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_22_0.575
GTGCACACA
1 Zscan4_primary_SCI09_U
2_e_k4me1_5_0.572
GCACAGCAGG
4 Zic1_secondary_SCI09_U,  Zic3_secondary_SCI09_U,  Zic2_secondary_SCI09_U,  NEUROD_02_M01288_T
3_e_k4me1_2_0.560
CACACGTGCC
7 CBF1_02_M01699_T,  MYC_Q2_M00799_T,  Arnt_MA0004.1_J,  Mycn_MA0104.1_J,  PIF1_01_M01585_T,  NMYC_01_M00055_T,  USF1_7_H
4_e_k36me3_254_0.560
CAGGCCACA
0
5_e_k4me3_357_0.442
ATAATCCG
0
6_h_k4me1_5_0.555
GGCCACTGGC
0
7_e_k4me3_271_0.445
AAATACCCG
0
8_e_k4me3_329_0.447
ACGACTTTA
0
9_e_k36me3_60_0.450
GGAGGATCACT
0
10_h_k4me1_9_0.550
TTGCAAAGCA
1 RBM35A_5_H
11_e_k36me3_192_0.452
GACGAGACT
0
12_e_k4me1_277_0.546
TGCCATGTGT
0
13_h_k4me3_1_0.454
AACTTCCG
24 ELK1_02_M00025_T,  Elk3_EMBO10_U,  Elk1_EMBO10_U,  SAP1A_01_M01167_T,  Ehf_primary_SCI09_U,  Ets1_EMBO10_U,  Gabpa_primary_SCI09_U,  Elf2_EMBO10_U,  Elk4_EMBO10_U,  GABPA_MA0062.1_J
14_h_k4me1_16_0.546
CAGGACATGC
0
15_e_k27me3_399_0.455
AGAAAATCG
0
16_e_k4me1_279_0.543
CCAGCAGGG
0
17_h_k36me3_28_0.541
TCGTGCAG
0
18_e_k27me3_184_0.460
AATTAGCG
4 EVX2_01_M01386_T,  Evx2_2645.3_Cell08_U,  Lhx8_2247.2_Cell08_U,  LHX8_01_M01440_T
19_e_k4me3_58_0.460
CTCGCGAGA
0
20_e_k4me3_376_0.462
ATACGATA
1 ABF1_02_M01289_T
21_e_k27me3_66_0.462
AACCCGGCG
0
22_e_k4me1_79_0.535
CTGTCCCCAT
0
23_e_k4me1_340_0.535
CATCCTGTC
0
24_h_k4me3_29_0.467
CTTAAGCGGA
0
25_e_k4me3_155_0.467
AGAGTCGCC
0
26_e_k36me3_264_0.468
AAACGAAAC
0
27_e_k36me3_101_0.468
CCTACTACG
0
28_h_k27me3_5_0.470
TCGGAGCG
0
29_e_k36me3_206_0.470
TCTCGAAGG
1 XBP1_Q2_M00683_T
30_h_k9me3_14_0.473
TCTTTTGATAGA
0
31_h_k9me3_24_0.474
TTGTCTAGGCTC
0
32_e_k4me1_245_0.524
AACCACATAC
0
33_e_k4me1_131_0.523
CCTCAGCCA
0
34_e_k27me3_408_0.477
AATACCGCC
0
35_h_k9me3_7_0.479
TACAAAAAGAGT
0
36_h_k9me3_16_0.481
CGCAGTTTTG
0
37_e_k4me3_52_0.483
CGCCGTCCG
0
38_h_k36me3_15_0.515
GCACCGAGGACC
0
39_h_k9me3_3_0.494
TGTTCAACTCTG
0
40_h_k9me3_26_0.496
AGGTGATGTAAC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 43

Matches to Query: 1_e_k4me1_22_0.575

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Summary 

Alignment 

Name Zscan4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.36066e-06
E-value 0.0215005
q-value 0.043001
Overlap 9
Offset 5
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 2_e_k4me1_5_0.572

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Summary 

Alignment 

Name Zic1_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.46032e-07
E-value 0.000426559
q-value 0.000501206
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Zic3_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.71587e-07
E-value 0.000501206
q-value 0.000501206
Overlap 10
Offset 2
Orientation Normal
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Summary 

Alignment 

Name Zic2_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.01501e-06
E-value 0.00296483
q-value 0.00197656
Overlap 10
Offset 2
Orientation Normal
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Summary 

Alignment 

Name NEUROD_02_M01288_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.0083e-06
E-value 0.0146292
q-value 0.00731462
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 3_e_k4me1_2_0.560

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Summary 

Alignment 

Name CBF1_02_M01699_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.30053e-07
E-value 0.00271668
q-value 0.00264574
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MYC_Q2_M00799_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.27818e-06
E-value 0.00957557
q-value 0.00290796
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name Arnt_MA0004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.03641e-06
E-value 0.0117904
q-value 0.00290796
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name Mycn_MA0104.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.03641e-06
E-value 0.0117904
q-value 0.00290796
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name PIF1_01_M01585_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.08892e-06
E-value 0.0119437
q-value 0.00290796
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name NMYC_01_M00055_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.31403e-06
E-value 0.0242853
q-value 0.0052558
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name USF1_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.01984e-05
E-value 0.0297895
q-value 0.00527483
Overlap 6
Offset -2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 4_e_k36me3_254_0.560

