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 nrmix.nseqs.100.100bp.seed.1.fa
Database contains 2100 sequences, 210000 residues
MOTIFS xstreme_example_output_files/streme_out/streme.xml (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
1-CCASYAGRGGGCGCY | 15 | CCACCAGGGGGCGCC |
2-GCTGAGTCATN | 11 | GCTGAGTCATG |
3-GCGCATGCGCAC | 12 | GCGCATGCGCAC |
4-AGATAAGG | 8 | AGATAAGG |
5-CACTTCCTGKT | 11 | CACTTCCTGTT |
6-CCCCGCCCCCD | 11 | CCCCGCCCCCT |
7-CAAGATGGC | 9 | CAAGATGGC |
8-GGTCACGTGAYGS | 13 | GGTCACGTGACGC |
Random model letter frequencies (xstreme_example_output_files/background):
A 0.222 C 0.278 G 0.278 T 0.222
Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|---|---|---|---|---|---|---|---|
7-CAAGATGGC | STREME-7 | 17 | + | 11811987 | 11811995 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 20204813 | 20204821 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 46049907 | 46049915 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 17 | - | 46969696 | 46969704 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 22 | - | 49448083 | 49448091 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 7 | + | 101459106 | 101459114 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 6 | + | 108881180 | 108881188 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 111991883 | 111991891 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 12 | - | 121454072 | 121454080 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 7 | - | 139477306 | 139477314 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 8 | - | 144691513 | 144691521 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 2 | + | 178837611 | 178837619 | 4.03e-06 | 0.122 | CAAGATGGC |
7-CAAGATGGC | STREME-7 | 19 | + | 5622592 | 5622600 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 1 | + | 5948572 | 5948580 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 11 | - | 10477459 | 10477467 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 6 | - | 30582716 | 30582724 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 9 | - | 36325131 | 36325139 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 10 | + | 59063366 | 59063374 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | X | + | 62654617 | 62654625 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 2 | - | 71357144 | 71357152 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 2 | + | 71558926 | 71558934 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | X | + | 154493683 | 154493691 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 6 | - | 167200226 | 167200234 | 7.25e-06 | 0.122 | CAAAATGGC |
7-CAAGATGGC | STREME-7 | 5 | + | 1799777 | 1799785 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | 20 | - | 5892040 | 5892048 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | 11 | - | 12915598 | 12915606 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | 19 | - | 38852962 | 38852970 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | 15 | - | 42565391 | 42565399 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | 11 | + | 66277926 | 66277934 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | X | + | 107408561 | 107408569 | 1.13e-05 | 0.14 | GAAGATGGC |
7-CAAGATGGC | STREME-7 | 12 | + | 6532681 | 6532689 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 6 | - | 31830559 | 31830567 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 6 | - | 31830571 | 31830579 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 33116333 | 33116341 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 11 | - | 72525157 | 72525165 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 5 | + | 82726245 | 82726253 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 12 | - | 93043686 | 93043694 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 1 | + | 109820001 | 109820009 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 9 | - | 115774341 | 115774349 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 11 | + | 125792908 | 125792916 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | X | - | 149885286 | 149885294 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 7 | - | 150755102 | 150755110 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 1 | + | 168147787 | 168147795 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 3 | + | 168582717 | 168582725 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 226814195 | 226814203 | 1.63e-05 | 0.14 | CAAGAGGGC |
7-CAAGATGGC | STREME-7 | 16 | + | 4743523 | 4743531 | 1.96e-05 | 0.157 | CAAGATGTC |
7-CAAGATGGC | STREME-7 | 17 | - | 80712772 | 80712780 | 1.96e-05 | 0.157 | CAAGATGTC |
7-CAAGATGGC | STREME-7 | 10 | + | 98590315 | 98590323 | 1.96e-05 | 0.157 | CAAGATGTC |
7-CAAGATGGC | STREME-7 | 17 | + | 1618603 | 1618611 | 2.46e-05 | 0.186 | CAAGACGGC |
7-CAAGATGGC | STREME-7 | 5 | - | 10334952 | 10334960 | 2.46e-05 | 0.186 | CAAGACGGC |
7-CAAGATGGC | STREME-7 | 7 | + | 106960368 | 106960376 | 2.46e-05 | 0.186 | CAAGACGGC |
