The database of the primary motif.

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The ID of the primary motif followed by the alternate ID in brackets if it has one.

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The logo of the primary motif.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

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The number of secondary motifs found that had significant spacings in the tested region.

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The list of secondary motifs found that had significant spacings in the tested region.

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The name of the sequence database.

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The last modified date of the sequence database.

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The number of sequences in the sequence database.

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The number of sequences in the sequence database which were excluded because they were shorter than twice the margin plus the primary motif length.

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The number of sequences in the sequence database which were excluded because they contained large runs of ambiguous symbols (normally wildcard masking) that could bias the results.

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The number of sequences in the sequence database which were excluded because no match to the primary motif could be found at a distance to the edges larger than the margin.

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The number of sequences in the sequence database which were excluded because they were largly identical to other sequences when aligned on the primary motif site.

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The number of sequences which were scanned with the secondary motifs.

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The name of the motif database derived from the file name.

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The date that the motif database was last modified.

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The number of motifs loaded from the motif database. Some motifs may have been excluded.

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The number of motifs with significant E-values whose significant spacings were not considered too similar to those of another motif.

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The number of motifs that while having significant spacings were less signficant than another motif that matched most of the same sites.

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This checkbox ensures the row stays visible after a filter operation that would normally hide it.

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The ID of the secondary motif.

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The alternate name of the secondary motif.

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The ID of the secondary motif followed by the alternate ID in brackets if it has one.

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The name of the cluster to which this secondary motif belongs. SpaMo assigns each secondary motif to a cluster, and names the cluster after the motif in it with the most significant spacing. SpaMo assigns two secondary motifs to the same cluster if the matches in their most significant spacings (from the primary motif) overlap substantially. Clustering is controlled by the -joint and -overlap options.

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The E-value is the lowest p-value of any spacing of the secondary motif times the number of secondary motifs. It estimates the expected number of random secondary motifs that would have the observed minimum p-value or less.

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The gap between the primary and secondary motifs for the most significant spacing.

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The strand and position of the secondary motif relative to the primary motif for the most significant spacing.

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The minimum score accepted as a match to either the primary or secondary motif. This value can greatly affect the results of SpaMo. If it is too high, there will be no matches to the primary motif. If too low, sequences with non-significant matches to the primary and/or secondary motif will reduce the effectiveness of the spacing analysis.

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The distance either side of the primary motif site which makes up the region that can contain the secondary motif site. Additionally it is the minimum gap between the primary motif site and the edge of the sequence. These constraints mean that input sequences shorter than the trimmed length of the primary motif plus two times the margin size can not be used by SpaMo.

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A histogram showing the counts for the orientation with the best spacing.

The significant spacings are highlighted in red.

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The primary motif is used as the reference point for all spacing calculation.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

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The secondary motif occurs at the spacings relative to the primary shown in the histogram below.

Sections of the motif with a gray background have been trimmed and were not used for scanning.

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The regions matching the secondary motif in the sequences with the given spacing are used to construct a motif. The logo for this "inferred" motif is shown aligned with that of the actual secondary motif.

The inferred secondary motif logo should closely resemble that of the secondary motif. If it does not, this may suggest that the observed spacing may actually be due to the enrichment of a motif that differs from the secondary motif.

You can download the inferred secondary motif by moving the mouse cursor over the logo and clicking "Download as MEME motif". You can then use this downloaded motif as an input to Tomtom to see what other known motifs it may resemble.

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These are the sequence logos created by aligning all of the sequences with the significant motif spacing. Alignments are centered on the match to the primary motif and done separately for each of the quadrants that contribute to the significant spacing. The logos extend in both directions (up to) 10 positions past the maximum region considered in the significance tests.

Note 1: If you don't see the complete logo(s), you can use the scroll bar underneath the Alignment window. If you don't see a scroll bar and are on a Mac, you can turn on scroll bars by clicking on the Apple Icon at the top left of your terminal and clicking: System Preferences/General/Show scroll bars/Always.

Note 2:These logos are useful for detecting cases where highly similar regions (such as DNA repeats) are present among the sequences with the significant motif spacing. Such cases may indicate that the spacing is due to recent duplication events rather than to a functional biological relationship between the primary and secondary motifs. Ideally, the regions around the primary and secondary motifs should have low information content and their logos in the alignment should closely match their motifs.

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This table shows the details of the significant spacings between the primary motif and the secondary motif currently selected in the "Secondaries" section, below. Click on a row in this table to select a particular spacing for detailed analysis.

Gap
is the space between the primary and secondary motifs where a value of zero means there is no space between them. Note that if a motif has had low information content areas trimmed off this is the gap to the first untrimmed position.
Orientation
is the combination of quadrants used. Possible values are: individual quadrants (up+, up-, dn+, dn-) which are important when neither motif is palindromic; the diagonally combined quadrants (up+/dn-, up-/dn+) which are important when only the primary motif is palindromic; the vertically combined quadrants (up+/up-, dn+/dn-) which are important when only the secondary motif is palindromic; and all quadrants combined together (all) which is important when both motifs are palindromes.
P-value
is the probability of the observed number (or more) sequences having the observed spacing between the primary and secondary motif, adjusted for multiple tests. The number of multiple tests is the number of spacing bins (the number of bars in one quadrant of the histogram) times the number of combinations of quadrants (nine) tested for significance.
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The histogram below shows the frequency of spacings from the primary motif to the secondary motif.

The two quadrants on the left show spacings where the secondary motif is upstream of the primary motif and the two quadrants on the right show spacings where the secondary motif is downstream of the primary motif.

The two quadrants on the top show spacings where the secondary motif is on the same strand as the primary motif and the two quadrants on the bottom show spacings where the secondary motif is on the opposite strand to the primary motif.

Histogram bars highlighted pink are part of one of the listed significant spacings. This feature can be disabled by unchecking the "highlight all" option under the spacings.

Histogram bars highlighted red are part of the currently selected significant spacing. This feature can be disabled by unchecking the "highlight selected" option under the spacings.

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The selected orientation graph shows the combined quadrants from the selected spacing with a zoomed view that only shows the portion of the graph for which significance testing was performed.

Histogram bars highlighted pink are one of the listed significant spacings for this orientation. This feature can be disabled by unchecking the "highlight all" option under the spacings.

The histogram bar highlighted red is the currently selected significant spacing. This feature can be disabled by unchecking the "highlight selected" option under the spacings.

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This lists the FASTA sequence identifiers of the subset of sequences that contain the significant motif spacing.

These identifiers can be cut-and-pasted into other programs for further analysis (e.g., Genome Ontology analysis or location analysis in the case ChIP-seq peak regions).

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Click on a row in this table to select one of the significant secondary motifs for detailed analysis. The details of the significant spacings between the primary motif and the secondary motif you select here will be displayed in the table and plots above.

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Specify which secondary motifs to display in the Secondaries table by checking one or more of the tick boxes below and then entering filter criteria. Then click "Update" to refresh the view of the Secondaries table.

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Specify the order in which secondary motifs are displayed in the Secondaries table by selecting a sorting criteria in the menu below. Then click "Update" to refresh the view of the Secondaries table.

