If you are still implementing threads: Don't forget to use flock while writing to file inside the threads, something like this:

use threads;
use Fcntl qw(:flock SEEK_END);


      if ($end >= $ref->{start} && $end <= $ref->{end}) {
    lock($out_fh);
    say $out_fh join("\t", $ID, $strand, $chr, $start, $end, $sequence
+, $numPositions, $mismatches||"", $ref->{info});
    unlock($out_fh);
      }


sub lock {
  my ($fh) = @_;
  flock($fh, LOCK_EX) or die $!;
  seek($fh, 0, SEEK_END) or die $!;
}
sub unlock {
  my ($fh) = @_;
  flock($fh, LOCK_UN) or die $!;
}
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Alternatively, use shared objects (collect it in an array or hash) and write it down later.