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



FIMO - Motif search tool

FIMO version 5.5.0, (Release date: Wed Sep 7 14:18:26 2022 -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 Clq2pp.fasta
Database contains 228 sequences, 3416 residues

MOTIFS meme_out/meme.xml (Protein)

MOTIF WIDTH BEST POSSIBLE MATCH
SKDLGYDYS 9 SKDLGYDYS
METSGCAPA 9 METSGCAPA
LCKGGRCWG 9 LCAGSRCWG
YTKHQIRQMEMK 12 YTKHQIRQMEMK
YTKVVHYRKWI 11 YTKVVHYRKWI
DNGDPLNNT 9 DNGDPLNNT
GNMRAILIDWLV 12 GNMRAILIDWLV
FSKEEWEKMKA 11 FSKEEWEKMKA
YWKFDPVKV 9 YWKFDPVKV
WTGPNCERK 9 WTGPNCERK

Random model letter frequencies (./background):
A 0.070 C 0.029 D 0.047 E 0.065 F 0.030 G 0.071 H 0.023 I 0.034 K 0.046 L 0.098 M 0.022 N 0.033 P 0.087 Q 0.036 R 0.066 S 0.083 T 0.059 V 0.056 W 0.016 Y 0.028


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
LCKGGRCWG MEME-3 MCKGSRCWGESSEDC + 1 9 2.49e-12 1.98e-09 MCKGSRCWG
LCKGGRCWG MEME-3 CHPCSPMCKGSRCWG + 7 15 2.49e-12 1.98e-09 MCKGSRCWG
LCKGGRCWG MEME-3 ACHQLCARGHCWGPG + 5 13 7.3e-12 2.9e-09 LCARGHCWG
LCKGGRCWG MEME-3 GLACHQLCARGHCWG + 7 15 7.3e-12 2.9e-09 LCARGHCWG

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_5 --bgfile ./background --motif LCKGGRCWG meme_out/meme.xml Clq2pp.fasta

Settings:

output_directory = fimo_out_5 MEME file name = meme_out/meme.xml sequence file name = Clq2pp.fasta
background file name = ./background alphabet = Protein max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = true
text only = false scan both strands = false 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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