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/BY4741--SWI1/BY4741--SWI1.fa
Database contains 923 sequences, 390882 residues

MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
CGCSTTA 7 CGCCTTA
CTBGGCCA 8 CTCGGCCA
GGTTCGA 7 GGTTCGA
ACCACKA 7 ACCACTA
ATGGGYG 7 ATGGGTG
TCCGBACA 8 TCCGTACA
GCKCTACC 8 GCGCTACC
TTTCTTB 7 TTTCTTT
ATGGCAWC 8 ATGGCAAC
CACGGYG 7 CACGGTG
CCCAYACA 8 CCCACACA
CTATCAC 7 CTATCAC
GATTWGAA 8 GATTAGAA
CCACACSC 8 CCACACCC
ATCKTGAG 8 ATCGTGAG
AYTCTCG 7 ATTCTCG
CTGAGCTA 8 CTGAGCTA
CAWATATA 8 CATATATA
TCKCCCA 7 TCTCCCA
ACCACTTK 8 ACCACTTG

Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/background):
A 0.320 C 0.180 G 0.180 T 0.320

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
ATGGCAWC DREME-9 chrV + 61923 61930 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrV + 86601 86608 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrV + 138679 138686 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrV + 138679 138686 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIII + 142734 142741 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX + 157810 157817 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX + 157810 157817 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVI + 181007 181014 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXIII + 183931 183938 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrII + 197662 197669 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrII + 197662 197669 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXV + 226644 226651 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXI + 327132 327139 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX + 355387 355394 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX + 396759 396766 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVII + 405483 405490 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrII + 405891 405898 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrII + 405891 405898 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV + 568895 568902 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV + 568895 568902 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXVI + 689754 689761 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXVI + 689754 689761 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVII + 736353 736360 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV + 835935 835942 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVII + 930986 930993 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrV - 67661 67668 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrV - 67661 67668 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV - 83576 83583 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXIII - 131874 131881 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVI - 162256 162263 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXI - 162536 162543 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXII - 168019 168026 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXIII - 259233 259240 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVIII - 262481 262488 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXV - 282192 282199 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVII - 346454 346461 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV - 359323 359330 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX - 374555 374562 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX - 531856 531863 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrX - 531856 531863 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXVI - 572297 572304 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXVI - 572297 572304 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXIII - 747941 747948 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVII - 828772 828779 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrVII - 845677 845684 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXVI - 860407 860414 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV - 992860 992867 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrXII - 1041749 1041756 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrIV - 1302864 1302871 1.1e-05 0.172 ATGGCAAC
ATGGCAWC DREME-9 chrI + 142173 142180 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrX + 378380 378387 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXI + 379700 379707 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrV + 423381 423388 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrV + 438720 438727 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrV + 469477 469484 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrV + 569523 569530 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXV + 780803 780810 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrVII + 823502 823509 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrIV + 1524547 1524554 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXV - 915 922 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrIII - 1166 1173 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrX - 58936 58943 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrVII - 73873 73880 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrVIII - 85342 85349 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrV - 207146 207153 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXI - 308188 308195 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXIV - 352198 352205 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXII - 370862 370869 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXII - 370862 370869 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXIII - 372489 372496 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrVII - 412338 412345 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXIII - 420632 420639 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrVII - 479662 479669 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrVII - 479662 479669 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXI - 513564 513571 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXV - 663856 663863 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXI - 665838 665845 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXII - 687903 687910 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXV - 960305 960312 2.2e-05 0.214 ATGGCATC
ATGGCAWC DREME-9 chrXIII + 25207 25214 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrIV + 117457 117464 3.43e-05 0.286 ATGGCAGC
ATGGCAWC DREME-9 chrXV + 254024 254031 3.43e-05 0.286 ATGGCAGC
ATGGCAWC DREME-9 chrII + 612386 612393 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrXV + 742909 742916 3.43e-05 0.286 ATGGCAGC
ATGGCAWC DREME-9 chrXII + 932129 932136 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrXI - 46910 46917 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrX - 121516 121523 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrXII - 241701 241708 3.43e-05 0.286 ATGGCAGC
ATGGCAWC DREME-9 chrV - 442436 442443 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrV - 442436 442443 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrIV - 551101 551108 3.43e-05 0.286 ATGGCACC
ATGGCAWC DREME-9 chrX - 703639 703646 3.43e-05 0.286 ATGGCAGC
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/BY4741--SWI1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa

Settings: 


  

    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/fimo_out_8
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa
  
  

    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/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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