Database and Motifs High-scoring Motif Occurences Debugging Information Results in TSV Format Results in GFF3 Format



FIMO - Motif search tool

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 AND MOTIFS

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


SECTION I: HIGH-SCORING MOTIF OCCURENCES

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

DEBUGGING INFORMATION

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.


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