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

FIMO - Motif search tool

FIMO version 5.4.0, (Release date: Mon Aug 16 16:18:19 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 nrmix.nseqs.100.100bp.seed.1.fa
Database contains 2100 sequences, 210000 residues

MOTIFS xstreme_example_output_files/streme_out/streme.xml (DNA)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
1-CCASYAGRGGGCGCY | 15 | CCACCAGGGGGCGCC
2-GCTGAGTCATN | 11 | GCTGAGTCATG
3-GCGCATGCGCAC | 12 | GCGCATGCGCAC
4-CACTTCCTGKT | 11 | CACTTCCTGTT
5-AGATAAGG | 8 | AGATAAGG
6-CCCCGCCCCCD | 11 | CCCCGCCCCCT
7-CAAGATGGC | 9 | CAAGATGGC
8-GGTCACGTGABBS | 13 | GGTCACGTGACGC

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 99 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
--- | --- | --- | --- | --- | --- | --- | --- | ---
7-CAAGATGGC | STREME-7 | 17 | + | 11811987 | 11811995 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 7 | + | 101459106 | 101459114 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 6 | + | 108881180 | 108881188 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 2 | + | 178837611 | 178837619 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 1 | - | 20204813 | 20204821 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 1 | - | 46049907 | 46049915 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 17 | - | 46969696 | 46969704 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 22 | - | 49448083 | 49448091 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 1 | - | 111991883 | 111991891 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 12 | - | 121454072 | 121454080 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 7 | - | 139477306 | 139477314 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 8 | - | 144691513 | 144691521 | 4.03e-06 | 0.122 | CAAGATGGC
7-CAAGATGGC | STREME-7 | 19 | + | 5622592 | 5622600 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 1 | + | 5948572 | 5948580 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 10 | + | 59063366 | 59063374 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | X | + | 62654617 | 62654625 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 2 | + | 71558926 | 71558934 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | X | + | 154493683 | 154493691 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 11 | - | 10477459 | 10477467 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 6 | - | 30582716 | 30582724 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 9 | - | 36325131 | 36325139 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 2 | - | 71357144 | 71357152 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 6 | - | 167200226 | 167200234 | 7.25e-06 | 0.122 | CAAAATGGC
7-CAAGATGGC | STREME-7 | 5 | + | 1799777 | 1799785 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | 11 | + | 66277926 | 66277934 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | X | + | 107408561 | 107408569 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | 20 | - | 5892040 | 5892048 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | 11 | - | 12915598 | 12915606 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | 19 | - | 38852962 | 38852970 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | 15 | - | 42565391 | 42565399 | 1.13e-05 | 0.14 | GAAGATGGC
7-CAAGATGGC | STREME-7 | 12 | + | 6532681 | 6532689 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 5 | + | 82726245 | 82726253 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 1 | + | 109820001 | 109820009 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 11 | + | 125792908 | 125792916 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 1 | + | 168147787 | 168147795 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 3 | + | 168582717 | 168582725 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 6 | - | 31830559 | 31830567 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 6 | - | 31830571 | 31830579 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 1 | - | 33116333 | 33116341 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 11 | - | 72525157 | 72525165 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 12 | - | 93043686 | 93043694 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 9 | - | 115774341 | 115774349 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | X | - | 149885286 | 149885294 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 7 | - | 150755102 | 150755110 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 1 | - | 226814195 | 226814203 | 1.63e-05 | 0.14 | CAAGAGGGC
7-CAAGATGGC | STREME-7 | 16 | + | 4743523 | 4743531 | 1.96e-05 | 0.157 | CAAGATGTC
7-CAAGATGGC | STREME-7 | 10 | + | 98590315 | 98590323 | 1.96e-05 | 0.157 | CAAGATGTC
7-CAAGATGGC | STREME-7 | 17 | - | 80712772 | 80712780 | 1.96e-05 | 0.157 | CAAGATGTC
