TOMTOM

Name	Preview	Matches	List
1_re_28_0.356	GGGATTACA	1	PITX2_Q2_M00482_T
2_re_23_0.361	GTCTCGAAC	1	RPC155_01_M01798_T
3_re_41_0.366	AGGCTGAGG	0
4_re_29_0.366	CTGGGCAACAGAG	0
5_re_37_0.366	CGATCTCGGC	0
6_re_3_0.367	ATCGCTTGAAC	0
7_re_94_0.374	TAGCTGGGA	1	LUN1_01_M00480_T
8_re_86_0.378	GCTCATGCC	0
9_re_40_0.379	TGGTGGCTCA	0
10_re_0_0.380	ACGCCTGTA	0
11_re_27_0.380	AACCCCGTC	0
12_re_13_0.382	CCGTCTCTA	0
13_re_67_0.385	GGGTTTCAC	0
14_re_19_0.390	AGGAGAATCG	0
15_re_176_0.393	GGAAGCCGAG	0
16_re_8_0.400	AAATTAGCC	0
17_re_100_0.400	GATCACACC	0
18_re_140_0.400	ATGGTCTCG	0
19_re_7_0.401	CCCGAGTAGC	0
20_re_42_0.404	AACATGGTGA	0
21_re_112_0.405	CACTTTGGG	0
22_re_181_0.407	CCATTGCAC	0
23_re_39_0.407	GCCCGCCACGAG	0
24_e_419_0.414	CTACGATT	0
25_re_129_0.415	AAGTGCTGG	0
26_e_118_0.576	ATGCAAATGA	10	OCT_C_M00210_T, OCT_Q6_M00795_T, IL24_5_H, nub_MA0453.1_J, Pou2f3_3986.2_Cell08_U, OCT1_Q5_01_M00930_T, POU2F3_01_M01476_T, OCT2_01_M01368_T, Pou2f2_3748.1_Cell08_U, OCT1_B_M00342_T
27_e_262_0.429	TAACGGGTA	0
28_h_5_0.568	GTAAGCAC	0
29_re_221_0.437	TGTGACGTCATC	10	Atf1_primary_SCI09_U, STF1_02_M01187_T, TGA2_01_M01586_T, ATF3_Q6_M00513_T, Jundm2_primary_SCI09_U, STF1_01_M01186_T, CREB_Q4_M00178_T, VJUN_01_M00036_T, ATF_B_M00338_T, CREB1_MA0018.2_J
30_h_11_0.560	CCTCTGAGCA	0
31_e_79_0.445	ATACCGAAA	0
32_h_13_0.550	GCTGTCAG	2	achi_MA0207.1_J, TGIF_01_M00418_T
33_re_247_0.454	CCACGATCA	0
34_re_174_0.544	CCATTCATT	2	Hbp1_primary_SCI09_U, THAP5_4_H
35_h_24_0.544	AAGTCACT	0
36_h_14_0.543	ACTTGTCC	0
37_e_268_0.542	GTGTATGCAT	0
38_e_12_0.537	CGTGTGTAC	0
39_e_297_0.535	ACAGAACAC	0
40_e_434_0.534	CCTTAATAC	0
41_h_18_0.533	ACAAACGC	0
42_e_175_0.470	GTCTTCGGA	0
43_h_25_0.530	ACCAACTG	2	Mybl1_secondary_SCI09_U, Myb_secondary_SCI09_U
44_e_314_0.523	AATGTGGCTATC	0
45_re_223_0.479	AGGAGGAAG	0
46_e_251_0.521	CCACTAGC	0
47_e_450_0.481	TCCAGGTA	0
48_e_112_0.485	AACTTTACG	0
49_e_568_0.493	CGTCTTTGTA	0
50_e_519_0.499	TATCGCTAA	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	29

Summary

Alignment

Name	PITX2_Q2_M00482_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.53844e-06
E-value	0.0190988
q-value	0.0381976
Overlap	9
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	RPC155_01_M01798_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.61585e-06
E-value	0.0222459
q-value	0.0444918
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	LUN1_01_M00480_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.51175e-07
E-value	0.00131788
q-value	0.00263576
Overlap	9
Offset	8
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT_C_M00210_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.1627e-07
E-value	0.00209222
q-value	0.00321474
Overlap	10
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT_Q6_M00795_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.65299e-06
E-value	0.00482838
q-value	0.00321474
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	IL24_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.99206e-06
E-value	0.0058188
q-value	0.00321474
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	nub_MA0453.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.31783e-06
E-value	0.00677037
q-value	0.00321474
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	Pou2f3_3986.2_Cell08_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.03031e-06
E-value	0.0117725
q-value	0.00321474
Overlap	10
Offset	4
Orientation	Normal

