TOMTOM

Name	Preview	Matches	List
1_h_k4me3-h1_0.620	GCGAAAAG	0
2_h_k4me3-h1_0.605	GTAAAACG	0
3_e_k4me3-h1_0.604	CGCGCCCCG	0
4_e_k4me3-h1_0.597	CCTTCGCGC	0
5_e_k4me3-tro_0.587	AACACCAGTG	0
6_e_k4me3-h1_0.583	AAGATCGC	0
7_e_k4me3-tro_0.580	CCAACACAG	0
8_e_k4me3-tro_0.579	AACTGAGGCA	0
9_h_k4me3-tro_0.579	ACCGAAGT	0
10_e_k4me3-h1_0.577	GAGGGGAGCG	1	ZMAT2_3_H
11_e_k4me3-tro_0.576	AGACCCACAA	0
12_e_k4me3-h1_0.574	TCCGTAAA	0
13_e_k4me3-tro_0.573	GAATATCAC	0
14_e_k4me3-tro_0.569	AGCAGCCCA	0
15_e_k4me3-h1_0.568	AATTTAGCC	0
16_e_k4me3-tro_0.568	AGCACTGGC	0
17_e_k4me3-tro_0.566	ATTTCTGTC	0
18_e_k4me3-h1_0.565	AGAAAGGGG	1	BPC1_Q2_M01126_T
19_e_k4me3-h1_0.565	ACGTGCAA	0
20_e_k4me3-h1_0.565	ATACGTGC	0
21_e_k4me3-tro_0.564	AGATGACAC	0
22_h_k4me3-h1_0.563	TTTTAATTAGTG	1	Vsx2_MA0180.1_J
23_e_k4me3-tro_0.562	TGCTGCATA	0
24_e_k4me3-tro_0.562	AAACTACTG	0
25_e_k4me3-h1_0.562	AAGACGCGC	0
26_e_k4me3-h1_0.561	CAACCTTT	0
27_h_k4me3-h1_0.561	TTGCTCGC	0
28_e_k4me3-h1_0.561	AATGGAGGG	0
29_e_k4me3-tro_0.560	AAGCTTGTC	0
30_e_k4me3-h1_0.559	CTGCAATCC	0
31_e_k4me3-tro_0.559	TCTGCCAGT	0
32_e_k4me3-h1_0.559	CCGTGTGAA	0
33_e_k4me3-h1_0.559	AAGCAAGCGG	0
34_h_k4me3-h1_0.557	GCCGGACCCCTA	0
35_e_k4me3-tro_0.557	CATTTTGAGC	1	ZNF205_10_H
36_e_k4me3-tro_0.557	CTCTAAGTC	0
37_e_k4me3-h1_0.556	CCCTAACG	0
38_e_k4me3-h1_0.556	AGACTATTG	0
39_e_k4me3-tro_0.556	AATAGGTCA	2	RORBETA_Q2_M01722_T, RORA_Q4_M01138_T
40_e_k4me3-tro_0.553	CTCCTGGCCA	0
41_e_k4me3-tro_0.552	GACCATGGC	0
42_e_k4me3-tro_0.552	GGCATAAAC	0
43_e_k4me3-tro_0.551	TCACGCCA	0
44_e_k4me3-h1_0.550	CGCAAACTC	0
45_e_k4me3-h1_0.550	AGCATTTAAA	0
46_e_k4me3-h1_0.548	AGGGAAATCT	1	TULP1_9_H
47_e_k4me3-h1_0.544	ATGCGATGGC	0
48_e_k4me3-h1_0.543	CACCTCGGG	0
49_e_k4me3-tro_0.543	AGCTCCACA	0
50_e_k4me3-tro_0.542	TCCAAGGAA	0
51_e_k4me3-tro_0.542	GGGCTACAC	0
52_e_k4me3-h1_0.541	CAGTCGTCC	0
53_e_k4me3-tro_0.541	ATTTGAACG	0
54_e_k4me3-h1_0.540	AATAGGATT	0
55_e_k4me3-tro_0.538	AAAAGAGTC	0
56_e_k4me3-h1_0.537	CTCATCCGA	0
57_e_k4me3-tro_0.534	GCACTACAG	0
58_e_k4me3-h1_0.522	TAGTGTGAA	0
59_e_k4me3-h1_0.517	AGTGAATAT	0
60_e_k4me3-tro_0.512	CCTATTTAA	0

