Database and Motifs | High-scoring Motif Occurences | Debugging Information |
FIMO version 4.10.0, (Release date: Tue May 06 16:46:04 2014 +1000)
For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net
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
memechip_example_output_files/sample-dna-Klf1.fa
Database contains
904
sequences,
452000
residues
MOTIFS memechip_example_output_files/dreme_out/dreme.xml (nucleotide)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
GGGYGK | 6 | GGGTGT |
TTATCW | 6 | TTATCT |
AGAWA | 5 | AGAAA |
Random model letter frequencies
(from memechip_example_output_files/background):
A 0.256 C 0.244 G 0.244 T 0.256
Motif | Sequence Name | Strand | Start | End | p-value | Matched Sequence |
---|
Command line:
/Users/cegrant/meme_4.10.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif TTATCW memechip_example_output_files/dreme_out/dreme.xml memechip_example_output_files/sample-dna-Klf1.fa
Settings:
output directory = memechip_example_output_files/fimo_out_2 | MEME file name = memechip_example_output_files/dreme_out/dreme.xml | sequence file name = memechip_example_output_files/sample-dna-Klf1.fa |
background file name = memechip_example_output_files/background | allow clobber = true | compute q-values = true |
parse genomic coord. = true | text only = false | scan both strands = true |
max sequence length = 250000000 | output threshold = 0.0001 | threshold type = p-value |
max stored scores = 100000 | pseudocount = 0.1 | verbosity = 1 |
selected motif = TTATCW |
This information can be useful in the event you wish to report a problem with the FIMO software.