#!/usr/bin/perl -w 
use strict;

use Bio::Tools::BPbl2seq;


my $AFILE = 'a.seq';
my $BFILE = 'b.seq';
my $OUTFILE = 'bl2seq.out';

system('blast/bl2seq', '-i', $AFILE,
                       '-j', $BFILE,
                       '-o', $OUTFILE,
                       '-p', 'blastn',
                       '-e', '1e-4');

my $report = Bio::Tools::BPbl2seq->new(-file => $OUTFILE,
                                       -queryname => 'a.seq');

my (@Aranges,@Branges);

while (my $hsp = $report->next_feature) {
   push @Aranges, [$hsp->query->start, $hsp->query->end];
   push @Branges, [$hsp->sbjct->start, $hsp->sbjct->end];
}

my $Arange_ref = \@Aranges;
my $Brange_ref = \@Branges;

my $sortedA = sort_array($Arange_ref);
my $sortedB = sort_array($Brange_ref);

my $Aseq = get_seq($AFILE);
my $Bseq = get_seq($BFILE);

my $Agaps = find_gaps(length $Aseq, $sortedA);
my $Bgaps = find_gaps(length $Bseq, $sortedB);

print_gaps('A',$Aseq,$Agaps);
print_gaps('B',$Bseq,$Bgaps);

#-------------
sub sort_array {
    my $array_ref = shift;
    my @array = @{$array_ref};
    for (my $i = 0; $i<((scalar @array)-1); $i++) {
        if ($array[$i][0] > $array[$i+1][0]) {
            ($array[$i], $array[$i+1]) = ($array[$i+1], $array[$i]);
        }
    }
    my $return_ref = \@array;
    return $return_ref;
}
#-------------
sub find_gaps {
    my $len = shift;
    my $array_ref = shift;
    my @array = @{$array_ref};
    my @gaps;
    if ($array[0][0] > 1) {
        push @gaps, (1, ($array[0]->[0]-1));
    }

    for (my $i = 1; $i<(scalar @array); $i++) {
        if ($array[$i-1][1] < $array[$i][0]) {
            push @gaps, [ ($array[$i-1][1]+1), ($array[$i][0]-1) ];
        }
    }

    if ($array[-1][1] < $len) {
        push @gaps, [ ($array[-1][1]+1), $len];
    }

    my $return_ref = \@gaps;
    return $return_ref;
}
#------------
sub get_seq {
    my $filename = shift;
    my $seq = '';
    open FILE, $filename or die "couldn't open $filename: $!\n";
    while (<FILE>) {
        chomp;
        if (/^>/) {
            next;
        }
        $seq .= $_;
    }
    close FILE;

    $seq;
}
#------------
sub print_gaps {
    my $seqname = shift;
    my $seqin = shift;
    my $array_ref = shift;
    my @array = @{$array_ref};

