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/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 600 sequences, 300000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CTTYAYCC 8 CTTCATCC
AGYTTSCC 8 AGCTTCCC
ACAGCAYA 8 ACAGCATA
CTGTRY 6 CTGTGT
RAGACCCA 8 AAGACCCA
AATGTHAA 8 AATGTAAA
CCAATTAA 8 CCAATTAA
TCTYACA 7 TCTTACA
RGCATTTA 8 GGCATTTA
TRTCAAAA 8 TATCAAAA
CCABTGG 7 CCATTGG
CTCTTGAA 8 CTCTTGAA
ATCTTGCM 8 ATCTTGCA
CCAGGAWA 8 CCAGGAAA
GGTACA 6 GGTACA
ACTATAG 7 ACTATAG
TGCAAARA 8 TGCAAAGA
GGGGAGRC 8 GGGGAGGC
AAGGTTAR 8 AAGGTTAG
CAATRTCA 8 CAATATCA
AAATGKGC 8 AAATGGGC
CTCTGTC 7 CTCTGTC

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.301 C 0.199 G 0.199 T 0.301


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
TRTCAAAA DREME-10 chr20 + 646756 646763 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr7 + 1688982 1688989 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr1 + 10087409 10087416 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr16 + 16571102 16571109 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr10 + 23101941 23101948 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr1 + 24251699 24251706 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr7 + 37231589 37231596 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr22 + 37436421 37436428 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr20 + 38458536 38458543 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr19 + 41815508 41815515 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr8 + 53998378 53998385 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr12 + 57866526 57866533 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr10 + 70648849 70648856 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr5 + 76165261 76165268 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr4 + 89516812 89516819 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr4 + 102604427 102604434 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr8 + 108301172 108301179 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr12 + 110870025 110870032 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr5 + 112660332 112660339 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr10 + 112875211 112875218 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr7 + 113953596 113953603 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr12 + 114041687 114041694 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr12 + 114043070 114043077 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr10 + 114649395 114649402 2.94e-05 0.317 tgtcAaaa
TRTCAAAA DREME-10 chrX + 123770369 123770376 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr9 + 132144917 132144924 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chrX + 150813466 150813473 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr6 + 151377235 151377242 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr3 + 189069440 189069447 2.94e-05 0.317 tgtcaaaa
TRTCAAAA DREME-10 chr1 - 14539453 14539460 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr16 - 15229783 15229790 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chrX - 15960415 15960422 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr8 - 18711483 18711490 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr14 - 21199967 21199974 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr1 - 29379656 29379663 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr6 - 36169774 36169781 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr19 - 46887403 46887410 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chrX - 47163344 47163351 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr18 - 55219982 55219989 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr2 - 68470681 68470688 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr4 - 75040646 75040653 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr14 - 77247174 77247181 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr17 - 78558346 78558353 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr6 - 81386531 81386538 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr14 - 92608224 92608231 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr15 - 101946125 101946132 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr10 - 103047535 103047542 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr12 - 106333175 106333182 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr12 - 107641317 107641324 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr12 - 123053386 123053393 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr5 - 142411148 142411155 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chrX - 150813477 150813484 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr1 - 204667259 204667266 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr2 - 234292890 234292897 2.94e-05 0.317 TGTCAAAA
TRTCAAAA DREME-10 chr11 + 1134933 1134940 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr12 + 2405262 2405269 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr19 + 12261751 12261758 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr16 + 19348341 19348348 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr10 + 21725100 21725107 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr22 + 27153112 27153119 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr22 + 29390252 29390259 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr17 + 30002302 30002309 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr6 + 32158279 32158286 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr4 + 39678015 39678022 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr7 + 46181492 46181499 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr13 + 46311452 46311459 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr17 + 47164491 47164498 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr1 + 47976937 47976944 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr10 + 52007270 52007277 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr17 + 58832731 58832738 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr3 + 61646572 61646579 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr17 + 66935960 66935967 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr11 + 73611455 73611462 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr18 + 74299379 74299386 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr14 + 76582695 76582702 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr14 + 77247002 77247009 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr1 + 82079833 82079840 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr7 + 98158077 98158084 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr5 + 103249317 103249324 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr11 + 119412255 119412262 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr12 + 120051746 120051753 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr8 + 130208202 130208209 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr3 + 130739924 130739931 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr3 + 161266516 161266523 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr1 + 207994274 207994281 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chr2 + 224421384 224421391 7.38e-05 0.401 tatcaaaa
TRTCAAAA DREME-10 chrUn_KI270466v1 - 359 366 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr20 - 3400397 3400404 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr1 - 15142292 15142299 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr2 - 20307451 20307458 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr22 - 26703465 26703472 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr15 - 29593975 29593982 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr6 - 33767099 33767106 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr7 - 37231770 37231777 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr14 - 54711481 54711488 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr3 - 55345667 55345674 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr2 - 62402320 62402327 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr3 - 67609885 67609892 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr7 - 72609028 72609035 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr13 - 72680539 72680546 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr4 - 85175306 85175313 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr6 - 100599549 100599556 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr15 - 101945903 101945910 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr5 - 135362082 135362089 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr1 - 164967345 164967352 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr4 - 187366244 187366251 7.38e-05 0.401 TATCAAAA
TRTCAAAA DREME-10 chr1 - 213180985 213180992 7.38e-05 0.401 TATCAAAA

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/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_28 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif TRTCAAAA /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_28 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/dreme_out/dreme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF529.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF529.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.


Go to top