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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.