# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SMP1/seqs-shuffled # positives: 511 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SMP1/seqs-centered (Sat Jan 18 20:39:19 PST 2020) # negatives: 511 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SMP1/seqs-shuffled (Sat Jan 18 20:39:19 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 20:50:44 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 0.298 C 0.204 G 0.206 T 0.293 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 92 10 1.3e-019 3.8e-015 # GGTTCGA TCGAACC 65 2 2.0e-018 6.1e-014 # GGTTCAA TTGAACC 31 8 1.1e-004 3.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 96 E= 3.8e-015 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 0.322917 0.000000 0.677083 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 34 1 6.1e-010 1.9e-005 # CTTGGCC GGCCAAG 21 1 4.5e-006 1.4e-001 # CTCGGCC GGCCGAG 16 0 1.4e-005 4.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.9e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.441176 0.000000 0.558824 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 MOTIF AWAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AWAAAAA TTTTTWT 137 64 5.4e-009 1.6e-004 # AAAAAAA TTTTTTT 101 44 1.9e-007 5.8e-003 # ATAAAAA TTTTTAT 55 30 3.1e-003 9.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 163 E= 1.6e-004 1.000000 0.000000 0.000000 0.000000 0.680982 0.000000 0.000000 0.319018 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 MOTIF ACCACTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACTW WAGTGGT 44 6 7.8e-009 2.3e-004 # ACCACTA TAGTGGT 28 2 3.1e-007 9.4e-003 # ACCACTT AAGTGGT 19 4 1.2e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 2.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.583333 0.000000 0.000000 0.416667 MOTIF GCGCYAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCGCYAC GTRGCGC 24 0 4.5e-008 1.3e-003 # GCGCTAC GTAGCGC 14 0 5.6e-005 1.7e+000 # GCGCCAC GTGGCGC 10 0 9.3e-004 2.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 1.3e-003 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 0.416667 0.000000 0.583333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 23 0 9.3e-008 2.8e-003 # GTGATAGT ACTATCAC 12 0 2.3e-004 6.8e+000 # GTGATAGC GCTATCAC 11 0 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-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 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 1.000000 0.000000 0.000000 0.478261 0.000000 0.521739 MOTIF CGCCTTAR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTAR YTAAGGCG 25 1 3.0e-007 9.1e-003 # CGCCTTAA TTAAGGCG 15 1 2.4e-004 7.0e+000 # CGCCTTAG CTAAGGCG 10 0 9.3e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.1e-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 0.600000 0.000000 0.400000 0.000000 MOTIF CRCCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 78 29 3.2e-007 9.4e-003 # CGCCCA TGGGCG 31 9 2.7e-004 7.9e+000 # CACCCA TGGGTG 48 20 3.0e-004 9.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 108 E= 9.4e-003 0.000000 1.000000 0.000000 0.000000 0.712963 0.000000 0.287037 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 1.000000 0.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 20 0 7.9e-007 2.3e-002 # CACCGTGG CCACGGTG 11 0 4.6e-004 1.4e+001 # CACCGTGC GCACGGTG 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.3e-002 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 0.000000 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 0.450000 0.550000 0.000000 MOTIF RCGGGGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 31 4 1.2e-006 3.6e-002 # ACGGGGA TCCCCGT 19 3 3.8e-004 1.1e+001 # GCGGGGA TCCCCGC 12 1 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 3.6e-002 0.612903 0.000000 0.387097 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAGTTGGK DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAGTTGGK MCCAACTG 19 0 1.6e-006 4.7e-002 # CAGTTGGT ACCAACTG 10 0 9.3e-004 2.7e+001 # CAGTTGGG CCCAACTG 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.7e-002 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 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 0.473684 0.526316 # Stopping reason: E-value threshold exceeded # Running time: 40.33 seconds