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 promotors.fasta
Database contains 5447 sequences, 544700 residues
MOTIFS meme_out/meme.txt (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | 35 | ATAAATGAAATAAATTTTAAACGAATTAAAAGATT |
VYSAAMMKAWBMKAMHGNDTGTTCAYKNSCWTK | 33 | GCGAAACGATTATACCGAGTGTTCATGAGCTTT |
CMSGHSCNGYGCGACMASSTCAASHRCRASYCGDC | 35 | CCGGTGCTGTGCGACCACCTCAAGAACGAGTCGTC |
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 |
---|---|---|---|---|---|---|---|---|
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | soxR | + | 53 | 87 | 5.35e-11 | 1e-05 | ATAGTTGAAGTAAAGTTTAAGTCAAGTCATGAATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221043452.1 | + | 21 | 55 | 5.56e-11 | 1e-05 | AAAAATGCTGTAATGTCACAACGATGTGAAAGATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044317.1 | + | 10 | 44 | 5.27e-10 | 6.31e-05 | AATTCTGGAACAAATTCTCAACTTCTAGACAAATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045447.1 | + | 22 | 56 | 2.32e-09 | 0.000209 | ACATATGGATTAAACTTTAATCGAATTTTAGCAGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042756.1 | + | 1 | 35 | 3.06e-09 | 0.00022 | AGACCTGGTCTATCTTCTAGACCAGGTCTAATATA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045501.1 | + | 59 | 93 | 3.92e-09 | 0.000235 | ATTAGTGAAACAACTTATTAGCGTAGCAACATCGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221046498.1 | + | 41 | 75 | 6.06e-09 | 0.000311 | ATAGTTGTTATATGTTTATAACAACTGATCGGATC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042174.1 | + | 35 | 69 | 2.32e-08 | 0.00104 | CTTCGATAAATATAGTAATGACGATTTTATCGATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221043121.1 | + | 55 | 89 | 6.31e-06 | 0.252 | ACAACTTGTGCAAAGTCCCGTTCAAGCAACCGCTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044826.1 | + | 8 | 42 | 9.22e-06 | 0.332 | CCTGCTTGAATGACGTCTCATTCTTGTCACCCATC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044769.1 | + | 63 | 97 | 1.08e-05 | 0.352 | ACAACTGAAATATTGTATCAGCTCAGATAAAAACC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045356.1 | + | 6 | 40 | 2.09e-05 | 0.627 | AGTTGCTTAACCAGTTCTTAACCAGGGGTCGCATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | ugpC | + | 31 | 65 | 4.52e-05 | 1 | GTTTTTGTTTTAATCTTCCAACGACGAATCGTCGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042334.1 | + | 48 | 82 | 6.72e-05 | 1 | ACAGCTGGATCATTCCTGCAACCAATTGTTGTGTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-MTY59_RS20085 | + | 27 | 61 | 8.48e-05 | 1 | ATCGTTGACACAACCTTCCAGCGACGCCTACGCTC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044991.1 | + | 50 | 84 | 0.000115 | 1 | ATACCTGCTACATAGCTTCCACACATAGATAGCTC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221043168.1 | + | 61 | 95 | 0.000132 | 1 | CAAGCTACGATATAGTTTCAGTTCATGCTAGGATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_064880192.1 | + | 6 | 40 | 0.000149 | 1 | ACAGCATGCGCATAGGTTTGGCATAGCGTCGGCTC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044674.1 | + | 6 | 40 | 0.000152 | 1 | GCTTGTTCTAAAAAGTAACGATCACGGCTAGACTC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042177.1 | + | 15 | 49 | 0.000153 | 1 | ATAGTAAAAATAGACTTTAGTCGTCGAAACGCGGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045401.1 | + | 58 | 92 | 0.000157 | 1 | GAATCTTAATTAAATTAAAACTGAGATTAAGGAGA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042319.1 | + | 48 | 82 | 0.000212 | 1 | ATACAGTGTGTATGTTAATACATACGGTATGTATC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044843.1 | + | 64 | 98 | 0.000227 | 1 | GTTGCTTCAGCGCAGTCACGACCTCTCCACAACTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045464.1 | + | 22 | 56 | 0.000339 | 1 | ACGCCTGGGACAACCTCAAGACCAGCTAGTGGATC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045203.1 | + | 1 | 35 | 0.000344 | 1 | ACTGGTTCGTAATCTTTTTGACTTACTCACACAGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044845.1 | + | 65 | 99 | 0.00035 | 1 | GCTGATGAAGCAAGGAATTGAGGAGGGCACAGCGA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042883.1 | + | 60 | 94 | 0.000387 | 1 | CACACTATCGCACCGTTTTAACCATGTGACACAGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | soxR | + | 64 | 98 | 