TOol for Motif TO Motif comparison (TOMTOM)

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

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

Query Motifs

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Name 

Preview 

Matches 

List 

STRGGTCAN
GTAGGTCAC
36 MA0066.1, M00515, M00157, M01138, MA0072.1, M01268, M01270, M00191, MA0258.1, MA0159.1, MA0071.1, M00959, M00156, MA0112.2, MA0160.1, MA0112.1, M01032, MA0074.1, M01202, MA0065.2

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2009.meme 476 11
transfac_matrix.meme 1226 25
uniprobe_mouse.meme 386 0

Matches to Query: STRGGTCAN

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Summary 

Alignment 

Name MA0066.1
Alt. Name PPARG
Database JASPAR_CORE_2009.meme
p-value 1.54217e-16
E-value 3.22004e-13
q-value 6.40581e-13
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name M00515
Alt. Name PPARgamma:RXRalpha,
Database transfac_matrix.meme
p-value 6.32802e-13
E-value 1.32129e-09
q-value 1.31426e-09
Overlap 9
Offset 2
Orientation Normal
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Summary 

Alignment 

Name M00157
Alt. Name RORalpha2
Database transfac_matrix.meme
p-value 1.87159e-06
E-value 0.00390789
q-value 0.00155483
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name M01138
Alt. Name RORalpha
Database transfac_matrix.meme
p-value 2.83024e-06
E-value 0.00590954
q-value 0.00195936
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0072.1
Alt. Name RORA_2
Database JASPAR_CORE_2009.meme
p-value 3.88856e-06
E-value 0.00811932
q-value 0.00230746
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name M01268
Alt. Name FXR
Database transfac_matrix.meme
p-value 1.94915e-05
E-value 0.0406982
q-value 0.0101204
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name M01270
Alt. Name PPARG
Database transfac_matrix.meme
p-value 4.13904e-05
E-value 0.0864232
q-value 0.0191029
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name M00191
Alt. Name ER
Database transfac_matrix.meme
p-value 7.58152e-05
E-value 0.158302
q-value 0.0314919
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0258.1
Alt. Name ESR2
Database JASPAR_CORE_2009.meme
p-value 8.94604e-05
E-value 0.186793
q-value 0.0337816
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0159.1
Alt. Name RXR::RAR_DR5
Database JASPAR_CORE_2009.meme
p-value 0.000151894
E-value 0.317154
q-value 0.0525776
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MA0071.1
Alt. Name RORA_1
Database JASPAR_CORE_2009.meme
p-value 0.000210068
E-value 0.438622
q-value 0.067121
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name M00959
Alt. Name ER
Database transfac_matrix.meme
p-value 0.000266538
E-value 0.556532
q-value 0.0790813
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name M00156
Alt. Name RORalpha1
Database transfac_matrix.meme
p-value 0.000306539
E-value 0.640053
q-value 0.0848861
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0112.2
Alt. Name ESR1
Database JASPAR_CORE_2009.meme
p-value 0.000429448
E-value 0.896688
q-value 0.111489
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0160.1
Alt. Name NR4A2
Database JASPAR_CORE_2009.meme
p-value 0.000740331
E-value 1.54581
q-value 0.170842
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0112.1
Alt. Name ESR1
Database JASPAR_CORE_2009.meme
p-value 0.00101281
E-value 2.11476
q-value 0.205449
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name M01032
Alt. Name HNF4
Database transfac_matrix.meme
p-value 0.00112829
E-value 2.35586
q-value 0.207355
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MA0074.1
Alt. Name RXRA::VDR
Database JASPAR_CORE_2009.meme
p-value 0.00122279
E-value 2.55319
q-value 0.207355
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name M01202
Alt. Name VDR:RXR
Database transfac_matrix.meme
p-value 0.00122279
E-value 2.55319
q-value 0.207355
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MA0065.2
Alt. Name PPARG::RXRA
Database JASPAR_CORE_2009.meme
p-value 0.00124799
E-value 2.6058
q-value 0.207355
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name M01248
Alt. Name Dax1
Database transfac_matrix.meme
p-value 0.0015006
E-value 3.13326
q-value 0.239737
Overlap 9
Offset 6
Orientation Normal
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Summary 

Alignment 

Name M00511
Alt. Name ERR
Database transfac_matrix.meme
p-value 0.00157765
E-value 3.29413
q-value 0.242711
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name M00528
Alt. Name PPAR
Database transfac_matrix.meme
p-value 0.00164774
E-value 3.44048
q-value 0.24444
Overlap 9
Offset 2
Orientation Normal
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Summary 

Alignment 

Name M01198
Alt. Name RXR:LXR-beta
Database transfac_matrix.meme
p-value 0.00193569
E-value 4.04172
q-value 0.277255
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name M01217
Alt. Name NUR77
Database transfac_matrix.meme
p-value 0.00221051
E-value 4.61555
q-value 0.287249
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name M00242
Alt. Name PPARalpha:RXRalpha
Database transfac_matrix.meme
p-value 0.00225302
E-value 4.70431
q-value 0.287249
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name M01033
Alt. Name HNF4
Database transfac_matrix.meme
p-value 0.0022814
E-value 4.76356
q-value 0.287249
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MA0451.1
Alt. Name kni
Database JASPAR_CORE_2009.meme
p-value 0.00230486
E-value 4.81254
q-value 0.287249
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name M01227
Alt. Name MAFB
Database transfac_matrix.meme
p-value 0.00235123
E-value 4.90936
q-value 0.287249
Overlap 5
Offset -4
Orientation Reverse Complement
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Summary 

Alignment 

Name M00202
Alt. Name CRP
Database transfac_matrix.meme
p-value 0.00264918
E-value 5.53149
q-value 0.308088
Overlap 9
Offset 13
Orientation Normal
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Summary 

Alignment 

Name M00226
Alt. Name P
Database transfac_matrix.meme
p-value 0.0026768
E-value 5.58916
q-value 0.308088
Overlap 6
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name M01282
Alt. Name PPARA
Database transfac_matrix.meme
p-value 0.00274432
E-value 5.73013
q-value 0.308088
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name M00763
Alt. Name PPAR
Database transfac_matrix.meme
p-value 0.00319369
E-value 6.66843
q-value 0.349101
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name M00172
Alt. Name AP-1
Database transfac_matrix.meme
p-value 0.00382363
E-value 7.98374
q-value 0.396792
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name M00965
Alt. Name LXR,
Database transfac_matrix.meme
p-value 0.00391656
E-value 8.17777
q-value 0.396792
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name M00762
Alt. Name PPAR,
Database transfac_matrix.meme
p-value 0.00437918
E-value 9.14373
q-value 0.433098
Overlap 7
Offset -2
Orientation Normal
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TOMTOM version
4.4.0 (Release date: Tue Apr 27 10:09:30 EST 2010)
Reference
Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble, "Quantifying similarity between motifs",
Genome Biology, 8:R24, 2007
Command line summary

Background letter frequencies (from first motif database):
A: 0.250   C: 0.250   G: 0.250   T: 0.250

Result calculation took 1.466 seconds
show model parameters...

Explanation of TOMTOM Results

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The TOMTOM results consist of

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 the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.