# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-shuffled # positives: 590 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-centered (Sat Jan 18 22:58:27 PST 2020) # negatives: 590 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-shuffled (Sat Jan 18 22:58:27 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:14:07 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 0.303 C 0.201 G 0.200 T 0.296 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 115 15 1.3e-022 3.9e-018 # GGTTCGA TCGAACC 80 5 7.1e-020 2.2e-015 # GGTTCAA TTGAACC 36 10 5.8e-005 1.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 3.9e-018 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 0.310345 0.000000 0.689655 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 44 1 5.9e-013 1.8e-008 # CTTGGCCA TGGCCAAG 16 0 1.4e-005 4.2e-001 # CTCGGCCA TGGCCGAG 19 1 1.8e-005 5.4e-001 # CTGGGCCA TGGCCCAG 9 0 1.9e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.8e-008 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.431818 0.204545 0.363636 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 BTAAGGCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 47 2 9.1e-013 2.8e-008 # TTAAGGCG CGCCTTAA 28 1 4.1e-008 1.3e-003 # CTAAGGCG CGCCTTAG 11 1 3.1e-003 9.4e+001 # GTAAGGCG CGCCTTAC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.8e-008 0.000000 0.234043 0.170213 0.595745 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 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 MOTIF ARAAAWA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ARAAAWA TWTTTYT 220 112 1.5e-012 4.7e-008 # AGAAAAA TTTTTCT 66 24 2.4e-006 7.4e-002 # AAAAATA TATTTTT 85 40 1.3e-005 4.1e-001 # AAAAAAA TTTTTTT 106 57 2.3e-005 7.1e-001 # AGAAATA TATTTCT 34 10 1.5e-004 4.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 269 E= 4.7e-008 1.000000 0.000000 0.000000 0.000000 0.643123 0.000000 0.356877 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 0.591078 0.000000 0.000000 0.408922 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 35 1 3.3e-010 1.0e-005 # GCGCTACC GGTAGCGC 24 0 4.7e-008 1.4e-003 # GCTCTACC GGTAGAGC 11 1 3.1e-003 9.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.0e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.685714 0.314286 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 MOTIF CCCATDC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 60 14 1.2e-008 3.7e-004 # CCCATTC GAATGGG 20 3 2.2e-004 6.6e+000 # CCCATGC GCATGGG 20 4 6.9e-004 2.1e+001 # CCCATAC GTATGGG 22 7 3.7e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 3.7e-004 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 0.000000 0.000000 0.000000 1.000000 0.354839 0.000000 0.322581 0.322581 0.000000 1.000000 0.000000 0.000000 MOTIF CACTTKCG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 22 0 2.0e-007 5.9e-003 # CACTTTCG CGAAAGTG 12 0 2.3e-004 7.0e+000 # CACTTGCG CGCAAGTG 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.9e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.545455 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGARTCAT DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGARTCAT ATGAYTCT 21 0 4.0e-007 1.2e-002 # AGAGTCAT ATGACTCT 11 0 4.7e-004 1.4e+001 # AGAATCAT ATGATTCT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.476190 0.000000 0.523810 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 0.000000 1.000000 MOTIF GGTCTM DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGTCTM KAGACC 66 22 6.0e-007 1.8e-002 # GGTCTA TAGACC 33 11 5.1e-004 1.5e+001 # GGTCTC GAGACC 33 11 5.1e-004 1.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 69 E= 1.8e-002 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 0.000000 0.000000 1.000000 0.478261 0.521739 0.000000 0.000000 MOTIF ACGKTGCC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACGKTGCC GGCAMCGT 20 0 8.1e-007 2.4e-002 # ACGTTGCC GGCAACGT 12 0 2.3e-004 6.9e+000 # ACGGTGCC GGCACCGT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-002 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 0.400000 0.600000 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 CCGKACA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCGKACA TGTMCGG 23 1 1.2e-006 3.6e-002 # CCGTACA TGTACGG 14 1 4.6e-004 1.4e+001 # CCGGACA TGTCCGG 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 3.6e-002 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 0.360000 0.640000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTCTGRC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTCTGRC GYCAGAC 23 1 1.2e-006 3.6e-002 # GTCTGGC GCCAGAC 14 1 4.6e-004 1.4e+001 # GTCTGAC GTCAGAC 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.6e-002 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 1.000000 0.000000 0.391304 0.000000 0.608696 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 49.95 seconds