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
4-EPETQB STREME-4 CEPETQDATYLWWVN + 2 7 4.55e-08 5.46e-05 EPETQD
4-EPETQB STREME-4 FTCEPETQDATYLWW + 4 9 4.55e-08 5.46e-05 EPETQD
4-EPETQB STREME-4 CEPEIQNTTYLWWVN + 2 7 5.75e-08 5.46e-05 EPEIQN
4-EPETQB STREME-4 LTCEPEIQNTTYLWW + 4 9 5.75e-08 5.46e-05 EPEIQN
4-EPETQB STREME-4 CEPEAQNTTYLWWVN + 2 7 7.85e-08 5.46e-05 EPEAQN
4-EPETQB STREME-4 FTCEPEAQNTTYLWW + 4 9 7.85e-08 5.46e-05 EPEAQN
4-EPETQB STREME-4 MLDLQPETTDLYCYE + 5 10 7.38e-07 0.00044 QPETTD
4-EPETQB STREME-4 VPRNQDWLGVSRQLR + 1 6 1.83e-06 0.000953 VPRNQD
4-EPETQB STREME-4 QYAAQNRRGLDLLFW + 1 6 2.42e-06 0.00112 QYAAQN
4-EPETQB STREME-4 LTSCGSSPVPGTTDG + 9 14 3.49e-06 0.00146 VPGTTD

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_4 --bgfile ./background --motif 4-EPETQB streme_out/streme.xml bigclq.txt

Settings:

output_directory = fimo_out_4 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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