#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %records;
until( eof( DATA ) ) {
    chomp( my $exon = <DATA> );
    push @{ $records{ $exon } }, {};

    my $seqs = 1;
    my $line = <DATA>;
    if( $line =~ m[(\d+) different hits] ) {
        $seqs = $1;
        chomp( $records{ $exon }[ -1 ]{ gene_id } = <DATA> );
    }
    else {
        chomp( $records{ $exon }[ -1 ]{ gene_id } = $line );
    }

    chomp( $records{ $exon }[ -1 ]{ Nm_id } = <DATA> );

    chomp( $records{ $exon }[ -1 ]{ snoRNA_key } = <DATA> );

    for( 1 .. $seqs ) {
        chomp( my $query = <DATA> );
        scalar (<DATA>);
        chomp( my $sbjct = <DATA> );
        push @{ $records{ $exon }[ -1 ]{ seqs } }, { $query => $sbjct };
    }

    chomp( $records{ $exon }[ -1 ]{ gene_name } = <DATA> );

    chomp( $records{ $exon }[ -1 ]{ web_link  } = <DATA> );
}

pp \%records;

__DATA__
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
4 different hits
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
4
GI:150418008
NM_206862.2
snoRNA 25, 26 and 27
Query  1     ACCTGGAGTCGAG  13
             |||||||||||||
Sbjct  4775  ACCTGGAGTCGAG  4763
Homo sapiens transforming, acidic coiled-coil containing protein 2 (TACC2), transcript variant 1, mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=10&list_uids=150418008

##</code><code>##

C:\test>junk55
{
  3  => [
          {
            Nm_id      => "NM_001040105.1",
            gene_id    => "GI:91982771",
            gene_name  => "Homo sapiens mucin 17, cell surface associated (MUC17), mRNA.",
            seqs       => [
                            {
                              "Query  4     TGGAGTCAAT  13" => "Sbjct  4854  TGGAGTCAAT  4845",
                            },
                          ],
            snoRNA_key => "snoRNA 10",
            web_link   => "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",
          },
          {
            Nm_id      => "NM_001100162.1",
            gene_id    => "GI:154448895",
            gene_name  => "Homo sapiens exportin 7 (XPO7), transcript variant 3, mRNA.",
            seqs       => [
                            {
                              "Query  2    CCTGGAGTCGAGTG  15" => "Sbjct  146  CCTGGAGTCGAGTG  133",
                            },
                          ],
            snoRNA_key => "snoRNA 25, 26 and 27",
            web_link   => "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",
          },
        ],
  4  => [
          {
            Nm_id      => "NM_206862.2",
            gene_id    => "GI:150418008",
            gene_name  => "Homo sapiens transforming, acidic coiled-coil containing protein 2 (TACC2), transcript variant 1, mRNA.",
            seqs       => [
                            {
                              "Query  1     ACCTGGAGTCGAG  13" => "Sbjct  4775  ACCTGGAGTCGAG  4763",
                            },
                          ],
            snoRNA_key => "snoRNA 25, 26 and 27",
            web_link   => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=10&list_uids=150418008",
          },
        ],
  31 => [
          {
            Nm_id      => "NM_002458.1",
            gene_id    => "GI:153945877",
            gene_name  => "Homo sapiens mucin 5B, oligomeric mucus/gel-forming (MUC5B), mRNA.",
            seqs       => [
                            {
                              "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",
                            },
                          ],
            snoRNA_key => "snoRNA 25, 26 and 27",
            web_link   => "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",
          },
        ],
}