Hi,
Try this 'compact' version if the lengths are similar.

@lines1= split(//,"CACTATGAGTGATCGC");
@lines2= split(//,"ACTGACTAATGCGTTG");
@array = map {   $lines1[$i++] eq $_  ?   $lines1[$i-1] : '*' } @lines
+2;
print join "",@array;
[download]

Artist