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 script_results/negative.fasta
Database contains 219 sequences, 21900 residues

MOTIFS meme_out_1/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GCGCMGGWAWHVBCS 15 GCGCCGGTAAACTCC
GCKGCTDBNNMGYCGWSTSSAWWTTCGYC 29 GCTGCTTTATCGCCGTCTCCATATTCGCC
CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS 47 CGGGCACTGCGGTAACGAGCACGACGACGCTTAAACGCAGTCTTACG

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
GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 2470507 + 56 84 4.64e-06 0.0708 GCCGTCTTGGCCTTCACACGTTGTTCGCC
GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 2718002 + 68 96 2.25e-05 0.172 TCTGTCTGGCTGGCGTGTTTTTTTTCATT
GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 3099912 + 9 37 3.49e-05 0.178 GGGGCTCTATCGCCAGAGGCGTTGGTGTC

DEBUGGING INFORMATION

Command line:

fimo --norc -motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC meme_out_1/meme.txt script_results/negative.fasta

Settings:

output_directory = fimo_out MEME file name = meme_out_1/meme.txt sequence file name = script_results/negative.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 = 0.0001 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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