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use strict;
use List::MoreUtils qw(uniq);
...
  my $E = binary($k);
  return $E . $b;
}

...G....C occurs in 1,2
.C......C occurs in 1,2
...
.C....T.. occurs in 0,1
AC....T.. occurs in 0,1
.C....... occurs in 0,1,2