Database and Motifs High-scoring Motif Occurences Debugging Information



FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

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 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 599 sequences, 299500 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GAGGCTAY 8 GAGGCTAC
CAGAAGCY 8 CAGAAGCC
GCTGGGAA 8 GCTGGGAA
CATAAATY 8 CATAAATT
AGTGYCTG 8 AGTGCCTG
RTGASTCA 8 ATGAGTCA
CYAAAAGC 8 CTAAAAGC
GTCAGAA 7 GTCAGAA
CTGTTYCC 8 CTGTTCCC
AGGGWGGG 8 AGGGAGGG
AARTAT 6 AAATAT
CYGTGCCA 8 CTGTGCCA

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.256 C 0.244 G 0.244 T 0.256


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
CTGTTYCC DREME-9 chr2 + 2900422 2900429 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr4 + 3755364 3755371 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr12 - 14258153 14258160 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr6 - 15553290 15553297 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr20 - 15775097 15775104 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr20 + 16418845 16418852 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr8 + 19537525 19537532 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr1 + 21939894 21939901 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr5 - 22026191 22026198 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr19 - 28956178 28956185 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr19 + 29295496 29295503 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr14 - 31241740 31241747 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr18 - 31795282 31795289 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr8 - 37479705 37479712 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr22 - 39452384 39452391 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr19 + 40715665 40715672 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr13 - 46120304 46120311 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr1 - 59266496 59266503 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr18 + 62311017 62311024 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr5 + 72282269 72282276 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr8 + 74099723 74099730 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr5 - 76790987 76790994 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr5 + 77029941 77029948 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr7 - 80734593 80734600 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr10 + 89862352 89862359 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr10 - 95813222 95813229 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr4 + 105708663 105708670 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr6 - 106911494 106911501 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr5 - 144037618 144037625 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr8 + 144068250 144068257 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr7 + 157889721 157889728 1.45e-05 0.213 ctgttccc
CTGTTYCC DREME-9 chr1 - 175471044 175471051 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr4 + 176619422 176619429 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr4 - 184617730 184617737 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr2 - 218707982 218707989 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr1 - 231067030 231067037 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr1 - 234523735 234523742 1.45e-05 0.213 CTGTTCCC
CTGTTYCC DREME-9 chr2 + 1578747 1578754 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr2 + 2900451 2900458 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr16 - 3191605 3191612 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr2 + 3575265 3575272 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr4 + 3852945 3852952 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr19 + 4724633 4724640 2.97e-05 0.213 Ctgtttcc
CTGTTYCC DREME-9 chr5 + 10304492 10304499 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr12 - 10362068 10362075 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr3 + 13031105 13031112 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr2 - 16254893 16254900 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr11 + 19769492 19769499 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr15 + 26724850 26724857 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr6 + 28941814 28941821 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr16 + 29943883 29943890 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr12 - 31749262 31749269 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr9 + 32498420 32498427 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr19 + 40715598 40715605 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr19 - 41501602 41501609 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr6 + 41767359 41767366 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr19 + 43662641 43662648 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr19 + 44212803 44212810 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr21 + 44939979 44939986 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr11 - 57735621 57735628 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr17 + 59619735 59619742 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr11 - 60925878 60925885 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr1 - 67700974 67700981 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr14 + 68089190 68089197 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr10 + 75469451 75469458 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr17 - 77234229 77234236 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr7 + 80734332 80734339 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr17 - 81394201 81394208 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr17 - 81980654 81980661 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr11 - 94768021 94768028 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr10 + 101164370 101164377 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr7 + 102572373 102572380 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr10 + 102767038 102767045 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr5 + 113187412 113187419 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr2 + 113809610 113809617 2.97e-05 0.213 ctgtttcc
CTGTTYCC DREME-9 chr1 - 120176524 120176531 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr12 + 120647045 120647052 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr5 + 138337402 138337409 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr5 - 181169675 181169682 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr3 + 181329283 181329290 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr2 - 190302231 190302238 2.97e-05 0.213 CTGTTTCC
CTGTTYCC DREME-9 chr7 + 620395 620402 5.94e-05 0.329 ctgttgcc
CTGTTYCC DREME-9 chr17 + 3890329 3890336 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr17 - 21040150 21040157 5.94e-05 0.329 CTGTTACC
CTGTTYCC DREME-9 chr16 - 22279971 22279978 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr16 + 22280150 22280157 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr1 - 27116360 27116367 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr6 - 28896430 28896437 5.94e-05 0.329 CTGTTACC
CTGTTYCC DREME-9 chr19 + 35386191 35386198 5.94e-05 0.329 ctgttgcc
CTGTTYCC DREME-9 chr22 - 40711942 40711949 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr13 + 44917710 44917717 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr13 - 52194497 52194504 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr13 - 67224466 67224473 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr14 - 69716183 69716190 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr5 - 71946282 71946289 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr14 + 77091314 77091321 5.94e-05 0.329 CTGTTACC
CTGTTYCC DREME-9 chr17 + 82494616 82494623 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr10 + 86879514 86879521 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr10 - 88093124 88093131 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr4 + 88456953 88456960 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr6 + 90218780 90218787 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr8 - 94648232 94648239 5.94e-05 0.329 CTGTTACC
CTGTTYCC DREME-9 chr12 - 103957159 103957166 5.94e-05 0.329 CTGTTGCC
CTGTTYCC DREME-9 chr6 + 106829891 106829898 5.94e-05 0.329 ctgttacc
CTGTTYCC DREME-9 chr5 + 168477779 168477786 5.94e-05 0.329 ctgttgcc

DEBUGGING INFORMATION

Command line:

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_14 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif CTGTTYCC /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_14 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF418.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/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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