Database and Motifs | High-scoring Motif Occurences | Debugging Information | Results in TSV Format | Results in GFF3 Format | Best Site per Sequence |
FIMO version 5.5.6, (Release date: Wed Jun 19 13:59:04 2024 -0700)
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/meme_out/meme.xml (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
TTTTYTTTTYTTTYW | 15 | TTTTTTTTTTTTTCT |
VATGACTCAG | 10 | GATGACTCAG |
SCCCCGCCCCC | 11 | GCCCCGCCCCC |
CCASYAGRKGGCRSY | 15 | CCACCAGGGGGCGCT |
CTTATCT | 7 | CTTATCT |
GACTACAWYTCCCAG | 15 | GACTACATCTCCCAG |
TGCACTCCAGCCTGG | 15 | TGCACTCCAGCCTGG |
AAASAGGAAGT | 11 | AAACAGGAAGT |
GCGCMTGCGCG | 11 | GCGCCTGCGCG |
RGCTCACTGCAGCCT | 15 | AGCTCACTGCAGCCT |
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 |
---|---|---|---|---|---|---|---|---|
GACTACAWYTCCCAG | MEME-6 | 19 | - | 44645482 | 44645496 | 7.56e-10 | 6.83e-05 | GACTACATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 20 | + | 48118366 | 48118380 | 7.56e-10 | 6.83e-05 | GACTACATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 17 | + | 65076890 | 65076904 | 7.56e-10 | 6.83e-05 | GACTACATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 6 | - | 119050296 | 119050310 | 7.56e-10 | 6.83e-05 | GACTACATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | X | - | 13510411 | 13510425 | 1.7e-09 | 0.000103 | GACTACATCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 14 | + | 68188940 | 68188954 | 1.7e-09 | 0.000103 | GACTACATCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 9 | + | 115774311 | 115774325 | 4.01e-09 | 0.000207 | AACTACATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 14 | - | 105881410 | 105881424 | 4.77e-09 | 0.000215 | AACTACATCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 15 | + | 52121594 | 52121608 | 6.73e-09 | 0.00027 | AACTACAACTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 17 | + | 74733809 | 74733823 | 1.17e-08 | 0.000422 | GACTACGTTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 18 | + | 56806837 | 56806851 | 1.9e-08 | 0.000625 | GACTACGATTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 224544291 | 224544305 | 2.36e-08 | 0.000709 | GACTACAACTCCCGG |
GACTACAWYTCCCAG | MEME-6 | 19 | - | 44617271 | 44617285 | 3.1e-08 | 0.000862 | GACTACACTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 7 | - | 129598505 | 129598519 | 3.87e-08 | 0.000999 | GAATACATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 19 | - | 15490545 | 15490559 | 6.71e-08 | 0.00162 | GACCACAACTCCCAT |
GACTACAWYTCCCAG | MEME-6 | 2 | + | 242447904 | 242447918 | 9.06e-08 | 0.00204 | GACTACAAGTCCCGG |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 142890895 | 142890909 | 1.24e-07 | 0.00244 | CACTACAATTCCCAT |
GACTACAWYTCCCAG | MEME-6 | 15 | + | 63481399 | 63481413 | 1.28e-07 | 0.00244 | AACTACAAGTCCCAT |
GACTACAWYTCCCAG | MEME-6 | 1 | - | 236445153 | 236445167 | 1.28e-07 | 0.00244 | GACCACAACTCCCAC |
GACTACAWYTCCCAG | MEME-6 | 19 | - | 48965542 | 48965556 | 2.04e-07 | 0.00358 | GCCTACATCTCCCAC |
GACTACAWYTCCCAG | MEME-6 | 19 | - | 633373 | 633387 | 2.08e-07 | 0.00358 | AACCACAACTCCCGG |
