TOMTOM

Name	Preview	Matches	List
1_e_k9me3-h1_0.593	GTGAGATGA	0
2_e_k9me3-npc_0.587	CAGCAACAGGA	1	RAV1_01_M00343_T
3_e_k9me3-npc_0.583	AGCTGCACA	0
4_e_k9me3-npc_0.581	CTGTTAAA	0
5_e_k9me3-h1_0.574	CTCAAACTC	0
6_h_k9me3-npc_0.570	GCATCTAAAG	0
7_h_k9me3-npc_0.569	AGGTCCAGAACC	0
8_e_k9me3-h1_0.568	CACTCCAGC	0
9_e_k9me3-npc_0.567	GGAAGTACAG	0
10_e_k9me3-h1_0.566	ACAGGCATG	0
11_e_k9me3-npc_0.565	GACTAATACT	0
12_e_k9me3-npc_0.564	GTTTGGAGA	0
13_e_k9me3-h1_0.564	CCGTCCAT	0
14_e_k9me3-h1_0.563	ACTCTGTCT	0
15_h_k9me3-npc_0.563	GCTGGTGCTGTT	0
16_e_k9me3-npc_0.561	ACGCTTCAT	0
17_e_k9me3-h1_0.561	CCTGGGTGAGA	0
18_h_k9me3-npc_0.560	ATTGTGTTCT	0
19_e_k9me3-npc_0.560	AACAGTTAC	0
20_e_k9me3-npc_0.560	CTGTTGTGAT	0
21_e_k9me3-npc_0.559	CTCAGTTTCT	0
22_e_k9me3-h1_0.559	TAGGGGTCAG	0
23_e_k9me3-h1_0.558	ATATGTATG	0
24_h_k9me3-npc_0.557	GGTGCTGCAGCA	0
25_e_k9me3-npc_0.557	CGTTTACCC	0
26_e_k9me3-h1_0.557	GAGGGCTCCC	0
27_e_k9me3-h1_0.557	GAGACCAGC	0
28_h_k9me3-npc_0.557	CACACAAC	0
29_e_k9me3-npc_0.556	TTAACCGCAG	0
30_e_k9me3-h1_0.556	CTGACCTCA	1	TERALPHA_Q6_M01724_T
31_e_k9me3-npc_0.555	GGAAGAGTA	0
32_e_k9me3-npc_0.555	ACATCACTGCC	0
33_e_k9me3-h1_0.555	GAGCCATG	0
34_e_k9me3-npc_0.554	ACAACGAG	0
35_e_k9me3-h1_0.553	GAGTCTTGCT	0
36_e_k9me3-h1_0.552	AGAGACGGG	0
37_e_k9me3-npc_0.552	CCAAGAACA	0
38_e_k9me3-h1_0.552	GTGGAAGGA	0
39_e_k9me3-npc_0.551	TCTTCAGCA	0
40_e_k9me3-h1_0.551	TGGCCGAAT	0
41_e_k9me3-npc_0.550	AAAGCGTTA	0
42_e_k9me3-h1_0.550	AGTGGGGAG	3	MZF1_01_M00083_T, YPR022C_01_M01647_T, MZF1_Q5_M01733_T
43_e_k9me3-h1_0.550	AACCTCCAC	0
44_e_k9me3-npc_0.550	ACTAAAGGC	0
45_e_k9me3-h1_0.549	CAGGGTTTC	0
