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 5.5.5, (Release date: Thu Sep 14 08:48:04 2023 +1000)

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/streme_out/streme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
1-CCASYAGRGGGCGCY 15 CCACCAGGGGGCGCC
2-GCTGAGTCATN 11 GCTGAGTCATG
3-GCGCATGCGCAC 12 GCGCATGCGCAC
4-CACTTCCTGKT 11 CACTTCCTGTT
5-AGATAAGG 8 AGATAAGG
6-CCCCGCCCCCD 11 CCCCGCCCCCT
7-CAAGATGGC 9 CAAGATGGC
8-GGTCACGTGABBS 13 GGTCACGTGACGC

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
4-CACTTCCTGKT STREME-4 9 + 37592411 37592421 1.99e-07 0.0282 CACTTCCTGTT
4-CACTTCCTGKT STREME-4 2 + 73162101 73162111 1.99e-07 0.0282 CACTTCCTGTT
4-CACTTCCTGKT STREME-4 X + 2549539 2549549 4.47e-07 0.0282 CACTTCCTGGT
4-CACTTCCTGKT STREME-4 X + 2549568 2549578 4.47e-07 0.0282 CACTTCCTGGT
4-CACTTCCTGKT STREME-4 9 - 100174678 100174688 4.47e-07 0.0282 CACTTCCTGGT
4-CACTTCCTGKT STREME-4 X + 100306664 100306674 4.47e-07 0.0282 CACTTCCTGGT
4-CACTTCCTGKT STREME-4 2 + 200320282 200320292 6.46e-07 0.0282 CACTTCCTGTA
4-CACTTCCTGKT STREME-4 4 + 10182693 10182703 8.95e-07 0.0282 CACTTCCTGTC
4-CACTTCCTGKT STREME-4 17 - 41150196 41150206 8.95e-07 0.0282 CACTTCCTGTC
4-CACTTCCTGKT STREME-4 17 + 45148509 45148519 8.95e-07 0.0282 CACTTCCTGTC
4-CACTTCCTGKT STREME-4 17 + 45148533 45148543 8.95e-07 0.0282 CACTTCCTGTC
4-CACTTCCTGKT STREME-4 15 + 85640353 85640363 8.95e-07 0.0282 CACTTCCTGTC
4-CACTTCCTGKT STREME-4 16 - 30961274 30961284 1.5e-06 0.0299 CACTTCCTGTG
4-CACTTCCTGKT STREME-4 10 + 64134797 64134807 1.5e-06 0.0299 AACTTCCTGTT
4-CACTTCCTGKT STREME-4 5 - 71894481 71894491 1.5e-06 0.0299 AACTTCCTGTT
4-CACTTCCTGKT STREME-4 10 + 73291290 73291300 1.5e-06 0.0299 CACTTCCTGTG
4-CACTTCCTGKT STREME-4 11 + 118747511 118747521 1.5e-06 0.0299 CACTTCCTGTG
4-CACTTCCTGKT STREME-4 1 - 155210888 155210898 1.5e-06 0.0299 CACTTCCTGTG
4-CACTTCCTGKT STREME-4 1 + 219328402 219328412 1.5e-06 0.0299 CACTTCCTGTG
4-CACTTCCTGKT STREME-4 17 - 27911736 27911746 1.66e-06 0.0314 TACTTCCTGTT
4-CACTTCCTGKT STREME-4 16 - 83973042 83973052 1.86e-06 0.0334 GACTTCCTGTT
4-CACTTCCTGKT STREME-4 16 + 27279965 27279975 2.11e-06 0.0362 CACTTCCGGTT
4-CACTTCCTGKT STREME-4 1 - 36863979 36863989 2.36e-06 0.0387 CACTTCCTGGA
4-CACTTCCTGKT STREME-4 12 - 8010450 8010460 3.34e-06 0.0445 CACTTCCTGGG
