The name of the primary motif.

[ close ]

The logo of the primary motif.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

[ close ]

The number of secondary motifs found that had significant spacings in the tested region.

[ close ]

The list of secondary motifs found that had significant spacings in the tested region.

[ close ]

The name of the sequence database.

[ close ]

The last modified date of the sequence database.

[ close ]

The number of sequences in the sequence database.

[ close ]

The number of sequences in the sequence database which were excluded because they were shorter than twice the margin plus the primary motif length.

[ close ]

The number of sequences in the sequence database which were excluded because no match to the primary motif could be found at a distance to the edges larger than the margin.

[ close ]

The number of sequences in the sequence database which were excluded because they were largly identical to other sequences when aligned on the primary motif site.

[ close ]

The number of sequences which were scanned with the secondary motifs.

[ close ]

The name of the motif database derived from the file name.

[ close ]

The date that the motif database was last modified.

[ close ]

The number of motifs loaded from the motif database. Some motifs may have been excluded.

[ close ]

The number of motifs with significant E-values whose significant spacings were not considered too similar to those of another motif.

[ close ]

The number of motifs that while having significant spacings were less signficant than another motif that matched most of the same sites.

[ close ]

The primary motif is used as the reference point for all spacing calculation.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

[ close ]

The secondary motif occurs at the spacings relative to the primary shown in the histogram below.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

[ close ]

The E-value is the lowest p-value of any spacing of the secondary motif times the number of secondary motifs. It estimates the expected number of random secondary motifs that would have the observed minimum p-value or less.

[ close ]

The histogram below shows the frequency of spacings from the primary motif to the secondary motif. Red bars indicate that a spacing has occured a statistically significant number of times.

Upstream
These are sequences where the secondary motif occurs before the primary motif.
Downstream
These are sequences where the secondary motif occurs after the primary motif.
Same Strand
These are sequences where the secondary motif is on the same strand as the primary motif.
Opposite Strand
These are sequences where the secondary motif is on the opposite strand to the primary motif.
[ close ]

The details of the significant spacings are shown in the four quadrants as they relate to the quadrants of the graph.

P-value
is the probability of the observed number (or more) sequences having the observed spacing between the primary and secondary motif, adjusted for multiple tests. The number of multiple tests is the number of spacing bins (the number of bars in the histogram) tested for significance.
Gap
is the space between the primary and secondary motifs where a value of zero means there is no space between them.
#
is the number of sequences where that spacing was observed.
[ close ]

The total number of sequences that have a match for both the primary motif and this secondary motif.

[ close ]

The motif database which this secondary motif came from.

[ close ]

The list of secondary motifs which have been identified as possibly similar to this motif because their most significant spacings overlaped with the most significant spacing of this motif. Check the boxes to show the possibly similar secondary motifs.

[ close ]

This shows the first secondary motif aligned with the current secondary motif by the most significant spacing.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

[ close ]

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use SpaMo in your research please cite the following paper:
Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey, "Inferring transcription factor complexes from ChIP-seq data", Nucleic Acids Research, 39(15):e98, 2011. [full text]

Primary Motif  |  Sequence Database  |  Secondary Databases  |  Spacing Analysis  |  Program information

Primary Motif

 Next Top
Name 
 Preview 
 Significant Secondaries 
 List 
UP00000 2 (Smad3 secondary)
TACGCCCCGCCACTCTG
67 UP00022 1 (Zfp740 primary),  UP00021 1 (Zfp281 primary),  UP00047 1 (Zbtb7b primary),  UP00099 2 (Ascl2 secondary),  UP00033 2 (Zfp410 secondary),  MA0079.3 (SP1),  UP00043 2 (Bcl6b secondary),  UP00002 1 (Sp4 primary),  1 (MEME),  UP00007 1 (Egr1 primary),  MA0162.2 (EGR1),  2 (MEME),  MA0528.1 (ZNF263),  MA0130.1 (ZNF354C),  MA0056.1 (MZF1 1-4),  MA0057.1 (MZF1 5-13),  CYGCCDCC (DREME),  UP00007 2 (Egr1 secondary),  MA0493.1 (Klf1),  MA0472.1 (EGR2)

Sequence Database

 Previous Next Top
Name 
 Last Modified 
 Loaded 
 Too Short 
 No Primary 
 Too Similar 
 Used 
Static Sex-independent Wed Jun 7 10:47:08 2017 67058 0 45433 1 21624

Secondary Databases

 Previous Next Top
Name 
 Last Modified 
 Number of Motifs 
 Motifs Significant 
 Motifs Redundant 
meme.xml Wed Jun 7 10:49:30 2017 3 2 0
dreme.xml Wed Jun 7 15:52:22 2017 63 6 1
JASPAR CORE 2014 vertebrates Wed Jun 7 10:46:42 2017 205 19 4
uniprobe mouse Wed Jun 7 10:46:42 2017 385 40 4

