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 3706 sequences, 92650 residues

MOTIFS meme_out/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CAGGA 5 CAGGA

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
CAGGA MEME-1 Seq1345 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1356 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq658 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2267 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2316 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq110 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq654 + 3 7 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3090 + 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3593 + 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2894 + 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2896 + 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2184 + 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1419 + 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3301 + 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2506 + 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq416 + 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1395 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3647 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2544 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2148 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq631 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2204 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq879 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1334 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2027 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq955 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3427 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1122 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1370 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1893 + 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2486 + 7 11 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3633 + 7 11 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2085 + 7 11 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1704 + 7 11 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2367 - 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3447 - 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3239 - 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1828 + 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3010 - 4 8 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2009 + 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq539 + 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3703 + 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq985 - 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2169 - 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq947 - 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2011 - 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3415 - 5 9 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2630 + 9 13 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1846 + 9 13 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3001 + 10 14 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2560 - 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2337 + 10 14 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3520 - 6 10 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq219 - 7 11 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1079 + 11 15 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2332 - 7 11 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2840 + 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq93 - 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1518 + 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq172 - 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq84 - 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1142 + 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1754 + 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2931 - 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3290 - 8 12 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2819 + 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2786 - 9 13 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1495 + 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq147 + 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2330 + 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3134 - 9 13 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3550 + 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1635 + 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq973 - 9 13 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2901 + 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3223 - 10 14 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3036 - 10 14 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1370 - 11 15 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2358 - 11 15 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3601 - 11 15 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq336 + 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2065 - 11 15 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1162 - 11 15 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3510 + 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq459 + 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3557 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2916 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2400 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2357 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq412 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2292 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2193 - 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1203 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3695 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq550 - 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3632 - 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3598 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1575 - 12 16 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1656 + 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1523 - 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq405 + 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq871 - 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3558 - 13 17 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1678 + 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq284 + 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1536 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2455 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq730 + 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2352 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1289 + 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1878 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq504 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3541 + 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1813 + 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3331 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1675 - 14 18 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq939 - 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1511 + 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq898 - 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1312 - 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq262 - 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2133 + 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3669 + 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3565 - 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq50 + 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3321 - 15 19 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2964 + 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1490 - 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2671 + 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2163 - 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3663 + 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1235 + 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3622 - 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1619 - 16 20 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1521 + 21 25 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2440 - 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq729 + 21 25 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2198 - 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3395 - 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq478 - 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1648 - 17 21 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2742 - 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2718 - 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq307 - 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1336 - 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1007 - 18 22 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2939 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2678 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2695 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2444 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2309 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1238 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq485 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1173 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1071 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1749 - 19 23 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq1353 - 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq436 - 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2200 - 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq3396 - 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2022 - 20 24 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2959 - 21 25 0.000864 0.824 CAGGA
CAGGA MEME-1 Seq2833 - 21 25 0.000864 0.824 CAGGA

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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