# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/seqs-shuffled # positives: 1112 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/seqs-centered (Sat Jan 18 20:11:10 PST 2020) # negatives: 1112 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/seqs-shuffled (Sat Jan 18 20:11:10 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 20:21:47 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 0.299 C 0.199 G 0.200 T 0.302 MOTIF TCTTCW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCTTCW WGAAGA 341 167 6.4e-019 2.2e-014 # TCTTCT AGAAGA 206 91 3.4e-013 1.2e-008 # TCTTCA TGAAGA 175 88 6.3e-009 2.2e-004 letter-probability matrix: alength= 4 w= 6 nsites= 407 E= 2.2e-014 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 0.464373 0.000000 0.000000 0.535627 MOTIF CCATBG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCATBG CVATGG 204 75 4.1e-017 1.4e-012 # CCATTG CAATGG 118 36 2.2e-012 7.5e-008 # CCATGG CCATGG 36 13 6.2e-004 2.1e+001 # CCATCG CGATGG 53 29 4.6e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 215 E= 1.4e-012 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 0.000000 0.255814 0.167442 0.576744 0.000000 0.000000 1.000000 0.000000 MOTIF CGGTR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGGTR YACCG 334 176 8.0e-016 2.7e-011 # CGGTA TACCG 199 94 2.3e-011 7.9e-007 # CGGTG CACCG 164 87 1.5e-007 5.0e-003 letter-probability matrix: alength= 4 w= 5 nsites= 393 E= 2.7e-011 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 0.554707 0.000000 0.445293 0.000000 MOTIF BTTGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST BTTGG CCAAV 685 520 1.3e-012 4.4e-008 # CTTGG CCAAG 277 162 5.3e-010 1.7e-005 # GTTGG CCAAC 261 184 2.7e-005 9.0e-001 # TTTGG CCAAA 353 302 1.0e-002 3.3e+002 letter-probability matrix: alength= 4 w= 5 nsites= 998 E= 4.4e-008 0.000000 0.302605 0.275551 0.421844 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 MOTIF AYCCRTAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 60 7 3.5e-012 1.1e-007 # ATCCGTAC GTACGGAT 21 1 5.0e-006 1.6e-001 # ACCCATAC GTATGGGT 23 4 1.4e-004 4.5e+000 # ATCCATAC GTATGGAT 14 1 4.7e-004 1.5e+001 # ACCCGTAC GTACGGGT 10 1 5.8e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 72 E= 1.1e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.472222 0.000000 0.527778 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.527778 0.000000 0.472222 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 MOTIF TMAACAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TMAACAA TTGTTKA 123 49 2.1e-009 6.5e-005 # TCAACAA TTGTTGA 74 27 9.5e-007 3.0e-002 # TAAACAA TTGTTTA 50 22 5.4e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 125 E= 6.5e-005 0.000000 0.000000 0.000000 1.000000 0.400000 0.600000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GATTCYA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GATTCYA TRGAATC 69 17 3.6e-009 1.1e-004 # GATTCTA TAGAATC 41 10 5.9e-006 1.8e-001 # GATTCCA TGGAATC 28 7 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 1.1e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 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 0.414286 0.000000 0.585714 1.000000 0.000000 0.000000 0.000000 MOTIF AAGGYTGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AAGGYTGC GCARCCTT 33 2 1.5e-008 4.6e-004 # AAGGCTGC GCAGCCTT 19 1 1.9e-005 5.8e-001 # AAGGTTGC GCAACCTT 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 4.6e-004 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 0.588235 0.000000 0.411765 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGSTTCGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGSTTCGA TCGAASCC 29 1 2.4e-008 7.5e-004 # GGGTTCGA TCGAACCC 18 0 3.6e-006 1.1e-001 # GGCTTCGA TCGAAGCC 11 1 3.1e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.5e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.379310 0.620690 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 ATTDGCTG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATTDGCTG CAGCHAAT 36 4 7.4e-008 2.3e-003 # ATTGGCTG CAGCCAAT 12 0 2.4e-004 7.3e+000 # ATTAGCTG CAGCTAAT 10 1 5.8e-003 1.8e+002 # ATTTGCTG CAGCAAAT 14 3 6.2e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 2.3e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.277778 0.000000 0.333333 0.388889 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCCTTA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 32 3 1.7e-007 5.4e-003 # CGCCTTA TAAGGCG 32 3 1.7e-007 5.4e-003 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 5.4e-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 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 GMAGTTGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GMAGTTGA TCAACTKC 37 5 1.8e-007 5.4e-003 # GAAGTTGA TCAACTTC 23 3 4.0e-005 1.2e+000 # GCAGTTGA TCAACTGC 14 2 2.0e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 5.4e-003 0.000000 0.000000 1.000000 0.000000 0.621622 0.378378 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 CTARACCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 22 0 2.1e-007 6.6e-003 # CTAAACCA TGGTTTAG 11 0 4.8e-004 1.5e+001 # CTAGACCA TGGTCTAG 11 0 4.8e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.6e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 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 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGTATGR DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TGGTATGR YCATACCA 38 6 3.7e-007 1.2e-002 # TGGTATGA TCATACCA 22 4 2.5e-004 7.7e+000 # TGGTATGG CCATACCA 16 2 6.3e-004 1.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.2e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.578947 0.000000 0.421053 0.000000 MOTIF TAAKAGCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TAAKAGCA TGCTMTTA 30 3 6.0e-007 1.8e-002 # TAAGAGCA TGCTCTTA 18 1 3.6e-005 1.1e+000 # TAATAGCA TGCTATTA 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.8e-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 0.600000 0.400000 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 GAACCAS DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GAACCAS STGGTTC 51 13 6.8e-007 2.1e-002 # GAACCAG CTGGTTC 25 6 4.1e-004 1.2e+001 # GAACCAC GTGGTTC 26 7 6.1e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 2.1e-002 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.509804 0.490196 0.000000 MOTIF CATCTRC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CATCTRC GYAGATG 45 10 7.8e-007 2.4e-002 # CATCTAC GTAGATG 29 5 1.7e-005 5.2e-001 # CATCTGC GCAGATG 17 5 8.2e-003 2.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 2.4e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.652174 0.000000 0.347826 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCTAGW DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CGCTAGW WCTAGCG 23 1 1.3e-006 4.1e-002 # CGCTAGA TCTAGCG 15 1 2.5e-004 7.6e+000 # CGCTAGT ACTAGCG 8 0 3.9e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 4.1e-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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.652174 0.000000 0.000000 0.347826 # Stopping reason: E-value threshold exceeded # Running time: 116.24 seconds