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/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CYRGGCCTGTGATGGGAGGGGC 22 CTGGGCCTGTGATGGGAGGGGC
CCTCCTAGGCCT 12 CCTCCTAGGCCT
AAAAAATGGTTT 12 AAAAAATGGTTT
CTSTGTGCAGCCTHG 15 CTGTGTGCAGCCTAG
GGRCCCTGGGCCY 13 GGGCCCTGGGCCT
CYRGGCCTGTGATGGG 16 CTGGGCCTGTGATGGG
GGCACCAAGTCC 12 GGCACCAAGTCC
RTGGGCY 7 GTGGGCC
CTGCTBTGTGCAGYCT 16 CTGCTTTGTGCAGTCT
RCTGCCCTGCACMRCCTCAGGA 22 ACTGCCCTGCACAACCTCAGGA

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.257 C 0.243 G 0.243 T 0.257


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
RTGGGCY MEME-8 chr10 - 96700 96706 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr4 + 203020 203026 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr10 - 7692557 7692563 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr19 + 7757730 7757736 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr11 + 9189051 9189057 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 - 12222878 12222884 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr1 + 12563314 12563320 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 + 15306556 15306562 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr20 - 19064993 19064999 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr2 - 20021593 20021599 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr9 + 20276790 20276796 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 20542311 20542317 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr8 + 22391517 22391523 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr7 - 23795181 23795187 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr10 - 24765185 24765191 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr12 + 25707249 25707255 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr18 - 32897363 32897369 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr12 + 33017233 33017239 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr15 - 35487605 35487611 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr18 + 36038415 36038421 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 39303009 39303015 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr2 - 39359880 39359886 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr2 + 40021201 40021207 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 + 40882482 40882488 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr21 + 41995774 41995780 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr21 + 44791367 44791373 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 + 45258239 45258245 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr22 - 45463879 45463885 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr19 + 49288421 49288427 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr13 + 50233741 50233747 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr12 + 50833974 50833980 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr13 + 52016491 52016497 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr15 - 55257299 55257305 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr14 + 55312796 55312802 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr12 - 55570231 55570237 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr15 - 56014876 56014882 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 + 56628842 56628848 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr19 - 57374395 57374401 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 - 58467420 58467426 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr17 - 69698544 69698550 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr13 + 72693085 72693091 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr2 - 73530964 73530970 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr2 - 73638603 73638609 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr2 - 73698271 73698277 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr17 - 74488927 74488933 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr1 - 75484977 75484983 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr15 + 75742512 75742518 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 76643793 76643799 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr14 + 77947539 77947545 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr11 + 78272829 78272835 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 - 78387050 78387056 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr15 - 78524439 78524445 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 - 80463464 80463470 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr17 + 81012723 81012729 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 82782184 82782190 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 + 82931000 82931006 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 + 82942543 82942549 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 - 83348574 83348580 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr6 - 84489791 84489797 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 - 86768989 86768995 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr1 - 86924756 86924762 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr10 + 87887795 87887801 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 + 88856580 88856586 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr12 + 89786367 89786373 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr11 - 91783352 91783358 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr11 + 91783384 91783390 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr12 + 94017429 94017435 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr9 + 94128790 94128796 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr13 - 96198242 96198248 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr3 - 99805351 99805357 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr1 - 101040825 101040831 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 - 103721403 103721409 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr14 + 103984364 103984370 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr14 - 104066927 104066933 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr7 + 104198853 104198859 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 - 105409922 105409928 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr6 + 105409954 105409960 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr7 - 105712200 105712206 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr12 + 107096693 107096699 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 - 108132573 108132579 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 + 109551446 109551452 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 - 113718812 113718818 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr10 + 115105596 115105602 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 + 115167082 115167088 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 - 115167197 115167203 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr8 + 116721137 116721143 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 116975712 116975718 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr11 - 117398798 117398804 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 - 118657791 118657797 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr11 + 120618606 120618612 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr11 + 120618710 120618716 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr7 - 121285270 121285276 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr7 + 124958151 124958157 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr4 + 125423317 125423323 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 125883371 125883377 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 - 128768388 128768394 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr3 - 129697424 129697430 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr2 - 135453236 135453242 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr6 - 136832357 136832363 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 - 137381727 137381733 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr9 - 137703175 137703181 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr6 + 139234403 139234409 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr8 + 140398921 140398927 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 - 143385213 143385219 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr7 + 144427725 144427731 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 + 146965318 146965324 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 - 146965410 146965416 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr1 + 151362544 151362550 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 + 151417924 151417930 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr4 + 151946990 151946996 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 153049296 153049302 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chrX + 153358085 153358091 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr6 + 159848742 159848748 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr5 - 172032070 172032076 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr3 - 172242654 172242660 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr5 + 174498802 174498808 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 - 180959787 180959793 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr3 + 181510707 181510713 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr4 + 186191153 186191159 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr2 + 197573755 197573761 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr2 + 204412982 204412988 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 + 220249705 220249711 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr2 - 220926458 220926464 5.29e-05 0.246 GTGGGCC
RTGGGCY MEME-8 chr1 + 225177561 225177567 5.29e-05 0.246 gtgggcc
RTGGGCY MEME-8 chr1 - 231686563 231686569 5.29e-05 0.246 GTGGGCC

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/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_8 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif RTGGGCY /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_8 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF585B.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF585B.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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