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Webserver for Aligning structural RNAs
Results
You can download the results in the following formats:
fasta
clustal
stockholm
col
The consensus is based on:
CMfinder
FoldalignM
LaRA
MASTR
RNAalifold
RNAforester
RNASampler
T-coffee consensus alignment
B
A
D
A
V
G
G
OOD
mir-100
U
A
U
U
-
G
A
G
G
C
C
U
-
-
-
-
G
U
U
G
-
C
C
A
C
A
A
A
C
C
C
G
U
A
G
A
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U
C
C
G
A
A
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C
U
U
G
U
G
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mir-373
C
-
G
A
G
G
A
G
C
U
C
A
U
A
-
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C
U
G
G
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G
A
U
A
C
-
U
C
A
A
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A
A
U
G
-
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G
G
G
G
C
G
-
-
C
U
U
U
C
C
-
-
-
-
-
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U
mir-516b-1
-
-
G
A
A
U
A
U
C
U
C
A
G
G
-
-
C
U
G
U
-
G
A
C
C
A
-
U
C
U
G
-
G
A
G
G
U
A
A
G
A
A
G
C
A
-
-
C
U
U
U
C
U
-
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-
-
-
-
G
mir-516b-2
-
-
G
A
A
G
A
U
C
U
C
A
U
G
-
-
A
U
G
U
-
G
A
C
C
A
-
U
C
U
G
-
G
A
G
G
U
A
A
G
A
A
G
C
A
-
-
C
U
U
U
G
U
-
-
-
-
-
-
G
mir-517a
A
-
G
A
A
G
A
U
C
U
C
A
G
G
-
-
C
A
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
U
G
-
-
-
G
A
A
G
C
A
-
-
C
U
G
U
C
U
-
-
-
-
-
-
G
mir-517b
A
-
G
A
A
G
A
C
C
U
C
A
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
U
G
-
-
-
G
A
A
G
C
A
-
-
C
U
G
U
C
U
-
-
-
-
-
-
G
mir-517c
A
-
G
A
A
G
A
U
C
U
C
A
G
G
-
-
C
A
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
U
G
-
-
-
G
A
A
G
C
A
-
-
C
U
G
U
C
U
-
-
-
-
-
-
G
mir-518b
A
A
G
A
A
U
A
U
G
U
C
A
U
G
-
-
C
U
G
U
-
G
G
C
C
C
-
U
C
C
A
-
G
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-518c
A
-
G
A
A
G
A
U
C
U
C
A
U
G
-
-
C
U
G
U
-
G
A
C
U
C
-
U
C
U
G
-
G
A
G
G
-
-
-
G
A
A
G
C
A
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-518e
-
-
C
A
A
G
A
U
C
U
C
A
G
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-518f
-
-
G
A
A
G
A
U
C
U
C
A
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
G
G
-
-
-
G
A
A
G
C
A
-
-
C
U
U
U
C
U
-
-
-
-
-
-
C
mir-519a-1
-
-
G
A
A
G
A
C
C
U
C
A
G
G
-
-
C
U
G
U
-
G
A
C
A
C
-
U
C
U
A
-
G
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-519a-2
A
-
G
A
A
G
A
U
C
U
C
A
G
G
-
-
C
U
G
U
-
G
U
C
C
C
-
U
C
U
A
-
C
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-519d
A
-
G
A
A
G
A
U
C
C
C
A
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
C
A
-
A
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
G
U
-
-
-
-
-
mir-519e
G
A
G
A
A
G
A
U
C
U
C
A
U
G
-
-
C
A
G
U
-
C
A
U
U
C
-
U
C
C
A
-
A
A
A
G
-
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-
G
G
A
G
C
A
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-520b
A
A
G
A
A
G
A
U
G
U
C
A
G
G
-
-
C
U
G
U
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G
U
C
C
C
-
U
C
U
A
-
C
A
G
G
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-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-520e
A
A
G
A
C
U
G
U
C
U
C
C
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
A
A
-
G
A
U
G
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-
-
G
A
A
G
C
A
-
-
G
U
U
U
C
U
-
-
-
-
-
-
G
mir-520f
-
-
G
A
G
G
A
U
C
U
C
A
G
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
A
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-520g
