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/BY4742--PDR1/BY4742--PDR1.fa
Database contains 581 sequences, 515404 residues

MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GGTTCRA 7 GGTTCGA
ARAAARA 7 AAAAAAA
TAAGGCR 7 TAAGGCG
ACCACTH 7 ACCACTA
ATGGCAWC 8 ATGGCAAC
ACCRACT 7 ACCAACT
ATCGTRAG 8 ATCGTGAG
ATGGYCA 7 ATGGTCA
CCGTGMTA 8 CCGTGATA
TCGGYCA 7 TCGGTCA
ASACCAC 7 ACACCAC
GYCCGGA 7 GTCCGGA
CRCCCA 6 CACCCA
RCGGGGA 7 GCGGGGA
GGATCGAA 8 GGATCGAA

Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/background):
A 0.313 C 0.187 G 0.187 T 0.313

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
ACCACTH DREME-4 chrI + 168 174 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI + 168 174 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrI + 203 209 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVII + 347 353 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI + 376 382 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXV + 418 424 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVII + 431 437 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI + 463 469 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII + 469 475 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII + 669 675 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrI + 693 699 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXV + 739 745 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII + 990 996 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVI + 5422 5428 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII + 5693 5699 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIV + 6794 6800 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIV + 6993 6999 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrII - 9594 9600 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 11459 11465 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 11655 11661 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 11739 11745 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 11977 11983 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII + 16544 16550 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrV - 68719 68725 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI - 84219 84225 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrV - 86615 86621 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXV + 92779 92785 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 97376 97382 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrV - 99816 99822 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX + 121288 121294 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII + 133088 133094 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII - 146404 146410 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 168006 168012 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrI + 182584 182590 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVI + 191594 191600 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 217038 217044 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrII - 227086 227092 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII - 227953 227959 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrI - 229894 229900 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIX - 248861 248867 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII + 259220 259226 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVI + 269436 269442 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXV - 274684 274690 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrV + 288505 288511 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII - 316121 316127 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII - 316202 316208 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIII - 316412 316418 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 341272 341278 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrII - 347614 347620 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrII + 350783 350789 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII + 353447 353453 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXV - 354140 354146 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 369193 369199 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX + 424496 424502 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 437783 437789 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIX - 439168 439174 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIX - 439412 439418 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIX - 439496 439502 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIX - 439708 439714 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXV + 446197 446203 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII + 452173 452179 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 488946 488952 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 519754 519760 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX + 524074 524080 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII - 556205 556211 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII - 556446 556452 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII - 556538 556544 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVIII - 556748 556754 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVII + 561724 561730 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 592600 592606 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX - 617930 617936 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI - 666004 666010 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI - 666243 666249 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXI - 666327 666333 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXVI - 689576 689582 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVII - 700686 700692 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIV + 726198 726204 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVII + 726652 726658 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXVI - 731894 731900 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 732101 732107 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX - 745240 745246 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX - 745324 745330 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrX - 745534 745540 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIV - 783703 783709 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 784365 784371 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrVII - 823477 823483 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV + 884707 884713 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII + 887287 887293 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII - 888312 888318 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII - 923639 923645 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXIII - 923878 923884 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII + 963036 963042 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV + 981036 981042 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 1018669 1018675 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 1064381 1064387 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrXII - 1064922 1064928 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV + 1150922 1150928 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 1305641 1305647 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV + 1489044 1489050 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 1524725 1524731 3.75e-05 0.38 ACCACTC
ACCACTH DREME-4 chrIV - 1525052 1525058 3.75e-05 0.38 ACCACTC
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/BY4742--PDR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/background --motif ACCACTH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/BY4742--PDR1.fa

Settings: 


  

    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/fimo_out_6
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/BY4742--PDR1.fa
  
  

    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/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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