Here is a standalone demonstration that the code I posted works just fine:

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

sub gen{
    return @_[1..$#_] if $_[0]==1;
    map{
        my $p=$_;
        map{ $p . $_ } gen($_[0]-1, @_[1..$#_] )
    } @_[1..$#_]
}

our $N //= 7;

my %seqs = map {
    if( length() ) {
        my( $id, @seq ) = split "\n", $_;
        $id => join '', @seq;
    }
    else { () }
} split '>', do{ local $/; uc( <DATA> ) };

my $start = time;
my %counts;
for my $seq ( values %seqs ) {
    ++$counts{ substr $seq, $_, $N } for 0 .. length( $seq ) -$N;
}
print "Took ", time - $start;

print "$_ ::= ", $counts{ $_ } // 0 for gen( $N, qw[A C G T] );


__DATA__
> DNA1
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
> DNA2
AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT
TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA
> DNA3
TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC
GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC
CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA
AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA
ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC
AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG
> DNA4
AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC
CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT
AAATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaac
ccatccctgagaatccaaaattctccgtgccacctatcacaccccatcct
aAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG
GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC
[download]

And some output:

C:\test>976237-2 -N=2
Took 0.000387907028198242
AA ::= 97
AC ::= 86
AG ::= 49
AT ::= 84
CA ::= 99
CC ::= 130
CG ::= 26
CT ::= 71
GA ::= 35
GC ::= 43
GG ::= 27
GT ::= 36
TA ::= 85
TC ::= 68
TG ::= 39
TT ::= 71
[download]