# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/seqs-shuffled # positives: 473 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/seqs-centered (Sat Jan 18 16:01:50 PST 2020) # negatives: 473 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/seqs-shuffled (Sat Jan 18 16:01:50 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:11:12 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 0.291 C 0.213 G 0.208 T 0.288 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 128 5 2.9e-036 7.7e-032 # GGTTCGA TCGAACC 97 3 7.4e-028 2.0e-023 # GGTTCAA TTGAACC 32 2 2.1e-008 5.7e-004 letter-probability matrix: alength= 4 w= 7 nsites= 129 E= 7.7e-032 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 0.248062 0.000000 0.751938 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 85 5 9.3e-022 2.4e-017 # AGTGGTT AACCACT 59 1 8.2e-018 2.1e-013 # AGTGGTA TACCACT 38 4 1.5e-008 4.0e-004 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 2.4e-017 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 0.380000 0.000000 0.000000 0.620000 MOTIF AYCCRTAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 74 2 2.0e-021 5.3e-017 # ACCCATAC GTATGGGT 39 2 1.9e-010 4.9e-006 # ATCCGTAC GTACGGAT 28 0 2.5e-009 6.5e-005 # ATCCATAC GTATGGAT 10 0 9.3e-004 2.4e+001 # ACCCGTAC GTACGGGT 7 0 7.6e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 5.3e-017 1.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.579545 0.000000 0.420455 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 58 4 2.6e-014 6.6e-010 # CGCCTTA TAAGGCG 44 4 3.2e-010 8.2e-006 # CGCGTTA TAACGCG 14 0 5.5e-005 1.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 6.6e-010 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 0.758621 0.241379 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 64 7 1.0e-013 2.6e-009 # CCAACTG CAGTTGG 32 3 1.3e-007 3.4e-003 # CCAACTT AAGTTGG 32 4 6.4e-007 1.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 2.6e-009 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 AARARA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AARARA TYTYTT 273 167 3.1e-012 8.1e-008 # AAGAAA TTTCTT 104 46 1.5e-007 3.8e-003 # AAAAAA TTTTTT 162 101 6.3e-006 1.6e-001 # AAGAGA TCTCTT 41 17 8.1e-004 2.1e+001 # AAAAGA TCTTTT 80 53 7.4e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 393 E= 8.1e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.679389 0.000000 0.320611 0.000000 1.000000 0.000000 0.000000 0.000000 0.740458 0.000000 0.259542 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAASGATG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 33 1 1.2e-009 2.9e-005 # CAACGATG CATCGTTG 23 1 1.2e-006 2.9e-002 # CAAGGATG CATCCTTG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.9e-005 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 0.696970 0.303030 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 0.000000 0.000000 1.000000 0.000000 MOTIF CATYACGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CATYACGC GCGTRATG 28 0 2.5e-009 6.1e-005 # CATCACGC GCGTGATG 15 0 2.7e-005 6.8e-001 # CATTACGC GCGTAATG 13 0 1.1e-004 2.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 6.1e-005 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.535714 0.000000 0.464286 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 CCGTGSA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 37 3 5.2e-009 1.3e-004 # CCGTGGA TCCACGG 23 1 1.2e-006 2.9e-002 # CCGTGCA TGCACGG 14 2 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.3e-004 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 0.378378 0.621622 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCTTSA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATCTTSA TSAAGAT 34 2 5.6e-009 1.4e-004 # ATCTTGA TCAAGAT 22 1 2.3e-006 5.6e-002 # ATCTTCA TGAAGAT 12 1 1.6e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.4e-004 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 0.352941 0.647059 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGSCCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 74 22 9.7e-009 2.4e-004 # CGCCCA TGGGCG 37 11 7.7e-005 1.9e+000 # CGGCCA TGGCCG 37 11 7.7e-005 1.9e+000 letter-probability matrix: alength= 4 w= 6 nsites= 76 E= 2.4e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.513158 0.486842 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 AGTCTKG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGTCTKG CMAGACT 29 1 1.9e-008 4.7e-004 # AGTCTGG CCAGACT 13 0 1.1e-004 2.7e+000 # AGTCTTG CAAGACT 16 1 1.2e-004 3.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 4.7e-004 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.448276 0.551724 0.000000 0.000000 1.000000 0.000000 MOTIF GCTACCGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCTACCGA TCGGTAGC 29 1 1.9e-008 4.6e-004 # GCTACCGA TCGGTAGC 29 1 1.9e-008 4.6e-004 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 4.6e-004 0.000000 0.000000 1.000000 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 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 MOTIF AGMAGAT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGMAGAT ATCTKCT 39 5 3.8e-008 9.1e-004 # AGCAGAT ATCTGCT 18 1 3.3e-005 8.0e-001 # AGAAGAT ATCTTCT 21 5 1.1e-003 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 9.1e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.538462 0.461538 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 0.000000 0.000000 0.000000 1.000000 MOTIF GCGTMTGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCGTMTGA TCAKACGC 23 0 9.1e-008 2.2e-003 # GCGTATGA TCATACGC 13 0 1.1e-004 2.7e+000 # GCGTCTGA TCAGACGC 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.2e-003 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 1.000000 0.565217 0.434783 0.000000 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 ATAGTKTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 30 3 4.8e-007 1.1e-002 # ATAGTGTA TACACTAT 16 0 1.3e-005 3.2e-001 # ATAGTTTA TAAACTAT 14 3 6.0e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.533333 0.466667 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCTATMA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GCTATMA TKATAGC 26 2 1.1e-006 2.7e-002 # GCTATCA TGATAGC 19 2 9.5e-005 2.3e+000 # GCTATAA TTATAGC 7 0 7.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 2.7e-002 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.269231 0.730769 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AACACSCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AACACSCA TGSGTGTT 23 1 1.2e-006 2.8e-002 # AACACCCA TGGGTGTT 13 1 8.5e-004 2.0e+001 # AACACGCA TGCGTGTT 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-002 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 0.000000 0.000000 0.000000 0.565217 0.434783 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 55.90 seconds