# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG1/seqs-shuffled # positives: 707 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG1/seqs-centered (Sat Jan 18 18:39:04 PST 2020) # negatives: 707 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG1/seqs-shuffled (Sat Jan 18 18:39:04 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:55:17 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 0.301 C 0.199 G 0.198 T 0.302 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 138 20 1.4e-025 4.7e-021 # GGTTCGA TCGAACC 96 7 1.1e-022 3.5e-018 # GGTTCAA TTGAACC 44 13 1.7e-005 5.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 140 E= 4.7e-021 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 0.314286 0.000000 0.685714 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 85 14 1.1e-014 3.5e-010 # AGTGGTT AACCACT 53 8 7.1e-010 2.4e-005 # AGTGGTA TACCACT 45 6 5.3e-009 1.7e-004 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 3.5e-010 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 0.450000 0.000000 0.000000 0.550000 MOTIF GTAAACAW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GTAAACAW WTGTTTAC 52 3 3.2e-013 1.1e-008 # GTAAACAA TTGTTTAC 42 3 2.5e-010 8.3e-006 # GTAAACAT ATGTTTAC 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 1.1e-008 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.811321 0.000000 0.000000 0.188679 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 35 0 1.9e-011 6.2e-007 # AACTTGGC GCCAAGTT 27 0 5.8e-009 1.9e-004 # AACTGGGC GCCCAGTT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 6.2e-007 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 0.228571 0.771429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAAAARWA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAAAARWA TWYTTTTT 163 73 7.2e-011 2.3e-006 # AAAAAGAA TTCTTTTT 60 20 2.4e-006 7.7e-002 # AAAAAATA TATTTTTT 56 22 4.8e-005 1.6e+000 # AAAAAAAA TTTTTTTT 71 39 9.8e-004 3.2e+001 # AAAAAGTA TACTTTTT 15 4 9.2e-003 3.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 192 E= 2.3e-006 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 0.614583 0.000000 0.385417 0.000000 0.661458 0.000000 0.000000 0.338542 1.000000 0.000000 0.000000 0.000000 MOTIF RCGCCTTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST RCGCCTTA TAAGGCGY 29 1 2.2e-008 7.2e-004 # GCGCCTTA TAAGGCGC 18 0 3.4e-006 1.1e-001 # ACGCCTTA TAAGGCGT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.2e-004 0.379310 0.000000 0.620690 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GRAGAAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GRAGAAAA TTTTCTYC 36 4 6.5e-008 2.1e-003 # GAAGAAAA TTTTCTTC 24 2 4.4e-006 1.4e-001 # GGAGAAAA TTTTCTCC 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 2.1e-003 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAATCAKA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TAATCAKA TMTGATTA 21 0 4.1e-007 1.3e-002 # TAATCATA TATGATTA 14 0 5.7e-005 1.9e+000 # TAATCAGA TCTGATTA 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-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 0.333333 0.666667 1.000000 0.000000 0.000000 0.000000 MOTIF TCCGKACA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TCCGKACA TGTMCGGA 21 0 4.1e-007 1.3e-002 # TCCGTACA TGTACGGA 14 0 5.7e-005 1.9e+000 # TCCGGACA TGTCCGGA 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 1.3e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.304348 0.695652 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 CTCTCSCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSCA TGSGAGAG 24 1 6.5e-007 2.1e-002 # CTCTCCCA TGGGAGAG 16 1 1.3e-004 4.1e+000 # CTCTCGCA TGCGAGAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CKTTGGGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 20 0 8.3e-007 2.7e-002 # CGTTGGGC GCCCAACG 13 0 1.2e-004 3.7e+000 # CTTTGGGC GCCCAAAG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.650000 0.350000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCAGWTC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCAGWTC GAWCTGG 29 3 1.0e-006 3.3e-002 # CCAGATC GATCTGG 16 1 1.3e-004 4.1e+000 # CCAGTTC GAACTGG 13 2 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.3e-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 0.000000 0.000000 1.000000 0.000000 0.551724 0.000000 0.000000 0.448276 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CSCGCTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CSCGCTA TAGCGSG 29 3 1.0e-006 3.3e-002 # CCCGCTA TAGCGGG 11 0 4.7e-004 1.5e+001 # CGCGCTA TAGCGCG 18 3 6.9e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.379310 0.620690 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAW WTGCCAT 55 16 1.1e-006 3.5e-002 # ATGGCAT ATGCCAT 31 8 1.2e-004 3.9e+000 # ATGGCAA TTGCCAT 24 8 3.2e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 3.5e-002 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 0.436364 0.000000 0.000000 0.563636 # Stopping reason: E-value threshold exceeded # Running time: 66.74 seconds