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For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use SpaMo in your research please cite the following paper:
Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey, "Inferring transcription factor complexes from ChIP-seq data", Nucleic Acids Research, 39(15):e98, 2011. [full text]

Primary Motif  |  Sequence Database  |  Secondary Databases  |  Spacing Analysis  |  Inputs and Settings  |  Program information

Primary Motifs

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Database
Name
Preview
Significant Secondaries
List
meme.xml YTCRCYMTGTTGSCCAGGCTGGWSTBSAAYKSCKS (MEME-3) 385
CYCCGTCTCWAMWAAAAAWAMA (MEME-5),  M6302_1.02 (HOXD13),  GAACCYRGGAGGYGGAGGTTGCAGTGAG (MEME-6),  TGCAGTGR (DREME-10),  AAAAATAC (DREME-5),  M6529_1.02 (UBP1),  M6342_1.02 (MEF2D),  M5616_1.02 (MEF2B),  M0442_1.02 ((ZBTB3)_(Mus_musculus)_(DBD_1.00)),  M1884_1.02 (MEF2A),  AGTAGAG (DREME-8),  M5553_1.02 (HOXC13),  M5557_1.02 (HOXD12),  M6237_1.02 (FOXD3),  M4467_1.02 (MEF2C),  M6251_1.02 (FUBP1),  M6149_1.02 (ARID5B),  M6187_1.02 (DDIT3),  M5583_1.02 (ISL2),  M6242_1.02 (FOXJ3),  ACCTC (DREME-6),  M6245_1.02 (FOXO1),  M6244_1.02 (FOXM1),  M6115_1.02 (TP73),  M2281_1.02 (FOXH1),  CCCAGCWMYTYGGGAGGCYGAGGCRGGAGRA (MEME-2),  M6279_1.02 (HMGA1),  M6490_1.02 (SRY),  M2283_1.02 (FOXP1),  M2306_1.02 (POU2F2),  M6376_1.02 (NKX2-5),  M4476_1.02 (RFX5),  M4451_1.02 (ATF3),  M6518_1.02 (TFEB),  M2292_1.02 (JUND),  M4481_1.02 (USF2),  M4469_1.02 (REST),  M4623_1.02 (JUNB),  M1528_1.02 ((RFX6)_(Mus_musculus)_(DBD_0.66)),  M0398_1.02 ((ZSCAN10)_(Mus_musculus)_(DBD_0.82)),  TCYCAAA (DREME-3),  M4708_1.02 (TBP),  M6517_1.02 (TFE3),  M5632_1.02 (MLX),  AGGCRYGHGCCACCACGCCY (MEME-4),  M4680_1.02 (BACH1),  M1529_1.02 ((RFX7)_(Mus_musculus)_(DBD_1.00)),  M2270_1.02 (DUX4),  M0396_1.02 ((OSR2)_(Mus_musculus)_(DBD_1.00)),  M1917_1.02 (USF1),  M2296_1.02 (MAFK),  M6141_1.02 (ALX1),  M4692_1.02 (SIX5),  M2314_1.02 (SP2),  M5339_1.02 (DLX1),  M5771_1.02 (RAX),  M6557_1.02 (ZNF384),  M4565_1.02 (FOSL2),  M1963_1.02 ((ZFY)_(Mus_musculus)_(DBD_0.97)),  M6236_1.02 (FOXC2),  M6163_1.02 (BPTF),  M6345_1.02 (MITF),  M6347_1.02 (MSX2),  M5500_1.02 (GSC),  M4526_1.02 (SMARCC1),  M6532_1.02 (VDR),  M5932_1.02 (TFEC),  M4681_1.02 (BACH2),  M0900_1.02 (SHOX),  M6322_1.02 (KLF1),  M6442_1.02 (PURA),  M6325_1.02 (KLF6),  M4619_1.02 (FOSL1),  M6330_1.02 (MAFA),  M0422_1.02 ((ZIC5)_(Mus_musculus)_(DBD_0.99)),  M6482_1.02 (SP3),  M6401_1.02 (OTX2),  M6550_1.02 (ZIC3),  M0216_1.02 ((NHLH2)_(Mus_musculus)_(DBD_1.00)),  M6146_1.02 (TFAP2D),  M4511_1.02 (RXRA),  M5345_1.02 (DMBX1),  M5501_1.02 (GSC2),  M5720_1.02 (PITX3),  M4438_1.02 (ESRRA),  M5717_1.02 (PITX1),  M6400_1.02 (OTX1),  M6418_1.02 (PITX2),  M5777_1.02 (RFX4),  M6144_1.02 (TFAP2B),  M1906_1.02 (SP1),  M6548_1.02 (ZIC1),  M6360_1.02 (NFE2L2),  M6391_1.02 (NR2E3),  M6553_1.02 (ZNF219),  CRGGAGGC (DREME-7),  M2065_1.02 (ESR2),  M6241_1.02 (FOXJ2),  GGGATTA (DREME-1),  M6123_1.02 ((ZNF281)_(Mus_musculus)_(DBD_1.00)),  M5705_1.02 (PAX4),  M5346_1.02 (DPRX),  M4572_1.02 (MAFF),  M6182_1.02 (CRX),  M4471_1.02 (PAX5),  M6263_1.02 (GFI1),  M6521_1.02 (THRA),  M2390_1.02 (EHF),  M6523_1.02 (THRB),  M6406_1.02 (PAX2),  M2273_1.02 (E2F6),  M6262_1.02 (GFI1B),  M6336_1.02 (MAZ),  M6422_1.02 (PLAGL1),  M6535_1.02 (WT1),  M5974_1.02 (ZNF524),  M5949_1.02 (VSX1),  M6514_1.02 (TFCP2),  M6271_1.02 (HES1),  M5965_1.02 (ZIC4),  M5672_1.02 (NOTO),  M6189_1.02 (DLX3),  CTTGAACC (DREME-9),  M6534_1.02 (VSX2),  M6272_1.02 (HESX1),  M6420_1.02 (PLAG1),  M5875_1.02 (TBX1),  GGTGRC (DREME-11),  AGSCWGG (DREME-2),  M4553_1.02 (BHLHE40),  M6289_1.02 (HOXA9),  M2388_1.02 (SREBF2),  M2387_1.02 (SREBF1),  M6410_1.02 (PAX6),  M1968_1.02 (EBF1),  M6461_1.02 (RXRB),  M6468_1.02 (SNAI1),  M6469_1.02 (SNAI2),  M4604_1.02 (ZNF263),  M6324_1.02 (KLF4),  M2303_1.02 (NR2C2),  M6264_1.02 (GLI1),  M5430_1.02 (FIGLA),  M6276_1.02 (HINFP),  M6364_1.02 (NFATC3),  M6273_1.02 (HEY2),  M4427_1.02 (CTCF),  M6176_1.02 (NR2F1),  M6353_1.02 (MYF6),  M4640_1.02 (ZBTB7A),  M6547_1.02 (ZFX),  M4612_1.02 (CTCFL),  M5962_1.02 (ZBTB7C),  M5873_1.02 (TBR1),  M5896_1.02 (TBX4),  M6552_1.02 (ZNF148),  M5628_1.02 (MGA),  M5116_1.02 ((ATOH8)_(Drosophila_melanogaster)_(DBD_0.70)),  M0633_1.02 (DMRT2),  M6281_1.02 (HNF1A),  M5711_1.02 (PAX9),  M5856_1.02 (SP8),  M6503_1.02 (TBX2),  M1950_1.02 (ZNF354C),  M6549_1.02 (ZIC2),  M6429_1.02 (POU6F1),  M6221_1.02 (ETS2),  M6505_1.02 (TBX5),  M6150_1.02 (ARNT2),  M6321_1.02 (KLF15),  M6331_1.02 (MAFB),  M5587_1.02 (JDP2),  M1926_1.02 (ZEB1),  M5209_1.02 ((SP5)_(Drosophila_melanogaster)_(DBD_0.93)),  M4536_1.02 (E2F1),  M2278_1.02 (FOS),  M6540_1.02 (ZBTB4),  M5571_1.02 (ID4),  M6366_1.02 (NFAT5),  M0405_1.02 ((KLF7)_(Mus_musculus)_(DBD_1.00)),  M0178_1.02 ((ASCL2)_(Mus_musculus)_(DBD_0.98)),  M6326_1.02 (KLF8),  M6483_1.02 (SP4),  M0443_1.02 ((KLF12)_(Mus_musculus)_(DBD_1.00)),  M1871_1.02 ((KLF2)_(Mus_musculus)_(DBD_0.95)),  M6385_1.02 (NR1I2),  M6210_1.02 (ENO1),  M6161_1.02 (BHLHE41),  M4569_1.02 (HSF1),  M6293_1.02 (HOXA7),  M2268_1.02 (CEBPB),  M1919_1.02 (YY1),  M6544_1.02 (HIVEP1),  M5660_1.02 (NFIA),  M5662_1.02 (NFIB),  M6464_1.02 (SMAD2),  M6201_1.02 (EGR4),  M6374_1.02 (NKX2-1),  M5506_1.02 (HES7),  M6375_1.02 (NKX2-2),  M6199_1.02 (EGR2),  M2391_1.02 (KLF5),  M6394_1.02 (NR4A2),  M6396_1.02 (NR5A2),  M6139_1.02 (AHR),  M5592_1.02 (KLF14),  M1868_1.02 (GATA2),  M6519_1.02 (TGIF1),  M1925_1.02 (CEBPA),  M6377_1.02 (NKX2-8),  M1928_1.02 (NFKB1),  M6259_1.02 (GCM1),  M6537_1.02 (YBX1),  M5634_1.02 (MNT),  M4484_1.02 (ZNF143),  M5504_1.02 (HES5),  M6185_1.02 (CXXC1),  M4971_1.02 ((FERD3L)_(Drosophila_melanogaster)_(DBD_0.89)),  CYATGTTGSCCAGGCT (MEME-9),  GACTCAK (DREME-4),  M6333_1.02 (MAFG),  M4444_1.02 (RELA),  M6173_1.02 (CEBPG),  M6208_1.02 (ELK3),  M6228_1.02 (FOSB),  M6542_1.02 (ZBTB6),  M6559_1.02 (ZNF589),  M2275_1.02 (ELF1),  M2277_1.02 (FLI1),  M2264_1.02 ((ATOH1)_(Mus_musculus)_(DBD_1.00)),  M6525_1.02 (TLX1),  M4452_1.02 (BATF),  M6457_1.02 (RUNX1),  M6448_1.02 (RELB),  M0212_1.02 ((TCFL5)_(Mus_musculus)_(DBD_1.00)),  M6352_1.02 (MYCN),  M6157_1.02 (BARX2),  M1934_1.02 (ESR1),  M2313_1.02 ((SOX6)_(Mus_musculus)_(DBD_1.00)),  M6339_1.02 (MECP2),  M6277_1.02 (HLF),  M5593_1.02 (KLF16),  M6212_1.02 (EPAS1),  M6275_1.02 (HIF1A),  M6155_1.02 (ATF6),  M6316_1.02 (TCF4),  M5425_1.02 (ETV6),  M6445_1.02 (RARB),  M1927_1.02 ((MYCL1)_(Mus_musculus)_(DBD_0.66)),  M6267_1.02 (GLIS3),  M4543_1.02 (MXI1),  M4537_1.02 (E2F4),  M5664_1.02 (NFIX),  M6539_1.02 (ZBTB7B),  M5512_1.02 (HIC2),  M6147_1.02 (ARID3A),  M1358_1.02 ((TERF2)_(Mus_musculus)_(DBD_0.92)),  M6475_1.02 (SOX2),  M1432_1.02 (NR2E1),  M1458_1.02 ((RORB)_(Tetraodon_nigroviridis)_(DBD_1.00)),  M5627_1.02 (MESP1),  M6246_1.02 (FOXO3),  M5652_1.02 (NEUROD2),  M5487_1.02 (GCM2),  TKTRTKTRTKTRTKTWTKTRTKTRTKTRTKT (MEME-1),  M6266_1.02 (GLI3),  M1970_1.02 (NFIC),  M6191_1.02 (E2F2),  M5653_1.02 (NEUROG2),  M5935_1.02 (TGIF2LX),  M6162_1.02 (ARNTL),  M5782_1.02 (RHOXF1),  M6411_1.02 (PAX8),  M6154_1.02 (ATF5),  M6449_1.02 (REL),  M6486_1.02 (SPZ1),  M5471_1.02 (FOXO6),  M5446_1.02 (FOXD4L2),  M6250_1.02 (FOXQ1),  M1882_1.02 (IRF1),  M6306_1.02 (INSM1),  M5509_1.02 (HEY1),  M4459_1.02 (EGR1),  M6234_1.02 (FOXA3),  M6373_1.02 (NFYC),  M6463_1.02 (SMAD1),  M6456_1.02 (RREB1),  M6312_1.02 (IRF7),  M6527_1.02 (TWIST1),  M6192_1.02 (E2F3),  M5722_1.02 (PKNOX2),  M6114_1.02 (FOXA1),  M0199_1.02 ((HES2)_(Mus_musculus)_(DBD_0.83)),  M6303_1.02 (HOXD4),  M0728_1.02 ((FOXJ1)_(Mus_musculus)_(DBD_1.00)),  M6419_1.02 (PKNOX1),  M6238_1.02 (FOXF1),  M6349_1.02 (MYBL2),  M5746_1.02 (POU6F2),  M6370_1.02 (NFKB2),  M4532_1.02 (MYC),  M6205_1.02 (ELF3),  M5934_1.02 (TGIF2),  M6346_1.02 (MLXIPL),  M6309_1.02 (IRF3),  M6556_1.02 (ZNF350),  M5980_1.02 (ZNF784),  M6545_1.02 (HIVEP2),  M5697_1.02 (ONECUT3),  M6399_1.02 (ONECUT2),  M4567_1.02 (FOXA2),  M6131_1.02 ((TFCP2L1)_(Mus_musculus)_(DBD_0.95)),  M6344_1.02 (MEIS2),  M6292_1.02 (HOXA5),  M5377_1.02 (ELF4),  M6343_1.02 (MEIS1),  M5551_1.02 (HOXC12),  M1628_1.02 ((TBX10)_(Mus_musculus)_(DBD_0.87)),  M5321_1.02 (CLOCK),  M0736_1.02 ((FOXK2)_(Mus_musculus)_(DBD_0.90)),  M6247_1.02 (FOXO4),  M4479_1.02 (TCF12),  M4629_1.02 (NFE2),  M6239_1.02 (FOXF2),  M6358_1.02 (NEUROD1),  M6381_1.02 (NR0B1),  M4635_1.02 (STAT2),  YTYTYTCYYTTYYTYTCTYTC (MEME-8),  M5743_1.02 (POU4F3),  M5740_1.02 (POU4F1),  M6378_1.02 (NKX3-1),  M5729_1.02 (POU2F3),  M5744_1.02 (POU5F1B),  M5637_1.02 (MSX1),  M0428_1.02 ((ZNF691)_(Mus_musculus)_(DBD_0.97)),  M6510_1.02 (TEF),  M6249_1.02 (FOXP3),  M6171_1.02 (CEBPD),  M6465_1.02 (SMAD3),  M6299_1.02 (HOXC6),  M2287_1.02 ((HOXC9)_(Mus_musculus)_(DBD_0.98)),  M0300_1.02 ((ATF2)_(Mus_musculus)_(DBD_1.00)),  M6555_1.02 (ZNF333),  M1915_1.02 ((ZNF76)_(Xenopus_laevis)_(DBD_0.84)),  M4525_1.02 (TFAP2C),  M5955_1.02 (YY2),  M6037_1.02 ((IRX1)_(Mus_musculus)_(DBD_1.00)),  M0737_1.02 ((FOXB2)_(Mus_musculus)_(DBD_0.94)),  M4461_1.02 (ETS1),  M5460_1.02 (FOXL1),  M6413_1.02 (PBX2),  M5335_1.02 (CUX2),  M5292_1.02 (ATF4),  M2385_1.02 (FOXP2),  M6268_1.02 (HAND1),  M5702_1.02 (PAX1),  M5517_1.02 (HMBOX1),  M1582_1.02 ((HMG20B)_(Mus_musculus)_(DBD_0.94)),  M6265_1.02 (GLI2),  M5643_1.02 (MYBL1),  M5320_1.02 (CENPB),  M6278_1.02 (HLTF),  M5544_1.02 (HOXC10),  M2321_1.02 (TP63),  M6478_1.02 (SOX9),  M5325_1.02 (CREB3L1),  M6546_1.02 (ZFHX3),  M6323_1.02 (KLF3),  M6290_1.02 (HOXA13),  M0413_1.02 ((ZBTB1)_(Mus_musculus)_(DBD_0.99)),  M5497_1.02 (GRHL1),  M6432_1.02 (PPARD),  M5883_1.02 (TBX20),  M6504_1.02 (TBX3),  M2310_1.02 (RUNX2),  M6226_1.02 (FEV),  AAATAAAT (DREME-12),  M5584_1.02 (ISX),  M6357_1.02 (NANOG),  M6301_1.02 (HOXD10),  M6152_1.02 (ATF1),  M5738_1.02 (POU3F4),  M6507_1.02 (TEAD1),  M6311_1.02 (IRF5),  M5348_1.02 (DRGX)

