# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/seqs-shuffled # positives: 638 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/seqs-centered (Sat Jan 18 09:22:29 PST 2020) # negatives: 638 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/seqs-shuffled (Sat Jan 18 09:22:29 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 09:38:11 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 0.302 C 0.191 G 0.192 T 0.314 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 90 7 4.9e-021 1.5e-016 # GGTTCGA TCGAACC 61 2 5.3e-017 1.7e-012 # GGTTCAA TTGAACC 29 5 1.5e-005 4.8e-001 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 1.5e-016 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 0.322222 0.000000 0.677778 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAAGGCR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 72 4 2.7e-018 8.3e-014 # TAAGGCG CGCCTTA 51 0 1.6e-016 4.9e-012 # TAAGGCA TGCCTTA 24 4 7.7e-005 2.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 8.3e-014 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.320000 0.000000 0.680000 0.000000 MOTIF ACTBGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 51 1 4.3e-015 1.3e-010 # ACTTGGCC GGCCAAGT 25 0 2.3e-008 7.2e-004 # ACTCGGCC GGCCGAGT 24 0 4.8e-008 1.5e-003 # ACTGGGCC GGCCCAGT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 1.3e-010 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 0.392157 0.196078 0.411765 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 TAGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 46 3 1.7e-011 5.1e-007 # TAGTGGTA TACCACTA 27 2 6.4e-007 2.0e-002 # TAGTGGTT AACCACTA 19 1 1.8e-005 5.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 5.1e-007 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 0.586957 0.000000 0.000000 0.413043 MOTIF CAASA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAASA TSTTG 328 217 2.2e-010 6.6e-006 # CAACA TGTTG 183 112 1.5e-006 4.7e-002 # CAAGA TCTTG 190 131 8.9e-005 2.7e+000 letter-probability matrix: alength= 4 w= 5 nsites= 444 E= 6.6e-006 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 0.468468 0.531532 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGAGABC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GGAGABC GVTCTCC 43 4 7.6e-010 2.2e-005 # GGAGACC GGTCTCC 18 2 1.8e-004 5.4e+000 # GGAGAGC GCTCTCC 13 1 8.7e-004 2.6e+001 # GGAGATC GATCTCC 12 1 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 2.2e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.418605 0.302326 0.279070 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 33 1 1.4e-009 4.0e-005 # GCGCTACC GGTAGCGC 20 0 8.2e-007 2.4e-002 # GCTCTACC GGTAGAGC 13 1 8.7e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.0e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.606061 0.393939 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 ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 33 2 1.3e-008 3.7e-004 # ATGGCAAC GTTGCCAT 22 1 2.4e-006 7.1e-002 # ATGGCATC GATGCCAT 11 1 3.1e-003 9.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 3.7e-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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 0 9.7e-008 2.9e-003 # ACTGAGCT AGCTCAGT 23 0 9.7e-008 2.9e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.9e-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 RAARAAAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RAARAAAA TTTTYTTY 105 47 3.2e-007 9.5e-003 # AAAAAAAA TTTTTTTT 52 20 6.8e-005 2.0e+000 # GAAAAAAA TTTTTTTC 40 15 3.9e-004 1.2e+001 # GAAGAAAA TTTTCTTC 23 6 1.0e-003 3.0e+001 # AAAGAAAA TTTTCTTT 28 12 7.5e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 127 E= 9.5e-003 0.598425 0.000000 0.401575 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.590551 0.000000 0.409449 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 TCTTCTGR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TCTTCTGR YCAGAAGA 24 1 6.3e-007 1.9e-002 # TCTTCTGA TCAGAAGA 13 0 1.1e-004 3.4e+000 # TCTTCTGG CCAGAAGA 11 1 3.1e-003 9.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.9e-002 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 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 0.541667 0.000000 0.458333 0.000000 MOTIF CACTATAK DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACTATAK MTATAGTG 20 0 8.2e-007 2.4e-002 # CACTATAT ATATAGTG 12 0 2.3e-004 6.8e+000 # CACTATAG CTATAGTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-002 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 MOTIF AGTMATAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGTMATAC GTATKACT 23 1 1.2e-006 3.6e-002 # AGTCATAC GTATGACT 11 0 4.7e-004 1.4e+001 # AGTAATAC GTATTACT 12 1 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.521739 0.478261 0.000000 0.000000 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 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 55.07 seconds