Spacings of "UP00022 1 (Zfp740 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00022 1 (Zfp740 primary) 
 E-value
TACGCCCCGCCACTCTG
CCCCCCCCCCCACTTG
3.6e-101
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
5.4e-104 0 172  
4.6e-41 1 102  
1.7e-22 2 76  
6.5e-07 3 48  
2.3e-07 5 49  
P-value Gap #  
1.7e-36 0 96  
8.7e-09 2 52  
0.016 3 37  
0.016 141 37  

Total sequences with primary and secondary motif 

9879

Motif Database 

uniprobe mouse

Secondary motifs with similar spacings 
Similar Secondary: UP00088 2 (Plagl1 secondary)
Same Strand
Opposite Strand
P-value Gap #  
2.5e-05 1 25  
0.039 7 19  

Total sequences with primary and secondary motif 

3771

Alignment by most significant spacings 

Best Similar
Secondary
CAAGTGGGGGGGGGGG
This Similar
Secondary
  GCTGGGGGGTACCCCTT

Spacings of "UP00021 1 (Zfp281 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00021 1 (Zfp281 primary) 
 E-value
TACGCCCCGCCACTCTG
TCCCCCCCCCCCCCC
3e-80
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
4.6e-83 0 158  
3.1e-23 1 82  
8.5e-12 2 62  
4.4e-16 3 70  
0.00074 4 44  
5.4e-05 5 47  
0.018 6 40  
0.00032 137 45  
P-value Gap #  
1.9e-26 0 87  
2.4e-09 1 57  
1.7e-07 2 53  
2.2e-05 3 48  
8.5e-06 4 49  
0.018 7 40  
0.037 8 39  

Total sequences with primary and secondary motif 

10792

Motif Database 

uniprobe mouse

Spacings of "UP00047 1 (Zbtb7b primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00047 1 (Zbtb7b primary) 
 E-value
TACGCCCCGCCACTCTG
AAGCCCCCCAAAAAT
7e-28
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
2e-19 0 65  
8.2e-08 1 45  
0.032 2 32  
0.014 3 33  
0.00038 5 37  
P-value Gap #  
1.1e-30 0 81  
7.9e-09 1 47  
0.00098 2 36  
0.00098 3 36  
0.006 6 34  
0.032 9 32  

Total sequences with primary and secondary motif 

8319

Motif Database 

uniprobe mouse

Spacings of "UP00099 2 (Ascl2 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00099 2 (Ascl2 secondary) 
 E-value
TACGCCCCGCCACTCTG
CTATCCCCGCCCTATT
3.9e-21
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0003 0 52  
2.5e-05 1 55  
3.4e-17 2 81  
5.9e-24 3 93  
4.3e-15 4 77  
2.5e-05 5 55  
0.003 8 49  
0.049 12 45  
P-value Gap #  
1.6e-08 0 63  
2.9e-07 1 60  
1.2e-16 2 80  
6.1e-09 3 64  
8.1e-10 4 66  
0.025 5 46  
4.5e-06 9 57  
0.025 11 46  

Total sequences with primary and secondary motif 

13767

Motif Database 

uniprobe mouse

Secondary motifs with similar spacings 
Similar Secondary: UP00093 1 (Klf7 primary)
Same Strand
Opposite Strand
P-value Gap #  
0.011 0 44  
9.2e-16 1 74  
1.3e-22 2 86  
3.6e-11 3 65  
0.023 4 43  
0.0053 7 45  
4e-05 9 51  
0.0011 11 47  
0.045 12 42  
0.0053 25 45  
P-value Gap #  
0.0025 0 46  
1.2e-11 1 66  
2.7e-06 2 54  
0.00022 3 49  
0.0053 8 45  
0.0011 10 47  
0.023 12 43  

Total sequences with primary and secondary motif 

12325

Alignment by most significant spacings 

Best Similar
Secondary
CTATCCCCGCCCTATT
This Similar
Secondary
TCGACCCCGCCCCTAT
Similar Secondary: MA0039.2 (Klf4)
Same Strand
Opposite Strand
P-value Gap #  
0.042 0 43  
4.1e-11 1 66  
8.2e-22 2 86  
4.1e-11 3 66  
0.042 4 43  
0.0011 6 48  
0.0049 7 46  
0.00048 9 49  
0.021 11 44  
0.021 12 44  
P-value Gap #  
3.9e-05 0 52  
6e-08 1 59  
2.7e-06 2 55  
0.042 3 43  
0.021 5 44  
3.9e-05 6 52  
1.6e-05 8 53  
0.01 10 45  
0.00048 12 49  

