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# ----- prediction on sequence number 1 (length = 105, name = seq_01) 
+--
#
...
# Predicted genes for sequence number 3 on both strands
# start gene g4 ....
[as same as above]......so on and on...

FILE 1:
>seq_01 g1
...
>seq_03 g4
......so on...

#!/usr/bin/perl
open(FH,$ARGV[0]);
...
  print OUT1 "$1";
  print OUT2 "$2";
}