# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/seqs-shuffled # positives: 551 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/seqs-centered (Sat Jan 18 07:55:26 PST 2020) # negatives: 551 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/seqs-shuffled (Sat Jan 18 07:55:26 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 08:08:45 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 0.292 C 0.209 G 0.209 T 0.289 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 136 12 1.5e-031 4.4e-027 # GGTTCGA TCGAACC 97 7 2.0e-023 6.0e-019 # GGTTCAA TTGAACC 41 5 1.2e-008 3.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 138 E= 4.4e-027 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 0.297101 0.000000 0.702899 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 84 12 7.1e-016 2.1e-011 # AGTGGTT AACCACT 57 6 2.4e-012 7.1e-008 # AGTGGTA TACCACT 38 6 2.9e-007 8.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 2.1e-011 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 0.404040 0.000000 0.000000 0.595960 MOTIF AAAAAWAW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWAW WTWTTTTT 125 41 5.2e-013 1.5e-008 # AAAAAAAT ATTTTTTT 68 13 4.4e-011 1.3e-006 # AAAAAAAA TTTTTTTT 48 17 4.8e-005 1.4e+000 # AAAAATAA TTATTTTT 34 15 4.0e-003 1.2e+002 # AAAAATAT ATATTTTT 23 8 4.8e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 138 E= 1.5e-008 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 0.630435 0.000000 0.000000 0.369565 1.000000 0.000000 0.000000 0.000000 0.485507 0.000000 0.000000 0.514493 MOTIF ACCRACT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 59 7 3.3e-012 9.7e-008 # ACCAACT AGTTGGT 40 4 4.7e-009 1.4e-004 # ACCGACT AGTCGGT 19 3 3.8e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 9.7e-008 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.683333 0.000000 0.316667 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 MOTIF CABACGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CABACGC GCGTVTG 51 6 1.1e-010 3.2e-006 # CATACGC GCGTATG 21 2 2.8e-005 8.3e-001 # CACACGC GCGTGTG 18 2 1.8e-004 5.3e+000 # CAGACGC GCGTCTG 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 3.2e-006 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.352941 0.235294 0.411765 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 MOTIF AAGGCGM DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGGCGM KCGCCTT 44 4 3.6e-010 1.1e-005 # AAGGCGC GCGCCTT 26 1 1.6e-007 4.6e-003 # AAGGCGA TCGCCTT 19 3 3.8e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 1.1e-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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.422222 0.577778 0.000000 0.000000 MOTIF CGSCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 79 22 1.0e-009 2.9e-005 # CGCCCA TGGGCG 47 14 8.1e-006 2.4e-001 # CGGCCA TGGCCG 32 8 7.0e-005 2.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 80 E= 2.9e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 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 GGATCRAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GGATCRAA TTYGATCC 37 3 5.7e-009 1.7e-004 # GGATCGAA TTCGATCC 26 1 1.6e-007 4.6e-003 # GGATCAAA TTTGATCC 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.7e-004 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 1.000000 0.000000 0.000000 0.315789 0.000000 0.684211 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCABAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 36 3 1.1e-008 3.2e-004 # ACCCATAC GTATGGGT 14 0 5.6e-005 1.6e+000 # ACCCACAC GTGTGGGT 16 3 2.1e-003 5.9e+001 # ACCCAGAC GTCTGGGT 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 3.2e-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 0.500000 0.159091 0.340909 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GYGCCAGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GYGCCAGA TCTGGCRC 22 0 1.9e-007 5.5e-003 # GTGCCAGA TCTGGCAC 12 0 2.3e-004 6.6e+000 # GCGCCAGA TCTGGCGC 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.000000 0.545455 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAGAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAAAAGAA TTCTTTTT 34 4 2.0e-007 5.8e-003 # AAAAAGAA TTCTTTTT 34 4 2.0e-007 5.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 5.8e-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 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 ATGGCAWC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 31 3 2.7e-007 7.7e-003 # ATGGCAAC GTTGCCAT 18 1 3.4e-005 9.7e-001 # ATGGCATC GATGCCAT 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 7.7e-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 0.580645 0.000000 0.000000 0.419355 0.000000 1.000000 0.000000 0.000000 MOTIF TGTTGWA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TGTTGWA TWCAACA 41 8 5.9e-007 1.7e-002 # TGTTGTA TACAACA 18 1 3.4e-005 9.7e-001 # TGTTGAA TTCAACA 24 7 1.5e-003 4.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.7e-002 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 1.000000 0.000000 0.571429 0.000000 0.000000 0.428571 1.000000 0.000000 0.000000 0.000000 MOTIF CCAACWGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCAACWGA TCWGTTGG 20 0 8.0e-007 2.3e-002 # CCAACTGA TCAGTTGG 12 0 2.3e-004 6.6e+000 # CCAACAGA TCTGTTGG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.3e-002 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 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTGGAG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGAG CTCCAYGG 20 0 8.0e-007 2.3e-002 # CCGTGGAG CTCCACGG 11 0 4.6e-004 1.3e+001 # CCATGGAG CTCCATGG 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.450000 0.000000 0.550000 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 MOTIF GGTCAGAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GGTCAGAA TTCTGACC 19 0 1.6e-006 4.6e-002 # GGTCAGAA TTCTGACC 19 0 1.6e-006 4.6e-002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.6e-002 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 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 MOTIF TCKCAAGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST TCKCAAGA TCTTGMGA 19 0 1.6e-006 4.6e-002 # TCTCAAGA TCTTGAGA 10 0 9.4e-004 2.7e+001 # TCGCAAGA TCTTGCGA 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.6e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.473684 0.526316 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 62.94 seconds