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/BY4742--MOT3/BY4742--MOT3.fa
Database contains 850 sequences, 467554 residues

MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GRVTCGAA 8 GAATCGAA
TGTAYGGR 8 TGTATGGA
CTBGGCCA 8 CTCGGCCA
CGCSTTA 7 CGCCTTA
AGARA 5 AGAAA
TAGTGGTW 8 TAGTGGTA
GCKCTACC 8 GCGCTACC
ATGGCAWC 8 ATGGCAAC
RCACCCA 7 ACACCCA
CCGMTGA 7 CCGATGA
CACGGYG 7 CACGGTG
ACCGGKG 7 ACCGGGG
ACWAGACC 8 ACTAGACC
GTGATAGY 8 GTGATAGC
ACCGAAAK 8 ACCGAAAG

Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/background):
A 0.308 C 0.192 G 0.192 T 0.308

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
ACCGGKG DREME-12 chrV + 61908 61914 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV + 61908 61914 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXV + 92908 92914 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXV + 92908 92914 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV + 131100 131106 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIII + 142719 142725 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIII + 168319 168325 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV + 177143 177149 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXIII + 183916 183922 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIX + 197636 197642 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrII + 197647 197653 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXIII + 290845 290851 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII + 328627 328633 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV + 354978 354984 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV + 354978 354984 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIX + 370461 370467 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXII + 448668 448674 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII + 541894 541900 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIV + 645171 645177 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrII + 645211 645217 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXII + 797222 797228 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIV + 802749 802755 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXII + 820345 820351 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII + 930971 930977 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIII - 82481 82487 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIV - 83592 83598 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrX - 115958 115964 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIX - 131907 131913 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVIII - 134366 134372 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXI - 141037 141043 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVI - 162272 162278 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXVI - 210211 210217 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV - 250331 250337 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXV - 282208 282214 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII - 311560 311566 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII - 311560 311566 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII - 311560 311566 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrII - 350872 350878 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII - 401546 401552 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV - 487350 487356 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIV - 521017 521023 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrX - 531872 531878 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrX - 531872 531878 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXVI - 572313 572319 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXII - 646020 646026 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXII - 646020 646026 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII - 788429 788435 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrVII - 845693 845699 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrXVI - 860423 860429 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIV - 992876 992882 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrIV - 1017226 1017232 1.53e-05 0.278 ACCGGGG
ACCGGKG DREME-12 chrV + 69067 69073 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 232533 232539 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 232533 232539 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 232533 232539 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 232533 232539 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 232533 232539 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII - 232532 232538 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII - 232532 232538 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII - 232532 232538 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII - 232532 232538 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII - 232532 232538 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 233196 233202 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 233196 233202 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 233196 233202 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 233196 233202 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 233196 233202 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXI - 326946 326952 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXI - 326946 326952 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXI - 326946 326952 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXI - 326946 326952 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII + 451446 451452 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII + 451446 451452 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII + 451446 451452 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII + 451446 451452 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII - 451445 451451 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII - 451445 451451 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII - 451445 451451 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVIII - 451445 451451 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 481873 481879 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 481873 481879 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 481873 481879 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 481873 481879 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 481873 481879 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXIII + 500397 500403 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXIII - 500396 500402 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXIII - 511556 511562 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrII + 606837 606843 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrII + 613636 613642 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 639062 639068 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII + 661944 661950 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXVI + 701391 701397 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 814751 814757 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 838578 838584 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 838578 838584 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 838578 838584 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXII + 838578 838584 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXV - 866770 866776 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXV + 866931 866937 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII + 883180 883186 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII + 883180 883186 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII + 883180 883186 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 883179 883185 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 883179 883185 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrVII - 883179 883185 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrXIII - 888827 888833 4e-05 0.33 ACCGGTG
ACCGGKG DREME-12 chrV - 23735 23741 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 25161 25167 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 25161 25167 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 25161 25167 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 25161 25167 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 25161 25167 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrI + 70135 70141 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrI - 72291 72297 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrI - 72291 72297 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrI - 72291 72297 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrI - 72291 72297 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrI - 72291 72297 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVIII + 85411 85417 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII - 86984 86990 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrII + 88636 88642 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrV - 140737 140743 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVIII + 146260 146266 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVIII + 146354 146360 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXV + 160060 160066 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXV + 160324 160330 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrII + 165153 165159 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrX + 197331 197337 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrIX - 210616 210622 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXV - 216431 216437 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXI - 219941 219947 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 226118 226124 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIV - 234507 234513 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrXII - 283162 283168 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII - 283162 283168 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII + 306310 306316 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII - 374307 374313 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrIX + 394991 394997 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrIV - 410425 410431 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrV + 434654 434660 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrIV - 437911 437917 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVIII - 452603 452609 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVIII - 452603 452609 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVIII - 452603 452609 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVIII - 452603 452609 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVII + 482456 482462 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVII + 482456 482462 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVII + 482456 482462 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVII + 482456 482462 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrVII + 482456 482462 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrV - 491374 491380 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrV + 492462 492468 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVIII - 499665 499671 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXI - 518034 518040 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVIII + 554160 554166 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVIII + 554160 554166 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXV - 619400 619406 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII + 656952 656958 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVII - 736291 736297 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVII - 774395 774401 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII - 806365 806371 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrXVI + 810616 810622 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII + 856335 856341 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXII + 856335 856341 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXVI - 856854 856860 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXVI - 856948 856954 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVII - 857265 857271 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrXV - 866846 866852 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXV - 866866 866872 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrXIII - 887472 887478 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrXV + 968377 968383 8e-05 0.413 ACCGGAG
ACCGGKG DREME-12 chrVII - 987310 987316 8e-05 0.413 ACCGGCG
ACCGGKG DREME-12 chrXV - 1005813 1005819 8e-05 0.413 ACCGGAG
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/BY4742--MOT3/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/background --motif ACCGGKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/BY4742--MOT3.fa

Settings: 


  

    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/fimo_out_11
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/BY4742--MOT3.fa
  
  

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