You have the coordinates of the subsequences? Then this should work: 
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]

In reply to Re: Intersecting Two Strings by lima1
in thread Intersecting Two Strings by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.