TOMTOM

Name	Preview	Matches	List
CSABTCCA	CCATTCCA	0
GKAATGSA	GGAATGGA	0
GARTWGAA	GAATTGAA	0
CRARTGGA	CGAATGGA	0
AAMGGAA	AAAGGAA	1	MA0370.1 (RME1)
GWTTMCA	GATTCCA	0
AATGCAM	AATGCAA	0
TCYCAGAA	TCTCAGAA	0
CTYTGTGA	CTTTGTGA	0
TAVACAGA	TAGACAGA	0
ATAGAR	ATAGAA	0
ATAKCTTC	ATATCTTC	0
GTTTCAAA	GTTTCAAA	0
ATWCTACA	ATTCTACA	0
TCCRGGAA	TCCAGGAA	3	MA0137.3 (STAT1), MA0518.1 (Stat4), MA0532.1 (STAT92E)
SGAATGTA	GGAATGTA	0
AHCGAAAC	AACGAAAC	0
ATAAAMAC	ATAAAAAC	0
TCCAAATR	TCCAAATA	0
AAMAGAGT	AAAAGAGT	0
GCAKGGAA	GCATGGAA	0
CCTCAAAK	CCTCAAAG	0
AATAKACT	AATAGACT	0
AATCMACC	AATCAACC	0
ACWCGAAT	ACTCGAAT	0
AGAAAGKT	AGAAAGGT	0
CCTKTCCA	CCTTTCCA	0
ACTCCAWT	ACTCCATT	0
GGAAGTTA	GGAAGTTA	0
CAKAGCA	CAGAGCA	0
TGTGTGCR	TGTGTGCG	0
CCATGRCA	CCATGACA	0
ACCAYAG	ACCATAG	0
AGTSGAAT	AGTGGAAT	0
CACGTGB	CACGTGG	16	MA0104.3 (Mycn), MA0059.1 (MYC::MAX), MA0561.1 (PIF4), MA0560.1 (PIF3), MA0562.1 (PIF5), MA0004.1 (Arnt), MA0128.1 (EmBP-1), MA0570.1 (ABF1), MA0552.1 (PIL5), MA0357.1 (PHO4)
AKAACTGC	ATAACTGC	0
ATTCCWGG	ATTCCTGG	0
KCATATAA	TCATATAA	0
CACTGCAC	CACTGCAC	0

Database	Number of Motifs	Motifs Matched
JASPAR_CORE_2014.meme	593	20

Summary

Alignment

Name	MA0370.1
Alt. Name	RME1
Database	JASPAR_CORE_2014.meme
p-value	4.38945e-05
E-value	0.0260294
q-value	0.0517028
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0137.3
Alt. Name	STAT1
Database	JASPAR_CORE_2014.meme
p-value	1.93251e-06
E-value	0.00114598
q-value	0.00227434
Overlap	8
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0518.1
Alt. Name	Stat4
Database	JASPAR_CORE_2014.meme
p-value	1.18936e-05
E-value	0.00705288
q-value	0.00699867
Overlap	8
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0532.1
Alt. Name	STAT92E
Database	JASPAR_CORE_2014.meme
p-value	4.89887e-05
E-value	0.0290503
q-value	0.019218
Overlap	8
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0104.3
Alt. Name	Mycn
Database	JASPAR_CORE_2014.meme
p-value	2.54413e-07
E-value	0.000150867
q-value	0.000287908
Overlap	7
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0059.1
Alt. Name	MYC::MAX
Database	JASPAR_CORE_2014.meme
p-value	6.36032e-07
E-value	0.000377167
q-value	0.000359885
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0561.1
Alt. Name	PIF4
Database	JASPAR_CORE_2014.meme
p-value	1.57345e-06
E-value	0.000933057
q-value	0.000514332
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0560.1
Alt. Name	PIF3
Database	JASPAR_CORE_2014.meme
p-value	1.81798e-06
E-value	0.00107806
q-value	0.000514332
Overlap	7
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0562.1
Alt. Name	PIF5
Database	JASPAR_CORE_2014.meme
p-value	6.90754e-06
E-value	0.00409617
q-value	0.00128599
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0004.1
Alt. Name	Arnt
Database	JASPAR_CORE_2014.meme
p-value	9.33677e-06
E-value	0.0055367
q-value	0.00128599
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0128.1
Alt. Name	EmBP-1
Database	JASPAR_CORE_2014.meme
p-value	9.89501e-06
E-value	0.00586774
q-value	0.00128599
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0570.1
Alt. Name	ABF1
Database	JASPAR_CORE_2014.meme
p-value	1.02274e-05
E-value	0.00606484
q-value	0.00128599
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0552.1
Alt. Name	PIL5
Database	JASPAR_CORE_2014.meme
p-value	1.45738e-05
E-value	0.00864226
q-value	0.00138873
Overlap	7
Offset	7
Orientation	Normal

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Summary

Alignment

Name	MA0357.1
Alt. Name	PHO4
Database	JASPAR_CORE_2014.meme
p-value	1.47259e-05
E-value	0.00873247
q-value	0.00138873
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0550.1
Alt. Name	BZR1
Database	JASPAR_CORE_2014.meme
p-value	2.07031e-05
E-value	0.012277
q-value	0.00167349
Overlap	7
Offset	4
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0568.1
Alt. Name	MYC3
Database	JASPAR_CORE_2014.meme
p-value	3.50447e-05
E-value	0.0207815
q-value	0.00247866
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0549.1
Alt. Name	BES1
Database	JASPAR_CORE_2014.meme
p-value	5.18937e-05
E-value	0.030773
q-value	0.00316285
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0551.1
Alt. Name	HY5
Database	JASPAR_CORE_2014.meme
p-value	5.50265e-05
E-value	0.0326307
q-value	0.00316285
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0569.1
Alt. Name	MYC4
Database	JASPAR_CORE_2014.meme
p-value	5.58977e-05
E-value	0.0331473
q-value	0.00316285
Overlap	7
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0093.2
Alt. Name	USF1
Database	JASPAR_CORE_2014.meme
p-value	6.07167e-05
E-value	0.036005
q-value	0.00327193
Overlap	7
Offset	3
Orientation	Reverse Complement

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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.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: CSABTCCA

Matches to Query: GKAATGSA

Matches to Query: GARTWGAA

Matches to Query: CRARTGGA

Matches to Query: AAMGGAA

Summary

Alignment

Matches to Query: GWTTMCA

Matches to Query: AATGCAM

Matches to Query: TCYCAGAA

Matches to Query: CTYTGTGA

Matches to Query: TAVACAGA

Matches to Query: ATAGAR

Matches to Query: ATAKCTTC

Matches to Query: GTTTCAAA

Matches to Query: ATWCTACA

Matches to Query: TCCRGGAA

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: SGAATGTA

Matches to Query: AHCGAAAC

Matches to Query: ATAAAMAC

Matches to Query: TCCAAATR

Matches to Query: AAMAGAGT

Matches to Query: GCAKGGAA

Matches to Query: CCTCAAAK

Matches to Query: AATAKACT

Matches to Query: AATCMACC

Matches to Query: ACWCGAAT

Matches to Query: AGAAAGKT

Matches to Query: CCTKTCCA

Matches to Query: ACTCCAWT

Matches to Query: GGAAGTTA

Matches to Query: CAKAGCA

Matches to Query: TGTGTGCR

Matches to Query: CCATGRCA

Matches to Query: ACCAYAG

Matches to Query: AGTSGAAT

Matches to Query: CACGTGB

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

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Alignment

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Alignment

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Summary

Alignment