7-CAAGATGGC | STREME-7 | 17 | + | 1618603 | 1618611 | 2.46e-05 | 0.186 | CAAGACGGC
7-CAAGATGGC | STREME-7 | 7 | + | 106960368 | 106960376 | 2.46e-05 | 0.186 | CAAGACGGC
7-CAAGATGGC | STREME-7 | 5 | - | 10334952 | 10334960 | 2.46e-05 | 0.186 | CAAGACGGC
7-CAAGATGGC | STREME-7 | 17 | + | 80009603 | 80009611 | 2.86e-05 | 0.201 | CAAGATGCC
7-CAAGATGGC | STREME-7 | 6 | + | 139003836 | 139003844 | 2.86e-05 | 0.201 | CAAGATGCC
7-CAAGATGGC | STREME-7 | 7 | - | 40678492 | 40678500 | 2.86e-05 | 0.201 | CAAGATGCC
7-CAAGATGGC | STREME-7 | 13 | - | 110359350 | 110359358 | 2.86e-05 | 0.201 | CAAGATGCC
7-CAAGATGGC | STREME-7 | 1 | + | 44820889 | 44820897 | 3.19e-05 | 0.204 | CAAGATGGT
7-CAAGATGGC | STREME-7 | 12 | - | 104341807 | 104341815 | 3.19e-05 | 0.204 | CAAGATGGT
7-CAAGATGGC | STREME-7 | 7 | - | 153111006 | 153111014 | 3.19e-05 | 0.204 | CAAGATGGT
7-CAAGATGGC | STREME-7 | 17 | + | 13241095 | 13241103 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 12 | + | 55119000 | 55119008 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 9 | + | 112665807 | 112665815 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 3 | + | 129209012 | 129209020 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 3 | + | 180520616 | 180520624 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 8 | - | 29172212 | 29172220 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 1 | - | 39283801 | 39283809 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 11 | - | 123349092 | 123349100 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 1 | - | 203185307 | 203185315 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 1 | - | 246862445 | 246862453 | 3.59e-05 | 0.204 | CTAGATGGC
7-CAAGATGGC | STREME-7 | 2 | - | 60983197 | 60983205 | 3.91e-05 | 0.216 | CAATATGGC
7-CAAGATGGC | STREME-7 | 11 | - | 69271450 | 69271458 | 3.91e-05 | 0.216 | CAATATGGC
7-CAAGATGGC | STREME-7 | 10 | + | 21623998 | 21624006 | 4.23e-05 | 0.23 | CAAGATGAC
7-CAAGATGGC | STREME-7 | 19 | + | 3106981 | 3106989 | 4.55e-05 | 0.236 | CAAGATTGC
7-CAAGATGGC | STREME-7 | 1 | - | 206664185 | 206664193 | 4.55e-05 | 0.236 | CAAGATTGC
7-CAAGATGGC | STREME-7 | 16 | + | 8162549 | 8162557 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 10 | + | 27443072 | 27443080 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 1 | + | 33116323 | 33116331 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 14 | + | 102700915 | 102700923 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 2 | + | 178837587 | 178837595 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 14 | - | 23387912 | 23387920 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 9 | - | 112681178 | 112681186 | 4.88e-05 | 0.236 | GAAAATGGC
7-CAAGATGGC | STREME-7 | 6 | + | 20402364 | 20402372 | 5.28e-05 | 0.252 | CAAAAGGGC
7-CAAGATGGC | STREME-7 | 19 | + | 2051151 | 2051159 | 5.79e-05 | 0.257 | GAAGAGGGC
7-CAAGATGGC | STREME-7 | 11 | + | 10477424 | 10477432 | 5.79e-05 | 0.257 | GAAGAGGGC
7-CAAGATGGC | STREME-7 | 19 | + | 50373109 | 50373117 | 5.79e-05 | 0.257 | GAAGAGGGC
7-CAAGATGGC | STREME-7 | 19 | - | 18854117 | 18854125 | 5.79e-05 | 0.257 | GAAGAGGGC
7-CAAGATGGC | STREME-7 | 17 | - | 42402617 | 42402625 | 5.79e-05 | 0.257 | GAAGAGGGC
7-CAAGATGGC | STREME-7 | 5 | - | 56433907 | 56433915 | 5.79e-05 | 0.257 | GAAGAGGGC
7-CAAGATGGC | STREME-7 | 4 | - | 17473959 | 17473967 | 6.04e-05 | 0.265 | CAAAATGTC
7-CAAGATGGC | STREME-7 | 2 | - | 171217791 | 171217799 | 6.36e-05 | 0.276 | GAAGATGTC
7-CAAGATGGC | STREME-7 | 8 | + | 69608124 | 69608132 | 6.77e-05 | 0.281 | CAAGAGGTC
7-CAAGATGGC | STREME-7 | 13 | - | 52123168 | 52123176 | 6.77e-05 | 0.281 | CAAGAGGTC
7-CAAGATGGC | STREME-7 | 14 | - | 74192489 | 74192497 | 6.77e-05 | 0.281 | CAAGAGGTC
7-CAAGATGGC | STREME-7 | 3 | - | 122801150 | 122801158 | 6.77e-05 | 0.281 | CAAGAGGTC
7-CAAGATGGC | STREME-7 | 11 | + | 46615369 | 46615377 | 8e-05 | 0.325 | GAAGACGGC
7-CAAGATGGC | STREME-7 | 7 | + | 101512763 | 101512771 | 8e-05 | 0.325 | GAAGACGGC
7-CAAGATGGC | STREME-7 | 3 | + | 197676790 | 197676798 | 8.4e-05 | 0.338 | GAAGATGCC
7-CAAGATGGC | STREME-7 | 7 | - | 10980049 | 10980057 | 8.91e-05 | 0.355 | CAAGAGGCC
7-CAAGATGGC | STREME-7 | 22 | + | 22832560 | 22832568 | 9.16e-05 | 0.358 | CAAAATGGT
7-CAAGATGGC | STREME-7 | 21 | - | 40721592 | 40721600 | 9.16e-05 | 0.358 | CAAAATGGT

DEBUGGING INFORMATION

Command line:

    fimo --parse-genomic-coord --verbosity 1 --oc xstreme_example_output_files/fimo_out_10 --bgfile xstreme_example_output_files/background --motif 7-CAAGATGGC xstreme_example_output_files/streme_out/streme.xml nrmix.nseqs.100.100bp.seed.1.fa

Settings:

        output_directory = xstreme_example_output_files/fimo_out_10
        MEME file name = xstreme_example_output_files/streme_out/streme.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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