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 streme_out/streme.xml (Protein)

MOTIF WIDTH BEST POSSIBLE MATCH
1-ELPKP 5 ELPKP
2-SSKDLG 6 SSKDLG
3-SPSPME 6 SPSPME

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
2-SSKDLG STREME-2 ISSKDLGYDYSYLQD + 2 7 1.06e-07 6.04e-05 SSKDLG
2-SSKDLG STREME-2 FFISSKDLGYDYSYL + 4 9 1.06e-07 6.04e-05 SSKDLG
2-SSKDLG STREME-2 GDFFISSKDLGYDYS + 6 11 1.06e-07 6.04e-05 SSKDLG
2-SSKDLG STREME-2 LYRNGDFFISSKDLG + 10 15 1.06e-07 6.04e-05 SSKDLG

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 2-SSKDLG streme_out/streme.xml Clq2pp.fasta

Settings:

output_directory = fimo_out_3 MEME file name = streme_out/streme.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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