-
-
-
-
A
G
A
U
C
C
C
A
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
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G
-
-
-
G
A
A
G
C
A
-
-
C
U
U
U
C
U
G
U
U
U
-
-
G
mir-520h
-
-
G
A
A
G
A
U
C
C
C
A
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
-
G
-
-
-
G
A
A
G
C
A
-
-
C
U
U
U
C
U
G
U
U
U
-
-
G
mir-521-1
A
-
G
A
A
G
A
U
C
U
C
A
G
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
C
A
-
A
A
G
G
-
-
-
G
A
A
G
A
A
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-521-2
A
-
G
A
A
G
G
U
C
U
C
G
G
G
-
-
C
U
G
U
-
G
A
C
U
C
-
U
C
C
A
-
A
A
G
G
-
-
-
G
A
A
G
A
A
-
-
U
U
U
U
C
U
-
-
-
-
-
-
C
mir-522
-
-
G
A
A
G
A
U
C
U
C
A
G
G
-
-
C
U
G
U
-
G
U
C
C
C
-
U
C
U
A
-
G
A
G
G
-
-
-
G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-523
-
-
G
A
A
G
A
U
C
U
C
A
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
G
G
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G
A
A
G
C
G
-
-
C
U
U
U
C
U
-
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-
-
-
-
G
mir-526a-1
-
-
G
A
A
G
A
G
C
U
C
A
G
G
-
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C
U
G
U
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G
A
C
C
C
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U
C
U
A
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G
A
G
G
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G
A
A
G
C
A
-
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C
U
U
U
C
U
-
-
-
-
-
-
G
mir-526a-2
-
-
G
A
A
G
A
U
C
U
C
G
U
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
A
-
G
A
G
G
-
-
-
G
A
A
G
C
A
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-526b
-
-
G
A
A
G
A
U
G
U
C
A
G
G
-
-
C
U
G
U
-
G
A
C
C
C
-
U
C
U
U
-
G
A
G
G
-
-
-
G
A
A
G
C
A
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-527
A
A
G
A
A
G
A
U
C
U
C
A
A
G
-
-
C
U
G
U
-
G
A
-
-
C
-
U
G
C
A
-
A
A
G
G
-
-
-
G
A
A
G
C
C
-
-
C
U
U
U
C
U
-
-
-
-
-
-
G
mir-551b
G
-
A
U
G
U
G
C
-
U
C
U
-
-
C
C
U
G
G
-
C
C
C
A
U
G
-
A
A
A
U
-
C
A
A
-
G
C
G
-
-
U
G
G
G
U
G
-
A
G
A
-
-
C
C
U
G
G
U
G
mir-593
U
-
G
U
A
G
C
C
C
C
C
A
G
A
A
U
C
U
G
U
C
A
G
G
C
A
-
C
C
A
G
-
C
C
A
-
G
G
C
-
-
A
U
U
G
C
U
C
A
G
C
C
-
C
G
U
U
-
-
-
mir-99b
G
-
A
C
U
C
C
U
G
G
G
U
C
-
-
-
C
U
G
G
-
C
A
C
C
C
A
C
C
C
G
-
U
A
G
A
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-
A
C
C
G
A
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CONS STRUCTURE
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mir-100
-
G
-
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U
A
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A
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G
U
C
-
C
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C
A
C
A
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mir-373
U
U
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-
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G
U
C
U
G
U
A
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C
U
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G
A
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C
C
-
C
U
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U
U
U
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A
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mir-516b-1
U
U
U
-
U
G
U
G
A
A
A
G
A
-
A
A
A
G
A
A
A
G
U
G
-
-
C
U
U
C
C
U
U
U
C
A
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A
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-
