# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--HSF1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--HSF1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--HSF1/seqs-shuffled # positives: 514 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--HSF1/seqs-centered (Sat Jan 18 10:50:47 PST 2020) # negatives: 514 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--HSF1/seqs-shuffled (Sat Jan 18 10:50:47 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 11:01:38 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 0.210 G 0.209 T 0.287 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 79 1 2.8e-024 7.9e-020 # TGTATGGG CCCATACA 38 0 1.8e-012 5.0e-008 # TGTACGGA TCCGTACA 30 0 6.0e-010 1.7e-005 # TGTACGGG CCCGTACA 10 0 9.3e-004 2.6e+001 # TGTATGGA TCCATACA 12 1 1.6e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 94 E= 7.9e-020 0.000000 0.000000 0.000000 1.000000 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 0.436170 0.000000 0.563830 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.468085 0.000000 0.531915 0.000000 MOTIF RGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 104 11 1.7e-022 4.8e-018 # GGTTCGA TCGAACC 87 7 1.9e-020 5.2e-016 # AGTTCGA TCGAACT 22 4 2.3e-004 6.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 4.8e-018 0.182692 0.000000 0.817308 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 51 0 1.2e-016 3.3e-012 # CTCGGCCA TGGCCGAG 32 0 1.4e-010 3.9e-006 # CTTGGCCA TGGCCAAG 19 0 1.6e-006 4.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 3.3e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.627451 0.000000 0.372549 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 CGCCTTAR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTAR YTAAGGCG 50 1 6.9e-015 1.9e-010 # CGCCTTAA TTAAGGCG 37 0 3.7e-012 1.0e-007 # CGCCTTAG CTAAGGCG 13 1 8.6e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 1.9e-010 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 0.740000 0.000000 0.260000 0.000000 MOTIF ACCACTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCACTA TAGTGGT 48 1 2.9e-014 8.1e-010 # ACCACTA TAGTGGT 48 1 2.9e-014 8.1e-010 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 8.1e-010 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 1.000000 0.000000 0.000000 0.000000 MOTIF ARAAAAAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAAW WTTTTTYT 121 39 6.0e-013 1.6e-008 # AGAAAAAA TTTTTTCT 48 6 6.7e-010 1.8e-005 # AAAAAAAA TTTTTTTT 64 23 2.6e-006 7.1e-002 # AAAAAAAT ATTTTTTT 55 22 6.1e-005 1.7e+000 # AGAAAAAT ATTTTTCT 14 2 2.0e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 149 E= 1.6e-008 1.000000 0.000000 0.000000 0.000000 0.657718 0.000000 0.342282 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 0.597315 0.000000 0.000000 0.402685 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 44 2 6.4e-012 1.7e-007 # ATGGCAAC GTTGCCAT 32 2 2.2e-008 6.1e-004 # ATGGCATC GATGCCAT 12 0 2.3e-004 6.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.7e-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 0.727273 0.000000 0.000000 0.272727 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 1 9.0e-012 2.5e-007 # GCGCTACC GGTAGCGC 27 0 5.2e-009 1.4e-004 # GCTCTACC GGTAGAGC 13 1 8.6e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.5e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.675000 0.325000 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 CTATCACR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 0 1.4e-010 3.8e-006 # CTATCACA TGTGATAG 17 0 6.7e-006 1.8e-001 # CTATCACG CGTGATAG 15 0 2.8e-005 7.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 3.8e-006 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.531250 0.000000 0.468750 0.000000 MOTIF CACGGTGM DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 26 0 1.1e-008 2.9e-004 # CACGGTGA TCACCGTG 16 0 1.4e-005 3.7e-001 # CACGGTGC GCACCGTG 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.9e-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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.615385 0.384615 0.000000 0.000000 MOTIF CCASAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCASAC GTSTGG 83 29 3.4e-008 9.1e-004 # CCACAC GTGTGG 51 18 2.5e-005 6.7e-001 # CCAGAC GTCTGG 35 11 2.0e-004 5.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 90 E= 9.1e-004 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 0.611111 0.388889 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 24 0 4.5e-008 1.2e-003 # ACTGAGCT AGCTCAGT 24 0 4.5e-008 1.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.2e-003 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 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 0.000000 1.000000 MOTIF ATTAASAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 26 1 1.5e-007 4.1e-003 # ATTAAGAG CTCTTAAT 15 1 2.4e-004 6.3e+000 # ATTAACAG CTGTTAAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.1e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.423077 0.576923 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGSTCTC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGSTCTC GAGASCG 28 2 3.1e-007 8.4e-003 # CGCTCTC GAGAGCG 12 0 2.3e-004 6.1e+000 # CGGTCTC GAGACCG 16 2 6.0e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 8.4e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.571429 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 MOTIF TGGCGCAR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TGGCGCAR YTGCGCCA 24 1 6.0e-007 1.6e-002 # TGGCGCAA TTGCGCCA 12 0 2.3e-004 6.1e+000 # TGGCGCAG CTGCGCCA 12 1 1.6e-003 4.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-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 1.000000 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 0.500000 0.000000 0.500000 0.000000 MOTIF AKATCGG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AKATCGG CCGATMT 32 4 6.6e-007 1.8e-002 # ATATCGG CCGATAT 20 2 5.2e-005 1.4e+000 # AGATCGG CCGATCT 12 2 6.2e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 1.8e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.625000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCMCGGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GCMCGGA TCCGKGC 20 0 7.9e-007 2.1e-002 # GCACGGA TCCGTGC 12 0 2.3e-004 6.1e+000 # GCCCGGA TCCGGGC 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 21 E= 2.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.619048 0.380952 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 0.000000 MOTIF RGCCCAA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST RGCCCAA TTGGGCY 35 6 1.6e-006 4.3e-002 # GGCCCAA TTGGGCC 20 4 6.8e-004 1.8e+001 # AGCCCAA TTGGGCT 15 2 1.1e-003 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 4.3e-002 0.444444 0.000000 0.555556 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 62.07 seconds