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/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CWTCMTCMTCATCMTC 16 CATCATCATCATCATC
GATGATGATGAKGAWG 16 GATGATGATGATGATG
CHTCHTCHTCHTCMTC 16 CATCATCATCATCATC
RTGRTGATGRTG 12 GTGATGATGATG
GARGARGARGARGARG 16 GAAGAGGAGGAGGAAG
TGATGRTGA 9 TGATGGTGA
YTCYTCYTCYTC 12 TTCCTCTTCCTC
AGGARGA 7 AGGAGGA
AYCAYCA 7 ACCATCA
AAAAGTAAAACTTGCT 16 AAAAGTAAAACTTGCT

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.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
AAAAGTAAAACTTGCT MEME-10 chr10 - 72918058 72918073 2.83e-10 2.35e-05 AAAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr5 - 93683241 93683256 2.83e-10 2.35e-05 AAAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr10 - 96189743 96189758 2.83e-10 2.35e-05 AAAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr2 - 197380100 197380115 2.83e-10 2.35e-05 AAAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr1 + 27207390 27207405 2.83e-10 2.35e-05 AAAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr11 + 62331404 62331419 2.83e-10 2.35e-05 AAAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr5 + 171392915 171392930 2.83e-10 2.35e-05 AAAAGTAAAACTtgct
AAAAGTAAAACTTGCT MEME-10 chr10 + 124867969 124867984 1.02e-08 0.000736 ACAAGTAAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr12 + 112507161 112507176 3.79e-06 0.244 AAAAGCAGAAGTTGCT
AAAAGTAAAACTTGCT MEME-10 chr15 - 89135663 89135678 1.43e-05 0.831 TAAAGGAAAGCCTGCT
AAAAGTAAAACTTGCT MEME-10 chr17 + 58476056 58476071 3.32e-05 0.841 aaaCCTGCAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr12 - 65855876 65855891 3.32e-05 0.841 AAAAGAAAAAACAGCT
AAAAGTAAAACTTGCT MEME-10 chr4 + 68337015 68337030 3.32e-05 0.841 AAAAGTAGTACCTGAT
AAAAGTAAAACTTGCT MEME-10 chr15 - 71252724 71252739 3.32e-05 0.841 AAAAGTTAAATGAGCT
AAAAGTAAAACTTGCT MEME-10 chr10 - 75390249 75390264 3.32e-05 0.841 AAAAGCAAAGCTGGGT
AAAAGTAAAACTTGCT MEME-10 chr9 - 84604224 84604239 3.32e-05 0.841 ACAAGAAAAACATTCT
AAAAGTAAAACTTGCT MEME-10 chr1 + 92074462 92074477 3.32e-05 0.841 AAGACTGCAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr2 + 113226402 113226417 3.32e-05 0.841 AAAATTGAGACTTGCC
AAAAGTAAAACTTGCT MEME-10 chr9 + 128694044 128694059 3.32e-05 0.841 aaaagaaAATTTGGCT
AAAAGTAAAACTTGCT MEME-10 chr10 - 7388518 7388533 4.23e-05 0.841 AAAAAAAAAATTAGCT
AAAAGTAAAACTTGCT MEME-10 chr10 + 7505212 7505227 4.23e-05 0.841 ACAAGTAAAAATTTCA
AAAAGTAAAACTTGCT MEME-10 chr6 - 10415265 10415280 4.23e-05 0.841 AAAGGGAAAAGTTTCT
AAAAGTAAAACTTGCT MEME-10 chr7 + 27705347 27705362 4.23e-05 0.841 agaaataaaatatgct
AAAAGTAAAACTTGCT MEME-10 chr6 + 43352124 43352139 4.23e-05 0.841 aagagcaaaacttcgt
AAAAGTAAAACTTGCT MEME-10 chr1 + 51840154 51840169 4.23e-05 0.841 AAAAATAAAGCTTGAG
AAAAGTAAAACTTGCT MEME-10 chr18 - 55589546 55589561 4.23e-05 0.841 ATAAGAAAAAGTTGTT
AAAAGTAAAACTTGCT MEME-10 chr15 - 81117537 81117552 4.23e-05 0.841 AAAAAAAAAAGTAGCT
AAAAGTAAAACTTGCT MEME-10 chr10 + 120507406 120507421 4.23e-05 0.841 AACAGTAAACATTTCT
AAAAGTAAAACTTGCT MEME-10 chr10 - 123380874 123380889 4.23e-05 0.841 AATTCTAAAACTTGTT
AAAAGTAAAACTTGCT MEME-10 chr10 + 7388167 7388182 4.35e-05 0.841 aaaacaaaaaattcct
AAAAGTAAAACTTGCT MEME-10 chr17 + 7563427 7563442 8.97e-05 1 CATCGAAAAACCTGCT
AAAAGTAAAACTTGCT MEME-10 chr6 + 32978136 32978151 8.97e-05 1 ACATGAACAACTGGCT
AAAAGTAAAACTTGCT MEME-10 chr7 - 42237771 42237786 8.97e-05 1 AAAAGTAAGGCGAGCA
AAAAGTAAAACTTGCT MEME-10 chr12 + 62950614 62950629 8.97e-05 1 catagtaatactggcc
AAAAGTAAAACTTGCT MEME-10 chr10 - 71420791 71420806 8.97e-05 1 GACTGCCAAACTTGCT
AAAAGTAAAACTTGCT MEME-10 chr15 + 78090797 78090812 8.97e-05 1 ccaaggaaatctggct
AAAAGTAAAACTTGCT MEME-10 chr17 + 78934370 78934385 8.97e-05 1 AGAAGGGAGACTGGCT
AAAAGTAAAACTTGCT MEME-10 chr10 + 123380570 123380585 8.97e-05 1 AGAAGGAAGCCTTGCC
AAAAGTAAAACTTGCT MEME-10 chr1 - 235214133 235214148 8.97e-05 1 ACACGTGGAACCTGCT

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/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_5 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif AAAAGTAAAACTTGCT /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_5 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF513.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF513.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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