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/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CVGCCGGC 8 CGGCCGGC
RTCTCAAA 8 GTCTCAAA
AAATAAAT 8 AAATAAAT
ACAGAGY 7 ACAGAGC
CACGTGAC 8 CACGTGAC
AGSTGA 6 AGCTGA
ATGGMG 6 ATGGAG
GCCGGTK 7 GCCGGTG

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/background):
A 0.197 C 0.303 G 0.303 T 0.197


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
RTCTCAAA DREME-2 chrUn_GL000224v1 - 3747 3754 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr1 + 6404702 6404709 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr16 - 12062173 12062180 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr16 + 12062371 12062378 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr11 + 13200706 13200713 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr6 + 17217011 17217018 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr6 - 17217158 17217165 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr16 - 21821024 21821031 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr16 - 22295530 22295537 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr1 + 22980205 22980212 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chrX + 23771947 23771954 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chrX - 24144214 24144221 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr16 + 27663212 27663219 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr16 - 27663457 27663464 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr16 - 28974486 28974493 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr19 + 29505920 29505927 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr16 + 30052691 30052698 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr16 - 30570767 30570774 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr5 - 32157772 32157779 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr5 + 32157972 32157979 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr5 + 32158085 32158092 8.27e-06 0.0689 GTCTCAaa
RTCTCAAA DREME-2 chr5 - 32367228 32367235 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr19 + 33123066 33123073 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr9 + 33474670 33474677 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr19 + 33534695 33534702 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr19 + 35289809 35289816 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr1 - 35380342 35380349 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr17 - 35763691 35763698 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr17 + 35763891 35763898 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr22 - 36088735 36088742 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr21 - 36123008 36123015 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr21 + 36123182 36123189 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr1 - 36159071 36159078 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr5 + 36644006 36644013 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr19 + 37160336 37160343 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr17 + 38667233 38667240 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr19 + 39126180 39126187 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr19 + 40346437 40346444 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr19 + 40567291 40567298 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr20 - 43667893 43667900 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr19 - 43709421 43709428 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr19 + 43709683 43709690 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chrX - 45011800 45011807 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr20 + 45349379 45349386 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr20 - 45349528 45349535 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr18 - 48873779 48873786 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr18 + 48873980 48873987 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr4 + 49510237 49510244 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr18 - 49515227 49515234 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr5 + 55463630 55463637 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr12 - 56219809 56219816 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr12 + 56220011 56220018 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr10 - 72580491 72580498 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr15 + 78404983 78404990 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr12 + 96428773 96428780 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr10 + 101751966 101751973 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr10 - 101752212 101752219 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr12 - 110364365 110364372 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr12 - 110364742 110364749 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr1 - 113113577 113113584 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr7 + 115740196 115740203 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr5 + 122696844 122696851 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr11 - 126211552 126211559 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chr9 + 137038601 137038608 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chrX + 153937190 153937197 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr5 + 160008844 160008851 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr4 + 190112100 190112107 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr1 + 204720636 204720643 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr1 + 204720959 204720966 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr1 + 223187049 223187056 8.27e-06 0.0689 gtctcaaa