Sequence Databases

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Name
Last Modified
Contained
Too Short
Too Masked
No Primary
Too Similar
Used
ZSCAN23.IDR0.05.filt.narrowPeak.outsidePolsteinDNase.summitPlusMinus250bp Mon Jun 11 06:39:23 2018 600 0 0 478 39 83

Secondary Motif Databases

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Name
Last Modified
Number of Motifs
Motifs Significant
Motifs Redundant
meme.xml Mon Jun 11 07:46:39 2018 9 4 3
dreme.xml Mon Jun 11 07:47:30 2018 13 NaN NaN
Homo_sapiens Wed Sep 14 11:58:29 2016 733 NaN NaN

Settings

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Match Score Threshold
  
7 (bits)
Margin size
150
Width of histogram bins 1
Significance computed up to this distance    150
Secondary match handling Count only the best secondary match above the score threshold Count all secondary matches above the match score threshold
Maximum allowed sequence identity 0.5
Odds ratio for redundancy heuristic 20
Bin p-value cutoff 0.05
Secondary motif E-value cutoff 10
Overlapping bases for redundancy check 2
Fraction of sites for redundancy check 0.5
Pseudocount added to motifs 0.1
Background model for motifs /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN23.IDR0.05.filt.narrowPeak.outsidePolsteinDNase.summitPlusMinus250bp.MemeChipResults/background
Bit threshold for trimming motif edges 0.25
Primary and secondary motif alphabets Converting secondary alphabet to primary alphabet Primary and secondary alphabets must match
Random number seed 1
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Spacing Analysis for

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Secondary Motif:
Cluster:
E-value:
Best Gap:
Best Orientation:

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Secondary Motif Logo

Inferred Secondary Motif Logo

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Spacings

Gap
Gap
Orientation
Orientation
p-value
p-value
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Selected Orientation Graph

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Contributing Sequences ()


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Secondaries

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ID
Name
Cluster
E-value
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Spacings

Spacing Analysis for YTCRCYMTGTTGSCCAGGCTGGWSTBSAAYKSCKS (MEME-3)

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Secondary Motif: CYCCGTCTCWAMWAAAAAWAMA (MEME-5)
Cluster: CYCCGTCTCWAMWAAAAAWAMA (MEME-5)
E-value: 2.82e-126
Best Gap: 1
Best Orientation: upstream / opposite strand

Primary Motif Logo

Secondary Motif Logo

Inferred Secondary Motif Logo

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Spacings

Gap
Gap
Orientation
Orientation
p-value
p-value
1up-3.73e-129
1up+/up-3.85e-111
1up-/dn+3.85e-111
1all3.56e-93
108dn-3.13e-19
108up+/dn-2.12e-15
108dn+/dn-2.12e-15
108all1.19e-11
107dn-4.48e-9
107up+/dn-4.76e-7
107dn+/dn-4.76e-7
0up-3.99e-6
107all4.19e-5
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Overview Graph

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Selected Orientation Graph

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Contributing Sequences (60)


