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

FIMO - Motif search tool

FIMO version 5.5.5, (Release date: Thu Sep 14 08:48:04 2023 +1000)

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 78 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
--- | --- | --- | --- | --- | --- | --- | --- | ---
TGCACTCCAGCCTGG | MEME-7 | 19 | + | 3106995 | 3107009 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 12 | + | 8010490 | 8010504 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 1 | - | 17262603 | 17262617 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 10 | - | 28807621 | 28807635 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 1 | + | 29210654 | 29210668 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 19 | - | 35870404 | 35870418 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 17 | + | 61626653 | 61626667 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 2 | + | 70297677 | 70297691 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 17 | - | 74634299 | 74634313 | 1.49e-09 | 5.9e-05 | TGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 5 | - | 172215427 | 172215441 | 2.98e-09 | 0.000106 | TGCACACCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 8 | - | 67571272 | 67571286 | 4.17e-09 | 0.000135 | TGCACTCCAGTCTGG
TGCACTCCAGCCTGG | MEME-7 | 7 | - | 18040134 | 18040148 | 1.05e-08 | 0.000312 | TGCGCTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 10 | + | 72522524 | 72522538 | 1.42e-08 | 0.000391 | GGCACTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 11 | + | 46358332 | 46358346 | 3.53e-08 | 0.0009 | TGCACTCGAGGCTGG
TGCACTCCAGCCTGG | MEME-7 | 20 | - | 33254176 | 33254190 | 9.32e-08 | 0.00222 | TGCATTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 6 | - | 41863491 | 41863505 | 1.33e-07 | 0.00297 | TGCTCACCCGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 19 | - | 55887857 | 55887871 | 2.12e-07 | 0.00445 | TTCACACCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 21 | + | 47573140 | 47573154 | 7.94e-07 | 0.0158 | GGCGCTCGAGGCTGG
TGCACTCCAGCCTGG | MEME-7 | 1 | + | 40638199 | 40638213 | 2.19e-06 | 0.0392 | TGCACTCTATCCTGG
TGCACTCCAGCCTGG | MEME-7 | 7 | - | 99832832 | 99832846 | 2.2e-06 | 0.0392 | TGCACGCCAGACTGG
TGCACTCCAGCCTGG | MEME-7 | 16 | + | 4340213 | 4340227 | 2.48e-06 | 0.0402 | TGCATTCCAGCCTTG
TGCACTCCAGCCTGG | MEME-7 | 1 | + | 36864019 | 36864033 | 2.48e-06 | 0.0402 | TTCATTCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 5 | - | 126853467 | 126853481 | 2.78e-06 | 0.0413 | TGCACTCCTGCCTGC
TGCACTCCAGCCTGG | MEME-7 | 8 | - | 128866736 | 128866750 | 2.78e-06 | 0.0413 | TTCACTCCTGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 19 | - | 40030644 | 40030658 | 5.54e-06 | 0.0791 | TGCTCTCGCGCCCGG
