# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SMP1/seqs-shuffled # positives: 701 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SMP1/seqs-centered (Sat Jan 18 16:12:18 PST 2020) # negatives: 701 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SMP1/seqs-shuffled (Sat Jan 18 16:12:18 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:27:27 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 0.302 C 0.200 G 0.193 T 0.305 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 93 6 1.1e-022 3.3e-018 # ACCCATAC GTATGGGT 45 4 2.2e-010 6.9e-006 # ATCCGTAC GTACGGAT 34 1 7.1e-010 2.2e-005 # ACCCGTAC GTACGGGT 12 0 2.3e-004 7.2e+000 # ATCCATAC GTATGGAT 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 109 E= 3.3e-018 1.000000 0.000000 0.000000 0.000000 0.000000 0.541284 0.000000 0.458716 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.550459 0.000000 0.449541 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTYGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 85 4 3.5e-022 1.1e-017 # AGTTGGTT AACCAACT 34 3 4.4e-008 1.4e-003 # AGTTGGTA TACCAACT 24 0 4.9e-008 1.5e-003 # AGTCGGTA TACCGACT 13 0 1.2e-004 3.6e+000 # AGTCGGTT AACCGACT 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 85 E= 1.1e-017 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.317647 0.000000 0.682353 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.435294 0.000000 0.000000 0.564706 MOTIF CCACDCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCACDCG CGHGTGG 71 5 5.2e-017 1.6e-012 # CCACTCG CGAGTGG 31 1 5.6e-009 1.7e-004 # CCACACG CGTGTGG 26 2 1.2e-006 3.8e-002 # CCACGCG CGCGTGG 14 2 2.0e-003 6.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 1.6e-012 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 1.000000 0.000000 0.000000 0.375000 0.000000 0.194444 0.430556 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TCGAACCB DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 57 3 1.1e-014 3.3e-010 # TCGAACCC GGGTTCGA 29 2 1.8e-007 5.5e-003 # TCGAACCG CGGTTCGA 21 1 4.8e-006 1.5e-001 # TCGAACCT AGGTTCGA 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 3.3e-010 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.508772 0.368421 0.122807 MOTIF CGCSTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 62 9 1.3e-011 4.0e-007 # CGCCTTA TAAGGCG 50 7 1.1e-009 3.3e-005 # CGCGTTA TAACGCG 12 2 6.3e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 4.0e-007 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 0.806452 0.193548 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 MOTIF TAGTGGTW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 51 5 2.7e-011 8.2e-007 # TAGTGGTA TACCACTA 28 0 2.8e-009 8.6e-005 # TAGTGGTT AACCACTA 23 5 4.1e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 8.2e-007 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 1.000000 0.549020 0.000000 0.000000 0.450980 MOTIF CRCCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 131 57 3.6e-009 1.1e-004 # CACCCA TGGGTG 99 43 4.2e-007 1.3e-002 # CGCCCA TGGGCG 35 14 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 215 E= 1.1e-004 0.000000 1.000000 0.000000 0.000000 0.832558 0.000000 0.167442 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCMA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCMA TKGCCAT 55 11 8.8e-009 2.6e-004 # ATGGCAA TTGCCAT 34 8 2.7e-005 8.1e-001 # ATGGCCA TGGCCAT 21 3 1.2e-004 3.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 2.6e-004 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 0.618182 0.381818 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCACR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 30 1 1.1e-008 3.3e-004 # CTATCACG CGTGATAG 15 0 2.8e-005 8.5e-001 # CTATCACA TGTGATAG 15 1 2.4e-004 7.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.3e-004 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 MOTIF GCGCYAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCGCYAC GTRGCGC 36 3 1.2e-008 3.7e-004 # GCGCTAC GTAGCGC 18 1 3.5e-005 1.0e+000 # GCGCCAC GTGGCGC 18 2 1.8e-004 5.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.7e-004 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 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGAADA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGAADA THTTCT 249 154 1.3e-008 3.9e-004 # AGAAAA TTTTCT 150 89 9.4e-006 2.8e-001 # AGAATA TATTCT 71 43 4.0e-003 1.2e+002 # AGAAGA TCTTCT 65 41 9.9e-003 3.0e+002 letter-probability matrix: alength= 4 w= 6 nsites= 307 E= 3.9e-004 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 0.547231 0.000000 0.205212 0.247557 1.000000 0.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 27 1 8.5e-008 2.5e-003 # CACCGTGG CCACGGTG 15 0 2.8e-005 8.3e-001 # CACCGTGC GCACGGTG 12 1 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.5e-003 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 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 0.444444 0.555556 0.000000 MOTIF GTAKCTCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTAKCTCA TGAGMTAC 23 0 9.9e-008 2.9e-003 # GTATCTCA TGAGATAC 16 0 1.4e-005 4.1e-001 # GTAGCTCA TGAGCTAC 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.9e-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 0.000000 0.000000 0.291667 0.708333 0.000000 1.000000 0.000000 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 MOTIF AAGAGWC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAGAGWC GWCTCTT 39 7 6.3e-007 1.9e-002 # AAGAGAC GTCTCTT 21 3 1.2e-004 3.6e+000 # AAGAGTC GACTCTT 18 4 2.0e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 1.9e-002 1.000000 0.000000 0.000000 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 0.000000 0.525000 0.000000 0.000000 0.475000 0.000000 1.000000 0.000000 0.000000 MOTIF AKATTTC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AKATTTC GAAATMT 63 21 1.3e-006 3.7e-002 # ATATTTC GAAATAT 40 14 2.1e-004 6.1e+000 # AGATTTC GAAATCT 25 7 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 3.7e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.378788 0.621212 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RGTCAGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST RGTCAGA TCTGACY 34 5 9.0e-007 2.6e-002 # GGTCAGA TCTGACC 19 1 1.8e-005 5.2e-001 # AGTCAGA TCTGACT 15 4 9.2e-003 2.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.6e-002 0.441176 0.000000 0.558824 0.000000 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTGCAY DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCGTGCAY RTGCACGG 19 0 1.7e-006 4.9e-002 # CCGTGCAT ATGCACGG 11 0 4.7e-004 1.4e+001 # CCGTGCAC GTGCACGG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.9e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.421053 0.000000 0.578947 MOTIF GCGTGCSA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GCGTGCSA TSGCACGC 19 0 1.7e-006 4.9e-002 # GCGTGCCA TGGCACGC 10 0 9.5e-004 2.7e+001 # GCGTGCGA TCGCACGC 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.9e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.526316 0.473684 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 81.87 seconds