# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/seqs-shuffled # positives: 667 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/seqs-centered (Sat Jan 18 21:57:15 PST 2020) # negatives: 667 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/seqs-shuffled (Sat Jan 18 21:57:15 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:12:25 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 0.309 C 0.194 G 0.188 T 0.309 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 101 5 3.2e-026 9.6e-022 # GGTTCGA TCGAACC 86 4 1.5e-022 4.5e-018 # GGATCGA TCGATCC 24 2 4.4e-006 1.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 101 E= 9.6e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.198020 0.000000 0.000000 0.801980 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 CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 60 3 1.3e-015 3.9e-011 # CTCGGCCA TGGCCGAG 28 0 2.8e-009 8.4e-005 # CTTGGCCA TGGCCAAG 21 2 2.9e-005 8.7e-001 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 3.9e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.466667 0.183333 0.350000 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 CCWTAACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 48 0 1.5e-015 4.4e-011 # CCTTAACC GGTTAAGG 36 0 9.0e-012 2.7e-007 # CCATAACC GGTTATGG 12 0 2.3e-004 7.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 4.4e-011 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 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 CCVTACA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCVTACA TGTABGG 88 15 5.6e-015 1.7e-010 # CCGTACA TGTACGG 43 3 1.3e-010 3.8e-006 # CCATACA TGTATGG 40 11 2.1e-005 6.2e-001 # CCCTACA TGTAGGG 12 1 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 1.7e-010 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.457143 0.114286 0.428571 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 0 5.0e-013 1.5e-008 # GCGCTACC GGTAGCGC 26 0 1.2e-008 3.5e-004 # GCTCTACC GGTAGAGC 14 0 5.7e-005 1.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.5e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.650000 0.350000 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 CCACTAHA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCACTAHA TDTAGTGG 42 2 3.1e-011 9.1e-007 # CCACTAAA TTTAGTGG 19 1 1.8e-005 5.3e-001 # CCACTACA TGTAGTGG 14 1 4.6e-004 1.4e+001 # CCACTATA TATAGTGG 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 9.1e-007 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 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.452381 0.333333 0.000000 0.214286 1.000000 0.000000 0.000000 0.000000 MOTIF GTTRCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTTRCCA TGGYAAC 41 4 2.8e-009 8.2e-005 # GTTGCCA TGGCAAC 31 3 2.9e-007 8.5e-003 # GTTACCA TGGTAAC 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 8.2e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.243902 0.000000 0.756098 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 AKAAAAAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AKAAAAAA TTTTTTMT 87 28 3.8e-009 1.1e-004 # AGAAAAAA TTTTTTCT 46 13 6.3e-006 1.9e-001 # ATAAAAAA TTTTTTAT 42 16 3.3e-004 9.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 1.1e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.522727 0.477273 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCAY DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGACCAY RTGGTCT 40 5 2.5e-008 7.3e-004 # AGACCAC GTGGTCT 22 3 6.9e-005 2.0e+000 # AGACCAT ATGGTCT 18 2 1.8e-004 5.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 7.3e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.536585 0.000000 0.463415 MOTIF CRCCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 104 43 5.4e-008 1.6e-003 # CACCCA TGGGTG 73 33 3.3e-005 9.8e-001 # CGCCCA TGGGCG 33 11 5.2e-004 1.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 179 E= 1.6e-003 0.000000 1.000000 0.000000 0.000000 0.821229 0.000000 0.178771 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 GGAGASC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGAGASC GSTCTCC 27 1 8.4e-008 2.4e-003 # GGAGACC GGTCTCC 18 1 3.4e-005 1.0e+000 # GGAGAGC GCTCTCC 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.4e-003 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 21 0 4.1e-007 1.2e-002 # CGTGTTAA TTAACACG 11 0 4.7e-004 1.4e+001 # CGTGCTAA TTAGCACG 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.000000 0.523810 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 41 8 6.5e-007 1.9e-002 # TGGCGCA TGCGCCA 23 5 4.0e-004 1.2e+001 # TGGCGTA TACGCCA 18 3 6.9e-004 2.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.9e-002 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 0.000000 1.000000 0.000000 0.000000 0.560976 0.000000 0.439024 1.000000 0.000000 0.000000 0.000000 MOTIF AMTCCGAT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AMTCCGAT ATCGGAKT 20 0 8.3e-007 2.4e-002 # AATCCGAT ATCGGATT 12 0 2.3e-004 6.7e+000 # ACTCCGAT ATCGGAGT 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 2.4e-002 1.000000 0.000000 0.000000 0.000000 0.545455 0.454545 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CTATCACR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 23 1 1.2e-006 3.6e-002 # CTATCACA TGTGATAG 13 0 1.2e-004 3.3e+000 # CTATCACG CGTGATAG 10 1 5.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.6e-002 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.565217 0.000000 0.434783 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 68.31 seconds