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_k27ac-mes_0.589
GAGATAAG
11 Gata1_MA0035.2_J,  Tal1::Gata1_MA0140.1_J,  GATA2_02_M00348_T,  GATA2_03_M00349_T,  GATA3_02_M00350_T,  GATA_Q6_M00789_T,  Gata6_primary_SCI09_U,  Gata3_primary_SCI09_U,  GATA1_04_M00128_T,  GATA1_06_M00347_T
2_h_k27ac-h1_0.587
TTGTTATGCAAA
5 OCT4_01_M01125_T,  Pou5f1_MA0142.1_J,  Sox2_MA0143.1_J,  OCT4_02_M01124_T,  NFIX_2_H
3_e_k27ac-mes_0.546
TGGTGATAA
0
4_e_k27ac-mes_0.539
ACAGGAAGT
7 ETS2_B_M00340_T,  ETS1_B_M00339_T,  ETS_Q6_M00971_T,  ETS2_Q6_M01207_T,  ELK1_01_M00007_T,  TEL2_Q6_M00678_T,  SPI1_MA0080.2_J
5_e_k27ac-mes_0.536
CACAGATAAC
1 GATA1_05_M00346_T
6_e_k27ac-mes_0.532
CTGATTACA
0
7_e_k27ac-mes_0.532
CTCCAGGAA
0
8_e_k27ac-mes_0.531
GTCTGGCACA
0
9_e_k27ac-h1_0.529
ATACACGTG
0
10_e_k27ac-mes_0.526
GCAATGACTCAG
15 TCF11MAFG_01_M00284_T,  AP1_C_M00199_T,  GCN4_C_M00204_T,  NRF2_Q4_M00821_T,  NFE2_01_M00037_T,  AP1_Q6_01_M00925_T,  FRA1_Q5_M01267_T,  AP1_MA0099.2_J,  NFE2L2_MA0150.1_J,  AP1_01_M00517_T
11_e_k27ac-mes_0.524
GGAATTCA
0
12_e_k27ac-h1_0.523
CGCGATGCA
0
13_e_k27ac-mes_0.521
AGGGAGAAG
0
14_e_k27ac-h1_0.520
CGCGCGCACC
1 Zfp161_primary_SCI09_U
15_e_k27ac-mes_0.519
CGTCCTACA
0
16_h_k27ac-mes_0.519
GGGGCTTTAA
0
17_e_k27ac-h1_0.519
CGCCCGCCGTT
0
18_e_k27ac-mes_0.519
AGAGTCTGG
0
19_e_k27ac-mes_0.518
CAGAAGCCAC
0
20_e_k27ac-mes_0.517
AGCGTTTCC
1 DIS3_8_H
21_e_k27ac-h1_0.517
AAGTAGGTAT
0
22_e_k27ac-mes_0.517
GATACCCA
0
23_e_k27ac-mes_0.516
TCGCGTTA
0
24_e_k27ac-mes_0.516
GGCTCCGGA
0
25_e_k27ac-h1_0.516
GCTACTCAC
0
26_e_k27ac-h1_0.515
GCTACATCATG
0
27_e_k27ac-h1_0.513
GAACCGAAA
0
28_e_k27ac-mes_0.512
ATTTGGGGA
0
29_e_k27ac-mes_0.510
CCACCAAAC
2 ING4_01_M01743_T,  LIM1_01_M00506_T
30_e_k27ac-h1_0.507
CTAAGACG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 43

Matches to Query: 1_h_k27ac-mes_0.589

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Summary 

Alignment 

Name Gata1_MA0035.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.9079e-09
E-value 2.8941e-05
q-value 5.77048e-05
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name Tal1::Gata1_MA0140.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.72467e-08
E-value 7.95877e-05
q-value 7.65958e-05
Overlap 8
Offset 10
Orientation Normal
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Summary 

Alignment 

Name GATA2_02_M00348_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.94544e-08
E-value 0.000115246
q-value 7.65958e-05
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name GATA2_03_M00349_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.1678e-07
E-value 0.00121741
q-value 0.000606844
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name GATA3_02_M00350_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.59682e-07
E-value 0.00221903
q-value 0.000884896
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name GATA_Q6_M00789_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.9043e-06
E-value 0.00556245
q-value 0.00184847
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name Gata6_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.49737e-06
E-value 0.0160578
q-value 0.0045739
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Gata3_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.46536e-06
E-value 0.0188853
q-value 0.00470688
Overlap 8
Offset 6
Orientation Normal
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Summary 

Alignment 

Name GATA1_04_M00128_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.23027e-06
E-value 0.0269616
q-value 0.00597313
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name GATA1_06_M00347_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.18402e-05
E-value 0.0345851
q-value 0.00689585
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name GATA1_07_M01756_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.41912e-05
E-value 0.0414524
q-value 0.00751373
Overlap 6
Offset -1
Orientation Normal
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Matches to Query: 2_h_k27ac-h1_0.587

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Summary 

Alignment 

Name OCT4_01_M01125_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.25895e-16
E-value 1.24404e-12
q-value 2.4719e-12
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name Pou5f1_MA0142.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.57574e-14
E-value 2.79707e-10
q-value 2.77889e-10
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name Sox2_MA0143.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.91169e-09
E-value 5.58406e-06
q-value 3.6985e-06
Overlap 12
Offset 3
Orientation Normal
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Summary 

Alignment 

Name OCT4_02_M01124_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.0741e-09
E-value 8.97944e-06
q-value 4.46053e-06
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name NFIX_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.04712e-05
E-value 0.0305865
q-value 0.012155
Overlap 6
Offset -6
Orientation Normal
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Matches to Query: 3_e_k27ac-mes_0.546

