my @headerseq; my @headersec; my @sequence; my @secseq; while () { chomp; if ($_ =~ /sequence/){ @headerseq = split('\n',$_); # print "@headerseq\n"; } elsif ($_ =~ /secstr/){ @headersec = split ('\n',$_); # print "@headersec\n"; } elsif ($_ =~ /^(\w*)$/) { @sequence = $_; # print "@sequence\n"; } else { @secseq = split ('\n',$_); # print "@secseq\n"; } foreach my $headerseq(@headerseq){ foreach my $sequence(@sequence) { print OFILE1 "$headerseq\n$sequence\n"; } } }