# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--AFT1/seqs-shuffled # positives: 640 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--AFT1/seqs-centered (Sun Jan 19 05:26:36 PST 2020) # negatives: 640 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--AFT1/seqs-shuffled (Sun Jan 19 05:26:36 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:42:05 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 0.299 C 0.201 G 0.202 T 0.298 MOTIF GRNTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRNTCGAA TTCGANYC 151 9 1.4e-038 4.3e-034 # GAATCGAA TTCGATTC 33 0 7.6e-011 2.3e-006 # GGATCGAA TTCGATCC 33 2 1.3e-008 3.9e-004 # GAGTCGAA TTCGACTC 22 0 2.0e-007 6.1e-003 # GGGTCGAA TTCGACCC 15 0 2.8e-005 8.6e-001 # GGCTCGAA TTCGAGCC 14 1 4.6e-004 1.4e+001 # GATTCGAA TTCGAATC 12 1 1.6e-003 5.0e+001 # GGTTCGAA TTCGAACC 16 3 2.1e-003 6.3e+001 # GACTCGAA TTCGAGTC 12 2 6.2e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 152 E= 4.3e-034 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.440789 0.171053 0.243421 0.144737 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 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 75 3 3.1e-020 9.4e-016 # CCGTACAT ATGTACGG 28 0 2.8e-009 8.3e-005 # CCATACAT ATGTATGG 31 2 4.7e-008 1.4e-003 # CCGTACAC GTGTACGG 14 1 4.6e-004 1.4e+001 # CCATACAC GTGTATGG 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 89 E= 9.4e-016 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.516854 0.000000 0.483146 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 0.000000 0.280899 0.000000 0.719101 MOTIF ACCACTM DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 82 8 7.1e-018 2.1e-013 # ACCACTA TAGTGGT 50 3 1.1e-012 3.4e-008 # ACCACTC GAGTGGT 33 5 1.6e-006 4.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 83 E= 2.1e-013 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 0.602410 0.397590 0.000000 0.000000 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 44 1 6.3e-013 1.9e-008 # CAACTTGG CCAAGTTG 32 0 1.6e-010 4.7e-006 # CAACTGGG CCCAGTTG 12 1 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.9e-008 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.272727 0.727273 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 1 1.0e-011 3.1e-007 # GCGCTACC GGTAGCGC 29 0 1.3e-009 4.0e-005 # GCTCTACC GGTAGAGC 11 1 3.1e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.1e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.725000 0.275000 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 SAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 315 202 7.8e-011 2.3e-006 # CAAGA TCTTG 180 109 1.3e-006 3.9e-002 # GAAGA TCTTC 180 118 2.6e-005 7.8e-001 letter-probability matrix: alength= 4 w= 5 nsites= 437 E= 2.3e-006 0.000000 0.514874 0.485126 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 CGCCTTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 56 9 4.2e-010 1.2e-005 # CGCCTTA TAAGGCG 56 9 4.2e-010 1.2e-005 letter-probability matrix: alength= 4 w= 7 nsites= 56 E= 1.2e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGAGASC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GGAGASC GSTCTCC 38 2 4.5e-010 1.3e-005 # GGAGACC GGTCTCC 26 2 1.2e-006 3.5e-002 # GGAGAGC GCTCTCC 12 0 2.3e-004 6.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.3e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.684211 0.315789 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGTTGCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCCA TGGCAACG 30 0 6.6e-010 1.9e-005 # CGTTGCCA TGGCAACG 30 0 6.6e-010 1.9e-005 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.9e-005 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 CTATCACR DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 34 1 6.9e-010 2.0e-005 # CTATCACA TGTGATAG 17 0 6.9e-006 2.0e-001 # CTATCACG CGTGATAG 17 1 6.6e-005 1.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.0e-005 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 MOTIF CRCCCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 111 42 1.4e-009 3.9e-005 # CACCCA TGGGTG 69 29 1.7e-005 4.7e-001 # CGCCCA TGGGCG 42 14 8.5e-005 2.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 126 E= 3.9e-005 0.000000 1.000000 0.000000 0.000000 0.650794 0.000000 0.349206 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 RGTTCAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST RGTTCAA TTGAACY 55 12 2.4e-008 6.8e-004 # GGTTCAA TTGAACC 33 4 3.9e-007 1.1e-002 # AGTTCAA TTGAACT 22 8 7.5e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 6.8e-004 0.400000 0.000000 0.600000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF MACTATA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST MACTATA TATAGTK 44 8 1.2e-007 3.4e-003 # CACTATA TATAGTG 27 4 1.4e-005 3.9e-001 # AACTATA TATAGTT 17 4 3.4e-003 9.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 3.4e-003 0.386364 0.613636 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 CTGAGCTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 22 0 2.0e-007 5.5e-003 # CTGAGCTA TAGCTCAG 22 0 2.0e-007 5.5e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.5e-003 0.000000 1.000000 0.000000 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 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 MOTIF TGGCGYA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 44 9 3.7e-007 1.0e-002 # TGGCGCA TGCGCCA 25 3 1.1e-005 3.2e-001 # TGGCGTA TACGCCA 19 6 6.9e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 1.0e-002 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 0.568182 0.000000 0.431818 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 30 3 5.3e-007 1.5e-002 # AGTCATAC GTATGACT 17 1 6.6e-005 1.8e+000 # AGTCAGAC GTCTGACT 13 2 3.5e-003 9.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.5e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.433333 0.566667 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGGGSA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 23 1 1.2e-006 3.4e-002 # CGCGGGCA TGCCCGCG 13 0 1.1e-004 3.2e+000 # CGCGGGGA TCCCCGCG 10 1 5.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.4e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.565217 0.434783 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARGAAATA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ARGAAATA TATTTCYT 19 0 1.7e-006 4.6e-002 # AGGAAATA TATTTCCT 11 0 4.7e-004 1.3e+001 # AAGAAATA TATTTCTT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.6e-002 1.000000 0.000000 0.000000 0.000000 0.421053 0.000000 0.578947 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 74.39 seconds