# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HSF1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HSF1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HSF1/seqs-shuffled # positives: 530 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HSF1/seqs-centered (Sat Jan 18 01:28:55 PST 2020) # negatives: 530 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HSF1/seqs-shuffled (Sat Jan 18 01:28:55 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 01:40:52 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 0.291 C 0.210 G 0.211 T 0.288 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 109 12 3.4e-023 9.7e-019 # GGTTCGA TCGAACC 81 5 2.6e-020 7.3e-016 # GGTTCAA TTGAACC 29 7 1.2e-004 3.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 110 E= 9.7e-019 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 0.263636 0.000000 0.736364 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAYCCRTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CAYCCRTA TAYGGRTG 65 2 2.2e-018 6.1e-014 # CACCCATA TATGGGTG 26 1 1.6e-007 4.4e-003 # CATCCGTA TACGGATG 23 1 1.2e-006 3.4e-002 # CATCCATA TATGGATG 12 0 2.3e-004 6.5e+000 # CACCCGTA TACGGGTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 72 E= 6.1e-014 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.486111 0.000000 0.513889 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.541667 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 74 5 3.6e-018 1.0e-013 # CGCCTTA TAAGGCG 60 2 8.1e-017 2.3e-012 # CGCGTTA TAACGCG 14 3 6.0e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 1.0e-013 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 0.810811 0.189189 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 CTYGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 55 2 2.9e-015 8.1e-011 # CTCGGCCA TGGCCGAG 33 1 1.3e-009 3.5e-005 # CTTGGCCA TGGCCAAG 22 1 2.3e-006 6.6e-002 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 8.1e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 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 TCHAGAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TCHAGAA TTCTDGA 74 11 8.6e-014 2.4e-009 # TCTAGAA TTCTAGA 30 3 5.0e-007 1.4e-002 # TCAAGAA TTCTTGA 27 4 1.3e-005 3.7e-001 # TCCAGAA TTCTGGA 20 4 6.9e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 2.4e-009 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.341772 0.265823 0.000000 0.392405 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 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 0 3.8e-012 1.1e-007 # GCGCTACC GGTAGCGC 22 0 1.9e-007 5.3e-003 # GCTCTACC GGTAGAGC 15 0 2.8e-005 7.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.1e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.594595 0.405405 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 0.000000 1.000000 0.000000 0.000000 MOTIF ATAGTKTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 43 2 1.3e-011 3.6e-007 # ATAGTGTA TACACTAT 24 1 6.1e-007 1.7e-002 # ATAGTTTA TAAACTAT 19 1 1.7e-005 4.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 3.6e-007 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 0.558140 0.441860 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 43 2 1.3e-011 3.6e-007 # ATGGCAAC GTTGCCAT 31 1 5.0e-009 1.4e-004 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 3.6e-007 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 0.720930 0.000000 0.000000 0.279070 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 92 28 2.2e-010 6.0e-006 # CACCCA TGGGTG 51 16 5.9e-006 1.6e-001 # CGCCCA TGGGCG 43 12 1.0e-005 2.9e-001 letter-probability matrix: alength= 4 w= 6 nsites= 107 E= 6.0e-006 0.000000 1.000000 0.000000 0.000000 0.570093 0.000000 0.429907 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 ACTGMGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACTGMGC GCKCAGT 34 1 6.3e-010 1.7e-005 # ACTGAGC GCTCAGT 23 0 9.3e-008 2.6e-003 # ACTGCGC GCGCAGT 11 1 3.0e-003 8.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.7e-005 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 1.000000 0.000000 0.676471 0.323529 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 32 1 2.5e-009 6.9e-005 # GGCTATCA TGATAGCC 17 0 6.7e-006 1.8e-001 # GGTTATCA TGATAACC 15 1 2.4e-004 6.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.9e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.531250 0.000000 0.468750 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTGGTYTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTGGTYTA TARACCAC 35 2 3.1e-009 8.3e-005 # GTGGTCTA TAGACCAC 21 0 3.9e-007 1.1e-002 # GTGGTTTA TAAACCAC 14 2 2.0e-003 5.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 8.3e-005 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 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGGW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CACGGW WCCGTG 83 28 1.7e-008 4.6e-004 # CACGGT ACCGTG 36 9 2.3e-005 6.3e-001 # CACGGA TCCGTG 47 19 2.5e-004 6.9e+000 letter-probability matrix: alength= 4 w= 6 nsites= 86 E= 4.6e-004 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 0.581395 0.000000 0.000000 0.418605 MOTIF CTTCTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTTCTA TAGAAG 48 8 1.1e-008 2.9e-004 # CTTCTA TAGAAG 48 8 1.1e-008 2.9e-004 letter-probability matrix: alength= 4 w= 6 nsites= 49 E= 2.9e-004 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AARAAAAA TTTTTYTT 99 43 2.7e-007 7.1e-003 # AAGAAAAA TTTTTCTT 47 18 1.4e-004 3.7e+000 # AAAAAAAA TTTTTTTT 61 29 2.9e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 125 E= 7.1e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 43 10 1.6e-006 4.3e-002 # ATCGTGA TCACGAT 20 3 2.1e-004 5.7e+000 # ATCTTGA TCAAGAT 23 7 2.3e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 4.3e-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 0.465116 0.534884 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 CCAASAGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCAASAGA TCTSTTGG 28 3 1.7e-006 4.6e-002 # CCAACAGA TCTGTTGG 13 1 8.6e-004 2.3e+001 # CCAAGAGA TCTCTTGG 15 2 1.1e-003 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 4.6e-002 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 0.464286 0.535714 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 # Stopping reason: E-value threshold exceeded # Running time: 61.61 seconds