# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/seqs-shuffled # positives: 468 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/seqs-centered (Sun Jan 19 10:10:51 PST 2020) # negatives: 468 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/seqs-shuffled (Sun Jan 19 10:10:51 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:19:41 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 0.208 G 0.204 T 0.294 MOTIF GGDTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGDTCGA TCGAHCC 91 7 7.3e-022 1.9e-017 # GGTTCGA TCGAACC 76 4 6.9e-020 1.8e-015 # GGGTCGA TCGACCC 12 0 2.3e-004 6.0e+000 # GGATCGA TCGATCC 19 3 3.7e-004 9.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 1.9e-017 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.184783 0.000000 0.054348 0.760870 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 AYCCRTAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 75 3 1.3e-020 3.5e-016 # ACCCATAC GTATGGGT 40 0 3.8e-013 1.0e-008 # ATCCGTAC GTACGGAT 28 2 3.0e-007 8.0e-003 # ACCCGTAC GTACGGGT 8 0 3.8e-003 1.0e+002 # ATCCATAC GTATGGAT 10 1 5.6e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 3.5e-016 1.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.444444 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.577778 0.000000 0.422222 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 AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 83 6 3.2e-020 8.2e-016 # AGTGGTT AACCACT 60 3 7.2e-016 1.9e-011 # AGTGGTA TACCACT 35 3 1.9e-008 5.0e-004 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 8.2e-016 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 0.357143 0.000000 0.000000 0.642857 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 57 5 3.3e-013 8.6e-009 # CGCCTTA TAAGGCG 43 2 1.2e-011 3.0e-007 # CGCGTTA TAACGCG 14 3 6.0e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 8.6e-009 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 0.754386 0.245614 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 MOTIF CCAACTK DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCAACTK MAGTTGG 68 12 9.8e-012 2.5e-007 # CCAACTG CAGTTGG 34 3 3.7e-008 9.4e-004 # CCAACTT AAGTTGG 34 9 6.0e-005 1.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 68 E= 2.5e-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 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 0.500000 0.500000 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 42 2 2.3e-011 6.0e-007 # ATGGCAAC GTTGCCAT 31 1 4.7e-009 1.2e-004 # ATGGCATC GATGCCAT 11 1 3.0e-003 7.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 6.0e-007 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 0.738095 0.000000 0.000000 0.261905 0.000000 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 0 1.3e-010 3.4e-006 # CTATCACA TGTGATAG 16 0 1.3e-005 3.4e-001 # CTATCACG CGTGATAG 16 0 1.3e-005 3.4e-001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 3.4e-006 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 0.500000 0.000000 0.500000 0.000000 MOTIF CGGTAGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGGTAGC GCTACCG 30 0 5.8e-010 1.5e-005 # CGGTAGC GCTACCG 30 0 5.8e-010 1.5e-005 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.5e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AKCGTGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AKCGTGA TCACGMT 32 1 2.4e-009 6.0e-005 # AGCGTGA TCACGCT 15 0 2.7e-005 6.9e-001 # ATCGTGA TCACGAT 17 1 6.4e-005 1.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 6.0e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.468750 0.531250 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 CGTGGMG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGTGGMG CKCCACG 32 1 2.4e-009 6.0e-005 # CGTGGAG CTCCACG 16 0 1.3e-005 3.4e-001 # CGTGGCG CGCCACG 16 1 1.2e-004 3.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 6.0e-005 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 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF SAAGAAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST SAAGAAA TTTCTTS 61 14 5.4e-009 1.4e-004 # GAAGAAA TTTCTTC 32 6 8.4e-006 2.1e-001 # CAAGAAA TTTCTTG 30 8 1.8e-004 4.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 63 E= 1.4e-004 0.000000 0.492063 0.507937 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CRCCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 84 29 1.8e-008 4.4e-004 # CACCCA TGGGTG 48 17 4.4e-005 1.1e+000 # CGCCCA TGGGCG 37 12 1.7e-004 4.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 98 E= 4.4e-004 0.000000 1.000000 0.000000 0.000000 0.602041 0.000000 0.397959 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 AGTCAKAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 1 1.5e-007 3.7e-003 # AGTCATAC GTATGACT 13 0 1.1e-004 2.8e+000 # AGTCAGAC GTCTGACT 13 1 8.5e-004 2.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.7e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 22 0 1.9e-007 4.6e-003 # CGTGCTAA TTAGCACG 11 0 4.6e-004 1.1e+001 # CGTGTTAA TTAACACG 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.6e-003 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 0.500000 0.000000 0.500000 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 CTTGTTRG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTTGTTRG CYAACAAG 22 0 1.9e-007 4.6e-003 # CTTGTTGG CCAACAAG 15 0 2.7e-005 6.7e-001 # CTTGTTAG CTAACAAG 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.6e-003 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 0.000000 0.000000 1.000000 0.318182 0.000000 0.681818 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCSACAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GCSACAA TTGTSGC 20 0 7.8e-007 1.9e-002 # GCGACAA TTGTCGC 12 0 2.3e-004 5.6e+000 # GCCACAA TTGTGGC 8 0 3.8e-003 9.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 1.9e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 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 MOTIF TAAKCGCA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST TAAKCGCA TGCGMTTA 23 1 1.2e-006 2.8e-002 # TAAGCGCA TGCGCTTA 12 0 2.3e-004 5.6e+000 # TAATCGCA TGCGATTA 11 1 3.0e-003 7.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-002 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 0.000000 0.521739 0.478261 0.000000 1.000000 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 0.000000 MOTIF AATCTTYT DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AATCTTYT ARAAGATT 35 6 1.5e-006 3.8e-002 # AATCTTCT AGAAGATT 19 3 3.7e-004 9.2e+000 # AATCTTTT AAAAGATT 16 3 2.0e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 3.8e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.542857 0.000000 0.457143 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 58.11 seconds