# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/seqs-shuffled # positives: 484 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/seqs-centered (Fri Jan 17 23:46:17 PST 2020) # negatives: 484 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/seqs-shuffled (Fri Jan 17 23:46:17 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:55:41 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 0.289 C 0.212 G 0.211 T 0.288 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 124 9 1.0e-030 2.7e-026 # GGTTCGA TCGAACC 91 5 1.2e-023 3.3e-019 # GGTTCAA TTGAACC 35 4 1.0e-007 2.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 126 E= 2.7e-026 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 0.277778 0.000000 0.722222 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 62 1 9.2e-019 2.5e-014 # CTCGGCCA TGGCCGAG 31 1 4.8e-009 1.3e-004 # CTTGGCCA TGGCCAAG 20 0 7.8e-007 2.1e-002 # CTGGGCCA TGGCCCAG 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 2.5e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.177419 0.322581 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 ACCCADAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCCADAC GTHTGGGT 59 3 1.6e-015 4.2e-011 # ACCCATAC GTATGGGT 40 1 8.6e-012 2.3e-007 # ACCCAGAC GTCTGGGT 13 1 8.5e-004 2.3e+001 # ACCCAAAC GTTTGGGT 11 1 3.0e-003 8.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 4.2e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.164179 0.000000 0.194030 0.641791 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCCTTAMC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 46 0 4.6e-015 1.2e-010 # GCCTTAAC GTTAAGGC 35 0 1.5e-011 4.1e-007 # GCCTTACC GGTAAGGC 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 1.2e-010 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 0.760870 0.239130 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 45 1 2.4e-013 6.3e-009 # GCGCTACC GGTAGCGC 30 1 9.7e-009 2.5e-004 # GCTCTACC GGTAGAGC 15 0 2.7e-005 7.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 6.3e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 ATCCGTRC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATCCGTRC GYACGGAT 37 0 3.6e-012 9.4e-008 # ATCCGTAC GTACGGAT 29 0 1.2e-009 3.2e-005 # ATCCGTGC GCACGGAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 9.4e-008 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.720930 0.000000 0.279070 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 41 2 4.8e-011 1.3e-006 # ATGGCAAC GTTGCCAT 29 1 1.9e-008 5.1e-004 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.3e-006 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 0.707317 0.000000 0.000000 0.292683 0.000000 1.000000 0.000000 0.000000 MOTIF GGTCTM DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GGTCTM KAGACC 82 22 1.6e-010 4.2e-006 # GGTCTC GAGACC 43 11 4.0e-006 1.1e-001 # GGTCTA TAGACC 39 11 3.0e-005 7.7e-001 letter-probability matrix: alength= 4 w= 6 nsites= 85 E= 4.2e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.458824 0.541176 0.000000 0.000000 MOTIF ATAGTKTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 44 5 1.7e-009 4.4e-005 # ATAGTGTA TACACTAT 27 1 7.6e-008 2.0e-003 # ATAGTTTA TAAACTAT 17 4 3.3e-003 8.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 4.4e-005 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 0.613636 0.386364 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RGCSCAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RGCSCAA TTGSGCY 63 10 1.6e-011 4.3e-007 # GGCGCAA TTGCGCC 21 1 4.5e-006 1.2e-001 # GGCCCAA TTGGGCC 20 3 2.1e-004 5.5e+000 # AGCGCAA TTGCGCT 17 3 1.2e-003 3.0e+001 # AGCCCAA TTGGGCT 15 3 3.5e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 4.3e-007 0.445946 0.000000 0.554054 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.486486 0.513514 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 AARAAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AARAAA TTTYTT 218 131 3.8e-009 9.7e-005 # AAAAAA TTTTTT 158 90 3.6e-007 9.3e-003 # AAGAAA TTTCTT 102 69 3.4e-003 8.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 303 E= 9.7e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.676568 0.000000 0.323432 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 GTGATARC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTGATARC GYTATCAC 29 1 1.9e-008 4.9e-004 # GTGATAGC GCTATCAC 18 0 3.2e-006 8.2e-002 # GTGATAAC GTTATCAC 11 1 3.0e-003 7.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 4.9e-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 0.379310 0.000000 0.620690 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ARTCATAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ARTCATAC GTATGAYT 25 0 2.2e-008 5.5e-004 # AGTCATAC GTATGACT 14 0 5.5e-005 1.4e+000 # AATCATAC GTATGATT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 5.5e-004 1.000000 0.000000 0.000000 0.000000 0.440000 0.000000 0.560000 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 0.000000 1.000000 0.000000 0.000000 MOTIF GCCASAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCCASAC GTSTGGC 37 4 2.9e-008 7.3e-004 # GCCAGAC GTCTGGC 17 1 6.4e-005 1.6e+000 # GCCACAC GTGTGGC 20 3 2.1e-004 5.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 7.3e-004 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 0.540541 0.459459 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGGGS DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGS SCCCGCG 26 1 1.5e-007 3.8e-003 # CGCGGGC GCCCGCG 13 0 1.1e-004 2.8e+000 # CGCGGGG CCCCGCG 13 1 8.5e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.8e-003 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 0.500000 0.500000 0.000000 MOTIF ACTGAGCT DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 22 0 1.9e-007 4.7e-003 # ACTGAGCT AGCTCAGT 22 0 1.9e-007 4.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.7e-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 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 MOTIF ATCAKAAG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATCAKAAG CTTMTGAT 27 2 5.9e-007 1.5e-002 # ATCAGAAG CTTCTGAT 14 0 5.5e-005 1.4e+000 # ATCATAAG CTTATGAT 13 2 3.5e-003 8.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.5e-002 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 0.000000 0.518519 0.481481 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 GAGTTCRA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GAGTTCRA TYGAACTC 20 0 7.8e-007 2.0e-002 # GAGTTCAA TTGAACTC 11 0 4.6e-004 1.2e+001 # GAGTTCGA TCGAACTC 9 0 1.9e-003 4.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.0e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.550000 0.000000 0.450000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCTCCCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TCTCCCA TGGGAGA 20 0 7.8e-007 2.0e-002 # TCTCCCA TGGGAGA 20 0 7.8e-007 2.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 2.0e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 61.14 seconds