Instead of splitting you could use a regex like [AGCT]+ to pick the bits you need with optional Ns at the beginning or end of the string (modifying robby_dobby's example from above):

use strict;
use warnings;

while (my $line = <DATA>) {
        my @info = $line =~ /((?:^N+)?[ATGC]+(?:N+$)?)/g;
        print join(", ", @info), "\n";
}

__DATA__
NNNAAAATATGACAAAGGGGTTNNNNNNNNNNNNNNGATGTCTGGTCAATAGGAT
CGCAGCCATTAACATCTCAACAAGCCAAAAATTCCTTCTCAGAAATTCGGNNN
AAAATATGACAAAGGGGTTNNNNNNNNNNNNNNGATGTCTGGTCAATAGGAT
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