# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MAC1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MAC1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MAC1/seqs-shuffled # positives: 549 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MAC1/seqs-centered (Sun Jan 19 03:00:45 PST 2020) # negatives: 549 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MAC1/seqs-shuffled (Sun Jan 19 03:00:45 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 03:14:11 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 0.296 C 0.208 G 0.205 T 0.291 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 118 5 3.2e-032 9.7e-028 # GGTTCGA TCGAACC 97 4 2.3e-026 7.0e-022 # GGATCGA TCGATCC 30 1 1.0e-008 3.1e-004 letter-probability matrix: alength= 4 w= 7 nsites= 118 E= 9.7e-028 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.211864 0.000000 0.000000 0.788136 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 81 13 1.8e-014 5.6e-010 # AGTGGTT AACCACT 59 5 1.1e-013 3.4e-009 # AGTGGTA TACCACT 32 8 7.0e-005 2.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 5.6e-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 0.357895 0.000000 0.000000 0.642105 MOTIF AAWAAKA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAWAAKA TMTTWTT 166 75 1.7e-011 5.2e-007 # AAAAAGA TCTTTTT 67 24 1.5e-006 4.4e-002 # AAAAATA TATTTTT 74 37 1.4e-004 4.3e+000 # AATAATA TATTATT 27 10 3.3e-003 1.0e+002 # AATAAGA TCTTATT 25 10 7.5e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 201 E= 5.2e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.731343 0.000000 0.000000 0.268657 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.467662 0.532338 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 32 1 2.6e-009 7.6e-005 # CTTGGCCA TGGCCAAG 17 1 6.5e-005 1.9e+000 # CTGGGCCA TGGCCCAG 8 0 3.8e-003 1.1e+002 # CTCGGCCA TGGCCGAG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 7.6e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.218750 0.250000 0.531250 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 GCCWTAAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 28 0 2.6e-009 7.8e-005 # GCCTTAAC GTTAAGGC 16 0 1.4e-005 4.1e-001 # GCCATAAC GTTATGGC 12 0 2.3e-004 6.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 7.8e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.000000 0.000000 0.571429 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 MOTIF GATTDGAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GATTDGAA TTCHAATC 36 4 5.8e-008 1.7e-003 # GATTTGAA TTCAAATC 13 0 1.1e-004 3.4e+000 # GATTAGAA TTCTAATC 19 3 3.8e-004 1.1e+001 # GATTGGAA TTCCAATC 11 1 3.0e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.7e-003 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 0.000000 0.000000 1.000000 0.441860 0.000000 0.255814 0.302326 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 CKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CKCTACC GGTAGMG 35 4 1.1e-007 3.2e-003 # CGCTACC GGTAGCG 22 2 1.5e-005 4.5e-001 # CTCTACC GGTAGAG 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 3.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.628571 0.371429 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 CRCCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 80 30 2.8e-007 8.4e-003 # CACCCA TGGGTG 47 19 2.6e-004 7.7e+000 # CGCCCA TGGGCG 36 12 2.7e-004 8.1e+000 letter-probability matrix: alength= 4 w= 6 nsites= 98 E= 8.4e-003 0.000000 1.000000 0.000000 0.000000 0.612245 0.000000 0.387755 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 MOTIF TCAACAAW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TCAACAAW WTTGTTGA 24 1 6.1e-007 1.8e-002 # TCAACAAA TTTGTTGA 14 1 4.5e-004 1.3e+001 # TCAACAAT ATTGTTGA 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-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 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 0.583333 0.000000 0.000000 0.416667 MOTIF GGTCTM DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GGTCTM KAGACC 67 23 7.3e-007 2.1e-002 # GGTCTC GAGACC 31 9 2.7e-004 7.9e+000 # GGTCTA TAGACC 37 14 6.9e-004 2.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 70 E= 2.1e-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 0.000000 0.000000 0.000000 1.000000 0.528571 0.471429 0.000000 0.000000 MOTIF CGTMTGAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGTMTGAC GTCAKACG 20 0 8.0e-007 2.3e-002 # CGTATGAC GTCATACG 13 0 1.1e-004 3.3e+000 # CGTCTGAC GTCAGACG 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.650000 0.350000 0.000000 0.000000 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 1.000000 0.000000 0.000000 MOTIF ACGATGGS DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACGATGGS SCCATCGT 19 0 1.6e-006 4.7e-002 # ACGATGGC GCCATCGT 11 0 4.6e-004 1.3e+001 # ACGATGGG CCCATCGT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.7e-002 1.000000 0.000000 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 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 0.578947 0.421053 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 45.91 seconds