use Data::Dumper;

my %bighash;
my $motif;
my $score;
my %hoa;
my $tag;

while ( <DATA> )
{
  chomp;
  my @aoa;
  if ( /^TAG/ )
  {
    $tag = (split(/: /,$_))[1];
  }
  elsif(/^MOTIF/)
  {
     ($motif,$score)=(split (/[\s,]/,$_))[1,3]; 
      push @{$hoa{$motif}}, $score;
  }
  elsif(/^\d,-\d+,[ATCG]*$/)
  {
      @aoa = split(/,/,$_); 
      push @{$hoa{$motif}}, [ @aoa ];
      
  }
  #print Dumper \%hoa ;
  $bighash{$tag} = { %hoa }; 
}               # -----  end while  -----

print Dumper \%bighash;

__DATA__
TAG: Set1
>instances
MOTIF: CTTTTTAG, 10.6222222222222
Submotif: CTTTT TTTAT

2,-76,CTTTTTAG
2,-77,TCTTTTTA
3,-60,ACTTTTTG
Decompose:
2,-16,CGTTTTTT    CGTTT GTTTT TTTTT 
1,-72,AATTTTAC    ATTTT TTTTA TTTAC 
2,-76,CTTTTTAG    CTTTT TTTTT TTTTA TTTAG
=============

MOTIF: CTTTTATC, 9
Submotif: GTTTT TTTTT

2,-76,CTTTTTAG
Decompose:
2,-76,CTTTTTAG    CTTTT TTTTT 
=============

TAG: Set2
>instances

TAG: Set3
>instances
MOTIF: TAGTTGAAAAAAATT, 17.8181818181818
Submotif: AAAAA AAATA AAATT

1,-49,CACACAAAAAATAAA
1,-82,AGTTGAAAAAAATTT
Decompose:
1,-49,CACACAAAAAATAAA    AAAAA AAAAA AAAAT AAATA 
1,-82,AGTTGAAAAAAATTT    AAAAA AAAAA AAAAA AAAAT AAATT AATTT
=============


##</code><code>##

$VAR1 = {
          'Set1' => {
                      'CTTTTTAG' => [
                                      '10.6222222222222',
                                      [
                                        '2',
                                        '-76',
                                        'CTTTTTAG'
                                      ],
                                      [
                                        '2',
                                        '-77',
                                        'TCTTTTTA'
                                      ],
                                      [
                                        '3',
                                        '-60',
                                        'ACTTTTTG'
                                      ]
                                    ],
                      'CTTTTATC' => [
                                      '9',
                                      [
                                        '2',
                                        '-76',
                                        'CTTTTTAG'
                                      ]
                                    ]
                    },
          'Set3' => {
                      'TAGTTGAAAAAAATT' => [
                                             '17.8181818181818',
                                             [
                                               '1',
                                               '-49',
                                               'CACACAAAAAATAAA'
                                             ],
                                             [
                                               '1',
                                               '-82',
                                               'AGTTGAAAAAAATTT'
                                             ]
                                           ],

          'Set2' => { }
        };