OOPS, I see that yr already identified this approach.

If your lines are really all the same length, you could do the job via a seek() / read() loop. The example below needs error checking. I haven't done any speed tests.

#!/usr/bin/perl
use strict;
use warnings;

my $linesep_len = length($/);
my $rec_len = length('ACATCACCTCCCACAACGAGGACTACACCATCGTGGAACA') + $li
+nesep_len;
my $read_len = 1;
my $skip_len = $rec_len - $read_len;

binmode(DATA);
seek(DATA, 10, 1) or die "seek error";
my $buf = ' ' x $read_len;
while (read(DATA, $buf, $read_len) > 0) {
    print $buf, "\n";
    seek(DATA, $skip_len, 1) or last;
}

__DATA__
ACATCACCTCCCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCxCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCsCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCjCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCcCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCCCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCCCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCCCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTCCCACAACGAGGACTACACCATCGTGGAACA
ACATCACCTC-CACAACGAGGACTACACCATCGTGGAACA
[download]

Output:

C
x
s
j
c
C
C
C
C
-
[download]