# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/seqs-shuffled # positives: 965 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/seqs-centered (Sun Jan 19 00:59:24 PST 2020) # negatives: 965 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/seqs-shuffled (Sun Jan 19 00:59:24 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 01:14:31 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 0.293 C 0.208 G 0.206 T 0.293 MOTIF GGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 78 7 3.6e-017 1.3e-012 # GGTTCGA TCGAACC 78 7 3.6e-017 1.3e-012 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 1.3e-012 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 367 224 9.7e-013 3.6e-008 # AAAAAAA TTTTTTT 182 111 4.1e-006 1.5e-001 # AAGAAAA TTTTCTT 120 66 2.0e-005 7.3e-001 # AAGAAAT ATTTCTT 65 28 5.4e-005 2.0e+000 # AAAAAAT ATTTTTT 144 104 3.9e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 461 E= 3.6e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.605206 0.000000 0.394794 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 0.600868 0.000000 0.000000 0.399132 MOTIF BCACGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST BCACGG CCGTGV 145 55 7.3e-012 2.7e-007 # GCACGG CCGTGC 61 19 8.5e-007 3.1e-002 # CCACGG CCGTGG 49 17 3.9e-005 1.4e+000 # TCACGG CCGTGA 42 20 3.1e-003 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 155 E= 2.7e-007 0.000000 0.322581 0.406452 0.270968 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 MOTIF ATGTAYGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 47 3 1.1e-011 4.1e-007 # ATGTATGG CCATACAT 28 2 3.7e-007 1.3e-002 # ATGTACGG CCGTACAT 21 1 5.0e-006 1.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 4.1e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.415094 0.000000 0.584906 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCTTAAMC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCTTAAMC GKTTAAGG 43 4 9.4e-010 3.4e-005 # CCTTAACC GGTTAAGG 29 3 1.1e-006 3.9e-002 # CCTTAAAC GTTTAAGG 14 1 4.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 3.4e-005 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.325581 0.674419 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 33 1 1.6e-009 5.7e-005 # GCGCTACC GGTAGCGC 21 0 4.3e-007 1.6e-002 # GCTCTACC GGTAGAGC 12 1 1.7e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 5.7e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.636364 0.363636 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 CAGAARA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAGAARA TYTTCTG 86 27 4.5e-009 1.6e-004 # CAGAAGA TCTTCTG 46 9 1.5e-007 5.5e-003 # CAGAAAA TTTTCTG 41 20 4.4e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 87 E= 1.6e-004 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.471264 0.000000 0.528736 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 34 3 4.8e-008 1.7e-003 # CTCGGCCA TGGCCGAG 18 0 3.5e-006 1.3e-001 # CTTGGCCA TGGCCAAG 16 3 2.1e-003 7.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.7e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.529412 0.000000 0.470588 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 1.000000 0.000000 0.000000 0.000000 MOTIF CAACGWTG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAACGWTG CAWCGTTG 24 0 5.2e-008 1.9e-003 # CAACGATG CATCGTTG 20 0 8.6e-007 3.1e-002 # CAACGTTG CAACGTTG 13 0 1.2e-004 4.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 1.9e-003 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.606061 0.000000 0.000000 0.393939 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF DCACCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST DCACCCA TGGGTGH 61 16 7.0e-008 2.5e-003 # ACACCCA TGGGTGT 35 10 1.0e-004 3.8e+000 # GCACCCA TGGGTGC 17 4 3.4e-003 1.2e+002 # TCACCCA TGGGTGA 12 2 6.3e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 69 E= 2.5e-003 0.521739 0.000000 0.304348 0.173913 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 MOTIF AASAAGAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AASAAGAA TTCTTSTT 46 9 1.5e-007 5.5e-003 # AACAAGAA TTCTTGTT 22 3 7.1e-005 2.6e+000 # AAGAAGAA TTCTTCTT 24 6 6.6e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 5.5e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.479167 0.520833 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 1.000000 0.000000 0.000000 0.000000 MOTIF CACTATW DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACTATW WATAGTG 46 9 1.5e-007 5.4e-003 # CACTATA TATAGTG 26 4 2.6e-005 9.5e-001 # CACTATT AATAGTG 22 5 7.0e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 5.4e-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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.541667 0.000000 0.000000 0.458333 MOTIF ACTGAGCT DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 20 0 8.6e-007 3.1e-002 # ACTGAGCT AGCTCAGT 20 0 8.6e-007 3.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 3.1e-002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 81.98 seconds