cWW-tSH-tHW-tHW-cSH-F History status: Exact match	11	1
174	HL_22443.1 View exemplar Basepair signature: cWW-R-tWH-R-tWH-R-R-R History status: Exact match	10	1
175	HL_84861.1 View exemplar Basepair signature: cWW-F-cSH-F-F History status: Exact match	0	1
176	HL_97733.1 View exemplar Basepair signature: cWW-F-F-F-cSH-F History status: Exact match	0	1
177	HL_92488.1 View exemplar Basepair signature: cWW-cWW-F-cSS-F-F-F-F-F-F History status: Exact match	0	1
178	HL_32426.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	0	1
179	HL_56500.1 View exemplar Basepair signature: cWW-cWW-F-cSH-F-F History status: Exact match	0	1
180	HL_04641.1 View exemplar Basepair signature: cWW-F-F-F-F-F History status: Exact match	0	1
181	HL_19239.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F History status: Exact match	0	1
182	HL_39425.1 View exemplar Basepair signature: cWW-F-F-F-F-F-F-F-cSH History status: Exact match	11	1
183	HL_46771.1 View exemplar Basepair signature: cWW-tSS-F-F-F History status: Exact match	0	1
184	HL_98252.1 View exemplar Basepair signature: cWW-tWW-F-F-F-F History status: Exact match	0	1

Coloring options:
Nucleotide numbers

Exact match 184;

Hairpin Loop Motif Atlas Release 3.78 Download CSV JSON annotations

Hairpin Loop Motif Atlas Release 3.78

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