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my @array1 = sort getArray1;
my @array2 = sort getArray2;
...
  if ($array1[$i1] > $array2[$i2]) { $i2++; }
  else { $i1++; }
}

@array1 = ( "a", "a", ... );
@array2 = ( "a", "b", ... );

Results:
a is repeated at position array1[0] and array2[0]