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

FIMO - Motif search tool

FIMO version 4.8.0, (Release date: 1 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 crp0.s
Database contains 18 sequences, 1890 residues

MOTIFS meme.crp0.zoops (nucleotide)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
1 | 18 | AATTGTGACGTAGATCAC
1 | 18 | GTGATCTACGTCACAATT
2 | 8 | CGGTGGGG
2 | 8 | CCCCACCG

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 22 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 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.
- 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 | q-value | Matched Sequence
--- | --- | --- | --- | --- | --- | --- | ---
1 | ara | − | 59 | 76 | 4.92e-07 | 0.000591 | `AAGTGTGACGCCGTGCAA`
1 | lac | + | 9 | 26 | 4.92e-07 | 0.000591 | `TAATGTGAGTTAGCTCAC`
1 | malt | + | 41 | 58 | 5.86e-07 | 0.000591 | `AATTGTGACACAGTGCAA`
1 | ilv | − | 43 | 60 | 1.61e-06 | 0.00106 | `AATTGAGGGGTTGATCAC`
1 | deop2 | + | 60 | 77 | 1.74e-06 | 0.00106 | `AATTGTGATGTGTATCGA`
1 | pbr322 | − | 57 | 74 | 2.98e-06 | 0.00151 | `ATCTGTGCGGTATTTCAC`
1 | uxu1 | + | 17 | 34 | 4.31e-06 | 0.00186 | `TGTTGTGATGTGGTTAAC`
1 | ce1cg | − | 65 | 82 | 4.97e-06 | 0.00188 | `TTTTGTGAAAACGATCAA`
1 | trn9cat | + | 84 | 101 | 6.13e-06 | 0.00206 | `AAATGAGACGTTGATCGG`
2 | ilv | + | 5 | 12 | 6.67e-06 | 0.0235 | `CGGCGGGG`
1 | gale | − | 46 | 63 | 8.61e-06 | 0.00261 | `AAGTGTGACATGGAATAA`
1 | tnaa | − | 75 | 92 | 1.05e-05 | 0.00275 | `AAATGTGAATCGAATCAC`
1 | crp | − | 67 | 84 | 1.12e-05 | 0.00275 | `TAATGTGACGTCCTTTGC`
1 | cya | + | 50 | 67 | 1.27e-05 | 0.00275 | `AGGTGTTAAATTGATCAC`
1 | male | + | 14 | 31 | 1.27e-05 | 0.00275 | `TTCTGTAACAGAGATCAC`
2 | male | + | 41 | 48 | 1.48e-05 | 0.0261 | `CGGTGGGG`
1 | ompa | + | 48 | 65 | 1.54e-05 | 0.00311 | `ATGCCTGACGGAGTTCAC`
1 | malk | + | 61 | 78 | 2.09e-05 | 0.00396 | `TTTCGTGATGTTGCTTGC`
1 | tdc | − | 82 | 99 | 2.22e-05 | 0.00396 | `ATATGTGCGACCACTCAC`
1 | tnaa | + | 71 | 88 | 2.5e-05 | 0.00421 | `GATTGTGATTCGATTCAC`
1 | tdc | + | 78 | 95 | 5.8e-05 | 0.00925 | `ATTTGTGAGTGGTCGCAC`
1 | bglr1 | + | 76 | 93 | 8.35e-05 | 0.0126 | `AACTGTGAGCATGGTCAT`

DEBUGGING INFORMATION

Command line:

    fimo meme.crp0.zoops crp0.s

Settings:

    output directory = fimo_out
    MEME file name = meme.crp0.zoops
    sequence file name = crp0.s

    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 = 2

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

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