use strict;
use warnings;
use Data::Dumper;

my (%letters, $l);

while (<DATA>) {
    chomp; @_ = split //; $l++;
    $letters{$_[$_]}[$_]++ for (0..$#_);
}
for (keys %letters) {
    no warnings;
    $_ /= $l for @{$letters{$_}};
}

print Dumper(\%letters);

__DATA__
AAA
ATG
TTT
GTC

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In reply to Re: Position Weight Matrix of Set of Strings by TedPride
in thread Position Weight Matrix of Set of Strings by monkfan

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