G
G
U
U
A
C
-
U
C
U
U
U
G
A
G
A
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mir-516b-2
U
-
-
-
-
-
-
U
U
U
G
U
G
-
A
A
A
G
A
A
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G
U
G
-
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C
U
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C
U
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C
A
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A
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-
G
G
U
U
A
C
-
U
C
U
U
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G
A
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A
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mir-517a
U
U
G
-
U
A
U
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A
A
A
G
A
-
A
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G
A
U
C
G
U
G
-
-
C
A
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C
C
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A
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-
U
G
U
U
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C
-
U
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U
U
U
G
A
G
A
C
A
A
G
mir-517b
U
U
G
-
U
C
U
A
A
-
-
G
A
-
A
A
A
G
A
U
C
G
U
G
-
-
C
A
U
C
C
C
U
U
U
A
G
A
G
-
U
G
U
U
A
C
-
U
G
U
U
U
G
A
G
A
A
A
A
G
mir-517c
U
U
G
-
U
C
U
A
A
-
-
G
A
-
A
A
A
G
A
U
C
G
U
G
-
-
C
A
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C
C
U
U
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A
G
A
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-
U
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U
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C
-
U
G
U
U
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G
A
G
A
A
A
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mir-518b
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
A
C
A
A
A
G
C
G
-
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C
U
C
C
C
C
U
U
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A
G
A
G
-
G
U
U
U
A
C
-
G
G
U
U
U
G
A
G
U
A
A
A
G
mir-518c
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
A
C
A
A
A
G
C
G
-
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C
U
U
C
U
C
U
U
U
A
G
A
G
-
U
G
U
U
A
C
-
G
G
U
U
U
G
A
G
A
A
A
A
G
mir-518e
U
U
G
-
G
C
U
A
A
A
A
G
A
-
A
A
A
G
A
A
A
G
C
G
-
-
C
U
U
C
C
C
U
U
C
A
G
A
G
-
U
G
U
U
A
A
C
G
C
U
U
U
G
A
G
A
A
A
A
G
mir-518f
U
U
G
-
U
C
U
A
A
A
A
G
A
-
A
A
A
G
A
A
A
G
C
G
-
-
C
U
U
C
U
C
U
U
U
A
G
A
G
-
G
A
U
U
A
-
C
U
C
U
U
U
G
A
G
A
A
A
A
G
mir-519a-1
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
G
G
A
A
A
G
U
G
-
-
C
A
U
C
C
U
U
U
U
A
G
A
G
-
U
G
U
U
A
C
-
U
G
U
U
U
G
A
G
A
A
A
A
G
mir-519a-2
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
G
G
A
A
A
G
U
G
-
-
C
A
U
C
C
U
U
U
U
A
G
A
G
-
U
G
U
U
A
C
-
U
G
U
U
U
G
A
G
A
A
A
A
G
mir-519d
U
U
G
-
U
U
U
U
C
U
C
U
U
A
A
A
-
C
A
A
A
G
U
G
-
-
C
C
U
C
C
C
U
U
U
A
G
A
G
-
U
G
U
U
A
-
C
C
G
U
U
U
G
G
G
A
A
A
A
G
mir-519e
-
-
-
-
U
U
U
G
A
A
A
G
A
-
A
A
A
C
A
A
A
G
U
G
-
-
C
C
U
C
C
U
U
U
U
A
G
A
G
-
U
G
U
U
A
C
-
U
G
U
U
U
G
A
G
A
A
A
A
A
mir-520b
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
A
G
A
A
A
G
U
G
-
-
C
U
U
C
C
U
U
U
U
A
G
A
G
-
G
G
U
U
A
C
-
C
G
U
U
U
A
A
G
A
A
A
A
G
mir-520e
U
U
G
-
U
C
U
G
A
A
A
G
G
-
A
A
A
G
A
A
A
G
U
G
-
-
C
U
U
C
C
U
U
U
U
U
G
A
G
-
G
G
U
U
A
C
-
U
G
U
U
U
G
A
G
A
A
A
A
G
mir-520f
U
G
G
-
U
C
A
G
A
A
A
G
A
-
A
A
A
G
C
A
A
G
U
G
-
-
C
U
U
C
C
U
U
U
U
A
G
A
G
-
