#!/usr/bin/perl
use strict;
use warnings;

open SEQ,  '<', 'data1.dat' or die $!;
open MASK, '<', 'data2.dat' or die $!;

while ( my $seq = <SEQ> ) {
  my $mask = <MASK>;
  my $start  =  index( $mask, 'N' );
  my $length = rindex( $mask, 'N' ) - $start + 1;

  my $lc_seq = lc substr( $seq, $start, $length );

  substr( $seq, $start, $length, $lc_seq );

  print $seq;
}