# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-shuffled # positives: 836 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-centered (Fri Jan 17 22:25:34 PST 2020) # negatives: 836 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-shuffled (Fri Jan 17 22:25:34 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:41:59 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 0.206 G 0.203 T 0.297 MOTIF TCGAACCB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 80 3 1.6e-021 5.6e-017 # TCGAACCC GGGTTCGA 34 2 7.2e-009 2.6e-004 # TCGAACCG CGGTTCGA 28 1 4.5e-008 1.6e-003 # TCGAACCT AGGTTCGA 18 0 3.5e-006 1.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 80 E= 5.6e-017 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 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 0.425000 0.350000 0.225000 MOTIF AGTGGTWW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWW WWACCACT 68 3 6.9e-018 2.4e-013 # AGTGGTTA TAACCACT 32 0 1.7e-010 6.1e-006 # AGTGGTAA TTACCACT 17 1 6.7e-005 2.4e+000 # AGTGGTTT AAACCACT 15 1 2.5e-004 8.7e+000 # AGTGGTAT ATACCACT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 75 E= 2.4e-013 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.373333 0.000000 0.000000 0.626667 0.653333 0.000000 0.000000 0.346667 MOTIF SAAGAW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST SAAGAW WTCTTS 321 197 3.3e-011 1.2e-006 # GAAGAA TTCTTC 130 68 1.7e-006 5.9e-002 # CAAGAT ATCTTG 84 39 1.6e-005 5.6e-001 # CAAGAA TTCTTG 116 73 5.7e-004 2.0e+001 # GAAGAT ATCTTC 78 49 4.8e-003 1.7e+002 letter-probability matrix: alength= 4 w= 6 nsites= 421 E= 1.2e-006 0.000000 0.491686 0.508314 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 0.610451 0.000000 0.000000 0.389549 MOTIF CTTASC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTTASC GSTAAG 119 44 2.8e-010 9.8e-006 # CTTACC GGTAAG 70 22 1.3e-007 4.5e-003 # CTTAGC GCTAAG 51 22 3.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 128 E= 9.8e-006 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 0.000000 0.570312 0.429688 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTYGGCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 44 5 2.4e-009 8.3e-005 # CTTGGCC GGCCAAG 30 4 2.5e-006 8.7e-002 # CTCGGCC GGCCGAG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 8.3e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.318182 0.000000 0.681818 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 MOTIF CAACRATG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CAACRATG CATYGTTG 29 1 2.3e-008 7.9e-004 # CAACGATG CATCGTTG 18 1 3.5e-005 1.2e+000 # CAACAATG CATTGTTG 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.9e-004 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 0.379310 0.000000 0.620690 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 MOTIF TATAGTGW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TATAGTGW WCACTATA 28 1 4.5e-008 1.6e-003 # TATAGTGT ACACTATA 21 1 4.9e-006 1.7e-001 # TATAGTGA TCACTATA 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.6e-003 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 MOTIF GCCWTAAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 28 2 3.6e-007 1.2e-002 # GCCTTAAC GTTAAGGC 18 2 1.9e-004 6.4e+000 # GCCATAAC GTTATGGC 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.2e-002 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 GGATCRAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGATCRAA TTYGATCC 30 3 5.6e-007 1.9e-002 # GGATCGAA TTCGATCC 19 2 1.0e-004 3.5e+000 # GGATCAAA TTTGATCC 12 1 1.7e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.9e-002 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.387097 0.000000 0.612903 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAWAT DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAAAWAT ATWTTTT 157 87 7.7e-007 2.6e-002 # AAAAAAT ATTTTTT 117 63 1.3e-005 4.4e-001 # AAAATAT ATATTTT 57 31 2.9e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 180 E= 2.6e-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 0.694444 0.000000 0.000000 0.305556 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CCTGYAG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCTGYAG CTRCAGG 31 4 1.4e-006 4.8e-002 # CCTGTAG CTACAGG 18 2 1.9e-004 6.4e+000 # CCTGCAG CTGCAGG 14 2 2.0e-003 6.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 4.8e-002 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 1.000000 0.000000 0.000000 0.437500 0.000000 0.562500 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 61.71 seconds