$size = 0;
$count = 0;
$score = 0;

for ( $marker = 1; $marker <= $num_dna_col; $marker += 1 )
    {
    $temp = $ref[$marker][$j];	// 2D array of Modal alleles to compare against
    $temp0 = $dna_cols[$marker];	// Array of allele names
    $temp0 = $myrow[$temp0];	// Data array from database read
		
    if($temp)         // Do we have an allele in the Modal template? 
        if($temp0)  // Does the current participant have a corresponding allele?
            {
            $size2 += 1;   // Increment number of available alleles to compare
			if($temp)    // Does the Modal template have a corresponding allele? 
                {
                $size += 1;
                if($temp == $temp0)
                    $count += 1;    // Increment number of matches 
                else
                    {
                    $temp1 = ($temp - $temp0);
                    if ($temp1 < 0 )
                        $temp1 = -$temp1;
									
                    $temp2 = $mutate_coef[$marker];     // mutation coefficients
                    $temp2 = log($temp2);
                    $temp1 = $temp1 * $temp2;
									
                    $score = $score + $temp1;
                    }
                }
            }	
    }
 
if ($size)   // Avoid division by zero
   {
   $score = $score / $size;
   $score = exp($score);
   }
else
   {
   $score = 0;
   }
$score = (int)  (( $score * 1000. ) + 0.5);