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Matches to Query: 5_e_k4me3_357_0.442

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Matches to Query: 6_h_k4me1_5_0.555

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Matches to Query: 7_e_k4me3_271_0.445

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Matches to Query: 8_e_k4me3_329_0.447

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Matches to Query: 9_e_k36me3_60_0.450

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Matches to Query: 10_h_k4me1_9_0.550

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Summary 

Alignment 

Name RBM35A_5_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.90832e-06
E-value 0.0143372
q-value 0.0286458
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 11_e_k36me3_192_0.452

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Matches to Query: 12_e_k4me1_277_0.546

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Matches to Query: 13_h_k4me3_1_0.454

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Summary 

Alignment 

Name ELK1_02_M00025_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.99486e-06
E-value 0.00582699
q-value 0.00356178
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Elk3_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.8498e-06
E-value 0.00832427
q-value 0.00356178
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.6477e-06
E-value 0.0106549
q-value 0.00356178
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SAP1A_01_M01167_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.9779e-06
E-value 0.0145404
q-value 0.00356178
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Ehf_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.6325e-06
E-value 0.0164525
q-value 0.00356178
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name Ets1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.71921e-06
E-value 0.0167058
q-value 0.00356178
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gabpa_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.71921e-06
E-value 0.0167058
q-value 0.00356178
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf2_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.33656e-06
E-value 0.0185091
q-value 0.00356178
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.33656e-06
E-value 0.0185091
q-value 0.00356178
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABPA_MA0062.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.4433e-06
E-value 0.0246629
q-value 0.00356178
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name NRF2_01_M00108_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.4433e-06
E-value 0.0246629
q-value 0.00356178
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name GADP_01_M01258_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.74988e-06
E-value 0.0255584
q-value 0.00356178
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name RARG_9_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.59774e-06
E-value 0.028035
q-value 0.00356178
Overlap 6
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name GABPA_MA0062.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.62872e-06
E-value 0.0281255
q-value 0.00356178
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK4_MA0076.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.02447e-05
E-value 0.0299249
q-value 0.00356178
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gabpa_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.03796e-05
E-value 0.0303187
q-value 0.00356178
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.11981e-05
E-value 0.0327097
q-value 0.00356178
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name Erg_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.11981e-05
E-value 0.0327097
q-value 0.00356178
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Fli1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.33201e-05
E-value 0.0389081
q-value 0.00381306
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name Gm5454_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.33201e-05
E-value 0.0389081
q-value 0.00381306
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ETV4_13_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.41028e-05
E-value 0.0411941
q-value 0.00384485
Overlap 6
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name Etv4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.57345e-05
E-value 0.0459606
q-value 0.0039514
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELF2_10_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.68972e-05
E-value 0.0493567
q-value 0.0039514
Overlap 6
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name FLI1_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.68972e-05
E-value 0.0493567
q-value 0.0039514
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 14_h_k4me1_16_0.546

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Matches to Query: 15_e_k27me3_399_0.455

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Matches to Query: 16_e_k4me1_279_0.543

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Matches to Query: 17_h_k36me3_28_0.541

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Matches to Query: 18_e_k27me3_184_0.460

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Summary 

Alignment 

Name EVX2_01_M01386_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.50232e-06
E-value 0.0189933
q-value 0.0161774
Overlap 8
Offset 6
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Evx2_2645.3_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.50232e-06
E-value 0.0189933
q-value 0.0161774
Overlap 8
Offset 6
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Lhx8_2247.2_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.39346e-05
E-value 0.0407029
q-value 0.0161774
Overlap 8
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name LHX8_01_M01440_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.56085e-05
E-value 0.0455923
q-value 0.0161774
Overlap 8
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 19_e_k4me3_58_0.460

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Matches to Query: 20_e_k4me3_376_0.462

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Summary 

Alignment 

Name ABF1_02_M01289_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.49368e-05
E-value 0.0436304
q-value 0.0872608
Overlap 8
Offset 8
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 21_e_k27me3_66_0.462

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Matches to Query: 22_e_k4me1_79_0.535

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Matches to Query: 23_e_k4me1_340_0.535

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Matches to Query: 24_h_k4me3_29_0.467

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Matches to Query: 25_e_k4me3_155_0.467

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Matches to Query: 26_e_k36me3_264_0.468

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Matches to Query: 27_e_k36me3_101_0.468

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Matches to Query: 28_h_k27me3_5_0.470

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Matches to Query: 29_e_k36me3_206_0.470

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Summary 

Alignment 

Name XBP1_Q2_M00683_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.54644e-06
E-value 0.00451715
q-value 0.00903429
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 30_h_k9me3_14_0.473

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Matches to Query: 31_h_k9me3_24_0.474

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Matches to Query: 32_e_k4me1_245_0.524

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Matches to Query: 33_e_k4me1_131_0.523

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Matches to Query: 34_e_k27me3_408_0.477

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Matches to Query: 35_h_k9me3_7_0.479

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Matches to Query: 36_h_k9me3_16_0.481

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Matches to Query: 37_e_k4me3_52_0.483

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Matches to Query: 38_h_k36me3_15_0.515

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Matches to Query: 39_h_k9me3_3_0.494

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Matches to Query: 40_h_k9me3_26_0.496

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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 103.714 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.