Database and Motifs High-scoring Motif Occurences Debugging Information



FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)

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

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]


DATABASE AND MOTIFS

DATABASE /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
TGTWWRTRTGGTATAT 16 TGTTAATATGGTATAT
TRTGGTATATRT 12 TGTGGTATATAT
TGGAGAAGTGACWAGACAAA 20 TGGAGAAGTGACAAGACAAA
CACACACACACA 12 CACACACACACA
AWCAAAAGAAAGMTRGARTRGC 22 ATCAAAAGAAAGCTGGAGTGGC
GGKGTKTGKGBTKBKDKGKGTG 22 GGTGTGTGTGCTGGTAGGGGTG
TCAGACARAGYAGAYTTCAGAGCAARGAAAR 31 TCAGACAAAGCAGACTTCAGAGCAAGGAAAA
AAGRRTRATAAA 12 AAGGGTGATAAA
CCATCAATCAATGAGTGGATAA 22 CCATCAATCAATGAGTGGATAA
ARCYCYYRRGYCTAACTRCTTCTTTGGRKTT 31 AGCCCCTAGGTCTAACTGCTTCTTTGGGTTT

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.305 C 0.195 G 0.195 T 0.305


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
CCATCAATCAATGAGTGGATAA MEME-9 chr13 + 34609990 34610011 1.26e-13 1.7e-08 ccatcaatcaatgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr7 - 112948358 112948379 1.26e-13 1.7e-08 CCATCAATCAATGAGTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr4 + 122787093 122787114 1.26e-13 1.7e-08 ccatcaatcaatgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr10 - 12581272 12581293 2.07e-13 1.7e-08 CCATCAATCAACGAGTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr17 + 13451717 13451738 2.07e-13 1.7e-08 ccatcaatcaacgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr2 + 147940536 147940557 2.07e-13 1.7e-08 ccatcaatcaacgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr5 + 170851747 170851768 2.07e-13 1.7e-08 ccatcaatcaacgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr9 + 16300221 16300242 7.23e-13 5.19e-08 ccatcaatcaaagagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr17 - 65118855 65118876 1.43e-12 9.13e-08 CCATCAATCATCGAGTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr2 + 37210377 37210398 3.47e-12 1.99e-07 ccatcaactaatgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 42495198 42495219 1.72e-11 8.23e-07 CCATCAACCAATGAGTGAATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr5 - 96842173 96842194 1.72e-11 8.23e-07 CCATCAACCAATGAGTAGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 168934233 168934254 2.01e-11 8.9e-07 ACATCAATCAATGAGTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr9 - 85871960 85871981 4.85e-11 1.86e-06 CCATCAATGATAGACTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 109552107 109552128 4.85e-11 1.86e-06 CCATCAATGATAGACTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr9 - 113608277 113608298 7.7e-11 2.76e-06 CCATCAACTGATGAATGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 224577822 224577843 1.28e-10 4.26e-06 ccatcaaccaacaaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 65207931 65207952 1.33e-10 4.26e-06 CCATCAATGATGGACTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 38408948 38408969 1.8e-10 5.45e-06 ctaccaatcaatgagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 1303918 1303939 2.94e-10 8.44e-06 CCATCAATGTATGATTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr12 + 25315548 25315569 6.86e-10 1.88e-05 tcatcaattaacaagtggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 229937507 229937528 8.53e-10 2.23e-05 ccatcaacagttgaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr16 + 81422772 81422793 1.02e-09 2.49e-05 ccatcaatcaacaagtagacaa
CCATCAATCAATGAGTGGATAA MEME-9 chr2 - 226711829 226711850 1.04e-09 2.49e-05 CCATCAACTGATGAATGAATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr5 + 124433330 124433351 2.32e-09 5.34e-05 tcatcaatggataaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr4 + 140330059 140330080 2.56e-09 5.65e-05 ccatcagtcaatgagtggctaa
