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Table 1 The first column lists the Type ID for each gapped n -mer, the second column lists the binary representation of the Type ID, the third column lists the k/m representation for each binary representation, obtained by replacing each 0 with a k and each 1 with an m, and the fourth column lists the final corresponding k/m representation of each gapped n -mer, obtained by removing all leading k’s and adding an m to the end of each entry in column three

From: MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding

Type ID

Binary representation

k/m Representation

Gapped n -mer

0

00000

kkkkk

m

1

00001

kkkkm

mm

2

00010

kkkmk

mkm

3

00011

kkkmm

mmm

4

00100

kkmkk

mkkm

5

00101

kkmkm

mkmm

6

00110

kkmmk

mmkm

7

00111

kkmmm

mmmm

8

01000

kmkkk

mkkkm

9

01001

kmkkm

mkkmm

10

01010

kmkmk

mkmkm

11

01011

kmkmm

mkmmm

12

01100

kmmkk

mmkkm

13

01101

kmmkm

mmkmm

14

01110

kmmmk

mmmkm

15

01111

kmmmm

mmmmm

16

10000

mkkkk

mkkkkm

17

10001

mkkkm

mkkkmm

18

10010

mkkmk

mkkmkm

19

10011

mkkmm

mkkmmm

20

10100

mkmkk

mkmkkm

21

10101

mkmkm

mkmkmm

22

10110

mkmmk

mkmmkm

23

10111

mkmmm

mkmmmm

24

11000

mmkkk

mmkkkm

25

11001

mmkkm

mmkkmm

26

11010

mmkmk

mmkmkm

27

11011

mmkmm

mmkmmm

28

11100

mmmkk

mmmkkm

29

11101

mmmkm

mmmkmm

30

11110

mmmmk

mmmmkm

31

11111

mmmmm

mmmmmm

  1. The fourth column illustrates which nucleotides are considered (m) and which are ignored (k) when scoring a potential binding site.