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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
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OOD
hsa-mir-154
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hsa-mir-300
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A
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U
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G
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hsa-mir-329-1
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G
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U
U
A
A
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C
A
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U
G
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U
A
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C
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U
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C
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U
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hsa-mir-329-2
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G
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U
A
C
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U
A
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C
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G
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U
U
U
C
U
G
U
U
U
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C
U
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U
U
A
U
U
hsa-mir-376a-1
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-
-
-
-
C
C
U
U
C
U
U
U
G
-
G
U
A
U
U
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U
A
A
A
A
G
G
U
A
G
A
U
U
C
U
C
C
U
U
C
U
A
U
G
A
G
U
A
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C
A
-
U
U
A
U
U
hsa-mir-376a-2
-
A
A
-
-
A
C
C
U
U
C
U
U
U
G
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G
U
A
U
U
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U
A
A
A
A
G
G
U
A
G
A
U
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U
C
C
U
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C
U
A
U
G
G
U
U
A
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C
G
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U
G
U
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hsa-mir-376b
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G
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U
C
C
U
U
C
U
U
U
G
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G
U
A
U
U
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U
A
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A
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A
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C
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A
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U
U
U
A
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C
G
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G
A
U
U
hsa-mir-376c
-
A
A
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-
U
C
C
U
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C
U
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G
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G
U
A
U
U
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U
A
A
A
A
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U
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A
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A
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C
C
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C
U
A
U
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U
U
U
A
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U
G
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U
A
U
U
hsa-mir-377
-
-
-
-
-
C
U
G
A
U
G
U
U
U
G
-
A
C
C
C
U
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U
G
A
G
C
A
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A
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U
U
G
C
C
C
U
U
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G
U
G
A
A
U
U
C
G
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C
U
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U
A
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U
hsa-mir-379
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-
U
U
C
C
G
U
G
G
U
U
C
C
U
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G
A
A
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A
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A
U
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G
U
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A
C
U
A
U
G
G
A
A
C
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U
A
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C
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U
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A
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A
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U
hsa-mir-381
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-
C
U
A
U
U
G
U
U
U
G
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G
U
A
C
U
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U
A
A
A
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C
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A
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G
U
U
G
C
C
C
U
U
U
G
U
A
U
A
U
U
C
G
-
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G
U
-
U
U
A
U
U
hsa-mir-382
-
-
-
-
-
-
U
U
U
U
C
U
G
U
G
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G
U
A
C
U
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U
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A
A
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A
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A
A
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U
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U
U
C
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G
G
A
U
U
C
G
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C
U
