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/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GCAGCCAY 8 GCAGCCAT
GGAHTAC 7 GGAATAC
AGGMTGAG 8 AGGCTGAG
GGACATGR 8 GGACATGA
CAGCMTGG 8 CAGCATGG
ATASACCA 8 ATACACCA
ATGRAGC 7 ATGAAGC
TAAAAAYA 8 TAAAAATA
GGTGGCKC 8 GGTGGCGC
ATYCTCC 7 ATCCTCC
TAGAGA 6 TAGAGA
GAGKGCAC 8 GAGTGCAC
ARCCATCA 8 AACCATCA
CAAAGCTA 8 CAAAGCTA
GCCTCCC 7 GCCTCCC
AGCTACT 7 AGCTACT
AATGTGG 7 AATGTGG

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/background):
A 0.263 C 0.237 G 0.237 T 0.263


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
GGAHTAC DREME-2 chrX - 823271 823277 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 1021471 1021477 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 1021572 1021578 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 1021671 1021677 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 1021772 1021778 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 1021873 1021879 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr17 + 2653073 2653079 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 + 3539890 3539896 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr6 + 3735412 3735418 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 - 3898616 3898622 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr17 + 4143588 4143594 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr6 - 11957013 11957019 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr16 - 12803337 12803343 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 + 16915381 16915387 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr5 - 17357705 17357711 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX + 19511971 19511977 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr3 + 24572563 24572569 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 - 29210711 29210717 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 + 29379752 29379758 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 - 30291040 30291046 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 - 30398768 30398774 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 + 32458932 32458938 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 + 33312978 33312984 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 - 37076725 37076731 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 - 37594655 37594661 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 + 40080482 40080488 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 + 40091891 40091897 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr19 - 40964561 40964567 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 - 44220132 44220138 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 + 44253555 44253561 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr20 + 45657236 45657242 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr17 + 46922136 46922142 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr12 - 46974143 46974149 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 + 46990703 46990709 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr17 - 47321090 47321096 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr19 - 49946049 49946055 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 50906220 50906226 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 + 68384392 68384398 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 68560128 68560134 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr10 + 74457670 74457676 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chrX + 74701510 74701516 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chrX - 75348806 75348812 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX - 78226254 78226260 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr6 - 78666019 78666025 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr17 - 78862727 78862733 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr17 - 78862914 78862920 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chrX + 79934110 79934116 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chrX + 83990334 83990340 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chrX + 84796484 84796490 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chrX - 88008101 88008107 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 93911084 93911090 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr7 - 100940959 100940965 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr12 - 101560173 101560179 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr6 + 115941146 115941152 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chrX + 123722370 123722376 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr7 - 128194914 128194920 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr7 - 149379859 149379865 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr3 + 176094081 176094087 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr3 + 187023538 187023544 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr3 + 191646416 191646422 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 + 223283884 223283890 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 - 225233159 225233165 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 225310799 225310805 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 + 226432117 226432123 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 + 229798750 229798756 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 + 231948258 231948264 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 + 232156221 232156227 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 + 232158738 232158744 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 + 233828033 233828039 6.37e-05 0.51 ggaatac
GGAHTAC DREME-2 chr1 - 234762330 234762336 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 236186689 236186695 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 241425332 241425338 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 243528676 243528682 6.37e-05 0.51 GGAATAC
GGAHTAC DREME-2 chr1 - 244563086 244563092 6.37e-05 0.51 GGAATAC

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/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_4 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/background --motif GGAHTAC /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_4 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF280D.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/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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