use strict;
use warnings;

my %site_length_catch;
my $max = 0;
foreach (@file) {
  chomp;
  my @r = split /\t/;
  # cleaning from your second loop
  $r[13] =~ s/\D\.\D([0-9]+)\D/$1/; 
  $r[13] =~ s/(\*|\?|s\d+)//; 
  $site_length_catch{$r[0]}{$r[13]}++;
  $max = $r[13]>$max?$r[13]:$max;
}

foreach my $gene (keys %site_length_catch) {
  print $site_length_catch{$gene}{$_} // 0, "\t" for 1..$max;
  print "\n";
}