# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PHD1/seqs-shuffled # positives: 956 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PHD1/seqs-centered (Sat Jan 18 06:04:09 PST 2020) # negatives: 956 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PHD1/seqs-shuffled (Sat Jan 18 06:04:10 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:18:37 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 0.299 C 0.203 G 0.198 T 0.300 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 103 11 3.4e-021 1.2e-016 # GGTTCGA TCGAACC 87 7 9.8e-020 3.5e-015 # GGATCGA TCGATCC 27 4 1.5e-005 5.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 103 E= 1.2e-016 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.213592 0.000000 0.000000 0.786408 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 KAGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST KAGTGGTW WACCACTM 81 6 7.7e-019 2.7e-014 # TAGTGGTA TACCACTA 30 3 5.8e-007 2.1e-002 # TAGTGGTT AACCACTA 19 0 1.7e-006 6.2e-002 # GAGTGGTT AACCACTC 25 3 1.2e-005 4.3e-001 # GAGTGGTA TACCACTC 8 0 3.8e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 83 E= 2.7e-014 0.000000 0.000000 0.409639 0.590361 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 0.469880 0.000000 0.000000 0.530120 MOTIF CCVTACA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCVTACA TGTABGG 105 25 6.2e-014 2.2e-009 # CCATACA TGTATGG 51 13 6.4e-007 2.3e-002 # CCGTACA TGTACGG 43 10 2.1e-006 7.3e-002 # CCCTACA TGTAGGG 18 3 7.0e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 2.2e-009 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.475000 0.150000 0.375000 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 AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 50 4 1.1e-011 3.8e-007 # AACTTGGC GCCAAGTT 38 2 5.3e-010 1.9e-005 # AACTGGGC GCCCAGTT 12 2 6.3e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 3.8e-007 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 0.240000 0.760000 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 2 7.2e-011 2.5e-006 # GCGCTACC GGTAGCGC 31 1 6.1e-009 2.1e-004 # GCTCTACC GGTAGAGC 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.5e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.756098 0.243902 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 ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 44 3 7.9e-011 2.8e-006 # ATGGCAAC GTTGCCAT 29 2 1.9e-007 6.7e-003 # ATGGCATC GATGCCAT 15 1 2.5e-004 8.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.8e-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 0.659091 0.000000 0.000000 0.340909 0.000000 1.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 61 10 1.2e-010 4.1e-006 # CGCCTTA TAAGGCG 43 5 4.7e-009 1.6e-004 # CGCGTTA TAACGCG 18 5 5.1e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 4.1e-006 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 0.704918 0.295082 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 CRCCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 144 61 4.2e-010 1.5e-005 # CACCCA TGGGTG 91 40 2.3e-006 8.2e-002 # CGCCCA TGGGCG 56 23 9.8e-005 3.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 192 E= 1.5e-005 0.000000 1.000000 0.000000 0.000000 0.703125 0.000000 0.296875 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 ARAAAAR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAR YTTTTYT 268 164 7.9e-009 2.7e-004 # AGAAAAA TTTTTCT 93 50 1.2e-004 4.1e+000 # AGAAAAG CTTTTCT 42 16 3.6e-004 1.2e+001 # AAAAAAA TTTTTTT 141 97 1.4e-003 4.9e+001 # AAAAAAG CTTTTTT 99 64 2.6e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 332 E= 2.7e-004 1.000000 0.000000 0.000000 0.000000 0.638554 0.000000 0.361446 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 0.626506 0.000000 0.373494 0.000000 MOTIF AGGRAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGGRAG CTYCCT 88 29 8.1e-009 2.8e-004 # AGGAAG CTTCCT 65 21 6.4e-007 2.2e-002 # AGGGAG CTCCCT 26 8 1.3e-003 4.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 98 E= 2.8e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.734694 0.000000 0.265306 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GTCAKAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GTCAKAC GTMTGAC 41 5 1.6e-008 5.4e-004 # GTCATAC GTATGAC 26 3 6.7e-006 2.3e-001 # GTCAGAC GTCTGAC 15 2 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 5.4e-004 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 0.357143 0.642857 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACCRCTT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AACCRCTT AAGYGGTT 32 2 2.7e-008 9.4e-004 # AACCACTT AAGTGGTT 25 2 2.5e-006 8.4e-002 # AACCGCTT AAGCGGTT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.4e-004 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 0.000000 0.781250 0.000000 0.218750 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 MOTIF GTGGAGAY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTGGAGAY RTCTCCAC 24 0 5.2e-008 1.8e-003 # GTGGAGAC GTCTCCAC 12 0 2.4e-004 8.0e+000 # GTGGAGAT ATCTCCAC 12 0 2.4e-004 8.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-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 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 0.500000 0.000000 0.500000 MOTIF CACTATR DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CACTATR YATAGTG 40 7 4.0e-007 1.4e-002 # CACTATA TATAGTG 32 7 3.0e-005 1.0e+000 # CACTATG CATAGTG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 1.4e-002 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.800000 0.000000 0.200000 0.000000 MOTIF ASAAAGCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ASAAAGCA TGCTTTST 35 5 5.5e-007 1.9e-002 # ACAAAGCA TGCTTTGT 24 4 8.1e-005 2.8e+000 # AGAAAGCA TGCTTTCT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 1.9e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.694444 0.305556 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GYGGTCTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GYGGTCTA TAGACCRC 24 1 6.8e-007 2.3e-002 # GTGGTCTA TAGACCAC 14 0 5.8e-005 2.0e+000 # GCGGTCTA TAGACCGC 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.3e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.416667 0.000000 0.583333 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTRCGCC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTRCGCC GGCGYAGT 20 0 8.6e-007 2.9e-002 # ACTGCGCC GGCGCAGT 12 0 2.4e-004 8.0e+000 # ACTACGCC GGCGTAGT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.9e-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 0.400000 0.000000 0.600000 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 AATCCMAC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AATCCMAC GTKGGATT 23 1 1.3e-006 4.5e-002 # AATCCAAC GTTGGATT 16 1 1.3e-004 4.4e+000 # AATCCCAC GTGGGATT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 4.5e-002 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 0.708333 0.291667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGTGSC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CGCGTGSC GSCACGCG 23 1 1.3e-006 4.5e-002 # CGCGTGGC GCCACGCG 11 0 4.7e-004 1.6e+001 # CGCGTGCC GGCACGCG 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.5e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.521739 0.478261 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 114.10 seconds