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AABBC
BAABC
AABBD
AACBB

      A        B      C       D
1    0.75    0.25    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

foreach my $segment (@collection) {
    foreach $i (0..length($segment)) {
        if (substr($segment,$i,1) eq "A") {
...
        }
    }
}