Here are a couple of minor optimisations:

1)  In the transform sub you copy the contents of the @words array unnecessarily. Change:

     50     my @words = @{+shift};

     72             foreach my $word (@words) {

     95             foreach my $word (@words) {
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To:

     50     my $words = shift;

     72             foreach my $word (@$words) {

     95             foreach my $word (@$words) {
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2)  The four argument form of substr is more efficient then assigning to the three argument form of substr. Change:

    118         substr((my $pat = $word), $i, 1) = '.';
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To:

    118         substr my $pat = $word, $i, 1, '.';
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HTH