Database and Motifs | High-scoring Motif Occurences | Debugging Information

FIMO - Motif search tool

FIMO version 4.7.0, (Release date: 0 EST 20)

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.

DATABASE AND MOTIFS

DATABASE /Users/xuebing/Downloads/hotair-target.fa.fasta
Database contains 832 sequences, 573269 residues

MOTIFS AATAAA.motif (nucleotide)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
AATAAA | 6 | AATAAA
AATAAA | 6 | TTTATT

Random model letter frequencies (from non-redundant database):
A 0.275 C 0.225 G 0.225 T 0.275

SECTION I: HIGH-SCORING MOTIF OCCURENCES

- Each of the following 0 motif occurrences has p-value less than 0.0001
- 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 table is sorted by increasing p-value.
- If the start position is larger than the end position, the motif occurrence is on the reverse strand.

Motif | Sequence Name | Strand | Start | End | p-value | Matched Sequence
--- | --- | --- | --- | --- | --- | ---

DEBUGGING INFORMATION

Command line:

    fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta

Settings:

    output directory = fimo_out
    MEME file name = AATAAA.motif
    sequence file name = /Users/xuebing/Downloads/hotair-target.fa.fasta

    background file name = (null)
    motif name = motif
    allow clobber = true

    compute q-values = true
    output p-threshold set = false
    output q-threshold set = false

    text only = false
    scan both strands = true
    max sequence length = 250000000

    output q-value threshold =   1
    output p-value threshold = 0.0001
    pseudocount = 0.1

    verbosity = 1

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

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