# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/seqs-shuffled # positives: 544 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/seqs-centered (Sat Jan 18 10:06:16 PST 2020) # negatives: 544 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/seqs-shuffled (Sat Jan 18 10:06:16 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 10:19:17 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 0.307 C 0.193 G 0.192 T 0.308 MOTIF AGTGGTWA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWA TWACCACT 52 2 2.5e-014 7.5e-010 # AGTGGTTA TAACCACT 36 0 8.0e-012 2.4e-007 # AGTGGTAA TTACCACT 16 2 6.0e-004 1.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 7.5e-010 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 0.307692 0.000000 0.000000 0.692308 1.000000 0.000000 0.000000 0.000000 MOTIF SGGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 42 1 2.3e-012 6.8e-008 # GGGTTCGA TCGAACCC 23 0 9.4e-008 2.8e-003 # CGGTTCGA TCGAACCG 19 1 1.7e-005 5.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 6.8e-008 0.000000 0.452381 0.547619 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAACTKGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 41 1 4.6e-012 1.4e-007 # CAACTTGG CCAAGTTG 33 1 1.3e-009 3.8e-005 # CAACTGGG CCCAGTTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.4e-007 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.195122 0.804878 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF RCGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RCGCCTTA TAAGGCGY 32 0 1.5e-010 4.3e-006 # GCGCCTTA TAAGGCGC 22 0 1.9e-007 5.7e-003 # ACGCCTTA TAAGGCGT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 4.3e-006 0.312500 0.000000 0.687500 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 32 1 2.5e-009 7.6e-005 # GCGCTACC GGTAGCGC 17 0 6.7e-006 2.0e-001 # GCTCTACC GGTAGAGC 15 1 2.4e-004 7.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 7.6e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.531250 0.468750 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 CGWTGCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGWTGCC GGCAWCG 31 1 5.1e-009 1.5e-004 # CGTTGCC GGCAACG 23 1 1.2e-006 3.5e-002 # CGATGCC GGCATCG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 1.5e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.258065 0.000000 0.000000 0.741935 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 1.000000 0.000000 0.000000 MOTIF CAASAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAASAA TTSTTG 140 73 1.9e-007 5.7e-003 # CAACAA TTGTTG 78 37 3.5e-005 1.0e+000 # CAAGAA TTCTTG 69 39 1.6e-003 4.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 153 E= 5.7e-003 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 0.535948 0.464052 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 21 0 3.9e-007 1.1e-002 # ACTGAGCT AGCTCAGT 21 0 3.9e-007 1.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-002 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 ACMATTG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACMATTG CAATKGT 31 4 1.2e-006 3.6e-002 # ACCATTG CAATGGT 16 2 6.0e-004 1.8e+001 # ACAATTG CAATTGT 15 2 1.1e-003 3.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 3.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.483871 0.516129 0.000000 0.000000 1.000000 0.000000 0.000000 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 MOTIF AAARCCGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAARCCGA TCGGYTTT 19 0 1.6e-006 4.7e-002 # AAAACCGA TCGGTTTT 11 0 4.6e-004 1.3e+001 # AAAGCCGA TCGGCTTT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.7e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.578947 0.000000 0.421053 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 39.29 seconds