# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/seqs-shuffled # positives: 788 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/seqs-centered (Sun Jan 19 00:20:03 PST 2020) # negatives: 788 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/seqs-shuffled (Sun Jan 19 00:20:03 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:36:40 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 0.301 C 0.200 G 0.201 T 0.298 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 75 14 4.4e-012 1.5e-007 # GGTTCGA TCGAACC 61 9 2.6e-011 9.3e-007 # GGATCGA TCGATCC 22 5 6.9e-004 2.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 1.5e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.263158 0.000000 0.000000 0.736842 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 SAAGAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SAAGAW WTCTTS 326 203 3.3e-011 1.2e-006 # CAAGAA TTCTTG 123 66 6.2e-006 2.2e-001 # CAAGAT ATCTTG 77 38 1.0e-004 3.6e+000 # GAAGAA TTCTTC 119 72 1.8e-004 6.4e+000 # GAAGAT ATCTTC 88 48 2.2e-004 7.6e+000 letter-probability matrix: alength= 4 w= 6 nsites= 421 E= 1.2e-006 0.000000 0.482185 0.517815 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 0.596200 0.000000 0.000000 0.403800 MOTIF DACCAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST DACCAC GTGGTH 145 66 2.8e-009 9.6e-005 # TACCAC GTGGTA 65 24 4.6e-006 1.6e-001 # AACCAC GTGGTT 57 28 8.2e-004 2.8e+001 # GACCAC GTGGTC 39 16 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 167 E= 9.6e-005 0.365269 0.000000 0.239521 0.395210 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 MOTIF GTTAKTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GTTAKTA TAMTAAC 39 6 1.9e-007 6.5e-003 # GTTAGTA TACTAAC 19 2 1.0e-004 3.4e+000 # GTTATTA TAATAAC 20 4 7.1e-004 2.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 6.5e-003 0.000000 0.000000 1.000000 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 0.000000 0.487179 0.512821 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAARTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAAAARTA TAYTTTTT 65 20 2.6e-007 8.9e-003 # AAAAAATA TATTTTTT 45 13 1.1e-005 3.7e-001 # AAAAAGTA TACTTTTT 20 7 9.1e-003 3.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 66 E= 8.9e-003 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 0.681818 0.000000 0.318182 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCTTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCTTACC GGTAAGG 20 0 8.4e-007 2.9e-002 # CCTTACC GGTAAGG 20 0 8.4e-007 2.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 2.9e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGSGGAG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGSGGAG CTCCSCG 23 1 1.3e-006 4.3e-002 # CGGGGAG CTCCCCG 12 0 2.3e-004 7.9e+000 # CGCGGAG CTCCGCG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 4.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 39.87 seconds