# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/seqs-shuffled # positives: 1939 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/seqs-centered (Sat Jan 18 23:52:01 PST 2020) # negatives: 1939 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/seqs-shuffled (Sat Jan 18 23:52:01 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:02:24 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 0.308 C 0.190 G 0.189 T 0.313 MOTIF TCTTB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCTTB VAAGA 1553 1198 1.1e-036 3.9e-032 # TCTTC GAAGA 691 443 1.1e-018 4.1e-014 # TCTTG CAAGA 698 455 7.6e-018 2.8e-013 # TCTTT AAAGA 880 718 7.4e-008 2.7e-003 letter-probability matrix: alength= 4 w= 5 nsites= 2833 E= 3.9e-032 0.000000 0.000000 0.000000 1.000000 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 0.305330 0.301447 0.393223 MOTIF GGTAD DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTAD HTACC 942 606 1.6e-028 5.5e-024 # GGTAA TTACC 496 282 4.5e-018 1.6e-013 # GGTAT ATACC 394 235 2.4e-012 8.3e-008 # GGTAG CTACC 294 158 5.2e-012 1.8e-007 letter-probability matrix: alength= 4 w= 5 nsites= 1348 E= 5.5e-024 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 0.450297 0.000000 0.227745 0.321958 MOTIF GCTKCY DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCTKCY RGMAGC 335 166 2.5e-016 8.4e-012 # GCTTCC GGAAGC 106 42 4.2e-008 1.4e-003 # GCTTCT AGAAGC 110 46 9.1e-008 3.0e-003 # GCTGCT AGCAGC 107 56 2.8e-005 9.3e-001 # GCTGCC GGCAGC 61 28 2.6e-004 8.8e+000 letter-probability matrix: alength= 4 w= 6 nsites= 394 E= 8.4e-012 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 0.449239 0.550761 0.000000 1.000000 0.000000 0.000000 0.000000 0.421320 0.000000 0.578680 MOTIF CCAAAK DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCAAAK MTTTGG 322 165 1.3e-014 4.3e-010 # CCAAAG CTTTGG 166 68 1.6e-011 5.4e-007 # CCAAAT ATTTGG 172 103 9.6e-006 3.2e-001 letter-probability matrix: alength= 4 w= 6 nsites= 355 E= 4.3e-010 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.495775 0.504225 MOTIF TGATR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TGATR YATCA 932 727 1.7e-011 5.6e-007 # TGATG CATCA 537 394 4.5e-008 1.5e-003 # TGATA TATCA 565 431 4.9e-007 1.6e-002 letter-probability matrix: alength= 4 w= 5 nsites= 1197 E= 5.6e-007 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 0.516291 0.000000 0.483709 0.000000 MOTIF ACCABC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCABC GVTGGT 254 129 8.6e-012 2.7e-007 # ACCACC GGTGGT 125 52 9.8e-009 3.1e-004 # ACCAGC GCTGGT 83 44 2.8e-004 8.8e+000 # ACCATC GATGGT 65 36 2.3e-003 7.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 286 E= 2.7e-007 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 0.468531 0.304196 0.227273 0.000000 1.000000 0.000000 0.000000 MOTIF GTRTGGAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTRTGGAA TTCCAYAC 46 6 4.2e-009 1.3e-004 # GTATGGAA TTCCATAC 24 2 4.9e-006 1.5e-001 # GTGTGGAA TTCCACAC 22 4 2.6e-004 8.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 1.3e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.521739 0.000000 0.478261 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGAAAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGAAAC GTTTCCAT 45 6 7.5e-009 2.4e-004 # ATGGAAAC GTTTCCAT 45 6 7.5e-009 2.4e-004 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 2.4e-004 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 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 1.000000 0.000000 0.000000 MOTIF AAVGTTG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AAVGTTG CAACBTT 182 92 9.4e-009 2.9e-004 # AACGTTG CAACGTT 44 14 4.5e-005 1.4e+000 # AAGGTTG CAACCTT 68 34 4.2e-004 1.3e+001 # AAAGTTG CAACTTT 71 44 6.8e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 186 E= 2.9e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.381720 0.252688 0.365591 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 MOTIF TGACTCYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TGACTCYA TRGAGTCA 39 4 1.3e-008 4.2e-004 # TGACTCTA TAGAGTCA 17 0 7.4e-006 2.3e-001 # TGACTCCA TGGAGTCA 22 4 2.6e-004 8.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 4.2e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.564103 0.000000 0.435897 1.000000 0.000000 0.000000 0.000000 MOTIF TATRTRTA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TATRTRTA TAYAYATA 92 32 2.0e-008 6.3e-004 # TATGTGTA TACACATA 25 5 1.5e-004 4.8e+000 # TATATGTA TACATATA 32 9 2.0e-004 6.3e+000 # TATATATA TATATATA 28 9 1.2e-003 3.8e+001 # TATGTATA TATACATA 29 13 9.4e-003 2.