4-CACTTCCTGKT STREME-4 1 + 17262647 17262657 3.34e-06 0.0445 CACTTCCTGGG
4-CACTTCCTGKT STREME-4 6 - 112942710 112942720 3.34e-06 0.0445 AACTTCCTGGT
4-CACTTCCTGKT STREME-4 3 + 186600584 186600594 3.34e-06 0.0445 CACTTCCTGGG
4-CACTTCCTGKT STREME-4 1 - 5948648 5948658 3.54e-06 0.0445 CACTTCCTGAA
4-CACTTCCTGKT STREME-4 20 - 44834667 44834677 3.54e-06 0.0445 CACTTCCTGAA
4-CACTTCCTGKT STREME-4 X - 155117827 155117837 3.54e-06 0.0445 CACTTCCTGAA
4-CACTTCCTGKT STREME-4 19 + 8261389 8261399 4.14e-06 0.046 CACTTCCTCTT
4-CACTTCCTGKT STREME-4 6 - 36586656 36586666 4.14e-06 0.046 CACTTCCTCTT
4-CACTTCCTGKT STREME-4 15 + 45016494 45016504 4.14e-06 0.046 CACTTCCTCTT
4-CACTTCCTGKT STREME-4 6 + 97364948 97364958 4.14e-06 0.046 CACTTCCTCTT
4-CACTTCCTGKT STREME-4 4 + 109541474 109541484 4.79e-06 0.0503 AACTTCCTGTC
4-CACTTCCTGKT STREME-4 17 - 55456744 55456754 5.19e-06 0.0503 AACTTCCTGAT
4-CACTTCCTGKT STREME-4 14 + 68887064 68887074 5.19e-06 0.0503 AACTTCCTGAT
4-CACTTCCTGKT STREME-4 7 + 106415181 106415191 5.19e-06 0.0503 AACTTCCTGAT
4-CACTTCCTGKT STREME-4 10 + 121447430 121447440 5.19e-06 0.0503 AACTTCCTGAT
4-CACTTCCTGKT STREME-4 22 - 22020093 22020103 6.06e-06 0.0533 CACTTCCGGGT
4-CACTTCCTGKT STREME-4 8 + 27949631 27949641 6.06e-06 0.0533 CACTTCCGGGT
4-CACTTCCTGKT STREME-4 17 + 35969269 35969279 6.06e-06 0.0533 CACTTCCGGGT
4-CACTTCCTGKT STREME-4 19 - 52772641 52772651 6.06e-06 0.0533 CACTTCCGGGT
4-CACTTCCTGKT STREME-4 9 + 136218851 136218861 6.46e-06 0.0543 CACTTCCTAGT
4-CACTTCCTGKT STREME-4 9 + 136218851 136218861 6.46e-06 0.0543 CACTTCCTAGT
4-CACTTCCTGKT STREME-4 14 - 105533620 105533630 6.96e-06 0.0572 GACTTCCTGTC
4-CACTTCCTGKT STREME-4 19 + 1275606 1275616 7.36e-06 0.0592 TACTTCCTGAT
4-CACTTCCTGKT STREME-4 6 + 12093045 12093055 8.01e-06 0.063 GACTTCCTGTG
4-CACTTCCTGKT STREME-4 17 + 43657680 43657690 8.17e-06 0.063 CACTTCCTATA
4-CACTTCCTGKT STREME-4 19 - 11616444 11616454 8.48e-06 0.0641 CACTTCCGGTC
4-CACTTCCTGKT STREME-4 11 - 111435820 111435830 1.06e-05 0.0777 AACTTCCTGGC
4-CACTTCCTGKT STREME-4 18 + 45408133 45408143 1.11e-05 0.0777 AACTTCCTGGG
4-CACTTCCTGKT STREME-4 11 + 111957317 111957327 1.13e-05 0.0777 GACTTCCGGTT
4-CACTTCCTGKT STREME-4 1 - 160509925 160509935 1.15e-05 0.0777 CACTTCCTCTA
4-CACTTCCTGKT STREME-4 1 - 160509925 160509935 1.15e-05 0.0777 CACTTCCTCTA