CCATCAATCAATGAGTGGATAA MEME-9 chr3 + 43230690 43230711 4.56e-09 9.7e-05 acatcaaccaatgagcagataa
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 198762371 198762392 9.72e-09 0.000193 ccatcagttatagactgggcaa
CCATCAATCAATGAGTGGATAA MEME-9 chr19 + 40053660 40053681 9.76e-09 0.000193 ctgtctatcaatgaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr12 + 45212223 45212244 1.1e-08 0.000208 tcatcaatgatggactagataa
CCATCAATCAATGAGTGGATAA MEME-9 chr5 + 175340261 175340282 1.12e-08 0.000208 ctatcaatggtagactggttaa
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 36298227 36298248 1.87e-08 0.000337 CCATCAACAGGGGACTGGGTAA
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 235462984 235463005 3.24e-08 0.000564 ccatcaatcaatgagtaaagaa
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 208506936 208506957 4.26e-08 0.00072 ccaacaacagatgaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr10 + 118939575 118939596 4.4e-08 0.000722 ctgtcaactgatgaatagataa
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 184895946 184895967 4.62e-08 0.000737 GCACCAGCGGTTGATTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr14 + 68222281 68222302 7.44e-08 0.00116 ccatcagtcaatgagtatacaa
CCATCAATCAATGAGTGGATAA MEME-9 chr19 + 40088755 40088776 1.21e-07 0.00183 ctaacaatgaataaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr6 + 1303975 1303996 2.38e-07 0.00351 ccacgaatgtatgattggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr6 + 111235986 111236007 3.04e-07 0.00436 ccatcaagcaacaagttgataa
CCATCAATCAATGAGTGGATAA MEME-9 chr10 - 101409796 101409817 3.24e-07 0.00455 TTATCAACGAATAAACAGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr10 + 48221195 48221216 3.35e-07 0.00458 ccatcaatcaatgagtggtata
CCATCAATCAATGAGTGGATAA MEME-9 chr5 - 67358534 67358555 4.66e-07 0.00623 CCACTGACCAATGAGTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 + 27908134 27908155 5.09e-07 0.00666 ccaccaacagtgaattagataa
CCATCAATCAATGAGTGGATAA MEME-9 chr2 - 189955351 189955372 9.32e-07 0.0119 CCATCAATGGATAACTGGATTT
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 4838535 4838556 1.81e-06 0.0226 TTATCAGTCAACAAGTATATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr18 - 35016185 35016206 2.78e-06 0.034 CTATCCACAGTGGATTGGGTAA
CCATCAATCAATGAGTGGATAA MEME-9 chr18 - 3144884 3144905 8.62e-06 0.103 CTATCAATTATTGAGAGAGTAG
CCATCAATCAATGAGTGGATAA MEME-9 chr1 + 21104819 21104840 9.56e-06 0.112 ccttcaatggtagactaaagaa
CCATCAATCAATGAGTGGATAA MEME-9 chr19 + 40053664 40053685 1.28e-05 0.147 ctatcaatgaatggataaagaa
CCATCAATCAATGAGTGGATAA MEME-9 chr19 + 40053539 40053560 1.47e-05 0.165 ccagcaatctactactggatat
CCATCAATCAATGAGTGGATAA MEME-9 chr12 - 7015779 7015800 1.53e-05 0.169 CCACCAATCATCAAAGTAATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr20 - 32174117 32174138 1.64e-05 0.178 TTCTCAATCATTGATAGAATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr4 + 111243080 111243101 1.74e-05 0.185 taatcagtgagtgaatgggtga
CCATCAATCAATGAGTGGATAA MEME-9 chr9 - 136579792 136579813 1.77e-05 0.185 GAGTGAATGAATGAGTGAGTAA
CCATCAATCAATGAGTGGATAA MEME-9 chr4 - 27034322 27034343 2.03e-05 0.208 CCAGCTCACAATGAGTGAATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr19 + 434561 434582 2.55e-05 0.258 TCATGAGTGAGTGAGTGAGTGA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 13674883 13674904 2.7e-05 0.268 CCATCATTATGAGACTGAATCA
CCATCAATCAATGAGTGGATAA MEME-9 chr13 + 43948519 43948540 2.82e-05 0.275 tgttcaatggggaaatggataa
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 169447677 169447698 2.95e-05 0.282 GCATCTAACAACAAAGGGTTAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 83822856 83822877 3.02e-05 0.285 CCACCAACTGACGGATGATAAA
CCATCAATCAATGAGTGGATAA MEME-9 chr16 - 24379178 24379199 3.24e-05 0.3 AGAGCAATAAATGTGTGGATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 42495194 42495215 3.36e-05 0.306 CAACCAATGAGTGAATAAAGAA
