#! perl -slw
use strict;

my $s1 = "1,0,CTGCCACCGCTGT";
my $s2 = "1,5,ACCGCTGTGTTTCGGCCGGCGA";

my @s1 = split ',', $s1;
my @s2 = split ',', $s2;

if( $s1[0] == $s2[0] ) {
    if( $s1[1] > $s2[1] ) {
        my @temp = @s1;
        @s1 = @s2;
        @s2 = @temp;
    }
    if( $s2[1] < length( $s1 ) ) {
        ## Updated to correct the error pointed out by Lima1++ below
        my $l1 = length( $s1[2] ) - $s1[1] - $s2[1];
        my $l2 = length( $s2[2] );
        $l1 = $l2 if $l2 < $l1;
        
        print "The intersection between the strings:\n",
            $s1[2], "\n",
            ' ' x ( $s2[1] - $s1[1] ), $s2[2],
            "\nis\n", ' ' x $s2[1],
            substr $s1[2], $s2[1] - $s1[1], $l1;              ;

        print "\nand it occurs at a 1-based offset into the sequence of ",
            $s2[1] + 1;
    }
    else {
        print "The strings do not intersect";
    }
}
else {
    print 'Strings are not from the same sequence';
}

__END__
c:\test>junk
The intersection between the strings:
CTGCCACCGCTGT
     ACCGCTGTGTTTCGGCCGGCGA
is
     ACCGCTGT

and it occurs at a 1-based offset into the sequence of 6