BMC Bioinformatics

Table 1 The 20 most frequent 5’ bulges, 3’ bulges, and internal loop

From: Analysis of secondary structural elements in human microRNA hairpin precursors

	5’ Bulge			3’ Bulge			Internal Loops
#	Unpaired	Count	Fraction^a	Unpaired	Count	Fraction^a	Unpaired	Count	Fraction^a
1	U	257	0.236	A	215	0.233	G/G	325	0.084
2	A	212	0.195	U	195	0.211	A/C	295	0.076
3	C	163	0.150	C	165	0.179	C/A	290	0.075
4	G	123	0.113	G	85	0.092	U/U	288	0.075
5	CU	20	0.018	GA	15	0.016	U/C	220	0.057
6	UU	18	0.017	UU	12	0.013	C/U	199	0.052
7	UC	16	0.015	AU	11	0.012	A/A	147	0.038
8	UA	13	0.012	UC	9	0.010	C/C	130	0.034
9	GU	12	0.011	AA	8	0.009	G/A	130	0.034
10	AA	11	0.010	CC	8	0.009	A/G	113	0.029
11	CA	11	0.010	CA	7	0.008	UU/UU	26	0.007
12	CC	11	0.010	GU	7	0.008	CA/CA	21	0.005
13	GA	11	0.010	UA	7	0.008	GUUG/AA	15	0.004
14	AU	10	0.009	CU	6	0.006	A/GG	14	0.004
15	AC	9	0.008	AC	5	0.005	UU/U	14	0.004
16	AG	7	0.006	GC	5	0.005	U/CU	13	0.003
17	UG	7	0.006	GG	5	0.005	GA/A	12	0.003
18	GG	4	0.004	UG	5	0.005	AG/G	11	0.003
19	UCAACA	4	0.004	AAA	4	0.004	UU/CU	11	0.003
20	ACC	3	0.003	CUU	4	0.004	A/GC	10	0.003

^afraction of the unpaired nucleotide sequence (loop) in its category (5’ bulge, 3’ bulge, or internal loop)

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ISSN: 1471-2105

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