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 |
---|---|---|---|---|---|---|---|---|
1-ELPKP | STREME-1 | TITVSAELPKPSISS | + | 7 | 11 | 2.22e-06 | 0.00278 | ELPKP |
1-ELPKP | STREME-1 | TGQFRVYPELPKPSI | + | 9 | 13 | 2.22e-06 | 0.00278 | ELPKP |
1-ELPKP | STREME-1 | VIDKKLPKPLEKVPM | + | 5 | 9 | 8.88e-06 | 0.00369 | KLPKP |
1-ELPKP | STREME-1 | GKVIDKKLPKPLEKV | + | 7 | 11 | 8.88e-06 | 0.00369 | KLPKP |
1-ELPKP | STREME-1 | GWTGPNCERKKPPVI | + | 8 | 12 | 8.88e-06 | 0.00369 | ERKKP |
1-ELPKP | STREME-1 | KFGWTGPNCERKKPP | + | 10 | 14 | 8.88e-06 | 0.00369 | ERKKP |
1-ELPKP | STREME-1 | TITVYAEPPKPFITS | + | 7 | 11 | 1.33e-05 | 0.00474 | EPPKP |
1-ELPKP | STREME-1 | TQEAPRPASSLRPPR | + | 3 | 7 | 2.48e-05 | 0.00687 | EAPRP |
1-ELPKP | STREME-1 | PATQEAPRPASSLRP | + | 5 | 9 | 2.48e-05 | 0.00687 | EAPRP |
1-ELPKP | STREME-1 | PREGPLPAARPAGAT | + | 3 | 7 | 7.41e-05 | 0.0185 | EGPLP |
1-ELPKP | STREME-1 | RCKGPLPTDCCHEQC | + | 3 | 7 | 9.91e-05 | 0.0206 | KGPLP |
1-ELPKP | STREME-1 | CARCKGPLPTDCCHE | + | 5 | 9 | 9.91e-05 | 0.0206 | KGPLP |
Command line:
fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 1-ELPKP streme_out/streme.xml Clq2pp.fasta
Settings:
output_directory = fimo_out_1 | 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.