Each of the two rows in the alignment matrix is represented as a string
interspersed by space symbols “−”; for example AT−GTTAT− is a representation
of the row corresponding to v = ATGTTAT, while ATCGT−A−C is a
representation of the row corresponding to w = ATCGTAC. Another way to
represent the row AT−GTTAT− is 1 2 2 3 4 5 6 7 7,which shows the number of
symbols of v present up to a given position. Similarly, ATCGT−A−C is represented
as 1 2 3 4 5 5 6 6 7. When both rows of an alignment are represented
in this way (fig. 6.13, top), the resulting matrix is