# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--AFT1/seqs-shuffled # positives: 605 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--AFT1/seqs-centered (Sat Jan 18 03:22:38 PST 2020) # negatives: 605 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--AFT1/seqs-shuffled (Sat Jan 18 03:22:38 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:38:57 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 0.301 C 0.200 G 0.200 T 0.299 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 86 5 1.1e-021 3.5e-017 # GGTTCGA TCGAACC 67 5 6.0e-016 2.0e-011 # AGTTCGA TCGAACT 25 0 2.3e-008 7.5e-004 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 3.5e-017 0.255814 0.000000 0.744186 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARAAAAAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAAW WTTTTTYT 121 44 4.9e-011 1.6e-006 # AAAAAAAT ATTTTTTT 64 17 2.7e-008 8.7e-004 # AAAAAAAA TTTTTTTT 56 23 8.1e-005 2.6e+000 # AGAAAAAT ATTTTTCT 19 5 3.1e-003 9.8e+001 # AGAAAAAA TTTTTTCT 32 15 8.2e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 138 E= 1.6e-006 1.000000 0.000000 0.000000 0.000000 0.673913 0.000000 0.326087 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 0.514493 0.000000 0.000000 0.485507 MOTIF CGYTACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGYTACC GGTARCG 26 0 1.1e-008 3.6e-004 # CGCTACC GGTAGCG 18 0 3.4e-006 1.1e-001 # CGTTACC GGTAACG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 3.6e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 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 ACTBGGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 25 0 2.3e-008 7.4e-004 # ACTCGGCC GGCCGAGT 11 0 4.7e-004 1.5e+001 # ACTTGGCC GGCCAAGT 10 0 9.4e-004 3.0e+001 # ACTGGGCC GGCCCAGT 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.4e-004 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 0.440000 0.280000 0.280000 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 ADGAAGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ADGAAGA TCTTCHT 70 25 8.6e-007 2.8e-002 # AAGAAGA TCTTCTT 28 10 2.2e-003 7.1e+001 # AGGAAGA TCTTCCT 28 10 2.2e-003 7.1e+001 # ATGAAGA TCTTCAT 18 5 5.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 2.8e-002 1.000000 0.000000 0.000000 0.000000 0.381579 0.000000 0.368421 0.250000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 24.09 seconds