Fig. 1.

Conservation and orthologous bases of the top 200 human MER121 instances most similar to the consensus. Human instances are aligned to one another, starting from the copy most similar to consensus and following a progressive alignment strategy. This approach results in a multiple alignment with 200 rows, one for each human instance. To incorporate information about orthologous sequence in the other species, we replace each human base with its corresponding four-way HDMR multiple alignment column, thereby enlarging the alignment to 800 rows (= 200 × 4). (A) Positions are colored according to four-way conservation (red, bases with perfect four-way conservation; black, bases with four-way alignment but not perfect conservation; gray, human base lacks an orthologous base in at least one other species. (B) Positions are colored according to their DNA base (blue, A; green, G; orange, C; red, T).