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 /home/students/y22/mkd57/public_html/term4/neg.fa
Database contains 30 sequences, 3000 residues
MOTIFS meme.txt (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
TCTGGTABAGTYMYYHCHBGTT | 22 | TCTGGTATAGTTCTTCCCGGTT |
KGTASGVTGGW | 11 | TGTAGGATGGA |
CGGAAVCGGAG | 11 | CGGAAACGGAG |
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 |
---|---|---|---|---|---|---|---|---|
TCTGGTABAGTYMYYHCHBGTT | MEME-1 | 23 | - | 79 | 100 | 1.68e-05 | 0.0791 | GCTGCTAACCTCTTCATCGTTG |
CGGAAVCGGAG | MEME-3 | 16 | + | 6 | 16 | 3.18e-05 | 0.0935 | CGGAAGCGCAG |
CGGAAVCGGAG | MEME-3 | 3 | - | 17 | 27 | 3.78e-05 | 0.0935 | CGACACAGGCG |
TCTGGTABAGTYMYYHCHBGTT | MEME-1 | 14 | + | 4 | 25 | 9.26e-05 | 0.219 | GGGTGTGTAGTCCCGTTACGTG |
Command line:
fimo meme.txt /home/students/y22/mkd57/public_html/term4/neg.fa
Settings:
output_directory = fimo_out | MEME file name = meme.txt | sequence file name = /home/students/y22/mkd57/public_html/term4/neg.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.