4-CACTTCCTGKT STREME-4 6 - 33951967 33951977 1.17e-05 0.0777 TACTTCCTGGA
4-CACTTCCTGKT STREME-4 4 - 123286169 123286179 1.17e-05 0.0777 TACTTCCTGGA
4-CACTTCCTGKT STREME-4 1 + 45452805 45452815 1.24e-05 0.0797 GACTTCCTATT
4-CACTTCCTGKT STREME-4 11 - 120215039 120215049 1.27e-05 0.0797 CACTTCCTCTC
4-CACTTCCTGKT STREME-4 9 - 115774277 115774287 1.29e-05 0.0797 TACTTCCTGGC
4-CACTTCCTGKT STREME-4 7 + 98923294 98923304 1.32e-05 0.0797 CACTTCCGGGA
4-CACTTCCTGKT STREME-4 1 + 56982058 56982068 1.37e-05 0.0797 CACTTCCTCAT
4-CACTTCCTGKT STREME-4 5 - 95064484 95064494 1.39e-05 0.0797 AACTTCCTGAC
4-CACTTCCTGKT STREME-4 8 + 125462316 125462326 1.39e-05 0.0797 AACTTCCTGAC
4-CACTTCCTGKT STREME-4 1 + 68368511 68368521 1.43e-05 0.0797 AACTTCCTCTT
4-CACTTCCTGKT STREME-4 7 - 75443027 75443037 1.43e-05 0.0797 AACTTCCTCTT
4-CACTTCCTGKT STREME-4 9 + 101137395 101137405 1.43e-05 0.0797 CACTTCCTCTG
4-CACTTCCTGKT STREME-4 2 + 102690877 102690887 1.43e-05 0.0797 AACTTCCTCTT
4-CACTTCCTGKT STREME-4 8 - 62599939 62599949 1.51e-05 0.0826 GACTTCCTGGG
4-CACTTCCTGKT STREME-4 7 + 105658950 105658960 1.53e-05 0.0826 CACTTCCTAGA
4-CACTTCCTGKT STREME-4 5 + 14696181 14696191 1.65e-05 0.0874 GACTTCCTGAA
4-CACTTCCTGKT STREME-4 3 + 15419637 15419647 1.71e-05 0.0874 AACTTCCGGGT
4-CACTTCCTGKT STREME-4 17 - 80009566 80009576 1.71e-05 0.0874 CACTTCCGGGG
4-CACTTCCTGKT STREME-4 1 - 205296238 205296248 1.75e-05 0.0874 CACTTCCTAGC
4-CACTTCCTGKT STREME-4 10 + 33270637 33270647 1.78e-05 0.0874 CACTTCCTGCC
4-CACTTCCTGKT STREME-4 10 - 43892633 43892643 1.78e-05 0.0874 CACTTCCTGCC
4-CACTTCCTGKT STREME-4 10 - 73291303 73291313 1.78e-05 0.0874 CACTTCCTGCC
4-CACTTCCTGKT STREME-4 20 + 2506210 2506220 1.8e-05 0.0874 TACTTCCTGAC
4-CACTTCCTGKT STREME-4 1 - 116915637 116915647 2.06e-05 0.0987 CACTTCCTAAA
4-CACTTCCTGKT STREME-4 7 + 99214374 99214384 2.09e-05 0.0989 CACTTCCGGAC
4-CACTTCCTGKT STREME-4 2 + 9374859 9374869 2.16e-05 0.0997 CACATCCTGTT
4-CACTTCCTGKT STREME-4 1 - 109820011 109820021 2.16e-05 0.0997 CACATCCTGTT
4-CACTTCCTGKT STREME-4 8 - 10873860 10873870 2.23e-05 0.102 GACTTCCGGGT
4-CACTTCCTGKT STREME-4 16 - 2653102 2653112 2.31e-05 0.104 CACTTCCGGAG
4-CACTTCCTGKT STREME-4 9 - 33165726 33165736 2.39e-05 0.106 TACTTCCGGTA
4-CACTTCCTGKT STREME-4 6 + 139697085 139697095 2.52e-05 0.111 GACTTCCTGCT
4-CACTTCCTGKT STREME-4 3 + 156272891 156272901 2.81e-05 0.122 GACTTCCGGAT
