# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR8/seqs-shuffled # positives: 496 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR8/seqs-centered (Sun Jan 19 02:11:28 PST 2020) # negatives: 496 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR8/seqs-shuffled (Sun Jan 19 02:11:28 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:22:23 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 0.201 G 0.205 T 0.296 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 101 7 6.5e-025 1.9e-020 # GGTTCGA TCGAACC 74 3 3.3e-020 9.9e-016 # GGTTCAA TTGAACC 27 4 1.3e-005 3.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 101 E= 1.9e-020 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 0.267327 0.000000 0.732673 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF MAAAAAAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST MAAAAAAW WTTTTTTK 103 36 4.1e-010 1.2e-005 # AAAAAAAT ATTTTTTT 61 16 4.0e-008 1.2e-003 # AAAAAAAA TTTTTTTT 43 15 1.0e-004 3.0e+000 # CAAAAAAT ATTTTTTG 17 4 3.3e-003 9.8e+001 # CAAAAAAA TTTTTTTG 32 15 8.0e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 113 E= 1.2e-005 0.690265 0.309735 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.442478 0.000000 0.000000 0.557522 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 46 5 4.8e-010 1.4e-005 # CGCCTTA TAAGGCG 35 4 1.0e-007 3.0e-003 # CGCGTTA TAACGCG 11 1 3.0e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 1.4e-005 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 0.760870 0.239130 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 ACCAYT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCAYT ARTGGT 121 54 1.4e-008 4.1e-004 # ACCACT AGTGGT 69 23 2.6e-007 7.6e-003 # ACCATT AATGGT 53 31 8.1e-003 2.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 130 E= 4.1e-004 1.000000 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 0.000000 0.000000 0.000000 0.576923 0.000000 0.423077 0.000000 0.000000 0.000000 1.000000 MOTIF CACGGTGM DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 22 0 1.9e-007 5.5e-003 # CACGGTGA TCACCGTG 12 0 2.3e-004 6.6e+000 # CACGGTGC GCACCGTG 10 0 9.3e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.5e-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 1.000000 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 0.545455 0.454545 0.000000 0.000000 MOTIF CCWACAG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCWACAG CTGTWGG 25 1 3.0e-007 8.8e-003 # CCTACAG CTGTAGG 14 0 5.6e-005 1.6e+000 # CCAACAG CTGTTGG 11 1 3.0e-003 8.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 8.8e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.440000 0.000000 0.000000 0.560000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CAASTTGG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAASTTGG CCAASTTG 21 0 3.8e-007 1.1e-002 # CAACTTGG CCAAGTTG 18 0 3.3e-006 9.4e-002 # CAAGTTGG CCAACTTG 18 0 3.3e-006 9.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-002 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 0.619048 0.380952 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 0.000000 0.000000 1.000000 0.000000 MOTIF ATGTAYGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 19 0 1.6e-006 4.6e-002 # ATGTATGG CCATACAT 13 0 1.1e-004 3.3e+000 # ATGTACGG CCGTACAT 7 0 7.6e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.6e-002 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 0.363636 0.000000 0.636364 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 29.98 seconds