Table 3  A Structured Motif
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
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.