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 NEGATIVE.fasta
Database contains 3136 sequences, 78400 residues

MOTIFS meme_out/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
WWYWVAGGAR 10 ATTTGAGGAG

Random model letter frequencies (--nrdb--):
A 0.275 C 0.225 G 0.225 T 0.275


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
WWYWVAGGAR MEME-1 Seq1396 - 8 17 3.83e-06 0.385 ATCAGAGGAG
WWYWVAGGAR MEME-1 Seq1973 + 14 23 1.3e-05 0.652 TTTTCAGGAG
WWYWVAGGAR MEME-1 Seq534 - 6 15 4.04e-05 1 AATACAGGAG
WWYWVAGGAR MEME-1 Seq2077 + 12 21 4.6e-05 1 TATTCAGGAG
WWYWVAGGAR MEME-1 Seq1089 + 15 24 5.24e-05 1 ATCGCAGGAG
WWYWVAGGAR MEME-1 Seq549 + 13 22 6.04e-05 1 ATTTCAGGAA
WWYWVAGGAR MEME-1 Seq483 + 9 18 0.000117 1 TTGTCAGGAG
WWYWVAGGAR MEME-1 Seq2241 + 9 18 0.000123 1 AGTTCAGGAG
WWYWVAGGAR MEME-1 Seq901 - 8 17 0.000133 1 ATTTCAGGAT
WWYWVAGGAR MEME-1 Seq708 + 5 14 0.000137 1 GACTCAGGAG
WWYWVAGGAR MEME-1 Seq2048 - 11 20 0.000137 1 TGTTGAGGAG
WWYWVAGGAR MEME-1 Seq2971 + 14 23 0.000212 1 AACCCAGGAG
WWYWVAGGAR MEME-1 Seq632 + 2 11 0.000223 1 GTTAGAGGAA
WWYWVAGGAR MEME-1 Seq1413 + 10 19 0.000225 1 TAATCAGGAG
WWYWVAGGAR MEME-1 Seq2922 + 11 20 0.000237 1 GCCACAGGAG
WWYWVAGGAR MEME-1 Seq1554 - 5 14 0.000283 1 TATAGAGGAA
WWYWVAGGAR MEME-1 Seq1092 - 7 16 0.000283 1 GTGACAGGAG
WWYWVAGGAR MEME-1 Seq1737 - 5 14 0.000322 1 AACAGCGGAG
WWYWVAGGAR MEME-1 Seq1507 + 11 20 0.000348 1 TTATCAGGAA
WWYWVAGGAR MEME-1 Seq1812 - 6 15 0.000348 1 TATCCAGGAG
WWYWVAGGAR MEME-1 Seq1011 - 16 25 0.000348 1 ATGTCAGGAA
WWYWVAGGAR MEME-1 Seq45 + 12 21 0.00035 1 ACTGGAGGAG
WWYWVAGGAR MEME-1 Seq2405 - 12 21 0.000393 1 TACAGAGGAT
WWYWVAGGAR MEME-1 Seq1050 + 16 25 0.000401 1 ATTCCAGGAA
WWYWVAGGAR MEME-1 Seq2161 - 7 16 0.000439 1 ATATCAGGAT
WWYWVAGGAR MEME-1 Seq1452 - 11 20 0.000439 1 TTAACAGGAA
WWYWVAGGAR MEME-1 Seq1866 + 9 18 0.00045 1 TATTCAGGAT
WWYWVAGGAR MEME-1 Seq695 - 14 23 0.000474 1 CTTCCAGGAG
WWYWVAGGAR MEME-1 Seq2440 + 4 13 0.000491 1 AGCACAGGAA
WWYWVAGGAR MEME-1 Seq2141 - 5 14 0.000503 1 ATTGGAGGAT
WWYWVAGGAR MEME-1 Seq2183 + 15 24 0.000503 1 ACTTGAGGAT
WWYWVAGGAR MEME-1 Seq2028 + 5 14 0.00056 1 ATTTCCGGAA
WWYWVAGGAR MEME-1 Seq926 + 15 24 0.000565 1 ATCACCGGAA
WWYWVAGGAR MEME-1 Seq2161 - 16 25 0.000611 1 TGCACAGGAA
WWYWVAGGAR MEME-1 Seq1725 - 14 23 0.00062 1 ATCTGCGGAT
WWYWVAGGAR MEME-1 Seq2288 + 4 13 0.000676 1 TTCACCGGAA
WWYWVAGGAR MEME-1 Seq1785 + 5 14 0.000705 1 AAATCAGGAA
WWYWVAGGAR MEME-1 Seq685 + 6 15 0.000705 1 AAATCAGGAA
WWYWVAGGAR MEME-1 Seq2425 - 10 19 0.000705 1 AAATCAGGAA
WWYWVAGGAR MEME-1 Seq2099 + 2 11 0.000711 1 GTATCAGGAA
WWYWVAGGAR MEME-1 Seq2064 + 7 16 0.00072 1 TTTAAAGGAT
WWYWVAGGAR MEME-1 Seq840 - 14 23 0.00072 1 TGCTCAGGAT
WWYWVAGGAR MEME-1 Seq639 + 5 14 0.000746 1 GATTGAGGAT
WWYWVAGGAR MEME-1 Seq2755 + 15 24 0.000781 1 TTTTCAGGAC
WWYWVAGGAR MEME-1 Seq3110 + 3 12 0.000804 1 GCCGCAGGAG
WWYWVAGGAR MEME-1 Seq1989 + 12 21 0.000816 1 AAGTCAGGAA
WWYWVAGGAR MEME-1 Seq16 - 16 25 0.000832 1 TGTAGAGGAT
WWYWVAGGAR MEME-1 Seq2608 + 9 18 0.000841 1 GCCACAGGAA
WWYWVAGGAR MEME-1 Seq2854 - 16 25 0.000841 1 TAAAGAGGAA
WWYWVAGGAR MEME-1 Seq781 - 10 19 0.000855 1 GATTCCGGAG
WWYWVAGGAR MEME-1 Seq1961 - 13 22 0.000886 1 GCGTCAGGAG
WWYWVAGGAR MEME-1 Seq2554 - 11 20 0.000927 1 CAGAGAGGAG
WWYWVAGGAR MEME-1 Seq1728 - 7 16 0.000932 1 GTGCCAGGAG
WWYWVAGGAR MEME-1 Seq1872 + 11 20 0.000944 1 ACATCAGGAA
WWYWVAGGAR MEME-1 Seq1549 + 15 24 0.000966 1 CTATCAGGAA
WWYWVAGGAR MEME-1 Seq1241 + 3 12 0.00097 1 AACGCAGGAT
WWYWVAGGAR MEME-1 Seq1146 - 11 20 0.000983 1 AATTGCGGAA
WWYWVAGGAR MEME-1 Seq813 + 2 11 0.000993 1 GGCACAGGAA
WWYWVAGGAR MEME-1 Seq707 + 2 11 0.000993 1 GGCACAGGAA

DEBUGGING INFORMATION

Command line:

fimo --oc fimo_neg -thresh 0.001 meme_out/meme.txt NEGATIVE.fasta

Settings:

output_directory = fimo_neg MEME file name = meme_out/meme.txt sequence file name = NEGATIVE.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 = true 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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