Name

Preview

Matches

List

RORBETA_Q2_M01722_T, RORA_Q4_M01138_T

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	7

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

ZMAT2_3_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.40506e-06

E-value

0.00410418

q-value

0.00820019

Overlap

Offset

Orientation

Normal

Name

BPC1_Q2_M01126_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.54872e-05

E-value

0.045238

q-value

0.090476

Overlap

Offset

Orientation

Normal

Name

Vsx2_MA0180.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.52193e-06

E-value

0.00444555

q-value

0.0081682

Overlap

Offset

-1

Orientation

Normal

Name

ZNF205_10_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.20654e-06

E-value

0.0064453

q-value

0.0128906

Overlap

Offset

Orientation

Reverse Complement

Name

RORBETA_Q2_M01722_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.11273e-06

E-value

0.00325029

q-value

0.00648403

Overlap

Offset

-2

Orientation

Reverse Complement

Name

RORA_Q4_M01138_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.66025e-05

E-value

0.048496

q-value

0.0392602

Overlap

Offset

Orientation

Normal

Name

TULP1_9_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.71166e-05

E-value

0.0499975

q-value

0.099775

Overlap

Offset

-1

Orientation

Normal

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_k4me3-h1_0.620

Matches to Query: 2_h_k4me3-h1_0.605

Matches to Query: 3_e_k4me3-h1_0.604

Matches to Query: 4_e_k4me3-h1_0.597

Matches to Query: 5_e_k4me3-tro_0.587

Matches to Query: 6_e_k4me3-h1_0.583

Matches to Query: 7_e_k4me3-tro_0.580

Matches to Query: 8_e_k4me3-tro_0.579

Matches to Query: 9_h_k4me3-tro_0.579

Matches to Query: 10_e_k4me3-h1_0.577

Summary

Alignment

Matches to Query: 11_e_k4me3-tro_0.576

Matches to Query: 12_e_k4me3-h1_0.574

Matches to Query: 13_e_k4me3-tro_0.573

Matches to Query: 14_e_k4me3-tro_0.569

Matches to Query: 15_e_k4me3-h1_0.568

Matches to Query: 16_e_k4me3-tro_0.568

Matches to Query: 17_e_k4me3-tro_0.566

Matches to Query: 18_e_k4me3-h1_0.565

Summary

Alignment

Matches to Query: 19_e_k4me3-h1_0.565

Matches to Query: 20_e_k4me3-h1_0.565

Matches to Query: 21_e_k4me3-tro_0.564

Matches to Query: 22_h_k4me3-h1_0.563

Summary

Alignment

Matches to Query: 23_e_k4me3-tro_0.562

Matches to Query: 24_e_k4me3-tro_0.562

Matches to Query: 25_e_k4me3-h1_0.562

Matches to Query: 26_e_k4me3-h1_0.561

Matches to Query: 27_h_k4me3-h1_0.561

Matches to Query: 28_e_k4me3-h1_0.561

Matches to Query: 29_e_k4me3-tro_0.560

Matches to Query: 30_e_k4me3-h1_0.559

Matches to Query: 31_e_k4me3-tro_0.559

Matches to Query: 32_e_k4me3-h1_0.559

Matches to Query: 33_e_k4me3-h1_0.559

Matches to Query: 34_h_k4me3-h1_0.557

Matches to Query: 35_e_k4me3-tro_0.557

Summary

Alignment

Matches to Query: 36_e_k4me3-tro_0.557

Matches to Query: 37_e_k4me3-h1_0.556

Matches to Query: 38_e_k4me3-h1_0.556

Matches to Query: 39_e_k4me3-tro_0.556

Summary

Alignment

Summary

Alignment

Matches to Query: 40_e_k4me3-tro_0.553

Matches to Query: 41_e_k4me3-tro_0.552

Matches to Query: 42_e_k4me3-tro_0.552

Matches to Query: 43_e_k4me3-tro_0.551

Matches to Query: 44_e_k4me3-h1_0.550

Matches to Query: 45_e_k4me3-h1_0.550

Matches to Query: 46_e_k4me3-h1_0.548

Summary

Alignment

Matches to Query: 47_e_k4me3-h1_0.544

Matches to Query: 48_e_k4me3-h1_0.543

Matches to Query: 49_e_k4me3-tro_0.543

Matches to Query: 50_e_k4me3-tro_0.542

Matches to Query: 51_e_k4me3-tro_0.542

Matches to Query: 52_e_k4me3-h1_0.541

Matches to Query: 53_e_k4me3-tro_0.541

Matches to Query: 54_e_k4me3-h1_0.540

Matches to Query: 55_e_k4me3-tro_0.538

Matches to Query: 56_e_k4me3-h1_0.537

Matches to Query: 57_e_k4me3-tro_0.534