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# Write results to output file.
open my $out_fh, '>', $out_filename
...
say {$out_fh} $indata;
close $out_fh 
    or die "Couldn't close $out_filename";

XYZ XYZ XYZ XYZ XYZ 
XYZ xyz foo ATGC atgc JAPHATGC
XYZ 
XYZXYZXYZ