# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-shuffled # positives: 686 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-centered (Sat Jan 18 12:33:57 PST 2020) # negatives: 686 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-shuffled (Sat Jan 18 12:33:57 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 12:50:01 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 0.291 C 0.211 G 0.208 T 0.290 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 149 15 1.9e-032 6.4e-028 # GGTTCGA TCGAACC 105 2 5.6e-031 1.9e-026 # GGTTCAA TTGAACC 46 13 6.4e-006 2.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 151 E= 6.4e-028 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 0.304636 0.000000 0.695364 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAWR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWR YWTTTTT 267 131 3.0e-016 9.8e-012 # AAAAAAA TTTTTTT 148 66 5.7e-010 1.9e-005 # AAAAATA TATTTTT 98 35 4.3e-009 1.4e-004 # AAAAAAG CTTTTTT 99 48 5.4e-006 1.8e-001 # AAAAATG CATTTTT 59 31 1.5e-003 5.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 345 E= 9.8e-012 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 0.594203 0.000000 0.000000 0.405797 0.623188 0.000000 0.376812 0.000000 MOTIF AGTGGTWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWA TWACCACT 51 1 4.6e-015 1.5e-010 # AGTGGTTA TAACCACT 33 1 1.4e-009 4.6e-005 # AGTGGTAA TTACCACT 18 0 3.4e-006 1.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 1.5e-010 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 0.352941 0.000000 0.000000 0.647059 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAACTK DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCAACTK MAGTTGGT 43 2 1.6e-011 5.2e-007 # ACCAACTT AAGTTGGT 27 2 6.5e-007 2.1e-002 # ACCAACTG CAGTTGGT 16 0 1.4e-005 4.6e-001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 5.2e-007 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.372093 0.627907 MOTIF CCCATDC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 60 11 5.3e-010 1.7e-005 # CCCATGC GCATGGG 22 1 2.4e-006 8.0e-002 # CCCATAC GTATGGG 22 6 1.7e-003 5.5e+001 # CCCATTC GAATGGG 17 4 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 1.7e-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 0.000000 0.000000 0.000000 1.000000 0.360656 0.000000 0.360656 0.278689 0.000000 1.000000 0.000000 0.000000 MOTIF GYGGTCTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GYGGTCTA TAGACCRC 32 1 2.8e-009 9.1e-005 # GTGGTCTA TAGACCAC 24 1 6.4e-007 2.1e-002 # GCGGTCTA TAGACCGC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.1e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 30 1 1.1e-008 3.6e-004 # GCGCTACC GGTAGCGC 22 1 2.4e-006 8.0e-002 # GCTCTACC GGTAGAGC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.6e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.733333 0.266667 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 AMGTTGCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AMGTTGCC GGCAACKT 26 0 1.2e-008 3.8e-004 # ACGTTGCC GGCAACGT 15 0 2.8e-005 9.2e-001 # AAGTTGCC GGCAACTT 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.8e-004 1.000000 0.000000 0.000000 0.000000 0.423077 0.576923 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTAASAG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 24 1 6.4e-007 2.1e-002 # ATTAAGAG CTCTTAAT 13 0 1.2e-004 3.7e+000 # ATTAACAG CTGTTAAT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.458333 0.541667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CAGAYGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CAGAYGC GCRTCTG 27 2 6.5e-007 2.1e-002 # CAGATGC GCATCTG 15 1 2.4e-004 7.9e+000 # CAGACGC GCGTCTG 12 1 1.6e-003 5.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.1e-002 0.000000 1.000000 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 0.000000 0.444444 0.000000 0.555556 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CYATGGCC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CYATGGCC GGCCATRG 20 0 8.3e-007 2.7e-002 # CCATGGCC GGCCATGG 12 0 2.3e-004 7.5e+000 # CTATGGCC GGCCATAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 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 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 51.67 seconds