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Secondaries

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ID
Name
Cluster
E-value
Best Gap
Best Orientation
Spacings
CYCCGTCTCWAMWAAAAAWAMAMEME-5CYCCGTCTCWAMWAAAAAWAMA2.82e-1261upstream / opposite strand
M6302_1.02HOXD13CYCCGTCTCWAMWAAAAAWAMA1.23e-936upstream / opposite strand
GAACCYRGGAGGYGGAGGTTGCAGTGAGMEME-6GAACCYRGGAGGYGGAGGTTGCAGTGAG2.07e-658downstream / opposite strand
TGCAGTGRDREME-10GAACCYRGGAGGYGGAGGTTGCAGTGAG1.00e-629downstream / opposite strand
AAAAATACDREME-5CYCCGTCTCWAMWAAAAAWAMA5.88e-6014upstream / opposite strand
M6529_1.02UBP1CYCCGTCTCWAMWAAAAAWAMA5.67e-586upstream / opposite strand
M6342_1.02MEF2DCYCCGTCTCWAMWAAAAAWAMA1.10e-5712upstream / opposite strand
M5616_1.02MEF2BCYCCGTCTCWAMWAAAAAWAMA1.38e-5711upstream / opposite strand
M0442_1.02(ZBTB3)_(Mus_musculus)_(DBD_1.00)GAACCYRGGAGGYGGAGGTTGCAGTGAG1.11e-5610downstream / opposite strand
M1884_1.02MEF2ACYCCGTCTCWAMWAAAAAWAMA6.96e-5512upstream / opposite strand
AGTAGAGDREME-8CYCCGTCTCWAMWAAAAAWAMA1.77e-547upstream / same strand
M5553_1.02HOXC13CYCCGTCTCWAMWAAAAAWAMA1.69e-539upstream / opposite strand
M5557_1.02HOXD12CYCCGTCTCWAMWAAAAAWAMA2.08e-539upstream / opposite strand
M6237_1.02FOXD3CYCCGTCTCWAMWAAAAAWAMA5.30e-5214upstream / opposite strand
M4467_1.02MEF2CCYCCGTCTCWAMWAAAAAWAMA6.12e-5212upstream / opposite strand
M6251_1.02FUBP1CYCCGTCTCWAMWAAAAAWAMA7.81e-5212upstream / same strand
M6149_1.02ARID5BCYCCGTCTCWAMWAAAAAWAMA2.00e-5115upstream / same strand
M6187_1.02DDIT3GAACCYRGGAGGYGGAGGTTGCAGTGAG6.14e-4913downstream / opposite strand
M5583_1.02ISL2M5583_1.022.56e-4831downstream / same strand
M6242_1.02FOXJ3CYCCGTCTCWAMWAAAAAWAMA1.97e-4713upstream / opposite strand
ACCTCDREME-6CYCCGTCTCWAMWAAAAAWAMA6.42e-470downstream / primary palindromic
M6245_1.02FOXO1CYCCGTCTCWAMWAAAAAWAMA7.69e-4711upstream / opposite strand
M6244_1.02FOXM1CYCCGTCTCWAMWAAAAAWAMA9.85e-4714upstream / opposite strand
M6115_1.02TP73M6115_1.021.89e-4646downstream / same strand
M2281_1.02FOXH1CYCCGTCTCWAMWAAAAAWAMA1.73e-4517upstream / opposite strand
CCCAGCWMYTYGGGAGGCYGAGGCRGGAGRAMEME-2CCCAGCWMYTYGGGAGGCYGAGGCRGGAGRA3.36e-4511downstream / opposite strand
M6279_1.02HMGA1CYCCGTCTCWAMWAAAAAWAMA7.51e-4515upstream / opposite strand
M6490_1.02SRYCYCCGTCTCWAMWAAAAAWAMA1.77e-4418upstream / opposite strand
M2283_1.02FOXP1CYCCGTCTCWAMWAAAAAWAMA7.59e-4414upstream / opposite strand
M2306_1.02POU2F2CYCCGTCTCWAMWAAAAAWAMA2.08e-4316upstream / same strand
M6376_1.02NKX2-5M6376_1.023.54e-413downstream / same strand
M4476_1.02RFX5M6115_1.025.08e-4158all / both palindromic
M4451_1.02ATF3M4451_1.026.21e-413downstream / opposite strand
M6518_1.02TFEBM6518_1.028.65e-414downstream / opposite strand
M2292_1.02JUNDM2292_1.021.04e-4051downstream / opposite strand
M4481_1.02USF2M4481_1.021.39e-401downstream / opposite strand
M4469_1.02RESTM4469_1.023.84e-4028downstream / same strand
M4623_1.02JUNBM2292_1.021.27e-3951downstream / opposite strand
M1528_1.02(RFX6)_(Mus_musculus)_(DBD_0.66)M1528_1.022.47e-3964downstream / opposite strand
M0398_1.02(ZSCAN10)_(Mus_musculus)_(DBD_0.82)M0398_1.022.85e-3930downstream / same strand
TCYCAAADREME-3TCYCAAA3.46e-3927downstream / same strand
M4708_1.02TBPCYCCGTCTCWAMWAAAAAWAMA5.49e-3917upstream / opposite strand
M6517_1.02TFE3M6517_1.022.18e-384downstream / opposite strand
M5632_1.02MLXM5632_1.025.26e-382downstream / same strand
AGGCRYGHGCCACCACGCCYMEME-4M2292_1.025.80e-3847downstream / same strand
M4680_1.02BACH1M4680_1.029.34e-384downstream / opposite strand
M1529_1.02(RFX7)_(Mus_musculus)_(DBD_1.00)GAACCYRGGAGGYGGAGGTTGCAGTGAG1.21e-3710downstream / same strand
M2270_1.02DUX4M4469_1.021.42e-3735downstream / opposite strand
M0396_1.02(OSR2)_(Mus_musculus)_(DBD_1.00)M1528_1.022.13e-3762all / both palindromic
M1917_1.02USF1M1917_1.023.96e-374downstream / opposite strand
M2296_1.02MAFKM2296_1.026.18e-3731downstream / opposite strand
M6141_1.02ALX1M4469_1.027.03e-3735downstream / opposite strand
M4692_1.02SIX5CYCCGTCTCWAMWAAAAAWAMA2.47e-360upstream / opposite strand
M2314_1.02SP2GAACCYRGGAGGYGGAGGTTGCAGTGAG1.37e-3518downstream / opposite strand
M5339_1.02DLX1M5339_1.021.38e-35101downstream / same strand
M5771_1.02RAXM5339_1.021.38e-35101downstream / same strand
M6557_1.02ZNF384CYCCGTCTCWAMWAAAAAWAMA1.54e-3520upstream / opposite strand
M4565_1.02FOSL2M2292_1.022.90e-3549downstream / secondary palindromic
M1963_1.02(ZFY)_(Mus_musculus)_(DBD_0.97)M6115_1.025.43e-3549downstream / same strand
M6236_1.02FOXC2CYCCGTCTCWAMWAAAAAWAMA1.08e-3412upstream / opposite strand
M6163_1.02BPTFCYCCGTCTCWAMWAAAAAWAMA2.00e-3418upstream / same strand
M6345_1.02MITFM6345_1.022.50e-344downstream / opposite strand
M6347_1.02MSX2M5339_1.022.71e-34101downstream / same strand
M5500_1.02GSCM4469_1.023.13e-3440downstream / opposite strand
M4526_1.02SMARCC1M2292_1.024.95e-3452downstream / opposite strand
M6532_1.02VDRGAACCYRGGAGGYGGAGGTTGCAGTGAG7.66e-3430downstream / opposite strand
M5932_1.02TFECM5932_1.027.80e-342downstream / secondary palindromic
M4681_1.02BACH2M6115_1.028.95e-3448downstream / opposite strand
M0900_1.02SHOXM5339_1.022.37e-33101downstream / same strand
M6322_1.02KLF1M6115_1.022.52e-3349downstream / opposite strand
M6442_1.02PURAM6115_1.022.87e-3344downstream / same strand
M6325_1.02KLF6M6115_1.024.28e-3353downstream / opposite strand
M4619_1.02FOSL1M2292_1.021.07e-3251downstream / opposite strand
M6330_1.02MAFAM6115_1.021.97e-3239downstream / opposite strand
M0422_1.02(ZIC5)_(Mus_musculus)_(DBD_0.99)M0422_1.023.76e-3224downstream / opposite strand
M6482_1.02SP3GAACCYRGGAGGYGGAGGTTGCAGTGAG4.61e-3218downstream / opposite strand
M6401_1.02OTX2M4469_1.029.73e-3237downstream / opposite strand
M6550_1.02ZIC3M0422_1.021.21e-3124downstream / opposite strand
M0216_1.02(NHLH2)_(Mus_musculus)_(DBD_1.00)M1528_1.022.11e-3164downstream / same strand
M6146_1.02TFAP2DM6115_1.022.25e-3145downstream / same strand
M4511_1.02RXRAGAACCYRGGAGGYGGAGGTTGCAGTGAG5.88e-3130downstream / opposite strand
M5345_1.02DMBX1M4469_1.029.38e-3140downstream / opposite strand
M5501_1.02GSC2M4469_1.029.38e-3140downstream / opposite strand
M5720_1.02PITX3M4469_1.022.22e-3040downstream / opposite strand
M4438_1.02ESRRAGAACCYRGGAGGYGGAGGTTGCAGTGAG3.14e-306downstream / same strand
M5717_1.02PITX1M4469_1.027.52e-3040downstream / opposite strand
M6400_1.02OTX1M4469_1.027.52e-3040downstream / opposite strand
M6418_1.02PITX2M4469_1.021.19e-2938downstream / opposite strand
M5777_1.02RFX4M1528_1.021.95e-2964downstream / same strand
M6144_1.02TFAP2BM6115_1.022.00e-2949downstream / same strand
M1906_1.02SP1GAACCYRGGAGGYGGAGGTTGCAGTGAG3.24e-2919downstream / opposite strand
M6548_1.02ZIC1M0422_1.023.75e-2924downstream / opposite strand
