A little over 10x the data takes a little over 10x as long, 36 seconds, though it needed a few tweaks to stop it from blowing gobs of memory:

#! perl -slw
use strict;
use Time::HiRes qw[ time ];

my $sequence = join'', map{ ( qw[ A C G T ] )[ rand 4 ] } 1 .. 100_000
+;
$sequence x= 65;

my $start = time;
my( %one, %two, %three );

print 'starting one';
for( my $i=0; $i < length( $sequence ) - 100_000; $i += 100_000 ) {
    $one{ $_ }++ for unpack '(A1)*', substr $sequence, $i, 100_000;
}
print 'starting two';
for( my $i=0; $i < length( $sequence ) - 99_999; $i += 99_999 ) {
    $two{ $_ }++ for unpack '(A2X)*', substr $sequence, $i, 100_000;
}
delete @two{ (qw'A C G T') };;

print 'starting three';
for( my $i=0; $i < length( $sequence ) - 99_999; $i += 99_999 ) {
    $three{ $_ }++ for unpack '(A3XX)*', substr $sequence, $i, 100_002
+;
}
delete @three{ (qw'AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT') }
+;

printf "Elapsed: %3f seconds\n", time - $start;

<STDIN>;

print "one\n@{[%one]}";
print "two\n@{[%two ]}";
print "three\n@{[%three]}";

__END__
P:\test>499988
starting one
starting two
starting three
Elapsed: 36.257410 seconds

one
A 1604992 T 1613184 C 1589696 G 1592128
two
AC 404168 CC 403645 TG 409301 AT 408133 AA 413074 CT 409560 CG 399941 
+TA 409562 
GC 400133 CA 401370 GT 407740 AG 404684 TC 406569 GA 406053 TT 412940 
+GG 403062
three
GCC 97240 AGT 100880 TGT 105820 TGA 99385 CGA 99580 ATC 103155 AAC 102
+765 
AGC 100490 TAC 99060 TCG 100490 ACA 96460 CTG 103155 CCG 97500 GCA 986
+70 
GTG 100230 AAG 100750 CAC 98995 GTT 105820 AGA 102310 ACC 101660 CCA 1
+03480 
TGG 101985 CGC 98475 CTC 98995 TTG 105300 TAA 102700 CAG 100880 ACG 10
+1400 
AAA 105365 ATG 100620 GTA 100360 CTT 102570 TAG 104650 GGA 104780 GTC 
+101335 
TGC 102115 TCA 102765 ATT 102765 TAT 103155 AAT 104195 ACT 104650 GAC 
+103350 
CAA 100230 GGT 98865 TCC 104130 TTT 101790 AGG 101010 CGT 102180 CGG 9
+9710 
CAT 101270 ATA 101595 CCC 100620 GGG 100360 GAG 98410 TTA 102765 GAT 9
+9515 
CTA 104845 TCT 99190 TTC 103090 GCG 100555 GGC 99060 GAA 104780 GCT 10
+3675 
CCT 102050
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