# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-shuffled # positives: 386 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-centered (Sat Jan 18 00:37:40 PST 2020) # negatives: 386 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-shuffled (Sat Jan 18 00:37:40 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 00:43:44 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 0.206 G 0.208 T 0.291 MOTIF AGTGGTH DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTH DACCACT 98 9 6.6e-023 1.6e-018 # AGTGGTT AACCACT 66 3 5.7e-018 1.4e-013 # AGTGGTA TACCACT 36 5 2.1e-007 5.0e-003 # AGTGGTC GACCACT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 1.6e-018 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 0.310345 0.086207 0.000000 0.603448 MOTIF ACCRACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 72 6 4.2e-017 1.0e-012 # ACCAACT AGTTGGT 52 5 7.0e-012 1.7e-007 # ACCGACT AGTCGGT 20 1 8.3e-006 2.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 1.0e-012 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.722222 0.000000 0.277778 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 MOTIF AASGCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AASGCG CGCSTT 92 17 9.1e-016 2.2e-011 # AAGGCG CGCCTT 64 9 1.4e-012 3.4e-008 # AACGCG CGCGTT 28 10 2.0e-003 4.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 93 E= 2.2e-011 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.301075 0.698925 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 GGYTCGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGYTCGA TCGARCC 56 4 7.0e-014 1.7e-009 # GGTTCGA TCGAACC 48 2 2.7e-013 6.4e-009 # GGCTCGA TCGAGCC 14 2 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 1.7e-009 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.210526 0.000000 0.789474 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 CGSCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 66 11 6.1e-012 1.4e-007 # CGGCCA TGGCCG 41 6 3.9e-008 9.1e-004 # CGCCCA TGGGCG 25 5 1.3e-004 2.9e+000 letter-probability matrix: alength= 4 w= 6 nsites= 67 E= 1.4e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.388060 0.611940 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 ATGTAYGG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 43 3 7.9e-011 1.8e-006 # ATGTATGG CCATACAT 23 1 1.1e-006 2.5e-002 # ATGTACGG CCGTACAT 22 2 1.4e-005 3.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 1.8e-006 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.479167 0.000000 0.520833 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACACTAK DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACACTAK MTAGTGT 37 2 6.3e-010 1.5e-005 # ACACTAT ATAGTGT 27 1 7.0e-008 1.6e-003 # ACACTAG CTAGTGT 10 1 5.6e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.5e-005 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.263158 0.736842 MOTIF CGKTGCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGKTGCC GGCAMCG 32 1 2.1e-009 4.9e-005 # CGTTGCC GGCAACG 18 1 3.2e-005 7.4e-001 # CGGTGCC GGCACCG 14 0 5.4e-005 1.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 4.9e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.437500 0.562500 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 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 26 0 9.6e-009 2.2e-004 # CTATCACA TGTGATAG 15 0 2.7e-005 6.1e-001 # CTATCACG CGTGATAG 11 0 4.5e-004 1.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.2e-004 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 0.576923 0.000000 0.423077 0.000000 MOTIF SAAGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 192 118 3.8e-008 8.6e-004 # GAAGA TCTTC 103 55 1.2e-005 2.8e-001 # CAAGA TCTTG 116 81 2.5e-003 5.7e+001 letter-probability matrix: alength= 4 w= 5 nsites= 269 E= 8.6e-004 0.000000 0.546468 0.453532 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 1.000000 0.000000 0.000000 0.000000 MOTIF CGTGGMG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGTGGMG CKCCACG 28 1 3.5e-008 7.6e-004 # CGTGGCG CGCCACG 16 0 1.3e-005 2.9e-001 # CGTGGAG CTCCACG 12 1 1.6e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 7.6e-004 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 0.000000 1.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CAYACGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CAYACGC GCGTRTG 25 1 2.8e-007 6.1e-003 # CATACGC GCGTATG 12 0 2.2e-004 4.9e+000 # CACACGC GCGTGTG 13 1 8.4e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 6.1e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.520000 0.000000 0.480000 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 MOTIF ATCCGTRC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATCCGTRC GYACGGAT 19 0 1.5e-006 3.3e-002 # ATCCGTGC GCACGGAT 10 0 9.2e-004 2.0e+001 # ATCCGTAC GTACGGAT 9 0 1.9e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.473684 0.000000 0.526316 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 35.50 seconds