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/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/AWRI1631--MOT3.fa
Database contains 904 sequences, 974861 residues

MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
TCGAACCB 8 TCGAACCC
YGGTAR 6 TGGTAA
AAGAAAHA 8 AAGAAAAA
CGCCTTA 7 CGCCTTA
AASTTGGT 8 AAGTTGGT
AAGATK 6 AAGATT
AAAADAAA 8 AAAAAAAA
CAWCAAG 7 CAACAAG

Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/background):
A 0.305 C 0.195 G 0.195 T 0.305

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
CGCCTTA DREME-4 chrII - 9602 9608 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIII - 24210 24216 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXI - 74643 74649 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrV - 86622 86628 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIII - 90878 90884 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV - 102735 102741 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV - 104823 104829 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 113820 113826 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIII - 117374 117380 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIII - 127735 127741 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVIII - 127786 127792 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXI - 142783 142789 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVI - 167457 167463 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIII - 168815 168821 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIX - 175049 175055 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrI - 181160 181166 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII - 197443 197449 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII - 205540 205546 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrII - 227093 227099 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIII - 227960 227966 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 228350 228356 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIX - 248868 248874 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrII - 266396 266402 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 274691 274697 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 287811 287817 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 288212 288218 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIII - 295502 295508 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIX - 325766 325772 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV - 331460 331466 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV - 338015 338021 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrII - 347622 347628 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX - 354264 354270 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII - 371323 371329 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXVI - 407919 407925 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII - 423111 423117 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV - 437790 437796 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV - 443025 443031 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXI - 458576 458582 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 487458 487464 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV - 507004 507010 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV - 519762 519768 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII - 611750 611756 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX - 617938 617944 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII - 628402 628408 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV - 632618 632624 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXVI - 640961 640967 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXVI - 689583 689589 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII - 700694 700700 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX - 703657 703663 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII - 704315 704321 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII - 710647 710653 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII - 731156 731162 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII - 732109 732115 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII - 784372 784378 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXVI - 810695 810701 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIII - 837948 837954 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 842724 842730 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV - 842899 842905 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV - 946332 946338 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV - 1305648 1305654 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX + 59146 59152 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX + 75692 75698 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVIII + 116153 116159 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV + 136655 136661 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVI + 137532 137538 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 167999 168005 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrI + 182577 182583 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVI + 191587 191593 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX + 195855 195861 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVI + 210679 210685 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV + 216622 216628 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV + 230793 230799 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIII + 259213 259219 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 283913 283919 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrV + 288498 288504 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV + 354087 354093 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX + 424488 424494 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV + 434310 434316 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 516701 516707 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX + 524067 524073 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrX + 543016 543022 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV + 560739 560745 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 568787 568793 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 592592 592598 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII + 600189 600195 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrII + 681624 681630 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV + 707993 707999 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV + 725367 725373 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXIV + 726190 726196 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXV + 779962 779968 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 820330 820336 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrVII + 857464 857470 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 963028 963034 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrXII + 976029 976035 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV + 981029 981035 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV + 1150915 1150921 4.1e-05 0.82 CGCCTTA
CGCCTTA DREME-4 chrIV + 1461802 1461808 4.1e-05 0.82 CGCCTTA
DEBUGGING INFORMATION

Command line: 

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/background --motif CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/AWRI1631--MOT3.fa

Settings: 


  

    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/fimo_out_4
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/AWRI1631--MOT3.fa
  
  

    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MOT3/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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