M6360_1.02NFE2L2M6115_1.025.53e-2947downstream / same strand
M6391_1.02NR2E3CYCCGTCTCWAMWAAAAAWAMA7.58e-2917upstream / same strand
M6553_1.02ZNF219M6553_1.029.10e-2911downstream / opposite strand
CRGGAGGCDREME-7M6115_1.029.52e-2955downstream / opposite strand
M2065_1.02ESR2GAACCYRGGAGGYGGAGGTTGCAGTGAG1.70e-286downstream / opposite strand
M6241_1.02FOXJ2CYCCGTCTCWAMWAAAAAWAMA1.72e-2818upstream / opposite strand
GGGATTADREME-1M4469_1.022.41e-2839downstream / same strand
M6123_1.02(ZNF281)_(Mus_musculus)_(DBD_1.00)M6115_1.024.15e-2844downstream / opposite strand
M5705_1.02PAX4M5339_1.024.15e-28100downstream / same strand
M5346_1.02DPRXM4469_1.025.07e-2840downstream / opposite strand
M4572_1.02MAFFM4572_1.029.54e-2843downstream / opposite strand
M6182_1.02CRXM4469_1.021.08e-2740downstream / opposite strand
M4471_1.02PAX5M4471_1.022.99e-271downstream / opposite strand
M6263_1.02GFI1M4469_1.029.14e-2736downstream / same strand
M6521_1.02THRAM6521_1.021.39e-263downstream / opposite strand
M2390_1.02EHFM2390_1.022.75e-2646downstream / opposite strand
M6523_1.02THRBM6523_1.023.26e-2643downstream / same strand
M6406_1.02PAX2M2292_1.023.26e-2643downstream / opposite strand
M2273_1.02E2F6M2273_1.023.42e-2644downstream / opposite strand
M6262_1.02GFI1BM4469_1.024.00e-2636downstream / same strand
M6336_1.02MAZM6115_1.025.96e-2645downstream / opposite strand
M6422_1.02PLAGL1M6115_1.021.27e-2553downstream / opposite strand
M6535_1.02WT1GAACCYRGGAGGYGGAGGTTGCAGTGAG1.58e-2518downstream / opposite strand
M5974_1.02ZNF524GAACCYRGGAGGYGGAGGTTGCAGTGAG2.48e-2530downstream / same strand
M5949_1.02VSX1M5339_1.022.94e-25100downstream / same strand
M6514_1.02TFCP2M6115_1.023.76e-2545downstream / opposite strand
M6271_1.02HES1M6271_1.025.83e-2542downstream / same strand
M5965_1.02ZIC4M5965_1.027.79e-2523downstream / opposite strand
M5672_1.02NOTOM5339_1.028.06e-25100downstream / opposite strand
M6189_1.02DLX3M5339_1.028.26e-2599downstream / same strand
CTTGAACCDREME-9CTTGAACC8.58e-2531downstream / opposite strand
M6534_1.02VSX2M5339_1.022.74e-2499downstream / same strand
M6272_1.02HESX1M2292_1.023.61e-2446downstream / same strand
M6420_1.02PLAG1M6115_1.024.81e-2444downstream / opposite strand
M5875_1.02TBX1M2292_1.021.66e-2335downstream / same strand
GGTGRCDREME-11M2292_1.021.95e-2355downstream / opposite strand
AGSCWGGDREME-2AGSCWGG3.59e-2346downstream / opposite strand
M4553_1.02BHLHE40M4553_1.024.59e-234downstream / opposite strand
M6289_1.02HOXA9CYCCGTCTCWAMWAAAAAWAMA7.04e-2321upstream / opposite strand
M2388_1.02SREBF2M2388_1.021.14e-222downstream / same strand
M2387_1.02SREBF1M2387_1.021.37e-222downstream / same strand
M6410_1.02PAX6M2292_1.021.88e-2244downstream / opposite strand
M1968_1.02EBF1M1968_1.022.18e-221downstream / secondary palindromic
M6461_1.02RXRBM6461_1.025.11e-223downstream / opposite strand
M6468_1.02SNAI1M6468_1.027.09e-224downstream / same strand
M6469_1.02SNAI2M6469_1.027.09e-224downstream / same strand
M4604_1.02ZNF263GAACCYRGGAGGYGGAGGTTGCAGTGAG1.35e-2110downstream / opposite strand
M6324_1.02KLF4M6324_1.022.83e-2189downstream / opposite strand
M2303_1.02NR2C2M2303_1.023.30e-2115downstream / same strand
M6264_1.02GLI1M0422_1.023.39e-2123downstream / opposite strand
M5430_1.02FIGLAM5430_1.025.46e-214downstream / opposite strand
M6276_1.02HINFPM6276_1.026.61e-2116downstream / opposite strand
M6364_1.02NFATC3M6364_1.021.18e-2040downstream / same strand
M6273_1.02HEY2M6324_1.021.42e-2076downstream / opposite strand
M4427_1.02CTCFGAACCYRGGAGGYGGAGGTTGCAGTGAG1.50e-2018downstream / opposite strand
M6176_1.02NR2F1M6176_1.022.91e-2025downstream / opposite strand
M6353_1.02MYF6M6353_1.029.32e-203downstream / same strand
M4640_1.02ZBTB7AM4640_1.029.69e-2012downstream / opposite strand
M6547_1.02ZFXM6115_1.021.15e-1944downstream / opposite strand
M4612_1.02CTCFLGAACCYRGGAGGYGGAGGTTGCAGTGAG1.53e-1918downstream / opposite strand
M5962_1.02ZBTB7CGAACCYRGGAGGYGGAGGTTGCAGTGAG1.64e-1915downstream / opposite strand
M5873_1.02TBR1M5873_1.022.14e-1947downstream / same strand
M5896_1.02TBX4M5896_1.022.55e-1947downstream / same strand
M6552_1.02ZNF148M6552_1.023.09e-1944downstream / opposite strand
M5628_1.02MGAM5628_1.023.62e-1947downstream / same strand
M5116_1.02(ATOH8)_(Drosophila_melanogaster)_(DBD_0.70)M5116_1.025.48e-194downstream / opposite strand
M0633_1.02DMRT2M0633_1.025.72e-1922upstream / same strand
M6281_1.02HNF1AM5339_1.029.32e-1998downstream / opposite strand
M5711_1.02PAX9M5711_1.021.14e-180downstream / opposite strand
M5856_1.02SP8M6324_1.023.64e-1890downstream / opposite strand
M6503_1.02TBX2M6503_1.024.07e-1838downstream / opposite strand
M1950_1.02ZNF354CM6324_1.024.86e-1888downstream / opposite strand
M6549_1.02ZIC2M6324_1.025.89e-1889downstream / opposite strand
M6429_1.02POU6F1CYCCGTCTCWAMWAAAAAWAMA7.89e-1819upstream / same strand
M6221_1.02ETS2GAACCYRGGAGGYGGAGGTTGCAGTGAG8.33e-1822downstream / opposite strand
M6505_1.02TBX5M6505_1.021.14e-1747downstream / same strand
M6150_1.02ARNT2M6150_1.021.17e-1751downstream / same strand
M6321_1.02KLF15GAACCYRGGAGGYGGAGGTTGCAGTGAG1.43e-1717downstream / opposite strand
M6331_1.02MAFBGAACCYRGGAGGYGGAGGTTGCAGTGAG1.87e-176downstream / same strand
M5587_1.02JDP2M2292_1.021.93e-1751downstream / same strand
M1926_1.02ZEB1M1926_1.022.76e-174downstream / same strand
M5209_1.02(SP5)_(Drosophila_melanogaster)_(DBD_0.93)M5209_1.022.83e-179downstream / opposite strand
M4536_1.02E2F1M4536_1.022.90e-1712downstream / opposite strand
M2278_1.02FOSM2292_1.023.89e-1751downstream / opposite strand
M6540_1.02ZBTB4M6540_1.023.90e-1785downstream / opposite strand
M5571_1.02ID4M5571_1.028.10e-174downstream / same strand
M6366_1.02NFAT5M6366_1.021.29e-16124downstream / same strand
M0405_1.02(KLF7)_(Mus_musculus)_(DBD_1.00)M6324_1.022.63e-1691downstream / opposite strand
M0178_1.02(ASCL2)_(Mus_musculus)_(DBD_0.98)M0178_1.023.55e-164downstream / secondary palindromic
M6326_1.02KLF8M6324_1.025.32e-1691downstream / opposite strand
M6483_1.02SP4M6483_1.027.81e-1649downstream / opposite strand
M0443_1.02(KLF12)_(Mus_musculus)_(DBD_1.00)M6324_1.025.49e-1592downstream / opposite strand
M1871_1.02(KLF2)_(Mus_musculus)_(DBD_0.95)M6324_1.027.78e-1589downstream / opposite strand
M6385_1.02NR1I2M6385_1.029.73e-154downstream / same strand
M6210_1.02ENO1M6366_1.021.35e-14134downstream / opposite strand
M6161_1.02BHLHE41M6161_1.024.09e-1438downstream / same strand
M4569_1.02HSF1GAACCYRGGAGGYGGAGGTTGCAGTGAG4.46e-1425downstream / same strand
M6293_1.02HOXA7GAACCYRGGAGGYGGAGGTTGCAGTGAG5.15e-1433downstream / opposite strand
M2268_1.02CEBPBM6366_1.025.60e-14129downstream / primary palindromic
M1919_1.02YY1M6366_1.021.54e-13131downstream / opposite strand
