FIMO Results

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 /mnt/data/annotations/by_organism/mouse/mm10/GRCm38.genome.fa
  
  Database contains 96 sequences, 2740108151 residues

  MOTIFS combined.meme (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1
        7
        ACAAAGG
       
        2
        21
        GTCCATTGTTATGCAAATTAA
       
        3
        7
        ATGCAAA
       
        4
        16
        TCCTTTGTTATGCAAA
       
        5
        16
        CCATTGTTATGCAAAT
       
        6
        17
        TCCTTTGTTATGCAAAT
       
        7
        8
        TCTATTGT
       
        8
        11
        GCCTTTGTTCC
       
        9
        6
        ACAAAG
       
        10
        8
        TATTGTTA
       
        11
        8
        CCCCACCC
       
        12
        9
        TTTTGTTTT
       
        13
        12
        TCCTTTGTTCTC
       
        14
        16
        AAAGGGGCCTTTGTTC
       
        15
        14
        TCCTTTGATTTGCT
       
        16
        30
        AGGTAGGAAGGCTCCACCCTAGGTAATCTC
       
        17
        6
        TATTCA
       
        18
        16
        CAAAGGAGGCATTGTT
       
        19
        7
        AACAATA
       
        20
        11
        ATATGCAAATG
       
        21
        7
        CAGCAGG
       
        22
        16
        CTCATGAATATTCAAG
       
        23
        11
        GTTATGTAACA
       
        24
        7
        AGAAAAG
       
        25
        8
        CAAGGTCA
       
        26
        8
        CATTCAAA
       
        27
        16
        AATCGAATGCAAATAA
       
        28
        6
        CTTCCT
       
        29
        16
        CTCATGCATATGCATA
       
        30
        7
        CTGCCTC
       
        31
        8
        GTAAACAC
       
        32
        6
        CCCAGC
       
        33
        7
        CTAATTA
       
        34
        8
        AGATGGCT
       
        35
        7
        ATAAAAG
       
        36
        11
        AAATCAATGAA
       
        37
        8
        ATTTGCAA
       
        38
        11
        TGTTGCATAAC
       
        39
        7
        AATGGCT
       
        40
        8
        AGGTACTC
       
        41
        11
        GCCTTTGATGT
       
        42
        13
        CCCTTTGATGTGG
       
        43
        19
        ATTAATGGGATTTTAATTA
       
        44
        13
        TGTTAGTATTGTG
       
        45
        7
        CTGCAGA
       
        46
        8
        AGACACTG
       
        47
        13
        CTCATGAATATAT
       
        48
        7
        CACACCT
       
        49
        8
        ATGGAAAT
       
        50
        7
        CTCCGGA
       
        51
        6
        ACAGAG
       
        52
        9
        ATTAATGAC
       
        53
        11
        AGTTATGTAAT
       
        54
        8
        GACTTCCC
       
        55
        12
        ACCATTTGTTCC
       
        56
        8
        TTAATGGC
       
        57
        10
        CTATAAAAGG
       
        58
        8
        CTCAGGGC
       
        59
        12
        TTTAATTGTTTT
       
        60
        7
        CCATTCA
       
        61
        8
        AGTCTTAC
       
        62
        8
        AGCAACAG
       
        63
        12
        TGTTTGCTTTGC
       
        64
        10
        GATAATTACA
       
        65
        8
        ATTTCCTA
       
        66
        12
        GGCAGCCATTTT
       
        67
        8
        CCCCTCCC
       
        68
        6
        GAATTC
       
        69
        9
        TTGTTTATT
       
        70
        16
        AAAGATCAAAGGAAAC
       
        71
        12
        CAAGATGGCGGC
       
        72
        8
        ACAGGAGC
       
        73
        15
        TTTGTTTACTTAGCA
       
        74
        11
        GGTTGTGCAAT
       
        75
        9
        GCTAATTAA
       
        76
        8
        CCACTGAG
       
        77
        10
        GTTAATTAGT
       
        78
        8
        CCTTGAAC
       
        79
        9
        GCTAATGGA
       
        80
        8
        AGCAGGCT
       
        81
        9
        GCTGATTAC
       
        82
        7
        TTAATTG
       
        83
        11
        TTTATTGATTT
       
Random model letter frequencies (--nrdb--):

A 0.275 C 0.225 G 0.225 T 0.275

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 tab-delimited plain text output file fimo.txt, the GFF 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 --motif 1 combined.meme /mnt/data/annotations/by_organism/mouse/mm10/GRCm38.genome.fa

Settings:


  
    output_directory = fimo_out
    MEME file name = combined.meme
    sequence file name = /mnt/data/annotations/by_organism/mouse/mm10/GRCm38.genome.fa
  
  
    background file name = --nrdb--
    alphabet = DNA
    max stored scores = 100000
  
  
    allow clobber = true
    compute q-values = true
    parse genomic coord. = false
  
  
    text only = false
    scan both strands = true
    max strand = false
  
  
    threshold type = p-value
    output theshold = 0.0001
    pseudocount = 0.1
  
  
    alpha = 1
    verbosity = 2

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