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Table 3 A Structured Motif

From: SMOTIF: efficient structured pattern and profile motif search

Symbols

M 1

 

M 2

  

M 3

A

2

12

17

1

11

1

35

0

24

 

1

0

 

3

1

35

C

0

10

8

5

2

0

0

19

0

 

0

25

 

5

35

1

G

2

5

5

2

10

34

1

0

0

 

26

11

 

0

0

0

T

32

9

6

28

13

1

0

17

12

 

9

0

 

28

0

0

IUPAC

D

N

N

N

N

D

R

Y

W

 

D

S

 

H

M

M

  1. We aligned the 36 A. thaliana LTR retrotransposons from Repbase Update [2] database which belong to Copia group corresponding to genes encoding reverse transcriptase to obtain the structured motif M1 [2,5] M2 [6,7] M3. Rows 2–5 show the profile (the frequency of observing a DNA base in a given position), and the last row shows the corresponding pattern over the IUPAC alphabet.
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Algorithms for Molecular Biology

ISSN: 1748-7188