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/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
Database contains 598 sequences, 299000 residues

MOTIFS /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CACACACASACACACA 16 CACACACACACACACA
KGKRWKGRTGDDKGDGWKGRTG 22 TGTGAGGATGGGGGTGAGGATG
TGTGTGTGTGTG 12 TGTGTGTGTGTG
AYCAYCAYCATCAYCAYCAYYAY 23 ATCATCACCATCACCATCATCAC
GTGTGTG 7 GTGTGTG
CATCHHYMYMWCCATC 16 CATCACTCTCTCCATC
AATGGAATGGAATGGAAT 18 AATGGAATGGAATGGAAT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC 43 AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACTGGGCCC
CATCCATCC 9 CATCCATCC
ACACASASA 9 ACACACAGA

Random model letter frequencies (/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background):
A 0.260 C 0.240 G 0.240 T 0.260


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr14 + 103204911 103204953 1.2e-26 6.59e-21 agtgcactcagacccagtggattaacatccaaaaactgggccc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 + 37365145 37365187 4.63e-26 1.27e-20 agtgcactcagacccagaggattaacatccaaaaactgggccc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr13 - 41148842 41148884 8.15e-24 1.49e-18 AGTGCACTCAGACCCAGTGGATTTACATCCAAAATTCGGGCCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr4 + 25223942 25223984 1.13e-23 1.55e-18 agtgcactcagaaccagcagattaacatccgaaaactgggccc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr22 - 19316863 19316905 8.51e-23 9.32e-18 AGTGCACTCTGGCCTAGTGGATTAACATCCAAAGACCGGGCCT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr21 + 38229460 38229502 2.55e-14 2.33e-09 agtgtgctcaggcccagcagattaacaaccaaaggctgagtcc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr8 + 43124576 43124618 9.76e-11 7.63e-06 agtgcactcagacccagctgataacattcaaaaactgggccca
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr17 - 81170400 81170442 6.83e-07 0.0467 AGGCCAGACTGGAGCAGGGGGTCCTAATGCAATGACTGGGGCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr5 + 11240943 11240985 1.61e-06 0.0981 tgagcacacacacccaatacatatacacccacatcatgcacac
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 - 228782455 228782497 2.89e-06 0.158 AGACCACACACACACAGACCATGTACACACACAGACCATACAC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr16 - 57628709 57628751 4.27e-06 0.213 TCAGGATCCACCCCCAGAGGCTTAACCTGCCAGCCCTGGTCCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 + 29672100 29672142 5.97e-06 0.272 agaaaacacacaagcaatgaatagacaagcaaacagcaggtcc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 - 223629244 223629286 8.55e-06 0.36 AGACCACGCAGAGCCAGCTCTTCATTATCCAAGGTCAGGAGGG
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr20 + 31067187 31067229 9.61e-06 0.376 aatggaatcaacaccagtggaatgaaatggaaaggagcggaat
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 11374451 11374493 1.23e-05 0.436 agtgCTCTCTGGCCAGGTGCAATCTCCTTCCTGTTCAGCTCCT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr3 - 24265059 24265101 1.27e-05 0.436 AGTCTACTGATGGCTAACCCTTTTTTATCCAAAGGTCAGTTCT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr8 - 143598352 143598394 1.44e-05 0.465 GGTGCACTCGGGCCCGTAGATCTGGCGCGCGAAGGCCTCGGCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr20 + 44188724 44188766 1.62e-05 0.484 TGATAACTTAGGCCACGTGAAGTCACTGCGGAAGTCTTGTTCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr3 - 99868616 99868658 1.75e-05 0.484 AGAGCACCCAAACTGTAAGTTTAAAAACCCATTATTTGGCCTT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 33364501 33364543 1.77e-05 0.484 AGTCACCTCTGCCCAGGGAACTGTATAGCCCAAGACAGGTGCT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr17_KI270729v1_random + 24250 24292 2.66e-05 0.661 aatggaatcaacccgagtggaatggaatgcaatggcatggaat
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 225707025 225707067 2.71e-05 0.661 GGTGCTTAAAAAGCTTACACAGTAACCTCCAAGGACCAGGTTT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 - 1524838 1524880 2.78e-05 0.661 ACAATACCCAGACACAGCACAGGAACACACAAACACATGAACA
