if ( $return >> 8 ) {
       warn "fasta32.exe ended with non-zero exit status\n";
    }

##</code><code>##

while (<FASTA>)
{
   ...
   if ( /(\d+\.\d+)% identity/ ) {
      ...
      if ( $per > $cut ) {
         ...
         while (<FASTA>)
         {
            ...
         }
...