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 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


SECTION I: HIGH-SCORING MOTIF OCCURENCES

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

DEBUGGING INFORMATION

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.


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