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 - 41936729 41936771 3.95e-05 0.887 AAGTCACACTGATACAGACACACACCACACAAAAATGCTGCCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr2 - 171631507 171631549 4.34e-05 0.887 TAGGTGCACCAGCTCAGCGGATTTGCATCCAGAAGGCTGAGAC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 + 58182304 58182346 4.55e-05 0.887 AGAGCACCCTGGGCCCAAGGATGGGTGGCACACACCAGGTCCT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 25768969 25769011 4.63e-05 0.887 actacacacactcccctcacatatacatacactacacactccc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 - 234247493 234247535 4.93e-05 0.887 ACTGAACAATGGACCATCCAATCAACCTACTGAACAATGGACC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 - 1524702 1524744 5.08e-05 0.887 CAAACACACAAGCACACCACATGAACACACAACACCCAGACAC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 + 41916502 41916544 5.1e-05 0.887 ATCTCACACAGAAACAAAGACACAAAATCACAAATCCTAGACA
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr22 + 23954785 23954827 5.23e-05 0.887 agttcactcacatcacacacatatacacccacacataaacaca
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr12 + 132156509 132156551 5.33e-05 0.887 actacacacacaaccactacacgtaccactacacactacacac
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr10 - 79378639 79378681 5.5e-05 0.887 CGTGCACTCACACATCTCATATGTGCACACCCACACAGCTCAC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr22 + 23954745 23954787 5.51e-05 0.887 agttcactcacatcacacacatatacacccacatacacacagt
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr17_KI270729v1_random + 22961 23003 5.76e-05 0.899 aatggaatcatgccgagtggaatgtaatgtaatgtaatggaat
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr7 + 148921262 148921304 5.92e-05 0.899 TCAGCACACCTAAATCTCAGCCTCACATGCATACACTCTGCCc
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr14 - 103205047 103205089 6.31e-05 0.899 TATGCACCTGTCACAATTTGATTAACTGCCTATGTTCTGTCTC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 182236785 182236827 6.43e-05 0.899 gttgcaaatatacacagcacaaatacacacacaaatagaccac
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr7 + 158262489 158262531 6.65e-05 0.899 catacatgcacacacactgcacacacattcacacactgcacac
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr17 - 80219999 80220041 6.73e-05 0.899 AGGGCAGCAAAGGCTGGAGGAGTGAGCCCCAGCATCCAGCACC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 206004673 206004715 6.73e-05 0.899 cttacacacagaagcaacacatatgcataccacacacatgcac
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 - 39073940 39073982 7.06e-05 0.921 CCTCCCAGCAGAACCATTTCCTTTCATCCCAAACTTTGAGCTC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 - 40964377 40964419 7.52e-05 0.957 AGATCATTTGGACACAGGACAGGGAACAACACACACTGGGGCC
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr19 + 39319606 39319648 8.02e-05 0.998 AGAAAATACTGAACCACAGTAGCACAGTCAGTAGACAGGCCCA
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 32471604 32471646 8.35e-05 1 AGAGGACTCAGGTGAGCTCCCTTAGCATTCATCAGCCCTGCCA
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr1 + 235589126 235589168 8.89e-05 1 tgtcatcacagccatatagccataacatcggaaggctcatcat
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr10 + 41904200 41904242 9.74e-05 1 actgaaatcaacccgagtggaatggaatggaatggaatggact
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr5 - 49656411 49656453 9.74e-05 1 AATGGAATCAACCCGAGTGGAATGGCATGGAATGGAATGGAAT
AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC MEME-8 chr10 + 41904260 41904302 9.91e-05 1 aatggaatcaacccgagtggaatgaaatggaatggaatggagt

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/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_4 --bgfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/background --motif AGTGCACTCAGACCCAGTGGATTAACATCCAAAAACYGGGCCC /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa

Settings:

output_directory = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/fimo_out_4 MEME file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/meme_out/meme.xml sequence file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.MemeChipResults/ZNF311.IDR0.05.filt.narrowPeak.top600.summitPlusMinus250bp.fa
background file name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZNF311.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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