7-CAAGATGGC | STREME-7 | 7 | - | 40678492 | 40678500 | 2.86e-05 | 0.201 | CAAGATGCC |
7-CAAGATGGC | STREME-7 | 17 | + | 80009603 | 80009611 | 2.86e-05 | 0.201 | CAAGATGCC |
7-CAAGATGGC | STREME-7 | 13 | - | 110359350 | 110359358 | 2.86e-05 | 0.201 | CAAGATGCC |
7-CAAGATGGC | STREME-7 | 6 | + | 139003836 | 139003844 | 2.86e-05 | 0.201 | CAAGATGCC |
7-CAAGATGGC | STREME-7 | 1 | + | 44820889 | 44820897 | 3.19e-05 | 0.204 | CAAGATGGT |
7-CAAGATGGC | STREME-7 | 12 | - | 104341807 | 104341815 | 3.19e-05 | 0.204 | CAAGATGGT |
7-CAAGATGGC | STREME-7 | 7 | - | 153111006 | 153111014 | 3.19e-05 | 0.204 | CAAGATGGT |
7-CAAGATGGC | STREME-7 | 17 | + | 13241095 | 13241103 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 8 | - | 29172212 | 29172220 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 39283801 | 39283809 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 12 | + | 55119000 | 55119008 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 9 | + | 112665807 | 112665815 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 11 | - | 123349092 | 123349100 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 3 | + | 129209012 | 129209020 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 3 | + | 180520616 | 180520624 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 203185307 | 203185315 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 1 | - | 246862445 | 246862453 | 3.59e-05 | 0.204 | CTAGATGGC |
7-CAAGATGGC | STREME-7 | 2 | - | 60983197 | 60983205 | 3.91e-05 | 0.216 | CAATATGGC |
7-CAAGATGGC | STREME-7 | 11 | - | 69271450 | 69271458 | 3.91e-05 | 0.216 | CAATATGGC |
7-CAAGATGGC | STREME-7 | 10 | + | 21623998 | 21624006 | 4.23e-05 | 0.23 | CAAGATGAC |
7-CAAGATGGC | STREME-7 | 19 | + | 3106981 | 3106989 | 4.55e-05 | 0.236 | CAAGATTGC |
7-CAAGATGGC | STREME-7 | 1 | - | 206664185 | 206664193 | 4.55e-05 | 0.236 | CAAGATTGC |
7-CAAGATGGC | STREME-7 | 16 | + | 8162549 | 8162557 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 14 | - | 23387912 | 23387920 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 10 | + | 27443072 | 27443080 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 1 | + | 33116323 | 33116331 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 14 | + | 102700915 | 102700923 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 9 | - | 112681178 | 112681186 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 2 | + | 178837587 | 178837595 | 4.88e-05 | 0.236 | GAAAATGGC |
7-CAAGATGGC | STREME-7 | 6 | + | 20402364 | 20402372 | 5.28e-05 | 0.252 | CAAAAGGGC |
7-CAAGATGGC | STREME-7 | 19 | + | 2051151 | 2051159 | 5.79e-05 | 0.257 | GAAGAGGGC |
7-CAAGATGGC | STREME-7 | 11 | + | 10477424 | 10477432 | 5.79e-05 | 0.257 | GAAGAGGGC |
7-CAAGATGGC | STREME-7 | 19 | - | 18854117 | 18854125 | 5.79e-05 | 0.257 | GAAGAGGGC |
7-CAAGATGGC | STREME-7 | 17 | - | 42402617 | 42402625 | 5.79e-05 | 0.257 | GAAGAGGGC |
7-CAAGATGGC | STREME-7 | 19 | + | 50373109 | 50373117 | 5.79e-05 | 0.257 | GAAGAGGGC |
7-CAAGATGGC | STREME-7 | 5 | - | 56433907 | 56433915 | 5.79e-05 | 0.257 | GAAGAGGGC |
7-CAAGATGGC | STREME-7 | 4 | - | 17473959 | 17473967 | 6.04e-05 | 0.265 | CAAAATGTC |
7-CAAGATGGC | STREME-7 | 2 | - | 171217791 | 171217799 | 6.36e-05 | 0.276 | GAAGATGTC |
7-CAAGATGGC | STREME-7 | 13 | - | 52123168 | 52123176 | 6.77e-05 | 0.281 | CAAGAGGTC |
7-CAAGATGGC | STREME-7 | 8 | + | 69608124 | 69608132 | 6.77e-05 | 0.281 | CAAGAGGTC |
7-CAAGATGGC | STREME-7 | 14 | - | 74192489 | 74192497 | 6.77e-05 | 0.281 | CAAGAGGTC |
7-CAAGATGGC | STREME-7 | 3 | - | 122801150 | 122801158 | 6.77e-05 | 0.281 | CAAGAGGTC |
7-CAAGATGGC | STREME-7 | 11 | + | 46615369 | 46615377 | 8e-05 | 0.325 | GAAGACGGC |
7-CAAGATGGC | STREME-7 | 7 | + | 101512763 | 101512771 | 8e-05 | 0.325 | GAAGACGGC |
7-CAAGATGGC | STREME-7 | 3 | + | 197676790 | 197676798 | 8.4e-05 | 0.338 | GAAGATGCC |
7-CAAGATGGC | STREME-7 | 7 | - | 10980049 | 10980057 | 8.91e-05 | 0.355 | CAAGAGGCC |
7-CAAGATGGC | STREME-7 | 22 | + | 22832560 | 22832568 | 9.16e-05 | 0.358 | CAAAATGGT |
7-CAAGATGGC | STREME-7 | 21 | - | 40721592 | 40721600 | 9.16e-05 | 0.358 | CAAAATGGT |
Command line:
fimo --parse-genomic-coord --verbosity 1 --oc xstreme_example_output_files/fimo_out_10 --bgfile xstreme_example_output_files/background --motif 7-CAAGATGGC xstreme_example_output_files/streme_out/streme.xml nrmix.nseqs.100.100bp.seed.1.fa
Settings:
output_directory = xstreme_example_output_files/fimo_out_10 | MEME file name = xstreme_example_output_files/streme_out/streme.xml | sequence file name = nrmix.nseqs.100.100bp.seed.1.fa |
background file name = xstreme_example_output_files/background | alphabet = DNA | max stored scores = 100000 |
allow clobber = true | compute q-values = true | parse genomic coord. = true |
text only = false | scan both strands = true | max strand = false |
threshold type = p-value | output theshold = 0.0001 | pseudocount = 0.1 |
alpha = 1 | verbosity = 1 |
This information can be useful in the event you wish to report a problem with the FIMO software.