# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/seqs-shuffled # positives: 1004 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/seqs-centered (Sat Jan 18 23:36:37 PST 2020) # negatives: 1004 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/seqs-shuffled (Sat Jan 18 23:36:37 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:50:23 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 0.299 C 0.199 G 0.201 T 0.301 MOTIF SGGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 58 0 1.5e-018 5.4e-014 # GGGTTCGA TCGAACCC 40 0 6.1e-013 2.2e-008 # CGGTTCGA TCGAACCG 18 0 3.5e-006 1.3e-001 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 5.4e-014 0.000000 0.310345 0.689655 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 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 STTACCR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST STTACCR YGGTAAS 102 22 1.5e-014 5.5e-010 # CTTACCG CGGTAAG 27 4 1.5e-005 5.4e-001 # GTTACCA TGGTAAC 27 4 1.5e-005 5.4e-001 # GTTACCG CGGTAAC 23 4 1.4e-004 5.1e+000 # CTTACCA TGGTAAG 33 10 2.7e-004 9.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 111 E= 5.5e-010 0.000000 0.540541 0.459459 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.540541 0.000000 0.459459 0.000000 MOTIF AAGAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAGAAR YTTCTT 361 220 2.3e-012 8.4e-008 # AAGAAA TTTCTT 252 149 5.4e-009 1.9e-004 # AAGAAG CTTCTT 141 86 6.7e-005 2.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 454 E= 8.4e-008 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 0.636564 0.000000 0.363436 0.000000 MOTIF GTTRGTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GTTRGTA TACYAAC 69 13 5.0e-011 1.8e-006 # GTTAGTA TACTAAC 42 8 4.4e-007 1.5e-002 # GTTGGTA TACCAAC 29 5 1.7e-005 5.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 1.8e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.591549 0.000000 0.408451 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 MOTIF GCGYCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCGYCA TGRCGC 79 21 9.0e-010 3.2e-005 # GCGTCA TGACGC 43 10 2.1e-006 7.5e-002 # GCGCCA TGGCGC 36 12 3.1e-004 1.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 79 E= 3.2e-005 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 0.455696 0.000000 0.544304 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CMAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CMAAGA TCTTKG 170 84 4.4e-009 1.5e-004 # CCAAGA TCTTGG 81 26 2.1e-008 7.5e-004 # CAAAGA TCTTTG 97 59 9.8e-004 3.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 185 E= 1.5e-004 0.000000 1.000000 0.000000 0.000000 0.551351 0.448649 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 1.000000 0.000000 0.000000 0.000000 MOTIF CAKACGCG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAKACGCG CGCGTMTG 24 0 5.2e-008 1.8e-003 # CAGACGCG CGCGTCTG 12 0 2.4e-004 8.2e+000 # CATACGCG CGCGTATG 12 0 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-003 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 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 GCCTTAAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAAC GTTAAGGC 24 0 5.2e-008 1.8e-003 # GCCTTAAC GTTAAGGC 24 0 5.2e-008 1.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 27 1 9.2e-008 3.2e-003 # CTCGGCCA TGGCCGAG 17 0 7.1e-006 2.5e-001 # CTTGGCCA TGGCCAAG 10 1 5.8e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.629630 0.000000 0.370370 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 TACCRCTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TACCRCTA TAGYGGTA 23 0 1.0e-007 3.7e-003 # TACCACTA TAGTGGTA 13 0 1.2e-004 4.1e+000 # TACCGCTA TAGCGGTA 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.7e-003 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 0.565217 0.000000 0.434783 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 MOTIF ACCASCG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACCASCG CGSTGGT 40 6 1.2e-007 4.0e-003 # ACCACCG CGGTGGT 23 3 4.0e-005 1.4e+000 # ACCAGCG CGCTGGT 17 3 1.2e-003 4.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 4.0e-003 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 0.000000 0.604651 0.395349 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GRCAGCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GRCAGCA TGCTGYC 34 4 2.4e-007 8.4e-003 # GGCAGCA TGCTGCC 20 1 9.6e-006 3.3e-001 # GACAGCA TGCTGTC 14 3 6.2e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 8.4e-003 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKGCTAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCKGCTAA TTAGCMGC 20 0 8.7e-007 3.0e-002 # GCTGCTAA TTAGCAGC 12 0 2.4e-004 8.2e+000 # GCGGCTAA TTAGCCGC 8 0 3.9e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 3.0e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 88.44 seconds