Database and Motifs | High-scoring Motif Occurences | Debugging Information | Results in TSV Format | Results in GFF3 Format |
FIMO version 5.1.1, (Release date: Wed Jan 29 15:00:42 2020 -0800)
For further information on how to interpret these results please access http://meme-suite.org//doc/fimo-output-format.html.
To get a copy of the FIMO software please access http://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 Human_coronavirus_HKU1.fasta
Database contains 1 sequences, 29926 residues
MOTIFS meme_out.txt (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
AWSWSMTTAAATCTAAAC | 18 | ATCTCATTAAATCTAAAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | 48 | GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC |
CCWCCCA | 7 | CCACCCA |
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 |
---|---|---|---|---|---|---|---|---|
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 28242 | 28289 | 1.68e-29 | 4.47e-25 | GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 54 | 71 | 3.52e-11 | 2.34e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 21754 | 21771 | 3.52e-11 | 2.34e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 22924 | 22941 | 3.52e-11 | 2.34e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 27026 | 27043 | 3.52e-11 | 2.34e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 28295 | 28312 | 1.1e-09 | 5.84e-06 | AAGAGCTTAAATCTAAAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 1592 | 1639 | 1.1e-06 | 0.0147 | GTTTATTCAGGTGTAGTAGGTTGTAAATCTATTGTTAAAGAAACTGCT |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 17522 | 17539 | 1.19e-05 | 0.0526 | CTCGTATTAAAGCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 4449 | 4466 | 1.62e-05 | 0.0616 | CTATGGTTAAATCTAAAG |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 22670 | 22717 | 1.68e-05 | 0.14 | GGTGATAGTGGTTTTATTTCTATTTTATCTGGTCTTTTATATAATGTT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 15574 | 15621 | 2.11e-05 | 0.14 | GGTTGCTATTATGTTAAGCCTGGTGGTACTAGCAGTGGTGATGCAACT |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 17323 | 17340 | 2.81e-05 | 0.0935 | AAGTTTTTAAATATTAAC |
CCWCCCA | MEME-3 | NC_006577.2 | + | 190 | 196 | 4.06e-05 | 1 | CCTCCCA |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 20923 | 20970 | 4.37e-05 | 0.16 | AGAGTCTCTTTATGGAATTATGGTAAACCTATTAATTTGCCTACAGGC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 26293 | 26340 | 5.56e-05 | 0.16 | GTTAAAAGTCAATCTCCTCGTATTAATTTTTGTGGTAATGGTAATCAT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 19996 | 20043 | 5.74e-05 | 0.16 | GTTAAAGATAGTTTGTTTTGTAGTTCCACTTATGGTGTTTGTAAATAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 23731 | 23778 | 5.78e-05 | 0.16 | CGCCAATATCTTCTTAAATTTGACAACCGTGGTGTTATTACTAATGCT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 13981 | 14028 | 5.91e-05 | 0.16 | CGTAATGATTGTTCAATATTGTGTGAAATTCTTTGTGAGTATGCTGAT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_006577.2 | + | 10502 | 10549 | 6.01e-05 | 0.16 | CCAAAATATACTTTTGGTAATGTTAAACCTGGTGAAACTTTTACTGTT |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 20734 | 20751 | 7.79e-05 | 0.221 | AAGTCATTAAATTTGAGT |
CCWCCCA | MEME-3 | NC_006577.2 | + | 27595 | 27601 | 8.35e-05 | 1 | CCACCCA |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 22509 | 22526 | 9.74e-05 | 0.221 | GTTTTGATAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 23465 | 23482 | 9.74e-05 | 0.221 | ATTTTGATAAATCTGAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_006577.2 | + | 27606 | 27623 | 9.97e-05 | 0.221 | AGATTATTTAATCTAAAT |
Command line:
fimo --oc . --verbosity 1 --thresh 1.0E-4 --norc meme_out.txt Human_coronavirus_HKU1.fasta
Settings:
output_directory = . | MEME file name = meme_out.txt | sequence file name = Human_coronavirus_HKU1.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 = 0.0001 | pseudocount = 0.1 |
alpha = 1 | verbosity = 1 |
This information can be useful in the event you wish to report a problem with the FIMO software.