# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MGA2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MGA2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MGA2/seqs-shuffled # positives: 609 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MGA2/seqs-centered (Sat Jan 18 17:40:58 PST 2020) # negatives: 609 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MGA2/seqs-shuffled (Sat Jan 18 17:40:59 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:56:52 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 0.298 C 0.205 G 0.201 T 0.295 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 104 10 6.8e-023 2.1e-018 # GGTTCGA TCGAACC 88 8 1.1e-019 3.4e-015 # GGATCGA TCGATCC 24 2 4.3e-006 1.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 2.1e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.192308 0.000000 0.000000 0.807692 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 88 12 7.4e-017 2.3e-012 # AGTGGTT AACCACT 62 4 2.5e-015 7.6e-011 # AGTGGTA TACCACT 38 8 3.2e-006 9.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 2.3e-012 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 0.375000 0.000000 0.000000 0.625000 MOTIF CCCATRC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCCATRC GYATGGG 57 6 2.7e-012 8.3e-008 # CCCATAC GTATGGG 36 3 1.2e-008 3.5e-004 # CCCATGC GCATGGG 23 3 3.7e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 8.3e-008 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 0.000000 0.000000 1.000000 0.616667 0.000000 0.383333 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 59 7 3.7e-012 1.1e-007 # CGCCTTA TAAGGCG 42 6 2.9e-008 8.9e-004 # CGCGTTA TAACGCG 17 1 6.6e-005 2.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 1.1e-007 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 0.711864 0.288136 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 CCGTRCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCGTRCA TGYACGG 50 4 7.8e-012 2.4e-007 # CCGTACA TGTACGG 28 1 4.2e-008 1.3e-003 # CCGTGCA TGCACGG 24 3 2.1e-005 6.2e-001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 2.4e-007 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 0.555556 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 49 4 1.5e-011 4.5e-007 # CTTGGCC GGCCAAG 35 2 3.3e-009 9.8e-005 # CTCGGCC GGCCGAG 14 2 2.0e-003 5.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 4.5e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.714286 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 MOTIF AARAAAW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 229 128 1.3e-010 3.8e-006 # AAGAAAA TTTTCTT 72 30 8.8e-006 2.6e-001 # AAAAAAA TTTTTTT 113 61 1.3e-005 4.0e-001 # AAAAAAT ATTTTTT 106 60 7.9e-005 2.4e+000 # AAGAAAT ATTTCTT 36 17 5.4e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 278 E= 3.8e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.633094 0.000000 0.366906 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 0.568345 0.000000 0.000000 0.431655 MOTIF GCKCTACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 30 0 6.5e-010 1.9e-005 # GCGCTACC GGTAGCGC 20 0 8.1e-007 2.4e-002 # GCTCTACC GGTAGAGC 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.9e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 CCWTAACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 29 1 2.1e-008 6.2e-004 # CCATAACC GGTTATGG 16 0 1.4e-005 4.1e-001 # CCTTAACC GGTTAAGG 13 1 8.7e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.2e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.551724 0.000000 0.000000 0.448276 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CASACGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CASACGC GCGTSTG 34 3 4.2e-008 1.2e-003 # CACACGC GCGTGTG 17 1 6.6e-005 1.9e+000 # CAGACGC GCGTCTG 17 2 3.3e-004 9.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.2e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 1.000000 0.000000 0.000000 MOTIF CCGTGMTA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 24 0 4.7e-008 1.4e-003 # CCGTGATA TATCACGG 12 0 2.3e-004 6.8e+000 # CCGTGCTA TAGCACGG 12 0 2.3e-004 6.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-003 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 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GACTSTTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 23 0 9.6e-008 2.8e-003 # GACTCTTA TAAGAGTC 13 0 1.1e-004 3.4e+000 # GACTGTTA TAACAGTC 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-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 0.565217 0.434783 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 AKGAAGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AKGAAGA TCTTCMT 37 6 5.5e-007 1.6e-002 # AGGAAGA TCTTCCT 24 4 7.7e-005 2.3e+000 # ATGAAGA TCTTCAT 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.648649 0.351351 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCAGWA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TCAGWA TWCTGA 101 46 8.1e-007 2.4e-002 # TCAGAA TTCTGA 62 30 3.5e-004 1.0e+001 # TCAGTA TACTGA 40 17 1.3e-003 3.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 105 E= 2.4e-002 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 0.619048 0.000000 0.000000 0.380952 1.000000 0.000000 0.000000 0.000000 MOTIF GCACYCAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCACYCAC GTGRGTGC 20 0 8.1e-007 2.4e-002 # GCACTCAC GTGAGTGC 11 0 4.7e-004 1.4e+001 # GCACCCAC GTGGGTGC 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.450000 0.000000 0.550000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 62.10 seconds