# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-shuffled # positives: 511 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-centered (Sat Jan 18 11:35:53 PST 2020) # negatives: 511 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-shuffled (Sat Jan 18 11:35:53 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 11:57:19 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 0.200 T 0.301 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 70 1 2.6e-021 7.8e-017 # GGGTTCGA TCGAACCC 27 0 5.2e-009 1.6e-004 # CGGTTCGA TCGAACCG 22 0 1.9e-007 5.7e-003 # GAGTTCGA TCGAACTC 13 1 8.6e-004 2.6e+001 # CAGTTCGA TCGAACTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 70 E= 7.8e-017 0.000000 0.428571 0.571429 0.000000 0.300000 0.000000 0.700000 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 CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 39 2 2.0e-010 5.9e-006 # CGCCTTA TAAGGCG 28 1 3.9e-008 1.2e-003 # CGCGTTA TAACGCG 11 1 3.0e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 5.9e-006 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 0.717949 0.282051 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 AAAAARAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAARAA TTYTTTTT 84 24 3.9e-010 1.2e-005 # AAAAAAAA TTTTTTTT 50 16 9.1e-006 2.7e-001 # AAAAAGAA TTCTTTTT 42 12 1.6e-005 4.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 99 E= 1.2e-005 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 0.575758 0.000000 0.424242 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 21 0 3.9e-007 1.1e-002 # GCTCTACC GGTAGAGC 11 0 4.6e-004 1.4e+001 # GCGCTACC GGTAGCGC 10 0 9.3e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.476190 0.523810 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 ATAGTKTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 30 3 4.9e-007 1.5e-002 # ATAGTGTA TACACTAT 16 1 1.2e-004 3.7e+000 # ATAGTTTA TAAACTAT 14 2 2.0e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.5e-002 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 ATTGAAMC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATTGAAMC GKTTCAAT 20 0 7.9e-007 2.3e-002 # ATTGAACC GGTTCAAT 14 0 5.6e-005 1.6e+000 # ATTGAAAC GTTTCAAT 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 2.3e-002 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 24.41 seconds