Database and Motifs High-scoring Motif Occurences Debugging Information Results in TSV Format Results in GFF3 Format



FIMO - Motif search tool

FIMO version 5.2.0, (Release date: Wed Oct 14 12:02:54 2020 -0700)

For further information on how to interpret these results please access http://meme-suite.org//doc/fimo-output-format.html.
To get a copy of the FIMO software please access http://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 ./bZIP_intersect_summits.fasta
Database contains 5670 sequences, 2835000 residues

MOTIFS dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
MCAGCY 6 ACAGCT
CTGKCR 6 CTGTCA
ASGTGKC 7 ACGTGGC
GMCAACY 7 GACAACT
ATATMY 6 ATATCT
ARAGAVA 7 AAAGAAA
GSTGGM 6 GGTGGA
RGAAGAA 7 AGAAGAA
CAGMCTGK 8 CAGACTGT
AAAHAAAA 8 AAAAAAAA
CAGCTCAC 8 CAGCTCAC
ACCTGTM 7 ACCTGTA
CATCWTC 7 CATCATC
MRACGA 6 AAACGA
CHAAACC 7 CAAAACC
GGWAA 5 GGAAA
CTTAGCTA 8 CTTAGCTA
TGGAGRA 7 TGGAGAA
CAACTGTM 8 CAACTGTA

Random model letter frequencies (./background):
A 0.306 C 0.194 G 0.194 T 0.306


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_37 --bgfile ./background --motif GGWAA dreme_out/dreme.xml ./bZIP_intersect_summits.fasta

Settings:

output_directory = fimo_out_37 MEME file name = dreme_out/dreme.xml sequence file name = ./bZIP_intersect_summits.fasta
background file name = ./background alphabet = DNA max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = true
text only = false scan both strands = true 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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