#$pkey is just a counter
$c->{$pkey}{left_instance}{sequence}; 
$c->{$pkey}{right_instance}{sequence};
$c->{$pkey}{comments};
#i am guessing $c->{$pkey}{match} as well but don't know 
#what that does.

##</code><code>##

use strict;
use warnings;
use Data::Dumper;

$/ = "\n\n\n";

my $pkey = 1;
my $c = {};

while ( <DATA> ) {
  #get comments if any
  $c->{$pkey}{comments} = $1 if s/^(#[^\n]+)\n//;

  #get stats if any
  _load_stats($pkey,$1,$c) if !/^Sbjct/ and s/\s*(\d[^\n]+)//;

  #loop over remaining data to get sequences
  while ( /Sbjct: ([-ACGT]+)\s+\d+\n(?:\s*!\s+)?Sbjct: ([-ACTG]+)/g) {
     $c->{$pkey}{left_instance}{sequence} .= $1;
     $c->{$pkey}{right_instance}{sequence} .= $2;
  }

  #add 1 to $pkey for next one
  #though we should probably be using an AoH
  #instead of a HoA so we don't need the counter
  #and can just use push.
  $pkey++;
}

#print resulting structure for verification
print Dumper $c;


#don't know what _load_stats really does
#so this will need changing
sub _load_stats
{
  my ($pkey,$data,$href) = @_;
  $href->{$pkey}{stats} = [split ' ',$data];
}   ##_load_stats



__DATA__
# args=-supermax -d -l 50 -h 7 -seedlength 7 -evalue 0.0001 -s 60 /home/anonymous_monk/clusters/all/all_clusters
140     8778      333   D   140     8778      334  -7    3.60e-56   -259    95.00
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         393
       !
Sbjct: -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         394

Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         453
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         454

Sbjct: TTAAAATTCCCCCC-GGGGGG                                                474
                     !
Sbjct: TTAAAATTCCCCCCGGGGGGG                                                475


   170     8778      333   D   140     8778      334  -7    3.60e-56   -259    95.00
Sbjct: CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         393
       !
Sbjct: -CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         394

Sbjct: CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         453
Sbjct: TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         454

Sbjct: GTAAAATTCCCCCC-GGGGGG                                                474
                     !
Sbjct: GTAAAATTCCCCCCGGGGGGG                                                475


# args=-supermax -d -l 50 -h 7 -seedlength 7 -evalue 0.0001 -s 655 /home/anonymous_monk/clusters/all/all_clusters
Sbjct: CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         393
       !
Sbjct: -CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         394

Sbjct: CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         453
Sbjct: TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         454

Sbjct: CCAAAATTCCCCCC-GGGGGG                                                474
                     !
Sbjct: CCAAAATTCCCCCCGGGGGGG                                                475