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/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 599 sequences, 299500 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GGAAMC 6 GGAACC
CCGCVGCC 8 CCGCCGCC

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/background):
A 0.187 C 0.313 G 0.313 T 0.187


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
CCGCVGCC DREME-2 chr19 + 1652566 1652573 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr16 + 1964879 1964886 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr16 - 3135316 3135323 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr11 + 3136859 3136866 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr3 + 9731414 9731421 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 + 12881241 12881248 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr3 + 14178320 14178327 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr3 - 15860216 15860223 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr10 + 17201650 17201657 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 - 17337218 17337225 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr10 - 21495763 21495770 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr10 - 21495827 21495834 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 23167719 23167726 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 23167804 23167811 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 - 27794059 27794066 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 - 29665532 29665539 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr16 - 29811567 29811574 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr16 + 31073444 31073451 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr4 - 31996538 31996545 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr21 + 32278785 32278792 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 32292301 32292308 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr20 - 34111915 34111922 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr20 - 34112110 34112117 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 - 35259847 35259854 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 - 35727943 35727950 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 + 35987334 35987341 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 - 36242239 36242246 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr13 + 36346491 36346498 5.48e-05 0.341 ccgcagcc
CCGCVGCC DREME-2 chr5 - 36690151 36690158 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr20 - 37095877 37095884 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 - 37371364 37371371 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 37989841 37989848 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 - 38244028 38244035 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr19 + 40090865 40090872 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 - 40587569 40587576 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 + 44246391 44246398 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr21 - 44299711 44299718 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr7 + 44796455 44796462 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr20 - 46689339 46689346 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chrX - 47233228 47233235 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr16 - 50369043 50369050 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr20 - 50790930 50790937 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 53220598 53220605 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr12 + 56725067 56725074 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr12 - 56725224 56725231 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 + 60700112 60700119 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 - 60700177 60700184 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr17 - 62652593 62652600 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr9 + 62838159 62838166 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr17 + 63842604 63842611 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr17 - 67245942 67245949 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr17 - 67245983 67245990 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr16 - 67872980 67872987 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr12 - 68808784 68808791 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr15 - 70097986 70097993 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr15 + 72117702 72117709 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr10 + 73096696 73096703 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr14 - 73714144 73714151 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chrX - 73944175 73944182 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chrX - 73944192 73944199 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr15 - 75368457 75368464 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr17 + 82065771 82065778 5.48e-05 0.341 ccgcagcc
CCGCVGCC DREME-2 chr16 - 85303755 85303762 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 86704764 86704771 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 + 90474559 90474566 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 + 91280661 91280668 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 + 91280675 91280682 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 95234182 95234189 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr15 - 99565878 99565885 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr15 - 99566062 99566069 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr14 - 102592243 102592250 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr7 + 114086399 114086406 5.48e-05 0.341 ccgcagcc
CCGCVGCC DREME-2 chr7 - 114086455 114086462 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr13 + 114131581 114131588 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 + 116100820 116100827 5.48e-05 0.341 CCGCAgcc
CCGCVGCC DREME-2 chr6 + 131628513 131628520 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr5 + 132830134 132830141 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr7 - 149422310 149422317 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 151790536 151790543 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 155244640 155244647 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 + 159727018 159727025 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 + 170502921 170502928 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr6 + 170502921 170502928 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr2 - 176136504 176136511 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 182604259 182604266 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 182604500 182604507 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr3 + 183884805 183884812 5.48e-05 0.341 ccgcagcc
CCGCVGCC DREME-2 chr1 + 184386838 184386845 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr3 + 184711670 184711677 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr3 + 194135087 194135094 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 + 200669955 200669962 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 212699682 212699689 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 212699688 212699695 5.48e-05 0.341 CCGCAGCC
CCGCVGCC DREME-2 chr1 - 224615967 224615974 5.48e-05 0.341 CCGCAGCC

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/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_4 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/background --motif CCGCVGCC /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/fimo_out_4 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out/dreme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResultsDefaultMax/ZSCAN30.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZSCAN30.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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