# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--THP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--THP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--THP2/seqs-shuffled # positives: 851 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--THP2/seqs-centered (Sun Jan 19 09:26:04 PST 2020) # negatives: 851 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--THP2/seqs-shuffled (Sun Jan 19 09:26:04 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 09:42:05 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 0.300 C 0.199 G 0.203 T 0.298 MOTIF SAAGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 519 349 1.0e-016 3.2e-012 # GAAGA TCTTC 328 187 5.8e-014 1.8e-009 # CAAGA TCTTG 302 214 2.2e-006 6.8e-002 letter-probability matrix: alength= 4 w= 5 nsites= 731 E= 3.2e-012 0.000000 0.466484 0.533516 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 MOTIF GGTAD DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTAD HTACC 430 263 1.0e-016 3.1e-012 # GGTAA TTACC 214 132 4.9e-007 1.5e-002 # GGTAT ATACC 173 102 1.8e-006 5.6e-002 # GGTAG CTACC 123 65 4.6e-006 1.4e-001 letter-probability matrix: alength= 4 w= 5 nsites= 579 E= 3.1e-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 1.000000 0.000000 0.000000 0.000000 0.428325 0.000000 0.229706 0.341969 MOTIF CAWCGWTG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAWCGWTG CAWCGWTG 54 0 2.3e-017 6.8e-013 # CAACGATG CATCGTTG 32 0 1.7e-010 5.0e-006 # CAACGTTG CAACGTTG 16 0 1.4e-005 4.1e-001 # CATCGATG CATCGATG 13 0 1.2e-004 3.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 61 E= 6.8e-013 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.606557 0.000000 0.000000 0.393443 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.557377 0.000000 0.000000 0.442623 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACCCADA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCCADA THTGGGT 85 17 5.6e-013 1.6e-008 # ACCCATA TATGGGT 32 2 2.7e-008 7.7e-004 # ACCCAGA TCTGGGT 24 3 2.2e-005 6.3e-001 # ACCCAAA TTTGGGT 36 12 3.0e-004 8.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 1.6e-008 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 0.382979 0.000000 0.255319 0.361702 1.000000 0.000000 0.000000 0.000000 MOTIF CMTTAGCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CMTTAGCA TGCTAAKG 38 2 5.1e-010 1.5e-005 # CCTTAGCA TGCTAAGG 21 1 4.9e-006 1.4e-001 # CATTAGCA TGCTAATG 17 1 6.7e-005 1.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.5e-005 0.000000 1.000000 0.000000 0.000000 0.447368 0.552632 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTTCRA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTTCRA TYGAAC 174 87 2.8e-009 7.9e-005 # GTTCAA TTGAAC 119 61 3.0e-006 8.6e-002 # GTTCGA TCGAAC 57 33 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 184 E= 7.9e-005 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 0.684783 0.000000 0.315217 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCAGCAS DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCAGCAS STGCTGC 55 11 1.0e-008 2.9e-004 # GCAGCAG CTGCTGC 38 6 3.5e-007 9.9e-003 # GCAGCAC GTGCTGC 20 5 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 2.9e-004 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.366667 0.633333 0.000000 MOTIF ARCAGGTC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ARCAGGTC GACCTGYT 28 1 4.5e-008 1.3e-003 # AGCAGGTC GACCTGCT 15 0 2.9e-005 8.1e-001 # AACAGGTC GACCTGTT 13 1 8.8e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.3e-003 1.000000 0.000000 0.000000 0.000000 0.464286 0.000000 0.535714 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAACVCAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAACVCAA TTGBGTTG 39 4 1.1e-008 3.1e-004 # CAACACAA TTGTGTTG 22 4 2.4e-004 6.9e+000 # CAACGCAA TTGCGTTG 9 0 1.9e-003 5.4e+001 # CAACCCAA TTGGGTTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 3.1e-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 0.564103 0.205128 0.230769 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 CCGTACA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGTACA TGTACGG 31 2 5.1e-008 1.4e-003 # CCGTACA TGTACGG 31 2 5.1e-008 1.4e-003 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.4e-003 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 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 GCCTTMA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GCCTTMA TKAAGGC 49 10 8.6e-008 2.4e-003 # GCCTTCA TGAAGGC 22 3 7.1e-005 2.0e+000 # GCCTTAA TTAAGGC 27 7 3.7e-004 1.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 2.4e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.560000 0.440000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACGACGKC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACGACGKC GMCGTCGT 26 1 1.7e-007 4.9e-003 # ACGACGGC GCCGTCGT 14 0 5.8e-005 1.6e+000 # ACGACGTC GACGTCGT 12 1 1.7e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.9e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.538462 0.461538 0.000000 1.000000 0.000000 0.000000 MOTIF GASACC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GASACC GGTSTC 102 44 3.0e-007 8.4e-003 # GACACC GGTGTC 59 20 4.1e-006 1.1e-001 # GAGACC GGTCTC 45 24 6.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 105 E= 8.4e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 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 MOTIF GCYAGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCYAGA TCTRGC 99 41 1.8e-007 4.9e-003 # GCCAGA TCTGGC 54 20 3.4e-005 9.4e-001 # GCTAGA TCTAGC 45 21 1.8e-003 5.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 105 E= 4.9e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.533333 0.000000 0.466667 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 AABTGGT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AABTGGT ACCAVTT 85 33 3.9e-007 1.1e-002 # AAGTGGT ACCACTT 27 6 1.4e-004 3.9e+000 # AACTGGT ACCAGTT 25 9 4.2e-003 1.2e+002 # AATTGGT ACCAATT 36 18 9.0e-003 2.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 1.1e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.277778 0.300000 0.422222 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 MOTIF ASTATCAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ASTATCAC GTGATAST 21 0 4.2e-007 1.2e-002 # ACTATCAC GTGATAGT 14 0 5.8e-005 1.6e+000 # AGTATCAC GTGATACT 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GAAAGWGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GAAAGWGA TCWCTTTC 32 4 7.7e-007 2.1e-002 # GAAAGAGA TCTCTTTC 20 2 5.5e-005 1.5e+000 # GAAAGTGA TCACTTTC 12 2 6.3e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 2.1e-002 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 0.000000 0.000000 1.000000 0.000000 0.625000 0.000000 0.000000 0.375000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGATTGGY DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AGATTGGY RCCAATCT 29 3 1.1e-006 2.9e-002 # AGATTGGC GCCAATCT 14 1 4.7e-004 1.3e+001 # AGATTGGT ACCAATCT 15 2 1.1e-003 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 2.9e-002 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 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 0.482759 0.000000 0.517241 MOTIF CTYGGCCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 26 2 1.3e-006 3.5e-002 # CTCGGCCA TGGCCGAG 15 1 2.5e-004 6.8e+000 # CTTGGCCA TGGCCAAG 11 1 3.1e-003 8.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.5e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.576923 0.000000 0.423077 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 ATCGTTC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATCGTTC GAACGAT 23 1 1.3e-006 3.6e-002 # ATCGTTC GAACGAT 23 1 1.3e-006 3.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 MOTIF TTAGTKAA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST TTAGTKAA TTMACTAA 31 4 1.4e-006 3.8e-002 # TTAGTTAA TTAACTAA 16 2 6.2e-004 1.7e+001 # TTAGTGAA TTCACTAA 15 2 1.1e-003 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 3.8e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.483871 0.516129 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 103.56 seconds