Database and Motifs | High-scoring Motif Occurences | Debugging Information | Results in TSV Format | Results in GFF3 Format

FIMO - Motif search tool

FIMO version 5.5.1, (Release date: Sun Jan 29 10:33:12 2023 -0800)

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 nrmix.nseqs.100.100bp.seed.1.fa
Database contains 2100 sequences, 210000 residues

MOTIFS xstreme_example_output_files/meme_out/meme.xml (DNA)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
TTTTYTTTTYTTTYW | 15 | TTTTTTTTTTTTTCT
VATGACTCAG | 10 | GATGACTCAG
SCCCCGCCCCC | 11 | GCCCCGCCCCC
CCASYAGRKGGCRSY | 15 | CCACCAGGGGGCGCT
CTTATCT | 7 | CTTATCT
GACTACAWYTCCCAG | 15 | GACTACATCTCCCAG
TGCACTCCAGCCTGG | 15 | TGCACTCCAGCCTGG
AAASAGGAAGT | 11 | AAACAGGAAGT
GCGCMTGCGCG | 11 | GCGCCTGCGCG
RGCTCACTGCAGCCT | 15 | AGCTCACTGCAGCCT

Random model letter frequencies (xstreme_example_output_files/background):
A 0.222 C 0.278 G 0.278 T 0.222

