On first look, id use a hash to flag up positions that match
then just add up the total number of matches...
e.g.

my $s1 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';

# Here are the array of the substrings, note that the number of 
# substrings may differ from array to array
# and length of the substring may vary (defined as a parameter) 

my @ar  =  ('GATTACG','GCGCTCG','AACGGCA');  #21 (0,11,21)
my @ar2 =  ('GATTACG','TTACGAG','CGTGTAA');  #16
my @ar3 =  ('TACGAGT','GTGGCGC','GCTCGTG');  #17

print &score($s1,\@ar) , "\n";
print &score($s1,\@ar2) , "\n";
print &score($s1,\@ar3) , "\n";



sub score 
{
  my ($str,$array) = @_;
  my %position_score;
  
  for my $frag (@{$array}) {
      my $idx = index($s1, $frag) + 1;
      
      for my $pos ($idx .. $idx + (length($frag) - 1)) {
             $position_score{$pos} = 1;
      };
  };

  my $total_score = 0;

  for my $score (values %position_score) {
         $total_score += $score;
  };
  
  return $total_score;


};
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