Total sequences with primary and secondary motif 

12677

Alignment by most significant spacings 

Best Similar
Secondary
AATAGGGCGGGGATAG
This Similar
Secondary
   TGGGTGGGGC
Similar Secondary: MA0599.1 (KLF5)
Same Strand
Opposite Strand
P-value Gap #  
2.4e-14 1 72  
8.4e-20 2 82  
8e-12 3 67  
0.0078 4 45  
0.00078 6 48  
0.0017 7 47  
6.5e-05 8 51  
0.0078 9 45  
0.032 11 43  
0.032 12 43  
0.032 18 43  
0.032 46 43  
P-value Gap #  
1.8e-09 0 62  
8.2e-13 1 69  
3.9e-08 2 59  
1.1e-05 3 53  
0.0017 6 47  
0.00078 8 48  

Total sequences with primary and secondary motif 

12529

Alignment by most significant spacings 

Best Similar
Secondary
CTATCCCCGCCCTATT
This Similar
Secondary
   GCCCCGCCCC
Similar Secondary: CYCCDCCC (DREME)
Same Strand
Opposite Strand
P-value Gap #  
5.9e-13 2 54  
7.3e-18 3 62  
1.5e-13 4 55  
0.01 5 33  
3.5e-05 7 39  
0.01 8 33  
0.00026 9 37  
0.024 10 32  
P-value Gap #  
0.0017 1 35  
4.8e-08 2 45  
0.01 3 33  
4.7e-07 4 43  

Total sequences with primary and secondary motif 

8232

Alignment by most significant spacings 

Best Similar
Secondary
CTATCCCCGCCCTATT
This Similar
Secondary
    CCCCTCCC

Spacings of "UP00033 2 (Zfp410 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00033 2 (Zfp410 secondary) 
 E-value
TACGCCCCGCCACTCTG
TCACCCCGCCCCTAATT
5.7e-21
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
4.2e-08 0 67  
8.7e-24 1 99  
2.8e-16 2 85  
2e-12 3 77  
1.3e-10 4 73  
0.0019 5 54  
0.0039 6 53  
1.1e-07 7 66  
0.0039 10 53  
0.00093 11 55  
0.029 16 50  
0.00044 18 56  
P-value Gap #  
7e-13 0 78  
0.00021 3 57  
3.6e-06 4 62  
6.4e-07 6 64  
0.015 9 51  

Total sequences with primary and secondary motif 

15604

Motif Database 

uniprobe mouse

Spacings of "MA0079.3 (SP1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0079.3 (SP1) 
 E-value
TACGCCCCGCCACTCTG
GCCCCGCCCCC
1.4e-19
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
2.2e-22 0 89  
4.3e-20 1 85  
8.7e-17 2 79  
7.2e-10 3 65  
1.1e-05 4 55  
0.0015 5 49  
2.8e-07 6 59  
P-value Gap #  
0.0066 0 47  
0.00031 1 51  
1.1e-07 2 60  
0.0031 3 48  
1.1e-12 4 71  
0.013 9 46  

Total sequences with primary and secondary motif 

13217

Motif Database 

JASPAR CORE 2014 vertebrates

Secondary motifs with similar spacings 
Similar Secondary: MA0516.1 (SP2)
Same Strand
Opposite Strand
P-value Gap #  
3.9e-20 0 87  
3.9e-20 1 87  
8.3e-15 2 77  
2.4e-12 3 72  
0.0041 4 49  
0.0041 5 49  
1.8e-07 6 61  
0.0041 7 49  
0.017 8 47  
0.017 12 47  
0.033 17 46  
P-value Gap #  
0.00093 0 51  
3.7e-05 1 55  
0.00019 2 53  
6.1e-11 3 69  
1.6e-05 6 56  
0.002 8 50  
0.033 11 46  
0.033 13 46  

Total sequences with primary and secondary motif 

13654

Alignment by most significant spacings 

Best Similar
Secondary
GCCCCGCCCCC
This Similar
Secondary
GCCCCGCCCCCTCCC

Spacings of "UP00043 2 (Bcl6b secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00043 2 (Bcl6b secondary) 
 E-value
TACGCCCCGCCACTCTG
ATCCCCGCCCCTAAAA
5e-15
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
7.7e-18 0 88  
5.5e-12 1 76  
4.1e-05 2 59  
0.00089 3 55  
0.0074 10 52  
0.0037 17 53  
0.028 24 50  
P-value Gap #  
2.5e-14 0 81  
0.015 2 51  
0.0037 3 53  
6.1e-09 4 69  
2.5e-07 6 65  
1.8e-05 9 60  

Total sequences with primary and secondary motif 

15478

Motif Database 

uniprobe mouse

Spacings of "UP00002 1 (Sp4 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00002 1 (Sp4 primary) 
 E-value
TACGCCCCGCCACTCTG
GGTCCCGCCCCCTTCTC
6.2e-15
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
2.5e-14 0 65  
9.5e-18 1 71  
2.5e-14 2 65  
0.0063 3 40  
0.00022 4 44  
7.2e-07 5 50  
0.0028 6 41  
0.029 9 38  
0.029 28 38  
P-value Gap #  
0.0012 2 42  
1.1e-08 3 54  
2.6e-07 4 51  
8.8e-05 5 45  
0.029 9 38  
0.00052 10 43  
0.0063 14 40  
0.014 15 39  

