# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/seqs-shuffled # positives: 546 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/seqs-centered (Sun Jan 19 02:27:58 PST 2020) # negatives: 546 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/seqs-shuffled (Sun Jan 19 02:27:58 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:40:42 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 0.307 C 0.201 G 0.192 T 0.300 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 90 8 1.9e-020 5.4e-016 # TGTACGGA TCCGTACA 38 0 1.9e-012 5.3e-008 # TGTATGGG CCCATACA 40 6 9.0e-008 2.6e-003 # TGTATGGA TCCATACA 13 1 8.6e-004 2.4e+001 # TGTACGGG CCCGTACA 11 1 3.0e-003 8.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 106 E= 5.4e-016 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 0.481132 0.000000 0.518868 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.509434 0.000000 0.490566 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 71 2 2.9e-020 8.0e-016 # CTCGGCCA TGGCCGAG 37 0 3.9e-012 1.1e-007 # CTTGGCCA TGGCCAAG 22 2 1.5e-005 4.2e-001 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 6.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 8.0e-016 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.521127 0.169014 0.309859 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 BTAAGGCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 62 4 2.1e-015 5.8e-011 # TTAAGGCG CGCCTTAA 37 3 5.7e-009 1.6e-004 # CTAAGGCG CGCCTTAG 13 0 1.1e-004 3.2e+000 # GTAAGGCG CGCCTTAC 12 1 1.6e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 5.8e-011 0.000000 0.209677 0.193548 0.596774 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 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 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 49 1 1.5e-014 4.3e-010 # GCGCTACC GGTAGCGC 32 0 1.5e-010 4.1e-006 # GCTCTACC GGTAGAGC 17 1 6.5e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 4.3e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.653061 0.346939 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 CCCANAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCCANAC GTNTGGG 86 19 1.2e-012 3.4e-008 # CCCACAC GTGTGGG 45 11 1.6e-006 4.3e-002 # CCCAGAC GTCTGGG 16 1 1.2e-004 3.5e+000 # CCCAAAC GTTTGGG 19 5 3.0e-003 8.4e+001 # CCCATAC GTATGGG 13 2 3.5e-003 9.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 142 E= 3.4e-008 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 0.133803 0.661972 0.105634 0.098592 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTARACCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 42 2 2.7e-011 7.4e-007 # CTAGACCA TGGTCTAG 26 2 1.2e-006 3.2e-002 # CTAAACCA TGGTTTAG 16 0 1.4e-005 3.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 7.4e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.619048 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 0.000000 MOTIF ATAGTKTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 45 4 1.9e-010 5.1e-006 # ATAGTGTA TACACTAT 28 0 2.6e-009 7.2e-005 # ATAGTTTA TAAACTAT 17 4 3.3e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 5.1e-006 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 0.622222 0.377778 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAKCTCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 50 6 2.0e-010 5.6e-006 # TAGCTCA TGAGCTA 25 2 2.2e-006 6.1e-002 # TATCTCA TGAGATA 25 4 4.2e-005 1.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 5.6e-006 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.431034 0.568966 0.000000 1.000000 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 MOTIF TGGCGYA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 51 9 6.6e-009 1.8e-004 # TGGCGTA TACGCCA 23 3 3.7e-005 1.0e+000 # TGGCGCA TGCGCCA 28 6 7.8e-005 2.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 1.8e-004 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 0.000000 1.000000 0.000000 0.000000 0.549020 0.000000 0.450980 1.000000 0.000000 0.000000 0.000000 MOTIF CTKGCGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTKGCGC GCGCMAG 30 1 1.0e-008 2.8e-004 # CTTGCGC GCGCAAG 19 1 1.7e-005 4.7e-001 # CTGGCGC GCGCCAG 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 2.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 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 1.000000 0.000000 0.000000 MOTIF AGAARA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGAARA TYTTCT 154 79 1.9e-008 5.1e-004 # AGAAAA TTTTCT 126 67 1.8e-006 5.0e-002 # AGAAGA TCTTCT 39 18 3.0e-003 8.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 178 E= 5.1e-004 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 0.775281 0.000000 0.224719 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SGGTTCGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 24 0 4.6e-008 1.2e-003 # CGGTTCGA TCGAACCG 12 0 2.3e-004 6.2e+000 # GGGTTCGA TCGAACCC 12 0 2.3e-004 6.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.2e-003 0.000000 0.500000 0.500000 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 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 MOTIF ATGGCAWC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 36 4 5.8e-008 1.5e-003 # ATGGCAAC GTTGCCAT 24 3 2.0e-005 5.4e-001 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 1.5e-003 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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF GTGGTTAK DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GTGGTTAK MTAACCAC 30 2 8.6e-008 2.3e-003 # GTGGTTAT ATAACCAC 16 0 1.4e-005 3.6e-001 # GTGGTTAG CTAACCAC 15 2 1.1e-003 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.3e-003 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.483871 0.516129 MOTIF ATCCKTGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATCCKTGC GCAMGGAT 22 0 1.9e-007 5.1e-003 # ATCCGTGC GCACGGAT 13 0 1.1e-004 3.0e+000 # ATCCTTGC GCAAGGAT 10 0 9.4e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 5.1e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.583333 0.416667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTATKAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GTATKAC GTMATAC 37 6 5.2e-007 1.4e-002 # GTATGAC GTCATAC 24 3 2.0e-005 5.4e-001 # GTATTAC GTAATAC 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 1.4e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.531915 0.468085 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCCATKC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCCATKC GMATGGG 41 8 5.9e-007 1.6e-002 # CCCATTC GAATGGG 18 2 1.8e-004 4.8e+000 # CCCATGC GCATGGG 23 6 1.0e-003 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.6e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.560976 0.439024 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 64.06 seconds