# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-shuffled # positives: 990 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-centered (Sat Jan 18 06:20:43 PST 2020) # negatives: 990 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-shuffled (Sat Jan 18 06:20:43 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:33:36 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 0.305 C 0.192 G 0.194 T 0.310 MOTIF RTAAACA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RTAAACA TGTTTAY 231 51 5.7e-033 2.0e-028 # GTAAACA TGTTTAC 131 16 1.7e-025 6.0e-021 # ATAAACA TGTTTAT 109 36 1.2e-010 4.1e-006 letter-probability matrix: alength= 4 w= 7 nsites= 257 E= 2.0e-028 0.466926 0.000000 0.533074 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 MOTIF GGWTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 95 12 2.8e-018 9.7e-014 # GGTTCGA TCGAACC 75 8 1.4e-015 4.9e-011 # GGATCGA TCGATCC 22 4 2.5e-004 8.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 9.7e-014 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.221053 0.000000 0.000000 0.778947 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 MOTIF AGAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGAAR YTTCT 634 474 2.7e-013 9.3e-009 # AGAAA TTTCT 501 345 8.5e-013 2.9e-008 # AGAAG CTTCT 260 210 4.8e-003 1.7e+002 letter-probability matrix: alength= 4 w= 5 nsites= 968 E= 9.3e-009 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 0.671488 0.000000 0.328512 0.000000 MOTIF GGTADC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGTADC GHTACC 158 65 1.7e-011 5.7e-007 # GGTAGC GCTACC 43 12 1.3e-005 4.3e-001 # GGTAAC GTTACC 69 31 6.2e-005 2.1e+000 # GGTATC GATACC 49 25 3.0e-003 1.0e+002 letter-probability matrix: alength= 4 w= 6 nsites= 163 E= 5.7e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.435583 0.000000 0.263804 0.300613 0.000000 1.000000 0.000000 0.000000 MOTIF AACCAAYT DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AACCAAYT ARTTGGTT 43 3 1.5e-010 5.1e-006 # AACCAACT AGTTGGTT 22 1 2.6e-006 8.4e-002 # AACCAATT AATTGGTT 21 2 3.0e-005 9.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 5.1e-006 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.511628 0.000000 0.488372 0.000000 0.000000 0.000000 1.000000 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 30 0 7.5e-010 2.4e-005 # ATGGCAAC GTTGCCAT 20 0 8.7e-007 2.8e-002 # ATGGCATC GATGCCAT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.4e-005 1.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.645161 0.000000 0.000000 0.354839 0.000000 1.000000 0.000000 0.000000 MOTIF ACCWCT DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 153 71 3.2e-009 1.1e-004 # ACCACT AGTGGT 81 37 1.9e-005 6.1e-001 # ACCTCT AGAGGT 79 36 2.3e-005 7.5e-001 letter-probability matrix: alength= 4 w= 6 nsites= 170 E= 1.1e-004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.535294 0.000000 0.000000 0.464706 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CTTCMA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTTCMA TKGAAG 208 117 2.0e-008 6.6e-004 # CTTCCA TGGAAG 91 45 2.8e-005 9.0e-001 # CTTCAA TTGAAG 126 79 3.3e-004 1.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 236 E= 6.6e-004 0.000000 1.000000 0.000000 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 0.605932 0.394068 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTAWATA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTAWATA TATWTAC 90 34 1.1e-007 3.5e-003 # GTAAATA TATTTAC 66 26 1.2e-005 3.9e-001 # GTATATA TATATAC 27 10 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 96 E= 3.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.718750 0.000000 0.000000 0.281250 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAMCAAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CAMCAAG CTTGKTG 70 23 3.1e-007 9.9e-003 # CAACAAG CTTGTTG 47 17 9.0e-005 2.9e+000 # CACCAAG CTTGGTG 23 6 1.1e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 9.9e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.671429 0.328571 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 0.000000 0.000000 1.000000 0.000000 MOTIF CTCTAGM DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTCTAGM KCTAGAG 25 1 3.5e-007 1.1e-002 # CTCTAGC GCTAGAG 17 1 6.8e-005 2.2e+000 # CTCTAGA TCTAGAG 8 0 3.9e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 1.1e-002 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.320000 0.680000 0.000000 0.000000 MOTIF CACCASC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACCASC GSTGGTG 38 7 1.2e-006 3.9e-002 # CACCAGC GCTGGTG 20 3 2.3e-004 7.3e+000 # CACCACC GGTGGTG 21 4 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 3.9e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.454545 0.545455 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAASAAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CAASAAC GTTSTTG 63 21 1.6e-006 5.0e-002 # CAAGAAC GTTCTTG 31 9 3.0e-004 9.6e+000 # CAACAAC GTTGTTG 32 12 1.7e-003 5.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 5.0e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.515625 0.484375 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 # Stopping reason: E-value threshold exceeded # Running time: 79.59 seconds