# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SRB8/seqs-shuffled # positives: 857 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SRB8/seqs-centered (Sun Jan 19 05:43:30 PST 2020) # negatives: 857 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SRB8/seqs-shuffled (Sun Jan 19 05:43:30 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:59:28 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 0.313 C 0.190 G 0.185 T 0.311 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 100 7 1.2e-023 3.9e-019 # TGTACGGA TCCGTACA 41 0 2.8e-013 9.1e-009 # TGTATGGG CCCATACA 43 5 4.5e-009 1.5e-004 # TGTACGGG CCCGTACA 13 0 1.2e-004 3.8e+000 # TGTATGGA TCCATACA 14 2 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 114 E= 3.9e-019 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.491228 0.000000 0.508772 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.508772 0.000000 0.491228 0.000000 MOTIF GGHTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 113 13 9.9e-023 3.2e-018 # GGTTCGA TCGAACC 93 8 9.5e-021 3.1e-016 # GGATCGA TCGATCC 25 4 4.6e-005 1.5e+000 # GGCTCGA TCGAGCC 18 2 1.9e-004 6.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 113 E= 3.2e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.185841 0.079646 0.000000 0.734513 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 CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 68 2 5.7e-019 1.8e-014 # CTCGGCCA TGGCCGAG 35 2 3.7e-009 1.2e-004 # CTTGGCCA TGGCCAAG 22 0 2.1e-007 6.7e-003 # CTGGGCCA TGGCCCAG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 1.8e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.514706 0.161765 0.323529 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 84 9 1.9e-017 6.3e-013 # CGCCTTA TAAGGCG 68 5 5.2e-016 1.7e-011 # CGCGTTA TAACGCG 16 4 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 84 E= 6.3e-013 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 0.809524 0.190476 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-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 48 2 6.1e-013 1.9e-008 # GCGCTACC GGTAGCGC 33 1 1.5e-009 4.9e-005 # GCTCTACC GGTAGAGC 15 1 2.5e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 1.9e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.687500 0.312500 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 ACCCANAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 72 12 2.3e-012 7.5e-008 # ACCCACAC GTGTGGGT 35 7 6.0e-006 1.9e-001 # ACCCAGAC GTCTGGGT 16 1 1.3e-004 4.1e+000 # ACCCAAAC GTTTGGGT 16 3 2.1e-003 6.7e+001 # ACCCATAC GTATGGGT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 133 E= 7.5e-008 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.120301 0.676692 0.120301 0.082707 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGGTTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTW WAACCACT 46 2 2.4e-012 7.5e-008 # AGTGGTTA TAACCACT 30 1 1.2e-008 3.7e-004 # AGTGGTTT AAACCACT 16 1 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 7.5e-008 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 0.000000 0.000000 0.000000 1.000000 0.652174 0.000000 0.000000 0.347826 MOTIF AAAAADA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AAAAADA THTTTTT 297 183 5.3e-010 1.7e-005 # AAAAAGA TCTTTTT 92 42 4.2e-006 1.3e-001 # AAAAAAA TTTTTTT 174 106 5.6e-006 1.8e-001 # AAAAATA TATTTTT 123 80 8.2e-004 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 385 E= 1.7e-005 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 0.446753 0.000000 0.225974 0.327273 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 46 5 7.1e-010 2.2e-005 # ATGGCAAC GTTGCCAT 27 1 8.9e-008 2.8e-003 # ATGGCATC GATGCCAT 20 4 7.2e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.2e-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 0.574468 0.000000 0.000000 0.425532 0.000000 1.000000 0.000000 0.000000 MOTIF ACTGMGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACTGMGC GCKCAGT 37 2 9.9e-010 3.1e-005 # ACTGCGC GCGCAGT 18 0 3.5e-006 1.1e-001 # ACTGAGC GCTCAGT 19 2 1.0e-004 3.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 3.1e-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 0.000000 0.000000 1.000000 0.000000 0.513514 0.486486 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 33 1 1.5e-009 4.8e-005 # CTATCACA TGTGATAG 18 0 3.5e-006 1.1e-001 # CTATCACG CGTGATAG 15 1 2.5e-004 7.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.8e-005 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 MOTIF GRAGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GRAGA TCTYC 315 203 2.4e-009 7.5e-005 # GAAGA TCTTC 219 137 6.5e-007 2.0e-002 # GGAGA TCTCC 124 80 6.5e-004 2.0e+001 letter-probability matrix: alength= 4 w= 5 nsites= 394 E= 7.5e-005 0.000000 0.000000 1.000000 0.000000 0.644670 0.000000 0.355330 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 MOTIF AGARTCAT DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGARTCAT ATGAYTCT 30 1 1.2e-008 3.6e-004 # AGAGTCAT ATGACTCT 15 0 2.9e-005 8.8e-001 # AGAATCAT ATGATTCT 15 1 2.5e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.6e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 MOTIF CSACTAGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CSACTAGA TCTAGTSG 26 0 1.2e-008 3.8e-004 # CGACTAGA TCTAGTCG 14 0 5.8e-005 1.8e+000 # CCACTAGA TCTAGTGG 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.461538 0.538462 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCACRCG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CCACRCG CGYGTGG 35 4 1.3e-007 3.9e-003 # CCACACG CGTGTGG 23 2 8.6e-006 2.6e-001 # CCACGCG CGCGTGG 12 2 6.3e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 3.9e-003 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 0.657143 0.000000 0.342857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGATCGKG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 21 0 4.2e-007 1.3e-002 # AGATCGGG CCCGATCT 14 0 5.8e-005 1.8e+000 # AGATCGTG CACGATCT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 MOTIF GATATTTY DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GATATTTY RAAATATC 27 2 6.8e-007 2.1e-002 # GATATTTT AAAATATC 13 0 1.2e-004 3.5e+000 # GATATTTC GAAATATC 14 2 2.0e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.518519 0.000000 0.481481 MOTIF ATGGGYGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYGC GCRCCCAT 20 0 8.5e-007 2.6e-002 # ATGGGCGC GCGCCCAT 12 0 2.3e-004 7.1e+000 # ATGGGTGC GCACCCAT 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 98.19 seconds