# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-shuffled # positives: 658 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-centered (Sun Jan 19 04:04:18 PST 2020) # negatives: 658 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-shuffled (Sun Jan 19 04:04:18 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 04:21:01 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 0.197 G 0.200 T 0.300 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 84 6 4.6e-020 1.5e-015 # GGTTCGA TCGAACC 67 3 9.6e-018 3.1e-013 # GGATCGA TCGATCC 26 3 6.2e-006 2.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 84 E= 1.5e-015 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.261905 0.000000 0.000000 0.738095 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 ACCDCT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCDCT AGHGGT 146 54 6.4e-013 2.1e-008 # ACCACT AGTGGT 81 24 2.7e-009 8.9e-005 # ACCTCT AGAGGT 50 18 4.3e-005 1.4e+000 # ACCGCT AGCGGT 29 13 8.8e-003 2.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 171 E= 2.1e-008 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.526316 0.000000 0.175439 0.298246 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CCAAMAGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCAAMAGA TCTKTTGG 29 2 1.8e-007 5.7e-003 # CCAAAAGA TCTTTTGG 15 0 2.8e-005 9.1e-001 # CCAACAGA TCTGTTGG 14 2 2.0e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.7e-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 1.000000 0.000000 0.000000 0.000000 0.517241 0.482759 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 CTTACCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTTACCR YGGTAAG 36 6 1.0e-006 3.2e-002 # CTTACCG CGGTAAG 15 0 2.8e-005 9.1e-001 # CTTACCA TGGTAAG 21 6 2.7e-003 8.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.2e-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 0.583333 0.000000 0.416667 0.000000 MOTIF ARAAAAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAA TTTTTYT 153 86 1.1e-006 3.4e-002 # AAAAAAA TTTTTTT 107 57 1.9e-005 6.2e-001 # AGAAAAA TTTTTCT 69 36 5.2e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 175 E= 3.4e-002 1.000000 0.000000 0.000000 0.000000 0.668571 0.000000 0.331429 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 # Stopping reason: E-value threshold exceeded # Running time: 25.85 seconds