TGCACTCCAGCCTGG | MEME-7 | 10 | - | 43892702 | 43892716 | 5.97e-06 | 0.082 | CGCGCTCGCGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 12 | + | 110497954 | 110497968 | 6.73e-06 | 0.0865 | CCCACTCCAGTCTGG
TGCACTCCAGCCTGG | MEME-7 | 11 | + | 64426756 | 64426770 | 6.78e-06 | 0.0865 | TGCTCTCAACCCTGG
TGCACTCCAGCCTGG | MEME-7 | 16 | - | 1876596 | 1876610 | 1.18e-05 | 0.144 | GGCAGTCCAGCCCGG
TGCACTCCAGCCTGG | MEME-7 | 5 | - | 133702660 | 133702674 | 1.21e-05 | 0.144 | TGCGCACGAGTCTAG
TGCACTCCAGCCTGG | MEME-7 | 3 | - | 135914582 | 135914596 | 1.38e-05 | 0.159 | GGCGCTTGAGTCTGG
TGCACTCCAGCCTGG | MEME-7 | 8 | - | 8203896 | 8203910 | 1.51e-05 | 0.168 | GGCTCTTCCGGCTGG
TGCACTCCAGCCTGG | MEME-7 | 3 | + | 4283485 | 4283499 | 1.7e-05 | 0.184 | TGCACACGTGCTTGG
TGCACTCCAGCCTGG | MEME-7 | 6 | - | 136610402 | 136610416 | 1.84e-05 | 0.193 | TGCGAACCTGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 8 | + | 106334252 | 106334266 | 1.91e-05 | 0.194 | TGTTCTCCATTCTGG
TGCACTCCAGCCTGG | MEME-7 | 9 | + | 37592366 | 37592380 | 2.06e-05 | 0.194 | TGCTCTCCACGGTGG
TGCACTCCAGCCTGG | MEME-7 | 22 | + | 47249988 | 47250002 | 2.06e-05 | 0.194 | TGCTCTCCAGGATGA
TGCACTCCAGCCTGG | MEME-7 | 5 | + | 172215421 | 172215435 | 2.06e-05 | 0.194 | TGTTGTCCAGGCTGG
TGCACTCCAGCCTGG | MEME-7 | 1 | + | 45478445 | 45478459 | 2.18e-05 | 0.2 | TACACTCCCGTTTGG
TGCACTCCAGCCTGG | MEME-7 | 2 | - | 97616867 | 97616881 | 2.32e-05 | 0.207 | AGCGCTGCAGTCTGG
TGCACTCCAGCCTGG | MEME-7 | 7 | + | 116767611 | 116767625 | 2.85e-05 | 0.242 | TGCACCCCCTGCTGG
TGCACTCCAGCCTGG | MEME-7 | 8 | + | 126346350 | 126346364 | 2.85e-05 | 0.242 | AGCGCTCCAGGCTGT
TGCACTCCAGCCTGG | MEME-7 | 5 | - | 180631585 | 180631599 | 3.14e-05 | 0.261 | GGCGCTTCAGCCTGC
TGCACTCCAGCCTGG | MEME-7 | 14 | + | 105956890 | 105956904 | 3.33e-05 | 0.269 | GGCGGCCCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 12 | + | 105060951 | 105060965 | 3.57e-05 | 0.269 | TGCAATCTAGCCTTG
TGCACTCCAGCCTGG | MEME-7 | 12 | + | 105060951 | 105060965 | 3.57e-05 | 0.269 | TGCAATCTAGCCTTG
TGCACTCCAGCCTGG | MEME-7 | 10 | - | 105091877 | 105091891 | 3.57e-05 | 0.269 | TACACTCTAGCCTAG
TGCACTCCAGCCTGG | MEME-7 | 4 | - | 187766387 | 187766401 | 3.73e-05 | 0.269 | TGGACTTCAGCGTGG
TGCACTCCAGCCTGG | MEME-7 | 6 | + | 15793521 | 15793535 | 3.9e-05 | 0.269 | TGCCCTGCAGCATGG
TGCACTCCAGCCTGG | MEME-7 | 7 | - | 108208490 | 108208504 | 3.9e-05 | 0.269 | TGCACCACAGCCTGA
TGCACTCCAGCCTGG | MEME-7 | 4 | + | 6615063 | 6615077 | 3.92e-05 | 0.269 | TGCACTCTGGCCTGA
TGCACTCCAGCCTGG | MEME-7 | 6 | + | 160276033 | 160276047 | 3.92e-05 | 0.269 | CTCACTCAAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 5 | - | 75668384 | 75668398 | 4.06e-05 | 0.273 | AGAACTCCAGCCTGA
TGCACTCCAGCCTGG | MEME-7 | 11 | + | 6640407 | 6640421 | 4.53e-05 | 0.294 | TTCTCACCAGGCTTG
