<s>
MaMF	B-Algorithm
,	O
or	O
Mammalian	O
Motif	O
Finder	O
,	O
is	O
an	O
algorithm	O
for	O
identifying	O
motifs	O
to	O
which	O
transcription	O
factors	O
bind	O
.	O
</s>
<s>
This	O
index	B-Data_Structure
is	O
then	O
used	O
to	O
build	O
a	O
list	O
of	O
all	O
pairs	O
of	O
sequences	O
of	O
length	O
w	O
,	O
such	O
that	O
each	O
sequence	O
shares	O
an	O
n-mer	O
,	O
and	O
each	O
sequence	O
forms	O
an	O
ungapped	O
alignment	B-Algorithm
with	O
a	O
substring	O
of	O
length	O
w	O
from	O
the	O
string	O
of	O
length	O
2w	O
around	O
the	O
match	O
,	O
with	O
a	O
score	O
exceeding	O
a	O
cut-off	O
.	O
</s>