G
G
U
U
A
-
C
C
G
U
U
U
G
G
G
A
A
A
A
G
mir-520g
U
U
G
-
U
C
U
G
A
-
G
A
A
A
A
A
A
C
A
A
A
G
U
G
-
-
C
U
U
C
C
C
U
U
U
A
G
A
G
-
U
G
U
U
A
-
C
C
G
U
U
U
G
G
G
A
A
A
A
G
mir-520h
U
U
G
-
U
C
U
G
A
-
G
A
A
A
A
A
A
C
A
A
A
G
U
G
-
-
C
U
U
C
C
C
U
U
U
A
G
A
G
-
-
-
U
U
A
-
C
U
G
U
U
U
G
G
G
A
A
A
A
G
mir-521-1
U
U
G
-
U
C
U
A
A
A
A
G
A
-
A
A
A
G
A
A
C
G
C
A
-
-
C
U
U
C
C
C
U
U
U
A
G
A
G
-
U
G
U
U
A
-
C
C
G
U
G
U
G
A
G
A
A
A
A
G
mir-521-2
U
U
G
-
U
C
U
A
A
A
A
G
A
-
A
A
A
G
A
A
C
G
C
A
-
-
C
U
U
C
C
C
U
U
U
A
G
A
G
-
U
G
U
U
A
-
C
C
G
U
G
U
G
A
G
A
A
A
A
G
mir-522
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
A
G
A
A
A
A
U
G
-
-
G
U
U
C
C
C
U
U
U
A
G
A
G
-
U
G
U
U
A
C
-
G
C
U
U
U
G
A
G
A
A
A
A
G
mir-523
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
A
A
G
A
A
C
G
C
G
-
-
C
U
U
C
C
C
U
A
U
A
G
A
G
-
G
G
U
U
A
C
-
C
C
U
U
U
G
A
G
A
A
A
A
G
mir-526a-1
U
U
G
-
C
U
U
G
A
A
A
G
A
-
A
G
A
G
A
A
A
G
C
G
-
-
C
U
U
C
C
U
U
U
U
A
G
A
G
-
G
A
U
U
A
C
-
U
C
U
U
U
G
A
G
A
A
A
A
A
mir-526a-2
U
-
-
-
-
-
U
G
A
A
A
G
A
-
A
A
A
G
A
A
C
A
U
G
-
-
C
A
U
C
C
U
U
U
C
A
G
A
G
-
G
G
U
U
A
C
-
U
C
U
U
U
G
A
G
A
A
G
A
G
mir-526b
U
U
G
-
U
C
U
G
A
A
A
G
A
-
A
G
A
G
A
A
A
G
U
G
-
-
C
U
U
C
C
U
U
U
U
A
G
A
G
-
G
C
U
U
A
C
-
U
G
U
C
U
G
A
G
A
A
A
A
G
mir-527
U
U
G
-
U
C
U
A
A
A
A
G
A
-
A
A
A
G
A
A
A
G
U
G
-
-
C
U
U
C
C
C
U
U
U
G
G
U
G
-
A
A
U
U
A
-
C
G
G
U
U
U
G
A
G
A
A
A
A
G
mir-551b
C
A
G
-
A
A
C
G
G
G
A
A
G
-
G
C
G
A
-
-
-
-
-
-
C
C
C
A
U
A
C
U
U
G
G
U
U
U
C
-
A
G
A
G
G
C
-
U
G
-
-
U
G
A
G
A
A
U
A
A
mir-593
-
U
C
-
C
C
U
C
U
G
G
G
G
-
G
A
G
C
A
A
G
G
A
G
U
G
G
U
G
C
U
G
G
G
U
U
U
G
U
-
C
U
C
U
G
C
-
-
-
-
-
-
U
G
G
G
G
U
U
-
mir-99b
-
G
G
G
C
C
U
U
C
G
C
C
G
-
C
A
C
A
C
A
A
G
C
U
-
-
C
G
U
G
U
C
U
G
U
G
-
-
G
G
U
C
C
G
-
-
-
U
G
U
C
G
G
G
G
G
C
U
C
A
CONS STRUCTURE
.
.
.
.
(
(
.
.
.
.
.
)
)
.
.
.
)
)
)
)
)
)
)
)
.
.
)
)
)
)
)
)
)
)
)
)
)
)
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
mir-100
C
A
C
G
-
G
-
A
C
mir-373
C
A
U
C
-
-
-
-
-
mir-516b-1
C
A
-
-
-
-
-
-
-
mir-516b-2
C
A
G
C
A
U
-
-
U
mir-517a
C
A
A
C
-
-
-
-
-
mir-517b
C
A
A
C
G
-
-
-
U
mir-517c
C
A
A
C
G
-
-
-
U
mir-518b
C
A
G
-
-
-
-
-
-
mir-518c
C
A
A
C
-
-
-
-
-
mir-518e
C
A
A
C
-
-
-
-
-
mir-518f
C
A
A
C
G
-
-
-
-
mir-519a-1
C
A
A
C
A
-
-
-
-
mir-519a-2
C
A
A
C
-
-
-
-
-
mir-519d
C
C
A
-
-
-
-
-
-
mir-519e
C
C
A
C
G
-
-
-
U
mir-520b
C
A
A
-
-
-
-
-
-
mir-520e
C
A
A
-
-
-
-
-
-
mir-520f
C
A
A
U
G
-
-
-
-
mir-520g
C
A
G
U
-
-
-
-
-
mir-520h
C
A
G
U
-
-
-
-
-
mir-521-1
C
A
A
C
-
-
-
-
-
mir-521-2
C
A
A
U
-
-
-
-
-
mir-522
C
A
U
C
G
-
-
-
-
mir-523
C
A
G
C
A
-
-
-
-
mir-526a-1
C
A
A
C
A
-
-
-
-
mir-526a-2
C
A
A
C
G
U
U
U
A
mir-526b
C
A
A
C
G
-
-
-
-
mir-527
C
A
A
C
G
-
-
-
-
mir-551b
C
U
G
C
-
-
-
A
A
mir-593
-
-
-
U
-
-
-
C
-
mir-99b
C
C
A
U
C
G
-
C
G
CONS STRUCTURE
.
.
.
.
.
.
.
.
.
Consensus
CPU time:
0.00
Average sequence ID:
0.6343746226
Average free energy:
-19.4119354839
Average covariation:
-0.0234115347019
Average basepair probability:
0.757860729014
Canonical basepairs:
NA
Sequence and structure consensus for Consensus
AaGAAGAUCUCAKGmyCUGUcGACCCaUCYAgGAGGkmmGAAGCRykCUUUCUsyuuguGUUGkUCUGAAAGAaAAASAAMGYGysCUUC CYUUUAGAGrKGUUACcYSUUUGAGAAAAGCAACrkumu
...........................((((.((((...((((((..((((((...........((.....))...))))))))..)))) ))))))))...............................
The alignment colored using colorrna.pl of the Vienna package
Cluster tree of the methods
Table
WAR
