# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP1/seqs-shuffled # positives: 641 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP1/seqs-centered (Fri Jan 17 22:08:20 PST 2020) # negatives: 641 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP1/seqs-shuffled (Fri Jan 17 22:08:20 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:24:55 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 0.304 C 0.192 G 0.195 T 0.309 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 72 14 1.8e-011 5.9e-007 # GGTTCGA TCGAACC 48 7 3.3e-009 1.1e-004 # GGTTCAA TTGAACC 24 7 1.5e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 5.9e-007 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 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 363 254 7.2e-010 2.3e-005 # CAAGA TCTTG 207 133 1.8e-006 5.9e-002 # GAAGA TCTTC 213 160 6.8e-004 2.2e+001 letter-probability matrix: alength= 4 w= 5 nsites= 529 E= 2.3e-005 0.000000 0.476371 0.523629 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 ACCARCT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCARCT AGYTGGT 32 2 2.4e-008 7.6e-004 # ACCAACT AGTTGGT 23 2 8.2e-006 2.6e-001 # ACCAGCT AGCTGGT 9 0 1.9e-003 5.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 7.6e-004 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 0.727273 0.000000 0.272727 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GGTADC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGTADC GHTACC 94 36 4.3e-008 1.3e-003 # GGTAGC GCTACC 26 6 2.3e-004 7.1e+000 # GGTAAC GTTACC 42 19 1.8e-003 5.6e+001 # GGTATC GATACC 28 12 7.5e-003 2.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 97 E= 1.3e-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 1.000000 0.000000 0.000000 0.000000 0.443299 0.000000 0.268041 0.288660 0.000000 1.000000 0.000000 0.000000 MOTIF GTGGTCWA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTGGTCWA TWGACCAC 22 0 2.0e-007 6.1e-003 # GTGGTCTA TAGACCAC 14 0 5.7e-005 1.7e+000 # GTGGTCAA TTGACCAC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.1e-003 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 0.000000 1.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.636364 1.000000 0.000000 0.000000 0.000000 MOTIF GTGRTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTGRTA TAYCAC 80 30 3.5e-007 1.1e-002 # GTGGTA TACCAC 39 13 1.6e-004 4.8e+000 # GTGATA TATCAC 43 17 4.0e-004 1.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 86 E= 1.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.523256 0.000000 0.476744 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAARAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAAARAAA TTTYTTTT 88 37 9.4e-007 2.9e-002 # AAAAAAAA TTTTTTTT 56 21 2.5e-005 7.5e-001 # AAAAGAAA TTTCTTTT 36 16 3.3e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 94 E= 2.9e-002 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 0.617021 0.000000 0.382979 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 # Stopping reason: E-value threshold exceeded # Running time: 32.88 seconds