GACTACAWYTCCCAG | MEME-6 | 19 | + | 51014319 | 51014333 | 2.44e-07 | 0.00401 | GACTACGACTCCCGT |
GACTACAWYTCCCAG | MEME-6 | 10 | + | 74114168 | 74114182 | 2.99e-07 | 0.00469 | AACTACGCCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 16 | + | 3314384 | 3314398 | 4.26e-07 | 0.00625 | GCCCACGTCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 244615362 | 244615376 | 4.33e-07 | 0.00625 | GACTACAAATCCCAG |
GACTACAWYTCCCAG | MEME-6 | 12 | + | 124055732 | 124055746 | 6.77e-07 | 0.0094 | GACTCCATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 9 | + | 128023833 | 128023847 | 8.39e-07 | 0.0112 | AACTACAGCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 14 | - | 55221779 | 55221793 | 8.67e-07 | 0.0112 | ACCTACATTTCCCGC |
GACTACAWYTCCCAG | MEME-6 | 18 | - | 56806774 | 56806788 | 1.13e-06 | 0.0137 | AACTACCACTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 73309517 | 73309531 | 1.14e-06 | 0.0137 | AACTCCATCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 65625534 | 65625548 | 3.31e-06 | 0.0386 | GACTCCATTTCCCGT |
GACTACAWYTCCCAG | MEME-6 | 2 | - | 53994508 | 53994522 | 3.76e-06 | 0.0425 | AACTACAATACCCAC |
GACTACAWYTCCCAG | MEME-6 | 18 | + | 32627283 | 32627297 | 8.24e-06 | 0.0902 | ACCTACAATTCACAT |
GACTACAWYTCCCAG | MEME-6 | 1 | - | 202489650 | 202489664 | 1.04e-05 | 0.11 | ACCTAGAAGTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 11 | + | 73309480 | 73309494 | 1.28e-05 | 0.132 | TACTACAGTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 7 | + | 150755127 | 150755141 | 1.42e-05 | 0.143 | GACTACGCGTTCCAG |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 59578050 | 59578064 | 1.72e-05 | 0.168 | GAACACAACTTCCGG |
GACTACAWYTCCCAG | MEME-6 | 22 | + | 41682151 | 41682165 | 1.77e-05 | 0.169 | AACTACCCGTCCCAT |
GACTACAWYTCCCAG | MEME-6 | 12 | - | 49626770 | 49626784 | 2.3e-05 | 0.213 | CCCCACATTCCCCAG |
GACTACAWYTCCCAG | MEME-6 | 9 | - | 33165743 | 33165757 | 2.73e-05 | 0.246 | CACCACGTTGCCCAT |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 201672058 | 201672072 | 3.01e-05 | 0.265 | AACAACCACTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 9 | - | 132404567 | 132404581 | 3.13e-05 | 0.269 | GACCACAGCTCTCAG |
GACTACAWYTCCCAG | MEME-6 | 7 | - | 39052901 | 39052915 | 3.28e-05 | 0.27 | GTCCACAGCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 16 | + | 67281139 | 67281153 | 3.29e-05 | 0.27 | GCCTCCGAGTCCCGG |
GACTACAWYTCCCAG | MEME-6 | 20 | + | 44007431 | 44007445 | 3.97e-05 | 0.31 | ACCTCCACCTCCCAC |
GACTACAWYTCCCAG | MEME-6 | 20 | + | 48909032 | 48909046 | 4.1e-05 | 0.31 | GCCCAAGCTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 14 | - | 94575670 | 94575684 | 4.1e-05 | 0.31 | GACCATAACTCCAAG |
GACTACAWYTCCCAG | MEME-6 | 4 | + | 89508386 | 89508400 | 4.13e-05 | 0.31 | CAACACAATTCACAT |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 65625577 | 65625591 | 4.35e-05 | 0.314 | GACTCCGTTACCCAG |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 21985783 | 21985797 | 4.47e-05 | 0.314 | CCGCACGTCTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 65625625 | 65625639 | 4.47e-05 | 0.314 | GCCTACATTTCCCTA |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 57282586 | 57282600 | 4.52e-05 | 0.314 | GTCCACAATGCCCAG |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 111957370 | 111957384 | 4.8e-05 | 0.323 | GGCGACAATTCCCAC |