SECTION I: HIGH-SCORING MOTIF OCCURENCES

- There were 87 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
--- | --- | --- | --- | --- | --- | --- | --- | ---
RGCTCACTGCAGCCT | MEME-10 | 20 | + | 33254202 | 33254216 | 1.19e-09 | 0.000107 | AGCTCACTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 1 | - | 36863991 | 36864005 | 1.19e-09 | 0.000107 | AGCTCACTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 4 | + | 74021829 | 74021843 | 1.19e-09 | 0.000107 | AGCTCACTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 10 | + | 105091905 | 105091919 | 1.19e-09 | 0.000107 | AGCTCACTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 4 | - | 71601604 | 71601618 | 6.3e-09 | 0.000454 | AGCTCACAGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 1 | - | 29210626 | 29210640 | 1.03e-08 | 0.000499 | AGCTCACTGCAACCT
RGCTCACTGCAGCCT | MEME-10 | 17 | + | 74634327 | 74634341 | 1.03e-08 | 0.000499 | AGCTCACTGCAACCT
RGCTCACTGCAGCCT | MEME-10 | 4 | - | 6615035 | 6615049 | 1.25e-08 | 0.000499 | AGCTCACTGCAGTCT
RGCTCACTGCAGCCT | MEME-10 | 21 | + | 40721515 | 40721529 | 1.25e-08 | 0.000499 | GGCTCATTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 11 | - | 46358304 | 46358318 | 1.8e-08 | 0.000646 | GGCTCACCGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 1 | + | 241759995 | 241760009 | 2.86e-08 | 0.000934 | GGGTCACTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 19 | + | 49587717 | 49587731 | 3.26e-08 | 0.000979 | GGCTCACTGCAACCT
RGCTCACTGCAGCCT | MEME-10 | 9 | - | 132388024 | 132388038 | 9.58e-08 | 0.00264 | GGCTCACCGCAACCT
RGCTCACTGCAGCCT | MEME-10 | 6 | + | 16131162 | 16131176 | 1.02e-07 | 0.00264 | AGGTCATTGCAGACT
RGCTCACTGCAGCCT | MEME-10 | 19 | - | 48824764 | 48824778 | 2.09e-07 | 0.00469 | AGGTCACCGCAGGCT
RGCTCACTGCAGCCT | MEME-10 | 2 | - | 85006921 | 85006935 | 2.09e-07 | 0.00469 | GGCTAACAGCAGACT
RGCTCACTGCAGCCT | MEME-10 | 12 | - | 8010462 | 8010476 | 2.49e-07 | 0.00527 | GGCTCATTCCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 1 | - | 230262735 | 230262749 | 5.26e-07 | 0.0105 | GGCTCACAGCAGGAT
RGCTCACTGCAGCCT | MEME-10 | 5 | - | 139990698 | 139990712 | 5.56e-07 | 0.0105 | AGCTAAAAGCAGACT
RGCTCACTGCAGCCT | MEME-10 | 7 | + | 116570486 | 116570500 | 8.39e-07 | 0.0151 | AGCTAATCGCAGTAT
RGCTCACTGCAGCCT | MEME-10 | 8 | - | 17123860 | 17123874 | 9.99e-07 | 0.0171 | AGGTAATCACAGCCT
RGCTCACTGCAGCCT | MEME-10 | 19 | + | 35870432 | 35870446 | 1.1e-06 | 0.0181 | GGCTGACTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 17 | - | 61626625 | 61626639 | 1.23e-06 | 0.0193 | GGCTCACTGTAGCCT
RGCTCACTGCAGCCT | MEME-10 | 15 | - | 85493671 | 85493685 | 1.66e-06 | 0.0248 | AGCTTACTGCAGTCT
RGCTCACTGCAGCCT | MEME-10 | 1 | - | 40638171 | 40638185 | 1.73e-06 | 0.0248 | AGCTCACTGTAACCT
RGCTCACTGCAGCCT | MEME-10 | 1 | + | 17262631 | 17262645 | 2.58e-06 | 0.0357 | GGCTTACTGCAGTCT
RGCTCACTGCAGCCT | MEME-10 | 17 | + | 66015880 | 66015894 | 4.18e-06 | 0.0558 | GGGTCACCACAGGAT
RGCTCACTGCAGCCT | MEME-10 | 7 | + | 108208518 | 108208532 | 4.54e-06 | 0.0584 | GGCTCACCTCAACCT
RGCTCACTGCAGCCT | MEME-10 | 1 | + | 154856428 | 154856442 | 5.66e-06 | 0.0703 | GGCTCATACCAAAAT
