Thanks so much again rnahi.
I hope you don't mind looking at my other instances. I'm really sorry, I didn't mentioned it before because I thought it may appear too complex and too discouraging to read.
Suppose I have this: 
my $fseq6 =   'CCGCGCTC';
my @nsub6 = ( 'CCGCG',
               '*****',
                 'CGCTC'
                 '*****',);

my $fseq5 =   'CCGCGCTC';
my @nsub5 = ( 'CCGCG',
               '*****',
               '*****',
                 'CGCTC');

my $fseq4  =  'CCCCGCGC';
my @nsub4  = ('CCCCG',
              '*****',
                 'CGCGC');

[download]


I would like to produce this: 
$result4 = [
            [ 0,'CCG--'],
            [ 1,'*****'],
            [ 2,'--CTC']
          ];

$result5 = [
            [ 0,'CCG--'],
            [ 1,'*****'],
            [ 2,'*****'],
            [ 3,'--CTC']
          ];

$result6 = [
            [ 0,'CCG--'],
            [ 1,'*****'],
            [ 2,'--CTC']
            [ 3,'*****'],
          ];

[download]


Basically 'skipping' the asterisk(*) but yet still keep its position in array in place.

Update: I've finally succeeded in improving your code such that it can take care those situations. It is not entirely neat and 'super-naive' but it does the job. I think I can't use "grep" function in this case because I still need to keep '*' in its position.

My sincere thanks, for providing an excellent starting point to me.
Here is the final code: 
my $count;
my @ar;
foreach (@nsub)
{
   $c++ if ($_ =~ /[ATCG]/);
   next if ($_ =~ /^\*/);
   push @ar, $_;
   last if ($count == 2);
}
my $sec_str= $ar[$#ar]; #Second non-* strings
print "$llm\n";

my @results;
my %seen;

my $previous = $nsub[0];
my $tmp = $previous;

my ($found) = "$nsub[0]#$sec_str" =~ /(\w+)#\1/;
if ($found) 
{
    $tmp =~ s/$found$/"-" x length($found)/e;
}


push @results, [ 0, $tmp ];

for (1 .. $#nsub)
{
    my $current = $nsub[$_];

    if ($current =~ /^\*/) 
    {
        push @results, [ $_, $current] unless $seen{$_}++;
    } 
    elsif ( "$previous#$current" =~ /(\w+)#\1/ ) 
    {
        my $found = $1;
        (my $tmp = $current) =~ s/^$found/"-" x length($found)/e;
        push @results, [ $_, $tmp];
        $previous = $current;
    } 
    else 
    {
        push @results, [$_,$previous];
        push @results, [$_+1,$current];
        #printf "%d -> no overlap\n", $_;
        $previous = $current;
    }
}

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

[download]


Please kindly advice. Really hope to hear from you again.
Regards,
Edward

In reply to Re^4: Identifying Overlapping Area in a Set of Strings by monkfan
in thread Identifying Overlapping Area in a Set of Strings by monkfan

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