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_h_k4me3_3_0.388
AAACGCGA
0
2_e_k4me3_1_0.393
ACGCGGCGGC
0
3_h_k4me3_1_0.408
CGCCGAAT
0
4_e_k27ac_64_0.411
AAACAAAACCC
0
5_h_k4me3_24_0.412
TTCGAAACCGAA
1 Irf4_primary_SCI09_U
6_e_k27me3_37_0.417
AGCGCGCTC
0
7_e_k4me3_69_0.419
ACTTCCGGC
12 GADP_01_M01258_T,  ELF2_10_H,  ETV4_13_H,  GABP_B_M00341_T,  Eip74EF_MA0026.1_J,  ELK1_02_M00025_T,  Etv6_EMBO10_U,  Ehf_primary_SCI09_U,  ERG_01_M01752_T,  GABPA_MA0062.2_J
8_h_k4me3_10_0.420
AGCGGACT
0
9_h_k27ac_6_0.422
TTAACGAGCG
0
10_e_k4me3_57_0.425
AGATGGCGG
2 NFMUE1_Q6_M00651_T,  REX1_03_M01744_T
11_h_k27ac_11_0.425
GGGGGAAAAAAA
0
12_h_k4me3_7_0.431
CGTATCGT
0
13_e_k4me1_248_0.567
ACATGTGTG
0
14_e_k4me3_225_0.434
ACGTCATT
0
15_e_k4me3_323_0.434
ATAACGAA
0
16_e_k27ac_460_0.436
CGGCTCTAA
0
17_h_k4me3_16_0.437
ATTCGGATTTCC
0
18_e_k9me3_199_0.561
GAATTCACA
0
19_e_k4me3_243_0.439
AGTAACTCG
0
20_e_k9me3_373_0.559
AATGTGGAA
0
21_e_k9me3_38_0.558
ATAAATGTA
0
22_e_k9me3_77_0.556
ACATCAGAGT
0
23_e_k9me3_324_0.551
ATGCCATGC
0
24_e_k9me3_489_0.549
ACCATAGCA
0
25_h_k4me3_18_0.451
CTTAACTT
0
26_e_k36me3_361_0.547
CATGTCCAC
0
27_e_k27ac_442_0.459
GGCTCTGAA
0
28_e_k36me3_322_0.539
AGGTGACATG
0
29_e_k27ac_226_0.534
CACAAAGGG
1 SOX10_MA0442.1_J
30_e_k36me3_276_0.530
AACACAGGTGA
1 sna_MA0086.1_J
31_e_k36me3_113_0.528
AGCACAGTGTAAC
0
32_h_k36me3_4_0.528
GATGACCTCCAC
0
33_e_k36me3_291_0.528
CACCAGGC
0
34_e_k27me3_261_0.524
ACTGAGGCT
0
35_e_k4me1_548_0.523
AGTCACCAC
0
36_e_k36me3_272_0.522
GGCCACACC
1 MET31_01_M01688_T
37_e_k27me3_246_0.521
CTTCCTGGA
1 Stat3_MA0144.1_J
38_e_k36me3_318_0.519
AGGGTGGTAC
0
39_e_k36me3_203_0.515
CCCCAGGTAAG
0
40_e_k36me3_119_0.508
CTGCAGTGAC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 19

Matches to Query: 1_h_k4me3_3_0.388

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Matches to Query: 2_e_k4me3_1_0.393

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Matches to Query: 3_h_k4me3_1_0.408

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Matches to Query: 4_e_k27ac_64_0.411

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Matches to Query: 5_h_k4me3_24_0.412

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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
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Matches to Query: 6_e_k27me3_37_0.417

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Matches to Query: 7_e_k4me3_69_0.419

