The name of the primary motif.

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The logo of the primary motif.

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

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

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

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The name of the sequence database.

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The last modified date of the sequence database.

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The number of sequences in the sequence database.

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

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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.

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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.

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

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

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The date that the motif database was last modified.

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

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

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

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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.

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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.

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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.

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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.

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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.

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

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The motif database which this secondary motif came from.

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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.

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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.

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# SpaMo

## Spaced Motif Analysis Tool

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
--- | --- | --- | ---
1 (MEME) | C A G C C A C A C C C A | 4 | MA0309.1 (GZF3), 3 (MEME), 2 (MEME), MA0207.1 (achi)

## Sequence Database | Previous Next Top

Name | Last Modified | Loaded | Too Short | No Primary | Too Similar | Used
--- | --- | --- | --- | --- | --- | ---
sample-dna-Klf1 | Tue Oct 7 14:14:10 2014 | 904 | 0 | 439 | 50 | 415

## Secondary Databases | Previous Next Top

Name | Last Modified | Number of Motifs | Motifs Significant | Motifs Redundant
--- | --- | --- | --- | ---
meme.xml | Tue Oct 7 17:17:30 2014 | 2 | 2 | 0
dreme.xml | Tue Oct 7 17:17:48 2014 | 3 | 0 | 1
JASPAR CORE 2009 | Wed Dec 5 17:04:00 2012 | 476 | 2 | 5

## Spacings of "MA0309.1 (GZF3)" relative to "1 (MEME)" | Previous Next Top

Primary: 1 (MEME) | Secondary: MA0309.1 (GZF3) | E-value
--- | --- | ---
C A G C C A C A C C C A | T G A T A A G A | 0.0064

Motif Spacing Histogram |  | Significant Motif Spacings (p<0.05) |
--- | --- | --- | ---
Upstream | Downstream |  | Upstream | Downstream | Other Details
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.004 | 15 | 6 |
1.3e-05 | 24 | 8 |
| #### Total sequences with primary and secondary motif 256 #### Motif Database JASPAR CORE 2009 #### Secondary motifs with similar spacings MA0289.1 (DAL80)MA0300.1 (GAT1)

Similar Secondary: MA0289.1 (DAL80)
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.026 | 1 | 5 |
P-value | Gap | # |
--- | --- | --- | ---
0.026 | 15 | 5 |
8.6e-05 | 24 | 7 |
| #### Total sequences with primary and secondary motif 219 #### Alignment by most significant spacings
Best Similar Secondary | T G A T A A G A
This Similar Secondary | C G A T A A G

Similar Secondary: MA0300.1 (GAT1)
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.033 | 15 | 5 |
0.0022 | 24 | 6 |
| #### Total sequences with primary and secondary motif 230 #### Alignment by most significant spacings
Best Similar Secondary | T G A T A A G A
This Similar Secondary | C C G A T A A G

## Spacings of "3 (MEME)" relative to "1 (MEME)" | Previous Next Top

Primary: 1 (MEME) | Secondary: 3 (MEME) | E-value
--- | --- | ---
C A G C C A C A C C C A | C T G C A T C T C T T C A A G A C A C A C C T A A C T G C | 0.0081

Motif Spacing Histogram |  | Significant Motif Spacings (p<0.05) |
--- | --- | --- | ---
Upstream | Downstream |  | Upstream | Downstream | Other Details
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
1.7e-05 | 2 | 3 |
| #### Total sequences with primary and secondary motif 4 #### Motif Database meme.xml

## Spacings of "2 (MEME)" relative to "1 (MEME)" | Previous Next Top

Primary: 1 (MEME) | Secondary: 2 (MEME) | E-value
--- | --- | ---
C A G C C A C A C C C A | C A G A T A A G | 0.13

Motif Spacing Histogram |  | Significant Motif Spacings (p<0.05) |
--- | --- | --- | ---
Upstream | Downstream |  | Upstream | Downstream | Other Details
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.00027 | 15 | 7 |
0.0043 | 24 | 6 |
| #### Total sequences with primary and secondary motif 259 #### Motif Database meme.xml #### Secondary motifs with similar spacings TTATCW (DREME)MA0035.2 (Gata1)MA0140.1 (Tal1::Gata1)MA0307.1 (GLN3)

Similar Secondary: TTATCW (DREME)
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.00028 | 15 | 7 |
0.0044 | 24 | 6 |
| #### Total sequences with primary and secondary motif 262 #### Alignment by most significant spacings
Best Similar Secondary | C T T A T C T G
This Similar Secondary | T T A T C T

Similar Secondary: MA0035.2 (Gata1)
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.001 | 15 | 7 |
0.013 | 24 | 6 |
| #### Total sequences with primary and secondary motif 316 #### Alignment by most significant spacings
Best Similar Secondary | C A G A T A A G
This Similar Secondary | A C A G A T A A G A A

Similar Secondary: MA0140.1 (Tal1::Gata1)
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.013 | 3 | 6 |
0.013 | 12 | 6 |
P-value | Gap | # |
--- | --- | --- | ---
0.001 | 5 | 7 |
| #### Total sequences with primary and secondary motif 298 #### Alignment by most significant spacings
Best Similar Secondary | C A G A T A A G
This Similar Secondary | C T G G T G G G G A C A G A T A A G

Similar Secondary: MA0307.1 (GLN3)
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.0018 | 16 | 7 |
0.0018 | 25 | 7 |
| #### Total sequences with primary and secondary motif 350 #### Alignment by most significant spacings
Best Similar Secondary | C A G A T A A G
This Similar Secondary | G A T A A

## Spacings of "MA0207.1 (achi)" relative to "1 (MEME)" | Previous Next Top

Primary: 1 (MEME) | Secondary: MA0207.1 (achi) | E-value
--- | --- | ---
C A G C C A C A C C C A | T G A C A G | 5.9

Motif Spacing Histogram |  | Significant Motif Spacings (p<0.05) |
--- | --- | --- | ---
Upstream | Downstream |  | Upstream | Downstream | Other Details
| Same Strand Opposite Strand |
P-value | Gap | # |
--- | --- | --- | ---
0.012 | 12 | 5 |
| #### Total sequences with primary and secondary motif 187 #### Motif Database JASPAR CORE 2009

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

spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_1 -bgfile memechip_example_output_files/background -primary 1 memechip_example_output_files/sample-dna-Klf1.fa memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Result calculation took 14 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.
show model parameters...

##### Model parameters

seed = 1 margin = 150 bin_size = 1 bin_pvalue_calc_range = 150 bin_pvalue_cutoff = 0.05 motif_evalue_cutoff = 10 seq_max_shared_fract = 0.5 seq_min_hit_score = 7 redundant_overlap = 2 redundant_joint = 0.5 motif_pseudocount = 0.1 motif_trim = 0.25 bin_max = 8 host = IMB12-010665 when = Tue Oct 7 17:18:24 2014
hide model parameters...