TGCACTCCAGCCTGG | MEME-7 | 1 | - | 227636790 | 227636804 | 4.53e-05 | 0.294 | TGCTCAACAGGCTGC
TGCACTCCAGCCTGG | MEME-7 | 1 | + | 20204777 | 20204791 | 4.87e-05 | 0.305 | TGTACACGTGGCTGG
TGCACTCCAGCCTGG | MEME-7 | 14 | + | 99654945 | 99654959 | 4.87e-05 | 0.305 | GGCTCCCGCGGCTGG
TGCACTCCAGCCTGG | MEME-7 | 12 | + | 49626759 | 49626773 | 5.11e-05 | 0.314 | GGTTCAGCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 1 | - | 234634753 | 234634767 | 5.75e-05 | 0.348 | GGCGCACCATCCGGG
TGCACTCCAGCCTGG | MEME-7 | 16 | - | 3245963 | 3245977 | 6.27e-05 | 0.373 | TGCTCTACCGGCTGA
TGCACTCCAGCCTGG | MEME-7 | 3 | - | 129118647 | 129118661 | 7.17e-05 | 0.413 | TTAAGACCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 6 | + | 136610396 | 136610410 | 7.17e-05 | 0.413 | GGGTCTCCAGGCAGG
TGCACTCCAGCCTGG | MEME-7 | 16 | + | 1614305 | 1614319 | 7.67e-05 | 0.425 | GGCACCCCCTGCTGG
TGCACTCCAGCCTGG | MEME-7 | 12 | + | 131356192 | 131356206 | 7.67e-05 | 0.425 | CGCGCTCCCGGCTCG
TGCACTCCAGCCTGG | MEME-7 | 22 | + | 19711586 | 19711600 | 7.91e-05 | 0.425 | TGCGCTCCCGGCCCG
TGCACTCCAGCCTGG | MEME-7 | 22 | + | 22555460 | 22555474 | 8.06e-05 | 0.425 | TGCAGACCAGCAGGG
TGCACTCCAGCCTGG | MEME-7 | 11 | - | 47429795 | 47429809 | 8.16e-05 | 0.425 | GGCGCTTCCGCCTCG
TGCACTCCAGCCTGG | MEME-7 | 5 | + | 149380014 | 149380028 | 8.22e-05 | 0.425 | TGCGCTTGCGCCAGG
TGCACTCCAGCCTGG | MEME-7 | 13 | + | 99739732 | 99739746 | 8.22e-05 | 0.425 | GGCGCGCCAGGCGGG
TGCACTCCAGCCTGG | MEME-7 | 22 | - | 28838174 | 28838188 | 8.35e-05 | 0.426 | AGCACACCAGCCCAG
TGCACTCCAGCCTGG | MEME-7 | 10 | - | 79734121 | 79734135 | 8.68e-05 | 0.436 | AGGACTCAAGTCTGG
TGCACTCCAGCCTGG | MEME-7 | 18 | - | 45408089 | 45408103 | 8.86e-05 | 0.436 | CACACTCCAGTTTGG
TGCACTCCAGCCTGG | MEME-7 | 19 | + | 39601042 | 39601056 | 8.92e-05 | 0.436 | TGGTCTGAAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 18 | + | 33077740 | 33077754 | 9.08e-05 | 0.437 | TGGACTCCAAGCTGT
TGCACTCCAGCCTGG | MEME-7 | 8 | - | 27949588 | 27949602 | 9.31e-05 | 0.437 | TGTTGTCCAGCCTAG
TGCACTCCAGCCTGG | MEME-7 | 5 | + | 172215433 | 172215447 | 9.31e-05 | 0.437 | TGGTGTGCAGCCTGG
TGCACTCCAGCCTGG | MEME-7 | 1 | - | 32405431 | 32405445 | 9.86e-05 | 0.453 | TGCTAGCCAGCCTTG
TGCACTCCAGCCTGG | MEME-7 | 7 | + | 99036229 | 99036243 | 9.89e-05 | 0.453 | GACTCACGCGGCTGG

DEBUGGING INFORMATION

Command line:

    fimo --verbosity 1 --oc xstreme_example_output_files/fimo_out_11 --bgfile xstreme_example_output_files/background --motif TGCACTCCAGCCTGG xstreme_example_output_files/meme_out/meme.xml nrmix.nseqs.100.100bp.seed.1.fa

Settings:

        output_directory = xstreme_example_output_files/fimo_out_11
        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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