AABBC
BAABC
AABBD
AACBB
##</code><code>##

	  A	    B	  C       D
1	0.75	0.25	0.00	0.00
2    1.00	0.00	0.00	0.00
3	0.25	0.50	0.25	0.00
4	0.00	1.00	0.00	0.00
5	0.00	0.25	0.50	0.25

##</code><code>##

foreach my $segment (@collection) {
	foreach $i (0..length($segment)) {
		if (substr($segment,$i,1) eq "A") {
			$score[$i][1] = 1;
			$score[$i][2] = 0;
			$score[$i][3] = 0;
			$score[$i][4] = 0;
		} elsif (substr($segment,$i,1) eq "B") {
			$score[$i][1] = 0;
			$score[$i][2] = 1;
			$score[$i][3] = 0;
			$score[$i][4] = 0;
		} elsif (substr($segment,$i,1) eq "C") {
			$score[$i][1] = 0;
			$score[$i][2] = 0;
			$score[$i][3] = 1;
			$score[$i][4] = 0;
		} elsif (substr($segment,$i,1) eq "D") {
			$score[$i][1] = 0;
			$score[$i][2] = 0;
			$score[$i][3] = 0;
			$score[$i][4] = 1;
		}
	}
}