TOMTOM

Name	Preview	Matches	List
1_h_8_0.595	TTTTCCGC	1	Sp100_primary_SCI09_U
2_h_26_0.592	GCGGCGAC	0
3_re_55_0.416	CCTGGCACA	0
4_e_37_0.583	ACGCCGAGA	0
5_e_13_0.583	CTCGCGAGA	0
6_e_202_0.580	AAATACGCA	0
7_re_50_0.421	CACACGTGA	0
8_re_5_0.425	ACGTGGCCT	0
9_re_6_0.426	CACGTGGCC	11	ABF1_02_M00400_T, ABF_Q2_M00442_T, GBF_Q2_M00441_T, PIF3_01_M00434_T, CG1_Q6_M00440_T, PIF3_02_M00435_T, GBP_Q6_M00182_T, EMBP1_Q2_M00366_T, ABF1_01_M00399_T, CMYC_02_M01154_T
10_e_177_0.573	GGAAAAAAA	1	NFAT1_Q6_M01281_T
11_e_45_0.573	CAGCGACG	0
12_e_21_0.571	GCGGCCGGAC	0
13_e_36_0.571	AGGACCGCG	0
14_re_72_0.430	ACAGTGCCT	0
15_h_18_0.569	GCGGAGTTAA	0
16_e_355_0.568	CGTAATTAA	0
17_e_368_0.568	AACGATAC	0
18_h_6_0.567	CGCCGAACAA	0
19_re_3_0.434	CTCTGTGCCTT	0
20_e_329_0.565	ATTAACGAG	0
21_e_5_0.564	CGCCTGCGC	3	ZFP206_01_M01742_T, HIST1H2BN_4_H, TRIM69_7_H
22_re_61_0.438	AGATGAGGAC	0
23_re_19_0.438	AGCACCTACA	0
24_h_10_0.560	GCGTTGCTTT	0
25_re_35_0.440	GTGTGTGCA	0
26_re_48_0.440	CACGTGCTG	0
27_e_238_0.559	AACTACG	0
28_e_81_0.557	GCGCGTCTT	0
29_e_361_0.557	AAATAACGG	0
30_e_362_0.556	GGCATTTT	0
31_re_83_0.445	ACTGTGCTAG	0
32_re_57_0.446	CAGAGCTGGA	0
33_e_35_0.553	CGCGTTCCCA	0
34_e_83_0.551	ACGCGTCCC	0
35_h_21_0.550	CCGATTGT	0
36_e_370_0.550	AAACGGTTA	3	MYBPH3_01_M00218_T, myb.Ph3_MA0054.1_J, Kr_MA0452.1_J
37_e_65_0.549	TCAGCGGCT	0
38_re_51_0.452	GGGCAGGGAT	1	HLCS_2_H
39_re_66_0.454	TACCTCTCTG	0
40_e_171_0.543	GAAAGGAAAA	0
41_e_15_0.540	CCGGAGCCG	0
42_re_27_0.460	CTCAGTTTCT	0
43_re_49_0.462	CCTCCCCAC	1	MZF1_Q5_M01733_T
44_re_65_0.464	TGTGGCTGC	0
45_e_360_0.535	CGGTAAACA	2	FKH2_MA0297.1_J, FOXO3_MA0157.1_J
46_e_99_0.531	CAGCCTCGC	0
47_re_78_0.484	CAGGTATTC	0
48_e_354_0.513	GGAATTCCA	0
49_h_4_0.512	CACATTCC	2	TEAD1_MA0090.1_J, TEF_01_M01305_T
50_re_79_0.489	ACATGTAAAA	2	HMRA2_MA0318.1_J, HMRA2_01_M01607_T

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	27

Summary

Alignment

Name	Sp100_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.42662e-05
E-value	0.0416716
q-value	0.0830307
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	ABF1_02_M00400_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.78163e-08
E-value	0.000198091
q-value	0.000382237
Overlap	9
Offset	10
Orientation	Normal

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Summary

Alignment

Name	ABF_Q2_M00442_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.23945e-06
E-value	0.00362045
q-value	0.00254984
Overlap	9
Offset	5
Orientation	Normal

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Summary

Alignment

Name	GBF_Q2_M00441_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.35717e-06
E-value	0.0039643
q-value	0.00254984
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	PIF3_01_M00434_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.74432e-06
E-value	0.00801617
q-value	0.0030936
Overlap	9
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	CG1_Q6_M00440_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.74192e-06
E-value	0.0196932
q-value	0.00515658
Overlap	9
Offset	2
Orientation	Normal