4-CACTTCCTGKT STREME-4 11 - 95930928 95930938 2.83e-05 0.122 CACTTCCTCAA
4-CACTTCCTGKT STREME-4 7 + 102004044 102004054 2.89e-05 0.123 GACTTCCGGTG
4-CACTTCCTGKT STREME-4 17 - 72304281 72304291 2.98e-05 0.125 CACTTCCTACT
4-CACTTCCTGKT STREME-4 10 + 94515962 94515972 3.07e-05 0.127 CACTTCCTCAC
4-CACTTCCTGKT STREME-4 17 + 25801001 25801011 3.15e-05 0.129 AACTTCCTCTC
4-CACTTCCTGKT STREME-4 1 - 207483188 207483198 3.32e-05 0.135 CACTTCCCGTT
4-CACTTCCTGKT STREME-4 12 + 696911 696921 3.61e-05 0.141 CACTTACTGAT
4-CACTTCCTGKT STREME-4 9 - 19380103 19380113 3.63e-05 0.141 CACTTCCGCTA
4-CACTTCCTGKT STREME-4 17 - 41150234 41150244 3.63e-05 0.141 CACTTCCGCTA
4-CACTTCCTGKT STREME-4 13 - 25192646 25192656 3.7e-05 0.141 TACTTCCGGGA
4-CACTTCCTGKT STREME-4 15 - 41408625 41408635 3.7e-05 0.141 TACTTCCGGGA
4-CACTTCCTGKT STREME-4 3 + 152153590 152153600 3.7e-05 0.141 GACTTCCTCTC
4-CACTTCCTGKT STREME-4 5 - 10334942 10334952 3.78e-05 0.143 CACTTCCTCCT
4-CACTTCCTGKT STREME-4 8 + 8203919 8203929 3.87e-05 0.143 GACTTCCTCAT
4-CACTTCCTGKT STREME-4 6 - 29520301 29520311 3.87e-05 0.143 GACTTCCTCAT
4-CACTTCCTGKT STREME-4 21 + 30365073 30365083 4.06e-05 0.146 CACTTCCGCTC
4-CACTTCCTGKT STREME-4 19 + 44645520 44645530 4.06e-05 0.146 CACTTCCGCTC
4-CACTTCCTGKT STREME-4 5 - 157285973 157285983 4.06e-05 0.146 CACTTCCGCTC
4-CACTTCCTGKT STREME-4 9 + 19380038 19380048 4.36e-05 0.154 AACTTCCGCTT
4-CACTTCCTGKT STREME-4 5 + 60627866 60627876 4.36e-05 0.154 CACTTCCGCTG
4-CACTTCCTGKT STREME-4 X - 62654540 62654550 4.43e-05 0.155 AACATCCTGTT
4-CACTTCCTGKT STREME-4 13 + 115000129 115000139 4.47e-05 0.155 GACTTCCGGGG
4-CACTTCCTGKT STREME-4 2 - 178548059 178548069 4.63e-05 0.159 AACTTCCGGAG
4-CACTTCCTGKT STREME-4 16 - 84220481 84220491 4.7e-05 0.16 GACTTCCTGCC
4-CACTTCCTGKT STREME-4 17 - 46555645 46555655 4.76e-05 0.161 GACTTCCGGAA
4-CACTTCCTGKT STREME-4 16 - 77690889 77690899 5.21e-05 0.174 AACTTCCTCGG
4-CACTTCCTGKT STREME-4 15 - 35261817 35261827 5.41e-05 0.178 AACTTCCGGCT
4-CACTTCCTGKT STREME-4 2 - 12310248 12310258 5.42e-05 0.178 CACTTACTATT
4-CACTTCCTGKT STREME-4 11 - 13010898 13010908 5.5e-05 0.178 CACTTCCTACC
4-CACTTCCTGKT STREME-4 20 - 32006928 32006938 5.54e-05 0.178 TACTTCCTAAC
4-CACTTCCTGKT STREME-4 16 + 83928872 83928882 5.56e-05 0.178 CACTTACTGGC
