# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/seqs-shuffled # positives: 807 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/seqs-centered (Sat Jan 18 19:27:26 PST 2020) # negatives: 807 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/seqs-shuffled (Sat Jan 18 19:27:26 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 19:42:15 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 0.204 G 0.204 T 0.297 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 113 12 1.5e-023 5.3e-019 # GGTTCGA TCGAACC 91 5 7.3e-023 2.5e-018 # AGTTCGA TCGAACT 28 7 2.2e-004 7.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 113 E= 5.3e-019 0.230088 0.000000 0.769912 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 72 5 3.3e-017 1.1e-012 # CCATACAT ATGTATGG 30 2 9.7e-008 3.3e-003 # CCGTACAT ATGTACGG 30 3 5.6e-007 1.9e-002 # CCGTACAC GTGTACGG 13 1 8.8e-004 3.0e+001 # CCATACAC GTGTATGG 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 84 E= 1.1e-012 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.000000 0.523810 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 0.000000 0.238095 0.000000 0.761905 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 62 2 3.6e-017 1.2e-012 # CTCGGCCA TGGCCGAG 27 0 6.0e-009 2.0e-004 # CTTGGCCA TGGCCAAG 22 1 2.5e-006 8.5e-002 # CTGGGCCA TGGCCCAG 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 1.2e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.435484 0.209677 0.354839 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 GCKCTMCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTMCC GGKAGMGC 49 2 2.9e-013 1.0e-008 # GCGCTACC GGTAGCGC 24 1 6.6e-007 2.2e-002 # GCTCTACC GGTAGAGC 15 0 2.9e-005 9.7e-001 # GCTCTCCC GGGAGAGC 10 1 5.7e-003 1.9e+002 # GCGCTCCC GGGAGCGC 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 1.0e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.489796 0.510204 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.734694 0.265306 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCCTTAMC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 48 2 5.8e-013 2.0e-008 # GCCTTAAC GTTAAGGC 35 1 3.8e-010 1.3e-005 # GCCTTACC GGTAAGGC 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 2.0e-008 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.729167 0.270833 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGRTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTGRTA TAYCAC 125 50 9.5e-010 3.2e-005 # GTGATA TATCAC 76 27 3.3e-007 1.1e-002 # GTGGTA TACCAC 50 23 8.3e-004 2.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 129 E= 3.2e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.596899 0.000000 0.403101 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGMAG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGMAG CTKCT 312 206 1.0e-008 3.3e-004 # AGAAG CTTCT 222 149 9.8e-006 3.3e-001 # AGCAG CTGCT 137 83 5.7e-005 1.9e+000 letter-probability matrix: alength= 4 w= 5 nsites= 419 E= 3.3e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.651551 0.348449 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GGCSCAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GGCSCAA TTGSGCC 42 6 3.4e-008 1.1e-003 # GGCCCAA TTGGGCC 22 2 1.6e-005 5.2e-001 # GGCGCAA TTGCGCC 20 4 7.1e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.1e-003 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 0.523810 0.476190 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 MOTIF AKCGTGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AKCGTGA TCACGMT 42 7 1.2e-007 4.0e-003 # ATCGTGA TCACGAT 22 2 1.6e-005 5.2e-001 # AGCGTGA TCACGCT 20 5 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 4.0e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 1.000000 0.000000 0.000000 0.000000 MOTIF CACGGYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 37 5 1.6e-007 5.2e-003 # CACGGTG CACCGTG 23 2 8.5e-006 2.7e-001 # CACGGCG CGCCGTG 14 3 6.1e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 5.2e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.378378 0.000000 0.621622 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGCAAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAAC GTTGCCAT 29 3 1.0e-006 3.4e-002 # ATGGCAAC GTTGCCAT 29 3 1.0e-006 3.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.4e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGGGS DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGS SCCCGCG 29 3 1.0e-006 3.3e-002 # CGCGGGC GCCCGCG 14 1 4.6e-004 1.5e+001 # CGCGGGG CCCCGCG 16 2 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.3e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.448276 0.551724 0.000000 MOTIF AATMCAAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AATMCAAC GTTGKATT 31 4 1.4e-006 4.5e-002 # AATCCAAC GTTGGATT 20 3 2.2e-004 7.2e+000 # AATACAAC GTTGTATT 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 4.5e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.343750 0.656250 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 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 70.11 seconds