Total sequences with primary and secondary motif 

10502

Motif Database 

uniprobe mouse

Spacings of "1 (MEME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: 1 (MEME) 
 E-value
TACGCCCCGCCACTCTG
CCCGCGCCCCCTCCCGCCCCGCCTCCGCC
1.1e-14
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
3.8e-07 0 55  
0.0025 1 45  
1.6e-17 2 76  
1.6e-05 3 51  
0.0053 7 44  
0.046 10 41  
P-value Gap #  
0.023 0 42  
6.9e-09 1 59  
9.3e-05 2 49  
5.3e-08 3 57  
0.0025 4 45  
0.00022 6 48  
0.046 8 41  
0.0025 9 45  
0.046 27 41  

Total sequences with primary and secondary motif 

10399

Motif Database 

meme.xml

Spacings of "UP00007 1 (Egr1 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00007 1 (Egr1 primary) 
 E-value
TACGCCCCGCCACTCTG
TCCGCCCCCGCATT
1.5e-14
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
2.3e-17 0 67  
0.0045 1 38  
0.0045 2 38  
0.0019 3 39  
0.049 8 35  
P-value Gap #  
1.4e-15 0 64  
0.01 3 37  
0.049 4 35  
0.00013 5 42  
0.00033 6 41  
0.00013 11 42  

Total sequences with primary and secondary motif 

9541

Motif Database 

uniprobe mouse

Spacings of "MA0162.2 (EGR1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0162.2 (EGR1) 
 E-value
TACGCCCCGCCACTCTG
CCCCCGCCCCCGCC
3.7e-12
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
5.7e-15 0 72  
0.00081 1 47  
1.1e-05 4 52  
0.0039 5 45  
0.017 6 43  
0.0039 14 45  
P-value Gap #  
0.00081 1 47  
0.0039 2 45  
0.0083 3 44  
1.9e-10 4 63  
0.017 9 43  
0.00036 10 48  
0.035 12 42  
0.0039 13 45  

Total sequences with primary and secondary motif 

12004

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "2 (MEME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: 2 (MEME) 
 E-value
TACGCCCCGCCACTCTG
GTGTGTGTGTG
4.4e-12
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
6.7e-15 0 42  

Total sequences with primary and secondary motif 

4402

Motif Database 

meme.xml

Spacings of "MA0528.1 (ZNF263)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0528.1 (ZNF263) 
 E-value
TACGCCCCGCCACTCTG
GGAGGAGGAGGGGGAGGAGGA
4.8e-11
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
7.1e-12 0 68  
0.00062 1 49  
7.4e-14 2 72  
1.2e-08 3 61  
0.0061 5 46  
P-value Gap #  
2.3e-07 0 58  
0.00062 1 49  
1.2e-08 2 61  
0.013 129 45  

Total sequences with primary and secondary motif 

11830

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0130.1 (ZNF354C)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0130.1 (ZNF354C) 
 E-value
TACGCCCCGCCACTCTG
ATCCAC
5e-11
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
3.2e-05 0 61  
0.039 4 51  
0.039 135 51  
P-value Gap #  
7.7e-14 1 82  
0.00033 2 58  
0.021 4 52  

Total sequences with primary and secondary motif 

16346

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0056.1 (MZF1 1-4)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0056.1 (MZF1 1-4) 
 E-value
TACGCCCCGCCACTCTG
TGGGGA
2.4e-10
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0024 0 50  
2.9e-11 1 70  
3.6e-13 2 74  
1.8e-09 3 66  
1.5e-06 4 59  
4.7e-05 5 55  
4.7e-05 6 55  
0.039 8 46  
P-value Gap #  
4.7e-05 0 55  
4.7e-05 1 55  
0.00053 2 52  
0.01 3 48  
0.005 5 49  

Total sequences with primary and secondary motif 

14322

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0057.1 (MZF1 5-13)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0057.1 (MZF1 5-13) 
 E-value
TACGCCCCGCCACTCTG
GGAGGGGGAA
4.3e-08
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
6.5e-11 0 67  
0.045 1 44  
0.00011 3 52  
0.0012 5 49  
0.0012 6 49  
0.023 9 45  
P-value Gap #  
0.0056 0 47  

Total sequences with primary and secondary motif 

13309

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "CYGCCDCC (DREME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: CYGCCDCC (DREME) 
 E-value
TACGCCCCGCCACTCTG
CTGCCGCC
4.7e-08
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.023 7 25  
P-value Gap #  
7.1e-11 0 41  
0.00036 12 29  

