# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT1/seqs-shuffled # positives: 498 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT1/seqs-centered (Sun Jan 19 08:02:29 PST 2020) # negatives: 498 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT1/seqs-shuffled (Sun Jan 19 08:02:29 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 08:13:26 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 0.302 C 0.197 G 0.197 T 0.304 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 77 7 1.8e-017 5.4e-013 # GGTTCGA TCGAACC 57 6 2.1e-012 6.2e-008 # GGATCGA TCGATCC 25 1 3.0e-007 9.0e-003 # GGCTCGA TCGAGCC 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 5.4e-013 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.311688 0.064935 0.000000 0.623377 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 AARAAAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAAA TTTTYTT 157 69 1.5e-011 4.4e-007 # AAAAAAA TTTTTTT 115 49 9.8e-009 2.9e-004 # AAGAAAA TTTTCTT 74 25 1.1e-007 3.3e-003 letter-probability matrix: alength= 4 w= 7 nsites= 195 E= 4.4e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.635897 0.000000 0.364103 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 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 49 8 5.6e-009 1.7e-004 # AGTGGTT AACCACT 31 5 4.6e-006 1.3e-001 # AGTGGTA TACCACT 22 3 6.5e-005 1.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 1.7e-004 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 0.407407 0.000000 0.000000 0.592593 MOTIF CACCCAY DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CACCCAY RTGGGTG 38 5 7.2e-008 2.1e-003 # CACCCAT ATGGGTG 24 3 2.0e-005 5.8e-001 # CACCCAC GTGGGTG 16 3 2.0e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 2.1e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.538462 0.000000 0.461538 MOTIF CTTGRCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTTGRCC GGYCAAG 29 2 1.6e-007 4.7e-003 # CTTGGCC GGCCAAG 17 0 6.6e-006 1.9e-001 # CTTGACC GGTCAAG 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 4.7e-003 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 0.413793 0.000000 0.586207 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF KAGTGGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST KAGTGGA TCCACTM 19 0 1.6e-006 4.7e-002 # TAGTGGA TCCACTA 12 0 2.3e-004 6.6e+000 # GAGTGGA TCCACTC 7 0 7.6e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 19 E= 4.7e-002 0.000000 0.000000 0.368421 0.631579 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 23.13 seconds