# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/seqs-shuffled # positives: 485 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/seqs-centered (Sat Jan 18 08:54:20 PST 2020) # negatives: 485 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/seqs-shuffled (Sat Jan 18 08:54:20 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 09:04:05 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 0.294 C 0.208 G 0.206 T 0.293 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 88 3 8.7e-025 2.4e-020 # TGTATGGG CCCATACA 38 1 3.6e-011 9.6e-007 # TGTACGGA TCCGTACA 35 1 3.0e-010 8.0e-006 # TGTACGGG CCCGTACA 13 0 1.1e-004 3.1e+000 # TGTATGGA TCCATACA 12 1 1.6e-003 4.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 102 E= 2.4e-020 0.000000 0.000000 0.000000 1.000000 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 0.490196 0.000000 0.509804 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.490196 0.000000 0.509804 0.000000 MOTIF BGGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BGGTTCGA TCGAACCV 73 1 2.3e-022 6.1e-018 # GGGTTCGA TCGAACCC 40 1 8.6e-012 2.3e-007 # CGGTTCGA TCGAACCG 26 0 1.1e-008 2.8e-004 # TGGTTCGA TCGAACCA 7 0 7.6e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 6.1e-018 0.000000 0.356164 0.547945 0.095890 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 65 0 2.7e-021 7.3e-017 # CTCGGCCA TGGCCGAG 34 0 3.2e-011 8.5e-007 # 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= 65 E= 7.3e-017 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.523077 0.169231 0.307692 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 CTWRACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTWRACC GGTYWAG 97 11 1.7e-020 4.5e-016 # CTTAACC GGTTAAG 36 6 8.8e-007 2.3e-002 # CTAGACC GGTCTAG 23 1 1.2e-006 3.1e-002 # CTTGACC GGTCAAG 19 0 1.6e-006 4.2e-002 # CTAAACC GGTTTAG 19 4 1.2e-003 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 97 E= 4.5e-016 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.432990 0.000000 0.000000 0.567010 0.567010 0.000000 0.432990 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 1 4.2e-012 1.1e-007 # GCGCTACC GGTAGCGC 25 0 2.2e-008 5.7e-004 # GCTCTACC GGTAGAGC 16 1 1.2e-004 3.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.1e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.609756 0.390244 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 CRCCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 98 30 4.2e-011 1.1e-006 # CACCCA TGGGTG 66 24 2.0e-006 5.3e-002 # CGCCCA TGGGCG 34 6 2.8e-006 7.3e-002 letter-probability matrix: alength= 4 w= 6 nsites= 117 E= 1.1e-006 0.000000 1.000000 0.000000 0.000000 0.692308 0.000000 0.307692 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 ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 2 9.6e-011 2.5e-006 # ATGGCAAC GTTGCCAT 28 2 3.1e-007 8.0e-003 # ATGGCATC GATGCCAT 12 0 2.3e-004 5.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.5e-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 0.700000 0.000000 0.000000 0.300000 0.000000 1.000000 0.000000 0.000000 MOTIF ATAGTKTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 43 3 9.9e-011 2.6e-006 # ATAGTGTA TACACTAT 25 0 2.2e-008 5.6e-004 # ATAGTTTA TAAACTAT 18 3 6.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.6e-006 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 0.581395 0.418605 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 32 1 2.4e-009 6.2e-005 # GGCTATCA TGATAGCC 18 0 3.2e-006 8.4e-002 # GGTTATCA TGATAACC 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.2e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.562500 0.000000 0.437500 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 MOTIF GTCTGRC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GTCTGRC GYCAGAC 32 1 2.4e-009 6.2e-005 # GTCTGAC GTCAGAC 16 0 1.3e-005 3.5e-001 # GTCTGGC GCCAGAC 16 1 1.2e-004 3.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 6.2e-005 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 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 27 0 5.1e-009 1.3e-004 # CACCGTGG CCACGGTG 14 0 5.5e-005 1.4e+000 # CACCGTGC GCACGGTG 13 0 1.1e-004 2.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.3e-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 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 0.481481 0.518519 0.000000 MOTIF AAGGCGCM DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAGGCGCM KGCGCCTT 29 1 1.9e-008 5.0e-004 # AAGGCGCC GGCGCCTT 20 1 8.8e-006 2.3e-001 # AAGGCGCA TGCGCCTT 9 0 1.9e-003 4.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.0e-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 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 1.000000 0.000000 0.000000 0.310345 0.689655 0.000000 0.000000 MOTIF TTTCTTB DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 109 47 3.5e-008 9.1e-004 # TTTCTTG CAAGAAA 36 10 5.5e-005 1.4e+000 # TTTCTTC GAAGAAA 34 12 6.3e-004 1.6e+001 # TTTCTTT AAAGAAA 48 25 3.5e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 9.1e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.278689 0.295082 0.426230 MOTIF GGATTTKA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GGATTTKA TMAAATCC 26 1 1.5e-007 3.9e-003 # GGATTTTA TAAAATCC 18 1 3.3e-005 8.4e-001 # GGATTTGA TCAAATCC 8 0 3.8e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.9e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.307692 0.692308 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 43 9 5.5e-007 1.4e-002 # TGGCGCA TGCGCCA 23 5 3.9e-004 9.8e+000 # TGGCGTA TACGCCA 20 4 6.8e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 1.4e-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 0.534884 0.000000 0.465116 1.000000 0.000000 0.000000 0.000000 MOTIF TAATCAKA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TAATCAKA TMTGATTA 24 1 5.9e-007 1.5e-002 # TAATCAGA TCTGATTA 12 0 2.3e-004 5.8e+000 # TAATCATA TATGATTA 12 1 1.6e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 1 1.2e-006 3.0e-002 # ACTGAGCT AGCTCAGT 23 1 1.2e-006 3.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.0e-002 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 CYTGCGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CYTGCGC GCGCARG 28 3 1.7e-006 4.3e-002 # CTTGCGC GCGCAAG 17 2 3.3e-004 8.3e+000 # CCTGCGC GCGCAGG 11 1 3.0e-003 7.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 4.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.366667 0.000000 0.633333 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 59.73 seconds