Total sequences with primary and secondary motif 

5670

Motif Database 

dreme.xml

Spacings of "UP00007 2 (Egr1 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00007 2 (Egr1 secondary) 
 E-value
TACGCCCCGCCACTCTG
TGCGGAGTGGGACTGG
1.6e-07
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
1.1e-05 0 54  
1.1e-07 1 59  
1.9e-06 2 56  
2.4e-10 3 65  
0.015 4 45  
7e-10 5 64  
0.0035 6 47  
P-value Gap #  
0.0016 0 48  
0.0016 4 48  

Total sequences with primary and secondary motif 

12973

Motif Database 

uniprobe mouse

Spacings of "MA0493.1 (Klf1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0493.1 (Klf1) 
 E-value
TACGCCCCGCCACTCTG
GGCCACACCCA
2e-07
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
6.9e-07 1 48  
3e-10 2 55  
5.3e-06 3 46  
0.0033 9 39  
0.036 18 36  
P-value Gap #  
0.0033 0 39  
9.3e-09 1 52  
5.3e-06 2 46  
0.00058 5 41  
0.017 8 37  
0.036 10 36  
0.036 12 36  

Total sequences with primary and secondary motif 

9831

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0472.1 (EGR2)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0472.1 (EGR2) 
 E-value
TACGCCCCGCCACTCTG
CCCCCGCCCACGCAC
2.5e-06
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
3.8e-09 0 54  
0.0014 1 41  
0.0075 4 39  
0.0014 5 41  
1.6e-05 15 46  
P-value Gap #  
1.6e-05 0 46  
0.0001 1 44  
1e-07 3 51  
0.0075 4 39  
0.00061 11 42  

Total sequences with primary and secondary motif 

10206

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "UP00042 2 (Gm397 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00042 2 (Gm397 secondary) 
 E-value
TACGCCCCGCCACTCTG
AGCGGCACACACGCAA
6.4e-06
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
9.8e-09 1 40  

Total sequences with primary and secondary motif 

6200

Motif Database 

uniprobe mouse

Spacings of "UP00096 2 (Sox13 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00096 2 (Sox13 secondary) 
 E-value
TACGCCCCGCCACTCTG
GTATTGGGTGGGTATTT
1.6e-05
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
2.4e-08 1 65  
1.6e-07 2 63  
0.013 3 49  
1.3e-05 4 58  
0.025 10 48  
P-value Gap #  
3.1e-05 0 57  
0.0065 2 50  
5.7e-06 3 59  

Total sequences with primary and secondary motif 

14395

Motif Database 

uniprobe mouse

Spacings of "MA0073.1 (RREB1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0073.1 (RREB1) 
 E-value
TACGCCCCGCCACTCTG
CCCCAAACCACCCCCCCCCC
6.9e-05
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0014 0 17  
P-value Gap #  
1.1e-07 0 23  
0.00033 1 18  
0.00033 2 18  

Total sequences with primary and secondary motif 

2259

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "UP00077 2 (Srf secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00077 2 (Srf secondary) 
 E-value
TACGCCCCGCCACTCTG
GTTAAAAAAAAAAATTT
0.00044
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0088 141 30  
P-value Gap #  
0.00048 141 33  
P-value Gap #  
6.7e-07 141 39  
P-value Gap #  
0.0035 139 31  
6.7e-07 141 39  

Total sequences with primary and secondary motif 

7036

Motif Database 

uniprobe mouse

Spacings of "UP00057 1 (Zic2 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00057 1 (Zic2 primary) 
 E-value
TACGCCCCGCCACTCTG
CCCCCCCGGGGGGGT
0.00072
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
1.1e-06 0 41  
0.0015 1 34  

Total sequences with primary and secondary motif 

7576

Motif Database 

uniprobe mouse

Spacings of "UP00024 1 (Glis2 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00024 1 (Glis2 primary) 
 E-value
TACGCCCCGCCACTCTG
TATCGACCCCCCACAG
0.00099
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
1.5e-06 0 41  
0.00076 1 35  
0.028 5 31  
P-value Gap #  
3.8e-05 0 38  
0.0019 1 34  
0.012 2 32  
0.028 4 31  

Total sequences with primary and secondary motif 

7769

Motif Database 

uniprobe mouse

Spacings of "UP00037 1 (Zfp105 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00037 1 (Zfp105 primary) 
 E-value
TACGCCCCGCCACTCTG
AACAAACAACAAGAG
0.008
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.012 138 31  
P-value Gap #  
0.012 124 31  
P-value Gap #  
0.029 138 30  
0.002 139 33  
1.2e-05 140 38  

