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if($sequence[1] =~ m/^(.*)$reg(.*)$/i){
          $aligned[$posCount][0] = $1;
          $aligned[$posCount][1] = $2;
          $aligned[$posCount][2] = $3;
}

if($sequence[1] =~ m/^(.*)$reg(.*)$/i){
         for(my $x = 0; $x < $numInsertionDeletes; $x++){
               $aligned[$posCount][$x] = ????????;
         }
      }