while (<IFILE>) {
        ...
        elsif ($_ =~ /^(\w*)$/) {
        @sequence = $_;
        }
        ...
        foreach my $sequence(@sequence) {
        print OFILE1 "$headerseq\n$sequence\n";

       }
        ...
}
[download]

I'm not familiar with processing FASTA sequence data, but a couple of things strike me in the code fragment originally posted by anonym:

• The statement
      @sequence = $_;
  will only assign a single element to the  @sequence array which, by the operation of the posted code alone, will never contain other than zero or one elements. Then
      foreach my $sequence(@sequence) {
      print OFILE1 "$headerseq\n$sequence\n";
      }
  loops over this zero or one element array to output to a file. This seems suspicious.
• I'm assuming that other code sets up  $/ to read multi-line FASTA records. The regex  /^(\w*)$/ in the  elsif condition statement above will only match records that have no whitespace (except that  $ could match a newline at the very end of the string), but all the records in the sample input shown by anonym have embedded whitespace.

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