# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/seqs-shuffled # positives: 470 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/seqs-centered (Sat Jan 18 19:43:32 PST 2020) # negatives: 470 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/seqs-shuffled (Sat Jan 18 19:43:32 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 19:52:50 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 0.288 C 0.213 G 0.213 T 0.286 MOTIF GGWTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCRA TYGAWCC 147 18 2.7e-031 7.0e-027 # GGTTCGA TCGAACC 95 8 2.9e-022 7.7e-018 # GGTTCAA TTGAACC 33 4 3.4e-007 9.1e-003 # GGATCGA TCGATCC 23 5 3.8e-004 1.0e+001 # GGATCAA TTGATCC 11 1 3.0e-003 8.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 155 E= 7.0e-027 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.212903 0.000000 0.000000 0.787097 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.283871 0.000000 0.716129 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 84 7 1.1e-019 2.9e-015 # AGTGGTT AACCACT 60 2 6.4e-017 1.7e-012 # AGTGGTA TACCACT 36 5 2.3e-007 6.1e-003 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 2.9e-015 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 0.367347 0.000000 0.000000 0.632653 MOTIF ACCCADAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCCADAC GTHTGGGT 60 2 6.4e-017 1.7e-012 # ACCCATAC GTATGGGT 40 0 3.8e-013 1.0e-008 # ACCCAGAC GTCTGGGT 13 0 1.1e-004 2.9e+000 # ACCCAAAC GTTTGGGT 12 2 6.2e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 1.7e-012 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.176471 0.000000 0.191176 0.632353 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 42 1 2.0e-012 5.2e-008 # AACTTGGC GCCAAGTT 31 0 2.8e-010 7.2e-006 # AACTGGGC GCCCAGTT 11 1 3.0e-003 7.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 5.2e-008 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.261905 0.738095 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCCGTRC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATCCGTRC GYACGGAT 35 0 1.5e-011 3.9e-007 # ATCCGTAC GTACGGAT 27 0 5.1e-009 1.3e-004 # ATCCGTGC GCACGGAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 3.9e-007 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.707317 0.000000 0.292683 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 38 1 3.5e-011 8.9e-007 # GCGCTACC GGTAGCGC 27 0 5.1e-009 1.3e-004 # GCTCTACC GGTAGAGC 11 1 3.0e-003 7.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 8.9e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.710526 0.289474 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AARAAAW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 177 87 3.8e-011 9.9e-007 # AAAAAAT ATTTTTT 81 34 1.8e-006 4.6e-002 # AAAAAAA TTTTTTT 89 46 4.2e-005 1.1e+000 # AAGAAAT ATTTCTT 34 9 6.0e-005 1.6e+000 # AAGAAAA TTTTCTT 48 25 3.5e-003 9.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 212 E= 9.9e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.641509 0.000000 0.358491 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 0.523585 0.000000 0.000000 0.476415 MOTIF GTGATAGY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 33 0 6.5e-011 1.6e-006 # GTGATAGC GCTATCAC 18 0 3.2e-006 8.2e-002 # GTGATAGT ACTATCAC 16 0 1.3e-005 3.4e-001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.6e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.529412 0.000000 0.470588 MOTIF CRCACGCC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CRCACGCC GGCGTGYG 30 0 5.8e-010 1.5e-005 # CACACGCC GGCGTGTG 20 0 7.8e-007 2.0e-002 # CGCACGCC GGCGTGCG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.5e-005 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GYGCCTTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GYGCCTTA TAAGGCRC 34 1 5.8e-010 1.5e-005 # GCGCCTTA TAAGGCGC 23 0 9.0e-008 2.3e-003 # GTGCCTTA TAAGGCAC 11 1 3.0e-003 7.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.5e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.676471 0.000000 0.323529 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 GATTAASA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GATTAASA TSTTAATC 26 0 1.0e-008 2.6e-004 # GATTAAGA TCTTAATC 14 0 5.5e-005 1.4e+000 # GATTAACA TGTTAATC 12 0 2.3e-004 5.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.6e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.461538 0.538462 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGAGACC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GGAGACC GGTCTCC 26 0 1.0e-008 2.6e-004 # GGAGACC GGTCTCC 26 0 1.0e-008 2.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 2.6e-004 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 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 ATGGCAWC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 35 3 1.9e-008 4.8e-004 # ATGGCAAC GTTGCCAT 25 2 2.1e-006 5.3e-002 # ATGGCATC GATGCCAT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 4.8e-004 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 0.714286 0.000000 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 MOTIF TGGCGCW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TGGCGCW WGCGCCA 33 3 7.0e-008 1.7e-003 # TGGCGCA TGCGCCA 22 2 1.5e-005 3.6e-001 # TGGCGCT AGCGCCA 11 1 3.0e-003 7.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.7e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 MOTIF TCGGYCAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TCGGYCAA TTGRCCGA 23 0 9.0e-008 2.3e-003 # TCGGCCAA TTGGCCGA 14 0 5.5e-005 1.4e+000 # TCGGTCAA TTGACCGA 9 0 1.9e-003 4.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.3e-003 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 0.608696 0.000000 0.391304 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCTTYTG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 32 3 1.3e-007 3.3e-003 # ATCTTCTG CAGAAGAT 18 2 1.8e-004 4.4e+000 # ATCTTTTG CAAAAGAT 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 3.3e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.562500 0.000000 0.437500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTAWATC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTAWATC GATWTAG 29 2 1.6e-007 3.9e-003 # CTATATC GATATAG 15 1 2.3e-004 5.8e+000 # CTAAATC GATTTAG 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 3.9e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.466667 0.000000 0.000000 0.533333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GACAASC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GACAASC GSTTGTC 31 3 2.5e-007 6.2e-003 # GACAACC GGTTGTC 17 2 3.2e-004 8.0e+000 # GACAAGC GCTTGTC 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 6.2e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.548387 0.451613 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCATGGGW DREME-19 # Word RC Word Pos Neg P-value E-value # BEST GCATGGGW WCCCATGC 25 1 3.0e-007 7.3e-003 # GCATGGGT ACCCATGC 16 1 1.2e-004 3.0e+000 # GCATGGGA TCCCATGC 9 0 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.3e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 0.360000 0.000000 0.000000 0.640000 MOTIF CGATCTKG DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CGATCTKG CMAGATCG 21 0 3.8e-007 9.3e-003 # CGATCTGG CCAGATCG 12 0 2.3e-004 5.6e+000 # CGATCTTG CAAGATCG 9 0 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 MOTIF CGCGGGSA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 21 0 3.8e-007 9.3e-003 # CGCGGGGA TCCCCGCG 11 0 4.6e-004 1.1e+001 # CGCGGGCA TGCCCGCG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.523810 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 64.86 seconds