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



FIMO - Motif search tool

FIMO version 5.5.1, (Release date: Sun Jan 29 10:33:12 2023 -0800)

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 proms.fasta
Database contains 1031 sequences, 51550 residues

MOTIFS meme_out_multi/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
MAGGAGH 7 AAGGAGC

Random model letter frequencies (--nrdb--):
A 0.275 C 0.225 G 0.225 T 0.275


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
MAGGAGH MEME-1 "cysZ" + 33 39 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "yaeD" + 36 42 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2698" + 38 44 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "yihD" + 38 44 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "rpsF" + 38 44 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "pckA" + 38 44 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF0865" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1804" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1058" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1596" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2994" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1843" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1252" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2051" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1439" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1037" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1428" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1356" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2547" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2620" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "yeiG" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2756" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF2181" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF0881" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "yhiE" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF3749" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF1900" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF3801" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "SF0302" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "yjgA" + 39 45 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "yidH" + 40 46 5.35e-05 0.151 AAGGAGC
MAGGAGH MEME-1 "hyfA" + 40 46 5.35e-05 0.151 AAGGAGC

DEBUGGING INFORMATION

Command line:

fimo --oc fimo_proms_multi meme_out_multi/meme.txt proms.fasta

Settings:

output_directory = fimo_proms_multi MEME file name = meme_out_multi/meme.txt sequence file name = proms.fasta
background file name = --nrdb-- alphabet = DNA max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = false
text only = false scan both strands = true max strand = false
threshold type = p-value output theshold = 0.0001 pseudocount = 0.1
alpha = 1 verbosity = 2

This information can be useful in the event you wish to report a problem with the FIMO software.


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