Database and Motifs | High-scoring Motif Occurences | Debugging Information |
FIMO version 4.9.1, (Release date: Fri Aug 23 16:49:42 2013 +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.
DATABASE
crp0.fasta
Database contains
18
sequences,
5670
residues
MOTIFS crp0.meme.html (nucleotide)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
1 | 18 | AATTGTGACGTAGATCAC |
2 | 8 | CGGTGGGG |
3 | 11 | CCTGGTGTGCC |
Random model letter frequencies
(from non-redundant database):
A 0.275 C 0.225 G 0.225 T 0.275
Motif | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|---|---|---|---|---|---|---|
3 | lac | − | 33 | 43 | 1.13e-07 | 0.000388 | CCTGGGGTGCC |
1 | lac | + | 9 | 26 | 4.53e-07 | 0.000654 | TAATGTGAGTTAGCTCAC |
1 | ara | − | 59 | 76 | 4.91e-07 | 0.000654 | AAGTGTGACGCCGTGCAA |
3 | trn9cat | + | 36 | 46 | 5.03e-07 | 0.00086 | CCTGGTGTCCC |
1 | malt | + | 41 | 58 | 6.49e-07 | 0.000654 | AATTGTGACACAGTGCAA |
1 | deop2 | + | 60 | 77 | 1.7e-06 | 0.00106 | AATTGTGATGTGTATCGA |
1 | ilv | − | 43 | 60 | 1.75e-06 | 0.00106 | AATTGAGGGGTTGATCAC |
1 | pbr322 | − | 57 | 74 | 2.97e-06 | 0.0015 | ATCTGTGCGGTATTTCAC |
1 | uxu1 | + | 17 | 34 | 3.9e-06 | 0.00168 | TGTTGTGATGTGGTTAAC |
1 | ce1cg | − | 65 | 82 | 4.57e-06 | 0.00173 | TTTTGTGAAAACGATCAA |
1 | trn9cat | + | 84 | 101 | 6.27e-06 | 0.00211 | AAATGAGACGTTGATCGG |
2 | ilv | + | 5 | 12 | 6.67e-06 | 0.0235 | CGGCGGGG |
1 | gale | − | 46 | 63 | 8.7e-06 | 0.00253 | AAGTGTGACATGGAATAA |
1 | tnaa | − | 75 | 92 | 9.72e-06 | 0.00253 | AAATGTGAATCGAATCAC |
1 | crp | − | 67 | 84 | 1.01e-05 | 0.00253 | TAATGTGACGTCCTTTGC |
1 | male | + | 14 | 31 | 1.18e-05 | 0.00268 | TTCTGTAACAGAGATCAC |
1 | cya | + | 50 | 67 | 1.24e-05 | 0.00268 | AGGTGTTAAATTGATCAC |
2 | male | + | 41 | 48 | 1.48e-05 | 0.0261 | CGGTGGGG |
1 | ompa | + | 48 | 65 | 1.52e-05 | 0.00307 | ATGCCTGACGGAGTTCAC |
1 | malk | + | 61 | 78 | 1.85e-05 | 0.0035 | TTTCGTGATGTTGCTTGC |
1 | tdc | − | 82 | 99 | 2e-05 | 0.00355 | ATATGTGCGACCACTCAC |
1 | tnaa | + | 71 | 88 | 2.37e-05 | 0.00398 | GATTGTGATTCGATTCAC |
1 | tdc | + | 78 | 95 | 5.68e-05 | 0.00904 | ATTTGTGAGTGGTCGCAC |
1 | bglr1 | + | 76 | 93 | 8.97e-05 | 0.0136 | AACTGTGAGCATGGTCAT |
Command line:
fimo --oc fimo_example_output_files crp0.meme.html crp0.fasta
Settings:
output directory = fimo_example_output_files | MEME file name = crp0.meme.html | sequence file name = crp0.fasta |
allow clobber = true | compute q-values = true | parse genomic coord. = false |
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 = 2 | = |
This information can be useful in the event you wish to report a problem with the FIMO software.