# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/seqs-shuffled # positives: 721 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/seqs-centered (Sat Jan 18 02:13:53 PST 2020) # negatives: 721 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/seqs-shuffled (Sat Jan 18 02:13:53 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 02:29:23 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 0.294 C 0.205 G 0.204 T 0.296 MOTIF CCRTRCA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCRTRCA TGYAYGG 111 22 4.2e-017 1.4e-012 # CCATACA TGTATGG 48 8 1.3e-008 4.4e-004 # CCGTACA TGTACGG 41 8 6.7e-007 2.2e-002 # CCGTGCA TGCACGG 19 3 3.9e-004 1.3e+001 # CCATGCA TGCATGG 17 4 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 133 E= 1.4e-012 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.533835 0.000000 0.466165 0.000000 0.000000 0.000000 0.000000 1.000000 0.729323 0.000000 0.270677 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SGGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 64 3 9.0e-017 3.0e-012 # CGGTTCGA TCGAACCG 28 0 2.9e-009 9.4e-005 # GGGTTCGA TCGAACCC 36 3 1.2e-008 4.1e-004 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 3.0e-012 0.000000 0.437500 0.562500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 ACTYGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACTYGGCC GGCCRAGT 43 0 6.0e-014 2.0e-009 # ACTTGGCC GGCCAAGT 26 0 1.2e-008 3.9e-004 # ACTCGGCC GGCCGAGT 25 0 2.4e-008 8.0e-004 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.0e-009 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 0.488372 0.000000 0.511628 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 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 68 9 3.5e-013 1.1e-008 # CGCCTTA TAAGGCG 56 7 2.9e-011 9.6e-007 # CGCGTTA TAACGCG 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 68 E= 1.1e-008 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 0.823529 0.176471 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 TAGTGGTW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 43 2 1.6e-011 5.4e-007 # TAGTGGTA TACCACTA 25 1 3.3e-007 1.1e-002 # TAGTGGTT AACCACTA 18 1 3.5e-005 1.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 5.4e-007 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 0.000000 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 0.581395 0.000000 0.000000 0.418605 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 44 3 6.8e-011 2.2e-006 # ATGGCAAC GTTGCCAT 30 3 5.5e-007 1.8e-002 # ATGGCATC GATGCCAT 14 0 5.7e-005 1.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.2e-006 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 0.681818 0.000000 0.000000 0.318182 0.000000 1.000000 0.000000 0.000000 MOTIF CACGGYG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 42 3 2.5e-010 8.3e-006 # CACGGTG CACCGTG 29 3 1.0e-006 3.3e-002 # CACGGCG CGCCGTG 13 0 1.2e-004 3.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 8.3e-006 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 0.000000 0.309524 0.000000 0.690476 0.000000 0.000000 1.000000 0.000000 MOTIF AARARA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AARARA TYTYTT 404 291 1.7e-009 5.5e-005 # AAGAAA TTTCTT 161 100 1.9e-005 6.3e-001 # AAGAGA TCTCTT 70 35 2.6e-004 8.5e+000 # AAAAAA TTTTTT 223 165 3.5e-004 1.2e+001 # AAAAGA TCTTTT 134 94 2.4e-003 7.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 595 E= 5.5e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.633613 0.000000 0.366387 0.000000 1.000000 0.000000 0.000000 0.000000 0.719328 0.000000 0.280672 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 28 0 2.9e-009 9.2e-005 # AGTCAGAC GTCTGACT 14 0 5.7e-005 1.8e+000 # AGTCATAC GTATGACT 14 0 5.7e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.2e-005 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 33 3 8.3e-008 2.7e-003 # GCGCTACC GGTAGCGC 22 2 1.6e-005 5.0e-001 # GCTCTACC GGTAGAGC 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.7e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 AAATCCR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAATCCR YGGATTT 50 11 1.3e-007 4.3e-003 # AAATCCA TGGATTT 28 6 8.3e-005 2.6e+000 # AAATCCG CGGATTT 22 5 6.9e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 4.3e-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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.568627 0.000000 0.431373 0.000000 MOTIF ATAGTKTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 34 4 2.2e-007 7.1e-003 # ATAGTGTA TACACTAT 18 0 3.4e-006 1.1e-001 # ATAGTTTA TAAACTAT 16 4 5.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 7.1e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.529412 0.470588 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCAVAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 36 5 2.8e-007 9.0e-003 # ACCCAGAC GTCTGGGT 13 1 8.7e-004 2.8e+001 # ACCCAAAC GTTTGGGT 13 2 3.5e-003 1.1e+002 # ACCCACAC GTGTGGGT 13 2 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 9.0e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.325000 0.350000 0.325000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGGBG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATGGGBG CVCCCAT 46 10 3.9e-007 1.3e-002 # ATGGGCG CGCCCAT 19 4 1.2e-003 3.8e+001 # ATGGGTG CACCCAT 17 4 3.4e-003 1.1e+002 # ATGGGGG CCCCCAT 13 2 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 1.3e-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 0.000000 1.000000 0.000000 0.000000 0.380000 0.260000 0.360000 0.000000 0.000000 1.000000 0.000000 MOTIF ACGYCAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACGYCAC GTGRCGT 29 3 1.0e-006 3.2e-002 # ACGCCAC GTGGCGT 22 3 6.9e-005 2.2e+000 # ACGTCAC GTGACGT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.2e-002 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 0.758621 0.000000 0.241379 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 70.70 seconds