M6544_1.02HIVEP1M6366_1.021.79e-13127downstream / same strand
M5660_1.02NFIAM5660_1.022.96e-134downstream / same strand
M5662_1.02NFIBM5662_1.022.96e-134downstream / same strand
M6464_1.02SMAD2M6324_1.023.41e-1392downstream / same strand
M6201_1.02EGR4M6201_1.024.17e-1355downstream / opposite strand
M6374_1.02NKX2-1M6374_1.027.13e-13139upstream / same strand
M5506_1.02HES7M5506_1.021.10e-1278downstream / opposite strand
M6375_1.02NKX2-2M6375_1.021.29e-1234downstream / opposite strand
M6199_1.02EGR2M6199_1.021.52e-1212downstream / opposite strand
M2391_1.02KLF5M6324_1.021.64e-1289downstream / opposite strand
M6394_1.02NR4A2M6394_1.024.29e-1222downstream / same strand
M6396_1.02NR5A2M6396_1.024.82e-1217downstream / same strand
M6139_1.02AHRM6324_1.025.58e-1291downstream / same strand
M5592_1.02KLF14M6324_1.025.79e-1289downstream / opposite strand
M1868_1.02GATA2CYCCGTCTCWAMWAAAAAWAMA6.93e-120upstream / same strand
M6519_1.02TGIF1M6519_1.027.09e-120downstream / same strand
M1925_1.02CEBPAM1925_1.027.29e-12128upstream / primary palindromic
M6377_1.02NKX2-8M6377_1.027.80e-122downstream / same strand
M1928_1.02NFKB1M1928_1.021.23e-11125downstream / same strand
M6259_1.02GCM1M6259_1.021.23e-11135downstream / same strand
M6537_1.02YBX1M6537_1.021.67e-1138downstream / same strand
M5634_1.02MNTM5634_1.021.82e-112downstream / same strand
M4484_1.02ZNF143GAACCYRGGAGGYGGAGGTTGCAGTGAG2.90e-1117downstream / opposite strand
M5504_1.02HES5M2292_1.023.63e-1148downstream / same strand
M6185_1.02CXXC1M6185_1.025.15e-1155downstream / opposite strand
M4971_1.02(FERD3L)_(Drosophila_melanogaster)_(DBD_0.89)M4971_1.028.34e-114downstream / opposite strand
CYATGTTGSCCAGGCTMEME-9CYATGTTGSCCAGGCT1.50e-10134downstream / same strand
GACTCAKDREME-4M2292_1.021.63e-1051downstream / opposite strand
M6333_1.02MAFGM2292_1.022.20e-1054downstream / opposite strand
M4444_1.02RELAM6366_1.022.81e-10126downstream / same strand
M6173_1.02CEBPGM6366_1.022.93e-10127downstream / primary palindromic
M6208_1.02ELK3M6208_1.023.49e-1021downstream / opposite strand
M6228_1.02FOSBM2292_1.029.47e-1051downstream / opposite strand
M6542_1.02ZBTB6M6542_1.029.69e-1017downstream / opposite strand
M6559_1.02ZNF589M6559_1.021.26e-910downstream / opposite strand
M2275_1.02ELF1M2275_1.021.40e-922downstream / opposite strand
M2277_1.02FLI1M2277_1.021.58e-921downstream / opposite strand
M2264_1.02(ATOH1)_(Mus_musculus)_(DBD_1.00)M6115_1.021.89e-955downstream / same strand
M6525_1.02TLX1M6366_1.022.44e-9136downstream / opposite strand
M4452_1.02BATFCYCCGTCTCWAMWAAAAAWAMA2.69e-94upstream / same strand
M6457_1.02RUNX1CYCCGTCTCWAMWAAAAAWAMA2.78e-90upstream / opposite strand
M6448_1.02RELBM6366_1.023.89e-9126downstream / same strand
M0212_1.02(TCFL5)_(Mus_musculus)_(DBD_1.00)M0212_1.026.19e-92downstream / secondary palindromic
M6352_1.02MYCNM6352_1.027.86e-91downstream / same strand
M6157_1.02BARX2M6157_1.028.94e-997downstream / same strand
M1934_1.02ESR1GAACCYRGGAGGYGGAGGTTGCAGTGAG1.01e-86downstream / opposite strand
M2313_1.02(SOX6)_(Mus_musculus)_(DBD_1.00)M2313_1.021.31e-839downstream / same strand
M6339_1.02MECP2GAACCYRGGAGGYGGAGGTTGCAGTGAG1.80e-826downstream / same strand
M6277_1.02HLFM6366_1.022.10e-8129downstream / primary palindromic
M5593_1.02KLF16M5593_1.022.39e-819downstream / opposite strand
M6212_1.02EPAS1M6212_1.022.91e-860all / both palindromic
M6275_1.02HIF1AM6324_1.023.64e-890downstream / opposite strand
M6155_1.02ATF6M6155_1.023.97e-816downstream / opposite strand
M6316_1.02TCF4M6316_1.024.06e-847upstream / same strand
M5425_1.02ETV6M5425_1.024.32e-817downstream / opposite strand
M6445_1.02RARBM6445_1.024.37e-819downstream / same strand
M1927_1.02(MYCL1)_(Mus_musculus)_(DBD_0.66)M1927_1.028.82e-81downstream / same strand
M6267_1.02GLIS3GAACCYRGGAGGYGGAGGTTGCAGTGAG8.97e-822downstream / opposite strand
M4543_1.02MXI1M4543_1.021.03e-71downstream / same strand
M4537_1.02E2F4M4537_1.021.07e-713downstream / opposite strand
M5664_1.02NFIXM5664_1.021.24e-74downstream / opposite strand
M6539_1.02ZBTB7BM6539_1.021.43e-718downstream / opposite strand
M5512_1.02HIC2M5512_1.021.63e-712downstream / opposite strand
M6147_1.02ARID3ACYCCGTCTCWAMWAAAAAWAMA1.78e-713upstream / same strand
M1358_1.02(TERF2)_(Mus_musculus)_(DBD_0.92)M1358_1.021.82e-7125downstream / opposite strand
M6475_1.02SOX2M6115_1.022.23e-739downstream / opposite strand
M1432_1.02NR2E1M1432_1.022.71e-722downstream / same strand
M1458_1.02(RORB)_(Tetraodon_nigroviridis)_(DBD_1.00)M1458_1.022.71e-722downstream / same strand
M5627_1.02MESP1GAACCYRGGAGGYGGAGGTTGCAGTGAG3.13e-721downstream / opposite strand
M6246_1.02FOXO3CYCCGTCTCWAMWAAAAAWAMA4.88e-714upstream / opposite strand
M5652_1.02NEUROD2M5652_1.025.32e-779downstream / secondary palindromic
M5487_1.02GCM2M5487_1.026.36e-714downstream / opposite strand
TKTRTKTRTKTRTKTWTKTRTKTRTKTRTKTMEME-1CYCCGTCTCWAMWAAAAAWAMA6.48e-78upstream / same strand
M6266_1.02GLI3M6266_1.026.77e-710downstream / opposite strand
M1970_1.02NFICM6259_1.029.09e-7140downstream / secondary palindromic
M6191_1.02E2F2M6191_1.021.03e-69downstream / opposite strand
M5653_1.02NEUROG2M5653_1.021.23e-679downstream / secondary palindromic
M5935_1.02TGIF2LXM5935_1.021.64e-643downstream / opposite strand
M6162_1.02ARNTLM6162_1.021.69e-632downstream / opposite strand
M5782_1.02RHOXF1M5782_1.021.78e-649downstream / secondary palindromic
M6411_1.02PAX8M6411_1.021.95e-69downstream / same strand
M6154_1.02ATF5M6154_1.022.03e-618downstream / opposite strand
M6449_1.02RELM6449_1.022.67e-6125downstream / secondary palindromic
M6486_1.02SPZ1M6486_1.023.61e-61downstream / opposite strand
M5471_1.02FOXO6M6259_1.024.10e-6131downstream / opposite strand
M5446_1.02FOXD4L2CYCCGTCTCWAMWAAAAAWAMA4.33e-614upstream / opposite strand
M6250_1.02FOXQ1CYCCGTCTCWAMWAAAAAWAMA4.65e-616upstream / opposite strand
M1882_1.02IRF1M1882_1.024.66e-610upstream / opposite strand
M6306_1.02INSM1M6306_1.025.58e-660downstream / opposite strand
M5509_1.02HEY1M5509_1.026.76e-679downstream / same strand
M4459_1.02EGR1M4459_1.026.79e-615downstream / opposite strand
M6234_1.02FOXA3CYCCGTCTCWAMWAAAAAWAMA7.02e-615upstream / opposite strand
M6373_1.02NFYCM6373_1.027.24e-625downstream / opposite strand
M6463_1.02SMAD1M6463_1.027.96e-614downstream / same strand
M6456_1.02RREB1GAACCYRGGAGGYGGAGGTTGCAGTGAG8.60e-611downstream / opposite strand
M6312_1.02IRF7CYCCGTCTCWAMWAAAAAWAMA9.10e-611upstream / opposite strand
M6527_1.02TWIST1M6366_1.029.10e-6133downstream / same strand
M6192_1.02E2F3M6192_1.021.00e-560downstream / same strand
M5722_1.02PKNOX2M5722_1.021.06e-543downstream / opposite strand
M6114_1.02FOXA1CYCCGTCTCWAMWAAAAAWAMA1.24e-515upstream / opposite strand