GACTACAWYTCCCAG | MEME-6 | 8 | + | 38009322 | 38009336 | 4.83e-05 | 0.323 | AACCACCTTTCCCAA |
GACTACAWYTCCCAG | MEME-6 | 11 | - | 62432642 | 62432656 | 4.93e-05 | 0.324 | CCCCACCACTCCCGG |
GACTACAWYTCCCAG | MEME-6 | 5 | + | 96425023 | 96425037 | 5.21e-05 | 0.336 | GACCACAGCTCTCAT |
GACTACAWYTCCCAG | MEME-6 | 3 | - | 197517942 | 197517956 | 5.49e-05 | 0.343 | GCCGCCATTTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 6 | + | 106773452 | 106773466 | 5.58e-05 | 0.343 | CACCACAAGTCCAGT |
GACTACAWYTCCCAG | MEME-6 | 19 | - | 49680228 | 49680242 | 5.65e-05 | 0.343 | AACCACATCTTGCAG |
GACTACAWYTCCCAG | MEME-6 | 1 | - | 63988795 | 63988809 | 5.69e-05 | 0.343 | GCCTAGAACTCCCCG |
GACTACAWYTCCCAG | MEME-6 | 3 | - | 126704786 | 126704800 | 5.84e-05 | 0.346 | GCCTGCAATTACCAG |
GACTACAWYTCCCAG | MEME-6 | 2 | - | 242447968 | 242447982 | 6.42e-05 | 0.374 | GACTAGGGGTCCCAG |
GACTACAWYTCCCAG | MEME-6 | 17 | - | 40729532 | 40729546 | 6.78e-05 | 0.386 | AACTACAACGTCCGG |
GACTACAWYTCCCAG | MEME-6 | 1 | - | 75941389 | 75941403 | 6.87e-05 | 0.386 | AACCACCACACCCAG |
GACTACAWYTCCCAG | MEME-6 | 1 | + | 212458538 | 212458552 | 6.95e-05 | 0.386 | GCACACACTCCCCAG |
GACTACAWYTCCCAG | MEME-6 | 14 | - | 91976685 | 91976699 | 7.26e-05 | 0.397 | GCACACACCGCCCAG |
GACTACAWYTCCCAG | MEME-6 | 18 | - | 72166845 | 72166859 | 7.42e-05 | 0.4 | CACTGCAACACCCAG |
GACTACAWYTCCCAG | MEME-6 | 22 | + | 19928260 | 19928274 | 7.71e-05 | 0.409 | CACCATGCCTCCCAT |
GACTACAWYTCCCAG | MEME-6 | 1 | - | 58666136 | 58666150 | 7.98e-05 | 0.416 | AATTACACCTTCCAG |
GACTACAWYTCCCAG | MEME-6 | 12 | + | 133022564 | 133022578 | 8.11e-05 | 0.416 | GACCACAAGTCACCG |
GACTACAWYTCCCAG | MEME-6 | 17 | + | 65241156 | 65241170 | 8.21e-05 | 0.416 | GCCCCCGACTCCCGC |
GACTACAWYTCCCAG | MEME-6 | 12 | + | 123868274 | 123868288 | 8.32e-05 | 0.416 | AAACACCCCTCCCAC |
GACTACAWYTCCCAG | MEME-6 | 17 | - | 7486896 | 7486910 | 8.41e-05 | 0.416 | CACTCCGCCTCCCGT |
GACTACAWYTCCCAG | MEME-6 | X | + | 47518025 | 47518039 | 8.77e-05 | 0.423 | CACCGCAAGTCCCGC |
GACTACAWYTCCCAG | MEME-6 | 15 | - | 41408661 | 41408675 | 8.78e-05 | 0.423 | GAACAAATATCCCAG |
GACTACAWYTCCCAG | MEME-6 | 2 | - | 11999084 | 11999098 | 9.1e-05 | 0.433 | CAATGCACCTCCCAC |
GACTACAWYTCCCAG | MEME-6 | 1 | - | 229650376 | 229650390 | 9.38e-05 | 0.44 | GACTACATGGCCTAC |
GACTACAWYTCCCAG | MEME-6 | 12 | - | 107528413 | 107528427 | 9.66e-05 | 0.445 | GACCACCACTCCAAC |
GACTACAWYTCCCAG | MEME-6 | 8 | - | 26148687 | 26148701 | 9.72e-05 | 0.445 | CCCTCCGTGTCCCGG |
Command line:
fimo --verbosity 1 --oc xstreme_example_output_files/fimo_out_7 --bgfile xstreme_example_output_files/background --motif GACTACAWYTCCCAG xstreme_example_output_files/meme_out/meme.xml nrmix.nseqs.100.100bp.seed.1.fa
Settings:
output_directory = xstreme_example_output_files/fimo_out_7 | MEME file name = xstreme_example_output_files/meme_out/meme.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.