P:\test>457797
"my" variable $seq masks earlier declaration in same scope at P:\test\457797.pl line 37.
"my" variable %alignment masks earlier declaration in same scope at P:\test\457797.pl line 38.
$VAR1 = {
          'S1' => 'C-D',
          'S2' => 'C-D',
          'S4' => 'CID',
          'S3' => 'CAD'
        };
$VAR1 = {
          'S1' => 'C-D',
          'S2' => 'C-D',
          'S4' => 'CID',
          'S3' => 'CAD'
        };
From LOOP
$VAR1 = {
          'S1' => 'C-D',
          'S2' => 'C-D',
          'S4' => 'CID',
          'S3' => 'CAD'
        };