M0199_1.02(HES2)_(Mus_musculus)_(DBD_0.83)M0199_1.021.27e-579downstream / same strand
M6303_1.02HOXD4M6303_1.021.27e-5100downstream / same strand
M0728_1.02(FOXJ1)_(Mus_musculus)_(DBD_1.00)CYCCGTCTCWAMWAAAAAWAMA1.35e-515upstream / opposite strand
M6419_1.02PKNOX1M2292_1.021.45e-550downstream / same strand
M6238_1.02FOXF1CYCCGTCTCWAMWAAAAAWAMA1.50e-510upstream / opposite strand
M6349_1.02MYBL2GAACCYRGGAGGYGGAGGTTGCAGTGAG1.52e-514downstream / same strand
M5746_1.02POU6F2M0633_1.021.65e-524upstream / opposite strand
M6370_1.02NFKB2M6370_1.021.98e-5124downstream / opposite strand
M4532_1.02MYCM4532_1.021.98e-580downstream / secondary palindromic
M6205_1.02ELF3M1882_1.022.09e-523upstream / primary palindromic
M5934_1.02TGIF2M5934_1.022.37e-543downstream / opposite strand
M6346_1.02MLXIPLM6346_1.022.82e-5122downstream / same strand
M6309_1.02IRF3M6309_1.023.97e-515upstream / opposite strand
M6556_1.02ZNF350M6556_1.024.16e-50downstream / same strand
M5980_1.02ZNF784M5980_1.024.36e-512downstream / opposite strand
M6545_1.02HIVEP2M6545_1.024.48e-538downstream / opposite strand
M5697_1.02ONECUT3CYCCGTCTCWAMWAAAAAWAMA4.56e-515upstream / same strand
M6399_1.02ONECUT2CYCCGTCTCWAMWAAAAAWAMA6.63e-514upstream / same strand
M4567_1.02FOXA2CYCCGTCTCWAMWAAAAAWAMA7.79e-515upstream / opposite strand
M6131_1.02(TFCP2L1)_(Mus_musculus)_(DBD_0.95)M6131_1.029.12e-546downstream / same strand
M6344_1.02MEIS2M6344_1.029.70e-542downstream / opposite strand
M6292_1.02HOXA5CYCCGTCTCWAMWAAAAAWAMA1.08e-421upstream / opposite strand
M5377_1.02ELF4M5377_1.021.14e-496upstream / opposite strand
M6343_1.02MEIS1M6343_1.021.38e-443downstream / opposite strand
M5551_1.02HOXC12CYCCGTCTCWAMWAAAAAWAMA1.41e-420upstream / same strand
M1628_1.02(TBX10)_(Mus_musculus)_(DBD_0.87)M1628_1.021.62e-448downstream / same strand
M5321_1.02CLOCKM5321_1.021.66e-444downstream / same strand
M0736_1.02(FOXK2)_(Mus_musculus)_(DBD_0.90)CYCCGTCTCWAMWAAAAAWAMA1.68e-414upstream / opposite strand
M6247_1.02FOXO4CYCCGTCTCWAMWAAAAAWAMA1.78e-413upstream / opposite strand
M4479_1.02TCF12M6316_1.021.85e-448upstream / secondary palindromic
M4629_1.02NFE2M2292_1.021.92e-451downstream / same strand
M6239_1.02FOXF2M6309_1.021.96e-411upstream / opposite strand
M6358_1.02NEUROD1M6358_1.021.99e-46downstream / opposite strand
M6381_1.02NR0B1M6381_1.022.51e-457downstream / primary palindromic
M4635_1.02STAT2M6309_1.022.53e-416upstream / opposite strand
YTYTYTCYYTTYYTYTCTYTCMEME-8M1882_1.022.72e-49upstream / same strand
M5743_1.02POU4F3M5743_1.022.76e-442upstream / secondary palindromic
M5740_1.02POU4F1M5743_1.022.84e-442upstream / secondary palindromic
M6378_1.02NKX3-1M6378_1.023.18e-422upstream / secondary palindromic
M5729_1.02POU2F3M5729_1.023.22e-4104downstream / same strand
M5744_1.02POU5F1BM5744_1.023.22e-4104downstream / same strand
M5637_1.02MSX1CYCCGTCTCWAMWAAAAAWAMA3.76e-415upstream / same strand
M0428_1.02(ZNF691)_(Mus_musculus)_(DBD_0.97)M0428_1.023.97e-430downstream / opposite strand
M6510_1.02TEFCYCCGTCTCWAMWAAAAAWAMA4.19e-411upstream / same strand
M6249_1.02FOXP3M6249_1.024.43e-418upstream / opposite strand
M6171_1.02CEBPDM1925_1.024.44e-4128upstream / primary palindromic
M6465_1.02SMAD3M6465_1.024.96e-464downstream / opposite strand
M6299_1.02HOXC6CYCCGTCTCWAMWAAAAAWAMA5.40e-412upstream / opposite strand
M2287_1.02(HOXC9)_(Mus_musculus)_(DBD_0.98)CYCCGTCTCWAMWAAAAAWAMA6.01e-411upstream / opposite strand
M0300_1.02(ATF2)_(Mus_musculus)_(DBD_1.00)M2313_1.026.45e-436downstream / opposite strand
M6555_1.02ZNF333M6555_1.026.97e-450upstream / opposite strand
M1915_1.02(ZNF76)_(Xenopus_laevis)_(DBD_0.84)M1915_1.027.02e-423downstream / opposite strand
M4525_1.02TFAP2CM4525_1.027.37e-422downstream / opposite strand
M5955_1.02YY2M5955_1.027.70e-440upstream / opposite strand
M6037_1.02(IRX1)_(Mus_musculus)_(DBD_1.00)M6366_1.028.37e-4131downstream / same strand
M0737_1.02(FOXB2)_(Mus_musculus)_(DBD_0.94)CYCCGTCTCWAMWAAAAAWAMA8.61e-415upstream / opposite strand
M4461_1.02ETS1M4461_1.028.76e-416downstream / opposite strand
M5460_1.02FOXL1CYCCGTCTCWAMWAAAAAWAMA9.78e-418upstream / opposite strand
M6413_1.02PBX2CYCCGTCTCWAMWAAAAAWAMA9.84e-417upstream / opposite strand
M5335_1.02CUX2M5743_1.021.40e-333upstream / same strand
M5292_1.02ATF4M1925_1.021.42e-3128upstream / primary palindromic
M2385_1.02FOXP2CYCCGTCTCWAMWAAAAAWAMA1.44e-313upstream / opposite strand
M6268_1.02HAND1M6268_1.021.52e-361downstream / secondary palindromic
M5702_1.02PAX1M5702_1.021.72e-30downstream / opposite strand
M5517_1.02HMBOX1M5517_1.021.77e-397downstream / same strand
M1582_1.02(HMG20B)_(Mus_musculus)_(DBD_0.94)M6555_1.021.88e-350upstream / opposite strand
M6265_1.02GLI2M6265_1.021.92e-3126upstream / same strand
M5643_1.02MYBL1M5643_1.021.97e-3127downstream / opposite strand
M5320_1.02CENPBM5320_1.022.10e-32upstream / opposite strand
M6278_1.02HLTFM6278_1.022.26e-312downstream / opposite strand
M5544_1.02HOXC10CYCCGTCTCWAMWAAAAAWAMA2.33e-321upstream / same strand
M2321_1.02TP63M2321_1.022.42e-380downstream / same strand
M6478_1.02SOX9CYCCGTCTCWAMWAAAAAWAMA2.93e-317upstream / opposite strand
M5325_1.02CREB3L1M5325_1.022.99e-333upstream / opposite strand
M6546_1.02ZFHX3CYCCGTCTCWAMWAAAAAWAMA3.30e-314upstream / secondary palindromic
M6323_1.02KLF3M6323_1.023.87e-320downstream / opposite strand
M6290_1.02HOXA13M6290_1.024.24e-350upstream / opposite strand
M0413_1.02(ZBTB1)_(Mus_musculus)_(DBD_0.99)M0413_1.024.32e-358downstream / opposite strand
M5497_1.02GRHL1M6316_1.024.65e-348upstream / same strand
M6432_1.02PPARDM6432_1.025.11e-336downstream / same strand
M5883_1.02TBX20M5883_1.025.34e-326downstream / same strand
M6504_1.02TBX3M6504_1.025.45e-335downstream / same strand
M2310_1.02RUNX2M2310_1.025.57e-336upstream / same strand
M6226_1.02FEVM1882_1.026.25e-322upstream / primary palindromic
AAATAAATDREME-12M6378_1.026.50e-331upstream / opposite strand
M5584_1.02ISXM6378_1.026.75e-324upstream / same strand
M6357_1.02NANOGM6357_1.026.96e-384downstream / same strand
M6301_1.02HOXD10M6301_1.026.97e-322upstream / opposite strand
M6152_1.02ATF1M2313_1.027.11e-334downstream / opposite strand
M5738_1.02POU3F4M5738_1.027.11e-3104downstream / same strand
M6507_1.02TEAD1M6507_1.027.59e-382downstream / secondary palindromic
M6311_1.02IRF5M1882_1.027.86e-314upstream / opposite strand
M5348_1.02DRGXCYCCGTCTCWAMWAAAAAWAMA7.91e-318upstream / opposite strand
Previous Top
SpaMo version
4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700)
Reference
Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey, "Inferring transcription factor complexes from ChIP-seq data", Nucleic Acids Research, 39(15):e98, 2011.
Command line


Result calculation took 14 seconds