# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG2/seqs-shuffled # positives: 908 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG2/seqs-centered (Sun Jan 19 07:32:54 PST 2020) # negatives: 908 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG2/seqs-shuffled (Sun Jan 19 07:32:54 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 07:47:46 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 0.295 C 0.209 G 0.204 T 0.292 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 79 6 2.7e-018 9.6e-014 # GGTTCGA TCGAACC 60 4 1.5e-014 5.5e-010 # GGATCGA TCGATCC 20 1 9.5e-006 3.4e-001 # GGCTCGA TCGAGCC 18 1 3.5e-005 1.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 81 E= 9.6e-014 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.222222 0.135802 0.000000 0.641975 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-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 68 3 7.7e-018 2.7e-013 # CTCGGCCA TGGCCGAG 30 0 7.3e-010 2.6e-005 # CTTGGCCA TGGCCAAG 22 2 1.6e-005 5.8e-001 # CTGGGCCA TGGCCCAG 16 1 1.3e-004 4.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 2.7e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.441176 0.235294 0.323529 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 GCKCTACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 44 1 7.8e-013 2.8e-008 # GCGCTACC GGTAGCGC 31 1 6.0e-009 2.1e-004 # GCTCTACC GGTAGAGC 13 0 1.2e-004 4.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.8e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.704545 0.295455 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 BTAAGGCG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 55 5 2.6e-012 9.2e-008 # TTAAGGCG CGCCTTAA 32 3 1.7e-007 5.9e-003 # GTAAGGCG CGCCTTAC 11 0 4.7e-004 1.7e+001 # CTAAGGCG CGCCTTAG 12 2 6.3e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 9.2e-008 0.000000 0.218182 0.200000 0.581818 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 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 MOTIF CTARACCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 38 2 5.2e-010 1.9e-005 # CTAGACCA TGGTCTAG 25 1 3.4e-007 1.2e-002 # CTAAACCA TGGTTTAG 13 1 8.8e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.9e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.342105 0.000000 0.657895 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 MOTIF AYCCGTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AYCCGTA TACGGRT 41 3 5.4e-010 1.9e-005 # ATCCGTA TACGGAT 27 2 6.9e-007 2.4e-002 # ACCCGTA TACGGGT 14 1 4.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 1.9e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.325581 0.000000 0.674419 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 1.000000 0.000000 0.000000 0.000000 MOTIF CGTTGCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCCA TGGCAACG 28 0 3.0e-009 1.1e-004 # CGTTGCCA TGGCAACG 28 0 3.0e-009 1.1e-004 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.1e-004 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 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 1.000000 0.000000 0.000000 0.000000 MOTIF TAKCTCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 49 8 8.5e-009 3.0e-004 # TATCTCA TGAGATA 32 7 3.0e-005 1.0e+000 # TAGCTCA TGAGCTA 17 1 6.8e-005 2.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 3.0e-004 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.314815 0.685185 0.000000 1.000000 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 ACGGTR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACGGTR YACCGT 116 48 1.4e-008 4.9e-004 # ACGGTA TACCGT 63 23 5.9e-006 2.1e-001 # ACGGTG CACCGT 58 26 2.3e-004 8.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 122 E= 4.9e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.516393 0.000000 0.483607 0.000000 MOTIF ACCCAWAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACCCAWAC GTWTGGGT 36 4 7.0e-008 2.5e-003 # ACCCATAC GTATGGGT 26 3 6.6e-006 2.3e-001 # ACCCAAAC GTTTGGGT 12 1 1.7e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 2.5e-003 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 0.315789 0.000000 0.000000 0.684211 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGAAR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGAAR YTTCT 457 347 1.3e-007 4.4e-003 # AGAAA TTTCT 319 238 2.3e-005 8.0e-001 # AGAAG CTTCT 200 153 3.2e-003 1.1e+002 letter-probability matrix: alength= 4 w= 5 nsites= 633 E= 4.4e-003 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 0.638231 0.000000 0.361769 0.000000 MOTIF ACCAGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACCAGC GCTGGT 47 11 7.1e-007 2.4e-002 # ACCAGC GCTGGT 47 11 7.1e-007 2.4e-002 letter-probability matrix: alength= 4 w= 6 nsites= 53 E= 2.4e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 75.96 seconds