Database and Motifs High-scoring Motif Occurences Debugging Information Results in TSV Format Results in GFF3 Format Best Site per Sequence



FIMO - Motif search tool

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 AND MOTIFS

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


SECTION I: HIGH-SCORING MOTIF OCCURENCES

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

DEBUGGING INFORMATION

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.


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