I am having trouble running this subroutine. Unless the 4 characters are in common in the string at each position once in the string (so that $a,$c,$g,$t = 1 or greater) then it generates errors about having an uninitialized variable when it returns the values. I can't figure out a way around this, especially since the variable seems to have been initialized with a value. 
sub comNucCount {

    my($string1, $string2) = @_;
    $string1 = lc $string1;
    $string2 = lc $string2;
    # we assume that the strings have the same length
    my($length) = length($string1);
    my($position);
    my($a,$c,$g,$t) = "0";

    for ($position=0; $position < $length ; ++$position) {
        if(substr($string1,$position,1) eq substr($string2,$position,1
+)) {
      if(substr($string1,$position,1) eq 'a'){$a++}
      if(substr($string1,$position,1) eq 'c'){$c++}
      if(substr($string1,$position,1) eq 'g'){$g++}
      if(substr($string1,$position,1) eq 't'){$t++}
        }
    }

    return "A=$a, C=$c, G=$g, T=$t";
  }

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In reply to String/Integer Concatenation by dunno260

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