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 |
---|---|---|---|---|---|---|---|---|
3-LEPLJP | STREME-3 | LEPSIPWKSKLL | + | 1 | 6 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | ILEPSIPWKSKLLTL | + | 2 | 7 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | HILEPSIPWKSKLLT | + | 3 | 8 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | DHILEPSIPWKSK | + | 4 | 9 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | DHILEPSIPWKS | + | 4 | 9 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | LDHILEPSIPWKSKL | + | 5 | 10 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | LNDHILEPSIPWKSK | + | 6 | 11 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | HSNLDHILEPSIPWK | + | 8 | 13 | 1.99e-06 | 0.00104 | LEPSIP |
3-LEPLJP | STREME-3 | EQKLISEEDLLRKRR | + | 1 | 6 | 4.61e-06 | 0.00193 | EQKLIS |
3-LEPLJP | STREME-3 | AEEQKLISEEDLLRK | + | 3 | 8 | 4.61e-06 | 0.00193 | EQKLIS |
3-LEPLJP | STREME-3 | LSQETFSDLWKLLPE | + | 9 | 14 | 5.63e-06 | 0.00211 | LWKLLP |
3-LEPLJP | STREME-3 | LLEPLLPLKSKLLTL | + | 2 | 7 | 6.56e-06 | 0.00211 | LEPLLP |
3-LEPLJP | STREME-3 | DHLLEPLLPLKSKL | + | 4 | 9 | 6.56e-06 | 0.00211 | LEPLLP |
3-LEPLJP | STREME-3 | EPEPVKEEKLSPEPI | + | 7 | 12 | 8.9e-06 | 0.00211 | EEKLSP |
3-LEPLJP | STREME-3 | EPEPEPVKEEKLSPE | + | 9 | 14 | 8.9e-06 | 0.00211 | EEKLSP |
3-LEPLJP | STREME-3 | EWKLLSETEKRPFID | + | 1 | 6 | 9.59e-06 | 0.00211 | EWKLLS |
3-LEPLJP | STREME-3 | RLGAEWKLLSETEKR | + | 5 | 10 | 9.59e-06 | 0.00211 | EWKLLS |
3-LEPLJP | STREME-3 | SKRLGAEWKLLSETE | + | 7 | 12 | 9.59e-06 | 0.00211 | EWKLLS |
3-LEPLJP | STREME-3 | EISKRLGAEWKLLSE | + | 9 | 14 | 9.59e-06 | 0.00211 | EWKLLS |
3-LEPLJP | STREME-3 | KNRETIEKLLSKLL | + | 6 | 11 | 2.25e-05 | 0.0047 | IEKLLS |
3-LEPLJP | STREME-3 | WGSIEPEEFLTPKKL | + | 7 | 12 | 3.07e-05 | 0.00612 | EEFLTP |
3-LEPLJP | STREME-3 | PAAPAPAPSWPLSSS | + | 9 | 14 | 8.24e-05 | 0.0156 | SWPLSS |
3-LEPLJP | STREME-3 | IQKLTGDENFTIPYW | + | 1 | 6 | 9.04e-05 | 0.0164 | IQKLTG |
Command line:
fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 3-LEPLJP streme_out/streme.xml bigclq.txt
Settings:
output_directory = fimo_out_3 | 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.