You can read your whole window at once by setting $/ to a reference to it's literal constant width.

{
    open (FH, "<ciona_fasta_two") or die $!;
    local ($/, $_) = (\500);
    while (<FH>) {
        my ($first, $last) = (substr($_,0,1), substr($_,-1,1));
        # do other stuff
    }
    close FH or die $!;
}
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