46_e_k9me3-h1_0.549	CATTCCCAAG	2	IK1_01_M00086_T, LARP4_9_H
47_e_k9me3-h1_0.548	CCATAAAGG	0
48_e_k9me3-h1_0.547	ATCACTTGA	0
49_e_k9me3-h1_0.547	GTGTGAGCAC	0
50_h_k9me3-npc_0.547	CAATGACAATGC	0
51_e_k9me3-npc_0.546	CTAGGTGACT	0
52_h_k9me3-npc_0.545	ATCCGTGGAG	0
53_e_k9me3-h1_0.545	GGAGATCGA	0
54_e_k9me3-npc_0.545	ACGATCCA	0
55_e_k9me3-npc_0.545	AAAATACAC	0
56_e_k9me3-h1_0.544	CCATGTTA	0
57_e_k9me3-npc_0.544	GAAAGAAGA	0
58_e_k9me3-npc_0.543	AAATCCTAG	0
59_e_k9me3-h1_0.542	GATTTCTGC	0
60_e_k9me3-npc_0.542	CTCATTTGC	2	OCT_C_M00210_T, nub_MA0453.1_J
61_e_k9me3-h1_0.541	AACCAGTCA	0
62_e_k9me3-h1_0.540	GAGGAATAAA	0
63_e_k9me3-npc_0.539	AGGTGACAT	0
64_e_k9me3-npc_0.538	AAGTATGGG	0
65_e_k9me3-npc_0.538	AGACGTGGG	0
66_e_k9me3-npc_0.536	CCAGTGGCC	0
67_e_k9me3-npc_0.536	TGAGCGCG	0
68_e_k9me3-h1_0.536	AAACTGCCT	0
69_e_k9me3-h1_0.536	AGATATTTC	0
70_h_k9me3-npc_0.536	TGCCTGAAGT	0
71_e_k9me3-npc_0.535	GAGACCTAA	0
72_e_k9me3-h1_0.535	AATCGCTTA	0
73_h_k9me3-h1_0.534	GACGGTCCCA	0
74_e_k9me3-h1_0.534	GATCCTGGAA	0
75_e_k9me3-h1_0.532	CATAGCTCA	0
76_e_k9me3-h1_0.530	AATAAATCT	0
77_e_k9me3-npc_0.530	ATTGATACC	0
78_e_k9me3-h1_0.529	GTGAATAA	0
79_e_k9me3-h1_0.529	TGTCCCTTG	0
80_e_k9me3-h1_0.528	TCTAACACA	0
81_e_k9me3-h1_0.528	ATCCTCAAA	0
82_e_k9me3-npc_0.527	CCATTGCACT	0
83_e_k9me3-h1_0.524	GTGGCTATA	0
84_h_k9me3-h1_0.524	AGATCGCC	1	NFMUE1_Q6_M00651_T
85_h_k9me3-h1_0.523	CTTGAAAGGGGA	2	MSN4_MA0342.1_J, RGM1_MA0366.1_J
86_e_k9me3-h1_0.522	TCTCTGGGTC	0
87_e_k9me3-npc_0.518	GATGGGGTA	0
88_e_k9me3-h1_0.515	CATTACCAC	1	Ubx_MA0094.1_J
89_e_k9me3-npc_0.505	CAGCCTGGGC	0
90_h_k9me3-h1_0.505	ACTGCTCAATCA	0

