TOMTOM

Name	Preview	Matches	List
1_e_134_0.556	CAGCCTCCAG	0
2_re_30_0.447	TCCTCCTTCCCT	0
3_e_334_0.550	CTCATGAGA	0
4_re_65_0.452	AGAGAAGAG	0
5_e_55_0.545	AACGTGGTGA	1	TAF9_2_H
6_re_40_0.455	ATTCATTCA	1	Hbp1_primary_SCI09_U
7_re_43_0.456	GGATGAGGAA	0
8_re_60_0.458	CAGGCACTG	0
9_e_176_0.542	CCAGTCTCGG	0
10_re_38_0.459	GCCTGGCAC	0
11_e_345_0.540	CAAGATGGC	2	YY1_02_M00069_T, YY1_Q6_M00793_T
12_e_211_0.540	ACATGGTGG	0
13_re_19_0.460	AGGAAGAAAA	0
14_re_13_0.460	CTCTGTGCC	0
15_re_71_0.461	TGCCAGGCA	0
16_re_63_0.461	GGGGAAAAA	0
17_re_48_0.461	TGGGCAGGGAT	0
18_re_64_0.464	CAGAGCTGGA	0
19_e_259_0.536	ACCATATCA	0
20_e_197_0.535	GGGTGACATA	0
21_e_100_0.535	TATCACAGCA	0
22_re_57_0.465	TACAGATGACG	0
23_e_249_0.534	CCAACGTGAG	0
24_re_68_0.467	GCACAGTGC	0
25_e_309_0.532	GAGAACAGCAG	0
26_e_226_0.532	ACTAATACA	0
27_re_28_0.469	AATACACGT	0
28_e_376_0.531	ACAATCACG	0
29_re_82_0.470	ATACTTACG	0
30_re_22_0.470	CCTCAGTTTC	0
31_re_56_0.471	GCAAGGTCAC	8	ERR2_01_M01589_T, NR4A2_MA0160.1_J, DAX1_01_M01248_T, SF1_Q6_M00727_T, GTF3C5_2_H, ESR1_MA0112.2_J, NUR77_Q5_M01217_T, SF1_Q6_01_M01132_T
32_re_2_0.472	TTTTAAAAA	0
33_e_332_0.527	GAACTGTGA	0
34_re_46_0.474	AATATATGC	0
35_e_52_0.525	ACAGCGTGG	0
36_re_21_0.476	CAGCACCTACA	0
37_re_0_0.476	TAAAATACGTA	0
38_re_76_0.477	AGTATTTAC	0
39_re_66_0.477	GACGTGTTTC	0
40_h_19_0.523	GATTGGCT	5	NFY_C_M00209_T, CAAT_01_M00254_T, CCAAT-box_POL004.1_J, NFYA_MA0060.1_J, NFY_01_M00287_T
41_re_7_0.477	GAAATGTATATT	0
42_re_78_0.478	AAACGTATGT	0
43_e_181_0.522	CCATCACGCC	0
44_e_303_0.521	ACTGCATTC	0
45_e_281_0.521	AGAGGTTTAC	0
46_e_359_0.521	AGGTTCAAC	0
47_h_30_0.520	GAGTGGAGTGGA	0
48_re_45_0.480	AGCACGTGGC	2	Myc_MA0147.1_J, Mycn_MA0104.2_J
49_re_80_0.481	ACAGCCACAGG	0
50_re_67_0.482	CATAAACGC	1	CKMT1B_2_H
51_e_282_0.518	AATACGCTC	0
52_e_263_0.517	CAGATCTC	0
53_e_69_0.517	CCAACGTAGG	0
54_e_351_0.516	ACTGGGTA	0
55_e_406_0.516	CTCGTAGTC	0
56_e_62_0.514	GACACATCAC	0
57_e_242_0.513	CATACCTGAG	0
58_e_399_0.512	CACATCCTG	0
59_e_366_0.510	GAGTTCACA	0
60_e_203_0.510	GGAAGTCCA	0
61_e_284_0.509	CACATGGGAC	0
62_e_160_0.509	GATTCTACA	0
63_e_16_0.509	ATTCGAGTCC	0
64_e_355_0.507	AGACATGCC	1	P53_01_M00034_T
65_e_354_0.506	GAATAAGTC	0
66_e_34_0.505	ACCACCTGC	2	HLH-2_HLH-3_Cell09_U, hlh-2::hlh-3_PL0002.1_J
67_e_401_0.505	CAGGCATAG	0
68_e_279_0.504	CCAGCGACA	1	BEN_02_M01241_T
69_e_261_0.503	ATCTTCACA	0
70_e_165_0.500	CAGCTGAGCA	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	24

