# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CIN5/seqs-shuffled # positives: 583 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CIN5/seqs-centered (Sun Jan 19 01:37:39 PST 2020) # negatives: 583 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CIN5/seqs-shuffled (Sun Jan 19 01:37:39 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 01:52:52 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 0.297 C 0.203 G 0.201 T 0.299 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 120 13 1.5e-025 4.6e-021 # GGTTCGA TCGAACC 87 4 4.7e-023 1.5e-018 # GGTTCAA TTGAACC 35 9 3.9e-005 1.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 4.6e-021 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 0.286885 0.000000 0.713115 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAADA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADA THTTTTT 213 101 7.4e-014 2.3e-009 # AAAAATA TATTTTT 82 31 2.5e-007 7.7e-003 # AAAAAAA TTTTTTT 116 58 1.2e-006 3.6e-002 # AAAAAGA TCTTTTT 76 32 5.5e-006 1.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 262 E= 2.3e-009 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 0.427481 0.000000 0.274809 0.297710 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAACTK DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCAACTK MAGTTGGT 41 0 2.2e-013 6.7e-009 # ACCAACTT AAGTTGGT 23 0 9.6e-008 2.9e-003 # ACCAACTG CAGTTGGT 18 0 3.3e-006 1.0e-001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 6.7e-009 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 0.439024 0.560976 MOTIF AGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 77 16 8.6e-012 2.6e-007 # AGTGGTT AACCACT 50 8 3.6e-009 1.1e-004 # AGTGGTA TACCACT 38 8 3.1e-006 9.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 91 E= 2.6e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.439560 0.000000 0.000000 0.560440 MOTIF CACGGYG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 32 0 1.5e-010 4.5e-006 # CACGGTG CACCGTG 20 0 8.1e-007 2.4e-002 # CACGGCG CGCCGTG 12 0 2.3e-004 7.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 4.5e-006 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 0.375000 0.000000 0.625000 0.000000 0.000000 1.000000 0.000000 MOTIF GCMAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCMAGA TCTKGC 78 23 4.3e-009 1.3e-004 # GCCAGA TCTGGC 41 5 1.3e-008 3.8e-004 # GCAAGA TCTTGC 37 18 6.1e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 78 E= 1.3e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.474359 0.525641 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 AAGCGCS DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAGCGCS SGCGCTT 31 1 5.2e-009 1.6e-004 # AAGCGCC GGCGCTT 19 1 1.8e-005 5.2e-001 # AAGCGCG CGCGCTT 12 0 2.3e-004 6.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 1.6e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.612903 0.387097 0.000000 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 31 2 4.6e-008 1.4e-003 # ATGGCAAC GTTGCCAT 22 2 1.5e-005 4.5e-001 # ATGGCATC GATGCCAT 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.4e-003 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 0.709677 0.000000 0.000000 0.290323 0.000000 1.000000 0.000000 0.000000 MOTIF GMTACCGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 27 1 8.1e-008 2.4e-003 # GCTACCGA TCGGTAGC 18 1 3.4e-005 1.0e+000 # GATACCGA TCGGTATC 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.4e-003 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTCTCSC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSC GSGAGAG 29 2 1.7e-007 5.0e-003 # CTCTCCC GGGAGAG 18 1 3.4e-005 1.0e+000 # CTCTCGC GCGAGAG 11 1 3.1e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 5.0e-003 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.620690 0.379310 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGGRGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGCGGRGA TCYCCGCG 21 0 4.0e-007 1.2e-002 # CGCGGGGA TCCCCGCG 14 0 5.6e-005 1.7e+000 # CGCGGAGA TCTCCGCG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCRC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGACCRC GYGGTCT 35 5 4.7e-007 1.4e-002 # AGACCGC GCGGTCT 12 0 2.3e-004 6.8e+000 # AGACCAC GTGGTCT 23 5 4.0e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.4e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.657143 0.000000 0.342857 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCTTYTG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 24 1 6.2e-007 1.8e-002 # ATCTTCTG CAGAAGAT 14 0 5.6e-005 1.7e+000 # ATCTTTTG CAAAAGAT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.583333 0.000000 0.416667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GTAWGAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GTAWGAC GTCWTAC 24 1 6.2e-007 1.8e-002 # GTATGAC GTCATAC 17 1 6.5e-005 1.9e+000 # GTAAGAC GTCTTAC 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 1.8e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.291667 0.000000 0.000000 0.708333 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 56.13 seconds