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use strict;
use warnings;
...
  $length = $.;
}
close $fh;

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miR156a AT3G19833 151 0.607541 
miR156a AT3G19883 11 0.607541 
...
miR156a AT3G19773 15 0.607541 
miR156a AT3G19833 161 0.607541
miR156a AT3G19780 163 0.607541