# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG1/seqs-shuffled # positives: 791 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG1/seqs-centered (Sat Jan 18 02:38:39 PST 2020) # negatives: 791 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG1/seqs-shuffled (Sat Jan 18 02:38:39 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 02:55:16 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 0.298 C 0.194 G 0.203 T 0.305 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 90 18 9.3e-014 3.3e-009 # GGTTCGA TCGAACC 59 8 2.2e-011 7.8e-007 # GGTTCAA TTGAACC 31 10 6.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 3.3e-009 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.358696 0.000000 0.641304 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAWA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 171 71 1.3e-012 4.5e-008 # AAAAAATA TATTTTTT 60 20 2.5e-006 8.9e-002 # AAGAAAAA TTTTTCTT 53 16 2.9e-006 1.0e-001 # AAAAAAAA TTTTTTTT 75 38 2.0e-004 7.1e+000 # AAGAAATA TATTTCTT 27 9 1.8e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 196 E= 4.5e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.653061 0.000000 0.346939 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 0.586735 0.000000 0.000000 0.413265 1.000000 0.000000 0.000000 0.000000 MOTIF CTWGACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 43 4 8.6e-010 3.0e-005 # CTAGACC GGTCTAG 21 1 4.9e-006 1.7e-001 # CTTGACC GGTCAAG 22 3 7.0e-005 2.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 3.0e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.477273 0.000000 0.000000 0.522727 0.000000 0.000000 1.000000 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 MOTIF GGTATS DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGTATS SATACC 84 27 9.1e-009 3.2e-004 # GGTATG CATACC 43 13 2.7e-005 9.6e-001 # GGTATC GATACC 42 15 1.8e-004 6.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 88 E= 3.2e-004 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 0.000000 1.000000 0.000000 0.488636 0.511364 0.000000 MOTIF ARGAAG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ARGAAG CTTCYT 157 79 2.2e-008 7.6e-004 # AAGAAG CTTCTT 111 56 4.2e-006 1.5e-001 # AGGAAG CTTCCT 57 24 1.1e-004 3.8e+000 letter-probability matrix: alength= 4 w= 6 nsites= 185 E= 7.6e-004 1.000000 0.000000 0.000000 0.000000 0.686486 0.000000 0.313514 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCCWTAAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 28 1 4.5e-008 1.5e-003 # GCCTTAAC GTTAAGGC 18 1 3.5e-005 1.2e+000 # GCCATAAC GTTATGGC 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.357143 0.000000 0.000000 0.642857 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RCGGGGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 31 4 1.4e-006 4.8e-002 # ACGGGGA TCCCCGT 17 2 3.4e-004 1.2e+001 # GCGGGGA TCCCCGC 14 2 2.0e-003 6.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 4.8e-002 0.548387 0.000000 0.451613 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 40.20 seconds