# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-shuffled # positives: 813 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-centered (Sat Jan 18 20:39:51 PST 2020) # negatives: 813 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-shuffled (Sat Jan 18 20:39:51 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 20:55:45 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 0.309 C 0.196 G 0.191 T 0.305 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 112 10 9.2e-025 3.0e-020 # GGTTCGA TCGAACC 97 8 5.7e-022 1.9e-017 # GGATCGA TCGATCC 25 2 2.4e-006 8.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 3.0e-020 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.187500 0.000000 0.000000 0.812500 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 CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 79 7 1.4e-017 4.8e-013 # CGCCTTA TAAGGCG 63 3 2.1e-016 6.9e-012 # CGCGTTA TAACGCG 16 4 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 4.8e-013 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 0.797468 0.202532 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 TGTAYGGR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 78 11 1.6e-014 5.3e-010 # TGTACGGA TCCGTACA 31 2 5.1e-008 1.7e-003 # TGTATGGG CCCATACA 32 4 7.6e-007 2.5e-002 # TGTACGGG CCCGTACA 10 1 5.7e-003 1.9e+002 # TGTATGGA TCCATACA 15 4 9.3e-003 3.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 91 E= 5.3e-010 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 0.000000 0.472527 0.000000 0.527473 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.538462 0.000000 0.461538 0.000000 MOTIF ACCACTV DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACTV BAGTGGT 101 22 1.7e-014 5.7e-010 # ACCACTA TAGTGGT 51 10 2.8e-008 9.3e-004 # ACCACTC GAGTGGT 33 9 1.1e-004 3.7e+000 # ACCACTG CAGTGGT 17 3 1.2e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 101 E= 5.7e-010 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 0.504950 0.326733 0.168317 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 35 0 2.0e-011 6.5e-007 # GCGCTACC GGTAGCGC 26 0 1.2e-008 4.0e-004 # GCTCTACC GGTAGAGC 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 6.5e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.742857 0.257143 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-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 39 1 2.4e-011 7.8e-007 # ATGGCAAC GTTGCCAT 22 1 2.5e-006 8.2e-002 # ATGGCATC GATGCCAT 17 0 7.0e-006 2.3e-001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 7.8e-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 0.564103 0.000000 0.000000 0.435897 0.000000 1.000000 0.000000 0.000000 MOTIF CTTGRCC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTTGRCC GGYCAAG 62 12 6.4e-010 2.1e-005 # CTTGGCC GGCCAAG 40 7 3.8e-007 1.2e-002 # CTTGACC GGTCAAG 22 5 6.9e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 2.1e-005 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 0.354839 0.000000 0.645161 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 42 5 8.0e-009 2.6e-004 # TGGCGTA TACGCCA 20 2 5.5e-005 1.8e+000 # TGGCGCA TGCGCCA 22 3 7.0e-005 2.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 2.6e-004 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 0.523810 0.000000 0.476190 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AARAAAR YTTTYTT 246 150 1.8e-008 5.8e-004 # AAGAAAA TTTTCTT 84 38 9.3e-006 3.0e-001 # AAAAAAG CTTTTTT 92 52 3.1e-004 1.0e+001 # AAGAAAG CTTTCTT 42 18 1.1e-003 3.6e+001 # AAAAAAA TTTTTTT 119 84 5.3e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 306 E= 5.8e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.604575 0.000000 0.395425 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 0.627451 0.000000 0.372549 0.000000 MOTIF GTGATAGY DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 27 1 8.8e-008 2.8e-003 # GTGATAGC GCTATCAC 16 0 1.4e-005 4.6e-001 # GTGATAGT ACTATCAC 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.8e-003 0.000000 0.000000 1.000000 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.592593 0.000000 0.407407 MOTIF TAGCTCR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TAGCTCR YGAGCTA 30 2 9.7e-008 3.1e-003 # TAGCTCA TGAGCTA 22 2 1.6e-005 5.1e-001 # TAGCTCG CGAGCTA 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 3.1e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.733333 0.000000 0.266667 0.000000 MOTIF CRCCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 113 51 1.9e-007 6.2e-003 # CACCCA TGGGTG 75 36 8.2e-005 2.6e+000 # CGCCCA TGGGCG 40 16 7.7e-004 2.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 183 E= 6.2e-003 0.000000 1.000000 0.000000 0.000000 0.770492 0.000000 0.229508 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 CCGTGSA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 36 5 2.9e-007 9.3e-003 # CCGTGGA TCCACGG 21 3 1.3e-004 4.0e+000 # CCGTGCA TGCACGG 15 2 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 9.3e-003 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 0.416667 0.583333 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGCGWGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 24 1 6.6e-007 2.1e-002 # AAGCGTGA TCACGCTT 13 0 1.2e-004 3.7e+000 # AAGCGAGA TCTCGCTT 11 1 3.1e-003 9.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.458333 0.000000 0.000000 0.541667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AACCRACT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AACCRACT AGTYGGTT 32 4 7.6e-007 2.4e-002 # AACCGACT AGTCGGTT 12 0 2.3e-004 7.4e+000 # AACCAACT AGTTGGTT 20 4 7.1e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 2.4e-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 0.000000 1.000000 0.000000 0.000000 0.625000 0.000000 0.375000 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 # Stopping reason: E-value threshold exceeded # Running time: 79.32 seconds