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_re_6_0.319
GTCTCGAACT
1 RPC155_01_M01798_T
2_re_8_0.322
AGGAGTTCGA
1 RPC155_01_M01798_T
3_re_35_0.328
CTGTAATCCC
0
4_re_21_0.329
GTAATCCCA
1 PITX2_Q2_M00482_T
5_re_23_0.332
GCCTCCCAAG
1 IK_Q5_M01169_T
6_re_72_0.337
AGGCTGAGG
0
7_re_29_0.337
ATCGCTTGAA
0
8_re_10_0.339
GAGAATCGCTTG
0
9_re_19_0.343
CTCTACTAAA
0
10_re_0_0.345
ACGCCTGTA
0
11_re_42_0.346
AGGCGTGAG
0
12_re_108_0.351
GGTGAAACC
0
13_re_11_0.352
CGTGGTGGC
0
14_re_52_0.352
ACTTTGGGAG
1 LUN1_01_M00480_T
15_re_37_0.353
TGGTGGCTCA
0
16_re_65_0.355
CCGAGGCGG
1 ETF_Q6_M00695_T
17_re_66_0.355
AAAATTAGC
0
18_re_56_0.357
AGTAGCTGG
1 LUN1_01_M00480_T
19_re_111_0.359
CTGGAGTGC
0
20_re_69_0.359
GATCTCGGC
0
21_re_81_0.359
ATGGTCTCG
0
22_re_40_0.360
AGCCGGGCG
0
23_re_106_0.361
CAATCTCGG
0
24_re_53_0.363
CAACATGGTG
0
25_re_7_0.372
ATCGCGCCA
0
26_re_75_0.374
AGAGCGAGA
0
27_re_13_0.379
CCGAGTAGC
0
28_e_492_0.380
AATTCCAGC
0
29_re_22_0.381
GCAACCTCCG
0
30_re_18_0.391
GGCGACAGAGCG
0
31_e_34_0.598
GTGCACACA
1 Zscan4_primary_SCI09_U
32_re_174_0.403
GGAAGCGGA
0
33_e_389_0.405
CCGGGTTT
0
34_e_412_0.591
GATGCACA
0
35_e_311_0.410
GCTTCGGC
0
36_h_9_0.589
CATGCAGCGT
0
37_e_315_0.411
CACTCGCC
0
38_h_14_0.578
TGCTTAGCAC
0
39_e_25_0.564
GCTGTGTGA
0
40_e_469_0.563
GAAACAGCTG
3 HLH-2_CND-1_Cell09_U,  hlh-2::cnd-1_PL0003.1_J,  RP58_01_M00532_T
41_h_26_0.551
GACATGCT
0
42_e_329_0.544
GGAGGGACA
0
43_h_3_0.543
GTTAATGATTAA
6 HNF1_Q6_M00790_T,  HNF1_C_M00206_T,  HNF1_01_M00132_T,  HNF1A_MA0046.1_J,  HNF1_Q6_01_M01011_T,  HNF1B_MA0153.1_J
44_e_10_0.464
CGTGCGTGC
1 BZR1_01_M01156_T
45_re_215_0.535
CACGTGACG
10 TYE7_MA0409.1_J,  CBF1_02_M01699_T,  TYE7_01_M01558_T,  Tye7_GR09_U,  Arnt_MA0004.1_J,  STRA13_01_M00985_T,  Cbf1_NBT06_U,  Mycn_MA0104.1_J,  TFEB_01_M01768_T,  HLH-30_Cell09_U
46_e_485_0.468
GAACGGAT
0
47_e_143_0.471
GATGAGGGCGG
0
48_e_341_0.527
TGTACCGA
0
49_e_277_0.477
ATCATCGTC
0
50_e_289_0.490
AGAACGTGG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 26

Matches to Query: 1_re_6_0.319

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Summary 

Alignment 

Name RPC155_01_M01798_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.59083e-06
E-value 0.0134098
q-value 0.0268196
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 2_re_8_0.322

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Summary 

Alignment 

Name RPC155_01_M01798_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.27687e-06
E-value 0.00372973
q-value 0.00745946
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 3_re_35_0.328

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Matches to Query: 4_re_21_0.329

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Summary 

Alignment 

Name PITX2_Q2_M00482_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.88233e-06
E-value 0.0113403
q-value 0.0226806
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 5_re_23_0.332

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Summary 

Alignment 

Name IK_Q5_M01169_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.47994e-06
E-value 0.00432292
q-value 0.00864584
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 6_re_72_0.337

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Matches to Query: 7_re_29_0.337

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Matches to Query: 8_re_10_0.339

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Matches to Query: 9_re_19_0.343

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Matches to Query: 10_re_0_0.345

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Matches to Query: 11_re_42_0.346

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Matches to Query: 12_re_108_0.351

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Matches to Query: 13_re_11_0.352