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 108 E= 6.3e-004 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.564815 0.000000 0.435185 0.000000 0.000000 0.000000 0.000000 1.000000 0.509259 0.000000 0.490741 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCTSTAGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCTSTAGA TCTASAGG 29 1 2.6e-008 8.2e-004 # CCTGTAGA TCTACAGG 19 1 1.9e-005 6.0e-001 # CCTCTAGA TCTAGAGG 10 0 9.7e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 8.2e-004 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 0.344828 0.655172 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 1.000000 0.000000 0.000000 0.000000 MOTIF CAATGGCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CAATGGCA TGCCATTG 37 4 4.5e-008 1.4e-003 # CAATGGCA TGCCATTG 37 4 4.5e-008 1.4e-003 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.4e-003 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 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 MOTIF CAGCAGW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CAGCAGW WCTGCTG 64 17 5.3e-008 1.7e-003 # CAGCAGA TCTGCTG 31 7 5.4e-005 1.7e+000 # CAGCAGT ACTGCTG 33 10 2.8e-004 8.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 1.7e-003 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 0.000000 1.000000 0.000000 0.484375 0.000000 0.000000 0.515625 MOTIF CTACWAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTACWAC GTWGTAG 72 23 1.7e-007 5.4e-003 # CTACAAC GTTGTAG 46 14 1.8e-005 5.7e-001 # CTACTAC GTAGTAG 26 9 2.9e-003 9.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 5.4e-003 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 0.638889 0.000000 0.000000 0.361111 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGAYGAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGAYGAC GTCRTCG 52 12 1.9e-007 5.8e-003 # CGACGAC GTCGTCG 23 4 1.5e-004 4.6e+000 # CGATGAC GTCATCG 29 8 3.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 5.8e-003 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 0.442308 0.000000 0.557692 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF KACAGTAA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST KACAGTAA TTACTGTM 37 5 1.9e-007 6.0e-003 # TACAGTAA TTACTGTA 26 5 9.1e-005 2.8e+000 # GACAGTAA TTACTGTC 11 0 4.8e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 6.0e-003 0.000000 0.000000 0.297297 0.702703 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACCAA TTGGT 398 278 2.2e-007 6.9e-003 # ACCAA TTGGT 398 278 2.2e-007 6.9e-003 letter-probability matrix: alength= 4 w= 5 nsites= 439 E= 6.9e-003 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAGARG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AAGARG CYTCTT 79 28 3.0e-007 9.1e-003 # AAGAAG CTTCTT 45 14 2.9e-005 8.8e-001 # AAGAGG CCTCTT 34 14 2.6e-003 8.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 79 E= 9.1e-003 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 0.569620 0.000000 0.430380 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCAAKTC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CCAAKTC GAMTTGG 75 26 4.1e-007 1.2e-002 # CCAATTC GAATTGG 43 14 6.9e-005 2.1e+000 # CCAAGTC GACTTGG 32 12 1.7e-003 5.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 1.2e-002 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 0.000000 0.000000 0.426667 0.573333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TGYTCAA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST TGYTCAA TTGARCA 125 60 5.6e-007 1.7e-002 # TGCTCAA TTGAGCA 55 21 5.2e-005 1.6e+000 # TGTTCAA TTGAACA 72 40 1.4e-003 4.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 129 E= 1.7e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.426357 0.000000 0.573643 0.000000 0.000000 0.000000 1.000000 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 TGTTGTTR DREME-22 # Word RC Word Pos Neg P-value E-value # BEST TGTTGTTR YAACAACA 55 15 6.7e-007 2.0e-002 # TGTTGTTG CAACAACA 34 10 1.8e-004 5.5e+000 # TGTTGTTA TAACAACA 22 5 7.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 56 E= 2.0e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.375000 0.000000 0.625000 0.000000 MOTIF AATGGTAC DREME-23 # Word RC Word Pos Neg P-value E-value # BEST AATGGTAC GTACCATT 26 2 1.4e-006 4.3e-002 # AATGGTAC GTACCATT 26 2 1.4e-006 4.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.3e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 219.91 seconds