# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/seqs-shuffled # positives: 425 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/seqs-centered (Sat Jan 18 09:39:12 PST 2020) # negatives: 425 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/seqs-shuffled (Sat Jan 18 09:39:12 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 09:46:16 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 0.295 C 0.208 G 0.208 T 0.289 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 119 11 7.4e-028 1.8e-023 # GGTTCGA TCGAACC 94 4 5.7e-026 1.4e-021 # GGTTCAA TTGAACC 27 7 3.2e-004 7.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 121 E= 1.8e-023 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 0.223140 0.000000 0.776860 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCRACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 70 3 4.0e-019 9.5e-015 # ACCAACT AGTTGGT 53 2 8.6e-015 2.1e-010 # ACCGACT AGTCGGT 17 1 6.3e-005 1.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 9.5e-015 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.757143 0.000000 0.242857 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 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 81 9 2.2e-017 5.2e-013 # AGTGGTT AACCACT 61 4 2.6e-015 6.1e-011 # AGTGGTA TACCACT 33 5 1.3e-006 3.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 97 E= 5.2e-013 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 0.340206 0.000000 0.000000 0.659794 MOTIF CCRTACA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 71 6 1.1e-016 2.7e-012 # CCATACA TGTATGG 39 3 1.3e-009 3.1e-005 # CCGTACA TGTACGG 39 3 1.3e-009 3.1e-005 letter-probability matrix: alength= 4 w= 7 nsites= 89 E= 2.7e-012 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.539326 0.000000 0.460674 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 ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 41 2 4.3e-011 1.0e-006 # ATGGCAAC GTTGCCAT 31 2 4.0e-008 9.3e-004 # ATGGCATC GATGCCAT 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.0e-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 0.756098 0.000000 0.000000 0.243902 0.000000 1.000000 0.000000 0.000000 MOTIF AMACTAT DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AMACTAT ATAGTKT 55 8 1.2e-010 2.9e-006 # ACACTAT ATAGTGT 26 3 5.6e-006 1.3e-001 # AAACTAT ATAGTTT 29 5 1.4e-005 3.2e-001 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 2.9e-006 1.000000 0.000000 0.000000 0.000000 0.526316 0.473684 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 MOTIF GSGCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GSGCCA TGGCSC 66 14 2.8e-010 6.4e-006 # GCGCCA TGGCGC 47 8 1.6e-008 3.7e-004 # GGGCCA TGGCCC 19 6 6.6e-003 1.5e+002 letter-probability matrix: alength= 4 w= 6 nsites= 66 E= 6.4e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.712121 0.287879 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 CGCSTTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 46 6 1.9e-009 4.5e-005 # CGCCTTA TAAGGCG 32 4 6.1e-007 1.4e-002 # CGCGTTA TAACGCG 14 2 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 4.5e-005 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 0.695652 0.304348 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 ATCKTGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 41 4 2.0e-009 4.7e-005 # ATCGTGA TCACGAT 21 1 4.4e-006 1.0e-001 # ATCTTGA TCAAGAT 20 3 2.1e-004 4.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 4.7e-005 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 0.512195 0.487805 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 27 0 4.9e-009 1.1e-004 # AGTCAGAC GTCTGACT 14 0 5.5e-005 1.3e+000 # AGTCATAC GTATGACT 13 0 1.1e-004 2.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.1e-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 0.518519 0.481481 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCCATKC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCCATKC GMATGGG 35 3 1.8e-008 4.1e-004 # CCCATGC GCATGGG 19 1 1.7e-005 3.8e-001 # CCCATTC GAATGGG 16 2 5.9e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 4.1e-004 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.542857 0.457143 0.000000 1.000000 0.000000 0.000000 MOTIF ATCTTYTG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 32 2 2.0e-008 4.6e-004 # ATCTTCTG CAGAAGAT 20 0 7.6e-007 1.7e-002 # ATCTTTTG CAAAAGAT 12 2 6.1e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 4.6e-004 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 0.625000 0.000000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCRTGGAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGAG CTCCAYGG 25 0 2.1e-008 4.7e-004 # CCGTGGAG CTCCACGG 16 0 1.3e-005 3.0e-001 # CCATGGAG CTCCATGG 9 0 1.9e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 4.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.360000 0.000000 0.640000 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 MOTIF AAAAAAAW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAAW WTTTTTTT 74 24 4.0e-008 9.1e-004 # AAAAAAAA TTTTTTTT 51 15 2.2e-006 5.0e-002 # AAAAAAAT ATTTTTTT 45 15 3.8e-005 8.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 87 E= 9.1e-004 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.551724 0.000000 0.000000 0.448276 MOTIF CGGCCAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGGCCAA TTGGCCG 24 0 4.3e-008 9.6e-004 # CGGCCAA TTGGCCG 24 0 4.3e-008 9.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 9.6e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 22 0 1.8e-007 4.1e-003 # CGTGCTAA TTAGCACG 12 0 2.3e-004 5.1e+000 # CGTGTTAA TTAACACG 10 0 9.3e-004 2.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.1e-003 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 0.545455 0.000000 0.454545 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATGGTCA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AATGGTCA TGACCATT 20 0 7.6e-007 1.7e-002 # AATGGTCA TGACCATT 20 0 7.6e-007 1.7e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.7e-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 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 ACAAGGMT DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACAAGGMT AKCCTTGT 19 0 1.6e-006 3.5e-002 # ACAAGGCT AGCCTTGT 11 0 4.6e-004 1.0e+001 # ACAAGGAT ATCCTTGT 8 0 3.8e-003 8.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.5e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.421053 0.578947 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ACKGAAGA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACKGAAGA TCTTCMGT 19 0 1.6e-006 3.5e-002 # ACTGAAGA TCTTCAGT 10 0 9.3e-004 2.1e+001 # ACGGAAGA TCTTCCGT 9 0 1.9e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.5e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.473684 0.526316 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 54.43 seconds