The problem appears when I also have Ns at the beginning or end of the sequence
So, remove the N's at the beginning and at the end, and use your old algorithm: 
$sequence =~ s/^N+|N+$//g;

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In reply to Re: Splitting only on internal pattern, not at start or end of string by choroba
in thread Splitting only on internal pattern, not at start or end of string by BiologySwede

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