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Summary 

Alignment 

Name GADP_01_M01258_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.63291e-07
E-value 0.000769073
q-value 0.00151968
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name ELF2_10_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.83879e-06
E-value 0.00537111
q-value 0.00246688
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name ETV4_13_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.83879e-06
E-value 0.00537111
q-value 0.00246688
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name GABP_B_M00341_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.11024e-06
E-value 0.00616401
q-value 0.00246688
Overlap 9
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name Eip74EF_MA0026.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.13699e-06
E-value 0.00624214
q-value 0.00246688
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name ELK1_02_M00025_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.90424e-06
E-value 0.0114043
q-value 0.00375579
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name Etv6_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.17254e-06
E-value 0.020951
q-value 0.00591413
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Ehf_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.92933e-06
E-value 0.0290036
q-value 0.00654399
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name ERG_01_M01752_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.05361e-05
E-value 0.0307759
q-value 0.00654399
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name GABPA_MA0062.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.13377e-05
E-value 0.0331176
q-value 0.00654399
Overlap 8
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name Ehf_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.27556e-05
E-value 0.0372592
q-value 0.00669307
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name ELK4_MA0076.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.57055e-05
E-value 0.0458759
q-value 0.00755418
Overlap 9
Offset 0
Orientation Reverse Complement
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Matches to Query: 8_h_k4me3_10_0.420

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Matches to Query: 9_h_k27ac_6_0.422

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Matches to Query: 10_e_k4me3_57_0.425

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Summary 

Alignment 

Name NFMUE1_Q6_M00651_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.6036e-06
E-value 0.0134471
q-value 0.0201237
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name REX1_03_M01744_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.88932e-06
E-value 0.0201237
q-value 0.0201237
Overlap 9
Offset 1
Orientation Normal
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Matches to Query: 11_h_k27ac_11_0.425

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Matches to Query: 12_h_k4me3_7_0.431

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Matches to Query: 13_e_k4me1_248_0.567

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Matches to Query: 14_e_k4me3_225_0.434

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Matches to Query: 15_e_k4me3_323_0.434

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Matches to Query: 16_e_k27ac_460_0.436

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Matches to Query: 17_h_k4me3_16_0.437

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Matches to Query: 18_e_k9me3_199_0.561

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Matches to Query: 19_e_k4me3_243_0.439

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Matches to Query: 20_e_k9me3_373_0.559

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Matches to Query: 21_e_k9me3_38_0.558

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Matches to Query: 22_e_k9me3_77_0.556

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Matches to Query: 23_e_k9me3_324_0.551

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Matches to Query: 24_e_k9me3_489_0.549

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Matches to Query: 25_h_k4me3_18_0.451

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Matches to Query: 26_e_k36me3_361_0.547

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Matches to Query: 27_e_k27ac_442_0.459

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Matches to Query: 28_e_k36me3_322_0.539

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Matches to Query: 29_e_k27ac_226_0.534

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Summary 

Alignment 

Name SOX10_MA0442.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.77166e-07
E-value 0.0028543
q-value 0.00570861
Overlap 6
Offset -1
Orientation Reverse Complement
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Matches to Query: 30_e_k36me3_276_0.530

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Summary 

Alignment 

Name sna_MA0086.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.9206e-06
E-value 0.0114521
q-value 0.0227955
Overlap 6
Offset -4
Orientation Normal
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Matches to Query: 31_e_k36me3_113_0.528

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Matches to Query: 32_h_k36me3_4_0.528

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Matches to Query: 33_e_k36me3_291_0.528

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Matches to Query: 34_e_k27me3_261_0.524

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Matches to Query: 35_e_k4me1_548_0.523

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Matches to Query: 36_e_k36me3_272_0.522

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Summary 

Alignment 

Name MET31_01_M01688_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.90478e-06
E-value 0.00556386
q-value 0.0111224
Overlap 8
Offset -1
Orientation Reverse Complement
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Matches to Query: 37_e_k27me3_246_0.521

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Summary 

Alignment 

Name Stat3_MA0144.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.98698e-08
E-value 0.00029172
q-value 0.000581252
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 38_e_k36me3_318_0.519

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Matches to Query: 39_e_k36me3_203_0.515

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Matches to Query: 40_e_k36me3_119_0.508

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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 98.080 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.