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  1. or download this
    #$pkey is just a counter
$c->{$pkey}{left_instance}{sequence}; 
...
$c->{$pkey}{comments};
#i am guessing $c->{$pkey}{match} as well but don't know 
#what that does.
  2. or download this
    use strict;
use warnings;
...
Sbjct: CCAAAATTCCCCCC-GGGGGG                                          
+      474
                     !
Sbjct: CCAAAATTCCCCCCGGGGGGG                                          
+      475