A black square followed diagonally by one or more red squares indicates matching strings in
both sequences. These need not occur on the principle diagonal. A string at the end of one
sequence may match a string at the start of the other. Just to convince you that long matching
strings are unlikely to occur by chance, on the next page I've put the same program, but now
both sequences are of length 20 with randomly chosen residues.
But before we do that, press
the more button and input the strings "ASDFGHJKL" and "ASDFTJKL". This will give you an idea
of what to look for when you have a string that's a little broken, but almost intact.