Total sequences with primary and secondary motif 

7476

Motif Database 

uniprobe mouse

Spacings of "UP00006 1 (Zic3 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00006 1 (Zic3 primary) 
 E-value
TACGCCCCGCCACTCTG
CCCCCCCGGGGGGGT
0.014
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
2.1e-05 0 43  
P-value Gap #  
5.6e-05 0 42  
P-value Gap #  
0.00037 0 40  

Total sequences with primary and secondary motif 

9165

Motif Database 

uniprobe mouse

Spacings of "MA0597.1 (THAP1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0597.1 (THAP1) 
 E-value
TACGCCCCGCCACTCTG
CTGCCCGCA
0.055
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
8.4e-05 1 62  
P-value Gap #  
0.04 0 53  
0.04 33 53  

Total sequences with primary and secondary motif 

16864

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "CCCGCCC (DREME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: CCCGCCC (DREME) 
 E-value
TACGCCCCGCCACTCTG
CCCGCCC
0.064
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00035 2 24  
9.7e-05 4 25  
P-value Gap #  
0.00035 3 24  
0.035 4 20  
9.7e-05 10 25  
0.012 12 21  

Total sequences with primary and secondary motif 

4142

Motif Database 

dreme.xml

Spacings of "UP00085 1 (Sfpi1 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00085 1 (Sfpi1 primary) 
 E-value
TACGCCCCGCCACTCTG
TTAAGAGGAAGTTA
0.075
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00011 0 48  

Total sequences with primary and secondary motif 

11677

Motif Database 

uniprobe mouse

Spacings of "UP00070 1 (Gcm1 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00070 1 (Gcm1 primary) 
 E-value
TACGCCCCGCCACTCTG
TCGTACCCGCATCATT
0.077
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00012 0 30  
0.023 1 25  
P-value Gap #  
0.0031 16 27  

Total sequences with primary and secondary motif 

5674

Motif Database 

uniprobe mouse

Spacings of "MA0504.1 (NR2C2)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0504.1 (NR2C2) 
 E-value
TACGCCCCGCCACTCTG
AGGGGTCAGAGGTCA
0.12
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00019 2 32  

Total sequences with primary and secondary motif 

6192

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "UP00102 1 (Zic1 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00102 1 (Zic1 primary) 
 E-value
TACGCCCCGCCACTCTG
CACCCCCGGGGGGG
0.17
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0017 0 37  
P-value Gap #  
0.00027 0 39  

Total sequences with primary and secondary motif 

8704

Motif Database 

uniprobe mouse

Spacings of "UP00028 1 (Tcfap2e primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00028 1 (Tcfap2e primary) 
 E-value
TACGCCCCGCCACTCTG
ATTGCCTGAGGCGAT
0.21
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0044 0 38  
0.00032 1 41  

Total sequences with primary and secondary motif 

9531

Motif Database 

uniprobe mouse

Spacings of "MA0471.1 (E2F6)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0471.1 (E2F6) 
 E-value
TACGCCCCGCCACTCTG
GGGCGGGAAGG
0.29
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0075 4 32  
P-value Gap #  
0.00044 1 35  

Total sequences with primary and secondary motif 

7634

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0009.1 (T)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0009.1 (T) 
 E-value
TACGCCCCGCCACTCTG
CTAGGTGTGAA
0.31
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00047 66 9  

Total sequences with primary and secondary motif 

543

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0475.1 (FLI1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0475.1 (FLI1) 
 E-value
TACGCCCCGCCACTCTG
ACAGGAAGTGG
0.32
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00048 5 42  

Total sequences with primary and secondary motif 

10045

Motif Database 

JASPAR CORE 2014 vertebrates

Secondary motifs with similar spacings 
Similar Secondary: MA0098.2 (Ets1)
Same Strand
Opposite Strand
P-value Gap #  
0.0022 5 40  

Total sequences with primary and secondary motif 

9961

Alignment by most significant spacings 

Best Similar
Secondary
 CCACTTCCTGT
This Similar
Secondary
CCCACTTCCTGTCTC

Spacings of "UP00002 2 (Sp4 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00002 2 (Sp4 secondary) 
 E-value
TACGCCCCGCCACTCTG
CAAAGGCGTGGCCAG
0.5
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.00077 2 41  
P-value Gap #  
0.00077 1 41  
0.044 2 36  
0.0042 9 39  
0.021 10 37  
0.0042 22 39  

Total sequences with primary and secondary motif 

9942

Motif Database 

uniprobe mouse

Spacings of "GGGMGGGA (DREME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: GGGMGGGA (DREME) 
 E-value
TACGCCCCGCCACTCTG
GGGAGGGA
0.76
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0012 5 17  

Total sequences with primary and secondary motif 

2398

Motif Database 

dreme.xml

Spacings of "UP00391 1 (Hoxa3 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00391 1 (Hoxa3 primary) 
 E-value
TACGCCCCGCCACTCTG
TGGAGGTAATTAAC
0.84
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0013 79 16  