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Summary

Alignment

Name	OCT1_Q5_01_M00930_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.46217e-06
E-value	0.013034
q-value	0.00321474
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	POU2F3_01_M01476_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.48275e-06
E-value	0.0130941
q-value	0.00321474
Overlap	10
Offset	4
Orientation	Normal

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Summary

Alignment

Name	OCT2_01_M01368_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.97718e-06
E-value	0.0145383
q-value	0.00321474
Overlap	10
Offset	4
Orientation	Normal

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Summary

Alignment

Name	Pou2f2_3748.1_Cell08_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.97718e-06
E-value	0.0145383
q-value	0.00321474
Overlap	10
Offset	4
Orientation	Normal

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Summary

Alignment

Name	OCT1_B_M00342_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.10174e-05
E-value	0.0321817
q-value	0.00640446
Overlap	9
Offset	1
Orientation	Normal

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Summary

Alignment

Name	Atf1_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.34048e-07
E-value	0.00185205
q-value	0.00145072
Overlap	12
Offset	2
Orientation	Normal

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Summary

Alignment

Name	STF1_02_M01187_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.47072e-07
E-value	0.0024743
q-value	0.00145072
Overlap	12
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TGA2_01_M01586_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.06631e-06
E-value	0.00311468
q-value	0.00145072
Overlap	12
Offset	0
Orientation	Normal

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Summary

Alignment

Name	ATF3_Q6_M00513_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.15024e-06
E-value	0.00335984
q-value	0.00145072
Overlap	12
Offset	1
Orientation	Normal

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Summary

Alignment

Name	Jundm2_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.39192e-06
E-value	0.00406579
q-value	0.00145072
Overlap	12
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	STF1_01_M01186_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.01601e-06
E-value	0.00588878
q-value	0.00145072
Overlap	12
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	CREB_Q4_M00178_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.40575e-06
E-value	0.0099482
q-value	0.00217846
Overlap	12
Offset	0
Orientation	Normal

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Summary

Alignment

Name	VJUN_01_M00036_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.22042e-06
E-value	0.0181698
q-value	0.00358096
Overlap	12
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	ATF_B_M00338_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.58101e-06
E-value	0.0250651
q-value	0.00436604
Overlap	11
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	CREB1_MA0018.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.10099e-06
E-value	0.026584
q-value	0.00436604
Overlap	8
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	achi_MA0207.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.58025e-06
E-value	0.0221419
q-value	0.0233646
Overlap	6
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	TGIF_01_M00418_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.03031e-06
E-value	0.0234565
q-value	0.0233646
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	Hbp1_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.71038e-06
E-value	0.00499603
q-value	0.00999071
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	THAP5_4_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.27326e-05
E-value	0.037192
q-value	0.037187
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Mybl1_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.39189e-06
E-value	0.00990772
q-value	0.0183977
Overlap	8
Offset	2
Orientation	Normal

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Summary

Alignment

Name	Myb_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.29841e-06
E-value	0.0183977
q-value	0.0183977
Overlap	8
Offset	2
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_re_28_0.356

Summary

Alignment

Matches to Query: 2_re_23_0.361

Summary

Alignment

Matches to Query: 3_re_41_0.366

Matches to Query: 4_re_29_0.366

Matches to Query: 5_re_37_0.366

Matches to Query: 6_re_3_0.367

Matches to Query: 7_re_94_0.374

Summary

Alignment

Matches to Query: 8_re_86_0.378

Matches to Query: 9_re_40_0.379

Matches to Query: 10_re_0_0.380

Matches to Query: 11_re_27_0.380

Matches to Query: 12_re_13_0.382

Matches to Query: 13_re_67_0.385

Matches to Query: 14_re_19_0.390

Matches to Query: 15_re_176_0.393

Matches to Query: 16_re_8_0.400

Matches to Query: 17_re_100_0.400

Matches to Query: 18_re_140_0.400

Matches to Query: 19_re_7_0.401

Matches to Query: 20_re_42_0.404

Matches to Query: 21_re_112_0.405

Matches to Query: 22_re_181_0.407

Matches to Query: 23_re_39_0.407

Matches to Query: 24_e_419_0.414

Matches to Query: 25_re_129_0.415

Matches to Query: 26_e_118_0.576

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 27_e_262_0.429

Matches to Query: 28_h_5_0.568

Matches to Query: 29_re_221_0.437

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment