# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/seqs-shuffled # positives: 622 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/seqs-centered (Sun Jan 19 09:54:03 PST 2020) # negatives: 622 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/seqs-shuffled (Sun Jan 19 09:54:03 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:09:36 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 0.307 C 0.200 G 0.190 T 0.303 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 88 1 5.7e-027 1.7e-022 # GGGTTCGA TCGAACCC 37 0 4.2e-012 1.2e-007 # CGGTTCGA TCGAACCG 30 1 1.1e-008 3.1e-004 # GAGTTCGA TCGAACTC 13 0 1.1e-004 3.4e+000 # CAGTTCGA TCGAACTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 1.7e-022 0.000000 0.431818 0.568182 0.000000 0.238636 0.000000 0.761364 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 98 14 2.4e-018 7.1e-014 # AGTGGTT AACCACT 71 6 2.9e-016 8.3e-012 # AGTGGTA TACCACT 42 8 3.6e-007 1.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 7.1e-014 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 0.362069 0.000000 0.000000 0.637931 MOTIF CAYCCRTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAYCCRTA TAYGGRTG 60 3 1.2e-015 3.4e-011 # CATCCGTA TACGGATG 21 0 4.0e-007 1.2e-002 # CACCCATA TATGGGTG 23 2 8.2e-006 2.4e-001 # CACCCGTA TACGGGTG 8 0 3.8e-003 1.1e+002 # CATCCATA TATGGATG 10 1 5.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 66 E= 3.4e-011 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.530303 0.000000 0.469697 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTBGGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 48 1 3.6e-014 1.0e-009 # ACTTGGCC GGCCAAGT 29 1 2.1e-008 6.1e-004 # ACTGGGCC GGCCCAGT 12 0 2.3e-004 6.7e+000 # ACTCGGCC GGCCGAGT 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 1.0e-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 0.145833 0.250000 0.604167 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-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 59 6 7.7e-013 2.2e-008 # CGCCTTA TAAGGCG 42 2 2.9e-011 8.5e-007 # CGCGTTA TAACGCG 17 4 3.4e-003 9.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 2.2e-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 0.711864 0.288136 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 GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 35 0 1.8e-011 5.1e-007 # GCGCTACC GGTAGCGC 26 0 1.1e-008 3.3e-004 # GCTCTACC GGTAGAGC 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 5.1e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.742857 0.257143 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 CCCAHACA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCCAHACA TGTDTGGG 56 9 4.1e-010 1.2e-005 # CCCATACA TGTATGGG 21 0 4.0e-007 1.2e-002 # CCCACACA TGTGTGGG 26 8 1.3e-003 3.7e+001 # CCCAAACA TGTTTGGG 11 1 3.1e-003 8.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 1.2e-005 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 0.134146 0.609756 0.000000 0.256098 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 ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 35 2 3.3e-009 9.4e-005 # ATGGCAAC GTTGCCAT 20 1 9.1e-006 2.6e-001 # ATGGCATC GATGCCAT 15 1 2.4e-004 6.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 9.4e-005 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 0.571429 0.000000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 MOTIF CACCGTG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACCGTG CACGGTG 26 0 1.1e-008 3.3e-004 # CACCGTG CACGGTG 26 0 1.1e-008 3.3e-004 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.3e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTCWCG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACTCWCG CGWGAGT 25 0 2.3e-008 6.6e-004 # ACTCACG CGTGAGT 18 0 3.4e-006 9.6e-002 # ACTCTCG CGAGAGT 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 6.6e-004 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 1.000000 0.000000 0.000000 0.720000 0.000000 0.000000 0.280000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGACCACR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGACCACR YGTGGTCT 24 0 4.8e-008 1.3e-003 # AGACCACA TGTGGTCT 12 0 2.3e-004 6.6e+000 # AGACCACG CGTGGTCT 12 0 2.3e-004 6.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.3e-003 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 0.500000 0.000000 0.500000 0.000000 MOTIF AYTGCGCC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AYTGCGCC GGCGCART 23 0 9.7e-008 2.7e-003 # ATTGCGCC GGCGCAAT 13 0 1.1e-004 3.3e+000 # ACTGCGCC GGCGCAGT 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.434783 0.000000 0.565217 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ARAAAW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ARAAAW WTTTYT 362 271 1.6e-007 4.5e-003 # AGAAAT ATTTCT 73 39 5.0e-004 1.4e+001 # AGAAAA TTTTCT 132 87 5.1e-004 1.5e+001 # AAAAAA TTTTTT 189 138 6.3e-004 1.8e+001 # AAAAAT ATTTTT 186 147 7.4e-003 2.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 550 E= 4.5e-003 1.000000 0.000000 0.000000 0.000000 0.636364 0.000000 0.363636 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 0.530909 0.000000 0.000000 0.469091 MOTIF CACATYAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 31 3 2.8e-007 7.7e-003 # CACATCAC GTGATGTG 16 1 1.3e-004 3.5e+000 # CACATTAC GTAATGTG 15 2 1.1e-003 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 7.7e-003 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 0.000000 1.000000 0.000000 0.516129 0.000000 0.483871 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CKAGAATC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CKAGAATC GATTCTMG 23 1 1.2e-006 3.4e-002 # CGAGAATC GATTCTCG 13 0 1.1e-004 3.2e+000 # CTAGAATC GATTCTAG 10 1 5.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.565217 0.434783 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CKTTGGGC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 20 0 8.2e-007 2.2e-002 # CGTTGGGC GCCCAACG 10 0 9.4e-004 2.6e+001 # CTTTGGGC GCCCAAAG 10 0 9.4e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 66.29 seconds