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Matches to Query: 14_re_52_0.352

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Summary 

Alignment 

Name LUN1_01_M00480_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.49004e-06
E-value 0.0101944
q-value 0.0203888
Overlap 9
Offset 8
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 15_re_37_0.353

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Matches to Query: 16_re_65_0.355

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Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.81909e-06
E-value 0.0286816
q-value 0.0570297
Overlap 7
Offset -2
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 17_re_66_0.355

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Matches to Query: 18_re_56_0.357

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Summary 

Alignment 

Name LUN1_01_M00480_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.38329e-08
E-value 4.04058e-05
q-value 8.08116e-05
Overlap 9
Offset 6
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 19_re_111_0.359

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Matches to Query: 20_re_69_0.359

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Matches to Query: 21_re_81_0.359

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Matches to Query: 22_re_40_0.360

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Matches to Query: 23_re_106_0.361

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Matches to Query: 24_re_53_0.363

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Matches to Query: 25_re_7_0.372

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Matches to Query: 26_re_75_0.374

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Matches to Query: 27_re_13_0.379

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Matches to Query: 28_e_492_0.380

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Matches to Query: 29_re_22_0.381

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Matches to Query: 30_re_18_0.391

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Matches to Query: 31_e_34_0.598

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Summary 

Alignment 

Name Zscan4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.16424e-06
E-value 0.0267687
q-value 0.0535375
Overlap 9
Offset 5
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 32_re_174_0.403

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Matches to Query: 33_e_389_0.405

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Matches to Query: 34_e_412_0.591

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Matches to Query: 35_e_311_0.410

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Matches to Query: 36_h_9_0.589

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Matches to Query: 37_e_315_0.411

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Matches to Query: 38_h_14_0.578

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Matches to Query: 39_e_25_0.564

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Matches to Query: 40_e_469_0.563

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Summary 

Alignment 

Name HLH-2_CND-1_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.51995e-06
E-value 0.0102818
q-value 0.0101813
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name hlh-2::cnd-1_PL0003.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.51995e-06
E-value 0.0102818
q-value 0.0101813
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name RP58_01_M00532_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.05358e-06
E-value 0.0206035
q-value 0.0136015
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 41_h_26_0.551

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Matches to Query: 42_e_329_0.544

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Matches to Query: 43_h_3_0.543

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Summary 

Alignment 

Name HNF1_Q6_M00790_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.71036e-08
E-value 0.00013759
q-value 0.000236295
Overlap 12
Offset 2
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1_C_M00206_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.4579e-08
E-value 0.000247055
q-value 0.000236295
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name HNF1_01_M00132_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.97263e-07
E-value 0.000576205
q-value 0.000260418
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name HNF1A_MA0046.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.34446e-07
E-value 0.000684816
q-value 0.000260418
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name HNF1_Q6_01_M01011_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.68487e-07
E-value 0.00107635
q-value 0.000294135
Overlap 12
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name HNF1B_MA0153.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.6273e-06
E-value 0.0105954
q-value 0.00184253
Overlap 12
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 44_e_10_0.464

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Summary 

Alignment 

Name BZR1_01_M01156_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34447e-05
E-value 0.0392719
q-value 0.0785439
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 45_re_215_0.535

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Summary 

Alignment 

Name TYE7_MA0409.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.09179e-07
E-value 0.00119521
q-value 0.00192474
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name CBF1_02_M01699_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.47919e-06
E-value 0.0043207
q-value 0.00192474
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name TYE7_01_M01558_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.69558e-06
E-value 0.00495278
q-value 0.00192474
Overlap 9
Offset 7
Orientation Normal
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Summary 

Alignment 

Name Tye7_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.69558e-06
E-value 0.00495278
q-value 0.00192474
Overlap 9
Offset 7
Orientation Normal
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Summary 

Alignment 

Name Arnt_MA0004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.35963e-06
E-value 0.00689247
q-value 0.00206949
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name STRA13_01_M00985_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.79679e-06
E-value 0.00816943
q-value 0.00206949
Overlap 9
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name Cbf1_NBT06_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.79341e-06
E-value 0.0169226
q-value 0.00298927
Overlap 9
Offset 7
Orientation Reverse Complement
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Summary 

Alignment 

Name Mycn_MA0104.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.60712e-06
E-value 0.0222204
q-value 0.00332124
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name TFEB_01_M01768_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.45215e-05
E-value 0.0424174
q-value 0.00549471
Overlap 8
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HLH-30_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.63656e-05
E-value 0.0478039
q-value 0.00580544
Overlap 9
Offset 5
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 46_e_485_0.468

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Matches to Query: 47_e_143_0.471

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Matches to Query: 48_e_341_0.527

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Matches to Query: 49_e_277_0.477

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Matches to Query: 50_e_289_0.490

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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 119.299 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.