# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MOT3/seqs-shuffled # positives: 824 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MOT3/seqs-centered (Sat Jan 18 21:24:20 PST 2020) # negatives: 824 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MOT3/seqs-shuffled (Sat Jan 18 21:24:20 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 21:38:59 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 0.293 C 0.203 G 0.209 T 0.295 MOTIF TCGAACCB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 93 2 8.2e-027 2.8e-022 # TCGAACCC GGGTTCGA 45 1 3.7e-013 1.3e-008 # TCGAACCG CGGTTCGA 32 0 1.7e-010 5.9e-006 # TCGAACCT AGGTTCGA 16 1 1.3e-004 4.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 93 E= 2.8e-022 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 0.483871 0.344086 0.172043 MOTIF ACCAYT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCAYT ARTGGT 187 78 1.1e-013 3.9e-009 # ACCACT AGTGGT 107 37 4.4e-010 1.5e-005 # ACCATT AATGGT 82 43 1.9e-004 6.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 210 E= 3.9e-009 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 0.590476 0.000000 0.409524 0.000000 0.000000 0.000000 1.000000 MOTIF AAGAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAGAAR YTTCTT 265 140 4.7e-013 1.6e-008 # AAGAAA TTTCTT 196 105 3.9e-009 1.3e-004 # AAGAAG CTTCTT 100 44 6.1e-007 2.1e-002 letter-probability matrix: alength= 4 w= 6 nsites= 342 E= 1.6e-008 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 1.000000 0.000000 0.000000 0.000000 0.654971 0.000000 0.345029 0.000000 MOTIF CGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 46 2 2.3e-012 7.8e-008 # CGCCTTA TAAGGCG 46 2 2.3e-012 7.8e-008 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 7.8e-008 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 41 1 6.0e-012 2.0e-007 # ATGTACGG CCGTACAT 21 0 4.2e-007 1.4e-002 # ATGTATGG CCATACAT 23 1 1.3e-006 4.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.0e-007 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.468085 0.000000 0.531915 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF RGAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST RGAAGA TCTTCY 132 55 1.1e-009 3.8e-005 # AGAAGA TCTTCT 71 24 3.6e-007 1.2e-002 # GGAAGA TCTTCC 65 31 2.3e-004 7.8e+000 letter-probability matrix: alength= 4 w= 6 nsites= 140 E= 3.8e-005 0.528571 0.000000 0.471429 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAACTKGG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 42 4 1.6e-009 5.5e-005 # CAACTTGG CCAAGTTG 31 4 1.4e-006 4.7e-002 # CAACTGGG CCCAGTTG 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 5.5e-005 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.261905 0.738095 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CACGGTGM DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 29 1 2.3e-008 7.6e-004 # CACGGTGA TCACCGTG 16 0 1.4e-005 4.7e-001 # CACGGTGC GCACCGTG 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.6e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.551724 0.448276 0.000000 0.000000 MOTIF CCAYAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCAYAC GTRTGG 101 41 7.6e-008 2.5e-003 # CCACAC GTGTGG 63 22 2.9e-006 9.6e-002 # CCATAC GTATGG 42 19 1.9e-003 6.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 113 E= 2.5e-003 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 0.592920 0.000000 0.407080 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCGCTACC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCGCTACC GGTAGCGC 23 0 1.0e-007 3.4e-003 # GCGCTACC GGTAGCGC 23 0 1.0e-007 3.4e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.4e-003 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 0.000000 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 MOTIF ATGGCAWC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 36 5 2.9e-007 9.7e-003 # ATGGCAAC GTTGCCAT 23 4 1.4e-004 4.6e+000 # ATGGCATC GATGCCAT 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 9.7e-003 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 0.638889 0.000000 0.000000 0.361111 0.000000 1.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 24 1 6.6e-007 2.2e-002 # AGATCGGG CCCGATCT 17 1 6.7e-005 2.2e+000 # AGATCGTG CACGATCT 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.708333 0.291667 0.000000 0.000000 1.000000 0.000000 MOTIF CTATCACR DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 4 7.7e-007 2.5e-002 # CTATCACG CGTGATAG 14 1 4.7e-004 1.5e+001 # CTATCACA TGTGATAG 18 3 7.0e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 2.5e-002 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 0.562500 0.000000 0.437500 0.000000 MOTIF CTTACC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTTACC GGTAAG 51 14 1.5e-006 4.8e-002 # CTTACC GGTAAG 51 14 1.5e-006 4.8e-002 letter-probability matrix: alength= 4 w= 6 nsites= 51 E= 4.8e-002 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 74.57 seconds