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 test.fasta
Database contains 4123 sequences, 412200 residues
MOTIFS meme_out/meme.txt (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC | 40 | CGGCGACGATGCAGAGCGCAGCGATGAGGAGGAGCAGCGC |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | 49 | TTCTAACAATTAAATATTAGATGTAAACGAATTATATACAGGATAGGCT |
TRWCWSWAGRCAKMAAGACHMGTTWTAWA | 29 | TAACACAAGACATCAAGACACGTTATATA |
Random model letter frequencies (--nrdb--):
A 0.282 C 0.222 G 0.229 T 0.267
Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|---|---|---|---|---|---|---|---|
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_00349 | + | 46 | 94 | 2.58e-17 | 5.52e-12 | TTCTGATAATCAAATGTTTGATGTAAACGAATGCTTATCACGATAGGAT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_02917 | + | 46 | 94 | 3.94e-12 | 4.22e-07 | TTCTTTCAAGCTAATTAGACGTTCTAACGACTACTATTAAGAAAAAGCT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_00092 | + | 39 | 87 | 3.23e-11 | 1.8e-06 | CACTATCTGATAAATTCTTCAACTCGTCAACCGATGTAACGCTGAAGCT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_02106 | + | 44 | 92 | 3.83e-11 | 1.8e-06 | TACCTACATGTTAAGTCGAGAACGACAATATGGTCATATACCACATGAT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_02094 | + | 26 | 74 | 4.2e-11 | 1.8e-06 | TATCGATTATTAAGAAGTAAATGTAATCGTAATAATTACACGTCACGCT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_02757 | + | 20 | 68 | 2.13e-10 | 7.6e-06 | TTCTAACAGACAACAATTTGAACGTTAGATCCTATAGACTGTATCGTCA |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_03932 | + | 44 | 92 | 3.41e-10 | 1.04e-05 | ATATCAGAATATATGATCATATGTTCATTTATTTCTTTGGGGATAGGCT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_00341 | + | 48 | 96 | 8.86e-06 | 0.237 | CTTCTAGAGATTAGATATTTATTCTTCCGTTATCTTGTCGTAATCTGCT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_01484 | + | 35 | 83 | 0.000921 | 1 | GTATACGTTCTAAATAATCAATGTCGACGATGGTCAGATGCTAGACTTT |
TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT | MEME-2 | MNBBKBOB_03335 | + | 1 | 49 | 0.00098 | 1 | ACGTCTTTCGACAAAACAAGATCCAATGGTCGACAAAACAGGACAAACT |
Command line:
fimo --norc -motif TWCTNAYARDYWAADWYKWSAWSKWMACDWMYKHYWTWMASSAYARGCT -thresh 0.001 meme_out/meme.txt test.fasta
Settings:
output_directory = fimo_out | MEME file name = meme_out/meme.txt | sequence file name = test.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 = false | max strand = false |
threshold type = p-value | output theshold = 0.001 | 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.