# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-shuffled # positives: 597 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-centered (Sun Jan 19 07:28:31 PST 2020) # negatives: 597 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-shuffled (Sun Jan 19 07:28:31 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 07:44:55 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 0.195 G 0.199 T 0.304 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 91 12 1.0e-017 3.3e-013 # GGTTCGA TCGAACC 61 3 5.5e-016 1.8e-011 # GGTTCAA TTGAACC 34 9 6.5e-005 2.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 3.3e-013 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.357895 0.000000 0.642105 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 107 40 1.8e-009 5.7e-005 # ACCACT AGTGGT 72 21 1.6e-008 5.1e-004 # ACCTCT AGAGGT 39 19 5.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 121 E= 5.7e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.661157 0.000000 0.000000 0.338843 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AAAAADAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 122 53 9.2e-009 2.9e-004 # AAAAATAA TTATTTTT 50 19 8.0e-005 2.5e+000 # AAAAAAAA TTTTTTTT 50 20 1.5e-004 4.7e+000 # AAAAAGAA TTCTTTTT 43 21 3.3e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 141 E= 2.9e-004 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 0.368794 0.000000 0.283688 0.347518 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAASAGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAASAGA TCTSTTG 44 9 3.6e-007 1.1e-002 # CAAGAGA TCTCTTG 23 5 4.0e-004 1.3e+001 # CAACAGA TCTGTTG 21 4 4.0e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 1.1e-002 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 0.477273 0.522727 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 ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 23 1 1.2e-006 3.8e-002 # ATGGCAAC GTTGCCAT 15 1 2.4e-004 7.5e+000 # ATGGCATC GATGCCAT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.8e-002 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 0.652174 0.000000 0.000000 0.347826 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 23.59 seconds