# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/seqs-shuffled # positives: 637 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/seqs-centered (Sun Jan 19 06:46:14 PST 2020) # negatives: 637 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/seqs-shuffled (Sun Jan 19 06:46:14 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 07:01:43 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 0.204 G 0.201 T 0.295 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 130 12 3.8e-029 1.2e-024 # GGTTCGA TCGAACC 94 7 3.0e-022 9.3e-018 # GGTTCAA TTGAACC 38 6 3.1e-007 9.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 132 E= 1.2e-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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.287879 0.000000 0.712121 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AYCCRTAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 68 2 3.5e-019 1.1e-014 # ACCCATAC GTATGGGT 33 1 1.4e-009 4.2e-005 # ATCCGTAC GTACGGAT 27 0 5.6e-009 1.7e-004 # ATCCATAC GTATGGAT 10 1 5.7e-003 1.8e+002 # ACCCGTAC GTACGGGT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 1.1e-014 1.000000 0.000000 0.000000 0.000000 0.000000 0.524390 0.000000 0.475610 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.560976 0.000000 0.439024 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 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 63 2 1.3e-017 3.9e-013 # CTCGGCCA TGGCCGAG 32 1 2.7e-009 8.4e-005 # CTTGGCCA TGGCCAAG 19 0 1.7e-006 5.1e-002 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 63 E= 3.9e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.507937 0.190476 0.301587 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-4 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 60 4 1.0e-014 3.1e-010 # TTAAGGCG CGCCTTAA 37 2 8.8e-010 2.7e-005 # CTAAGGCG CGCCTTAG 13 1 8.7e-004 2.7e+001 # GTAAGGCG CGCCTTAC 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 3.1e-010 0.000000 0.216667 0.166667 0.616667 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 ACTARACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACTARACC GGTYTAGT 33 0 7.6e-011 2.3e-006 # ACTAGACC GGTCTAGT 19 0 1.7e-006 5.1e-002 # ACTAAACC GGTTTAGT 14 0 5.7e-005 1.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.3e-006 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 0.424242 0.000000 0.575758 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 CGCKCTAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGCKCTAC GTAGMGCG 34 1 6.8e-010 2.1e-005 # CGCGCTAC GTAGCGCG 24 1 6.3e-007 1.9e-002 # CGCTCTAC GTAGAGCG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.1e-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 0.000000 0.705882 0.294118 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 MOTIF AAGAMAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAGAMAAA TTTKTCTT 62 13 1.6e-009 4.7e-005 # AAGAAAAA TTTTTCTT 50 12 3.4e-007 1.0e-002 # AAGACAAA TTTGTCTT 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 4.7e-005 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 0.781250 0.218750 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 GTGATAGY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 31 1 5.4e-009 1.6e-004 # GTGATAGC GCTATCAC 18 0 3.4e-006 1.0e-001 # GTGATAGT ACTATCAC 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 1.6e-004 0.000000 0.000000 1.000000 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.562500 0.000000 0.437500 MOTIF GAASTCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GAASTCA TGASTTC 36 3 1.2e-008 3.6e-004 # GAAGTCA TGACTTC 20 2 5.4e-005 1.6e+000 # GAACTCA TGAGTTC 16 1 1.3e-004 3.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.6e-004 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 0.444444 0.555556 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 GTWGCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GTWGCCA TGGCWAC 50 9 1.3e-008 4.0e-004 # GTTGCCA TGGCAAC 33 5 1.6e-006 4.7e-002 # GTAGCCA TGGCTAC 17 4 3.4e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 4.0e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 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 CCGTGSA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 37 4 3.3e-008 1.0e-003 # CCGTGGA TCCACGG 23 2 8.2e-006 2.5e-001 # CCGTGCA TGCACGG 14 2 2.0e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.0e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.378378 0.621622 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AYCAGAAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AYCAGAAG CTTCTGRT 24 0 4.8e-008 1.4e-003 # ATCAGAAG CTTCTGAT 15 0 2.8e-005 8.5e-001 # ACCAGAAG CTTCTGGT 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.625000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 MOTIF ACTGMGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACTGMGC GCKCAGT 38 5 8.1e-008 2.4e-003 # ACTGAGC GCTCAGT 23 1 1.2e-006 3.7e-002 # ACTGCGC GCGCAGT 15 4 9.2e-003 2.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 2.4e-003 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 1.000000 0.000000 0.605263 0.394737 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF SCGCTTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST SCGCTTA TAAGCGS 28 2 3.3e-007 1.0e-002 # GCGCTTA TAAGCGC 17 1 6.6e-005 2.0e+000 # CCGCTTA TAAGCGG 11 1 3.1e-003 9.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 1.0e-002 0.000000 0.392857 0.607143 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GARTCATA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GARTCATA TATGAYTC 21 0 4.0e-007 1.2e-002 # GAGTCATA TATGACTC 12 0 2.3e-004 6.9e+000 # GAATCATA TATGATTC 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACACTATA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 24 1 6.3e-007 1.9e-002 # ACACTATA TATAGTGT 24 1 6.3e-007 1.9e-002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.9e-002 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 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 ACGCGRG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACGCGRG CYCGCGT 24 1 6.3e-007 1.9e-002 # ACGCGAG CTCGCGT 14 1 4.6e-004 1.4e+001 # ACGCGGG CCCGCGT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 1.9e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.583333 0.000000 0.416667 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAAGCGTG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGTG CACGCTTT 19 0 1.7e-006 5.0e-002 # AAAGCGTG CACGCTTT 19 0 1.7e-006 5.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 5.0e-002 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 0.000000 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 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 76.59 seconds