# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-shuffled # positives: 818 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-centered (Sat Jan 18 06:35:04 PST 2020) # negatives: 818 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-shuffled (Sat Jan 18 06:35:04 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:48:32 PST 2020 MEME version 4.12.0 ALPHABET "DNA" DNA-LIKE A "Adenine" CC0000 ~ T "Thymine" 008000 C "Cytosine" 0000CC ~ G "Guanine" FFB300 N "Any base" = ACGT X = ACGT . = ACGT V "Not T" = ACG H "Not G" = ACT D "Not C" = AGT B "Not A" = CGT M "Amino" = AC R "Purine" = AG W "Weak" = AT S "Strong" = CG Y "Pyrimidine" = CT K "Keto" = GT U = T END ALPHABET strands: + - Background letter frequencies (from dataset): A 0.298 C 0.203 G 0.202 T 0.297 MOTIF GGTTCGAB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGAB VTCGAACC 59 2 3.0e-016 1.0e-011 # GGTTCGAT ATCGAACC 21 0 4.2e-007 1.4e-002 # GGTTCGAC GTCGAACC 19 0 1.7e-006 5.9e-002 # GGTTCGAG CTCGAACC 19 2 1.0e-004 3.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 1.0e-011 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.322034 0.322034 0.355932 MOTIF ACCRACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 73 7 7.3e-016 2.5e-011 # ACCAACT AGTTGGT 52 5 1.6e-011 5.5e-007 # ACCGACT AGTCGGT 21 2 3.0e-005 1.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 73 E= 2.5e-011 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.712329 0.000000 0.287671 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AGAARM DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGAARM KYTTCT 375 220 9.5e-016 3.2e-011 # AGAAGA TCTTCT 113 50 1.1e-007 3.9e-003 # AGAAAA TTTTCT 199 118 2.5e-007 8.6e-003 # AGAAAC GTTTCT 86 49 5.7e-004 2.0e+001 # AGAAGC GCTTCT 68 39 2.5e-003 8.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 509 E= 3.2e-011 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.634578 0.000000 0.365422 0.000000 0.693517 0.306483 0.000000 0.000000 MOTIF ACCAYT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCAYT ARTGGT 160 70 7.7e-011 2.6e-006 # ACCACT AGTGGT 95 31 1.2e-009 4.2e-005 # ACCATT AATGGT 68 41 4.8e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 178 E= 2.6e-006 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.589888 0.000000 0.410112 0.000000 0.000000 0.000000 1.000000 MOTIF AGAGCGY DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGAGCGY RCGCTCT 31 2 5.1e-008 1.7e-003 # AGAGCGT ACGCTCT 18 0 3.5e-006 1.2e-001 # AGAGCGC GCGCTCT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 1.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.437500 0.000000 0.562500 MOTIF GTCAKAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTCAKAC GTMTGAC 34 4 2.3e-007 7.6e-003 # GTCATAC GTATGAC 20 2 5.5e-005 1.8e+000 # GTCAGAC GTCTGAC 14 2 2.0e-003 6.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 7.6e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.411765 0.588235 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TACCRA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TACCRA TYGGTA 98 41 2.5e-007 8.2e-003 # TACCGA TCGGTA 49 12 6.4e-007 2.1e-002 # TACCAA TTGGTA 52 29 5.9e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 104 E= 8.2e-003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.528846 0.000000 0.471154 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCMACAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCMACAC GTGTKGC 35 5 5.3e-007 1.7e-002 # GCAACAC GTGTTGC 20 1 9.4e-006 3.1e-001 # GCCACAC GTGTGGC 15 4 9.3e-003 3.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.7e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTGGGR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACTGGGR YCCCAGT 32 4 7.6e-007 2.5e-002 # ACTGGGA TCCCAGT 17 2 3.4e-004 1.1e+001 # ACTGGGG CCCCAGT 15 2 1.1e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 2.5e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.531250 0.000000 0.468750 0.000000 MOTIF GCCRTTAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCCRTTAC GTAAYGGC 23 1 1.3e-006 4.2e-002 # GCCGTTAC GTAACGGC 14 1 4.7e-004 1.5e+001 # GCCATTAC GTAATGGC 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.2e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.391304 0.000000 0.608696 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 55.74 seconds