TOMTOM

Name	Preview	Matches	List
1_e_k9me3-mes_0.544	AAAACTAGAC	0
2_e_k9me3-h1_0.543	AGGTACCAG	0
3_e_k9me3-h1_0.542	AGCCAAGAT	1	YY1_02_M00069_T
4_e_k9me3-mes_0.542	CAAAACTGC	0
5_e_k9me3-mes_0.540	ATGCACACA	0
6_e_k9me3-mes_0.540	ACCATAGGCCTCA	0
7_e_k9me3-mes_0.540	CTCAGAAACT	0
8_e_k9me3-mes_0.539	AGTGTTTCAA	0
9_e_k9me3-mes_0.539	CCTCAAAGCGC	0
10_e_k9me3-mes_0.539	GCTCAATCA	1	ZID_01_M00085_T
11_e_k9me3-h1_0.538	GACTAATACA	0
12_e_k9me3-h1_0.538	CTGTTCCTAT	0
13_e_k9me3-mes_0.538	ACAGAGTTG	0
14_e_k9me3-h1_0.538	TCACTATCA	0
15_e_k9me3-mes_0.537	GCAAGTGGATAT	0
16_e_k9me3-mes_0.537	CTTTTTGTA	0
17_e_k9me3-mes_0.537	CTTCACGTA	0
18_e_k9me3-h1_0.536	AAGACAATG	0
19_e_k9me3-h1_0.535	CCATATCAT	0
20_e_k9me3-mes_0.535	AGACAGAAGCATT	0
21_e_k9me3-mes_0.534	ATCTCACAGA	0
22_e_k9me3-h1_0.534	GGGTGGGGAGG	2	MZF1_Q5_M01733_T, MZF1_01_M00083_T
23_e_k9me3-h1_0.534	GGTACCTCA	0
24_e_k9me3-h1_0.534	GGCATTAGA	0
25_e_k9me3-h1_0.533	GTAATGTTA	0
26_e_k9me3-h1_0.533	TATGGTTTG	0
27_e_k9me3-h1_0.532	GATCTCCTGA	0
28_e_k9me3-h1_0.532	CGAGGAGCC	1	ANXA11_6_H
29_e_k9me3-mes_0.531	AGGTTCAACT	0
30_e_k9me3-h1_0.531	GTGAGACAA	0
31_e_k9me3-h1_0.530	GCAAGCTCC	0
32_e_k9me3-h1_0.530	TAGTAAAGA	0
33_e_k9me3-mes_0.530	CCGGTATAG	0
34_e_k9me3-h1_0.530	AAAATGTGGGA	0
35_e_k9me3-h1_0.530	GATCTCAGC	0
36_e_k9me3-h1_0.530	CATGATCTC	0
37_e_k9me3-h1_0.530	AGAACAGCAGTAA	0
38_e_k9me3-h1_0.530	GGAAATGCAT	2	SCMH1_9_H, BCL11A_7_H
39_e_k9me3-mes_0.529	CAAATGTCC	0
40_h_k9me3-h1_0.529	CAAGGCGTCA	0
41_e_k9me3-h1_0.529	GGAAGCAGAC	0
42_e_k9me3-h1_0.529	ACTCGTATG	0
43_e_k9me3-h1_0.529	ATCAGGCATT	0
44_e_k9me3-h1_0.529	ACCTGGAAA	0
45_e_k9me3-mes_0.527	ACTCGCAGA	0
46_e_k9me3-mes_0.527	ATCACAGGA	1	Tcf7_primary_SCI09_U
47_e_k9me3-h1_0.525	CATGTGCAGT	0
48_e_k9me3-mes_0.523	TCGCTTGAA	0
49_e_k9me3-h1_0.523	CACTTTTAA	0
50_e_k9me3-h1_0.522	CCACCTCAGC	1	ROM_Q2_M00700_T
51_e_k9me3-h1_0.521	CCTTCCTAGA	0
52_e_k9me3-h1_0.512	CGCACACCAC	0
53_e_k9me3-mes_0.510	AATGGAATG	0
54_e_k9me3-mes_0.509	CCCACGAGGG	0
55_e_k9me3-mes_0.509	ACCACTGCA	0
56_e_k9me3-mes_0.507	TGCCTGTAA	0
57_e_k9me3-mes_0.505	AACCTGGGA	0
58_e_k9me3-mes_0.505	TACGCTGGAGA	1	UGP2_3_H
59_e_k9me3-mes_0.505	CTAGGTGAC	0
60_e_k9me3-mes_0.505	GACACAGCC	0

