From the dates in the file header, this looks like a file you've inherited. Perhaps the first thing to do is write a small script that just contains this

my @satfile = <STDIN>;
my @satseq = @satfile;
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and see if it runs out of memory. If so, your datafiles are too big to read in and make a copy and you'll want to deal with one line at a time, e.g.

my $sorsz = 3;
while (my $line = <STDIN>) {
    chomp $line;    # to remove newlines

    if ( $. <= 3 ) {    # input line numbers start from 1
        push @satseq, $line;
    }
    elsif ( $line =~ /\#/ ) {
        $satseq[$sorsz] .= $line;    # concatenates line onto the end
        $sorsz++;
    }
    else{
        $satseq[$sorsz] .= $line;
    }
}
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which is a more memory efficient way to deal with large files.

If the concatenation is still killing memory, try substr($satseq[$sorsz],length($satseq[$sorsz]),0) = $line