# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MCM1/seqs-shuffled # positives: 800 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MCM1/seqs-centered (Sat Jan 18 18:38:09 PST 2020) # negatives: 800 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--MCM1/seqs-shuffled (Sat Jan 18 18:38:09 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:52:20 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 0.296 C 0.201 G 0.202 T 0.300 MOTIF TCGAACCB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 84 5 9.2e-021 3.1e-016 # TCGAACCC GGGTTCGA 40 2 1.3e-010 4.4e-006 # TCGAACCG CGGTTCGA 29 1 2.3e-008 7.6e-004 # TCGAACCT AGGTTCGA 15 2 1.1e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 84 E= 3.1e-016 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 0.476190 0.345238 0.178571 MOTIF ACCACTM DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 78 9 7.9e-016 2.6e-011 # ACCACTA TAGTGGT 44 4 4.6e-010 1.5e-005 # ACCACTC GAGTGGT 34 5 9.3e-007 3.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 2.6e-011 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.556962 0.443038 0.000000 0.000000 MOTIF RAGAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST RAGAAA TTTCTY 275 151 1.3e-012 4.4e-008 # AAGAAA TTTCTT 195 105 4.9e-009 1.6e-004 # GAGAAA TTTCTC 100 55 9.2e-005 3.1e+000 letter-probability matrix: alength= 4 w= 6 nsites= 325 E= 4.4e-008 0.676923 0.000000 0.323077 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 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 58 7 9.3e-012 3.1e-007 # CGCCTTA TAAGGCG 48 6 9.3e-010 3.1e-005 # CGCGTTA TAACGCG 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 3.1e-007 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 0.827586 0.172414 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 GTGATAGY DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 33 0 8.3e-011 2.7e-006 # GTGATAGC GCTATCAC 17 0 7.0e-006 2.3e-001 # GTGATAGT ACTATCAC 16 0 1.4e-005 4.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.7e-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 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 0.515152 0.000000 0.484848 MOTIF CCAAVAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCAAVAGA TCTBTTGG 41 3 5.1e-010 1.7e-005 # CCAACAGA TCTGTTGG 13 0 1.2e-004 3.8e+000 # CCAAGAGA TCTCTTGG 17 2 3.4e-004 1.1e+001 # CCAAAAGA TCTTTTGG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.7e-005 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 0.000000 0.268293 0.317073 0.414634 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 MOTIF CRCCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 100 34 1.1e-009 3.7e-005 # CGCCCA TGGGCG 42 10 3.3e-006 1.1e-001 # CACCCA TGGGTG 59 25 9.1e-005 3.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 111 E= 3.7e-005 0.000000 1.000000 0.000000 0.000000 0.612613 0.000000 0.387387 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 AACTKGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AACTKGG CCMAGTT 66 16 5.0e-009 1.6e-004 # AACTTGG CCAAGTT 43 9 7.1e-007 2.3e-002 # AACTGGG CCCAGTT 23 8 5.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 1.6e-004 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 0.000000 1.000000 0.000000 0.000000 0.348485 0.651515 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 34 2 7.1e-009 2.3e-004 # GCGCTACC GGTAGCGC 22 0 2.1e-007 6.7e-003 # GCTCTACC GGTAGAGC 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.3e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.647059 0.352941 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 CGTTGCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCCA TGGCAACG 25 0 2.5e-008 8.0e-004 # CGTTGCCA TGGCAACG 25 0 2.5e-008 8.0e-004 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.0e-004 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 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 CACTATA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACTATA TATAGTG 28 1 4.5e-008 1.4e-003 # CACTATA TATAGTG 28 1 4.5e-008 1.4e-003 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 1.4e-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 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGKGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CGCGKGC GCMCGCG 26 1 1.7e-007 5.6e-003 # CGCGGGC GCCCGCG 15 1 2.4e-004 7.9e+000 # CGCGTGC GCACGCG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 5.6e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.576923 0.423077 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TCYGTACA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TCYGTACA TGTACRGA 26 1 1.7e-007 5.6e-003 # TCCGTACA TGTACGGA 18 1 3.5e-005 1.1e+000 # TCTGTACA TGTACAGA 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.6e-003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.655172 0.000000 0.344828 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AKATTAT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AKATTAT ATAATMT 68 22 3.1e-007 1.0e-002 # AGATTAT ATAATCT 33 7 1.7e-005 5.5e-001 # ATATTAT ATAATAT 39 15 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 1.0e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.458333 0.541667 1.000000 0.000000 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 0.000000 0.000000 1.000000 MOTIF AGYCAGAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGYCAGAC GTCTGRCT 21 0 4.2e-007 1.3e-002 # AGTCAGAC GTCTGACT 13 0 1.2e-004 3.7e+000 # AGCCAGAC GTCTGGCT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.380952 0.000000 0.619048 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 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 78.22 seconds