6
GI:50845406
NM_031444.2  
snoRNA3 -9 Box D except for snoRNA4
Query  3     CTGGAGTCAAGGCT  16
             ||||||||||||||
Sbjct  1297  CTGGAGTCAAGGCT  1284
Homo sapiens chromosome 22 open reading frame 13 (C22orf13), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UEDK8KR6016&log%24=nuclalign&blast_rank=13&list_uids=50845406
5
GI:38327560
NM_006282.2  
snoRNA3 -9 Box D except for snoRNA4
Query  5     GGAGTCAAGGCTAC  18
             ||||||||||||||
Sbjct  5129  GGAGTCAAGGCTAC  5116
Homo sapiens serine/threonine kinase 4 (STK4), mRNA
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UEDK8KR6016&log%24=nuclalign&blast_rank=14&list_uids=38327560
3
GI:91982771
NM_001040105.1  
snoRNA 10
Query  4     TGGAGTCAAT  13
             ||||||||||
Sbjct  4854  TGGAGTCAAT  4845
Homo sapiens mucin 17, cell surface associated (MUC17), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDU305DZ01N&log%24=nuclalign&blast_rank=97&list_uids=91982771
3
GI:154448895
NM_001100162.1  
snoRNA 25, 26 and 27
Query  2    CCTGGAGTCGAGTG  15
            ||||||||||||||
Sbjct  146  CCTGGAGTCGAGTG  133
Homo sapiens exportin 7 (XPO7), transcript variant 3, mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=2&list_uids=154448895					
31
GI:153945877
NM_002458.1  
snoRNA 25, 26 and 27
Query  3     CTGGAGTCGAGTG  15
             |||||||||||||
Sbjct  6818  CTGGAGTCGAGTG  6806
Query  3     CTGGAGTCGAGTG  15
             |||||||||||||
Sbjct  8489  CTGGAGTCGAGTG  8477
Query  3      CTGGAGTCGAGTG  15
              |||||||||||||
Sbjct  10589  CTGGAGTCGAGTG  10577
Query  3      CTGGAGTCGAGTG  15
              |||||||||||||
Sbjct  12260  CTGGAGTCGAGTG  12248
Homo sapiens mucin 5B, oligomeric mucus/gel-forming (MUC5B), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=9&list_uids=153945877

##</code><code>##

'snoRNA 25,26 and 27'=>[
        { 
          GI=>'GI:15444889',
          NM=>'NM_001100162.1',
          exon=>'3',
          seq=>[
                Query  2    CCTGGAGTCGAGTG  15
                             ||||||||||||||
                Sbjct  146  CCTGGAGTCGAGTG  133
                      ],
           geneName =>'Homo sapiens mucin 17, cell surface associated (MUC17), mRNA.',
           weblink=>'http://......'
                },
        {
          GI=>'GI:153945877',
          NM=>'NM_002458.1'
          exon=>'31',
          seq=>[
                  #more than one seq   
                    ]
                },
    ],
'snoRNA3 -9 Box D except for snoRNA4'=>[
                     #more than record once again
                      .......
                       ]

##</code><code>##

use strict;
use Data::Dump qw[ pp ];

my %records;
until(eof(DATA)){
        chomp(my $snoRNA = <DATA>);
        push @{$records{$snoRNA}},{} ;
        my $seqs = 1;
        my $line = <DATA>;
        if( $line =~ m[(\d+) different hits] ) {
                $seqs = $1;
                chomp( $records{ $snoRNA }[ -1 ]{ exon } = <DATA> );
                 } else {
                        chomp( $records{ $snoRNA }[ -1 ]{ exon } = $line );
                        }
    chomp( $records{ $snoRNA }[ -1 ]{ GeneID } = <DATA> );
    chomp( $records{ $snoRNA }[ -1 ]{ NM_ID } = <DATA> );
    for( 1 .. $seqs ) {
        chomp( my $query = <DATA> );
        scalar (<DATA>);
        chomp( my $sbjct = <DATA> );
        push @{ $records{ $snoRNA }[ -1 ]{ seqs } }, { $query => $sbjct };
    }
    chomp( $records{ $snoRNA }[ -1 ]{ gene_name } = <DATA> );
    chomp( $records{ $snoRNA }[ -1 ]{ web_link  } = <DATA> );
        }
        
pp \%records;
__DATA__
snoRNA 25, 26 and 27
2
GI:142387131
NM_006299.3
Query  2    CCTGGAGTCGAGT  14
            |||||||||||||
Sbjct  371  CCTGGAGTCGAGT  359
Homo sapiens zinc finger protein 193 (ZNF193), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=11&list_uids=142387131
snoRNA 25, 26 and 27
1
NM_001005236.3
GI:256773198
Query  3    CTGGAGTCGAGTGTCT  18
            |||||| |||||||||
Sbjct  168  CTGGAGACGAGTGTCT  153
Homo sapiens olfactory receptor, family 1, subfamily L, member 1 (OR1L1), mRNA.
http://www.ncbi.nlm.nih.gov/
snoRNA 25, 26 and 27
4 different hits
31
GI:153945877
NM_002458.1
Query  3     CTGGAGTCGAGTG  15
             |||||||||||||
Sbjct  6818  CTGGAGTCGAGTG  6806
Query  3     CTGGAGTCGAGTG  15
             |||||||||||||
Sbjct  8489  CTGGAGTCGAGTG  8477
Query  3      CTGGAGTCGAGTG  15
              |||||||||||||
Sbjct  10589  CTGGAGTCGAGTG  10577
Query  3      CTGGAGTCGAGTG  15
              |||||||||||||
Sbjct  12260  CTGGAGTCGAGTG  12248
Homo sapiens mucin 5B, oligomeric mucus/gel-forming (MUC5B), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=9&list_uids=153945877

##</code><code>##