As long as you are not allowing overlaps, an alternative to toolic's regex solution would be to use unpack.
johngg@shiraz:~/perl/Monks > perl -Mstrict -Mwarnings -E '
my $str = q{BEBEBEHUHUHUJJFAFALL};
my %cnt;
$cnt{ $_ } ++ for unpack q{(a2)*}, $str;
say qq{$_ -> $cnt{ $_ }} for sort keys %cnt;'
BE -> 3
FA -> 2
HU -> 3
JJ -> 1
LL -> 1
I hope this is of interest.
Update: A bit of a lash-up allowing for overlaps.
johngg@shiraz:~/perl/Monks > perl -Mstrict -Mwarnings -E '
my $str = q{BEBEBEHUHUHUJJFAFALL};
my %cnt;
my $len = shift || 2;
my $overlap = shift || 0;
my $fmt
= $overlap
? qq{(a${len}X@{ [ $len - 1 ] })*}
: qq{(a${len})*};
$cnt{ $_ } ++ for grep { length == $len } unpack $fmt, $str;
say qq{$_ -> $cnt{ $_ }} for sort keys %cnt;'
BE -> 3
FA -> 2
HU -> 3
JJ -> 1
LL -> 1
johngg@shiraz:~/perl/Monks > perl -Mstrict -Mwarnings -E '
my $str = q{BEBEBEHUHUHUJJFAFALL};
my %cnt;
my $len = shift || 2;
my $overlap = shift || 0;
my $fmt
= $overlap
? qq{(a${len}X@{ [ $len - 1 ] })*}
: qq{(a${len})*};
$cnt{ $_ } ++ for grep { length == $len } unpack $fmt, $str;
say qq{$_ -> $cnt{ $_ }} for sort keys %cnt;' 2 1
AF -> 1
AL -> 1
BE -> 3
EB -> 2
EH -> 1
FA -> 2
HU -> 3
JF -> 1
JJ -> 1
LL -> 1
UH -> 2
UJ -> 1
johngg@shiraz:~/perl/Monks > perl -Mstrict -Mwarnings -E '
my $str = q{BEBEBEHUHUHUJJFAFALL};
my %cnt;
my $len = shift || 2;
my $overlap = shift || 0;
my $fmt
= $overlap
? qq{(a${len}X@{ [ $len - 1 ] })*}
: qq{(a${len})*};
$cnt{ $_ } ++ for grep { length == $len } unpack $fmt, $str;
say qq{$_ -> $cnt{ $_ }} for sort keys %cnt;' 3
AFA -> 1
BEB -> 1
EBE -> 1
HUH -> 1
JJF -> 1
UHU -> 1
johngg@shiraz:~/perl/Monks > perl -Mstrict -Mwarnings -E '
my $str = q{BEBEBEHUHUHUJJFAFALL};
my %cnt;
my $len = shift || 2;
my $overlap = shift || 0;
my $fmt
= $overlap
? qq{(a${len}X@{ [ $len - 1 ] })*}
: qq{(a${len})*};
$cnt{ $_ } ++ for grep { length == $len } unpack $fmt, $str;
say qq{$_ -> $cnt{ $_ }} for sort keys %cnt;' 3 1
AFA -> 1
ALL -> 1
BEB -> 2
BEH -> 1
EBE -> 2
EHU -> 1
FAF -> 1
FAL -> 1
HUH -> 2
HUJ -> 1
JFA -> 1
JJF -> 1
UHU -> 2
UJJ -> 1
