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/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
AAAGAYAT 8 AAAGACAT
ATYTGTR 7 ATCTGTG
CAAGHAG 7 CAAGAAG
AAWTTTGG 8 AAATTTGG
ATRTGTRG 8 ATATGTAG
ATTATYTC 8 ATTATTTC
TATTTGAA 8 TATTTGAA
ATGAMAGR 8 ATGAAAGA
AAAACTYC 8 AAAACTTC
ATAAACHC 8 ATAAACTC
GAADCTCA 8 GAAGCTCA
AATRGCTG 8 AATGGCTG
AACTGATG 8 AACTGATG
AACTCYAA 8 AACTCCAA
GGCCAARA 8 GGCCAAAA

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.314 C 0.186 G 0.186 T 0.314


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
ATTATYTC DREME-6 chr5 + 452098 452105 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr16 + 2357578 2357585 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr18 - 2815101 2815108 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr4 + 2856545 2856552 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 + 3231061 3231068 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 - 4112391 4112398 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr20 + 4352599 4352606 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr20 - 4578744 4578751 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr3 + 5155466 5155473 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr19 - 8815942 8815949 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr3 + 14222097 14222104 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr16 - 14223802 14223809 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr3 + 14750866 14750873 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr19 - 15104137 15104144 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr10 + 15705224 15705231 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr11 - 17404289 17404296 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 - 18049391 18049398 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 - 18049407 18049414 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr20 - 18331850 18331857 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr9 - 18896163 18896170 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr16 - 20706152 20706159 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr18 - 21032056 21032063 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr22 + 24024585 24024592 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 + 24740799 24740806 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 - 25205784 25205791 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr13 + 26596705 26596712 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr13 + 26596776 26596783 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr9 - 26937801 26937808 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr9 - 26937985 26937992 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr7 - 29906622 29906629 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr19 + 29936630 29936637 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr19 - 30180835 30180842 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr15 + 31012679 31012686 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr21 - 32167676 32167683 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr14 + 32209816 32209823 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr21 + 32716710 32716717 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr9 + 34712362 34712369 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr19 - 36647147 36647154 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr21 + 36681488 36681495 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr8 + 37457280 37457287 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 + 38102998 38103005 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr20 + 38116985 38116992 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr17 + 38315728 38315735 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr3 + 38387208 38387215 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr22 + 38810171 38810178 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr20 + 41198757 41198764 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr20 - 41479271 41479278 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 + 41957174 41957181 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr4 + 42379278 42379285 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 - 42545123 42545130 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr10 - 42545230 42545237 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr10 - 42917155 42917162 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr19 - 44255872 44255879 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr21 + 45401483 45401490 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr1 + 45821361 45821368 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr12 - 46046628 46046635 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr10 + 46170044 46170051 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr19 + 46380933 46380940 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chrX + 46989767 46989774 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr17 + 50009514 50009521 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr18 + 50534048 50534055 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 - 55803204 55803211 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 + 57165289 57165296 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr14 - 58415792 58415799 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr20 + 58531450 58531457 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 - 63600684 63600691 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 + 64987992 64987999 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr2 - 68757255 68757262 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr14 + 68801837 68801844 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 + 69272878 69272885 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr15 + 69777581 69777588 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr15 + 69777746 69777753 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr6 + 71465477 71465484 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr15 + 72438131 72438138 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 - 73306285 73306292 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 73334774 73334781 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr17 - 73621717 73621724 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr17 - 73621875 73621882 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chrX + 74339064 74339071 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr11 + 75052647 75052654 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 - 75312567 75312574 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr9 + 75889669 75889676 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr15 - 76003525 76003532 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr9 + 79847293 79847300 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 + 80296930 80296937 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr10 - 80297082 80297089 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr1 - 81489554 81489561 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr17 - 82609807 82609814 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr10 - 83357158 83357165 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 84771413 84771420 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 84771554 84771561 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr15 + 85132267 85132274 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr9 + 86573157 86573164 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr15 + 89611546 89611553 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr7 + 95458198 95458205 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr9 + 97403924 97403931 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr2 - 100163609 100163616 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr13 - 102659305 102659312 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr12 + 106217942 106217949 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr1 - 109937323 109937330 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr12 + 109977834 109977841 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr9 + 114044017 114044024 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr1 - 114479252 114479259 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 + 115345561 115345568 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr12 + 115555937 115555944 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr12 + 117013994 117014001 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr12 - 119745049 119745056 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 120192426 120192433 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 121011155 121011162 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr8 + 123308359 123308366 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr2 + 126817381 126817388 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr6 + 128616586 128616593 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chrX - 130658707 130658714 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr9 + 134076792 134076799 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr11 - 134132026 134132033 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 - 134982272 134982279 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 - 134982287 134982294 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr3 + 136281194 136281201 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr6 + 139341314 139341321 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr8 + 144031676 144031683 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr4 + 144399977 144399984 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr8 - 144741930 144741937 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 144749346 144749353 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr2 - 148007659 148007666 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr6 - 163768887 163768894 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 - 172760261 172760268 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 - 172760300 172760307 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr5 + 174785509 174785516 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr3 - 185830564 185830571 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr3 - 193416804 193416811 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr1 - 221331672 221331679 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr1 - 227987339 227987346 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr1 + 229685373 229685380 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr1 - 236779368 236779375 5.58e-05 0.244 ATTATTTC
ATTATYTC DREME-6 chr1 + 244401161 244401168 5.58e-05 0.244 attatttc
ATTATYTC DREME-6 chr7 + 316737 316744 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr7 - 316851 316858 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr17 - 683228 683235 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr18 - 2687409 2687416 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr5 - 4786365 4786372 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr18 - 26071175 26071182 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr17 - 29034818 29034825 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr22 + 32294302 32294309 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr19 + 33898207 33898214 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr19 + 33898383 33898390 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr19 + 33898536 33898543 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr20 - 34237902 34237909 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr20 + 36282940 36282947 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr20 + 41479191 41479198 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr20 + 46660703 46660710 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr12 + 50800226 50800233 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr5 + 56420531 56420538 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr15 - 57152771 57152778 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr17 - 58989823 58989830 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr10 - 60711662 60711669 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr17 + 62531167 62531174 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr10 - 63600629 63600636 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr15 + 67905887 67905894 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr15 + 68444548 68444555 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr5 - 73346868 73346875 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr15 + 85131965 85131972 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr1 - 90675586 90675593 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr7 + 95458283 95458290 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr6 - 110089506 110089513 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr9 - 112712941 112712948 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr7 + 128586938 128586945 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr5 + 132621913 132621920 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr2 - 150791743 150791750 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr5 - 158297332 158297339 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr5 - 158297516 158297523 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr6 + 159730019 159730026 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr6 + 163683303 163683310 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr6 + 163683333 163683340 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr3 - 196866311 196866318 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr2 + 202939205 202939212 8.89e-05 0.296 attatctc
ATTATYTC DREME-6 chr1 - 221331909 221331916 8.89e-05 0.296 ATTATCTC
ATTATYTC DREME-6 chr2 + 237907377 237907384 8.89e-05 0.296 attatctc

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/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_15 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif ATTATYTC /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_15 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF558.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF558.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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