# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CIN5/seqs-shuffled # positives: 633 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CIN5/seqs-centered (Sat Jan 18 15:48:30 PST 2020) # negatives: 633 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CIN5/seqs-shuffled (Sat Jan 18 15:48:31 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:04:22 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 0.207 G 0.206 T 0.291 MOTIF GTTCGAHY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGAHY RDTCGAAC 102 4 1.1e-027 3.4e-023 # GTTCGATC GATCGAAC 29 0 1.3e-009 4.3e-005 # GTTCGATT AATCGAAC 27 3 3.4e-006 1.1e-001 # GTTCGAAT ATTCGAAC 15 0 2.8e-005 9.0e-001 # GTTCGACT AGTCGAAC 14 1 4.6e-004 1.5e+001 # GTTCGAAC GTTCGAAC 9 0 1.9e-003 6.1e+001 # GTTCGACC GGTCGAAC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 102 E= 3.4e-023 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 0.235294 0.215686 0.000000 0.549020 0.000000 0.450980 0.000000 0.549020 MOTIF AGTGGTWW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWW WWACCACT 74 4 6.5e-019 2.1e-014 # AGTGGTTA TAACCACT 39 1 2.1e-011 6.7e-007 # AGTGGTAA TTACCACT 20 1 9.1e-006 2.9e-001 # AGTGGTTT AAACCACT 16 1 1.3e-004 4.0e+000 # AGTGGTAT ATACCACT 11 1 3.1e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 86 E= 2.1e-014 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 0.360465 0.000000 0.000000 0.639535 0.686047 0.000000 0.000000 0.313953 MOTIF CAACTKGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 44 0 2.6e-014 8.3e-010 # CAACTTGG CCAAGTTG 35 0 1.8e-011 5.7e-007 # CAACTGGG CCCAGTTG 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 8.3e-010 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 0.204545 0.795455 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAAARWA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAAARWA TWYTTTT 242 127 6.5e-013 2.1e-008 # AAAAATA TATTTTT 92 35 5.2e-008 1.7e-003 # AAAAAAA TTTTTTT 120 56 1.2e-007 3.8e-003 # AAAAGTA TACTTTT 36 17 5.4e-003 1.7e+002 # AAAAGAA TTCTTTT 61 37 7.6e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 300 E= 2.1e-008 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 0.686667 0.000000 0.313333 0.000000 0.596667 0.000000 0.000000 0.403333 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 52 5 1.3e-011 4.1e-007 # CGCCTTA TAAGGCG 40 3 8.7e-010 2.7e-005 # CGCGTTA TAACGCG 12 2 6.2e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 4.1e-007 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 0.769231 0.230769 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-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 39 1 2.1e-011 6.6e-007 # GCGCTACC GGTAGCGC 28 1 4.2e-008 1.3e-003 # GCTCTACC GGTAGAGC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 6.6e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.717949 0.282051 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 ATGGCAW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAW WTGCCAT 59 9 7.0e-011 2.2e-006 # ATGGCAT ATGCCAT 30 2 9.1e-008 2.8e-003 # ATGGCAA TTGCCAT 30 7 7.7e-005 2.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 2.2e-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 0.500000 0.000000 0.000000 0.500000 MOTIF CACGGYG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 35 1 3.4e-010 1.1e-005 # CACGGTG CACCGTG 25 1 3.2e-007 1.0e-002 # CACGGCG CGCCGTG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.1e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 1.000000 0.000000 MOTIF CAASAGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAASAGA TCTSTTG 42 7 1.1e-007 3.4e-003 # CAACAGA TCTGTTG 18 2 1.8e-004 5.7e+000 # CAAGAGA TCTCTTG 24 5 2.4e-004 7.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 3.4e-003 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 0.428571 0.571429 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 GGTTCRA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 63 18 1.1e-007 3.4e-003 # GGTTCGA TCGAACC 30 5 8.7e-006 2.7e-001 # GGTTCAA TTGAACC 33 13 1.9e-003 5.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 63 E= 3.4e-003 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 0.523810 0.000000 0.476190 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACRGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACRGA TCYGTG 67 21 1.9e-007 5.8e-003 # CACAGA TCTGTG 30 8 1.9e-004 6.0e+000 # CACGGA TCCGTG 38 13 2.4e-004 7.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 68 E= 5.8e-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 0.441176 0.000000 0.558824 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 36 5 2.7e-007 8.2e-003 # TGGCGCA TGCGCCA 20 3 2.2e-004 6.7e+000 # TGGCGTA TACGCCA 16 2 6.1e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 8.2e-003 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 0.555556 0.000000 0.444444 1.000000 0.000000 0.000000 0.000000 MOTIF STTAAGCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST STTAAGCA TGCTTAAS 25 1 3.2e-007 9.8e-003 # GTTAAGCA TGCTTAAC 17 1 6.6e-005 2.0e+000 # CTTAAGCA TGCTTAAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.8e-003 0.000000 0.320000 0.680000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 27 2 6.4e-007 1.9e-002 # AGTCATAC GTATGACT 15 1 2.4e-004 7.3e+000 # AGTCAGAC GTCTGACT 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.9e-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 0.444444 0.555556 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TAATCAKA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TAATCAKA TMTGATTA 34 5 8.7e-007 2.6e-002 # TAATCAGA TCTGATTA 15 1 2.4e-004 7.3e+000 # TAATCATA TATGATTA 19 4 1.2e-003 3.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.6e-002 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.441176 0.558824 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGCSCA TGSGCG 70 25 9.0e-007 2.7e-002 # CGCCCA TGGGCG 44 18 4.9e-004 1.5e+001 # CGCGCA TGCGCG 26 7 5.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 71 E= 2.7e-002 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 0.633803 0.366197 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 67.25 seconds