substr( $mask_input, $lastEnd, $start ) =~ tr[\x00-\xff][N];
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Why use tr at all? Just use substr:

# Assuming $lastEnd is initialized to 0 above

my $length = $start - $lastEnd;
if ($length) {
    my $replacement = 'N' x $length;
    substr( $mask_input, $lastEnd, $length, $replacement );
}
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