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use strict;
use warnings;
...

    return @cons;
}

  my %H = ( A=>[], T=>[], C=>[], G=>[] );
  my @mi_letters = map { [split '', uc $_] } @mi;
...

  # note: to avoid warnings, change the sort further down to include t
+his (the '||0'):
  #    ($H{$b}->[$B]||0) <=> ($H{$a}->[$B]||0)