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_NL63.fasta
Database contains 1 sequences, 27553 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_005831.2 | + | 14872 | 14919 | 1.78e-06 | 0.0364 | GGTACCTATTATTTGCCTTACCCAGATCCTAGTAGGATCTTGTCAGCT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 24638 | 24685 | 4.4e-06 | 0.0364 | CGTGACAATCTTAAACCTGTTACTACACTTAGTACTATTACTGCTTAT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 2780 | 2827 | 4.51e-06 | 0.0364 | TTAGACACTTGTTTTGGTGTTAGTAAACCTAATGCCATTGATGTTGAA |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_005831.2 | + | 26107 | 26124 | 1.16e-05 | 0.274 | GCTTCATTTAATCTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_005831.2 | + | 1731 | 1748 | 2.81e-05 | 0.274 | GTGATGTTAAATTTAAAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_005831.2 | + | 9384 | 9401 | 3.2e-05 | 0.274 | ATGTACATACACCTAAAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 11993 | 12040 | 3.99e-05 | 0.121 | GCCACAATTCGTCTACAAGCTGGTAAACAAACTGAATTGGCTGTTAAT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 22794 | 22841 | 4.11e-05 | 0.121 | GTTGAGTACCTCCAAATTACTAGTACTCCAATAGTTGTTGATTGTGCT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 26805 | 26852 | 4.11e-05 | 0.121 | GCTGATAAGCCTTCTCAGTTGAAGAAACCTCGTTGGAAGCGTGTTCCT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 280 | 327 | 4.81e-05 | 0.121 | GCTAACCATGTTTTACAATCAAGTGACACTTGCTGTTGCAAGTGATTC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 17293 | 17340 | 5.27e-05 | 0.121 | ACTAATGTTCCTTTACAGGTTGGTTTTTCAAATGGTGTTAATTTTGTT |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 5126 | 5173 | 5.34e-05 | 0.121 | GGTGTTGACTCTTTTGAAGGTGTTTTACCTATTAATACTGATACTGTC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_005831.2 | + | 26392 | 26409 | 5.34e-05 | 0.286 | AGGACCTTAAATTCAGAC |
AWSWSMTTAAATCTAAAC | MEME-1 | NC_005831.2 | + | 8520 | 8537 | 5.57e-05 | 0.286 | TAGTTACTAAATTTAAAC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 22929 | 22976 | 5.73e-05 | 0.121 | CTTAGTGCTCATTTGGAAACTAATGATGTTAGTAGTATGCTAACTTTC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 15829 | 15876 | 5.78e-05 | 0.121 | TATAAGTCTACTGTAACTACTAAGTTAGTTCCTGGTATGATTTTTGTC |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 3959 | 4006 | 6.01e-05 | 0.121 | GATGGTTTTGGTGTCTTTGACATTAAAAATAGTAGTGTTAATACTGTT |
CCWCCCA | MEME-3 | NC_005831.2 | + | 21579 | 21585 | 8.35e-05 | 1 | CCACCCA |
GGTAACTATCGTTTACCGTCTAGTAAACCTAGTGGTATGGATACTGCC | MEME-2 | NC_005831.2 | + | 14413 | 14460 | 9.86e-05 | 0.183 | GGTTTTTATTTTAAGCCAGGTGGTACGACTTCTGGTGACGCTAGTACA |
Command line:
fimo --oc . --verbosity 1 --thresh 1.0E-4 --norc meme_out.txt Human_Coronavirus_NL63.fasta
Settings:
output_directory = . | MEME file name = meme_out.txt | sequence file name = Human_Coronavirus_NL63.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.