# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MAC1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MAC1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MAC1/seqs-shuffled # positives: 691 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MAC1/seqs-centered (Sun Jan 19 01:53:01 PST 2020) # negatives: 691 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MAC1/seqs-shuffled (Sun Jan 19 01:53:01 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:08:48 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 0.298 C 0.203 G 0.203 T 0.296 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 96 10 2.5e-020 8.0e-016 # GGTTCGA TCGAACC 85 8 1.2e-018 3.7e-014 # GGATCGA TCGATCC 18 2 1.8e-004 5.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 96 E= 8.0e-016 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.000000 0.833333 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 BTAAGGCG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 66 1 9.5e-020 3.0e-015 # TTAAGGCG CGCCTTAA 37 0 4.4e-012 1.4e-007 # CTAAGGCG CGCCTTAG 18 1 3.5e-005 1.1e+000 # GTAAGGCG CGCCTTAC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 66 E= 3.0e-015 0.000000 0.272727 0.166667 0.560606 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 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 MOTIF CAYCCRTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAYCCRTA TAYGGRTG 67 2 8.4e-019 2.7e-014 # CACCCATA TATGGGTG 25 0 2.4e-008 7.6e-004 # CATCCGTA TACGGATG 23 1 1.3e-006 4.0e-002 # CATCCATA TATGGATG 13 1 8.7e-004 2.8e+001 # CACCCGTA TACGGGTG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 74 E= 2.7e-014 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.486486 0.000000 0.513514 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.527027 0.000000 0.472973 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 71 5 5.1e-017 1.6e-012 # CTCGGCCA TGGCCGAG 35 1 3.5e-010 1.1e-005 # CTTGGCCA TGGCCAAG 24 3 2.1e-005 6.7e-001 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 1.6e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.492958 0.169014 0.338028 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-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 43 1 1.3e-012 4.3e-008 # GCGCTACC GGTAGCGC 26 0 1.2e-008 3.7e-004 # GCTCTACC GGTAGAGC 17 1 6.6e-005 2.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 4.3e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.604651 0.395349 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 2 8.1e-012 2.6e-007 # ATGGCAAC GTTGCCAT 33 0 7.9e-011 2.5e-006 # ATGGCATC GATGCCAT 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 2.6e-007 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 0.733333 0.000000 0.000000 0.266667 0.000000 1.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 34 0 3.8e-011 1.2e-006 # GTGATAGC GCTATCAC 20 0 8.3e-007 2.6e-002 # GTGATAGT ACTATCAC 15 0 2.8e-005 8.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.2e-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 0.571429 0.000000 0.428571 MOTIF CACTADA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CACTADA THTAGTG 76 17 5.8e-011 1.8e-006 # CACTATA TATAGTG 33 4 4.0e-007 1.3e-002 # CACTAGA TCTAGTG 17 4 3.4e-003 1.1e+002 # CACTAAA TTTAGTG 27 10 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 1.8e-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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.350649 0.000000 0.220779 0.428571 1.000000 0.000000 0.000000 0.000000 MOTIF ARAARAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ARAARAAA TTTYTTYT 129 52 4.1e-010 1.3e-005 # AGAAAAAA TTTTTTCT 44 11 2.9e-006 9.1e-002 # AAAAGAAA TTTCTTTT 41 13 6.5e-005 2.1e+000 # AAAAAAAA TTTTTTTT 64 29 1.1e-004 3.6e+000 # AGAAGAAA TTTCTTCT 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 151 E= 1.3e-005 1.000000 0.000000 0.000000 0.000000 0.695364 0.000000 0.304636 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.655629 0.000000 0.344371 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 MOTIF CCCAHACA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCCAHACA TGTDTGGG 49 7 1.9e-009 6.1e-005 # CCCATACA TGTATGGG 22 3 6.9e-005 2.2e+000 # CCCACACA TGTGTGGG 17 2 3.4e-004 1.1e+001 # CCCAAACA TGTTTGGG 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 6.1e-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 0.230769 0.346154 0.000000 0.423077 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 AGTCAKAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 31 1 5.6e-009 1.7e-004 # AGTCATAC GTATGACT 16 0 1.4e-005 4.4e-001 # AGTCAGAC GTCTGACT 15 1 2.4e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.7e-004 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 0.483871 0.516129 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGGAGAY DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTGGAGAY RTCTCCAC 26 0 1.2e-008 3.7e-004 # GTGGAGAC GTCTCCAC 14 0 5.7e-005 1.8e+000 # GTGGAGAT ATCTCCAC 12 0 2.3e-004 7.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.7e-004 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 0.538462 0.000000 0.461538 MOTIF TGGCGCW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TGGCGCW WGCGCCA 41 5 1.4e-008 4.3e-004 # TGGCGCA TGCGCCA 27 5 4.8e-005 1.5e+000 # TGGCGCT AGCGCCA 14 0 5.7e-005 1.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 4.3e-004 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 0.658537 0.000000 0.000000 0.341463 MOTIF AHATCTTG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AHATCTTG CAAGATDT 41 6 5.7e-008 1.8e-003 # AAATCTTG CAAGATTT 18 3 6.9e-004 2.1e+001 # ATATCTTG CAAGATAT 16 3 2.1e-003 6.5e+001 # ACATCTTG CAAGATGT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.8e-003 1.000000 0.000000 0.000000 0.000000 0.439024 0.170732 0.000000 0.390244 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 0.000000 1.000000 0.000000 MOTIF ACTGAGCT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 0 9.9e-008 3.1e-003 # ACTGAGCT AGCTCAGT 23 0 9.9e-008 3.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.1e-003 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 MOTIF GAYTAGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GAYTAGA TCTARTC 37 5 1.5e-007 4.7e-003 # GATTAGA TCTAATC 24 4 7.8e-005 2.4e+000 # GACTAGA TCTAGTC 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 4.7e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.351351 0.000000 0.648649 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGTCW DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATGGTCW WGACCAT 38 6 3.2e-007 1.0e-002 # ATGGTCA TGACCAT 25 5 1.4e-004 4.4e+000 # ATGGTCT AGACCAT 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 1.0e-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 0.641026 0.000000 0.000000 0.358974 MOTIF AKCGCAAG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AKCGCAAG CTTGCGMT 23 1 1.3e-006 3.9e-002 # AGCGCAAG CTTGCGCT 13 0 1.2e-004 3.6e+000 # ATCGCAAG CTTGCGAT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.9e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.565217 0.434783 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 1.000000 0.000000 MOTIF STTAAGCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST STTAAGCA TGCTTAAS 23 1 1.3e-006 3.9e-002 # GTTAAGCA TGCTTAAC 15 1 2.4e-004 7.5e+000 # CTTAAGCA TGCTTAAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.9e-002 0.000000 0.347826 0.652174 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 88.38 seconds