# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ARR1/seqs-shuffled # positives: 658 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ARR1/seqs-centered (Sat Jan 18 04:11:12 PST 2020) # negatives: 658 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ARR1/seqs-shuffled (Sat Jan 18 04:11:12 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 04:27:14 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 0.207 G 0.206 T 0.292 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 120 10 1.3e-027 4.4e-023 # GGTTCGA TCGAACC 99 7 1.0e-023 3.3e-019 # GGATCGA TCGATCC 28 3 1.8e-006 6.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 4.4e-023 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.208333 0.000000 0.000000 0.791667 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 90 13 1.1e-016 3.5e-012 # AGTGGTA TACCACT 42 2 3.0e-011 9.8e-007 # AGTGGTT AACCACT 62 11 1.6e-010 5.2e-006 letter-probability matrix: alength= 4 w= 7 nsites= 107 E= 3.5e-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 0.401869 0.000000 0.000000 0.598131 MOTIF AACTKGGC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 42 1 2.6e-012 8.4e-008 # AACTTGGC GCCAAGTT 32 1 2.8e-009 8.8e-005 # AACTGGGC GCCCAGTT 10 0 9.4e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 8.4e-008 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 0.238095 0.761905 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 AARAAAWA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 129 46 6.4e-012 2.1e-007 # AAGAAAAA TTTTTCTT 41 8 6.4e-007 2.1e-002 # AAAAAATA TATTTTTT 46 14 1.4e-005 4.5e-001 # AAAAAAAA TTTTTTTT 54 29 3.1e-003 9.9e+001 # AAGAAATA TATTTCTT 15 3 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 145 E= 2.1e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.655172 0.000000 0.344828 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 0.641379 0.000000 0.000000 0.358621 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 32 1 2.8e-009 8.8e-005 # GCGCTACC GGTAGCGC 22 1 2.4e-006 7.8e-002 # GCTCTACC GGTAGAGC 10 0 9.4e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.8e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.687500 0.312500 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 AAGGCG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGGCG CGCCTT 72 19 3.2e-009 1.0e-004 # AAGGCG CGCCTT 72 19 3.2e-009 1.0e-004 letter-probability matrix: alength= 4 w= 6 nsites= 72 E= 1.0e-004 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 CCABAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCABAC GTVTGG 138 61 1.7e-009 5.4e-005 # CCATAC GTATGG 54 22 1.0e-004 3.3e+000 # CCACAC GTGTGG 60 27 1.7e-004 5.3e+000 # CCAGAC GTCTGG 31 14 7.2e-003 2.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 157 E= 5.4e-005 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 0.452229 0.191083 0.356688 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCGTGSA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 46 8 3.9e-008 1.2e-003 # CCGTGGA TCCACGG 25 3 1.1e-005 3.6e-001 # CCGTGCA TGCACGG 22 5 6.8e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 1.2e-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 0.000000 0.468085 0.531915 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGAGACM DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGAGACM KGTCTCT 26 1 1.7e-007 5.2e-003 # AGAGACC GGTCTCT 15 0 2.8e-005 8.8e-001 # AGAGACA TGTCTCT 11 1 3.1e-003 9.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 5.2e-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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.407407 0.592593 0.000000 0.000000 MOTIF ATCKTGAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 26 1 1.7e-007 5.1e-003 # ATCGTGAG CTCACGAT 17 1 6.6e-005 2.1e+000 # ATCTTGAG CTCAAGAT 9 0 1.9e-003 5.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.1e-003 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 0.653846 0.346154 0.000000 0.000000 0.000000 1.000000 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 GACTSTTA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 25 1 3.2e-007 1.0e-002 # GACTCTTA TAAGAGTC 14 1 4.6e-004 1.4e+001 # GACTGTTA TAACAGTC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-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 0.000000 0.000000 1.000000 0.000000 0.560000 0.440000 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 CAAAWCCG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CAAAWCCG CGGWTTTG 21 0 4.1e-007 1.3e-002 # CAAAACCG CGGTTTTG 12 0 2.3e-004 7.2e+000 # CAAATCCG CGGATTTG 9 0 1.9e-003 5.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGCAWC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 35 5 4.9e-007 1.5e-002 # ATGGCAAC GTTGCCAT 21 4 4.1e-004 1.3e+001 # ATGGCATC GATGCCAT 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.5e-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 0.600000 0.000000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCAKAAG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATCAKAAG CTTMTGAT 24 1 6.4e-007 2.0e-002 # ATCATAAG CTTATGAT 14 0 5.7e-005 1.8e+000 # ATCAGAAG CTTCTGAT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.416667 0.583333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCGGGSA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 20 0 8.2e-007 2.6e-002 # CGCGGGCA TGCCCGCG 10 0 9.4e-004 2.9e+001 # CGCGGGGA TCCCCGCG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 65.44 seconds