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/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CARGAARA 8 CAAGAAGA
RGACAAGA 8 GGACAAGA
ATKAGG 6 ATGAGG
AGRGTGAG 8 AGGGTGAG
THAATAAA 8 TCAATAAA
CAVTTGTC 8 CAGTTGTC
ATYCTTC 7 ATTCTTC
CNTGGGAC 8 CTTGGGAC
RGGCAGA 7 AGGCAGA
ACTCRGGA 8 ACTCAGGA
ARGGTGRA 8 AGGGTGGA
CACDGACA 8 CACAGACA
ATGCWGAC 8 ATGCTGAC
GAACAGC 7 GAACAGC
CTCAGTAA 8 CTCAGTAA
GCTCCTY 7 GCTCCTC
CCACCRAA 8 CCACCAAA
TCAGCTAR 8 TCAGCTAG
GACRC 5 GACAC
ATGYG 5 ATGTG
CATGTM 6 CATGTC
GGTACM 6 GGTACA
CRTGAGAC 8 CATGAGAC

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.252 C 0.248 G 0.248 T 0.252

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
RGGCAGA DREME-9 chr5 - 342616 342622 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chrX - 984344 984350 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr16 - 4244019 4244025 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr9 - 6708957 6708963 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 8939336 8939342 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr12 - 8956083 8956089 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr3 - 9619612 9619618 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr10 - 11730393 11730399 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr10 - 11730533 11730539 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr9 - 12958628 12958634 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr12 - 13317036 13317042 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 13827347 13827353 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr11 - 15378670 15378676 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr21 - 17191305 17191311 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr8 - 17748357 17748363 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr7 - 20529123 20529129 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr22 - 24038618 24038624 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr12 - 24803199 24803205 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr2 - 30497873 30497879 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr19 - 32638407 32638413 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr11 - 32704920 32704926 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr19 - 32937216 32937222 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr8 - 33659713 33659719 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr19 - 36710916 36710922 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr21 - 36959777 36959783 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr13 - 38086563 38086569 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 38801737 38801743 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr19 - 38862227 38862233 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr14 - 39441739 39441745 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chrX - 40810217 40810223 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 41162680 41162686 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr17 - 41678401 41678407 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr22 - 41683985 41683991 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr19 - 42378364 42378370 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr13 - 44459470 44459476 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chrX - 44976228 44976234 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr13 - 48551526 48551532 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr16 - 49680325 49680331 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 51060370 51060376 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 - 51867634 51867640 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr19 - 54449061 54449067 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr10 - 56317436 56317442 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 - 61670734 61670740 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr10 - 62465701 62465707 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr13 - 67107508 67107514 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr15 - 70089151 70089157 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 - 73037038 73037044 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr11 - 74261239 74261245 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr5 - 74430318 74430324 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr13 - 74923150 74923156 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr18 - 75483831 75483837 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr16 - 79808588 79808594 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr12 - 84032950 84032956 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr5 - 85368751 85368757 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr9 - 85744377 85744383 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr10 - 89020654 89020660 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 89073363 89073369 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 90433974 90433980 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr9 - 91327575 91327581 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr14 - 103162184 103162190 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chrX - 105050537 105050543 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr7 - 107360191 107360197 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr7 - 107360316 107360322 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr7 - 108580095 108580101 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 124978911 124978917 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 125143202 125143208 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr9 - 125529796 125529802 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 132876994 132877000 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 - 132877175 132877181 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chrX - 135917569 135917575 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr5 - 141681533 141681539 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr5 - 141681688 141681694 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr5 - 141681806 141681812 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 - 142336174 142336180 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr2 - 146720964 146720970 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 152477458 152477464 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 - 152752162 152752168 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr2 - 177834141 177834147 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 217969156 217969162 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr2 - 220192796 220192802 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 233066151 233066157 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 - 238745097 238745103 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 + 2981435 2981441 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr19 + 5533532 5533538 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr17 + 8040446 8040452 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 9031251 9031257 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr8 + 11169198 11169204 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr9 + 12958497 12958503 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr21 + 15743392 15743398 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr7 + 17101553 17101559 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 17790410 17790416 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 21036119 21036125 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr18 + 21863423 21863429 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr12 + 30470638 30470644 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 30498295 30498301 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr12 + 31362823 31362829 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr7 + 32948635 32948641 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr5 + 33041077 33041083 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr3 + 33467679 33467685 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr22 + 33619325 33619331 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr10 + 33637613 33637619 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr15 + 36067442 36067448 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr15 + 36328956 36328962 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chrX + 39060787 39060793 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr22 + 40753781 40753787 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 40967070 40967076 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 41288478 41288484 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 42513198 42513204 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 45541518 45541524 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr12 + 45696654 45696660 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr22 + 47167595 47167601 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr17 + 49017076 49017082 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr2 + 54121144 54121150 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 54393361 54393367 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr19 + 54448995 54449001 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr6 + 54667628 54667634 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr17 + 54836605 54836611 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr17 + 54836629 54836635 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr18 + 55789634 55789640 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 61670608 61670614 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 62072763 62072769 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr13 + 64075530 64075536 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr13 + 64075761 64075767 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr10 + 65581790 65581796 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 69895521 69895527 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr7 + 69911548 69911554 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr15 + 73892141 73892147 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr15 + 74882647 74882653 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 77474552 77474558 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chrX + 78810904 78810910 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 81439905 81439911 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr9 + 83128860 83128866 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 84585526 84585532 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 85140788 85140794 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr9 + 86125812 86125818 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 90434216 90434222 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr1 + 98650668 98650674 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chrX + 105050847 105050853 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr3 + 105759082 105759088 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr3 + 105759152 105759158 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 105933976 105933982 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr11 + 108628918 108628924 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 110138578 110138584 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 112979640 112979646 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 112979710 112979716 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 113423143 113423149 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr10 + 119748527 119748533 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr3 + 120507044 120507050 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr10 + 120989617 120989623 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 123436205 123436211 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr8 + 123754749 123754755 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 124978836 124978842 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 125453569 125453575 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr9 + 125529872 125529878 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr10 + 125567948 125567954 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 125952753 125952759 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr7 + 127608662 127608668 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr9 + 129032306 129032312 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr6 + 130749686 130749692 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr3 + 133487007 133487013 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chrX + 135669095 135669101 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chrX + 140560779 140560785 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr4 + 142336356 142336362 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr7 + 148672039 148672045 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr7 + 151958814 151958820 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr7 + 158707748 158707754 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 169997688 169997694 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 170923850 170923856 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 177834325 177834331 6.05e-05 0.2 AGGCAGA
RGGCAGA DREME-9 chr4 + 180866651 180866657 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 209615971 209615977 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr2 + 216425665 216425671 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 221309081 221309087 6.05e-05 0.2 aggcaga
RGGCAGA DREME-9 chr1 + 232013953 232013959 6.05e-05 0.2 aggcaga
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/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_33 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif RGGCAGA /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings: 


  

    output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_33
    MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml
    sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF680.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
  
  

    background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF680.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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