TOMTOM

Name	Preview	Matches	List
1_re_2_0.447	TTTTAAAAA	0
2_re_43_0.456	CTCCTTCCCA	0
3_re_30_0.458	AGGGGCAGGGAC	1	HLCS_2_H
4_re_41_0.459	GCCTGGCAC	0
5_re_3_0.459	TATTTTTAAC	2	AMEF2_Q6_M00403_T, MEF2_05_M01301_T
6_re_14_0.459	TATAAAATA	0
7_re_5_0.460	AATAAATAT	1	CROC_01_M00266_T
8_re_24_0.463	AAATAAATG	1	CSTF2_5_H
9_re_23_0.463	AGAGAAGAGG	0
10_e_41_0.536	GCGCTCCAAC	0
11_re_57_0.465	CAGGCACTG	0
12_h_9_0.534	GAGTGGAATGGA	0
13_e_235_0.534	ACTGCATTC	0
14_re_63_0.466	CAGAGCTGGA	0
15_re_45_0.467	CGTATTTTA	0
16_re_18_0.467	CAGGAAACTG	0
17_re_90_0.468	CTCCCCACC	3	MZF1_01_M00083_T, MZF1_Q5_M01733_T, YPR022C_01_M01647_T
18_re_17_0.469	GGGAAAAAA	0
19_re_70_0.470	GAGAGGAAA	0
20_re_80_0.470	GAAATAATATA	0
21_re_12_0.472	TAATACGTAAA	0
22_e_186_0.528	GATACTACA	0
23_e_12_0.527	GAAACCCTAC	0
24_re_66_0.473	CTCTCTGCCT	0
25_re_20_0.473	CATTTTCTCT	0
26_h_16_0.525	ACATCACAAAGA	0
27_re_67_0.475	TACAGATGAGA	0
28_re_53_0.476	AATGAATGA	1	Hbp1_primary_SCI09_U
29_re_48_0.476	AACTGAGGC	0
30_e_107_0.524	TCTACAAAAA	0
31_h_3_0.524	CCTATGAATGTA	0
32_re_27_0.476	AGCACCTAC	0
33_e_49_0.523	GAATTCACAG	0
34_re_32_0.478	GGAAACGTAGG	2	DIS3_8_H, NFAT1_Q6_M01281_T
35_h_4_0.519	GAATTCATAC	0
36_re_60_0.481	GGAGGACAGAG	0
37_e_60_0.519	TCGAGTACA	0
38_e_16_0.518	CCACATTCAT	0
39_re_93_0.482	ACGTAATAT	0
40_e_99_0.518	ATGTGAAGA	0
41_e_321_0.516	TACACGCA	0
42_e_149_0.515	GAACGTTCA	0
43_e_145_0.515	ACTCGTACAG	0
44_e_442_0.515	ACTGGCTGAA	0
45_h_29_0.514	TACCTGCA	0
46_e_108_0.514	AGCGCTTTG	0
47_e_3_0.514	AATTCGATG	0
48_e_178_0.514	AATGTAGCG	0
49_re_71_0.486	AGGTCACACA	1	GTF3C5_2_H
50_h_6_0.514	GTTCAACTCTGT	0
51_e_98_0.514	CATCAAATG	0
52_re_65_0.486	CACGTGGAG	0
53_re_19_0.487	AAGCACGTGGC	3	Myc_MA0147.1_J, Mycn_MA0104.2_J, MYC::MAX_MA0059.1_J
54_re_69_0.487	CACGGTCACA	0
55_e_241_0.513	CATGCATGCA	1	PF14_0633_PNAS08_U
56_re_29_0.488	AGCTGTGTG	0
57_e_92_0.512	ATACGATTC	0
58_e_225_0.512	GACGTGTCC	0
59_re_42_0.488	GAAACACACA	0
60_h_1_0.512	GCTTCTGTCTAG	0
61_e_62_0.512	CATCAGAGAG	0
62_e_221_0.512	AATCAAAAG	0
63_e_158_0.511	GCCTTATGA	0
64_re_85_0.489	AAATGTCAC	0
65_e_367_0.511	CGTCACTGC	0
66_h_2_0.511	GTGGGAAAGCCT	0
67_e_360_0.511	AGAGATGTG	0
68_e_90_0.510	AGATATTTCC	0
69_e_413_0.510	GACCGTATC	0
70_e_416_0.510	GGTACACAC	0
71_e_148_0.510	CATAAAAAC	1	ABDB_Q6_M01094_T
72_e_44_0.510	ATGATTCCA	0
73_e_24_0.510	GCAAGTGGAGTT	0
74_e_295_0.509	AATGCTGA	0
75_h_24_0.509	GTCTAGTTTT	0
76_e_203_0.508	GTGTACTCA	0
77_e_7_0.508	CACACTGGAC	0
78_e_169_0.507	CATTCTTTA	0
79_e_364_0.507	ACACATAG	0
80_h_5_0.507	AATGCGGGAA	0
81_e_121_0.507	CCGTTCCAC	0
82_e_198_0.507	AACTCATAC	0
83_e_188_0.506	CTACACGGC	0
84_e_368_0.506	GCGTGCCTT	0
85_h_23_0.506	GTGACGATAT	0
86_e_456_0.506	GTTTCTGGA	0
87_e_227_0.505	CAAGTACGC	0
88_e_399_0.505	GGTAGAAAA	0
89_e_370_0.505	AGGTGTACG	0
90_e_330_0.504	CTGTCACGC	0
91_e_440_0.504	GAAACAGTC	0
92_e_143_0.503	CAGAGTTGAG	0
93_e_176_0.503	AGGCACGTA	0
94_e_428_0.503	AATGACAGCA	1	PKNOX2_7_H
95_e_447_0.502	ACTGTGAAA	1	MRPL1_5_H
96_e_150_0.502	ACGTTATTC	0
97_e_215_0.502	ACAGCCACA	0
98_e_427_0.501	CCCTGCACA	0
99_e_66_0.501	ATTCCTTAC	0
100_h_8_0.501	AGCTGCAAGGGA	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	19

