First off, why did you start a new thread after having asked the very same question (I suppose, because the latter is screwed up) in another thread?

Said this,

• I see no need for the intermediate @allowed variable: it only clobbers your logic - but this is only cosmetic;
• Coming to the regex:

  my $regex   = qr/ N+ | (?: (?=$allowed) . )*  . /x;
  [download]

  what is that "N"?!? Didn't you say that your string only contains the letters ACGT?
• I can't understand: it seems that (leaving N+ aside) you want to

  "match zero or more occurrencies of a group composed by an allowed sequence and any charachter followed by (another) any charachter (without including the allowed sequences in the match)."

  Is this what that you really want?

Whatever, the easiest solution I can think of to solve your problem would be of removing the newlines before processing your data. If that data is huge and e.g. read from a file, you may want to do so (joining lines or bunch of lines) in a smart way, which you will have to devise.