# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/seqs-shuffled # positives: 408 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/seqs-centered (Sat Jan 18 03:04:34 PST 2020) # negatives: 408 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/seqs-shuffled (Sat Jan 18 03:04:34 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:11:12 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 0.296 C 0.205 G 0.206 T 0.293 MOTIF AGTGGTW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 91 7 3.6e-022 9.0e-018 # AGTGGTT AACCACT 70 5 2.9e-017 7.3e-013 # AGTGGTA TACCACT 35 2 2.6e-009 6.4e-005 letter-probability matrix: alength= 4 w= 7 nsites= 109 E= 9.0e-018 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.321101 0.000000 0.000000 0.678899 MOTIF CCRTACA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 67 5 2.5e-016 6.2e-012 # CCGTACA TGTACGG 37 2 6.6e-010 1.6e-005 # CCATACA TGTATGG 35 3 1.8e-008 4.3e-004 letter-probability matrix: alength= 4 w= 7 nsites= 80 E= 6.2e-012 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.512500 0.000000 0.487500 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 MOTIF AASGCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AASGCG CGCSTT 95 19 2.0e-015 5.0e-011 # AAGGCG CGCCTT 66 10 1.8e-012 4.4e-008 # AACGCG CGCGTT 29 9 6.4e-004 1.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 96 E= 5.0e-011 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.302083 0.697917 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 SGGTTCGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 43 0 3.5e-014 8.5e-010 # GGGTTCGA TCGAACCC 26 0 9.9e-009 2.4e-004 # CGGTTCGA TCGAACCG 17 0 6.4e-006 1.6e-001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 8.5e-010 0.000000 0.395349 0.604651 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 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 CAACTKGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 48 3 2.7e-012 6.5e-008 # CAACTTGG CCAAGTTG 36 2 1.3e-009 3.1e-005 # CAACTGGG CCCAGTTG 12 1 1.6e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 6.5e-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 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TGGCGYA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 42 2 2.0e-011 4.9e-007 # TGGCGCA TGCGCCA 21 1 4.3e-006 1.0e-001 # TGGCGTA TACGCCA 21 1 4.3e-006 1.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 4.9e-007 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 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGCTWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCGCTWC GWAGCGCG 30 0 5.4e-010 1.3e-005 # CGCGCTAC GTAGCGCG 26 0 9.9e-009 2.4e-004 # CGCGCTTC GAAGCGCG 9 0 1.9e-003 4.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.3e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.766667 0.000000 0.000000 0.233333 0.000000 1.000000 0.000000 0.000000 MOTIF ACGKTGCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACGKTGCC GGCAMCGT 29 0 1.1e-009 2.6e-005 # ACGTTGCC GGCAACGT 16 0 1.3e-005 3.1e-001 # ACGGTGCC GGCACCGT 13 0 1.1e-004 2.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 2.6e-005 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 0.448276 0.551724 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 MOTIF SAAGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 206 128 1.9e-008 4.5e-004 # CAAGA TCTTG 127 71 3.2e-006 7.6e-002 # GAAGA TCTTC 107 72 2.0e-003 4.7e+001 letter-probability matrix: alength= 4 w= 5 nsites= 280 E= 4.5e-004 0.000000 0.571429 0.428571 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 AWAGCCG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AWAGCCG CGGCTWT 28 1 3.6e-008 8.1e-004 # ATAGCCG CGGCTAT 21 1 4.3e-006 9.8e-002 # AAAGCCG CGGCTTT 7 0 7.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 8.1e-004 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GWCTCCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GWCTCCA TGGAGWC 28 1 3.6e-008 8.1e-004 # GACTCCA TGGAGTC 16 0 1.3e-005 3.0e-001 # GTCTCCA TGGAGAC 12 1 1.6e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 8.1e-004 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.000000 0.428571 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCABA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACCCABA TVTGGGT 41 6 4.1e-008 9.1e-004 # ACCCATA TATGGGT 16 1 1.2e-004 2.7e+000 # ACCCAGA TCTGGGT 14 1 4.4e-004 1.0e+001 # ACCCACA TGTGGGT 15 4 8.9e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 9.1e-004 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 0.000000 0.333333 0.291667 0.375000 1.000000 0.000000 0.000000 0.000000 MOTIF GACTSTTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 24 0 4.2e-008 9.4e-004 # GACTCTTA TAAGAGTC 15 0 2.7e-005 6.0e-001 # GACTGTTA TAACAGTC 9 0 1.9e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 9.4e-004 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 0.625000 0.375000 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 ACACTAK DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACACTAK MTAGTGT 37 5 1.2e-007 2.6e-003 # ACACTAT ATAGTGT 27 4 1.2e-005 2.7e-001 # ACACTAG CTAGTGT 10 1 5.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 2.6e-003 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 0.263158 0.736842 MOTIF CTCTMCCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 26 1 1.4e-007 3.2e-003 # CTCTCCCA TGGGAGAG 14 0 5.4e-005 1.2e+000 # CTCTACCA TGGTAGAG 12 1 1.6e-003 3.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.2e-003 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 0.000000 1.000000 0.461538 0.538462 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 AAGCGWGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 21 0 3.7e-007 8.1e-003 # AAGCGTGA TCACGCTT 12 0 2.2e-004 5.0e+000 # AAGCGAGA TCTCGCTT 9 0 1.9e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 8.1e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 44.33 seconds