# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HAA1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HAA1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HAA1/seqs-shuffled # positives: 578 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HAA1/seqs-centered (Sat Jan 18 19:13:37 PST 2020) # negatives: 578 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HAA1/seqs-shuffled (Sat Jan 18 19:13:37 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 19:28:25 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 0.293 C 0.210 G 0.207 T 0.290 MOTIF GTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGA TCGAAC 144 16 8.6e-031 2.6e-026 # GTTCGA TCGAAC 144 16 8.6e-031 2.6e-026 letter-probability matrix: alength= 4 w= 6 nsites= 144 E= 2.6e-026 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 0.000000 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 93 7 4.2e-022 1.3e-017 # AGTGGTT AACCACT 63 4 1.1e-015 3.5e-011 # AGTGGTA TACCACT 42 3 2.2e-010 6.7e-006 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 1.3e-017 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 0.398148 0.000000 0.000000 0.601852 MOTIF CCVTACA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCVTACA TGTABGG 64 10 1.2e-011 3.6e-007 # CCGTACA TGTACGG 18 0 3.3e-006 1.0e-001 # CCATACA TGTATGG 26 6 2.2e-004 6.8e+000 # CCCTACA TGTAGGG 21 4 4.0e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 69 E= 3.6e-007 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.405797 0.304348 0.289855 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 1.000000 0.000000 0.000000 0.000000 MOTIF AACTTGRC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTTGRC GYCAAGTT 39 1 2.0e-011 6.0e-007 # AACTTGGC GCCAAGTT 32 1 2.6e-009 7.8e-005 # AACTTGAC GTCAAGTT 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 6.0e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.179487 0.000000 0.820513 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGGCG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAGGCG CGCCTT 73 15 2.7e-011 8.1e-007 # AAGGCG CGCCTT 73 15 2.7e-011 8.1e-007 letter-probability matrix: alength= 4 w= 6 nsites= 74 E= 8.1e-007 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 AAAAADA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAAAADA THTTTTT 189 93 2.8e-011 8.3e-007 # AAAAAAA TTTTTTT 111 52 3.8e-007 1.1e-002 # AAAAAGA TCTTTTT 64 23 2.9e-006 8.6e-002 # AAAAATA TATTTTT 66 28 2.8e-005 8.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 228 E= 8.3e-007 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 0.460526 0.000000 0.258772 0.280702 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCRC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGACCRC GYGGTCT 42 3 2.2e-010 6.5e-006 # AGACCAC GTGGTCT 29 1 2.1e-008 6.1e-004 # AGACCGC GCGGTCT 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 6.5e-006 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 0.000000 1.000000 0.000000 0.000000 0.690476 0.000000 0.309524 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 32 1 2.6e-009 7.7e-005 # ATGGCAAC GTTGCCAT 19 1 1.7e-005 5.2e-001 # ATGGCATC GATGCCAT 13 0 1.1e-004 3.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 7.7e-005 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 0.593750 0.000000 0.000000 0.406250 0.000000 1.000000 0.000000 0.000000 MOTIF ATCTTYTG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 31 1 5.2e-009 1.5e-004 # ATCTTCTG CAGAAGAT 18 0 3.3e-006 9.8e-002 # ATCTTTTG CAAAAGAT 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.5e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.580645 0.000000 0.419355 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AARATAT DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AARATAT ATATYTT 56 12 1.3e-008 3.8e-004 # AAAATAT ATATTTT 38 11 5.1e-005 1.5e+000 # AAGATAT ATATCTT 20 2 5.3e-005 1.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 3.8e-004 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CRTGCAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CRTGCAC GTGCAYG 25 0 2.3e-008 6.7e-004 # CGTGCAC GTGCACG 13 0 1.1e-004 3.3e+000 # CATGCAC GTGCATG 12 0 2.3e-004 6.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 6.7e-004 0.000000 1.000000 0.000000 0.000000 0.480000 0.000000 0.520000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGARTCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGARTCA TGAYTCT 34 3 4.1e-008 1.2e-003 # AGAGTCA TGACTCT 19 0 1.6e-006 4.8e-002 # AGAATCA TGATTCT 16 3 2.1e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.2e-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 0.457143 0.000000 0.542857 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 AGAYCGGG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGGG CCCGRTCT 24 0 4.7e-008 1.4e-003 # AGATCGGG CCCGATCT 14 0 5.6e-005 1.6e+000 # AGACCGGG CCCGGTCT 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-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 0.000000 0.416667 0.000000 0.583333 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 MOTIF GCGCTACC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCGCTACC GGTAGCGC 23 0 9.5e-008 2.8e-003 # GCGCTACC GGTAGCGC 23 0 9.5e-008 2.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-003 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 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 ACTCASG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTCASG CSTGAGT 32 3 1.5e-007 4.2e-003 # ACTCACG CGTGAGT 20 2 5.3e-005 1.5e+000 # ACTCAGG CCTGAGT 12 1 1.6e-003 4.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 4.2e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.625000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACCCWCAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACCCWCAC GTGWGGGT 29 2 1.7e-007 4.9e-003 # ACCCACAC GTGTGGGT 17 1 6.5e-005 1.9e+000 # ACCCTCAC GTGAGGGT 12 1 1.6e-003 4.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 4.9e-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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TCAGWA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST TCAGWA TWCTGA 90 38 6.6e-007 1.9e-002 # TCAGAA TTCTGA 53 22 1.4e-004 4.2e+000 # TCAGTA TACTGA 39 16 1.0e-003 3.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 97 E= 1.9e-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 0.546392 0.000000 0.000000 0.453608 1.000000 0.000000 0.000000 0.000000 MOTIF RCGGGGA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 31 4 1.3e-006 3.6e-002 # ACGGGGA TCCCCGT 14 0 5.6e-005 1.6e+000 # GCGGGGA TCCCCGC 17 4 3.4e-003 9.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 3.6e-002 0.451613 0.000000 0.548387 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 68.86 seconds