# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/seqs-shuffled # positives: 446 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/seqs-centered (Sat Jan 18 09:57:10 PST 2020) # negatives: 446 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/seqs-shuffled (Sat Jan 18 09:57:10 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 10:05:18 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 0.206 G 0.204 T 0.293 MOTIF CCRTACA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 79 3 5.6e-022 1.5e-017 # CCATACA TGTATGG 47 1 5.1e-014 1.3e-009 # CCGTACA TGTACGG 40 2 9.0e-011 2.3e-006 letter-probability matrix: alength= 4 w= 7 nsites= 96 E= 1.5e-017 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.562500 0.000000 0.437500 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 90 7 1.2e-021 3.1e-017 # AGTGGTT AACCACT 67 2 3.3e-019 8.4e-015 # AGTGGTA TACCACT 37 5 1.2e-007 3.2e-003 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 3.1e-017 1.000000 0.000000 0.000000 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 0.351852 0.000000 0.000000 0.648148 MOTIF GGHTCGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 85 7 4.5e-020 1.1e-015 # GGTTCGA TCGAACC 69 4 9.6e-018 2.5e-013 # GGCTCGA TCGAGCC 17 1 6.3e-005 1.6e+000 # GGATCGA TCGATCC 15 2 1.1e-003 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 88 E= 1.1e-015 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.170455 0.147727 0.000000 0.681818 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 AGTYGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 69 5 7.8e-017 2.0e-012 # AGTTGGTT AACCAACT 30 2 7.9e-008 2.0e-003 # AGTTGGTA TACCAACT 20 2 5.1e-005 1.3e+000 # AGTCGGTA TACCGACT 9 0 1.9e-003 4.8e+001 # AGTCGGTT AACCGACT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 69 E= 2.0e-012 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.275362 0.000000 0.724638 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.420290 0.000000 0.000000 0.579710 MOTIF CACGGW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACGGW WCCGTG 68 13 3.0e-011 7.6e-007 # CACGGA TCCGTG 38 6 2.6e-007 6.6e-003 # CACGGT ACCGTG 32 7 2.5e-005 6.2e-001 letter-probability matrix: alength= 4 w= 6 nsites= 70 E= 7.6e-007 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.542857 0.000000 0.000000 0.457143 MOTIF CRCCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 82 21 5.1e-011 1.3e-006 # CACCCA TGGGTG 54 12 3.0e-008 7.4e-004 # CGCCCA TGGGCG 28 9 1.0e-003 2.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 94 E= 1.3e-006 0.000000 1.000000 0.000000 0.000000 0.702128 0.000000 0.297872 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 1.000000 0.000000 0.000000 0.000000 MOTIF AASGCG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AASGCG CGCSTT 88 26 2.0e-010 4.8e-006 # AAGGCG CGCCTT 59 19 1.2e-006 3.0e-002 # AACGCG CGCGTT 29 7 1.2e-004 2.9e+000 letter-probability matrix: alength= 4 w= 6 nsites= 88 E= 4.8e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.329545 0.670455 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 MOTIF CCAAVAGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCAAVAGA TCTBTTGG 37 2 7.1e-010 1.7e-005 # CCAAGAGA TCTCTTGG 16 0 1.3e-005 3.3e-001 # CCAACAGA TCTGTTGG 11 1 3.0e-003 7.4e+001 # CCAAAAGA TCTTTTGG 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.7e-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 0.270270 0.297297 0.432432 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 GCGCTHCC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCGCTHCC GGDAGCGC 27 0 5.0e-009 1.2e-004 # GCGCTACC GGTAGCGC 12 0 2.3e-004 5.5e+000 # GCGCTCCC GGGAGCGC 8 0 3.8e-003 9.2e+001 # GCGCTTCC GGAAGCGC 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.2e-004 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 0.444444 0.296296 0.000000 0.259259 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGGCCAM DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGGCCAM KTGGCCG 35 3 1.9e-008 4.5e-004 # CGGCCAA TTGGCCG 25 2 2.1e-006 5.1e-002 # CGGCCAC GTGGCCG 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 4.5e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 MOTIF CGCCASAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGCCASAC GTSTGGCG 24 0 4.3e-008 1.1e-003 # CGCCACAC GTGTGGCG 15 0 2.7e-005 6.6e-001 # CGCCAGAC GTCTGGCG 9 0 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.625000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GACTSTTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 23 0 8.9e-008 2.2e-003 # GACTCTTA TAAGAGTC 13 0 1.1e-004 2.7e+000 # GACTGTTA TAACAGTC 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.2e-003 0.000000 0.000000 1.000000 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 0.000000 0.565217 0.434783 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 GCTAWCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCTAWCA TGWTAGC 28 2 3.0e-007 7.2e-003 # GCTATCA TGATAGC 17 1 6.3e-005 1.5e+000 # GCTAACA TGTTAGC 12 1 1.6e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 7.2e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.413793 0.000000 0.000000 0.586207 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 41 8 5.2e-007 1.3e-002 # ATCGTGA TCACGAT 15 1 2.3e-004 5.6e+000 # ATCTTGA TCAAGAT 26 7 5.4e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.3e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.365854 0.634146 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARAAAAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAA TTTTTYT 102 49 1.4e-006 3.4e-002 # AGAAAAA TTTTTCT 48 19 1.6e-004 3.8e+000 # AAAAAAA TTTTTTT 68 36 5.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 121 E= 3.4e-002 1.000000 0.000000 0.000000 0.000000 0.644628 0.000000 0.355372 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 AGACCACR DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGACCACR YGTGGTCT 19 0 1.6e-006 3.7e-002 # AGACCACG CGTGGTCT 10 0 9.3e-004 2.2e+001 # AGACCACA TGTGGTCT 9 0 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.7e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 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 0.473684 0.000000 0.526316 0.000000 MOTIF GCCATRGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GCCATRGA TCYATGGC 19 0 1.6e-006 3.7e-002 # GCCATAGA TCTATGGC 10 0 9.3e-004 2.2e+001 # GCCATGGA TCCATGGC 9 0 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.7e-002 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.526316 0.000000 0.473684 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 51.61 seconds