# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-shuffled # positives: 750 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-centered (Sun Jan 19 02:41:55 PST 2020) # negatives: 750 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-shuffled (Sun Jan 19 02:41:55 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:58:04 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 0.303 C 0.197 G 0.196 T 0.304 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 98 7 3.2e-023 1.1e-018 # GGTTCGA TCGAACC 84 4 8.4e-022 2.8e-017 # GGATCGA TCGATCC 18 3 6.9e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 1.1e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.153061 0.000000 0.000000 0.846939 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 100 14 1.2e-018 4.1e-014 # AGTGGTT AACCACT 73 9 1.7e-014 5.5e-010 # AGTGGTA TACCACT 41 5 1.4e-008 4.7e-004 letter-probability matrix: alength= 4 w= 7 nsites= 117 E= 4.1e-014 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 0.350427 0.000000 0.000000 0.649573 MOTIF ACCRACT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 73 9 1.7e-014 5.5e-010 # ACCAACT AGTTGGT 52 4 2.5e-012 8.3e-008 # ACCGACT AGTCGGT 21 5 1.1e-003 3.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 73 E= 5.5e-010 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 SAAGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 401 261 2.1e-013 6.9e-009 # CAAGA TCTTG 243 137 1.9e-010 6.2e-006 # GAAGA TCTTC 222 158 9.0e-005 3.0e+000 letter-probability matrix: alength= 4 w= 5 nsites= 563 E= 6.9e-009 0.000000 0.502664 0.497336 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 1.000000 0.000000 0.000000 0.000000 MOTIF CGCCASAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCCASAC GTSTGGCG 29 0 1.4e-009 4.5e-005 # CGCCACAC GTGTGGCG 19 0 1.7e-006 5.4e-002 # CGCCAGAC GTCTGGCG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 4.5e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.655172 0.344828 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GMTACCGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 28 0 2.9e-009 9.2e-005 # GCTACCGA TCGGTAGC 21 0 4.1e-007 1.3e-002 # GATACCGA TCGGTATC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.2e-005 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 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 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 ATYGTTGG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATYGTTGG CCAACRAT 25 0 2.4e-008 7.7e-004 # ATCGTTGG CCAACGAT 16 0 1.4e-005 4.5e-001 # ATTGTTGG CCAACAAT 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.7e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.640000 0.000000 0.360000 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 MOTIF ATACAACW DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATACAACW WGTTGTAT 32 3 1.6e-007 5.0e-003 # ATACAACA TGTTGTAT 26 3 6.4e-006 2.0e-001 # ATACAACT AGTTGTAT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 5.0e-003 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.794118 0.000000 0.000000 0.205882 MOTIF CGSCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 79 28 1.7e-007 5.2e-003 # CGGCCA TGGCCG 50 16 1.1e-005 3.5e-001 # CGCCCA TGGGCG 30 12 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 81 E= 5.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.382716 0.617284 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 AGACCAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGACCAC GTGGTCT 29 2 1.8e-007 5.7e-003 # AGACCAC GTGGTCT 29 2 1.8e-007 5.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 5.7e-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 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 MOTIF CCRTGGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGA TCCAYGG 41 7 2.1e-007 6.6e-003 # CCGTGGA TCCACGG 22 2 1.6e-005 5.0e-001 # CCATGGA TCCATGG 20 5 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 6.6e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.000000 0.523810 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACGKTGCC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACGKTGCC GGCAMCGT 28 2 3.5e-007 1.1e-002 # ACGTTGCC GGCAACGT 18 2 1.9e-004 5.8e+000 # ACGGTGCC GGCACCGT 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.1e-002 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 0.000000 0.357143 0.642857 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 1.000000 0.000000 0.000000 MOTIF AAGGCG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AAGGCG CGCCTT 60 19 1.2e-006 3.6e-002 # AAGGCG CGCCTT 60 19 1.2e-006 3.6e-002 letter-probability matrix: alength= 4 w= 6 nsites= 60 E= 3.6e-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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 64.87 seconds