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/aa_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Database contains 1020 sequences, 572147 residues

MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
RGTTCGA 7 GGTTCGA
DTCTTC 6 TTCTTC
CCWTAACC 8 CCTTAACC
GGAWGCA 7 GGAAGCA
ACCCAYAC 8 ACCCATAC
GTGRTA 6 GTGATA
GYCAAGA 7 GTCAAGA
CGCCASAC 8 CGCCACAC
CACGRTG 7 CACGGTG
TAAGCAVA 8 TAAGCAAA
TGGCAACR 8 TGGCAACG
GCKCTACC 8 GCGCTACC
AAAAARA 7 AAAAAAA

Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/background):
A 0.303 C 0.197 G 0.197 T 0.303

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
CACGRTG DREME-9 chrVII + 55968 55974 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIII + 82491 82497 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVIII + 122497 122503 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV - 130274 130280 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV - 130274 130280 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX - 139683 139689 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX - 139683 139689 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX - 139683 139689 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXI + 141047 141053 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXI - 141236 141242 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXV - 159867 159873 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXV - 159867 159873 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXV - 160434 160440 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIX + 183481 183487 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrI + 190545 190551 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXII + 202112 202118 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXVI + 210221 210227 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIX - 210689 210695 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVI + 225070 225076 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVI + 225070 225076 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXII + 254385 254391 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIII - 290835 290841 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIII + 306467 306473 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIII + 306467 306473 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIII - 306783 306789 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIII - 306783 306789 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXI - 326688 326694 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXI - 326688 326694 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXI - 327081 327087 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXI - 327081 327087 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 328617 328623 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXV - 347522 347528 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrV - 354968 354974 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV - 356374 356380 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV + 357255 357261 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIX - 370451 370457 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX + 374284 374290 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII + 401556 401562 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrV - 442107 442113 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrV - 442107 442113 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVIII + 452622 452628 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVIII + 452622 452628 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVIII + 452622 452628 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 482500 482506 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 482500 482506 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrV + 487360 487366 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIV + 495538 495544 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX - 526405 526411 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 541884 541890 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrII - 555942 555948 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIV + 569908 569914 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV + 580167 580173 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV + 580167 580173 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV + 580167 580173 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXV + 594575 594581 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX + 606380 606386 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX - 606886 606892 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrX - 663183 663189 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXII - 734826 734832 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXII - 737946 737952 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 739146 739152 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 739146 739152 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXII - 797212 797218 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXIII + 797861 797867 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII - 806782 806788 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXVI - 819553 819559 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVII + 856907 856913 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrXII + 950430 950436 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrIV + 1278876 1278882 2.7e-05 0.443 CACGGTG
CACGRTG DREME-9 chrVI + 31182 31188 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVIII + 56332 56338 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrV - 138726 138732 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrV - 138726 138732 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXI + 162490 162496 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVIII - 175460 175466 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXIV + 302035 302041 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXIV - 302088 302094 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrX - 355434 355440 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrX - 355434 355440 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXI + 355933 355939 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXI + 355933 355939 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrX + 374509 374515 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrV - 377834 377840 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrV - 377834 377840 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXI + 382394 382400 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXI + 385312 385318 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVII - 405530 405536 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrII - 405938 405944 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrII - 405938 405944 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrV - 423347 423353 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVIII - 504831 504837 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXVI - 520200 520206 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrX - 538445 538451 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXIII - 556968 556974 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVII + 557935 557941 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrIV - 568942 568948 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrII - 612279 612285 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVII + 641133 641139 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXII + 704304 704310 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXII - 704657 704663 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVII - 736400 736406 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXIII + 759258 759264 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXIII + 759258 759264 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXII - 797303 797309 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVII + 878977 878983 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrIV - 976717 976723 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXV + 989158 989164 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrVII - 1000280 1000286 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXV - 1028507 1028513 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrXV - 1028507 1028513 6.87e-05 0.7 CACGATG
CACGRTG DREME-9 chrIV + 1278900 1278906 6.87e-05 0.7 CACGATG
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/aa_results/AWRI1631--SOK2/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/background --motif CACGRTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/AWRI1631--SOK2.fa

Settings: 


  

    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/fimo_out_11
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
  
  

    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SOK2/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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