# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CIN5/seqs-shuffled # positives: 467 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CIN5/seqs-centered (Sat Jan 18 12:54:35 PST 2020) # negatives: 467 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CIN5/seqs-shuffled (Sat Jan 18 12:54:35 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 13:03:31 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 0.300 C 0.201 G 0.199 T 0.300 MOTIF CCRTRCA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCRTRCA TGYAYGG 97 8 6.5e-023 1.8e-018 # CCATACA TGTATGG 45 2 2.9e-012 7.9e-008 # CCGTACA TGTACGG 41 1 4.1e-012 1.1e-007 # CCATGCA TGCATGG 13 2 3.5e-003 9.5e+001 # CCGTGCA TGCACGG 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 1.8e-018 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.532787 0.000000 0.467213 0.000000 0.000000 0.000000 0.000000 1.000000 0.778689 0.000000 0.221311 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 60 2 6.4e-017 1.7e-012 # CTCGGCCA TGGCCGAG 30 0 5.8e-010 1.5e-005 # CTTGGCCA TGGCCAAG 18 1 3.3e-005 8.8e-001 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 4.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 1.7e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.200000 0.300000 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 CTTAAYCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTTAAYCA TGRTTAAG 43 0 4.1e-014 1.1e-009 # CTTAACCA TGGTTAAG 33 0 6.5e-011 1.7e-006 # CTTAATCA TGATTAAG 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.1e-009 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.767442 0.000000 0.232558 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACTAVAC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CACTAVAC GTBTAGTG 33 0 6.5e-011 1.7e-006 # CACTAAAC GTTTAGTG 13 0 1.1e-004 3.0e+000 # CACTACAC GTGTAGTG 12 0 2.3e-004 6.1e+000 # CACTAGAC GTCTAGTG 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 1.7e-006 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 0.393939 0.363636 0.242424 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGMGCG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGMGCG CGCKCT 61 13 1.9e-009 4.9e-005 # AGAGCG CGCTCT 29 3 8.9e-007 2.4e-002 # AGCGCG CGCGCT 32 11 7.5e-004 2.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 64 E= 4.9e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.468750 0.531250 0.000000 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 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 35 2 2.8e-009 7.5e-005 # ATGGCAAC GTTGCCAT 25 2 2.1e-006 5.6e-002 # ATGGCATC GATGCCAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 7.5e-005 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 0.694444 0.000000 0.000000 0.305556 0.000000 1.000000 0.000000 0.000000 MOTIF RCACCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST RCACCCA TGGGTGY 44 7 2.8e-008 7.5e-004 # ACACCCA TGGGTGT 33 5 1.4e-006 3.7e-002 # GCACCCA TGGGTGC 14 2 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 7.5e-004 0.653846 0.000000 0.346154 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCGCCTTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCGCCTTA TAAGGCGC 24 0 4.4e-008 1.2e-003 # GCGCCTTA TAAGGCGC 24 0 4.4e-008 1.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.2e-003 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 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 AARAAAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AARAAAAA TTTTTYTT 75 25 6.3e-008 1.7e-003 # AAGAAAAA TTTTTCTT 37 6 4.8e-007 1.3e-002 # AAAAAAAA TTTTTTTT 47 22 1.2e-003 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 87 E= 1.7e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.620690 0.000000 0.379310 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 TGGCGYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 40 7 2.9e-007 7.6e-003 # TGGCGCA TGCGCCA 22 2 1.5e-005 3.8e-001 # TGGCGTA TACGCCA 18 5 4.9e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 7.6e-003 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 0.550000 0.000000 0.450000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGC GCTCAGT 21 0 3.8e-007 9.8e-003 # ACTGAGC GCTCAGT 21 0 3.8e-007 9.8e-003 letter-probability matrix: alength= 4 w= 7 nsites= 21 E= 9.8e-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 MOTIF CTATCACR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 24 1 5.9e-007 1.5e-002 # CTATCACA TGTGATAG 14 1 4.5e-004 1.2e+001 # CTATCACG CGTGATAG 10 0 9.3e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-002 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 0.583333 0.000000 0.416667 0.000000 MOTIF TCAGAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TCAGAA TTCTGA 57 17 6.7e-007 1.7e-002 # TCAGAA TTCTGA 57 17 6.7e-007 1.7e-002 letter-probability matrix: alength= 4 w= 6 nsites= 61 E= 1.7e-002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATMCAAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AATMCAAC GTTGKATT 23 1 1.2e-006 3.0e-002 # AATCCAAC GTTGGATT 13 0 1.1e-004 2.9e+000 # AATACAAC GTTGTATT 10 1 5.6e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 3.0e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.416667 0.583333 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 0.000000 MOTIF CAGWCGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CAGWCGC GCGWCTG 23 1 1.2e-006 3.0e-002 # CAGACGC GCGTCTG 15 1 2.3e-004 6.0e+000 # CAGTCGC GCGACTG 8 0 3.8e-003 9.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.0e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.652174 0.000000 0.000000 0.347826 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATAGTGTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATAGTGTA TACACTAT 19 0 1.6e-006 4.1e-002 # ATAGTGTA TACACTAT 19 0 1.6e-006 4.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.1e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 51.24 seconds