Summary

Alignment

Name	HLCS_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.20819e-06
E-value	0.0122921
q-value	0.0245302
Overlap	5
Offset	-3
Orientation	Normal

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Summary

Alignment

Name	AMEF2_Q6_M00403_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.06287e-06
E-value	0.0147886
q-value	0.0295427
Overlap	10
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	MEF2_05_M01301_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.64803e-05
E-value	0.048139
q-value	0.0418087
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	CROC_01_M00266_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.33174e-06
E-value	0.012653
q-value	0.0251985
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	CSTF2_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.71188e-06
E-value	0.0196054
q-value	0.0391852
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MZF1_01_M00083_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.32834e-06
E-value	0.00680107
q-value	0.0135605
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	MZF1_Q5_M01733_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.13397e-06
E-value	0.0149963
q-value	0.0149504
Overlap	7
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	YPR022C_01_M01647_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.67471e-05
E-value	0.0489182
q-value	0.0325123
Overlap	6
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	Hbp1_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.63747e-05
E-value	0.0478306
q-value	0.0954888
Overlap	9
Offset	6
Orientation	Normal

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Summary

Alignment

Name	DIS3_8_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.31376e-07
E-value	0.00242845
q-value	0.00483368
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	NFAT1_Q6_M01281_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.43706e-06
E-value	0.0188026
q-value	0.0187128
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	GTF3C5_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.24386e-05
E-value	0.0363331
q-value	0.0724813
Overlap	6
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	Myc_MA0147.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.79e-06
E-value	0.0110706
q-value	0.0139182
Overlap	10
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	Mycn_MA0104.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.87026e-06
E-value	0.014226
q-value	0.0139182
Overlap	10
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	MYC::MAX_MA0059.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.58261e-06
E-value	0.0279908
q-value	0.0182567
Overlap	11
Offset	0
Orientation	Normal

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Summary

Alignment

Name	PF14_0633_PNAS08_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.92698e-06
E-value	0.0173127
q-value	0.0282636
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	ABDB_Q6_M01094_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.20817e-06
E-value	0.0210551
q-value	0.0421101
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	PKNOX2_7_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.07932e-06
E-value	0.0265207
q-value	0.0529612
Overlap	6
Offset	-3
Orientation	Normal

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Summary

Alignment

Name	MRPL1_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.79138e-06
E-value	0.0139956
q-value	0.0279912
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_re_2_0.447

Matches to Query: 2_re_43_0.456

Matches to Query: 3_re_30_0.458

Summary

Alignment

Matches to Query: 4_re_41_0.459

Matches to Query: 5_re_3_0.459

Summary

Alignment

Summary

Alignment

Matches to Query: 6_re_14_0.459

Matches to Query: 7_re_5_0.460

Summary

Alignment

Matches to Query: 8_re_24_0.463

Summary

Alignment

Matches to Query: 9_re_23_0.463

Matches to Query: 10_e_41_0.536

Matches to Query: 11_re_57_0.465

Matches to Query: 12_h_9_0.534

Matches to Query: 13_e_235_0.534

Matches to Query: 14_re_63_0.466

Matches to Query: 15_re_45_0.467

Matches to Query: 16_re_18_0.467

Matches to Query: 17_re_90_0.468

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 18_re_17_0.469

Matches to Query: 19_re_70_0.470

Matches to Query: 20_re_80_0.470

Matches to Query: 21_re_12_0.472

Matches to Query: 22_e_186_0.528

Matches to Query: 23_e_12_0.527

Matches to Query: 24_re_66_0.473

Matches to Query: 25_re_20_0.473

Matches to Query: 26_h_16_0.525

Matches to Query: 27_re_67_0.475

Matches to Query: 28_re_53_0.476

Summary

Alignment

Matches to Query: 29_re_48_0.476

Matches to Query: 30_e_107_0.524

Matches to Query: 31_h_3_0.524

Matches to Query: 32_re_27_0.476

Matches to Query: 33_e_49_0.523

Matches to Query: 34_re_32_0.478

Summary

Alignment

Summary

Alignment

Matches to Query: 35_h_4_0.519

Matches to Query: 36_re_60_0.481

Matches to Query: 37_e_60_0.519

Matches to Query: 38_e_16_0.518

Matches to Query: 39_re_93_0.482

Matches to Query: 40_e_99_0.518

Matches to Query: 41_e_321_0.516

Matches to Query: 42_e_149_0.515

Matches to Query: 43_e_145_0.515

Matches to Query: 44_e_442_0.515

Matches to Query: 45_h_29_0.514

Matches to Query: 46_e_108_0.514

Matches to Query: 47_e_3_0.514

Matches to Query: 48_e_178_0.514

Matches to Query: 49_re_71_0.486