Database and Motifs | High-scoring Motif Occurences | Debugging Information | Results in TSV Format | Results in GFF3 Format |
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 try.fa
Database contains 200 sequences, 20000 residues
MOTIFS meme.txt (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
KWSKYCVMWGGTTCGAATCCKTCABSVCSCACCACTTTWYT | 41 | GTGGTCGAAGGTTCGAATCCTTCACGGCCCACCACTTTATT |
GAAAGTGCATAAATCAGCGCAAYACC | 26 | GAAAGTGCATAAATCAGCGCAACACC |
TAGRGCAGTTGGCTTTTAACC | 21 | TAGAGCAGTTGGCTTTTAACC |
Random model letter frequencies (--nrdb--):
A 0.275 C 0.225 G 0.225 T 0.275
Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|---|---|---|---|---|---|---|---|
KWSKYCVMWGGTTCGAATCCKTCABSVCSCACCACTTTWYT | MEME-1 | 187 | + | 20 | 60 | 8.57e-06 | 0.206 | TATGTCATTAGTGTTATTACTGTTTGCGGTAACGGCTTTGG |
TAGRGCAGTTGGCTTTTAACC | MEME-3 | 148 | + | 65 | 85 | 1.18e-05 | 0.376 | TTTCGCAGTTGGCCTTTAACT |
GAAAGTGCATAAATCAGCGCAAYACC | MEME-2 | 160 | - | 48 | 73 | 1.8e-05 | 0.322 | GAGGTGGCAGAATCTACCGTAATACC |
GAAAGTGCATAAATCAGCGCAAYACC | MEME-2 | 153 | + | 39 | 64 | 2.15e-05 | 0.322 | GAGTCTGCCTAAGTAAGGGCAGCGCC |
KWSKYCVMWGGTTCGAATCCKTCABSVCSCACCACTTTWYT | MEME-1 | 16 | + | 53 | 93 | 3.12e-05 | 0.375 | CTGTATCTGGGCTGGGACCCGCTCGGATCCAACAATTATTA |
TAGRGCAGTTGGCTTTTAACC | MEME-3 | 46 | + | 62 | 82 | 7.72e-05 | 1 | AAAAGCGGTACACTTGTAAGC |
GAAAGTGCATAAATCAGCGCAAYACC | MEME-2 | 154 | + | 3 | 28 | 9.56e-05 | 0.954 | AAATGAGCAAAATTTCGTGCATTTGC |
Command line:
fimo meme.txt try.fa
Settings:
output_directory = fimo_out | MEME file name = meme.txt | sequence file name = try.fa |
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.