Total sequences with primary and secondary motif 

2113

Motif Database 

uniprobe mouse

Spacings of "CHGGRA (DREME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: CHGGRA (DREME) 
 E-value
TACGCCCCGCCACTCTG
CTGGGA
1.4
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0021 2 60  

Total sequences with primary and secondary motif 

18226

Motif Database 

dreme.xml

Spacings of "UP00408 2 (Gabpa secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00408 2 (Gabpa secondary) 
 E-value
TACGCCCCGCCACTCTG
CCGTCTTCCCCCTCAC
1.5
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0023 1 38  
P-value Gap #  
0.012 37 36  

Total sequences with primary and secondary motif 

9249

Motif Database 

uniprobe mouse

Spacings of "MA0111.1 (Spz1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0111.1 (Spz1) 
 E-value
TACGCCCCGCCACTCTG
AGGGTAACAGC
1.5
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.014 2 32  
0.032 3 31  
P-value Gap #  
0.0023 5 34  

Total sequences with primary and secondary motif 

7831

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "UP00108 1 (Alx3 3418.2)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00108 1 (Alx3 3418.2) 
 E-value
TACGCCCCGCCACTCTG
TAAACTAATTAGCTGAG
1.8
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0027 135 12  

Total sequences with primary and secondary motif 

1250

Motif Database 

uniprobe mouse

Secondary motifs with similar spacings 
Similar Secondary: UP00247 1 (Pax4 3989.2)
Same Strand
Opposite Strand
P-value Gap #  
0.0067 135 12  
P-value Gap #  
0.0067 76 12  

Total sequences with primary and secondary motif 

1361

Alignment by most significant spacings 

Best Similar
Secondary
TAAACTAATTAGCTGAG
This Similar
Secondary
TGAACTAATTAGCCCAC
Similar Secondary: UP00188 1 (Lmx1a 2238.2)
Same Strand
Opposite Strand
P-value Gap #  
0.0093 135 15  

Total sequences with primary and secondary motif 

2152

Alignment by most significant spacings 

Best Similar
Secondary
TAAACTAATTAGCTGAG
This Similar
Secondary
CGAATTAATTAAAAACC

Spacings of "UP00079 2 (Esrra secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00079 2 (Esrra secondary) 
 E-value
TACGCCCCGCCACTCTG
GGCGAGGGGTCAAGGGC
2.3
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0035 2 31  

Total sequences with primary and secondary motif 

7086

Motif Database 

uniprobe mouse

Spacings of "UP00004 2 (Sox14 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00004 2 (Sox14 secondary) 
 E-value
TACGCCCCGCCACTCTG
CTCACACAATGGCGC
2.4
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0036 139 34  

Total sequences with primary and secondary motif 

8117

Motif Database 

uniprobe mouse

Spacings of "UP00087 1 (Tcfap2c primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00087 1 (Tcfap2c primary) 
 E-value
TACGCCCCGCCACTCTG
ATTGCCTGAGGCGAA
2.4
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0037 0 37  

Total sequences with primary and secondary motif 

8898

Motif Database 

uniprobe mouse

Spacings of "UP00069 1 (Sox1 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00069 1 (Sox1 primary) 
 E-value
TACGCCCCGCCACTCTG
AATCAATTCAATAATT
2.6
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0039 115 25  

Total sequences with primary and secondary motif 

5084

Motif Database 

uniprobe mouse

Spacings of "UP00078 1 (Arid3a primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00078 1 (Arid3a primary) 
 E-value
TACGCCCCGCCACTCTG
GGGTTTAATTAAAATTC
2.6
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.004 136 23  

Total sequences with primary and secondary motif 

4383

Motif Database 

uniprobe mouse

Spacings of "CCBGCCTC (DREME)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: CCBGCCTC (DREME) 
 E-value
TACGCCCCGCCACTCTG
CCTGCCTC
2.7
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0042 5 18  

Total sequences with primary and secondary motif 

2932

Motif Database 

dreme.xml

Spacings of "UP00407 2 (Elf3 secondary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00407 2 (Elf3 secondary) 
 E-value
TACGCCCCGCCACTCTG
GTTCAAAAAAAAAATTC
2.8
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.011 121 28  
0.0043 135 29  
P-value Gap #  
0.0043 135 29  

Total sequences with primary and secondary motif 

6163

Motif Database 

uniprobe mouse

Spacings of "UP00071 1 (Sox21 primary)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00071 1 (Sox21 primary) 
 E-value
TACGCCCCGCCACTCTG
TTTAATTATAATTAAG
3.9
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.006 105 18  

Total sequences with primary and secondary motif 

2994

Motif Database 

uniprobe mouse

Spacings of "MA0068.1 (Pax4)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0068.1 (Pax4) 
 E-value
TACGCCCCGCCACTCTG
GAAAAATTTCCCATACTCCACTCCCCCCCC
4
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0061 0 30  
0.0061 1 30  
0.037 3 28  

