# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/seqs-shuffled # positives: 698 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/seqs-centered (Fri Jan 17 23:10:16 PST 2020) # negatives: 698 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/seqs-shuffled (Fri Jan 17 23:10:16 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:25:58 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 0.212 G 0.213 T 0.287 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 118 7 1.6e-029 5.4e-025 # GGTTCGA TCGAACC 98 6 3.1e-024 1.0e-019 # AGTTCGA TCGAACT 27 1 8.5e-008 2.8e-003 letter-probability matrix: alength= 4 w= 7 nsites= 118 E= 5.4e-025 0.194915 0.000000 0.805085 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 CCRTRCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTRCA TGYAYGG 115 16 1.3e-021 4.1e-017 # CCGTACA TGTACGG 43 3 1.3e-010 4.3e-006 # CCATACA TGTATGG 49 7 2.0e-009 6.4e-005 # CCATGCA TGCATGG 20 3 2.2e-004 7.3e+000 # CCGTGCA TGCACGG 20 3 2.2e-004 7.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 141 E= 4.1e-017 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.546099 0.000000 0.453901 0.000000 0.000000 0.000000 0.000000 1.000000 0.723404 0.000000 0.276596 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 59 3 2.7e-015 8.9e-011 # CTCGGCCA TGGCCGAG 31 1 5.6e-009 1.8e-004 # CTTGGCCA TGGCCAAG 17 2 3.4e-004 1.1e+001 # CTGGGCCA TGGCCCAG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 8.9e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.525424 0.186441 0.288136 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 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 43 0 5.8e-014 1.9e-009 # GCGCTACC GGTAGCGC 28 0 2.8e-009 9.2e-005 # GCTCTACC GGTAGAGC 15 0 2.8e-005 9.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.9e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.651163 0.348837 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 GCCWTAAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 46 1 1.6e-013 5.3e-009 # GCCTTAAC GTTAAGGC 35 1 3.6e-010 1.2e-005 # GCCATAAC GTTATGGC 12 0 2.3e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 5.3e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.255319 0.000000 0.000000 0.744681 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 1.000000 0.000000 0.000000 MOTIF AARAAAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 254 139 4.5e-012 1.5e-007 # AAAAAAA TTTTTTT 133 71 1.7e-006 5.4e-002 # AAGAAAT ATTTCTT 46 14 1.4e-005 4.7e-001 # AAGAAAA TTTTCTT 77 37 6.0e-005 2.0e+000 # AAAAAAT ATTTTTT 106 64 3.8e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 322 E= 1.5e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.627329 0.000000 0.372671 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 0.577640 0.000000 0.000000 0.422360 MOTIF ATAGTKTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 47 4 6.2e-011 2.0e-006 # ATAGTGTA TACACTAT 26 2 1.2e-006 4.0e-002 # ATAGTTTA TAAACTAT 22 2 1.6e-005 5.0e-001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 2.0e-006 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 0.541667 0.458333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 29 0 1.4e-009 4.5e-005 # AGATCGGG CCCGATCT 20 0 8.3e-007 2.7e-002 # AGATCGTG CACGATCT 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 4.5e-005 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 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 0.689655 0.310345 0.000000 0.000000 1.000000 0.000000 MOTIF ACTARACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACTARACC GGTYTAGT 33 1 1.4e-009 4.6e-005 # ACTAGACC GGTCTAGT 19 0 1.7e-006 5.4e-002 # ACTAAACC GGTTTAGT 14 1 4.6e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.6e-005 1.000000 0.000000 0.000000 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 0.424242 0.000000 0.575758 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 CGSTCTCC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGSTCTCC GGAGASCG 26 0 1.2e-008 3.8e-004 # CGGTCTCC GGAGACCG 16 0 1.4e-005 4.5e-001 # CGCTCTCC GGAGAGCG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.384615 0.615385 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAASGATG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 33 2 1.3e-008 4.2e-004 # CAACGATG CATCGTTG 22 1 2.5e-006 7.9e-002 # CAAGGATG CATCCTTG 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.2e-004 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 0.666667 0.333333 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 0.000000 1.000000 0.000000 MOTIF TAATCAKA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TAATCAKA TMTGATTA 35 3 2.3e-008 7.4e-004 # TAATCAGA TCTGATTA 17 1 6.6e-005 2.1e+000 # TAATCATA TATGATTA 18 2 1.8e-004 5.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 7.4e-004 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.485714 0.514286 1.000000 0.000000 0.000000 0.000000 MOTIF GCGCAAK DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCGCAAK MTTGCGC 46 8 4.1e-008 1.3e-003 # GCGCAAG CTTGCGC 29 3 1.0e-006 3.2e-002 # GCGCAAT ATTGCGC 19 6 6.9e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 1.3e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.660000 0.340000 MOTIF GTGGSGTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GTGGSGTA TACSCCAC 24 0 4.9e-008 1.6e-003 # GTGGCGTA TACGCCAC 15 0 2.8e-005 9.1e-001 # GTGGGGTA TACCCCAC 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-003 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 0.625000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 32 3 1.5e-007 4.9e-003 # GGCTATCA TGATAGCC 18 1 3.5e-005 1.1e+000 # GGTTATCA TGATAACC 14 2 2.0e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 4.9e-003 0.000000 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 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAGCRTG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AAAGCRTG CAYGCTTT 22 0 2.0e-007 6.4e-003 # AAAGCGTG CACGCTTT 14 0 5.7e-005 1.8e+000 # AAAGCATG CATGCTTT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.4e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.363636 0.000000 0.636364 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GARTCATA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GARTCATA TATGAYTC 25 1 3.3e-007 1.0e-002 # GAGTCATA TATGACTC 16 1 1.3e-004 4.1e+000 # GAATCATA TATGATTC 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.360000 0.000000 0.640000 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGTCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATGGTCA TGACCAT 27 2 6.5e-007 2.1e-002 # ATGGTCA TGACCAT 27 2 6.5e-007 2.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.1e-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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATTTCSTA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ATTTCSTA TASGAAAT 20 0 8.3e-007 2.6e-002 # ATTTCGTA TACGAAAT 12 0 2.3e-004 7.4e+000 # ATTTCCTA TAGGAAAT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-002 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 1 1.3e-006 4.0e-002 # ACTGAGCT AGCTCAGT 23 1 1.3e-006 4.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.0e-002 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 151.84 seconds