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 neg.fasta
Database contains 270 sequences, 27000 residues

MOTIFS meme_out/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC 40 CGGCGACGATGCAGAGCGCAGCGATGAGGAGGAGCAGCGC
TCTTGCCTTTDACWTCBAYCA 21 TCTTGCCTTTTACTTCGATCA
CVTWHHGATWATTAAVHNTWDRHTGTAADCSAADTVATAWCACG 44 CATATCGATAATTAAAAATAGAATGTAATCGAAGTCATAACACG

Random model letter frequencies (--nrdb--):
A 0.282 C 0.222 G 0.229 T 0.267


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
TCTTGCCTTTDACWTCBAYCA MEME-2 2424527 + 33 53 0.000152 1 TTTTGCCCGGGACCCCCGTCG
TCTTGCCTTTDACWTCBAYCA MEME-2 3997334 + 7 27 0.000225 1 TGCTGCTTGTTACGGTCCTCG
TCTTGCCTTTDACWTCBAYCA MEME-2 1477986 + 14 34 0.000527 1 CGTTGCCAGTCACATCCGGCG
TCTTGCCTTTDACWTCBAYCA MEME-2 1276771 + 76 96 0.000578 1 CCTTGCCGGTGGCGGCTTCCA
TCTTGCCTTTDACWTCBAYCA MEME-2 240931 + 24 44 0.000603 1 GATCGCCTTTGACGCCTATTC
TCTTGCCTTTDACWTCBAYCA MEME-2 392722 + 76 96 0.000663 1 TATGGCGGGTCACTGTCACCA
TCTTGCCTTTDACWTCBAYCA MEME-2 1818826 + 41 61 0.000665 1 GCTCGCCGGCGACTACCGGCA
TCTTGCCTTTDACWTCBAYCA MEME-2 3042133 + 77 97 0.000702 1 ACATGACGATGACGGCCACCG
TCTTGCCTTTDACWTCBAYCA MEME-2 4238598 + 57 77 0.000843 1 CCTTGCTGGTCACCGTCGCCA
TCTTGCCTTTDACWTCBAYCA MEME-2 530026 + 32 52 0.000858 1 GATCGCCTTCAACTCCGGGCT
TCTTGCCTTTDACWTCBAYCA MEME-2 2114090 + 76 96 0.0009 1 TCCAGGCGGTGGGTGCGATCA
TCTTGCCTTTDACWTCBAYCA MEME-2 3453181 + 72 92 0.000904 1 TCCCGAATTCGACCTCGACGC
TCTTGCCTTTDACWTCBAYCA MEME-2 999830 + 48 68 0.000948 1 GCTTGCCCAGTTCACCGGCCG
TCTTGCCTTTDACWTCBAYCA MEME-2 1366696 + 5 25 0.000991 1 CATTGAGTCGGTCAGCGACCA

DEBUGGING INFORMATION

Command line:

fimo --norc -motif TCTTGCCTTTDACWTCBAYCA -thresh 0.001 meme_out/meme.txt neg.fasta

Settings:

output_directory = fimo_out MEME file name = meme_out/meme.txt sequence file name = neg.fasta
background file name = --nrdb-- alphabet = DNA max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = false
text only = false scan both strands = false max strand = false
threshold type = p-value output theshold = 0.001 pseudocount = 0.1
alpha = 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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