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 meme_out/meme.xml (Protein)

MOTIF WIDTH BEST POSSIBLE MATCH
GSGSGSGMA 9 GSGSGSGMA
HEPENQDATYSW 12 HEPENQDATYSW
LEPSIPWKS 9 LEPSIPWKS
LVCNGVLQG 9 LVCNGVLQG
DDIEKWF 7 DDIEKWF
KIFYVYMKR 9 KIFYVYMKR
LKVEDPFYW 9 LKVEDPFYW
LSYTWDFGD 9 LSYTWDFGD
QASRIWS 7 QASRIWS
MPTPEATGMTPE 12 MSTPESTGMTPA
NWCMQI 6 NWCMQI
KLLMEKE 7 KLLMEKE
IHHNTHLCF 9 IHHNTHLCF
WLGVSRQLR 9 WLGVSRQLR
MHNSEISKR 9 MHNSEISKR
TLQGLGISW 9 TLQGLGISW
HCWGPGPTQCVN 12 HCWGPGPTQCVN
EPEPVKEEK 9 EPEPVKEEK
RELDLHF 7 RGLDLHF
CYHPDGGPVPI 11 EIFPDGGPVPS
KPTTSEKIH 9 KPTTSEKIH
TPTLQHY 7 TPTLQHY
QTYMNGSPTYSM 12 QTYMNGSPTYSM
TGDENFAJPYW 11 TGLESFALPMW
CQGGLPK 7 CQGGLPK
LGASLYLGW 9 LGASLYLGW
TAADMAAQITKR 12 TAADMAAQITKR
ANKEILDEAYVM 12 ANKEILDEAYVM
ICTIDVY 7 ICTIDVY
IPEEDLLKK 9 ASEEDLLKK

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
TAADMAAQITKR MEME-27 TAADMAAQITKRKWE + 1 12 1.94e-16 1.59e-13 TAADMAAQITKR
TAADMAAQITKR MEME-27 SWTAADMAAQITKRK + 3 14 1.94e-16 1.59e-13 TAADMAAQITKR

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_26 --bgfile ./background --motif TAADMAAQITKR meme_out/meme.xml bigclq.txt

Settings:

output_directory = fimo_out_26 MEME file name = meme_out/meme.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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