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