# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/seqs-shuffled # positives: 723 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/seqs-centered (Sat Jan 18 03:12:02 PST 2020) # negatives: 723 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/seqs-shuffled (Sat Jan 18 03:12:02 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:27:36 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 0.295 C 0.203 G 0.207 T 0.295 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 74 5 7.1e-018 2.4e-013 # ACCCATAC GTATGGGT 37 2 9.3e-010 3.1e-005 # ATCCGTAC GTACGGAT 26 1 1.7e-007 5.6e-003 # ACCCGTAC GTACGGGT 10 1 5.7e-003 1.9e+002 # ATCCATAC GTATGGAT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 86 E= 2.4e-013 1.000000 0.000000 0.000000 0.000000 0.000000 0.558140 0.000000 0.441860 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.558140 0.000000 0.441860 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 GCCTTAMC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 55 0 9.5e-018 3.1e-013 # GCCTTAAC GTTAAGGC 41 0 2.5e-013 8.3e-009 # GCCTTACC GGTAAGGC 14 0 5.7e-005 1.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 3.1e-013 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 0.745455 0.254545 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGTTCRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 104 19 7.4e-017 2.4e-012 # GGTTCGA TCGAACC 79 9 3.5e-016 1.1e-011 # GGTTCAA TTGAACC 27 11 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 106 E= 2.4e-012 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 0.254717 0.000000 0.745283 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 67 6 5.2e-015 1.7e-010 # CTCGGCCA TGGCCGAG 33 0 8.0e-011 2.6e-006 # CTGGGCCA TGGCCCAG 14 1 4.6e-004 1.5e+001 # CTTGGCCA TGGCCAAG 20 5 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 1.7e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.492537 0.208955 0.298507 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 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 50 3 1.3e-012 4.1e-008 # TAGTGGTA TACCACTA 32 0 1.6e-010 5.3e-006 # TAGTGGTT AACCACTA 18 3 6.9e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 4.1e-008 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.640000 0.000000 0.000000 0.360000 MOTIF MAGAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST MAGAW WTCTK 563 451 7.6e-011 2.5e-006 # AAGAA TTCTT 306 223 3.7e-006 1.2e-001 # AAGAT ATCTT 248 171 5.1e-006 1.6e-001 # CAGAT ATCTG 144 95 3.3e-004 1.1e+001 # CAGAA TTCTG 202 147 4.4e-004 1.4e+001 letter-probability matrix: alength= 4 w= 5 nsites= 1062 E= 2.5e-006 0.636535 0.363465 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 0.580979 0.000000 0.000000 0.419021 MOTIF GMGCTAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GMGCTAC GTAGCKC 41 3 4.9e-010 1.5e-005 # GCGCTAC GTAGCGC 28 2 3.4e-007 1.0e-002 # GAGCTAC GTAGCTC 13 1 8.7e-004 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.5e-005 0.000000 0.000000 1.000000 0.000000 0.317073 0.682927 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 1.000000 0.000000 0.000000 MOTIF CTCTMCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 30 0 6.9e-010 2.1e-005 # CTCTACCA TGGTAGAG 15 0 2.8e-005 8.5e-001 # CTCTCCCA TGGGAGAG 15 0 2.8e-005 8.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.1e-005 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 0.500000 0.500000 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 AGTCAKAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 31 1 5.6e-009 1.7e-004 # AGTCAGAC GTCTGACT 16 0 1.4e-005 4.2e-001 # AGTCATAC GTATGACT 15 1 2.4e-004 7.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.7e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.516129 0.483871 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAASGATG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 34 2 6.8e-009 2.0e-004 # CAACGATG CATCGTTG 23 1 1.3e-006 3.8e-002 # CAAGGATG CATCCTTG 11 1 3.1e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.0e-004 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 0.676471 0.323529 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CATYACGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CATYACGC GCGTRATG 25 0 2.4e-008 7.2e-004 # CATTACGC GCGTAATG 13 0 1.2e-004 3.5e+000 # CATCACGC GCGTGATG 12 0 2.3e-004 7.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 7.2e-004 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 0.500000 0.000000 0.500000 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 GRTCTCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GRTCTCCA TGGAGAYC 23 0 1.0e-007 3.0e-003 # GGTCTCCA TGGAGACC 14 0 5.7e-005 1.7e+000 # GATCTCCA TGGAGATC 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.0e-003 0.000000 0.000000 1.000000 0.000000 0.391304 0.000000 0.608696 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 40 6 1.0e-007 3.1e-003 # CGCCTTA TAAGGCG 24 4 7.9e-005 2.4e+000 # CGCGTTA TAACGCG 16 2 6.1e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 3.1e-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 0.600000 0.400000 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 ATAGTKTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 37 5 1.6e-007 4.6e-003 # ATAGTGTA TACACTAT 18 2 1.8e-004 5.5e+000 # ATAGTTTA TAAACTAT 19 3 3.9e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 4.6e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.486486 0.513514 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAACCSAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AAACCSAA TTSGGTTT 26 1 1.7e-007 5.0e-003 # AAACCCAA TTGGGTTT 15 0 2.8e-005 8.5e-001 # AAACCGAA TTCGGTTT 11 1 3.1e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.0e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.576923 0.423077 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 23 1 1.3e-006 3.8e-002 # CGTGCTAA TTAGCACG 13 1 8.7e-004 2.6e+001 # CGTGTTAA TTAACACG 10 0 9.5e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.8e-002 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 0.565217 0.000000 0.434783 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: 72.72 seconds