My code1

use 5.010;
use strict;
use warnings;

my @matrix;
$matrix[0][0]{score} = 0;
$matrix[0][0]{pointer} = "none";
for(my $j = 1; $j <= length($seq1); $j++) { 
   $matrix[0][$j]{score} = $GAP * $j; 
   $matrix[0][$j]{pointer} = "left"; 
}

for (my $i = 1; $i <= length($seq2); $i++) {
   $matrix[$i][0]{score} = $GAP * $i; 
   $matrix[$i][0]{pointer} = "up"; 
} 
for(my $i = 1; $i <= length($seq2); $i++) {
    for(my $j = 1; $j <= length($seq1); $j++) { 
        my ($diagonal_score, $left_score, $up_score); 
        my $letter1 = substr($seq1, $j-1, 1); 
        my $letter2 = substr($seq2, $i-1, 1); 
        if ($letter1 eq $letter2) { 
            $diagonal_score = $matrix[$i-1][$j-1]{score} + $MATCH; 
            }
        else { $diagonal_score = $matrix[$i-1][$j-1]{score} + $MISMATCH; 
            }
        $up_score = $matrix[$i-1][$j]{score} + $GAP;
        $left_score = $matrix[$i][$j-1]{score} + $GAP;
        if ($diagonal_score >= $up_score) { 
           if ($diagonal_score >= $left_score) {
              $matrix[$i][$j]{score} = $diagonal_score; 
              $matrix[$i][$j]{pointer} = "diagonal";
            }
            else { 
               $matrix[$i][$j]{score} = $left_score; 
               $matrix[$i][$j]{pointer} = "left"; 
            }
        }else { 
               if ($up_score >= $left_score) { 
                  $matrix[$i][$j]{score} = $up_score; 
                  $matrix[$i][$j]{pointer} = "up";
                } 
               else { 
                  $matrix[$i][$j]{score} = $left_score; 
                  $matrix[$i][$j]{pointer} = "left"; 
                } 
            } 
         } 
       }

my $align1 = "";
my $align2 = ""; 

my $j = length($seq1); 
my $i = length($seq2); 

while (1) { 
     last if $matrix[$i][$j]{pointer} eq "none";  
+f matrix 
     if ($matrix[$i][$j]{pointer} eq "diagonal") { 
        $align1 .= substr($seq1, $j-1, 1);
        $align2 .= substr($seq2, $i-1, 1); 
        $i--; 
        $j--;
      } 
     elsif ($matrix[$i][$j]{pointer} eq "left") { 
       $align1 .= substr($seq1, $j-1, 1); 
       $align2 .= "-"; $j--; 
     } 
     elsif ($matrix[$i][$j]{pointer} eq "up") { 
       $align1 .= "-";
       $align2 .= substr($seq2, $i-1, 1); 
       $i--;
     } 
   }

$align1 = reverse $align1; 
$align2 = reverse $align2; 
print "$align1\n"; 
print "$align2\n";