# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MCM1/seqs-shuffled # positives: 774 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MCM1/seqs-centered (Sat Jan 18 19:29:45 PST 2020) # negatives: 774 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MCM1/seqs-shuffled (Sat Jan 18 19:29:46 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 19:46:09 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 0.300 C 0.198 G 0.197 T 0.305 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 96 8 9.7e-022 3.4e-017 # GGTTCGA TCGAACC 71 5 6.1e-017 2.1e-012 # GGATCGA TCGATCC 31 4 1.4e-006 4.8e-002 letter-probability matrix: alength= 4 w= 7 nsites= 96 E= 3.4e-017 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.302083 0.000000 0.000000 0.697917 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 ARAAAAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAA TTTTTYT 194 102 1.6e-009 5.6e-005 # AAAAAAA TTTTTTT 136 71 7.5e-007 2.6e-002 # AGAAAAA TTTTTCT 92 45 1.7e-005 5.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 231 E= 5.6e-005 1.000000 0.000000 0.000000 0.000000 0.627706 0.000000 0.372294 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCTTAVC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCTTAVC GBTAAGG 61 13 3.2e-009 1.1e-004 # CCTTACC GGTAAGG 19 3 3.9e-004 1.4e+001 # CCTTAGC GCTAAGG 19 3 3.9e-004 1.4e+001 # CCTTAAC GTTAAGG 25 7 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 63 E= 1.1e-004 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 0.396825 0.301587 0.301587 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 24 0 5.0e-008 1.7e-003 # GGTTATCA TGATAACC 14 0 5.8e-005 2.0e+000 # GGCTATCA TGATAGCC 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.7e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.416667 0.000000 0.583333 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 MOTIF CMAGAAG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CMAGAAG CTTCTKG 52 13 3.5e-007 1.2e-002 # CCAGAAG CTTCTGG 21 3 1.3e-004 4.3e+000 # CAAGAAG CTTCTTG 31 10 6.3e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 0.596154 0.403846 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 0.000000 0.000000 1.000000 0.000000 MOTIF GMTACCGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 24 1 6.6e-007 2.2e-002 # GCTACCGA TCGGTAGC 16 1 1.3e-004 4.4e+000 # GATACCGA TCGGTATC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 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 ACCKTS DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCKTS SAMGGT 149 70 4.7e-009 1.6e-004 # ACCGTG CACGGT 33 12 1.1e-003 3.6e+001 # ACCGTC GACGGT 26 9 2.7e-003 9.3e+001 # ACCTTG CAAGGT 46 24 4.9e-003 1.7e+002 # ACCTTC GAAGGT 49 28 9.4e-003 3.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 161 E= 1.6e-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 0.000000 0.000000 0.372671 0.627329 0.000000 0.000000 0.000000 1.000000 0.000000 0.484472 0.515528 0.000000 MOTIF RGTGGTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST RGTGGTA TACCACY 42 8 4.0e-007 1.3e-002 # AGTGGTA TACCACT 28 5 2.8e-005 9.4e-001 # GGTGGTA TACCACC 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 1.3e-002 0.651163 0.000000 0.348837 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 1.000000 0.000000 0.000000 0.000000 MOTIF CAGCAG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAGCAG CTGCTG 40 8 1.2e-006 4.0e-002 # CAGCAG CTGCTG 40 8 1.2e-006 4.0e-002 letter-probability matrix: alength= 4 w= 6 nsites= 43 E= 4.0e-002 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 48.34 seconds