    if (scalar @array > 0) {
        print "$seqname gaps:\n";
        foreach my $gap (@array) {
            my $start = ${$gap}[0];
            my $end   = ${$gap}[1];
            my $seq   = substr ($seqin, $start, ($end-$start) );
            print "$start - $end:$seq\n";
        }
    }
}
<code>
Which results in this output:
<code>
A gaps:
320 - 338:ggctcctatcagcgggtc
361 - 418:atgcagtccagagaaaagtgcctcatttttcagtaaagtgacatattcctggtttag
892 - 3389:gtccctggcaaccttgtgtgtctatttcttactggatgaaggaaacattttaacagccactaaagtgtt
cacatcgatgtctttgtttaatattttaaggattcctctgtttgagttaccaaccgtgatctcagctgtggtccagacaa
agatatccctgggccgtttggaagactttctcaacactgaggagcttcttcctcaaagtattgaaacgaactatacagga
gatcatgctattgggtttacagatgcttctttctcctgggataaaacaggaatgccagttctaaaagaggctctgtggct
tatgtttctcagcaggcctggattcagaattgcattttgcaagaaaacattctctttggctccatcatgaagaaagagtt
ttatgagcaagtattggaagcctgtgctctccttccagatttggagcagttgccaaagggagatcaaactgagattggag
aaagagtaaggaaacggctgtgaatataagtgggggccagcagcatcgagtaagcctggccagagctgtctacagtgggg
ccgacgtctacctcctggatgatcccttgtctgctattgatgttcatgttggaaagcagctttttgaaaaagtgataggg
tccttgggccttttgaaaaaccgggtagccatagtttcatttatgctttcttgtggggcaggggatatatctagcactgt
gcctaaaattccatttattttgtttatttgttgaagcaaagtagtcacatttcacatgaaaaaaatgggatgctcagatt
gcaatttcacaggcaaatgtcaatgggtaatttttgaagttttacttacaagtttactctggtgacaatttatgtgattg
ttatctcttcatctaataccatatcctaaggggatgtatgtgccataatgaattgttgttgactcaagtgatttttacaa
tggtattttggtgcacaccaaaatattaataaaattttatattattaacatagcaatttgacattattatcacagcaatc
atagtgattcagctgttttgttaaagggccaagaagatgaaaattagtgtttaccagtacatgccatatttcacagggta
aattagttcaatccctatttcacacataaaggagctcagggctcacaatgacttgatataggttgctcaacttaagaaca
atagagatttttaaaagtatgtctgactccaaagccacattcttcataatatgtgtttatggaattattaatatagagaa
ctttgaaaatatatgtataaaattataaaatatatgtctcagtaaaaataaacaaacatctttatatattgacataaacc
caagattaaaaatgtcacacttaattgtatgtatatgtataaaataatatgaatgatttaaaaataaggactatgaatta
tgacttggattaaacactttttttgtaatggtactgtatatttaaaaataagcaagaatgacatatatgaaattgtttta
aatttgcaattaaattgattcatttctaatgaacgaaaaaatacccgaactaaagtgttaaaaatcacatttagaaacta
ttttctcatctagcagcatgtcattattccttgtaaaatacatagatgctgccttaaactggcacctaccaaaaatcata
ctctgaaatagtaaaggaaaaaagtcattgtagctttttttaaaaagccatttttcgtaatctctgagataaaacacttt
gtttttcagactcatattttagtgacacacaatctcacacttctgccacaaatgaatcttattgttgtaatgaaaagtgg
cagaatagctcaaatgggaatataccaggagctgctgtgtaaaaccaaaaatctcactaatttgcaccaagtcatcagtg
aacaagaaaaagctcatgctctaaagcaagtcagtgcaatcaactccagaactagaccaaaagacaaaatcctggagcaa
aaacatagtgggatatgagtccccttctgagagtcatgcaaggatttctaggcactgttaagaacccacgtagaaagaag
atgttaagtgacggtagaaccagttttcagggttgcctgattttttgaagcagcacttcacagaagtcgaggtgaccagg
attgacatgcaagttctaagagacaggccctcattggatcaaggaaaacagctctcaatgaaaaaagaaaagatccctgt
tggtgggttgaagttctccatcattctgcagtacctccaagcctttggctggctctgggtgtggctgactgtggtcactt
acttagggcagaatttggtgagcattggacagaatctatggcttagtgcatgggcaaaagaagcaaaaaacatgaatgag
ttcacagaatggaagcaaataagaagcaataaacttaatatctatggattattgggattaataaaaggtaaaagaaaatg
taaaaaaaaaaaaaaaaaaaaaaaaaaa
B gaps:
805 - 1073:cttacttttatcaaatgtttctcgacaaaagttttccactggggaaattattaacttgatgtcagcaac
tcatggacttgacagcaaacctcaatctcctctggtctgccccttttcaaatcctaatggccgtatatctcctttggcaa
gagctgggtccagcagtgttagcaggggtggcagtccttgtgtttgttataccaataaatgctttagctgcaactaaaat
aaaaaagttaaaggtaagaaaaaaaaaaaaaaaaaaaaa