Additional File 2. Description of Y-patch, AuxRE-like and ABRE-like coupling motifs, revealed by de novo motif search on the flanks of experimentally
proven AuxREs. For each motif we compiled the frequency matrix with the estimated threshold; #seq denotes the number of the sequence in the
Additional file 1; position, strand, PWM score, and sequences that passed the threshold. Logos constructed for these three sequence sets are shown on
Figure 1D-F.
Name of
motif
Y-patch
Frequency matrix and threshold for the
respective PWM
A 0 0 0 1 0 0 0 1
C 0 25 0 22 25 0 12 7
G 0 0 0 0 0 0 0 0
T 25 0 25 2 0 25 13 17
0.91
AuxRE-like
A
C
G
T
9 0 0
0 0 0
7 0 0
9 25 25
2 0 0 0
7 0 25 0
7 0 0 0
9 25 0 25
9
7
0
9
0.9997
ABRE-like
A
C
G
T
9
7
0
9
9 1 9 0 0 0 1
0 12 0 12 12 0 12
7 12 7 0 12 12 12
9 0 9 13 1 13 0
0.9949
#seq
18
12
24
10
13
17
21
7
2
11
5
12
15
18
20
23
24
3
9
11
13
21
6
13
22
8
23
9
Position,
strand
89+
81+
4396+
61+
32+
62+
11+
6585+
77+
1690+
30+
96100+
2286+
7115+
12+
73+
22+
102+
95+
724586+
PWM
score
1
0.9957
0.9825
0.9782
0.9301
0.9301
0.9301
0.9274
0.9231
0.9139
1
1
1
1
1
1
1
0.9997
0.9997
0.9997
0.9997
0.9997
1
1
1
0.9997
0.9997
0.9949
Sequence
TCTCCTCT
TCTCCTTT
TCTCCTCC
TCTCCTTC
TCTTCTCT
TCTTCTCT
TCTTCTCT
TCTCCTCA
TCTCCTTA
TCTACTCT
ATTTTCTT
TTTTTCTT
ATTTTCTT
ATTTTCTT
TTTTTCTA
TTTTTCTT
TTTTTCTT
ATTGTCTA
TTTGTCTA
ATTGTCTT
ATTCTCTT
ATTCTCTT
ATGTCGGC
TTCTCGGG
ATGTCGGG
TGGTCGGC
TGCTCCGG
ATGTCCTC