I haven't tested the code below very much; you should if you think you many want to use it.

#!/usr/bin/perl -wl
use strict;
use List::Util qw( min max sum );

sub score {
  my ($str, @array) = @_;
  my @pos =
    sort { $a->[ 0 ] <=> $b->[ 0 ] }
    map  [ $_->[ 0 ], $_->[ 0 ] + length $_->[ 1 ] ],
    grep $_->[ 0 ] > -1,
    map  [ index( $str, $_ ), $_ ],
      @array;

  for my $i ( reverse 0 .. $#pos - 1 ) {
    my $lefts  = [ sort { $a <=> $b } map $_->[ 0 ], @pos[ $i, $i + 1 
+] ];
    my $rights = [ sort { $b <=> $a } map $_->[ 1 ], @pos[ $i, $i + 1 
+] ];
    if ( $rights->[ 1 ] - $lefts->[ 1 ] > 0 ) {
      splice @pos, $i, 2, [ map $_->[ 0 ], $lefts, $rights ]
    }
  }
  return sum map $_->[ 1 ] - $_->[ 0 ], @pos;
}

my $s1 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';

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

print score( $s1, @$_ ) for \@ar, \@ar2, \@ar3;

__END__
% perl score.pl
21
16
17
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