Database and Motifs | High-scoring Motif Occurences | Debugging Information |
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 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/NR2C1-Antibody.IDR0.05.filt.narrowPeaksummitPlusMinus250bp.fa
Database contains 15672 sequences, 7836000 residues
MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
TGACCYB | 7 | TGACCTC |
CMGGAAGY | 8 | CCGGAAGT |
TTATCW | 6 | TTATCT |
CTGTAAYC | 8 | CTGTAATC |
CAYGTGAY | 8 | CACGTGAC |
GGAARTR | 7 | GGAAGTG |
GTGRCTCA | 8 | GTGGCTCA |
AANATGGC | 8 | AAGATGGC |
CCMCRCCC | 8 | CCCCACCC |
AGGCYGAG | 8 | AGGCTGAG |
AGKTCA | 6 | AGTTCA |
CAAAGKGC | 8 | CAAAGTGC |
HCCGGAA | 7 | CCCGGAA |
AAAATAMA | 8 | AAAATACA |
CAGCSTGG | 8 | CAGCCTGG |
AAATTAGC | 8 | AAATTAGC |
CHGCYTCC | 8 | CTGCCTCC |
TAGAGAYR | 8 | TAGAGACG |
RRGGTTA | 7 | AGGGTTA |
ATGACBCA | 8 | ATGACTCA |
GATCCRCC | 8 | GATCCGCC |
GCTGGGA | 7 | GCTGGGA |
GCDGCBGC | 8 | GCTGCGGC |
CACGTGK | 7 | CACGTGG |
TGGTGAAA | 8 | TGGTGAAA |
GAGGCCR | 7 | GAGGCCA |
GGMRGGA | 7 | GGAAGGA |
WAAATR | 6 | AAAATG |
GACGTCAY | 8 | GACGTCAC |
TGCAGTRA | 8 | TGCAGTGA |
GRACTACA | 8 | GGACTACA |
RGAAA | 5 | AGAAA |
CACACRCA | 8 | CACACACA |
CGACCTY | 7 | CGACCTC |
CGCCAY | 6 | CGCCAC |
GCGGAAS | 7 | GCGGAAG |
CAGCTRC | 7 | CAGCTGC |
ATAGATTC | 8 | ATAGATTC |
TGACBCA | 7 | TGACCCA |
GAAAATCC | 8 | GAAAATCC |
GTTAAAGA | 8 | GTTAAAGA |
ACATTGTA | 8 | ACATTGTA |
CCTCCCAS | 8 | CCTCCCAC |
TGATGTMA | 8 | TGATGTCA |
GCCTGGS | 7 | GCCTGGG |
ATGACGTA | 8 | ATGACGTA |
AGAGGGCR | 8 | AGAGGGCA |
GGGTCA | 6 | GGGTCA |
AGAATCGC | 8 | AGAATCGC |
AGTTCGAG | 8 | AGTTCGAG |
RCCAATCA | 8 | GCCAATCA |
CGCABGCG | 8 | CGCAGGCG |
ATCTCRGC | 8 | ATCTCAGC |
AAMCACA | 7 | AACCACA |
CGCCTRTA | 8 | CGCCTGTA |
Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/background):
A 0.244 C 0.256 G 0.256 T 0.244
Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|
Command line:
/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_42 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/background --motif RGAAA /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/NR2C1-Antibody.IDR0.05.filt.narrowPeaksummitPlusMinus250bp.fa
Settings:
output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_42 | MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml | sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/NR2C1-Antibody.IDR0.05.filt.narrowPeaksummitPlusMinus250bp.fa |
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/NR2C1-Antibody.IDR0.05.filt.narrowPeak.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.