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Summary

Alignment

Name	PIF3_02_M00435_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.32074e-06
E-value	0.0213839
q-value	0.00515658
Overlap	9
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	GBP_Q6_M00182_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.30191e-06
E-value	0.0242499
q-value	0.00515658
Overlap	9
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	EMBP1_Q2_M00366_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.69237e-06
E-value	0.0283114
q-value	0.00515658
Overlap	8
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	ABF1_01_M00399_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.30146e-05
E-value	0.0380157
q-value	0.00515658
Overlap	9
Offset	10
Orientation	Normal

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Summary

Alignment

Name	CMYC_02_M01154_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.32334e-05
E-value	0.0386547
q-value	0.00515658
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Mycn_MA0104.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.40762e-05
E-value	0.0411167
q-value	0.00515658
Overlap	8
Offset	2
Orientation	Normal

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Summary

Alignment

Name	NFAT1_Q6_M01281_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.61089e-06
E-value	0.0105474
q-value	0.0210448
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	ZFP206_01_M01742_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.22292e-07
E-value	0.00152561
q-value	0.00162183
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	HIST1H2BN_4_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.5523e-07
E-value	0.00162183
q-value	0.00162183
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TRIM69_7_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.31787e-06
E-value	0.00384951
q-value	0.00256634
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MYBPH3_01_M00218_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.75343e-06
E-value	0.00512177
q-value	0.0102435
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	myb.Ph3_MA0054.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.41507e-06
E-value	0.0216594
q-value	0.0204281
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Kr_MA0452.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.04903e-05
E-value	0.0306421
q-value	0.0204281
Overlap	9
Offset	2
Orientation	Normal

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Summary

Alignment

Name	HLCS_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.59597e-05
E-value	0.0466183
q-value	0.0930474
Overlap	5
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	MZF1_Q5_M01733_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.03991e-06
E-value	0.0118006
q-value	0.023529
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	FKH2_MA0297.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.0903e-07
E-value	0.00177898
q-value	0.00355135
Overlap	7
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	FOXO3_MA0157.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.38399e-05
E-value	0.0404264
q-value	0.0403513
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	TEAD1_MA0090.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.15037e-06
E-value	0.00628122
q-value	0.00628122
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	TEF_01_M01305_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.15037e-06
E-value	0.00628122
q-value	0.00628122
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	HMRA2_MA0318.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.92072e-06
E-value	0.0289784
q-value	0.0301255
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	HMRA2_01_M01607_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.2077e-05
E-value	0.0352768
q-value	0.0301255
Overlap	7
Offset	-1
Orientation	Normal

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The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

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.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: 1_h_8_0.595

Summary

Alignment

Matches to Query: 2_h_26_0.592

Matches to Query: 3_re_55_0.416

Matches to Query: 4_e_37_0.583

Matches to Query: 5_e_13_0.583

Matches to Query: 6_e_202_0.580

Matches to Query: 7_re_50_0.421

Matches to Query: 8_re_5_0.425

Matches to Query: 9_re_6_0.426

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 10_e_177_0.573

Summary

Alignment

Matches to Query: 11_e_45_0.573

Matches to Query: 12_e_21_0.571

Matches to Query: 13_e_36_0.571

Matches to Query: 14_re_72_0.430

Matches to Query: 15_h_18_0.569

Matches to Query: 16_e_355_0.568

Matches to Query: 17_e_368_0.568

Matches to Query: 18_h_6_0.567

Matches to Query: 19_re_3_0.434

Matches to Query: 20_e_329_0.565

Matches to Query: 21_e_5_0.564

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 22_re_61_0.438

Matches to Query: 23_re_19_0.438

Matches to Query: 24_h_10_0.560

Matches to Query: 25_re_35_0.440

Matches to Query: 26_re_48_0.440

Matches to Query: 27_e_238_0.559

Matches to Query: 28_e_81_0.557

Matches to Query: 29_e_361_0.557

Matches to Query: 30_e_362_0.556

Matches to Query: 31_re_83_0.445

Matches to Query: 32_re_57_0.446

Matches to Query: 33_e_35_0.553

Matches to Query: 34_e_83_0.551

Matches to Query: 35_h_21_0.550

Matches to Query: 36_e_370_0.550

Summary

Alignment

Summary