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Matches to Query: 4_e_k27ac-mes_0.539

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Summary 

Alignment 

Name ETS2_B_M00340_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.96841e-06
E-value 0.00574973
q-value 0.00665171
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name ETS1_B_M00339_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.29648e-06
E-value 0.00670802
q-value 0.00665171
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name ETS_Q6_M00971_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.72531e-06
E-value 0.0196446
q-value 0.00882215
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name ETS2_Q6_M01207_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.29298e-06
E-value 0.0213028
q-value 0.00882215
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name ELK1_01_M00007_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.61454e-06
E-value 0.0222421
q-value 0.00882215
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name TEL2_Q6_M00678_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.57908e-05
E-value 0.0461248
q-value 0.0131968
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name SPI1_MA0080.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.59465e-05
E-value 0.0465798
q-value 0.0131968
Overlap 7
Offset -2
Orientation Normal
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Matches to Query: 5_e_k27ac-mes_0.536

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Summary 

Alignment 

Name GATA1_05_M00346_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.28462e-06
E-value 0.0154364
q-value 0.0308727
Overlap 9
Offset -1
Orientation Normal
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Matches to Query: 6_e_k27ac-mes_0.532

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Matches to Query: 7_e_k27ac-mes_0.532

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Matches to Query: 8_e_k27ac-mes_0.531

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Matches to Query: 9_e_k27ac-h1_0.529

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Matches to Query: 10_e_k27ac-mes_0.526

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Summary 

Alignment 

Name TCF11MAFG_01_M00284_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.50885e-07
E-value 0.00102494
q-value 0.00203937
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name AP1_C_M00199_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.36196e-07
E-value 0.00244253
q-value 0.00243001
Overlap 9
Offset -3
Orientation Normal
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Summary 

Alignment 

Name GCN4_C_M00204_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.52275e-06
E-value 0.00444795
q-value 0.00243639
Overlap 10
Offset -1
Orientation Normal
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Summary 

Alignment 

Name NRF2_Q4_M00821_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.00595e-06
E-value 0.00585939
q-value 0.00243639
Overlap 10
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name NFE2_01_M00037_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.09597e-06
E-value 0.00612234
q-value 0.00243639
Overlap 9
Offset -3
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q6_01_M00925_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.52096e-06
E-value 0.00736372
q-value 0.002442
Overlap 9
Offset -3
Orientation Normal
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Summary 

Alignment 

Name FRA1_Q5_M01267_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.80526e-06
E-value 0.0111152
q-value 0.00255675
Overlap 8
Offset -3
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_MA0099.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.88603e-06
E-value 0.0113511
q-value 0.00255675
Overlap 7
Offset -4
Orientation Normal
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Summary 

Alignment 

Name NFE2L2_MA0150.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.95915e-06
E-value 0.0115647
q-value 0.00255675
Overlap 9
Offset -3
Orientation Normal
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Summary 

Alignment 

Name AP1_01_M00517_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.9918e-06
E-value 0.017502
q-value 0.00294655
Overlap 11
Offset -1
Orientation Normal
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Summary 

Alignment 

Name AP1_Q4_M00188_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.08367e-06
E-value 0.0177704
q-value 0.00294655
Overlap 10
Offset -2
Orientation Normal
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Summary 

Alignment 

Name AP1_Q6_M00174_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.08367e-06
E-value 0.0177704
q-value 0.00294655
Overlap 10
Offset -2
Orientation Normal
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Summary 

Alignment 

Name AP1_Q2_M00173_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.80449e-06
E-value 0.0227969
q-value 0.00325794
Overlap 10
Offset -2
Orientation Normal
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Summary 

Alignment 

Name AP1_Q4_01_M00926_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.84767e-06
E-value 0.0229231
q-value 0.00325794
Overlap 8
Offset -3
Orientation Reverse Complement
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Summary 

Alignment 

Name MAF_Q6_01_M00983_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.26226e-05
E-value 0.0368707
q-value 0.0048909
Overlap 9
Offset -3
Orientation Reverse Complement
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Matches to Query: 11_e_k27ac-mes_0.524

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Matches to Query: 12_e_k27ac-h1_0.523

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Matches to Query: 13_e_k27ac-mes_0.521

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Matches to Query: 14_e_k27ac-h1_0.520

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Summary 

Alignment 

Name Zfp161_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.34301e-06
E-value 0.0126859
q-value 0.0253379
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 15_e_k27ac-mes_0.519

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Matches to Query: 16_h_k27ac-mes_0.519

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Matches to Query: 17_e_k27ac-h1_0.519

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Matches to Query: 18_e_k27ac-mes_0.519

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Matches to Query: 19_e_k27ac-mes_0.518

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Matches to Query: 20_e_k27ac-mes_0.517

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Summary 

Alignment 

Name DIS3_8_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.70586e-06
E-value 0.0254298
q-value 0.050774
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 21_e_k27ac-h1_0.517

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Matches to Query: 22_e_k27ac-mes_0.517

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Matches to Query: 23_e_k27ac-mes_0.516

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Matches to Query: 24_e_k27ac-mes_0.516

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Matches to Query: 25_e_k27ac-h1_0.516

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Matches to Query: 26_e_k27ac-h1_0.515

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Matches to Query: 27_e_k27ac-h1_0.513

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Matches to Query: 28_e_k27ac-mes_0.512

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Matches to Query: 29_e_k27ac-mes_0.510

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Summary 

Alignment 

Name ING4_01_M01743_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34271e-06
E-value 0.00392207
q-value 0.00784413
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name LIM1_01_M00506_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.30004e-05
E-value 0.0379742
q-value 0.0379742
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 30_e_k27ac-h1_0.507

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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 69.108 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.