# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/seqs-shuffled # positives: 566 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/seqs-centered (Sat Jan 18 07:48:58 PST 2020) # negatives: 566 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/seqs-shuffled (Sat Jan 18 07:48:58 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 08:02:42 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 0.288 C 0.216 G 0.210 T 0.286 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 125 13 3.6e-027 1.0e-022 # GGTTCGA TCGAACC 95 6 1.2e-023 3.4e-019 # GGTTCAA TTGAACC 31 7 4.5e-005 1.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 126 E= 1.0e-022 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 0.246032 0.000000 0.753968 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 91 5 2.4e-023 6.8e-019 # CCGTACAT ATGTACGG 35 1 3.2e-010 9.2e-006 # CCATACAT ATGTATGG 38 4 1.7e-008 4.8e-004 # CCGTACAC GTGTACGG 17 0 6.8e-006 1.9e-001 # CCATACAC GTGTATGG 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 106 E= 6.8e-019 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.490566 0.000000 0.509434 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 0.264151 0.000000 0.735849 MOTIF CTYGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 75 1 7.9e-023 2.2e-018 # CTTGGCC GGCCAAG 46 0 5.5e-015 1.5e-010 # CTCGGCC GGCCGAG 40 1 9.7e-012 2.7e-007 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 2.2e-018 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.480000 0.000000 0.520000 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 88 10 2.7e-018 7.6e-014 # CGCCTTA TAAGGCG 70 5 6.8e-017 1.9e-012 # CGCGTTA TAACGCG 18 5 4.9e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 88 E= 7.6e-014 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 0.795455 0.204545 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 49 0 6.0e-016 1.7e-011 # GCGCTACC GGTAGCGC 34 0 3.5e-011 9.8e-007 # GCTCTACC GGTAGAGC 15 0 2.8e-005 7.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 1.7e-011 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.693878 0.306122 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 47 1 6.7e-014 1.9e-009 # AGTGGTTA TAACCACT 26 1 1.6e-007 4.4e-003 # AGTGGTAA TTACCACT 21 0 3.9e-007 1.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 1.9e-009 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 0.446809 0.000000 0.000000 0.553191 1.000000 0.000000 0.000000 0.000000 MOTIF ACACSC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACACSC GSGTGT 110 34 4.1e-012 1.1e-007 # ACACCC GGGTGT 70 25 8.1e-007 2.2e-002 # ACACGC GCGTGT 41 9 1.8e-006 4.9e-002 letter-probability matrix: alength= 4 w= 6 nsites= 171 E= 1.1e-007 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 0.760234 0.239766 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 46 3 1.5e-011 4.2e-007 # ATGGCAAC GTTGCCAT 29 1 2.0e-008 5.6e-004 # ATGGCATC GATGCCAT 17 2 3.3e-004 9.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 4.2e-007 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 0.630435 0.000000 0.000000 0.369565 0.000000 1.000000 0.000000 0.000000 MOTIF CACATYAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 32 0 1.5e-010 4.1e-006 # CACATCAC GTGATGTG 17 0 6.8e-006 1.9e-001 # CACATTAC GTAATGTG 15 0 2.8e-005 7.6e-001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 4.1e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.531250 0.000000 0.468750 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACCRACT DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AACCRACT AGTYGGTT 36 1 1.6e-010 4.4e-006 # AACCAACT AGTTGGTT 22 1 2.4e-006 6.5e-002 # AACCGACT AGTCGGTT 14 0 5.6e-005 1.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 4.4e-006 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 0.000000 0.611111 0.000000 0.388889 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 MOTIF AGAAAWA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGAAAWA TWTTTCT 92 34 2.2e-008 6.1e-004 # AGAAAAA TTTTTCT 69 24 6.2e-007 1.7e-002 # AGAAATA TATTTCT 26 10 5.0e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 97 E= 6.1e-004 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 1.000000 0.000000 0.000000 0.000000 0.731959 0.000000 0.000000 0.268041 1.000000 0.000000 0.000000 0.000000 MOTIF GATTAASA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GATTAASA TSTTAATC 25 0 2.3e-008 6.2e-004 # GATTAAGA TCTTAATC 14 0 5.6e-005 1.5e+000 # GATTAACA TGTTAATC 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 6.2e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.440000 0.560000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCTKTTG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATCTKTTG CAAMAGAT 33 3 7.6e-008 2.1e-003 # ATCTGTTG CAACAGAT 18 2 1.8e-004 4.9e+000 # ATCTTTTG CAAAAGAT 15 1 2.4e-004 6.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.1e-003 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 0.000000 1.000000 0.000000 0.000000 0.545455 0.454545 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 ATAGTKTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 30 2 8.7e-008 2.4e-003 # ATAGTGTA TACACTAT 16 1 1.2e-004 3.4e+000 # ATAGTTTA TAAACTAT 14 1 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.4e-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 0.533333 0.466667 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTRCGCC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTRCGCC GGCGYAGT 23 0 9.5e-008 2.6e-003 # ACTGCGCC GGCGCAGT 14 0 5.6e-005 1.5e+000 # ACTACGCC GGCGTAGT 9 0 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.6e-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 0.391304 0.000000 0.608696 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 AGCGCMAG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGCGCMAG CTKGCGCT 22 0 1.9e-007 5.3e-003 # AGCGCAAG CTTGCGCT 11 0 4.6e-004 1.3e+001 # AGCGCCAG CTGGCGCT 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.3e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGGYGC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYGC GCRCCCAT 22 0 1.9e-007 5.2e-003 # ATGGGCGC GCGCCCAT 12 0 2.3e-004 6.2e+000 # ATGGGTGC GCACCCAT 10 0 9.4e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.2e-003 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 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCGTGSA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 45 10 5.9e-007 1.6e-002 # CCGTGGA TCCACGG 27 5 4.6e-005 1.2e+000 # CCGTGCA TGCACGG 19 5 3.0e-003 8.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 1.6e-002 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 0.413043 0.586957 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAKCTCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 48 12 8.8e-007 2.4e-002 # TAGCTCA TGAGCTA 21 3 1.2e-004 3.2e+000 # TATCTCA TGAGATA 27 9 1.7e-003 4.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 2.4e-002 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.396226 0.603774 0.000000 1.000000 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 MOTIF CACGCGAS DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CACGCGAS STCGCGTG 19 0 1.6e-006 4.4e-002 # CACGCGAG CTCGCGTG 10 0 9.4e-004 2.5e+001 # CACGCGAC GTCGCGTG 9 0 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.4e-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 1.000000 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 0.000000 0.473684 0.526316 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 73.94 seconds