Total sequences with primary and secondary motif 

5931

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MA0003.2 (TFAP2A)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0003.2 (TFAP2A) 
 E-value
TACGCCCCGCCACTCTG
CATTGCCTCAGGGCA
4.3
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0066 0 39  

Total sequences with primary and secondary motif 

10082

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "UP00156 1 (Msx2 3449.1)" relative to "UP00000 2 (Smad3 secondary)"

 Previous Next Top
Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00156 1 (Msx2 3449.1) 
 E-value
TACGCCCCGCCACTCTG
GAAGACCAATTAGCGCT
4.5
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0069 28 13  

Total sequences with primary and secondary motif 

1609

Motif Database 

uniprobe mouse

Spacings of "UP00024 2 (Glis2 secondary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00024 2 (Glis2 secondary) 
 E-value
TACGCCCCGCCACTCTG
AATATTAATAAAGA
4.9
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0075 137 23  

Total sequences with primary and secondary motif 

4566

Motif Database 

uniprobe mouse

Spacings of "UP00003 1 (E2F3 primary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00003 1 (E2F3 primary) 
 E-value
TACGCCCCGCCACTCTG
ATAAGGGCGCGCGAT
5.7
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0086 16 25  

Total sequences with primary and secondary motif 

5195

Motif Database 

uniprobe mouse

Spacings of "UP00253 1 (Rax 3443.1)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00253 1 (Rax 3443.1) 
 E-value
TACGCCCCGCCACTCTG
TGCACTAATTAGCGCAC
5.8
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.0088 76 12  

Total sequences with primary and secondary motif 

1400

Motif Database 

uniprobe mouse

Spacings of "MA0060.2 (NFYA)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0060.2 (NFYA) 
 E-value
TACGCCCCGCCACTCTG
AGAGTGCTGATTGGTCCA
7.1
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.039 26 15  
P-value Gap #  
0.011 11 16  

Total sequences with primary and secondary motif 

2400

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "MCGTGR (DREME)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MCGTGR (DREME) 
 E-value
TACGCCCCGCCACTCTG
CCGTGG
7.3
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.011 6 30  

Total sequences with primary and secondary motif 

7271

Motif Database 

dreme.xml

Spacings of "MA0154.2 (EBF1)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: MA0154.2 (EBF1) 
 E-value
TACGCCCCGCCACTCTG
GTCCCCAGGGA
7.4
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.011 9 30  

Total sequences with primary and secondary motif 

7086

Motif Database 

JASPAR CORE 2014 vertebrates

Spacings of "UP00059 1 (Arid5a primary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00059 1 (Arid5a primary) 
 E-value
TACGCCCCGCCACTCTG
CTAATATTGCTAAA
7.9
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.012 139 17  

Total sequences with primary and secondary motif 

2826

Motif Database 

uniprobe mouse

Spacings of "UP00058 2 (Tcf3 secondary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00058 2 (Tcf3 secondary) 
 E-value
TACGCCCCGCCACTCTG
AGCCGAAAAAAAAAT
8.1
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.012 140 15  

Total sequences with primary and secondary motif 

2281

Motif Database 

uniprobe mouse

Spacings of "UP00034 1 (Sox7 primary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00034 1 (Sox7 primary) 
 E-value
TACGCCCCGCCACTCTG
AATAAAGAACAATAGAATTTCA
9
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.014 111 22  

Total sequences with primary and secondary motif 

4278

Motif Database 

uniprobe mouse

Spacings of "UP00001 1 (E2F2 primary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00001 1 (E2F2 primary) 
 E-value
TACGCCCCGCCACTCTG
ATAAAGGCGCGCGAT
9.1
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.014 1 30  

Total sequences with primary and secondary motif 

7214

Motif Database 

uniprobe mouse

Spacings of "UP00082 2 (Zfp187 secondary)" relative to "UP00000 2 (Smad3 secondary)"

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Primary: UP00000 2 (Smad3 secondary) 
 Secondary: UP00082 2 (Zfp187 secondary) 
 E-value
TACGCCCCGCCACTCTG
GAGCCCTTGTCCCTTG
9.1
Motif Spacing Histogram 
   Significant Motif Spacings (p<0.05) 
  
Upstream Downstream   Upstream Downstream Other Details
Same Strand
Opposite Strand
P-value Gap #  
0.014 0 39  

Total sequences with primary and secondary motif 

10365

Motif Database 

uniprobe mouse
Previous Top
SpaMo version
4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000)
Reference
Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey, "Inferring transcription factor complexes from ChIP-seq data", Nucleic Acids Research, 39(15):e98, 2011.
Command line summary

Result calculation took 14 minutes 17 seconds
Note that the random number generator was initilized with a seed of 1 so you need "-numgen 1" in the list of arguments to replicate the experiment.
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