# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--GAL11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--GAL11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--GAL11/seqs-shuffled # positives: 754 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--GAL11/seqs-centered (Sun Jan 19 09:14:01 PST 2020) # negatives: 754 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--GAL11/seqs-shuffled (Sun Jan 19 09:14:01 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 09:30:45 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 0.303 C 0.198 G 0.199 T 0.300 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 92 9 8.1e-020 2.8e-015 # GGTTCGA TCGAACC 76 8 5.0e-016 1.8e-011 # GGATCGA TCGATCC 25 2 2.4e-006 8.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 2.8e-015 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.228261 0.000000 0.000000 0.771739 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 TGGTWR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGGTWR YWACCA 211 101 1.4e-012 4.8e-008 # TGGTAG CTACCA 51 18 3.0e-005 1.0e+000 # TGGTAA TTACCA 66 30 9.6e-005 3.3e+000 # TGGTTA TAACCA 65 32 3.5e-004 1.2e+001 # TGGTTG CAACCA 55 30 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 241 E= 4.8e-008 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 0.510373 0.000000 0.000000 0.489627 0.547718 0.000000 0.452282 0.000000 MOTIF AAAAAADA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAAADA THTTTTTT 129 48 4.0e-011 1.3e-006 # AAAAAAAA TTTTTTTT 71 25 6.8e-007 2.3e-002 # AAAAAATA TATTTTTT 52 20 7.3e-005 2.5e+000 # AAAAAAGA TCTTTTTT 36 12 2.9e-004 1.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 145 E= 1.3e-006 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 1.000000 0.000000 0.000000 0.000000 0.475862 0.000000 0.227586 0.296552 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 368 268 1.2e-007 4.0e-003 # GAAGA TCTTC 234 157 3.8e-006 1.3e-001 # CAAGA TCTTG 218 146 9.2e-006 3.1e-001 letter-probability matrix: alength= 4 w= 5 nsites= 520 E= 4.0e-003 0.000000 0.492308 0.507692 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 1.000000 0.000000 0.000000 0.000000 MOTIF CACGGYG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 29 2 1.8e-007 6.0e-003 # CACGGTG CACCGTG 19 2 1.0e-004 3.3e+000 # CACGGCG CGCCGTG 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 6.0e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.344828 0.000000 0.655172 0.000000 0.000000 1.000000 0.000000 MOTIF CGGTAGM DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGGTAGM KCTACCG 26 2 1.3e-006 4.1e-002 # CGGTAGC GCTACCG 18 2 1.9e-004 6.1e+000 # CGGTAGA TCTACCG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 4.1e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.307692 0.692308 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 33.75 seconds