Summary

Alignment

Name	TAF9_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.66886e-05
E-value	0.0487473
q-value	0.0971627
Overlap	5
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	Hbp1_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.21272e-06
E-value	0.00646335
q-value	0.0129267
Overlap	9
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	YY1_02_M00069_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.85734e-07
E-value	0.000834629
q-value	0.00166926
Overlap	9
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	YY1_Q6_M00793_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.13967e-07
E-value	0.0026697
q-value	0.0026697
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	ERR2_01_M01589_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.00881e-06
E-value	0.00294675
q-value	0.0040789
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	NR4A2_MA0160.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.84027e-06
E-value	0.00537543
q-value	0.0040789
Overlap	8
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	DAX1_01_M01248_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.75732e-06
E-value	0.00805414
q-value	0.0040789
Overlap	10
Offset	5
Orientation	Normal

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Summary

Alignment

Name	SF1_Q6_M00727_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.81011e-06
E-value	0.00820834
q-value	0.0040789
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	GTF3C5_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.35912e-06
E-value	0.018575
q-value	0.00738425
Overlap	6
Offset	-4
Orientation	Reverse Complement

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Summary

Alignment

Name	ESR1_MA0112.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.27889e-05
E-value	0.0373564
q-value	0.0107724
Overlap	10
Offset	2
Orientation	Normal

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Summary

Alignment

Name	NUR77_Q5_M01217_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.29876e-05
E-value	0.0379368
q-value	0.0107724
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	SF1_Q6_01_M01132_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.48611e-05
E-value	0.0434094
q-value	0.0107855
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	NFY_C_M00209_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.38647e-06
E-value	0.00697088
q-value	0.0139418
Overlap	8
Offset	3
Orientation	Normal

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Summary

Alignment

Name	CAAT_01_M00254_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.28466e-06
E-value	0.0212785
q-value	0.0141857
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	CCAAT-box_POL004.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.28466e-06
E-value	0.0212785
q-value	0.0141857
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	NFYA_MA0060.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.43194e-05
E-value	0.0418269
q-value	0.0175711
Overlap	8
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	NFY_01_M00287_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.70087e-05
E-value	0.0496824
q-value	0.0175711
Overlap	8
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	Myc_MA0147.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.2872e-06
E-value	0.0154439
q-value	0.0252709
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Mycn_MA0104.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.82419e-06
E-value	0.0257755
q-value	0.0252709
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	CKMT1B_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.36057e-07
E-value	0.000689522
q-value	0.00137904
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	P53_01_M00034_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.50652e-05
E-value	0.0440053
q-value	0.0880106
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	HLH-2_HLH-3_Cell09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.42879e-06
E-value	0.0187785
q-value	0.0209202
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	hlh-2::hlh-3_PL0002.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.28141e-06
E-value	0.021269
q-value	0.0209202
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	BEN_02_M01241_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.474e-06
E-value	0.0218316
q-value	0.0436631
Overlap	8
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_e_134_0.556

Matches to Query: 2_re_30_0.447

Matches to Query: 3_e_334_0.550

Matches to Query: 4_re_65_0.452

Matches to Query: 5_e_55_0.545

Summary

Alignment

Matches to Query: 6_re_40_0.455

Summary

Alignment

Matches to Query: 7_re_43_0.456

Matches to Query: 8_re_60_0.458

Matches to Query: 9_e_176_0.542

Matches to Query: 10_re_38_0.459

Matches to Query: 11_e_345_0.540

Summary

Alignment

Summary

Alignment

Matches to Query: 12_e_211_0.540

Matches to Query: 13_re_19_0.460

Matches to Query: 14_re_13_0.460

Matches to Query: 15_re_71_0.461

Matches to Query: 16_re_63_0.461

Matches to Query: 17_re_48_0.461

Matches to Query: 18_re_64_0.464

Matches to Query: 19_e_259_0.536

Matches to Query: 20_e_197_0.535

Matches to Query: 21_e_100_0.535

Matches to Query: 22_re_57_0.465

Matches to Query: 23_e_249_0.534

Matches to Query: 24_re_68_0.467

Matches to Query: 25_e_309_0.532

Matches to Query: 26_e_226_0.532

Matches to Query: 27_re_28_0.469

Matches to Query: 28_e_376_0.531

Matches to Query: 29_re_82_0.470

Matches to Query: 30_re_22_0.470

Matches to Query: 31_re_56_0.471

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 32_re_2_0.472

Matches to Query: 33_e_332_0.527

Matches to Query: 34_re_46_0.474

Matches to Query: 35_e_52_0.525

Matches to Query: 36_re_21_0.476

Matches to Query: 37_re_0_0.476

Matches to Query: 38_re_76_0.477

Matches to Query: 39_re_66_0.477

Matches to Query: 40_h_19_0.523

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary