# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-shuffled # positives: 999 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-centered (Sun Jan 19 10:05:01 PST 2020) # negatives: 999 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-shuffled (Sun Jan 19 10:05:01 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:21:42 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 0.196 G 0.200 T 0.305 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 109 20 3.1e-017 1.1e-012 # GGTTCGA TCGAACC 71 7 3.4e-015 1.2e-010 # GGTTCAA TTGAACC 39 13 1.7e-004 6.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 110 E= 1.1e-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 0.354545 0.000000 0.645455 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAVC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCAVC GBTGGT 211 100 3.7e-012 1.3e-007 # ACCAAC GTTGGT 101 40 5.3e-008 1.9e-003 # ACCAGC GCTGGT 56 22 5.5e-005 2.0e+000 # ACCACC GGTGGT 71 41 2.3e-003 8.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 235 E= 1.3e-007 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 0.434043 0.327660 0.238298 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGMAGMT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGMAGMT AKCTKCT 123 41 8.2e-012 3.0e-007 # AGAAGAT ATCTTCT 54 20 3.6e-005 1.3e+000 # AGCAGAT ATCTGCT 25 5 1.5e-004 5.3e+000 # AGCAGCT AGCTGCT 19 5 3.2e-003 1.1e+002 # AGAAGCT AGCTTCT 28 11 4.4e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 131 E= 3.0e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.656489 0.343511 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.641221 0.358779 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GTGGTWA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GTGGTWA TWACCAC 58 9 1.8e-010 6.6e-006 # GTGGTTA TAACCAC 33 4 4.4e-007 1.6e-002 # GTGGTAA TTACCAC 27 6 1.5e-004 5.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 6.6e-006 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 0.450000 0.000000 0.000000 0.550000 1.000000 0.000000 0.000000 0.000000 MOTIF TCWTCAW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TCWTCAW WTGAWGA 176 84 5.1e-010 1.8e-005 # TCTTCAA TTGAAGA 67 31 1.3e-004 4.5e+000 # TCTTCAT ATGAAGA 44 17 3.0e-004 1.1e+001 # TCATCAT ATGATGA 42 19 1.9e-003 6.9e+001 # TCATCAA TTGATGA 41 21 6.8e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 203 E= 1.8e-005 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.433498 0.000000 0.000000 0.566502 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.551724 0.000000 0.000000 0.448276 MOTIF CAAGAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CAAGAW WTCTTG 223 134 1.2e-007 4.4e-003 # CAAGAA TTCTTG 139 77 4.9e-006 1.8e-001 # CAAGAT ATCTTG 98 60 1.0e-003 3.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 251 E= 4.4e-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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.585657 0.000000 0.000000 0.414343 MOTIF GTGATAGY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 24 1 6.8e-007 2.4e-002 # GTGATAGT ACTATCAC 15 1 2.5e-004 8.8e+000 # GTGATAGC GCTATCAC 9 0 1.9e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.4e-002 0.000000 0.000000 1.000000 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.000000 0.625000 MOTIF AMAAGTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AMAAGTA TACTTKT 73 26 6.9e-007 2.5e-002 # ACAAGTA TACTTGT 32 9 1.9e-004 6.7e+000 # AAAAGTA TACTTTT 42 18 1.1e-003 4.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 2.5e-002 1.000000 0.000000 0.000000 0.000000 0.578947 0.421053 0.000000 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RCGCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RCGCCA TGGCGY 64 20 4.8e-007 1.7e-002 # GCGCCA TGGCGC 36 9 2.7e-005 9.6e-001 # ACGCCA TGGCGT 28 12 7.8e-003 2.7e+002 letter-probability matrix: alength= 4 w= 6 nsites= 64 E= 1.7e-002 0.437500 0.000000 0.562500 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 1.000000 0.000000 0.000000 0.000000 MOTIF RATGGCAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RATGGCAA TTGCCATY 27 2 7.0e-007 2.4e-002 # GATGGCAA TTGCCATC 16 1 1.3e-004 4.6e+000 # AATGGCAA TTGCCATT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.4e-002 0.407407 0.000000 0.592593 0.000000 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 1.000000 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 MOTIF AAAAWAT DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAAAWAT ATWTTTT 183 107 8.5e-007 3.0e-002 # AAAAAAT ATTTTTT 125 77 2.3e-004 8.1e+000 # AAAATAT ATATTTT 74 38 3.0e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 201 E= 3.0e-002 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 0.631841 0.000000 0.000000 0.368159 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 74.48 seconds