OK, here's my suggestions : replace

my @alpha = qw(a b c d e f g h i j k l m n o p q r s t u v w x y z);
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with

my @alpha = ("a".."z");
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since it's smaller and more legible.

using

my $x=0;
my $y=0;
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is redundant; my'd variables are set to 0/""/undef unless explicitly set otherwise.

I'd also replace

while ($yy < 26) {
        $xx = 0;
        while ($xx < 26) {
                print " $outtie[$xx][$yy] ";
                $xx++;
        }
        print "\n";
        $yy++;
}
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with

foreach $yy (1..26) {
    foreach $xx (1..26) {
        print " $outtie[$xx][$yy] ";
    }
    print \n
}
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