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U
U
A
C
U
hsa-mir-410
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A
U
-
G
G
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C
A
C
U
C
U
G
G
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U
A
C
C
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A
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A
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U
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C
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A
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U
C
G
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C
U
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A
U
U
hsa-mir-411
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C
U
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A
C
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U
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A
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C
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U
A
U
A
G
C
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U
A
C
G
-
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C
U
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U
U
A
U
C
hsa-mir-487a
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C
G
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U
C
A
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C
C
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U
C
G
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U
A
C
U
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C
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C
G
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C
U
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A
A
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U
hsa-mir-487b
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U
G
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C
U
A
A
C
C
U
U
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G
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U
A
C
U
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C
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hsa-mir-494
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U
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G
C
U
A
A
U
C
U
U
C
G
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A
U
A
C
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C
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A
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U
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C
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C
U
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C
U
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A
U
U
hsa-mir-495
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U
G
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C
U
C
A
U
C
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C
U
G
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U
A
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C
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U
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C
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A
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C
G
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U
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A
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A
hsa-mir-496
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A
G
C
A
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C
C
A
A
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U
C
A
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G
U
A
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U
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A
A
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C
A
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U
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U
U
A
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hsa-mir-539
U
G
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-
C
U
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C
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G
U
U
U
C
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A
U
A
C
U
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U
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G
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U
C
G
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C
U
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U
A
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hsa-mir-543
-
U
G
-
-
C
U
G
A
C
G
U
G
C
G
-
G
U
A
C
U
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U
A
A
U
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A
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A
A
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U
U
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C
C
C
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U
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U
U
U
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U
C
G
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-
C
U
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U
U
A
U
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hsa-mir-655
-
A
-
-
-
C
U
A
U
G
C
A
A
G
G
-
A
U
A
U
U
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U
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U
U
A
U
C
C
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U
U
A
U
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U
U
C
G
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C
U
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U
C
A
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U
hsa-mir-656
A
G
U
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G
C
U
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C
U
C
A
G
U
-
G
G
U
A
C
C
