#! perl -slw
use strict;
require 5.008;
use Data::Dumper;
use re 'eval';

my $re_comment = qr[^ \# ( \s* [^\n]+ )(?{ $c->{comment} .= $^N; })]x;

my $re_stats = qr[^ \s+ ( \d+ [^\n]+ ) \n]x;

my $re_seq   = qr[^ Sbjct: \s+ ( [^ ]+ ) \s+ \d+ \n]x;

my $re_bang  = qr[^ \s* ! \s* \n]x;

my $re_pair  = qr[
	$re_seq (?{ $c->{left_instance} .= $^N; })
	(?:$re_bang)?
	$re_seq (?{ $c->{right_instance} .= $^N; })
	$re_comment? \n
]x;

my $re_record= qr[
	$re_stats (?{ $c->{stats} .= $^N })
	(?: $re_pair )+
]x;

local $/ = "\n\n\n";
while( <DATA> ) {
	our $c = {};
	print m[$re_record]mo
	? Dumper $c
	: 'Failed to match';
}

__DATA__
          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


          140 8778 333 D 140 8778 334 -7 3.60e-56 -259 95.00
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 393
!
Sbjct: -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 394
# some comment
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT 453
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT 454
# some more comment
Sbjct: TTAAAATTCCCCCC-GGGGGG 474
!
Sbjct: TTAAAATTCCCCCCGGGGGGG 475


          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


##</code><code>##

D:\Perl\test>254442
$VAR1 = {
          'right_instance' => '-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTTTTAAAATTCCCCCCGGGGGGG',
          'stats' => '140 8778 333 D 140 8778 334 -7 3.60e-56 -259 95.00',
          'left_instance' => 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTTTTAAAATTCCCCCC-GGGGGG'
        };

$VAR1 = {
          'comment' => ' some comment some more comment',
          'right_instance' => '-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTTTTAAAATTCCCCCCGGGGGGG',
          'stats' => '140 8778 333 D 140 8778 334 -7 3.60e-56 -259 95.00',
          'left_instance' => 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTTTTAAAATTCCCCCC-GGGGGG'
        };

$VAR1 = {
          'right_instance' => '-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTTTTAAAATTCCCCCCGGGGGGG',
          'stats' => '140 8778 333 D 140 8778 334 -7 3.60e-56 -259 95.00',
          'left_instance' => 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTTTTAAAATTCCCCCC-GGGGGG'
        };