open D1, 'data1.txt';
open D2, 'data2.txt';
my ($c1, $c2);
while (read D2, $c2, 1) {
    read D1, $c1, 1;
    print $c2 eq 'N' ? lc($c1) : $c1;
}
close D2;
close D1;

##</code><code>##

>seq1
GGTacacagaagccaaagcaggctccaggctctgagctgtcagcacagagaccgaT
>seq2
GTCTCTGTCTCtaaaataaataaacattaaaaaaattttaaaagaaaaGATTCTCTCC