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_strain_SC2628.fasta
Database contains 1 sequences, 29932 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 | KY983584.1 | + | 28248 | 28295 | 1.68e-29 | 4.32e-25 | GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 33 | 50 | 3.52e-11 | 2.32e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 21760 | 21777 | 3.52e-11 | 2.32e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 22930 | 22947 | 3.52e-11 | 2.32e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 27032 | 27049 | 3.52e-11 | 2.32e-07 | ATCTCATTAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 28301 | 28318 | 1.1e-09 | 5.79e-06 | AAGAGCTTAAATCTAAAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 1571 | 1618 | 1.1e-06 | 0.0142 | GTTTATTCAGGTGTAGTAGGTTGTAAATCTATTGTTAAAGAAACTGCT |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 17528 | 17545 | 1.19e-05 | 0.0521 | CTCGTATTAAAGCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 4455 | 4472 | 1.62e-05 | 0.061 | CTATGGTTAAATCTAAAG |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 22676 | 22723 | 1.68e-05 | 0.136 | GGTGATAGTGGTTTCATTTCTATTTTATCTGGTCTTTTATATAATGTT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 15580 | 15627 | 2.11e-05 | 0.136 | GGTTGCTATTATGTTAAGCCTGGTGGTACTAGCAGTGGTGATGCAACT |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 17329 | 17346 | 2.81e-05 | 0.0927 | AAGTTTTTAAATATTAAC |
CCWCCCA | MEME-3 | KY983584.1 | + | 169 | 175 | 4.06e-05 | 1 | CCTCCCA |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 20929 | 20976 | 4.37e-05 | 0.155 | AGAGTCTCTTTATGGAATTATGGTAAACCTATTAATTTGCCTACAGGC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 26299 | 26346 | 5.56e-05 | 0.155 | GTTAAAAGTCAATCTCCTCGTATTAATTTTTGTGGTAATGGTAATCAT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 20002 | 20049 | 5.74e-05 | 0.155 | GTTAAAGATAGTTTGTTTTGTAGTTCCACTTATGGTGTTTGTAAATAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 23737 | 23784 | 5.78e-05 | 0.155 | CGCCAATATCTTCTTAAATTTGACAACCGTGGTGTTATTACTAATGCT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 13987 | 14034 | 5.91e-05 | 0.155 | CGTAATGATTGTTCAATATTGTGTGAAATTCTTTGTGAGTATGCTGAT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | KY983584.1 | + | 10508 | 10555 | 6.01e-05 | 0.155 | CCAAAATATACTTTTGGTAATGTTAAACCTGGTGAAACTTTTACTGTT |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 20740 | 20757 | 7.79e-05 | 0.219 | AAGTCATTAAATTTGAGT |
CCWCCCA | MEME-3 | KY983584.1 | + | 27601 | 27607 | 8.35e-05 | 1 | CCACCCA |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 22515 | 22532 | 9.74e-05 | 0.219 | GTTTTGATAAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 23471 | 23488 | 9.74e-05 | 0.219 | ATTTTGATAAATCTGAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | KY983584.1 | + | 27612 | 27629 | 9.97e-05 | 0.219 | AGATTATTTAATCTAAAT |
Command line:
fimo --oc . --verbosity 1 --thresh 1.0E-4 --norc meme_out.txt Human_coronavirus_HKU1_strain_SC2628.fasta
Settings:
output_directory = . | MEME file name = meme_out.txt | sequence file name = Human_coronavirus_HKU1_strain_SC2628.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.