Perhaps not the best efficient way, but it does what you ask:

use warnings;
use Data::Dumper;

my $fseq =  'CCCCGCGC';
my @nsub =  ('CCCCG', 'CCCGC', 'CGCGC');

my @results;

for (1 .. $#nsub)
{
    my $current = $nsub[$_];
    my $previous = $nsub[$_ -1];
    # the "#" is used as a separator.
    # put a different character (or sequence of characters)
    # if you believe that it could also be in your strings
    if ( "$previous#$current" =~ /(\w+)#\1/ )
    {
        my $found = $1;
        printf "%d -> %s (%s) %d -> %s \n",
            $_ -1,
            $previous,
            $found,
            $_,
            $current;
        $current =~ s/^$found/"-" x length($found)/e;
        $previous =~ s/$found$/"-" x length($found)/e;
        push @results, [ $_ -1, $previous];
        push @results, [ $_, $current];

    }
    else
    {
        printf "%d -> no overlap\n", $_
    }
}

print Data::Dumper->Dump([ \@results], ['result']);

[download]

Result: (adjusted)

0 -> CCCCG (CCCG) 1 -> CCCGC
1 -> CCCGC (CGC) 2 -> CGCGC

$result = [
            [ 0, 'C----' ],
            [ 1,  '----C' ],
            [ 1, 'CC---' ],
            [   2, '---GC' ]
          ];

[download]

In reply to Re: Identifying Overlapping Area in a Set of Strings by rnahi
in thread Identifying Overlapping Area in a Set of Strings by monkfan

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