# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MOT3/seqs-shuffled # positives: 801 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MOT3/seqs-centered (Sat Jan 18 22:26:53 PST 2020) # negatives: 801 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MOT3/seqs-shuffled (Sat Jan 18 22:26:53 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:43:38 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 0.297 C 0.200 G 0.204 T 0.299 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 94 10 1.4e-019 5.0e-015 # GGTTCGA TCGAACC 73 5 1.7e-017 6.0e-013 # GGATCGA TCGATCC 28 5 2.8e-005 1.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 5.0e-015 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.276596 0.000000 0.000000 0.723404 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 AARAAR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAR YTTYTT 463 333 5.2e-011 1.9e-006 # AAGAAA TTTCTT 181 111 3.7e-006 1.3e-001 # AAAAAA TTTTTT 242 168 1.4e-005 5.0e-001 # AAGAAG CTTCTT 116 76 1.3e-003 4.7e+001 # AAAAAG CTTTTT 182 134 1.6e-003 5.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 697 E= 1.9e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.579627 0.000000 0.420373 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.628407 0.000000 0.371593 0.000000 MOTIF CCAASW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCAASW WSTTGG 212 117 2.5e-009 8.8e-005 # CCAACT AGTTGG 67 28 2.4e-005 8.2e-001 # CCAAGA TCTTGG 56 22 5.1e-005 1.8e+000 # CCAACA TGTTGG 71 43 4.2e-003 1.5e+002 # CCAAGT ACTTGG 49 28 9.5e-003 3.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 238 E= 8.8e-005 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 0.000000 0.554622 0.445378 0.000000 0.567227 0.000000 0.000000 0.432773 MOTIF CGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 32 2 2.6e-008 9.0e-004 # CGCCTTA TAAGGCG 32 2 2.6e-008 9.0e-004 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 9.0e-004 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 ACCACTM DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 57 14 7.3e-008 2.5e-003 # ACCACTA TAGTGGT 33 6 5.7e-006 2.0e-001 # ACCACTC GAGTGGT 24 9 6.3e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 2.5e-003 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 0.000000 0.000000 0.000000 1.000000 0.578947 0.421053 0.000000 0.000000 MOTIF GCGCTWCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCGCTWCC GGWAGCGC 21 0 4.2e-007 1.4e-002 # GCGCTACC GGTAGCGC 12 0 2.3e-004 8.0e+000 # GCGCTTCC GGAAGCGC 9 0 1.9e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.571429 0.000000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 35.58 seconds