use strict;
use warnings;

use List::Util qw(min);

use Data::Dumper;

my $seq1 = { id    => 1,
             start => 0,
             seq   => 'CTGCCACCGCTGT' };
my $seq2 = { id    => 1,
             start => 5,
             seq   => 'ACCGCTGTGTTTCGGCCGGCGA'}; 

print Dumper [ intersection($seq1, $seq2) ];

sub intersection {
        # make sure that seq1 is always the first
        # subsequence
        my ($seq1, $seq2)  = sort {$a->{start} <=> $b->{start} }@_; 

        # determine the start of intersected string ... 
        my $i_start  = $seq2->{start} - $seq1->{start};

        # ... and the length
        my $i_length = min(length(substr($seq1->{seq},$i_start)),
                           length($seq2->{seq}));
        return ($i_start+1, substr($seq2->{seq}, 0, $i_length));
}
[download]