TOMTOM

Name	Preview	Matches	List
AYTACA	ACTACA	0
CAKSCTGG	CAGCCTGG	0
GAGGCBGA	GAGGCTGA	0
TACWAAAA	TACAAAAA	0
CCCAGCW	CCCAGCA	0
TGCAGTGR	TGCAGTGA	0
AGGAGAAT	AGGAGAAT	0
CACCRYG	CACCACG	0
AWCTCCTG	AACTCCTG	0
GAGAYGGR	GAGACGGG	0
ATCTCRGC	ATCTCGGC	0
TCCCAGAR	TCCCAGAA	2	MA0144.2 (STAT3), MA0519.1 (Stat5a::Stat5b)
GTTCAAGY	GTTCAAGC	0
ATCACYTG	ATCACCTG	1	MA0086.1 (sna)
CGTAGTYY	CGTAGTCC	0
CYGGCTAA	CCGGCTAA	0
GHGACAGA	GAGACAGA	0
AAAWAAAA	AAAAAAAA	0
GCGTGARC	GCGTGAGC	0
CAABATGG	CAACATGG	1	MA0095.2 (YY1)

Name

Preview

Matches

List

MA0144.2 (STAT3), MA0519.1 (Stat5a::Stat5b)

Database	Number of Motifs	Motifs Matched
JASPAR_CORE_2014.meme	593	4

Database

Number of Motifs

Motifs Matched

JASPAR_CORE_2014.meme

593

Name

MA0144.2

Alt. Name

STAT3

Database

JASPAR_CORE_2014.meme

p-value

3.43543e-05

E-value

0.0203721

q-value

0.0260351

Overlap

Offset

Orientation

Reverse Complement

Name

MA0519.1

Alt. Name

Stat5a::Stat5b

Database

JASPAR_CORE_2014.meme

p-value

4.39812e-05

E-value

0.0260808

q-value

0.0260351

Overlap

Offset

Orientation

Normal

Name

MA0086.1

Alt. Name

sna

Database

JASPAR_CORE_2014.meme

p-value

1.36841e-05

E-value

0.00811466

q-value

0.0162146

Overlap

Offset

-2

Orientation

Reverse Complement

Name

MA0095.2

Alt. Name

YY1

Database

JASPAR_CORE_2014.meme

p-value

2.22097e-05

E-value

0.0131704

q-value

0.0263408

Overlap

Offset

Orientation

Normal

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: AYTACA

Matches to Query: CAKSCTGG

Matches to Query: GAGGCBGA

Matches to Query: TACWAAAA

Matches to Query: CCCAGCW

Matches to Query: TGCAGTGR

Matches to Query: AGGAGAAT

Matches to Query: CACCRYG

Matches to Query: AWCTCCTG

Matches to Query: GAGAYGGR

Matches to Query: ATCTCRGC

Matches to Query: TCCCAGAR

Summary

Alignment

Summary

Alignment

Matches to Query: GTTCAAGY

Matches to Query: ATCACYTG

Summary

Alignment

Matches to Query: CGTAGTYY

Matches to Query: CYGGCTAA

Matches to Query: GHGACAGA

Matches to Query: AAAWAAAA

Matches to Query: GCGTGARC

Matches to Query: CAABATGG

Summary

Alignment

TOMTOM version

Reference

Command line summary

Model parameters

Explanation of TOMTOM Results

The TOMTOM results consist of

Inputs

Query Motifs

Target Databases

Matches

Summary Table

Alignment

Create custom LOGO