# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MIG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MIG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MIG1/seqs-shuffled # positives: 834 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MIG1/seqs-centered (Sat Jan 18 11:13:01 PST 2020) # negatives: 834 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MIG1/seqs-shuffled (Sat Jan 18 11:13:01 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 11:27:14 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 0.292 C 0.207 G 0.209 T 0.292 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 103 11 2.3e-021 8.1e-017 # GGTTCGA TCGAACC 86 9 5.1e-018 1.8e-013 # AGTTCGA TCGAACT 21 3 1.3e-004 4.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 103 E= 8.1e-017 0.203883 0.000000 0.796117 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 ACCACYA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACYA TRGTGGT 72 7 1.4e-015 4.9e-011 # ACCACTA TAGTGGT 54 3 9.7e-014 3.4e-009 # ACCACCA TGGTGGT 18 4 2.1e-003 7.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 4.9e-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 0.270270 0.000000 0.729730 1.000000 0.000000 0.000000 0.000000 MOTIF CCTTAVC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCTTAVC GBTAAGG 95 20 5.8e-014 2.0e-009 # CCTTAGC GCTAAGG 31 4 1.4e-006 4.8e-002 # CCTTAAC GTTAAGG 41 11 1.4e-005 4.7e-001 # CCTTACC GGTAAGG 26 6 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 2.0e-009 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 1.000000 0.000000 0.000000 0.000000 0.418367 0.265306 0.316327 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGTADC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGTADC GHTACC 138 46 2.1e-013 7.1e-009 # GGTAGC GCTACC 42 11 8.4e-006 2.9e-001 # GGTAAC GTTACC 49 15 8.5e-006 2.9e-001 # GGTATC GATACC 52 21 1.4e-004 4.7e+000 letter-probability matrix: alength= 4 w= 6 nsites= 144 E= 7.1e-009 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 0.340278 0.000000 0.291667 0.368056 0.000000 1.000000 0.000000 0.000000 MOTIF ACCCABAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 38 1 4.8e-011 1.6e-006 # ACCCATAC GTATGGGT 19 1 1.8e-005 6.2e-001 # ACCCACAC GTGTGGGT 12 0 2.3e-004 8.0e+000 # ACCCAGAC GTCTGGGT 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.6e-006 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 0.000000 0.285714 0.238095 0.476190 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AMGWTG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AMGWTG CAWCKT 247 138 1.4e-010 4.8e-006 # ACGATG CATCGT 58 25 1.3e-004 4.6e+000 # AAGATG CATCTT 86 46 1.9e-004 6.3e+000 # ACGTTG CAACGT 42 19 1.9e-003 6.4e+001 # AAGTTG CAACTT 90 60 6.4e-003 2.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 287 E= 4.8e-006 1.000000 0.000000 0.000000 0.000000 0.644599 0.355401 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.519164 0.000000 0.000000 0.480836 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGGCTATY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGGCTATY RATAGCCG 28 0 3.0e-009 9.9e-005 # CGGCTATC GATAGCCG 20 0 8.5e-007 2.8e-002 # CGGCTATT AATAGCCG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.9e-005 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 MOTIF CACGGYG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 46 7 1.3e-008 4.2e-004 # CACGGTG CACCGTG 32 5 3.0e-006 1.0e-001 # CACGGCG CGCCGTG 14 2 2.0e-003 6.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 4.2e-004 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.304348 0.000000 0.695652 0.000000 0.000000 1.000000 0.000000 MOTIF GATRAAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GATRAAAA TTTTYATC 33 2 1.4e-008 4.6e-004 # GATGAAAA TTTTCATC 17 1 6.7e-005 2.2e+000 # GATAAAAA TTTTTATC 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.6e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.484848 0.000000 0.515152 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATMTTTTG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATMTTTTG CAAAAKAT 32 2 2.7e-008 8.8e-004 # ATATTTTG CAAAATAT 16 1 1.3e-004 4.3e+000 # ATCTTTTG CAAAAGAT 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.8e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAGAAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAGAAA TTTCTT 199 112 2.7e-008 9.1e-004 # AAGAAA TTTCTT 199 112 2.7e-008 9.1e-004 letter-probability matrix: alength= 4 w= 6 nsites= 222 E= 9.1e-004 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACTCGGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACTCGGC GCCGAGTG 24 0 5.0e-008 1.7e-003 # CACTCGGC GCCGAGTG 24 0 5.0e-008 1.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.7e-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 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 MOTIF ACSTTCT DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACSTTCT AGAASGT 38 6 3.5e-007 1.1e-002 # ACCTTCT AGAAGGT 20 3 2.2e-004 7.4e+000 # ACGTTCT AGAACGT 18 3 7.0e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.1e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.526316 0.473684 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 0.000000 1.000000 MOTIF GTMTTCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GTMTTCA TGAAKAC 40 7 3.9e-007 1.3e-002 # GTCTTCA TGAAGAC 24 5 2.5e-004 8.1e+000 # GTATTCA TGAATAC 16 2 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.3e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.390244 0.609756 0.000000 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 1.000000 0.000000 0.000000 0.000000 MOTIF CTTACCR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTTACCR YGGTAAG 32 4 7.7e-007 2.5e-002 # CTTACCA TGGTAAG 19 3 4.0e-004 1.3e+001 # CTTACCG CGGTAAG 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 2.5e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.575758 0.000000 0.424242 0.000000 MOTIF ATGGGYGC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYGC GCRCCCAT 20 0 8.5e-007 2.8e-002 # ATGGGCGC GCGCCCAT 12 0 2.3e-004 7.7e+000 # ATGGGTGC GCACCCAT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-002 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 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 105.28 seconds