while (<IFILE>) {
        chomp;
        if ($_ =~ /sequence/){
        @headerseq = split('\n',$_);
[download]

You don't show where you have set $/ to some kind of record seperator so you are reading in one line at a time. That means split('\n',$_) will return one element, the whole line. Each time you are setting @headerseq to the line that matches /sequence/.

The same applies to the other arrays. You are not actually using them as arrays since they only ever hold one element in this setup.