# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/seqs-shuffled # positives: 584 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/seqs-centered (Sat Jan 18 01:58:16 PST 2020) # negatives: 584 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/seqs-shuffled (Sat Jan 18 01:58:16 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 02:12:28 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 0.203 G 0.203 T 0.298 MOTIF GRNTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRNTCGAA TTCGANYC 127 13 1.1e-027 3.1e-023 # GAATCGAA TTCGATTC 30 2 8.8e-008 2.6e-003 # GGATCGAA TTCGATCC 23 1 1.2e-006 3.6e-002 # GAGTCGAA TTCGACTC 21 2 2.8e-005 8.3e-001 # GGTTCGAA TTCGAACC 12 1 1.6e-003 4.8e+001 # GGGTCGAA TTCGACCC 13 2 3.5e-003 1.0e+002 # GACTCGAA TTCGAGTC 10 1 5.7e-003 1.7e+002 # GATTCGAA TTCGAATC 12 2 6.2e-003 1.8e+002 # GGCTCGAA TTCGAGCC 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 127 E= 3.1e-023 0.000000 0.000000 1.000000 0.000000 0.551181 0.000000 0.448819 0.000000 0.417323 0.173228 0.267717 0.141732 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 84 2 2.2e-024 6.5e-020 # TGTATGGG CCCATACA 37 1 8.1e-011 2.4e-006 # TGTACGGA TCCGTACA 32 0 1.5e-010 4.4e-006 # TGTACGGG CCCGTACA 12 0 2.3e-004 6.7e+000 # TGTATGGA TCCATACA 14 1 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 97 E= 6.5e-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 0.463918 0.000000 0.536082 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.494845 0.000000 0.505155 0.000000 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 89 8 4.8e-020 1.4e-015 # AGTGGTT AACCACT 62 6 1.0e-013 2.9e-009 # AGTGGTA TACCACT 39 2 2.2e-010 6.2e-006 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 1.4e-015 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 0.380952 0.000000 0.000000 0.619048 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 60 4 9.1e-015 2.6e-010 # CGCCTTA TAAGGCG 45 3 3.0e-011 8.7e-007 # CGCGTTA TAACGCG 15 1 2.4e-004 6.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 2.6e-010 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 0.750000 0.250000 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 CTTGGCY DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTTGGCY RGCCAAG 53 3 1.3e-013 3.8e-009 # CTTGGCC GGCCAAG 41 1 4.9e-012 1.4e-007 # CTTGGCT AGCCAAG 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 3.8e-009 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.773585 0.000000 0.226415 MOTIF AGCGCGY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGCGCGY RCGCGCT 33 0 7.3e-011 2.1e-006 # AGCGCGC GCGCGCT 20 0 8.1e-007 2.3e-002 # AGCGCGT ACGCGCT 14 0 5.6e-005 1.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.1e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.588235 0.000000 0.411765 MOTIF TGGCGYA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 43 3 1.2e-010 3.3e-006 # TGGCGCA TGCGCCA 23 2 8.1e-006 2.3e-001 # TGGCGTA TACGCCA 20 1 9.0e-006 2.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 3.3e-006 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 GTGGAGAY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTGGAGAY RTCTCCAC 29 0 1.3e-009 3.7e-005 # GTGGAGAC GTCTCCAC 17 0 6.8e-006 1.9e-001 # GTGGAGAT ATCTCCAC 12 0 2.3e-004 6.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.7e-005 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 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 0.586207 0.000000 0.413793 MOTIF GATTWGAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 34 2 6.3e-009 1.8e-004 # GATTAGAA TTCTAATC 19 0 1.6e-006 4.6e-002 # GATTTGAA TTCAAATC 15 2 1.1e-003 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.8e-004 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 0.558824 0.000000 0.000000 0.441176 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 ACACSCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACACSCA TGSGTGT 50 9 1.2e-008 3.5e-004 # ACACCCA TGGGTGT 38 7 1.0e-006 2.9e-002 # ACACGCA TGCGTGT 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 3.5e-004 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 0.769231 0.230769 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAAMT DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAMT AKTTTTTT 91 34 3.7e-008 1.0e-003 # AAAAAAAT ATTTTTTT 70 26 1.6e-006 4.6e-002 # AAAAAACT AGTTTTTT 22 8 7.4e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 98 E= 1.0e-003 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.755102 0.244898 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ATGGCAWC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 33 3 7.7e-008 2.2e-003 # ATGGCAAC GTTGCCAT 22 2 1.5e-005 4.2e-001 # ATGGCATC GATGCCAT 11 1 3.1e-003 8.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.2e-003 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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF CCAACWG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCAACWG CWGTTGG 48 10 1.2e-007 3.3e-003 # CCAACTG CAGTTGG 29 7 1.3e-004 3.5e+000 # CCAACAG CTGTTGG 19 4 1.2e-003 3.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 3.3e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.395833 0.000000 0.000000 0.604167 0.000000 0.000000 1.000000 0.000000 MOTIF ACACTATA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 22 0 1.9e-007 5.4e-003 # ACACTATA TATAGTGT 22 0 1.9e-007 5.4e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.4e-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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GACTGTWA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GACTGTWA TWACAGTC 22 0 1.9e-007 5.4e-003 # GACTGTAA TTACAGTC 11 0 4.7e-004 1.3e+001 # GACTGTTA TAACAGTC 11 0 4.7e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.4e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGCGWGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 25 1 3.2e-007 8.8e-003 # AAGCGTGA TCACGCTT 14 0 5.6e-005 1.6e+000 # AAGCGAGA TCTCGCTT 11 1 3.1e-003 8.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.8e-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 0.440000 0.000000 0.000000 0.560000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCACR DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 4 6.9e-007 1.9e-002 # CTATCACG CGTGATAG 15 1 2.4e-004 6.7e+000 # CTATCACA TGTGATAG 17 3 1.2e-003 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 1.9e-002 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 0.531250 0.000000 0.468750 0.000000 MOTIF ATCTKG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATCTKG CMAGAT 94 41 7.5e-007 2.1e-002 # ATCTTG CAAGAT 64 27 3.5e-005 9.7e-001 # ATCTGG CCAGAT 32 14 4.9e-003 1.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 107 E= 2.1e-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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.308411 0.691589 0.000000 0.000000 1.000000 0.000000 MOTIF CCTTATKA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CCTTATKA TMATAAGG 20 0 8.1e-007 2.2e-002 # CCTTATGA TCATAAGG 13 0 1.1e-004 3.1e+000 # CCTTATTA TAATAAGG 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.2e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.650000 0.350000 1.000000 0.000000 0.000000 0.000000 MOTIF GACCATTR DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GACCATTR YAATGGTC 20 0 8.1e-007 2.2e-002 # GACCATTA TAATGGTC 12 0 2.3e-004 6.3e+000 # GACCATTG CAATGGTC 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.2e-002 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 1.000000 0.000000 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 0.600000 0.000000 0.400000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 76.57 seconds