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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 TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

Query Motifs | Target Databases | Matches | Program information | Explanation

## Query Motifs

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#### Name

#### Preview

#### Matches

#### List

1 | AGCCACACCCA | 1 | MA0039.2 (Klf4)
2 | AGATAAGG | 3 | MA0035.2 (Gata1), MA0140.1 (Tal1::Gata1), MA0309.1 (GZF3)
3 | CCATCCCTCTCCCTC | 0 |

## Target Databases

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#### Database

#### Number of Motifs

#### Motifs Matched

JASPAR_CORE_2009.meme | 476 | 4

## Matches to Query: 1

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#### Summary

#### Alignment

Name | MA0039.2
Alt. Name | Klf4
Database | JASPAR_CORE_2009.meme
p-value | 1.51819e-08
E-value | 7.22658e-06
q-value | 1.4358e-05
Overlap | 10
Offset | -1
Orientation | Reverse Complement

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## Matches to Query: 2

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#### Summary

#### Alignment

Name | MA0035.2
Alt. Name | Gata1
Database | JASPAR_CORE_2009.meme
p-value | 3.46735e-08
E-value | 1.65046e-05
q-value | 3.28615e-05
Overlap | 8
Offset | 2
Orientation | Normal

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#### Summary

#### Alignment

Name | MA0140.1
Alt. Name | Tal1::Gata1
Database | JASPAR_CORE_2009.meme
p-value | 7.35149e-05
E-value | 0.0349931
q-value | 0.0347993
Overlap | 7
Offset | 11
Orientation | Normal

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#### Summary

#### Alignment

Name | MA0309.1
Alt. Name | GZF3
Database | JASPAR_CORE_2009.meme
p-value | 0.000110155
E-value | 0.0524336
q-value | 0.0347993
Overlap | 8
Offset | 0
Orientation | Normal

Create custom LOGO ↧ | [Previous Match] [Query Top]

## Matches to Query: 3

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##### TOMTOM version

4.8.0 (Release date: Tue Jan 17 11:51:47 EST 2012)

##### Reference

Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

##### Command line summary

tomtom -verbosity 1 -oc memechip_out/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 0.1 -no-ssc memechip_out/meme_out/meme.txt JASPAR_CORE_2009.meme
Background letter frequencies (from first motif database):
A: 0.250 C: 0.250 G: 0.250 T: 0.250
Result calculation took 8.412 seconds
show model parameters...

##### Model parameters

distance_measure = value: "pearson" threshold = type: "evalue" background = from: "first_target", A: "0.25", C: "0.25", G: "0.25", T: "0.25" host = tlb-takumi-lt.imb.uq.edu.au when = Tue Jan 17 12:32:31 2012
hide model parameters...

## Explanation of TOMTOM Results

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#### The TOMTOM results consist of

- The query motifs with links to further information on matches. [View]
- The target databases with information on the number of matches. [View]
- The matches between query motifs and target motifs. [View]
  - The summary of match information.
  - An alignment of the two motifs.
- The program details including:
  1. The version of TOMTOM and the date it was released. [View]
  2. The reference to cite if you use TOMTOM in your research. [View]
  3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
- This explanation of how to interpret TOMTOM results.

#### Inputs

The important inputs to TOMTOM.

##### Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name
  The motif name.
Alt. Name
  The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website
  A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview
  The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches
  The number of significant matches.
List
  Links to the first 20 matches

##### Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database
  The database name.
Number of Motifs
  The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched
  The number of motifs that had a match with at least one of the query motifs.

#### Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

##### Summary Table

The summary gives the important statistics about the motif match.

Name
  The name of the matched motif.
Alt. Name
  The alternative name of the matched motif.
p-value
  The probability that the match occurred by random chance according to the null model.
E-value
  The expected number of false positives in the matches up to this point.
q-value
  The minimum False Discovery Rate required to include the match.
Overlap
  The number of letters that overlaped in the optimal alignment.
Offset
  The offset of the query motif to the matched motif in the optimal alignment.
Orientation
  The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.

##### Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

##### Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type
  Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars
  Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC
  Toggle adding pseudocounts for Small Sample Correction.
Flip
  Toggle a full reverse complement of the alignment.
Width
  Specify the width of the generated motif.
Height
  Specify the height of the generated motif.