FIMO Results

Database and Motifs

High-scoring Motif Occurences

Debugging Information

Results in TSV Format

Results in GFF3 Format

FIMO - Motif search tool

FIMO version 5.4.1, (Release date: Sat Aug 21 19:23:23 2021 -0700)

For further information on how to interpret these results please access https://meme-suite.org/meme/doc/fimo-output-format.html.
To get a copy of the FIMO software please access https://meme-suite.org

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 ./IFI16_D1_chip.MACS2_peaks.narrowPeak.chr-vs-BL-outersection1.fa
  
  Database contains 17848 sequences, 3569600 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-VTGASTCAB
        9
        ATGAGTCAT
       
        2-TTGMKCAA
        8
        TTGCGCAA
       
        3-ACATTCCW
        8
        ACATTCCT
       
        4-CCCCRCCCC
        9
        CCCCACCCC
       
        5-GATGACDHA
        9
        GATGACACA
       
        6-AGAAACA
        7
        AGAAACA
       
        7-TGASTCA
        7
        TGAGTCA
       
        8-AGGAAR
        6
        AGGAAG
       
        9-CATTCC
        6
        CATTCC
       
        10-CTTGGCAA
        8
        CTTGGCAA
       
        11-AAATRC
        6
        AAATGC
       
        12-AGTCACCT
        8
        AGTCACCT
       
        13-AAATATTTRTTG
        12
        AAATATTTATTG
       
        14-CCGCCTCCTC
        10
        CCGCCTCCTC
       
        15-AAACCWGT
        8
        AAACCTGT
       
        16-ATGATGCAATC
        11
        ATGATGCAATC
       
        17-ACACCCACAT
        10
        ACACCCACAT
       
        18-CTGGGA
        6
        CTGGGA
       
        19-TGCGCAGGCGCAV
        13
        TGCGCAGGCGCAA
       
        20-CRGCCAATC
        9
        CAGCCAATC
       
        21-CACACACACACACA
        14
        CACACACACACACA
       
        22-RGGYAGRG
        8
        AGGCAGAG
       
        23-GTGCCTGGCACABAG
        15
        GTGCCTGGCACATAG
       
        24-AATGAATGAATR
        12
        AATGAATGAATA
       
        25-CCWCCYACK
        9
        CCTCCCACT
       
Random model letter frequencies (./background):

A 0.258 C 0.242 G 0.242 T 0.258

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-VTGASTCAB	9	ATGAGTCAT
2-TTGMKCAA	8	TTGCGCAA
3-ACATTCCW	8	ACATTCCT
4-CCCCRCCCC	9	CCCCACCCC
5-GATGACDHA	9	GATGACACA
6-AGAAACA	7	AGAAACA
7-TGASTCA	7	TGAGTCA
8-AGGAAR	6	AGGAAG
9-CATTCC	6	CATTCC
10-CTTGGCAA	8	CTTGGCAA
11-AAATRC	6	AAATGC
12-AGTCACCT	8	AGTCACCT
13-AAATATTTRTTG	12	AAATATTTATTG
14-CCGCCTCCTC	10	CCGCCTCCTC
15-AAACCWGT	8	AAACCTGT
16-ATGATGCAATC	11	ATGATGCAATC
17-ACACCCACAT	10	ACACCCACAT
18-CTGGGA	6	CTGGGA
19-TGCGCAGGCGCAV	13	TGCGCAGGCGCAA
20-CRGCCAATC	9	CAGCCAATC
21-CACACACACACACA	14	CACACACACACACA
22-RGGYAGRG	8	AGGCAGAG
23-GTGCCTGGCACABAG	15	GTGCCTGGCACATAG
24-AATGAATGAATR	12	AATGAATGAATA
25-CCWCCYACK	9	CCTCCCACT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 0 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the TSV (tab-delimited values) output file fimo.tsv, the GFF3 file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
The table is sorted by increasing p-value.

Motif ID	Alt ID	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_7 --bgfile ./background --motif 8-AGGAAR streme_out/streme.xml ./IFI16_D1_chip.MACS2_peaks.narrowPeak.chr-vs-BL-outersection1.fa

Settings:


  
    output_directory = fimo_out_7
    MEME file name = streme_out/streme.xml
    sequence file name = ./IFI16_D1_chip.MACS2_peaks.narrowPeak.chr-vs-BL-outersection1.fa
  
  
    background file name = ./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.

Go to top

output_directory = fimo_out_7	MEME file name = streme_out/streme.xml	sequence file name = ./IFI16_D1_chip.MACS2_peaks.narrowPeak.chr-vs-BL-outersection1.fa
background file name = ./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