If you are going to match the same position more than once, as indicated by your code, then you should store the value from a single call to substr and use that in the subsequent if statements:

while(<IN>)
  {
      my $tmp = substr($_, 259, 1);
  
      if($tmp eq "B")
      {
          print B $_;
      }
      else if ($tmp eq "T")
      {
          print T $_;
      }
      else if ()
      {
          # and so on for at least 10 lines!...
      }
  }
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--
John.