# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--IES2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--IES2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--IES2/seqs-shuffled # positives: 713 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--IES2/seqs-centered (Sat Jan 18 16:28:57 PST 2020) # negatives: 713 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--IES2/seqs-shuffled (Sat Jan 18 16:28:57 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:47:19 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 0.312 C 0.187 G 0.184 T 0.317 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 97 12 3.6e-019 1.1e-014 # GGTTCGA TCGAACC 66 2 1.8e-018 5.5e-014 # GGTTCAA TTGAACC 32 10 4.0e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 1.1e-014 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.326531 0.000000 0.673469 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 1 7.7e-018 2.3e-013 # CTCGGCCA TGGCCGAG 30 0 6.8e-010 2.1e-005 # CTTGGCCA TGGCCAAG 19 1 1.8e-005 5.5e-001 # CTGGGCCA TGGCCCAG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 2.3e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.183333 0.316667 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 CTWAACCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTWAACCA TGGTTWAG 51 2 6.7e-014 2.0e-009 # CTTAACCA TGGTTAAG 37 0 4.5e-012 1.4e-007 # CTAAACCA TGGTTTAG 14 2 2.0e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 2.0e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.274510 0.000000 0.000000 0.725490 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 1.000000 0.000000 0.000000 0.000000 MOTIF TTTCTTB DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 158 64 3.0e-012 9.0e-008 # TTTCTTG CAAGAAA 39 10 1.4e-005 4.3e-001 # TTTCTTT AAAGAAA 84 41 3.7e-005 1.1e+000 # TTTCTTC GAAGAAA 46 16 6.3e-005 1.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 176 E= 9.0e-008 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.255682 0.227273 0.517045 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 0 4.5e-012 1.4e-007 # GCGCTACC GGTAGCGC 25 0 2.4e-008 7.2e-004 # GCTCTACC GGTAGAGC 12 0 2.3e-004 7.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.4e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.675676 0.324324 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 CCRTACA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 72 13 6.4e-012 1.9e-007 # CCGTACA TGTACGG 38 3 3.4e-009 1.0e-004 # CCATACA TGTATGG 41 10 5.2e-006 1.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 88 E= 1.9e-007 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.454545 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 CACTAKA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACTAKA TMTAGTG 52 7 3.3e-010 9.8e-006 # CACTATA TATAGTG 38 5 8.5e-008 2.5e-003 # CACTAGA TCTAGTG 14 2 2.0e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 9.8e-006 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 0.000000 0.000000 0.269231 0.730769 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 2 6.8e-009 2.0e-004 # ATGGCAAC GTTGCCAT 20 1 9.3e-006 2.8e-001 # ATGGCATC GATGCCAT 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.0e-004 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 0.588235 0.000000 0.000000 0.411765 0.000000 1.000000 0.000000 0.000000 MOTIF CAGRCGC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAGRCGC GCGYCTG 29 1 2.2e-008 6.6e-004 # CAGGCGC GCGCCTG 13 0 1.2e-004 3.4e+000 # CAGACGC GCGTCTG 16 1 1.3e-004 3.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 6.6e-004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.551724 0.000000 0.448276 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 AAAGCGWG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 27 1 8.6e-008 2.5e-003 # AAAGCGTG CACGCTTT 16 1 1.3e-004 3.8e+000 # AAAGCGAG CTCGCTTT 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.5e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.407407 0.000000 0.000000 0.592593 0.000000 0.000000 1.000000 0.000000 MOTIF CGCCACRC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGCCACRC GYGTGGCG 22 0 2.0e-007 6.0e-003 # CGCCACAC GTGTGGCG 15 0 2.8e-005 8.4e-001 # CGCCACGC GCGTGGCG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.0e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.681818 0.000000 0.318182 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 21 0 4.1e-007 1.2e-002 # CACCGTGG CCACGGTG 11 0 4.7e-004 1.4e+001 # CACCGTGC GCACGGTG 10 0 9.5e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 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 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 0.523810 0.000000 MOTIF AGTYATAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGTYATAC GTATRACT 23 1 1.3e-006 3.7e-002 # AGTCATAC GTATGACT 14 1 4.6e-004 1.4e+001 # AGTTATAC GTATAACT 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.7e-002 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 0.608696 0.000000 0.391304 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 1.000000 0.000000 0.000000 MOTIF TGGGTGTW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TGGGTGTW WACACCCA 23 1 1.3e-006 3.7e-002 # TGGGTGTA TACACCCA 12 0 2.3e-004 6.9e+000 # TGGGTGTT AACACCCA 11 1 3.1e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 3.7e-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 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 0.541667 0.000000 0.000000 0.458333 # Stopping reason: E-value threshold exceeded # Running time: 66.51 seconds