RTCTCAAA DREME-2 chr1 - 230626508 230626515 8.27e-06 0.0689 GTCTCAAA
RTCTCAAA DREME-2 chrUn_KI270467v1 - 2221 2228 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr5 + 1917586 1917593 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr16 + 5034064 5034071 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr6 - 17217221 17217228 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr19 - 18106585 18106592 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr16 + 21572537 21572544 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr1 - 22980354 22980361 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr19 - 31204166 31204173 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr5 + 32367430 32367437 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr19 - 33159125 33159132 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr19 - 33821511 33821518 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr17 - 39451572 39451579 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr19 - 40346541 40346548 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr12 - 48866627 48866634 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr18 + 49506598 49506605 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr15 - 70866162 70866169 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr15 - 75217795 75217802 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr15 - 75217975 75217982 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr10 - 113077715 113077722 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chrX + 115644592 115644599 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr4 + 141686290 141686297 1.36e-05 0.0868 atctcaaa
RTCTCAAA DREME-2 chr1 - 213016021 213016028 1.36e-05 0.0868 ATCTCAAA
RTCTCAAA DREME-2 chr1 - 3900903 3900910 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr3 - 9938953 9938960 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr16 - 14297423 14297430 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr17 - 26603802 26603809 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr19 + 32058509 32058516 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chr10 + 35686299 35686306 2.73e-05 0.147 ttctcaaa
RTCTCAAA DREME-2 chr22 + 36089001 36089008 2.73e-05 0.147 ctctcaaa
RTCTCAAA DREME-2 chr19 - 37506851 37506858 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chr19 - 37507036 37507043 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chr11 + 65712155 65712162 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr15 - 69128262 69128269 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr17 + 75456556 75456563 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chr11 - 114060417 114060424 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chr10 - 114649484 114649491 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chrX - 115644744 115644751 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chrX + 130516194 130516201 2.73e-05 0.147 TTCTCAAA
RTCTCAAA DREME-2 chr5 + 160009000 160009007 2.73e-05 0.147 CTCTCAAA
RTCTCAAA DREME-2 chr16 - 14297463 14297470 6.53e-05 0.276 GTCTTAAA
RTCTCAAA DREME-2 chrX - 24144030 24144037 6.53e-05 0.276 GTCTAAAA
RTCTCAAA DREME-2 chr17 - 26603816 26603823 6.53e-05 0.276 GTTTCAAA
RTCTCAAA DREME-2 chr11 - 32584192 32584199 6.53e-05 0.276 GTCTAAAA
RTCTCAAA DREME-2 chr10 - 35685905 35685912 6.53e-05 0.276 GTTTCAAA
RTCTCAAA DREME-2 chr12 - 48106239 48106246 6.53e-05 0.276 GTCTTAAA
RTCTCAAA DREME-2 chr17 - 49368662 49368669 6.53e-05 0.276 GTTTCAAA
RTCTCAAA DREME-2 chr17 - 50708026 50708033 6.53e-05 0.276 GTCTAAAA
RTCTCAAA DREME-2 chr15 - 78405043 78405050 6.53e-05 0.276 GTGTCAAA
RTCTCAAA DREME-2 chr3 - 122793876 122793883 6.53e-05 0.276 GTATCAAA
RTCTCAAA DREME-2 chrX - 153936991 153936998 6.53e-05 0.276 GTCTTAAA
RTCTCAAA DREME-2 chrX - 153937451 153937458 6.53e-05 0.276 GTCTTAAA
RTCTCAAA DREME-2 chr1 - 223186820 223186827 6.53e-05 0.276 GTTTCAAA
RTCTCAAA DREME-2 chr1 - 223993222 223993229 6.53e-05 0.276 GTTTCAAA
RTCTCAAA DREME-2 chr16 + 46718 46725 6.53e-05 0.276 gtcttaaa
RTCTCAAA DREME-2 chr12 + 4538372 4538379 6.53e-05 0.276 GTCTGAAA
RTCTCAAA DREME-2 chr6 + 17217126 17217133 6.53e-05 0.276 gtttcaaa
RTCTCAAA DREME-2 chr17 + 17591532 17591539 6.53e-05 0.276 GTCTAAAA
RTCTCAAA DREME-2 chr10 + 22325983 22325990 6.53e-05 0.276 GTCTAAAA
RTCTCAAA DREME-2 chr1 + 35641782 35641789 6.53e-05 0.276 GTGTCAAA
RTCTCAAA DREME-2 chr19 + 35882147 35882154 6.53e-05 0.276 gtctaaaa
RTCTCAAA DREME-2 chr17 + 39182695 39182702 6.53e-05 0.276 gtctAaaa
RTCTCAAA DREME-2 chr19 + 40567345 40567352 6.53e-05 0.276 GTCTTAAA
RTCTCAAA DREME-2 chr1 + 50968375 50968382 6.53e-05 0.276 GTCTTAAA
RTCTCAAA DREME-2 chrX + 53421957 53421964 6.53e-05 0.276 GTCTGAAA
RTCTCAAA DREME-2 chr9 + 128947793 128947800 6.53e-05 0.276 GTGTCAAA
RTCTCAAA DREME-2 chr5 + 157669399 157669406 6.53e-05 0.276 gtcttaaa
RTCTCAAA DREME-2 chr3 + 158801819 158801826 6.53e-05 0.276 GTCTGAAA
RTCTCAAA DREME-2 chr5 + 159263238 159263245 6.53e-05 0.276 GTTTCAAA
RTCTCAAA DREME-2 chr1 + 213015957 213015964 6.53e-05 0.276 GTCTTAAA

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/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_15 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/background --motif RTCTCAAA /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_15 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF704.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/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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