# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MSS11/seqs-shuffled # positives: 740 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MSS11/seqs-centered (Sat Jan 18 07:32:02 PST 2020) # negatives: 740 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MSS11/seqs-shuffled (Sat Jan 18 07:32:02 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 07:47:29 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 0.296 C 0.206 G 0.206 T 0.292 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 117 11 1.3e-025 4.2e-021 # GGTTCGA TCGAACC 97 8 4.3e-022 1.4e-017 # AGTTCGA TCGAACT 27 3 3.5e-006 1.2e-001 letter-probability matrix: alength= 4 w= 7 nsites= 117 E= 4.2e-021 0.196581 0.000000 0.803419 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 84 5 7.7e-021 2.6e-016 # TGTATGGG CCCATACA 39 2 2.5e-010 8.2e-006 # TGTACGGA TCCGTACA 33 1 1.4e-009 4.8e-005 # TGTATGGA TCCATACA 13 1 8.7e-004 2.9e+001 # TGTACGGG CCCGTACA 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 98 E= 2.6e-016 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 0.448980 0.000000 0.551020 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.489796 0.000000 0.510204 0.000000 MOTIF AGTYGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 71 4 7.0e-018 2.3e-013 # AGTTGGTT AACCAACT 30 2 9.5e-008 3.1e-003 # AGTTGGTA TACCAACT 20 1 9.3e-006 3.1e-001 # AGTCGGTT AACCGACT 11 0 4.7e-004 1.6e+001 # AGTCGGTA TACCGACT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 2.3e-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 0.295775 0.000000 0.704225 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.422535 0.000000 0.000000 0.577465 MOTIF AGTGGTWA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWA TWACCACT 54 3 8.7e-014 2.9e-009 # AGTGGTTA TAACCACT 37 3 6.6e-009 2.2e-004 # AGTGGTAA TTACCACT 17 0 7.0e-006 2.3e-001 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 2.9e-009 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 0.314815 0.000000 0.000000 0.685185 1.000000 0.000000 0.000000 0.000000 MOTIF GTWGCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTWGCCA TGGCWAC 55 8 2.3e-010 7.5e-006 # GTTGCCA TGGCAAC 37 7 1.9e-006 6.4e-002 # GTAGCCA TGGCTAC 18 1 3.5e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 7.5e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.327273 0.000000 0.000000 0.672727 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 AAGARA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGARA TYTCTT 233 133 1.0e-009 3.4e-005 # AAGAAA TTTCTT 180 102 1.5e-007 5.0e-003 # AAGAGA TCTCTT 69 36 5.5e-004 1.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 273 E= 3.4e-005 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 0.728938 0.000000 0.271062 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACACSC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACACSC GSGTGT 95 32 2.2e-009 7.3e-005 # ACACCC GGGTGT 54 16 1.8e-006 5.7e-002 # ACACGC GCGTGT 43 17 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 103 E= 7.3e-005 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 1.000000 0.000000 0.000000 0.000000 0.582524 0.417476 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTCTMCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 28 0 2.9e-009 9.2e-005 # CTCTCCCA TGGGAGAG 17 0 7.0e-006 2.2e-001 # CTCTACCA TGGTAGAG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.2e-005 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 0.000000 1.000000 0.392857 0.607143 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 MOTIF CTATCACR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 34 2 6.9e-009 2.2e-004 # CTATCACA TGTGATAG 18 1 3.5e-005 1.1e+000 # CTATCACG CGTGATAG 16 1 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.2e-004 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 0.529412 0.000000 0.470588 0.000000 MOTIF AAGGCGY DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAGGCGY RCGCCTT 38 5 8.6e-008 2.8e-003 # AAGGCGT ACGCCTT 16 1 1.3e-004 4.1e+000 # AAGGCGC GCGCCTT 22 4 2.4e-004 7.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 2.8e-003 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 0.000000 0.578947 0.000000 0.421053 MOTIF CACGCGAS DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACGCGAS STCGCGTG 23 0 1.0e-007 3.2e-003 # CACGCGAC GTCGCGTG 14 0 5.7e-005 1.8e+000 # CACGCGAG CTCGCGTG 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.608696 0.391304 0.000000 MOTIF CKTTGGGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 26 1 1.7e-007 5.4e-003 # CGTTGGGC GCCCAACG 18 1 3.5e-005 1.1e+000 # CTTTGGGC GCCCAAAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.4e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.692308 0.307692 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 MOTIF CGCGCTWC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGCGCTWC GWAGCGCG 22 0 2.0e-007 6.5e-003 # CGCGCTAC GTAGCGCG 13 0 1.2e-004 3.7e+000 # CGCGCTTC GAAGCGCG 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.5e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.590909 0.000000 0.000000 0.409091 0.000000 1.000000 0.000000 0.000000 MOTIF CGGCCAM DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGGCCAM KTGGCCG 41 7 2.1e-007 6.7e-003 # CGGCCAA TTGGCCG 26 5 8.3e-005 2.6e+000 # CGGCCAC GTGGCCG 15 2 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 6.7e-003 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 0.634146 0.365854 0.000000 0.000000 MOTIF TCTTCTGR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TCTTCTGR YCAGAAGA 21 0 4.1e-007 1.3e-002 # TCTTCTGA TCAGAAGA 14 0 5.7e-005 1.8e+000 # TCTTCTGG CCAGAAGA 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 MOTIF CACGGTGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGA TCACCGTG 20 0 8.4e-007 2.7e-002 # CACGGTGA TCACCGTG 20 0 8.4e-007 2.7e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-002 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 1.000000 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGAYCGG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGG CCGRTCT 42 9 1.2e-006 3.7e-002 # AGACCGG CCGGTCT 21 5 1.1e-003 3.6e+001 # AGATCGG CCGATCT 21 5 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 3.7e-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 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 82.05 seconds