4-CACTTCCTGKT STREME-4 19 - 633421 633431 6.15e-05 0.195 TACTTCCGGCT
4-CACTTCCTGKT STREME-4 7 + 132937541 132937551 6.19e-05 0.195 CACTTCCGCGC
4-CACTTCCTGKT STREME-4 2 + 128051525 128051535 6.29e-05 0.197 GACTTCCGGCT
4-CACTTCCTGKT STREME-4 2 + 172017088 172017098 6.56e-05 0.203 CACTTCCGCGG
4-CACTTCCTGKT STREME-4 3 - 10283989 10283999 6.61e-05 0.203 CACATCCTGGG
4-CACTTCCTGKT STREME-4 X + 124138657 124138667 6.67e-05 0.203 CACTTACTGAC
4-CACTTCCTGKT STREME-4 12 + 8179065 8179075 6.78e-05 0.204 CACTTCCTCCC
4-CACTTCCTGKT STREME-4 6 + 97364934 97364944 6.78e-05 0.204 CACTTCCTCCC
4-CACTTCCTGKT STREME-4 6 - 149350930 149350940 6.91e-05 0.206 AACTTACTGAT
4-CACTTCCTGKT STREME-4 16 + 14726453 14726463 7.03e-05 0.208 CACTTCCTCCG
4-CACTTCCTGKT STREME-4 8 - 61564902 61564912 7.31e-05 0.212 CACTTCCGCAC
4-CACTTCCTGKT STREME-4 5 + 125796037 125796047 7.31e-05 0.212 CACTTCCGCAC
4-CACTTCCTGKT STREME-4 9 + 101137441 101137451 7.91e-05 0.226 TACTTCCTCCT
4-CACTTCCTGKT STREME-4 16 + 15665488 15665498 8.02e-05 0.226 GACTTCCTCCT
4-CACTTCCTGKT STREME-4 1 - 31229452 31229462 8.02e-05 0.226 GACTTCCTCCT
4-CACTTCCTGKT STREME-4 12 - 53552128 53552138 8.02e-05 0.226 GACTTCCTCCT
4-CACTTCCTGKT STREME-4 15 + 89545534 89545544 8.41e-05 0.232 CACTTCCGCCT
4-CACTTCCTGKT STREME-4 9 - 128023799 128023809 8.41e-05 0.232 CACTTCCGCCT
4-CACTTCCTGKT STREME-4 5 + 55544872 55544882 8.43e-05 0.232 CACATCCTGCT
4-CACTTCCTGKT STREME-4 1 - 95743676 95743686 8.48e-05 0.232 TACATCCTGAT
4-CACTTCCTGKT STREME-4 2 - 128051561 128051571 8.75e-05 0.238 GACATCCTGTG
4-CACTTCCTGKT STREME-4 1 - 32405385 32405395 9.32e-05 0.252 AACATCCTGGA
4-CACTTCCTGKT STREME-4 1 + 1790059 1790069 9.57e-05 0.252 CACATCCTAAT
4-CACTTCCTGKT STREME-4 X - 65144722 65144732 9.62e-05 0.252 CACTTCCCCTT
4-CACTTCCTGKT STREME-4 7 + 117432229 117432239 9.62e-05 0.252 CACTTCCCCTT
4-CACTTCCTGKT STREME-4 5 - 133702706 133702716 9.62e-05 0.252 CACTTCCCCTT

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc xstreme_example_output_files/fimo_out_6 --bgfile xstreme_example_output_files/background --motif 4-CACTTCCTGKT xstreme_example_output_files/streme_out/streme.xml nrmix.nseqs.100.100bp.seed.1.fa

Settings:

output_directory = xstreme_example_output_files/fimo_out_6 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.


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