# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/seqs-shuffled # positives: 645 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/seqs-centered (Sun Jan 19 06:01:18 PST 2020) # negatives: 645 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/seqs-shuffled (Sun Jan 19 06:01:18 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 06:17:26 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 0.294 C 0.207 G 0.203 T 0.297 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 88 4 3.2e-023 1.0e-018 # TGTATGGG CCCATACA 38 1 4.3e-011 1.4e-006 # TGTACGGA TCCGTACA 35 2 3.4e-009 1.1e-004 # TGTACGGG CCCGTACA 13 0 1.1e-004 3.6e+000 # TGTATGGA TCCATACA 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 102 E= 1.0e-018 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 0.490196 0.000000 0.509804 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.490196 0.000000 0.509804 0.000000 MOTIF SGGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 64 0 1.0e-020 3.3e-016 # GGGTTCGA TCGAACCC 41 0 2.4e-013 7.5e-009 # CGGTTCGA TCGAACCG 23 0 9.8e-008 3.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 3.3e-016 0.000000 0.359375 0.640625 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 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 67 5 6.7e-016 2.1e-011 # CTCGGCCA TGGCCGAG 34 1 6.9e-010 2.2e-005 # CTTGGCCA TGGCCAAG 22 3 6.8e-005 2.1e+000 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 2.1e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.507463 0.164179 0.328358 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 CGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 64 4 6.9e-016 2.2e-011 # CGCCTTA TAAGGCG 64 4 6.9e-016 2.2e-011 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 2.2e-011 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACTANA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACTANA TNTAGTG 75 12 2.7e-013 8.3e-009 # CACTATA TATAGTG 30 4 2.4e-006 7.4e-002 # CACTAAA TTTAGTG 25 4 4.4e-005 1.4e+000 # CACTACA TGTAGTG 17 3 1.2e-003 3.8e+001 # CACTAGA TCTAGTG 12 1 1.6e-003 5.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 8.3e-009 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 0.337662 0.181818 0.155844 0.324675 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCAVAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 46 2 1.9e-012 6.1e-008 # ACCCAGAC GTCTGGGT 16 0 1.4e-005 4.3e-001 # ACCCACAC GTGTGGGT 19 1 1.8e-005 5.5e-001 # ACCCAAAC GTTTGGGT 15 1 2.4e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 6.1e-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 0.288462 0.403846 0.307692 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 41 1 5.2e-012 1.6e-007 # ATGGCAAC GTTGCCAT 30 1 1.1e-008 3.4e-004 # ATGGCATC GATGCCAT 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.6e-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 0.731707 0.000000 0.000000 0.268293 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 2 1.2e-010 3.6e-006 # GCGCTACC GGTAGCGC 25 1 3.2e-007 1.0e-002 # GCTCTACC GGTAGAGC 15 1 2.4e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.6e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.625000 0.375000 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 CACATYAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 30 0 6.6e-010 2.0e-005 # CACATCAC GTGATGTG 18 0 3.4e-006 1.0e-001 # CACATTAC GTAATGTG 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.0e-005 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 0.600000 0.000000 0.400000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 46 7 1.1e-008 3.4e-004 # TGGCGCA TGCGCCA 25 3 1.1e-005 3.5e-001 # TGGCGTA TACGCCA 21 4 4.1e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 3.4e-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 0.543478 0.000000 0.456522 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 48 9 4.1e-008 1.3e-003 # ATCTTGA TCAAGAT 31 6 1.6e-005 5.0e-001 # ATCGTGA TCACGAT 17 3 1.2e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 1.3e-003 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 0.354167 0.645833 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 ATGGGYG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYG CRCCCAT 48 9 4.1e-008 1.3e-003 # ATGGGTG CACCCAT 32 6 9.4e-006 2.9e-001 # ATGGGCG CGCCCAT 17 3 1.2e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 1.3e-003 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 0.340000 0.000000 0.660000 0.000000 0.000000 1.000000 0.000000 MOTIF CCGTGMTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 24 0 4.8e-008 1.5e-003 # CCGTGATA TATCACGG 13 0 1.1e-004 3.5e+000 # CCGTGCTA TAGCACGG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-003 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 0.541667 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CWGAAGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CWGAAGA TCTTCWG 42 7 1.1e-007 3.4e-003 # CTGAAGA TCTTCAG 16 1 1.3e-004 3.9e+000 # CAGAAGA TCTTCTG 27 6 1.4e-004 4.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 3.4e-003 0.000000 1.000000 0.000000 0.000000 0.642857 0.000000 0.000000 0.357143 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 MOTIF CGSTCTCC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGSTCTCC GGAGASCG 22 0 2.0e-007 6.1e-003 # CGGTCTCC GGAGACCG 13 0 1.1e-004 3.5e+000 # CGCTCTCC GGAGAGCG 9 0 1.9e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.409091 0.590909 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 30 3 5.3e-007 1.6e-002 # AGTCATAC GTATGACT 17 1 6.6e-005 2.0e+000 # AGTCAGAC GTCTGACT 13 2 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.6e-002 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 0.433333 0.566667 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 20 0 8.2e-007 2.5e-002 # ACTGAGCT AGCTCAGT 20 0 8.2e-007 2.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.5e-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 0.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 75.04 seconds