# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-shuffled # positives: 1025 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-centered (Sat Jan 18 07:16:29 PST 2020) # negatives: 1025 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-shuffled (Sat Jan 18 07:16:29 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 07:30:37 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 0.305 C 0.193 G 0.194 T 0.309 MOTIF AAGARA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AAGARA TYTCTT 381 214 2.4e-016 8.5e-012 # AAGAAA TTTCTT 296 158 1.1e-013 4.1e-009 # AAGAGA TCTCTT 117 74 6.8e-004 2.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 477 E= 8.5e-012 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 0.729560 0.000000 0.270440 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 80 11 6.6e-015 2.4e-010 # GGTTCGA TCGAACC 80 11 6.6e-015 2.4e-010 letter-probability matrix: alength= 4 w= 7 nsites= 80 E= 2.4e-010 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 ACCACTM DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 71 11 1.4e-012 4.9e-008 # ACCACTA TAGTGGT 42 6 3.7e-008 1.3e-003 # ACCACTC GAGTGGT 29 5 1.7e-005 5.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 4.9e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.591549 0.408451 0.000000 0.000000 MOTIF ATRGCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATRGCA TGCYAT 151 62 5.4e-011 1.9e-006 # ATGGCA TGCCAT 87 30 2.8e-008 9.8e-004 # ATAGCA TGCTAT 66 34 6.8e-004 2.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 158 E= 1.9e-006 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.417722 0.000000 0.582278 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 AGTYGGTW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 50 4 1.1e-011 4.0e-007 # AGTTGGTT AACCAACT 18 2 1.9e-004 6.6e+000 # AGTTGGTA TACCAACT 17 2 3.5e-004 1.2e+001 # AGTCGGTT AACCGACT 8 0 3.9e-003 1.4e+002 # AGTCGGTA TACCGACT 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 4.0e-007 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 0.300000 0.000000 0.700000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.480000 0.000000 0.000000 0.520000 MOTIF GCKKCTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKKCTA TAGMMGC 77 16 1.9e-011 6.6e-007 # GCGGCTA TAGCCGC 28 6 8.7e-005 3.0e+000 # GCTTCTA TAGAAGC 25 7 9.7e-004 3.4e+001 # GCTGCTA TAGCAGC 18 4 2.1e-003 7.3e+001 # GCGTCTA TAGACGC 8 0 3.9e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 80 E= 6.6e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.462500 0.537500 0.000000 0.000000 0.587500 0.412500 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 GAAAAMAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GAAAAMAA TTKTTTTC 99 37 1.9e-008 6.6e-004 # GAAAAAAA TTTTTTTC 77 29 9.5e-007 3.3e-002 # GAAAACAA TTGTTTTC 24 8 3.3e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 102 E= 6.6e-004 0.000000 0.000000 1.000000 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 0.764706 0.235294 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF KCGCCTTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST KCGCCTTA TAAGGCGM 28 1 4.7e-008 1.6e-003 # TCGCCTTA TAAGGCGA 16 1 1.3e-004 4.5e+000 # GCGCCTTA TAAGGCGC 12 0 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.6e-003 0.000000 0.000000 0.428571 0.571429 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 CCCATDC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 58 14 5.1e-008 1.8e-003 # CCCATTC GAATGGG 22 5 7.1e-004 2.5e+001 # CCCATGC GCATGGG 17 3 1.2e-003 4.3e+001 # CCCATAC GTATGGG 20 6 4.5e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 1.8e-003 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 0.338983 0.000000 0.288136 0.372881 0.000000 1.000000 0.000000 0.000000 MOTIF CWGACGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CWGACGC GCGTCWG 33 3 9.1e-008 3.2e-003 # CTGACGC GCGTCAG 18 1 3.6e-005 1.2e+000 # CAGACGC GCGTCTG 15 2 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 3.2e-003 0.000000 1.000000 0.000000 0.000000 0.454545 0.000000 0.000000 0.545455 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF KATATA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST KATATA TATATM 153 83 7.8e-007 2.7e-002 # TATATA TATATA 86 43 5.9e-005 2.0e+000 # GATATA TATATC 79 46 1.5e-003 5.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 167 E= 2.7e-002 0.000000 0.000000 0.461078 0.538922 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 1.000000 0.000000 0.000000 0.000000 MOTIF GTTAGTAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTTAGTAA TTACTAAC 20 0 8.7e-007 3.0e-002 # GTTAGTAA TTACTAAC 20 0 8.7e-007 3.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 3.0e-002 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 79.26 seconds