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A Structured Motif |
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| Symbols |
M1 |
M2 |
M3 |
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|
|
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| 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 |
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|
|
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| IUPAC |
D |
N |
N |
N |
N |
D |
R |
Y |
W |
D |
S |
H |
M |
M |
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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. | ||||||||||||||||
Zhang and Zaki Algorithms for Molecular Biology 2006 1:22 doi:10.1186/1748-7188-1-22 |
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