Name

Preview

Matches

List

MZF1_01_M00083_T, YPR022C_01_M01647_T, MZF1_Q5_M01733_T

IK1_01_M00086_T, LARP4_9_H

OCT_C_M00210_T, nub_MA0453.1_J

MSN4_MA0342.1_J, RGM1_MA0366.1_J

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	13

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

RAV1_01_M00343_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.52833e-05

E-value

0.0446426

q-value

0.0892853

Overlap

Offset

Orientation

Normal

Name

TERALPHA_Q6_M01724_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.43421e-06

E-value

0.0100313

q-value

0.0199702

Overlap

Offset

Orientation

Reverse Complement

Name

MZF1_01_M00083_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

7.44905e-06

E-value

0.0217587

q-value

0.0186431

Overlap

Offset

Orientation

Normal

Name

YPR022C_01_M01647_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

8.31279e-06

E-value

0.0242817

q-value

0.0186431

Overlap

Offset

-1

Orientation

Reverse Complement

Name

MZF1_Q5_M01733_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

9.59974e-06

E-value

0.0280408

q-value

0.0186431

Overlap

Offset

-2

Orientation

Normal

Name

IK1_01_M00086_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.49524e-06

E-value

0.00436759

q-value

0.00873517

Overlap

Offset

Orientation

Reverse Complement

Name

LARP4_9_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.04651e-05

E-value

0.0305685

q-value

0.0305685

Overlap

Offset

-2

Orientation

Reverse Complement

Name

OCT_C_M00210_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

6.16087e-06

E-value

0.0179959

q-value

0.0359374

Overlap

Offset

Orientation

Normal

Name

nub_MA0453.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.67145e-05

E-value

0.0488231

q-value

0.0487493

Overlap

Offset

Orientation

Reverse Complement

Name

NFMUE1_Q6_M00651_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

9.0318e-06

E-value

0.0263819

q-value

0.0527637

Overlap

Offset

Orientation

Reverse Complement

Name

MSN4_MA0342.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.66689e-05

E-value

0.0486898

q-value

0.048658

Overlap

Offset

-6

Orientation

Normal

Name

RGM1_MA0366.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.66689e-05

E-value

0.0486898

q-value

0.048658

Overlap

Offset

-6

Orientation

Normal

Name

Ubx_MA0094.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

E-value

q-value

Overlap

Offset

-1

Orientation

Reverse Complement

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-h1_0.593

Matches to Query: 2_e_k9me3-npc_0.587

Summary

Alignment

Matches to Query: 3_e_k9me3-npc_0.583

Matches to Query: 4_e_k9me3-npc_0.581

Matches to Query: 5_e_k9me3-h1_0.574

Matches to Query: 6_h_k9me3-npc_0.570

Matches to Query: 7_h_k9me3-npc_0.569

Matches to Query: 8_e_k9me3-h1_0.568

Matches to Query: 9_e_k9me3-npc_0.567

Matches to Query: 10_e_k9me3-h1_0.566

Matches to Query: 11_e_k9me3-npc_0.565

Matches to Query: 12_e_k9me3-npc_0.564

Matches to Query: 13_e_k9me3-h1_0.564

Matches to Query: 14_e_k9me3-h1_0.563

Matches to Query: 15_h_k9me3-npc_0.563

Matches to Query: 16_e_k9me3-npc_0.561

Matches to Query: 17_e_k9me3-h1_0.561

Matches to Query: 18_h_k9me3-npc_0.560

Matches to Query: 19_e_k9me3-npc_0.560

Matches to Query: 20_e_k9me3-npc_0.560

Matches to Query: 21_e_k9me3-npc_0.559

Matches to Query: 22_e_k9me3-h1_0.559

Matches to Query: 23_e_k9me3-h1_0.558

Matches to Query: 24_h_k9me3-npc_0.557

Matches to Query: 25_e_k9me3-npc_0.557

Matches to Query: 26_e_k9me3-h1_0.557

Matches to Query: 27_e_k9me3-h1_0.557

Matches to Query: 28_h_k9me3-npc_0.557

Matches to Query: 29_e_k9me3-npc_0.556

Matches to Query: 30_e_k9me3-h1_0.556

Summary

Alignment

Matches to Query: 31_e_k9me3-npc_0.555

Matches to Query: 32_e_k9me3-npc_0.555

Matches to Query: 33_e_k9me3-h1_0.555

Matches to Query: 34_e_k9me3-npc_0.554

Matches to Query: 35_e_k9me3-h1_0.553

Matches to Query: 36_e_k9me3-h1_0.552

Matches to Query: 37_e_k9me3-npc_0.552

Matches to Query: 38_e_k9me3-h1_0.552

Matches to Query: 39_e_k9me3-npc_0.551

Matches to Query: 40_e_k9me3-h1_0.551

Matches to Query: 41_e_k9me3-npc_0.550

Matches to Query: 42_e_k9me3-h1_0.550

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 43_e_k9me3-h1_0.550

Matches to Query: 44_e_k9me3-npc_0.550

Matches to Query: 45_e_k9me3-h1_0.549

Matches to Query: 46_e_k9me3-h1_0.549

Summary

Alignment

Summary

Alignment

Matches to Query: 47_e_k9me3-h1_0.548

Matches to Query: 48_e_k9me3-h1_0.547

Matches to Query: 49_e_k9me3-h1_0.547

Matches to Query: 50_h_k9me3-npc_0.547

Matches to Query: 51_e_k9me3-npc_0.546

Matches to Query: 52_h_k9me3-npc_0.545

Matches to Query: 53_e_k9me3-h1_0.545

Matches to Query: 54_e_k9me3-npc_0.545

Matches to Query: 55_e_k9me3-npc_0.545

Matches to Query: 56_e_k9me3-h1_0.544

Matches to Query: 57_e_k9me3-npc_0.544