RGCTCACTGCAGCCT | MEME-10 | 2 | - | 24680611 | 24680625 | 6.34e-06 | 0.0761 | CGGTCATTGCAGGCT
RGCTCACTGCAGCCT | MEME-10 | 10 | + | 28807649 | 28807663 | 6.86e-06 | 0.0797 | GGCTTACTGCAAGCT
RGCTCACTGCAGCCT | MEME-10 | 12 | + | 53764980 | 53764994 | 7.52e-06 | 0.0825 | AGCTCACGCCAGTCT
RGCTCACTGCAGCCT | MEME-10 | 15 | - | 42991213 | 42991227 | 7.56e-06 | 0.0825 | AGCTAATAACAATAT
RGCTCACTGCAGCCT | MEME-10 | 16 | - | 8162575 | 8162589 | 8.72e-06 | 0.0923 | GGCTCACTGCAAGCC
RGCTCACTGCAGCCT | MEME-10 | 1 | + | 68403331 | 68403345 | 1.15e-05 | 0.119 | GGCTCACCCCTGCCT
RGCTCACTGCAGCCT | MEME-10 | 16 | - | 4340185 | 4340199 | 1.31e-05 | 0.131 | GACTCACTCCAACCT
RGCTCACTGCAGCCT | MEME-10 | 9 | - | 131486933 | 131486947 | 1.83e-05 | 0.175 | GGCTCACAGCAGGAG
RGCTCACTGCAGCCT | MEME-10 | X | + | 10550412 | 10550426 | 1.84e-05 | 0.175 | AGGTAAAAGGAGCCT
RGCTCACTGCAGCCT | MEME-10 | 3 | + | 33133320 | 33133334 | 2.04e-05 | 0.188 | AGGGAAAAGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 22 | - | 22235795 | 22235809 | 2.18e-05 | 0.195 | GGGCCACCCCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 11 | - | 117314198 | 117314212 | 2.22e-05 | 0.195 | GCCTCACAACAGGCT
RGCTCACTGCAGCCT | MEME-10 | 2 | + | 70331740 | 70331754 | 2.39e-05 | 0.198 | GGCTAAACTCAGACT
RGCTCACTGCAGCCT | MEME-10 | 10 | - | 80853544 | 80853558 | 2.46e-05 | 0.198 | TGCTCACTGCGGCCT
RGCTCACTGCAGCCT | MEME-10 | 2 | - | 138815973 | 138815987 | 2.48e-05 | 0.198 | AGATAATAACAGACT
RGCTCACTGCAGCCT | MEME-10 | 12 | + | 104026297 | 104026311 | 2.49e-05 | 0.198 | AGCACACTGCACCCT
RGCTCACTGCAGCCT | MEME-10 | 17 | + | 25900892 | 25900906 | 2.52e-05 | 0.198 | GAGTCATCACAGCCT
RGCTCACTGCAGCCT | MEME-10 | 4 | + | 186425577 | 186425591 | 3.59e-05 | 0.275 | AGCTGGCCGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 8 | + | 27949615 | 27949629 | 4.02e-05 | 0.302 | CACTCACTGCAACCT
RGCTCACTGCAGCCT | MEME-10 | 22 | + | 22555433 | 22555447 | 4.11e-05 | 0.302 | GGGTCATTGCAAAAG
RGCTCACTGCAGCCT | MEME-10 | 12 | - | 116928266 | 116928280 | 4.23e-05 | 0.302 | ATCTAATTCCAGAAT
RGCTCACTGCAGCCT | MEME-10 | 19 | - | 16738805 | 16738819 | 4.39e-05 | 0.302 | AGCTCACTGGAGTTT
RGCTCACTGCAGCCT | MEME-10 | 18 | + | 45408117 | 45408131 | 4.4e-05 | 0.302 | TGCTCACTGCAGGTT
RGCTCACTGCAGCCT | MEME-10 | 6 | + | 7150840 | 7150854 | 4.5e-05 | 0.302 | AGCGACCTGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 9 | + | 26975640 | 26975654 | 4.64e-05 | 0.302 | GGCTCCTTGCATCCT
RGCTCACTGCAGCCT | MEME-10 | 18 | + | 19192021 | 19192035 | 4.7e-05 | 0.302 | GGCCCAGCGCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 17 | + | 40825579 | 40825593 | 4.76e-05 | 0.302 | AGCACAAACCAGGCT
RGCTCACTGCAGCCT | MEME-10 | 12 | - | 104358604 | 104358618 | 4.78e-05 | 0.302 | AGGTAACTCCAAACC
RGCTCACTGCAGCCT | MEME-10 | 11 | - | 62432607 | 62432621 | 5.04e-05 | 0.313 | AGCTAAAACCACACT
RGCTCACTGCAGCCT | MEME-10 | 13 | - | 49512782 | 49512796 | 5.48e-05 | 0.332 | AACTAAAAACAACCT
RGCTCACTGCAGCCT | MEME-10 | 12 | + | 53552150 | 53552164 | 5.53e-05 | 0.332 | AGGTCAGTGCAGAGT
RGCTCACTGCAGCCT | MEME-10 | 1 | - | 45296689 | 45296703 | 5.62e-05 | 0.332 | AGCTCACTGTAGCAC
