# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/seqs-shuffled # positives: 430 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/seqs-centered (Sun Jan 19 00:34:59 PST 2020) # negatives: 430 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/seqs-shuffled (Sun Jan 19 00:34:59 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:42:28 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 0.296 C 0.205 G 0.204 T 0.295 MOTIF SGGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCRA TYGAACCS 68 0 1.9e-022 4.8e-018 # GGGTTCGA TCGAACCC 27 0 4.9e-009 1.2e-004 # CGGTTCGA TCGAACCG 25 0 2.1e-008 5.2e-004 # GGGTTCAA TTGAACCC 9 0 1.9e-003 4.7e+001 # CGGTTCAA TTGAACCG 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 4.8e-018 0.000000 0.470588 0.529412 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 0.235294 0.000000 0.764706 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 57 0 9.5e-019 2.4e-014 # ACTTGGCC GGCCAAGT 27 0 4.9e-009 1.2e-004 # ACTCGGCC GGCCGAGT 26 0 1.0e-008 2.5e-004 # ACTGGGCC GGCCCAGT 12 0 2.3e-004 5.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 2.4e-014 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 0.385965 0.210526 0.403509 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 CCRTACAY DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 67 5 2.9e-016 7.1e-012 # CCGTACAT ATGTACGG 26 1 1.5e-007 3.6e-003 # CCATACAT ATGTATGG 26 3 5.6e-006 1.4e-001 # CCGTACAC GTGTACGG 14 1 4.4e-004 1.1e+001 # CCATACAC GTGTATGG 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 76 E= 7.1e-012 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.460526 0.000000 0.539474 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.289474 0.000000 0.710526 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 75 9 1.3e-015 3.3e-011 # CGCCTTA TAAGGCG 60 6 2.2e-013 5.5e-009 # CGCGTTA TAACGCG 15 3 3.5e-003 8.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 3.3e-011 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 0.800000 0.200000 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 42 1 1.8e-012 4.5e-008 # GCGCTACC GGTAGCGC 27 0 4.9e-009 1.2e-004 # GCTCTACC GGTAGAGC 15 1 2.3e-004 5.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 4.5e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.642857 0.357143 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 AGTGGTWA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWA TWACCACT 40 2 8.7e-011 2.1e-006 # AGTGGTAA TTACCACT 20 1 8.5e-006 2.1e-001 # AGTGGTTA TAACCACT 20 1 8.5e-006 2.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.1e-006 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 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 2 8.7e-011 2.1e-006 # ATGGCAAC GTTGCCAT 29 1 1.8e-008 4.4e-004 # ATGGCATC GATGCCAT 11 1 3.0e-003 7.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.1e-006 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 0.725000 0.000000 0.000000 0.275000 0.000000 1.000000 0.000000 0.000000 MOTIF CCASAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCASAC GTSTGG 82 23 3.0e-010 7.3e-006 # CCACAC GTGTGG 54 14 2.0e-007 4.9e-003 # CCAGAC GTCTGG 31 9 2.5e-004 6.1e+000 letter-probability matrix: alength= 4 w= 6 nsites= 88 E= 7.3e-006 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 0.647727 0.352273 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACCACTWG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACCACTWG CWAGTGGT 24 0 4.3e-008 1.0e-003 # ACCACTTG CAAGTGGT 16 0 1.3e-005 3.2e-001 # ACCACTAG CTAGTGGT 8 0 3.8e-003 9.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.0e-003 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 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 MOTIF CACCGTGS DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 27 1 7.3e-008 1.7e-003 # CACCGTGG CCACGGTG 15 0 2.7e-005 6.4e-001 # CACCGTGC GCACGGTG 12 1 1.6e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.7e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.444444 0.555556 0.000000 MOTIF CAMGGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAMGGA TCCKTG 59 16 9.5e-008 2.3e-003 # CACGGA TCCGTG 35 8 1.4e-005 3.2e-001 # CAAGGA TCCTTG 25 8 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 64 E= 2.3e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.453125 0.546875 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 AAGATWT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAGATWT AWATCTT 49 11 1.6e-007 3.7e-003 # AAGATTT AAATCTT 35 8 1.4e-005 3.2e-001 # AAGATAT ATATCTT 15 3 3.5e-003 8.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 3.7e-003 1.000000 0.000000 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 0.000000 0.000000 0.000000 1.000000 0.294118 0.000000 0.000000 0.705882 0.000000 0.000000 0.000000 1.000000 MOTIF AYTGCGCC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AYTGCGCC GGCGCART 22 0 1.8e-007 4.2e-003 # ACTGCGCC GGCGCAGT 11 0 4.6e-004 1.1e+001 # ATTGCGCC GGCGCAAT 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.2e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GACTSTTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 22 0 1.8e-007 4.2e-003 # GACTCTTA TAAGAGTC 12 0 2.3e-004 5.3e+000 # GACTGTTA TAACAGTC 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.2e-003 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 0.000000 0.000000 1.000000 0.000000 0.545455 0.454545 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 ATAGTKTA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 31 3 2.4e-007 5.7e-003 # ATAGTGTA TACACTAT 18 2 1.7e-004 4.1e+000 # ATAGTTTA TAAACTAT 13 1 8.5e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 5.7e-003 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 0.580645 0.419355 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTTSTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CTTSTA TASAAG 60 20 1.5e-006 3.6e-002 # CTTCTA TAGAAG 40 14 1.8e-004 4.1e+000 # CTTGTA TACAAG 23 6 9.8e-004 2.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 63 E= 3.6e-002 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 0.650794 0.349206 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTGAGCTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 19 0 1.6e-006 3.6e-002 # CTGAGCTA TAGCTCAG 19 0 1.6e-006 3.6e-002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.6e-002 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 1.000000 0.000000 0.000000 0.000000 MOTIF AACACSC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AACACSC GSGTGTT 25 2 2.1e-006 4.8e-002 # AACACCC GGGTGTT 13 0 1.1e-004 2.6e+000 # AACACGC GCGTGTT 12 2 6.1e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 4.8e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.520000 0.480000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 54.40 seconds