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 228823585 228823606 3.65e-05 0.328 CTTTCAACAATTAATAGGACAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 119308583 119308604 4.17e-05 0.369 CCATCTGTCAAGCAGTATGCAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 + 1303765 1303786 4.3e-05 0.374 gtatctacctaaaagaaaataa
CCATCAATCAATGAGTGGATAA MEME-9 chr17 - 28810596 28810617 4.54e-05 0.389 CCCCCAGATGTTGACTAGTTAA
CCATCAATCAATGAGTGGATAA MEME-9 chr2 + 174367987 174368008 5.09e-05 0.43 acataaattataaaggggtcaa
CCATCAATCAATGAGTGGATAA MEME-9 chr14 - 91049765 91049786 5.53e-05 0.461 CCATCTAGGTTTGTGTAAGTAA
CCATCAATCAATGAGTGGATAA MEME-9 chr7 - 148878560 148878581 5.66e-05 0.465 CTGCCAACAGGCGAATTAACAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 - 89122773 89122794 6.04e-05 0.489 CCATCTGTTGGAGAGTGAGTTC
CCATCAATCAATGAGTGGATAA MEME-9 chr3 + 65538840 65538861 6.55e-05 0.523 CCAACTACCAACAAACAGACAC
CCATCAATCAATGAGTGGATAA MEME-9 chr12 + 14270384 14270405 6.74e-05 0.526 ttgtcaatgaaggaaggaagaa
CCATCAATCAATGAGTGGATAA MEME-9 chr10 + 101546105 101546126 6.78e-05 0.526 gtaccatcaatcaagtggatat
CCATCAATCAATGAGTGGATAA MEME-9 chr12 + 51551629 51551650 7.21e-05 0.543 ctataaaccattaagaggggaa
CCATCAATCAATGAGTGGATAA MEME-9 chr17 + 29258678 29258699 7.23e-05 0.543 ATATCAGCTAAGAATTAGTTAC
CCATCAATCAATGAGTGGATAA MEME-9 chr13 + 95628635 95628656 7.27e-05 0.543 ccaataacagatgaataagcaa
CCATCAATCAATGAGTGGATAA MEME-9 chr4 + 111243084 111243105 7.4e-05 0.546 cagtgagtgaatgggtgaataa
CCATCAATCAATGAGTGGATAA MEME-9 chr19 + 40567294 40567315 7.62e-05 0.554 tcaaaaataaataaataaataa
CCATCAATCAATGAGTGGATAA MEME-9 chr2 + 95220755 95220776 7.74e-05 0.556 TCATCTAGCTTTGAAGGAACAA
CCATCAATCAATGAGTGGATAA MEME-9 chr6 + 3957925 3957946 8.13e-05 0.574 acaccaatctgaatctgcataa
CCATCAATCAATGAGTGGATAA MEME-9 chr20 - 14396292 14396313 8.19e-05 0.574 ACACCATTCTCTGAATGATTAA
CCATCAATCAATGAGTGGATAA MEME-9 chrX - 69170732 69170753 8.43e-05 0.584 GCATCAAATAGGGAATAGTTAC
CCATCAATCAATGAGTGGATAA MEME-9 chr5 + 60817949 60817970 8.73e-05 0.591 ccaccaatatgagacttgttta
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 180839873 180839894 8.73e-05 0.591 ACACCAACTTTGGTATGCATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr12 + 1924724 1924745 8.94e-05 0.597 CGGTCTGCCAAAGAGTGGATCC
CCATCAATCAATGAGTGGATAA MEME-9 chr22 - 28947249 28947270 9.19e-05 0.607 CTACTGACTGAAGAGTGGATAC
CCATCAATCAATGAGTGGATAA MEME-9 chr10 + 33589193 33589214 9.34e-05 0.609 tcaacagtcaaagacaggttta
CCATCAATCAATGAGTGGATAA MEME-9 chr1 - 154527812 154527833 9.58e-05 0.609 CCAGCAGTATAAAAATGGGCAG
CCATCAATCAATGAGTGGATAA MEME-9 chr3 + 65539005 65539026 9.7e-05 0.609 CCAACTACCATCAAACAGACAC
CCATCAATCAATGAGTGGATAA MEME-9 chr3 + 65539059 65539080 9.7e-05 0.609 CCAACTACCATCAAACAGACAC
CCATCAATCAATGAGTGGATAA MEME-9 chr19 - 30034616 30034637 9.75e-05 0.609 GTACCAATTAAAAGACAAATAA
CCATCAATCAATGAGTGGATAA MEME-9 chr15 - 68891506 68891527 9.9e-05 0.612 TTAACAACAATCAACTAGATAT

DEBUGGING INFORMATION

Command line:

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_7 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif CCATCAATCAATGAGTGGATAA /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_7 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF211.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background alphabet = DNA max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = true
text only = false scan both strands = true max strand = false
threshold type = p-value output theshold = 0.0001 pseudocount = 0.1
alpha = 1 verbosity = 1

This information can be useful in the event you wish to report a problem with the FIMO software.


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