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A
A
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A
U
A
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U
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C
C
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U
G
A
G
G
U
G
U
U
C
A
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C
U
-
U
U
C
U
A
hsa-mir-758
C
A
G
-
C
A
-
C
G
U
G
C
C
U
G
G
A
U
A
C
A
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A
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A
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C
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hsa-mir-889
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C
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A
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U
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G
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CONS STRUCTURE
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hsa-mir-154
U
G
U
G
A
C
G
A
A
U
C
A
U
A
C
A
C
G
G
U
U
G
A
C
C
U
A
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U
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U
C
A
G
U
A
C
C
A
A
A
U
C
C
C
G
C
C
-
-
U
U
G
hsa-mir-300
U
G
C
A
A
U
G
-
A
U
U
A
U
A
C
A
A
G
G
G
C
A
G
A
C
U
C
U
C
U
C
U
G
G
G
G
A
G
C
A
A
A
U
C
C
U
G
C
C
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U
G
G
hsa-mir-329-1
G
A
G
G
A
C
G
A
A
A
C
A
C
A
C
C
U
G
G
U
U
A
A
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C
U
C
U
U
U
U
C
C
A
G
U
A
U
C
A
A
A
U
C
C
C
A
U
C
-
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-
U
hsa-mir-329-2
G
A
G
G
A
C
G
A
A
A
C
A
C
A
C
C
U
G
G
U
U
A
A
C
C
U
C
U
U
U
U
C
C
A
G
U
A
U
C
A
A
A
U
C
C
C
A
U
C
-
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U
hsa-mir-376a-1
U
A
U
G
A
U
U
A
A
U
C
A
U
A
G
A
G
G
A
A
A
A
U
C
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A
C
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U
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U
A
U
C
A
A
A
U
G
C
U
G
C
U
-
-
U
U
G
hsa-mir-376a-2
G
A
U
G
G
U
U
A
A
U
C
A
U
A
G
A
G
G
A
A
A
A
U
C
C
A
C
G
U
U
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U
C
A
G
U
A
U
C
A
A
A
U
G
C
U
G
C
C
-
-
-
-
-
hsa-mir-376b
C
C
U
G
G
U
U
A
A
U
C
A
U
A
G
A
G
G
A
A
A
A
U
C
C
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A
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U
A
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A
A
A
U
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C
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C
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U
hsa-mir-376c
U
A
U
G
G
U
U
A
A
A
C
A
U
A
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A
G
G
A
A
A
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C
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A
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A
U
C
A
A
A
U
G
C
U
G
C
U
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hsa-mir-377
U
A
U
G
U
U
G
A
A
U
C
A
C
A
C
A
A
A
G
G
C
A
A
C
U
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U
G
A
G
U
A
U
C
A
A
A
U
C
C
U
G
C
U
-
-
-
U
G
hsa-mir-379
U
C
U
G
A
C
C
U
A
U
G
U
A
A
C
A
U
G
G
U
C
C
A
C
U
A
A
C
U
-
C
U
C
A
G
U
A
U
C
C
A
A
U
C
C
A
U
C
C
U
C
-
-
-
hsa-mir-381
G
A
C
A
U
G
G
A
A
U
-
A
U
A
C
A
A
G
G
G
C
A
A
G
C
U
C
U
C
U
G
U
G
A
G
U
A
U
C
A
A
A
C
C
U
U
G
U
C
-
-
U
U
G
hsa-mir-382
U
A
U
G
A
C
G
A
A
U
C
A
U
U
C
A
C
G
G
A
C
A
A
C
A
C
U
U
U
U
U
U
C
A
G
U
A
C
C
A
A
A
U
G
C
U
A
C
C
-
-
U
C
U
hsa-mir-410
A
A
U
G
A
C
G
A
A
U
A
U
A
A
C
A
C
A
G
A
U
G
G
C
C
U
G
U
U
U
U
C
-
A
G
U
A
C
C
G
C
U
A
C
C
G
C
C
C
-
-
-
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hsa-mir-411
U
G
U
G
A
C
G
U
A
U
G
U
A
A
C
A
C
G
G
U
C
C
A
C
U
A
A
C
C
-
C
U
C
A
G
U
A
U
C
A
A
A
U
C
C
A
U
C
C
C
C
G
A
G
hsa-mir-487a
U
A
U
G
A
C
G
A
A
U
C
A
U
A
C
A
G
G
G
A
C
A
U
C
C
A
G
U
U
U
U
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C
A
G
U
A
U
C
A
A
A
U
A
C
U
G
C
U
-
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hsa-mir-487b
C
A
U
G
U
C
G
A
A
U
C
G
U
A
C
A
G
G
G
U
C
A
U
C
C
A
C
U
U
U
U
U
C
A
G
U
A
U
C
A
A
G
A
G
C
-
G
C
A
-
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-
-
G
hsa-mir-494
U
A
U
G
A
U
G
A
A
A
C
A
U
A
C
A
C
G
G
G
A
A
A
C
C
U
C
U
U
U
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U
U
A
G
U
A
U
C
A
A
A
U
C
C
C
A
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hsa-mir-495
U
G
U
G
A
C
G
A
A
A
C
A
A
A
C
A
U
G
G
U
G
C
A
C
U
U
C
U
U
U
U
U
C
G
G
U
A
U
C
A
A
A
U
A
U
C
U
C
C
-
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hsa-mir-496
U
A
U
G
A
U
G
A
G
U
A
U
U
A
C
A
U
G
G
C
C
A
A
U
C
U
C
C
U
U
-
U
C
G
G
U
A
C
U
C
A
A
U
U
C
U
U
C
-
-
-
-
-
-
hsa-mir-539
U
A
U
G
A
U
G
A
A
U
C
A
U
A
C
A
A
G
G
A
C
A
A
U
U
U
C
U
U
U
U
U
G
A
G
U
A
U
C
A
A
A
U
C
U
U
G
C
C
-
-
-
-
-
hsa-mir-543
U
G
U
G
A
C
G
A
A
A
C
A
U
U
C
G
C
G
G
U
G
C
A
C
U
U
C
U
U
U
U
U
C
A
G
U
A
U
C
C
U
A
U
U
C
U
G
C
C
-
-
-
-
-
hsa-mir-655
C
A
U
C
A
U
G
A
A
U
A
A
U
A
C
A
U
G
G
U
U
A
A
C
C
U
C
U
U
U
U
U
G
A
A
U
A
U
C
A
G
A
C
U
C
U
G
C
C
-
-
-
-
U
hsa-mir-656
U
A
U
G
A
U
G
A
A
U
A
U
U
A
U
A
C
A
G
U
C
A
A
C
C
U
C
U
U
-
U
C
C
G
A
U
A
U
C
G
A
A
U
C
C
C
A
C
-
-
-
-
-
C
hsa-mir-758
U
G
U
G
C
C
G
U
U
U
G
U
G
A
C
C
U
G
G
U
C
C
A
C
U
A
A
C
-
C
C
U
C
A
G
U
A
U
C
U
A
A
U
G
C
C
C
C
C
-
-
-
-
U
hsa-mir-889
U
A
U
G
A
U
G
A
U
U
A
A
U
A
U
-
C
G
G
A
C
A
A
C
C
A
U
U
G
U
U
U
U
A
G
U
A
U
C
C
A
A
A
U
U
U
G
C
U
-
-
-
-
U
CONS STRUCTURE
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Consensus
CPU time:
0.00
Average sequence ID:
0.555744054288
Average free energy:
-21.0552
Average covariation:
0.237126436782
Average basepair probability:
0.722648326132
Canonical basepairs:
NA
Sequence and structure consensus for Consensus
mRgcrCYVWYSUKUGgGUACUcURARRRGWRGUURYCCSUGKURYGUUCGcgCUwUUAUUURUGAYGAAUCAUACASGGWCAACCWCUUU UUSAGUAUCAAAUSCYGCCycuuK
..............(.(((((..((((((((((((((((((....(((((...............)))))....)))))))))))))))) )).))))))...............
The alignment colored using colorrna.pl of the Vienna package
Cluster tree of the methods
Table
WAR