# WARNING: this file is not sorted! # db id alt consensus E-value adj_p-value log_adj_p-value bin_location bin_width total_width sites_in_bin total_sites p_success p-value mult_tests 1 GGSSGGGSSGGRGSHGGVGGVRGGGSVGGG MEME-1 GGSSGGGSSGGRGSHGGVGGVRGGGSVGGG 2.9e-003 9.0e-005 -9.32 0.0 17 755 325 10778 0.02252 2.4e-007 377 1 WGGGGGCGGGGCCWS MEME-2 WGGGGGCGGGGCCWS 5.8e-017 1.8e-018 -40.85 0.0 292 770 4652 11003 0.37922 4.7e-021 384 2 GGGCGGRR DREME-1 GGGCGGGG 6.2e-035 2.0e-036 -82.22 0.0 287 777 1918 4087 0.36937 5.0e-039 388 2 HTTYCY DREME-2 HTTYCY 6.7e-012 2.1e-013 -29.19 0.0 445 779 9304 15427 0.57125 5.4e-016 389 2 CCASYAGG DREME-4 CCASYAGG 4.8e-068 1.5e-069 -158.46 0.0 429 777 2562 3677 0.55212 3.9e-072 388 2 CYCCWCCC DREME-5 CYCCWCCC 3.0e-004 9.5e-006 -11.56 0.0 477 777 4047 6251 0.61390 2.5e-008 388 2 CMCGCCYC DREME-6 CMCGCCYC 4.3e-018 1.3e-019 -43.46 0.0 331 777 2053 4099 0.42600 3.4e-022 388 2 CTVCAGS DREME-7 CTSCAGS 7.7e-003 2.4e-004 -8.33 0.0 126 778 1861 10348 0.16195 6.2e-007 388 2 ATGYWAAT DREME-9 ATGYWAAT 8.0e-037 2.5e-038 -86.58 0.0 147 777 916 3191 0.18919 6.5e-041 388 2 ATTGGCYR DREME-11 ATTGGCYR 2.6e-023 8.0e-025 -55.48 0.0 295 777 929 1845 0.37967 2.1e-027 388 2 CTSCCTCY DREME-13 CTSCCTCY 1.1e-002 3.5e-004 -7.96 0.0 35 777 329 5571 0.04505 9.0e-007 388 2 CASGTR DREME-16 CAGGTR 1.5e0000 4.6e-002 -3.08 0.0 39 779 610 10502 0.05006 1.2e-004 389 2 CCAATCAS DREME-18 CCAATCAS 9.7e-025 3.0e-026 -58.75 0.0 329 777 688 1177 0.42342 7.8e-029 388 2 GCCACRCC DREME-21 GCCACRCC 3.4e-008 1.1e-009 -20.66 0.0 331 777 634 1207 0.42600 2.7e-012 388 2 GAGTSAC DREME-22 GAGTSAC 4.7e-001 1.5e-002 -4.23 0.0 254 778 878 2407 0.32648 3.8e-005 388 2 CCDCCTCC DREME-23 CCDCCTCC 1.6e0000 4.9e-002 -3.01 0.0 29 777 226 4716 0.03732 1.3e-004 388 2 CCACTAGA DREME-24 CCACTAGA 4.0e-009 1.2e-010 -22.81 0.0 377 777 354 554 0.48520 3.2e-013 388 2 GAATGY DREME-25 GAATGY 8.1e-032 2.5e-033 -75.06 0.0 183 779 2452 8331 0.23492 6.5e-036 389 2 ACCAATMG DREME-26 ACCAATMG 8.4e-006 2.6e-007 -15.16 0.0 133 777 127 440 0.17117 6.8e-010 388 2 ACAAAGVC DREME-27 ACAAAGVC 3.8e-007 1.2e-008 -18.24 0.0 91 777 320 1901 0.11712 3.1e-011 388 ## # Detailed descriptions of columns in this file: # # db: The name of the database (file name) that contains the motif. # id: A name for the motif that is unique in the motif database file. # alt: An alternate name of the motif that may be provided # in the motif database file. # consensus: A consensus sequence computed from the motif. # E-value: The expected number motifs that would have least one. # region as enriched for best matches to the motif as the reported region. # The E-value is the p-value multiplied by the number of motifs in the # input database(s). # adj_p-value: The probability that any tested region would be as enriched for # best matches to this motif as the reported region is. # By default the p-value is calculated by using the one-tailed binomial # test on the number of sequences with a match to the motif # that have their best match in the reported region, corrected for # the number of regions and score thresholds tested. # The test assumes that the probability that the best match in a sequence # falls in the region is the region width divided by the # number of places a motif # can align in the sequence (sequence length minus motif width plus 1). # When CentriMo is run in discriminative mode with a negative # set of sequences, the p-value of a region is calculated # using the Fisher exact test on the # enrichment of best matches in the positive sequences relative # to the negative sequences, corrected # for the number of regions and score thresholds tested. # The test assumes that the probability that the best match (if any) # falls into a given region # is the same for all positive and negative sequences. # log_adj_p-value: Log of adjusted p-value. # bin_location: Location of the center of the most enriched region. # bin_width: The width (in sequence positions) of the most enriched region. # A best match to the motif is counted as being in the region if the # center of the motif falls in the region. # total_width: The window maximal size which can be reached for this motif: # rounded(sequence length - motif length +1)/2 # sites_in_bin: The number of (positive) sequences whose best match to the motif # falls in the reported region. # Note: This number may be less than the number of # (positive) sequences that have a best match in the region. # The reason for this is that a sequence may have many matches that score # equally best. # If n matches have the best score in a sequence, 1/n is added to the # appropriate bin for each match. # total_sites: The number of sequences containing a match to the motif # above the score threshold. # p_success: The probability of falling in the enriched window: # bin width / total width # p-value: The uncorrected p-value before it gets adjusted to the # number of multiple tests to give the adjusted p-value. # mult_tests: This is the number of multiple tests (n) done for this motif. # It was used to correct the original p-value of a region for # multiple tests using the formula: # p' = 1 - (1-p)^n where p is the uncorrected p-value. # The number of multiple tests is the number of regions # considered times the number of score thresholds considered. # It depends on the motif length, sequence length, and the type of # optimizations being done (central enrichment, local enrichment, # score optimization).