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.

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_e_k4me1_5_0.567
GTGCACACA
1 Zscan4_primary_SCI09_U
2_e_k4me1_248_0.565
ACATGTGTG
0
3_e_k27ac_447_0.440
CTCGAATTA
0
4_e_k4me1_245_0.553
AGGTCACAC
0
5_e_k4me3_136_0.448
CGGCG
0
6_h_k4me3_2_0.450
CAATTCCG
2 STAT1_02_M00492_T,  STAT1_01_M00224_T
7_e_k27ac_123_0.455
GGAAAAAAA
1 NFAT1_Q6_M01281_T
8_e_k4me3_90_0.456
CGGCGTCTC
0
9_h_k4me3_3_0.456
AAACGCGA
0
10_e_k4me3_48_0.456
CGCCGCTTC
0
11_h_k9me3_15_0.542
GAGCATGCATGC
0
12_e_k4me3_278_0.460
TCGATATT
0
13_e_k4me1_476_0.539
CAGCAAATG
0
14_h_k4me3_7_0.461
CGTATCGT
0
15_e_k4me1_477_0.536
GAAAGCATG
0
16_e_k4me1_548_0.535
AGTCACCAC
0
17_h_k4me3_24_0.470
TTCGAAACCGAA
1 Irf4_primary_SCI09_U
18_e_k36me3_50_0.472
CATCTACGA
0
19_e_k36me3_187_0.472
CTGTACTCCA
0
20_e_k27ac_46_0.516
GAGCAGGGA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 5

Matches to Query: 1_e_k4me1_5_0.567

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Summary 

Alignment 

Name Zscan4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.01477e-06
E-value 0.0175692
q-value 0.0351383
Overlap 9
Offset 5
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 2_e_k4me1_248_0.565

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Matches to Query: 3_e_k27ac_447_0.440

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Matches to Query: 4_e_k4me1_245_0.553

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Matches to Query: 5_e_k4me3_136_0.448

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Matches to Query: 6_h_k4me3_2_0.450

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Summary 

Alignment 

Name STAT1_02_M00492_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.51167e-06
E-value 0.0131786
q-value 0.0259727
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name STAT1_01_M00224_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.50445e-05
E-value 0.0439449
q-value 0.0433039
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 7_e_k27ac_123_0.455

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Summary 

Alignment 

Name NFAT1_Q6_M01281_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.97784e-06
E-value 0.0174613
q-value 0.0348517
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 8_e_k4me3_90_0.456

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Matches to Query: 9_h_k4me3_3_0.456

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Matches to Query: 10_e_k4me3_48_0.456

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Matches to Query: 11_h_k9me3_15_0.542

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Matches to Query: 12_e_k4me3_278_0.460

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Matches to Query: 13_e_k4me1_476_0.539

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Matches to Query: 14_h_k4me3_7_0.461

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Matches to Query: 15_e_k4me1_477_0.536

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Matches to Query: 16_e_k4me1_548_0.535

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Matches to Query: 17_h_k4me3_24_0.470

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Summary 

Alignment 

Name Irf4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.32519e-05
E-value 0.0387087
q-value 0.0774173
Overlap 12
Offset 3
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 18_e_k36me3_50_0.472

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Matches to Query: 19_e_k36me3_187_0.472

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Matches to Query: 20_e_k27ac_46_0.516

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TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 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

Background letter frequencies (from first motif database):
A: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 42.690 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 of the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.