Update: This solution, though correct (I think), is unnecessarily complicated and slow. The idea of using bit vectors, which is ideal for counting the size of embedded substrings, is not particularly well-suited for this new problem. See the one in my follow-up to this node instead.

This is a straightforward adaptation of the solution proposed by Roy Johnson (and minimally tweaked by YT) to your earlier problem: 

sub append_n {
    my ($str, $array) = @_;
    my $vec = '';
    for (@$array) {
        my $ofs = 0;
        while ( ( my $idx = index $str, $_, $ofs ) > -1 ) {
          # Set bits at each matched location
          vec( $vec, $_, 1 ) = 1 for $idx .. $idx + length() - 1;
          $ofs = $idx + 1;
        }
    }
    # Count set bits
    vec( $vec, $_, 1 ) or substr( $str, $_, 1 ) = 'N'
      for 0 .. -1 + length $str;
    return $str;
}
__END__
GATTACGNNNNGCGCTCGNNNAACGGCA
GATTACGAGNNNNNNNCGTGTAANNNNN
NNNTACGAGTGGCGCTCGTGNNNNNNNN
NNNNNNNNNNGGNNNNNNNNNNNNGGNN

[download]

Update: Edited the name of the sub to match the one given in the head node.

the lowliest monk

In reply to Re: Recovering Substrings to String with Gap by tlm
in thread Recovering Substrings to String with Gap by monkfan

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