RGCTCACTGCAGCCT | MEME-10 | 22 | - | 40228653 | 40228667 | 6.16e-05 | 0.355 | TTGTCACTGCAGACT
RGCTCACTGCAGCCT | MEME-10 | 15 | - | 45016446 | 45016460 | 6.21e-05 | 0.355 | ACATCATTGCAGGCT
RGCTCACTGCAGCCT | MEME-10 | 14 | + | 79163713 | 79163727 | 7.03e-05 | 0.377 | AGGTCTCTGCAGATT
RGCTCACTGCAGCCT | MEME-10 | 10 | - | 115548378 | 115548392 | 7.12e-05 | 0.377 | GAGTCATTCCAACAT
RGCTCACTGCAGCCT | MEME-10 | 11 | - | 120215001 | 120215015 | 7.12e-05 | 0.377 | GGCAAACCACAACAT
RGCTCACTGCAGCCT | MEME-10 | 7 | + | 93442816 | 93442830 | 7.29e-05 | 0.377 | ATGACACTGCAGACT
RGCTCACTGCAGCCT | MEME-10 | 17 | + | 61626651 | 61626665 | 7.37e-05 | 0.377 | AGTGCACTCCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 6 | + | 15793567 | 15793581 | 7.44e-05 | 0.377 | AGCTCACAGGTGTCT
RGCTCACTGCAGCCT | MEME-10 | 8 | - | 116680932 | 116680946 | 7.55e-05 | 0.377 | ATCTTACTGCAATCT
RGCTCACTGCAGCCT | MEME-10 | 15 | + | 91384181 | 91384195 | 7.58e-05 | 0.377 | AGCTCCCTCCACCCT
RGCTCACTGCAGCCT | MEME-10 | 7 | + | 18040162 | 18040176 | 7.61e-05 | 0.377 | CGCTGACTGCAAGCT
RGCTCACTGCAGCCT | MEME-10 | 16 | + | 80361647 | 80361661 | 7.69e-05 | 0.377 | AGTTAATTGAAGACT
RGCTCACTGCAGCCT | MEME-10 | 16 | - | 89768294 | 89768308 | 7.76e-05 | 0.377 | GGCTCTTCCCAGGAT
RGCTCACTGCAGCCT | MEME-10 | 5 | + | 56737411 | 56737425 | 8.09e-05 | 0.38 | AGCTCCCAGGAGGCT
RGCTCACTGCAGCCT | MEME-10 | 14 | + | 68188946 | 68188960 | 8.09e-05 | 0.38 | ATCTCCCAGCAGGCT
RGCTCACTGCAGCCT | MEME-10 | 5 | - | 123985337 | 123985351 | 8.16e-05 | 0.38 | AGGTCACTGAAACCA
RGCTCACTGCAGCCT | MEME-10 | X | - | 155227122 | 155227136 | 8.23e-05 | 0.38 | AGATAACTGCAGCAG
RGCTCACTGCAGCCT | MEME-10 | 12 | - | 124975328 | 124975342 | 8.35e-05 | 0.381 | AGCTCTTATCAGACT
RGCTCACTGCAGCCT | MEME-10 | 6 | - | 12092966 | 12092980 | 8.65e-05 | 0.386 | GGCTAGTTGCAGCCA
RGCTCACTGCAGCCT | MEME-10 | 6 | + | 7975164 | 7975178 | 8.68e-05 | 0.386 | GGCTCTCTGCGGCAT
RGCTCACTGCAGCCT | MEME-10 | 21 | - | 38738760 | 38738774 | 8.81e-05 | 0.387 | AGGTAACGGCAGATT
RGCTCACTGCAGCCT | MEME-10 | 1 | + | 201672071 | 201672085 | 9.28e-05 | 0.399 | AGCTCCCAGCAGCAG
RGCTCACTGCAGCCT | MEME-10 | 1 | + | 36864017 | 36864031 | 9.32e-05 | 0.399 | ACTTCATTCCAGCCT
RGCTCACTGCAGCCT | MEME-10 | 12 | + | 122017058 | 122017072 | 9.89e-05 | 0.414 | CGGTAACAGCAGCCC
RGCTCACTGCAGCCT | MEME-10 | 12 | + | 9892362 | 9892376 | 9.96e-05 | 0.414 | ACCTCCCTGCAAGCT
RGCTCACTGCAGCCT | MEME-10 | 17 | - | 46795032 | 46795046 | 0.0001 | 0.414 | AAGTTATTGCAGTCT

DEBUGGING INFORMATION

Command line:

    fimo --parse-genomic-coord --verbosity 1 --oc xstreme_example_output_files/fimo_out_12 --bgfile xstreme_example_output_files/background --motif RGCTCACTGCAGCCT xstreme_example_output_files/meme_out/meme.xml nrmix.nseqs.100.100bp.seed.1.fa

Settings:

        output_directory = xstreme_example_output_files/fimo_out_12
        MEME file name = xstreme_example_output_files/meme_out/meme.xml
        sequence file name = nrmix.nseqs.100.100bp.seed.1.fa

        background file name = xstreme_example_output_files/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.

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