# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-shuffled # positives: 552 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-centered (Sat Jan 18 09:13:16 PST 2020) # negatives: 552 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-shuffled (Sat Jan 18 09:13:16 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 09:27:04 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 0.305 C 0.198 G 0.197 T 0.301 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 93 9 1.5e-020 4.6e-016 # GGTTCGA TCGAACC 72 7 6.9e-016 2.1e-011 # AGTTCGA TCGAACT 24 2 4.2e-006 1.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 93 E= 4.6e-016 0.236559 0.000000 0.763441 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 ACTBGGCC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 38 0 1.9e-012 5.7e-008 # ACTTGGCC GGCCAAGT 20 0 8.0e-007 2.4e-002 # ACTCGGCC GGCCGAGT 15 0 2.8e-005 8.4e-001 # ACTGGGCC GGCCCAGT 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 5.7e-008 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 0.342105 0.236842 0.421053 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 KCGCCTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST KCGCCTTA TAAGGCGM 30 0 6.2e-010 1.9e-005 # GCGCCTTA TAAGGCGC 18 0 3.3e-006 1.0e-001 # TCGCCTTA TAAGGCGA 12 0 2.3e-004 6.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.9e-005 0.000000 0.000000 0.600000 0.400000 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 MOTIF AAAAADAA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 124 53 3.2e-009 9.5e-005 # AAAAATAA TTATTTTT 42 15 1.6e-004 4.9e+000 # AAAAAAAA TTTTTTTT 62 31 5.3e-004 1.6e+001 # AAAAAGAA TTCTTTTT 39 18 3.0e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 141 E= 9.5e-005 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 0.425532 0.000000 0.276596 0.297872 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATAGTKTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 34 2 6.1e-009 1.8e-004 # ATAGTGTA TACACTAT 21 1 4.6e-006 1.4e-001 # ATAGTTTA TAAACTAT 13 1 8.6e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.8e-004 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 0.617647 0.382353 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTAC GTAGMGC 26 0 1.1e-008 3.3e-004 # GCGCTAC GTAGCGC 18 0 3.3e-006 9.9e-002 # GCTCTAC GTAGAGC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.3e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.692308 0.307692 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 CCCATDC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 57 13 2.0e-008 6.1e-004 # CCCATGC GCATGGG 17 2 3.3e-004 9.8e+000 # CCCATAC GTATGGG 21 6 2.7e-003 8.0e+001 # CCCATTC GAATGGG 19 5 3.0e-003 9.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 6.1e-004 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 0.000000 0.000000 0.000000 1.000000 0.368421 0.000000 0.298246 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 25 0 2.3e-008 6.7e-004 # ATGGCAAC GTTGCCAT 14 0 5.6e-005 1.7e+000 # ATGGCATC GATGCCAT 11 0 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 6.7e-004 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 0.560000 0.000000 0.000000 0.440000 0.000000 1.000000 0.000000 0.000000 MOTIF KAGTGGTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST KAGTGGTA TACCACTM 27 2 6.1e-007 1.8e-002 # TAGTGGTA TACCACTA 20 2 5.2e-005 1.5e+000 # GAGTGGTA TACCACTC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.8e-002 0.000000 0.000000 0.285714 0.714286 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 19 0 1.6e-006 4.8e-002 # ATCGTGAG CTCACGAT 11 0 4.6e-004 1.4e+001 # ATCTTGAG CTCAAGAT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.8e-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 0.578947 0.421053 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 MOTIF CATCCGTR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CATCCGTR YACGGATG 19 0 1.6e-006 4.8e-002 # CATCCGTG CACGGATG 11 0 4.6e-004 1.4e+001 # CATCCGTA TACGGATG 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.8e-002 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 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 0.500000 0.000000 0.500000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 42.89 seconds