Name

Preview

Matches

List

MZF1_Q5_M01733_T, MZF1_01_M00083_T

SCMH1_9_H, BCL11A_7_H

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	10

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

YY1_02_M00069_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.21469e-05

E-value

0.0354812

q-value

0.0709624

Overlap

Offset

Orientation

Reverse Complement

Name

ZID_01_M00085_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

6.48185e-06

E-value

0.0189335

q-value

0.037867

Overlap

Offset

Orientation

Normal

Name

MZF1_Q5_M01733_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.4657e-06

E-value

0.00720231

q-value

0.0143011

Overlap

Offset

-3

Orientation

Normal

Name

MZF1_01_M00083_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.63642e-05

E-value

0.0477999

q-value

0.0474563

Overlap

Offset

-1

Orientation

Normal

Name

ANXA11_6_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.77292e-07

E-value

0.00110207

q-value

0.00220414

Overlap

Offset

-1

Orientation

Normal

Name

SCMH1_9_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

4.28947e-06

E-value

0.0125295

q-value

0.0246172

Overlap

Offset

-1

Orientation

Normal

Name

BCL11A_7_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

8.52583e-06

E-value

0.0249039

q-value

0.0246172

Overlap

Offset

-1

Orientation

Normal

Name

Tcf7_primary_SCI09_U

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.65765e-05

E-value

0.04842

q-value

0.0481826

Overlap

Offset

Orientation

Normal

Name

ROM_Q2_M00700_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.5095e-05

E-value

0.0440924

q-value

0.0881849

Overlap

Offset

Orientation

Normal

Name

UGP2_3_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

8.44326e-06

E-value

0.0246628

q-value

0.0493255

Overlap

Offset

-4

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_e_k9me3-mes_0.544

Matches to Query: 2_e_k9me3-h1_0.543

Matches to Query: 3_e_k9me3-h1_0.542

Summary

Alignment

Matches to Query: 4_e_k9me3-mes_0.542

Matches to Query: 5_e_k9me3-mes_0.540

Matches to Query: 6_e_k9me3-mes_0.540

Matches to Query: 7_e_k9me3-mes_0.540

Matches to Query: 8_e_k9me3-mes_0.539

Matches to Query: 9_e_k9me3-mes_0.539

Matches to Query: 10_e_k9me3-mes_0.539

Summary

Alignment

Matches to Query: 11_e_k9me3-h1_0.538

Matches to Query: 12_e_k9me3-h1_0.538

Matches to Query: 13_e_k9me3-mes_0.538

Matches to Query: 14_e_k9me3-h1_0.538

Matches to Query: 15_e_k9me3-mes_0.537

Matches to Query: 16_e_k9me3-mes_0.537

Matches to Query: 17_e_k9me3-mes_0.537

Matches to Query: 18_e_k9me3-h1_0.536

Matches to Query: 19_e_k9me3-h1_0.535

Matches to Query: 20_e_k9me3-mes_0.535

Matches to Query: 21_e_k9me3-mes_0.534

Matches to Query: 22_e_k9me3-h1_0.534

Summary

Alignment

Summary

Alignment

Matches to Query: 23_e_k9me3-h1_0.534

Matches to Query: 24_e_k9me3-h1_0.534

Matches to Query: 25_e_k9me3-h1_0.533

Matches to Query: 26_e_k9me3-h1_0.533

Matches to Query: 27_e_k9me3-h1_0.532

Matches to Query: 28_e_k9me3-h1_0.532

Summary

Alignment

Matches to Query: 29_e_k9me3-mes_0.531

Matches to Query: 30_e_k9me3-h1_0.531

Matches to Query: 31_e_k9me3-h1_0.530

Matches to Query: 32_e_k9me3-h1_0.530

Matches to Query: 33_e_k9me3-mes_0.530

Matches to Query: 34_e_k9me3-h1_0.530

Matches to Query: 35_e_k9me3-h1_0.530

Matches to Query: 36_e_k9me3-h1_0.530

Matches to Query: 37_e_k9me3-h1_0.530

Matches to Query: 38_e_k9me3-h1_0.530

Summary

Alignment

Summary

Alignment

Matches to Query: 39_e_k9me3-mes_0.529

Matches to Query: 40_h_k9me3-h1_0.529

Matches to Query: 41_e_k9me3-h1_0.529

Matches to Query: 42_e_k9me3-h1_0.529

Matches to Query: 43_e_k9me3-h1_0.529

Matches to Query: 44_e_k9me3-h1_0.529

Matches to Query: 45_e_k9me3-mes_0.527

Matches to Query: 46_e_k9me3-mes_0.527

Summary

Alignment

Matches to Query: 47_e_k9me3-h1_0.525

Matches to Query: 48_e_k9me3-mes_0.523

Matches to Query: 49_e_k9me3-h1_0.523

Matches to Query: 50_e_k9me3-h1_0.522

Summary

Alignment

Matches to Query: 51_e_k9me3-h1_0.521

Matches to Query: 52_e_k9me3-h1_0.512

Matches to Query: 53_e_k9me3-mes_0.510