ok, you can put those lines into temp file and after indexing over you can replace file1 with temp file. For example:

While<file1>
 {  $f1=$_;
   While<file1>
    { $f2= $_;
       if($f1 eq $f2)
          {
            print TF "$f2\n";
          }
     }
       print TF "$f1\n";
    }

close TF;

open F_1,"file1.txt";
while(<F_1>)
{
 print F_1 "$_\n";
}

close F_1;
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