0.000389 | 1 | AAAGTTTAAGTCAAGTCATGAATTCGAGAAGGCCA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045425.1 | + | 42 | 76 | 0.000472 | 1 | AAATTTGAATCTAAATTAAACCAAGCTGTCAGCGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044865.1 | + | 32 | 66 | 0.000512 | 1 | ATTCGTAAACCAAGTAGAAGATCTCGATAACTCTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042917.1 | + | 10 | 44 | 0.000522 | 1 | AAAACCTAAATGAGTTCTAATCGAAAGGAAGTGGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045157.1 | + | 59 | 93 | 0.000536 | 1 | AGTAGCTGTGCTACGACACGTCCACGAATCGTAGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_250160605.1 | + | 59 | 93 | 0.000553 | 1 | ACTAGTGAACAATCTAATCAACGTTTCAAGGAGGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045516.1 | + | 4 | 38 | 0.00057 | 1 | GTTAGATAACCAAAGTCTTGGAATAGCAACGGCTG |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042768.1 | + | 11 | 45 | 0.000581 | 1 | AAAGTAGTGCCAAAGCCAACTCGTTTCCATAACGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221046544.1 | + | 47 | 81 | 0.000592 | 1 | ACTTTTGTAATAAAAGTTAATTCTCTACGTCTCGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221046349.1 | + | 38 | 72 | 0.000606 | 1 | AAACATGCATTGTCCGTGCATCGTTGCCACGACGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221041827.1 | + | 2 | 36 | 0.00063 | 1 | CCTAGAGATGTAGAGGATAGACTCCTTCTTCTAGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042850.1 | + | 36 | 70 | 0.000644 | 1 | CTTAATCGAACATTGTTTACGCGTCAGTCTAAATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042977.1 | + | 10 | 44 | 0.000685 | 1 | AGCACTGGTGGAACGTCTGGTCGCGGCCTAGCATA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042991.1 | + | 41 | 75 | 0.000691 | 1 | CGATATCGATCAGGCCAAAGACCTTTTGTCGGCGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042027.1 | + | 5 | 39 | 0.000723 | 1 | AGAGGTGTTCGACCGTATCGTCGCCTCCATCACGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045213.1 | + | 56 | 90 | 0.000729 | 1 | CGACTCGGTTGAATTCCATGATGACGCGATGGCTA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042461.1 | + | 47 | 81 | 0.000732 | 1 | TGTGGTGCCACAAGCTATAGTTGTGTCACACGATT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-MTY59_RS04730 | + | 52 | 86 | 0.000734 | 1 | CGAGTAGCTATATCCCATTAGCAAGGTATATCTTC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045455.1 | + | 61 | 95 | 0.000815 | 1 | ACCGGTTCAGCATTTTTTGAGTCTATGTTAAATTA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221043904.1 | + | 60 | 94 | 0.00082 | 1 | TTCAGTTGATTAATGTTTAACAAACTGAAAGGCTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045043.1 | + | 9 | 43 | 0.000829 | 1 | CTATATCCTGGAGCTTAAAAGCATGTTGACATTTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221043922.1 | + | 40 | 74 | 0.000874 | 1 | AGTAGAGTTTGATTGTCAACTCAACTGTAACAGTT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042962.1 | + | 21 | 55 | 0.000895 | 1 | AATGCTGATGTAGTTTTTCCTCGTCGCCACTCGGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045226.1 | + | 30 | 64 | 0.000923 | 1 | AGAAGTGTCAAAAATGAGTAGCCTCGAAACACAGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221045531.1 | + | 36 | 70 | 0.000923 | 1 | ACACGTTGTCGAAAGTTCCGACACCGTGTTGACTG |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042175.1 | + | 33 | 67 | 0.000927 | 1 | CTGGCTTAGCTATTTTAGCAGTAATGATATAAATA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221044750.1 | + | 16 | 50 | 0.000942 | 1 | CTTAAAGTTGCGTGGCCTTGGCCAAGGCCACCAGT |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | rpsE | + | 41 | 75 | 0.000942 | 1 | CGCTCTTGCCTAACGTTAAGACTACCTGTTCTCGA |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221046564.1 | + | 35 | 69 | 0.000949 | 1 | CGACGAGGACTGGTCTTTCGGCCACGGTAGGGCGC |
AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT | MEME-1 | cds-WP_221042470.1 | + | 14 | 48 | 0.000971 | 1 | CGCGATGCCGTGAGTTCGTGTCGTTGTAACGGATA |
Command line:
fimo --norc -motif AWWNNTGRWRTAWMKTHWHAACSAHKTNWHRDATT -thresh 0.001 meme_out/meme.txt promotors.fasta
Settings:
output_directory = fimo_out | MEME file name = meme_out/meme.txt | sequence file name = promotors.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.