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%alphabet = (%alphabet, map { $_ => 1 } @chars);

@alphabet{@chars} = (); # No need to set values to 1 as you only ever 
+use keys

    if(defined $sorted{$characters}) {
...
    else {
        $sorted{$characters} = [$line];
    }

push @{$sorted{$characters}}, $line;

    foreach (my $pos2 = 0; $pos2 < $count; $pos2++) {
        next if $pos2 < $pos1;

for (my $pos2 = $pos1; $pos2 < $count; $pos2++) {