Table 3.
A Structured Motif
| Symbols | M1 | M2 | M3 | |||||||||||||
| 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.