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 bigclq.txt
Database contains 424 sequences, 6316 residues
MOTIFS streme_out/streme.xml (Protein)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
1-SGSGS | 5 | SGSGS |
2-QGGLPK | 6 | QGGLPK |
3-LEPLJP | 6 | LEPLIP |
4-EPETQB | 6 | EPETQD |
Random model letter frequencies (./background):
A 0.067 C 0.020 D 0.043 E 0.065 F 0.025 G 0.087 H 0.015 I 0.038 K 0.061
L 0.108 M 0.030 N 0.028 P 0.081 Q 0.034 R 0.043 S 0.096 T 0.047 V 0.049
W 0.034 Y 0.029
Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|---|---|---|---|---|---|---|---|
2-QGGLPK | STREME-2 | LQGISPKIMPKKPAE | + | 2 | 7 | 1.67e-07 | 0.000136 | QGISPK |
2-QGGLPK | STREME-2 | GRLQGISPKIMPKKP | + | 4 | 9 | 1.67e-07 | 0.000136 | QGISPK |
2-QGGLPK | STREME-2 | TFGRLQGISPKIMPK | + | 6 | 11 | 1.67e-07 | 0.000136 | QGISPK |
2-QGGLPK | STREME-2 | QMTFGRLQGISPKIM | + | 8 | 13 | 1.67e-07 | 0.000136 | QGISPK |
2-QGGLPK | STREME-2 | RPQMTFGRLQGISPK | + | 10 | 15 | 1.67e-07 | 0.000136 | QGISPK |
2-QGGLPK | STREME-2 | CQGGLPKEACMEISS | + | 2 | 7 | 3.17e-07 | 0.000161 | QGGLPK |
2-QGGLPK | STREME-2 | VSCQGGLPKEACMEI | + | 4 | 9 | 3.17e-07 | 0.000161 | QGGLPK |
2-QGGLPK | STREME-2 | LTVSCQGGLPKEACM | + | 6 | 11 | 3.17e-07 | 0.000161 | QGGLPK |
2-QGGLPK | STREME-2 | LDLLFWEQGGLCK | + | 8 | 13 | 8.53e-07 | 0.000346 | QGGLCK |
2-QGGLPK | STREME-2 | RGLDLLFWEQGGLCK | + | 10 | 15 | 8.53e-07 | 0.000346 | QGGLCK |
2-QGGLPK | STREME-2 | GAQGQFPRVCMTVDS | + | 3 | 8 | 6.19e-06 | 0.00228 | QGQFPR |
2-QGGLPK | STREME-2 | DQLGYPQHPGLNAHG | + | 2 | 7 | 8.79e-06 | 0.00297 | QLGYPQ |
2-QGGLPK | STREME-2 | IGEVDVEQHTLAKYL | + | 8 | 13 | 1.1e-05 | 0.00327 | QHTLAK |
2-QGGLPK | STREME-2 | GGQLQPGYPALASRH | + | 5 | 10 | 1.13e-05 | 0.00327 | QPGYPA |
2-QGGLPK | STREME-2 | SQQGTPGMALGSMGS | + | 2 | 7 | 1.5e-05 | 0.00406 | QQGTPG |
Command line:
fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_8 --bgfile ./background --motif 2-QGGLPK streme_out/streme.xml bigclq.txt
Settings:
output_directory = fimo_out_8 | MEME file name = streme_out/streme.xml | sequence file name = bigclq.txt |
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.