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 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
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 |
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.