# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NRG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NRG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NRG1/seqs-shuffled # positives: 688 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NRG1/seqs-centered (Sat Jan 18 08:44:56 PST 2020) # negatives: 688 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NRG1/seqs-shuffled (Sat Jan 18 08:44:56 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 09:01:04 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 0.289 C 0.211 G 0.210 T 0.290 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 128 8 9.0e-032 3.0e-027 # GGTTCGA TCGAACC 103 4 7.2e-028 2.4e-023 # GGATCGA TCGATCC 33 4 4.0e-007 1.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 128 E= 3.0e-027 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.234375 0.000000 0.000000 0.765625 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 BTAAGGCG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 56 2 2.0e-015 6.7e-011 # TTAAGGCG CGCCTTAA 35 1 3.5e-010 1.2e-005 # GTAAGGCG CGCCTTAC 10 0 9.4e-004 3.2e+001 # CTAAGGCG CGCCTTAG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 56 E= 6.7e-011 0.000000 0.196429 0.178571 0.625000 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-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAWA TWTTTYT 253 128 2.7e-014 9.0e-010 # AAAAAAA TTTTTTT 141 63 1.8e-009 6.0e-005 # AGAAAAA TTTTTCT 92 35 5.9e-008 2.0e-003 # AGAAATA TATTTCT 31 10 6.2e-004 2.1e+001 # AAAAATA TATTTTT 75 43 1.4e-003 4.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 305 E= 9.0e-010 1.000000 0.000000 0.000000 0.000000 0.649180 0.000000 0.350820 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 0.688525 0.000000 0.000000 0.311475 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 52 3 3.2e-013 1.0e-008 # CTTGGCCA TGGCCAAG 18 0 3.4e-006 1.1e-001 # CTCGGCCA TGGCCGAG 24 2 4.4e-006 1.5e-001 # CTGGGCCA TGGCCCAG 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 1.0e-008 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.461538 0.192308 0.346154 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 ACCACTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCACTA TAGTGGT 49 4 1.7e-011 5.5e-007 # ACCACTA TAGTGGT 49 4 1.7e-011 5.5e-007 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 5.5e-007 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CDCCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CDCCCA TGGGHG 141 60 3.2e-010 1.1e-005 # CGCCCA TGGGCG 56 20 1.3e-005 4.4e-001 # CACCCA TGGGTG 61 26 6.9e-005 2.3e+000 # CTCCCA TGGGAG 33 16 9.5e-003 3.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 162 E= 1.1e-005 0.000000 1.000000 0.000000 0.000000 0.450617 0.000000 0.345679 0.203704 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 GMTACCGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 34 1 7.1e-010 2.3e-005 # GCTACCGA TCGGTAGC 27 1 8.5e-008 2.8e-003 # GATACCGA TCGGTATC 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.3e-005 0.000000 0.000000 1.000000 0.000000 0.205882 0.794118 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 CTATCACR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 25 0 2.4e-008 7.8e-004 # CTATCACG CGTGATAG 14 0 5.7e-005 1.9e+000 # CTATCACA TGTGATAG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.8e-004 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 0.440000 0.000000 0.560000 0.000000 MOTIF CAWAACCG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAWAACCG CGGTTWTG 30 2 9.3e-008 3.0e-003 # CAAAACCG CGGTTTTG 15 1 2.4e-004 7.9e+000 # CATAACCG CGGTTATG 15 1 2.4e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.0e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 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 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCGTGSA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 43 8 2.2e-007 7.1e-003 # CCGTGCA TGCACGG 18 2 1.8e-004 6.0e+000 # CCGTGGA TCCACGG 25 6 3.9e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 7.1e-003 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 0.409091 0.590909 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGTTGKA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TGTTGKA TMCAACA 49 11 2.2e-007 7.1e-003 # TGTTGTA TACAACA 25 5 1.4e-004 4.5e+000 # TGTTGGA TCCAACA 25 6 3.9e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 7.1e-003 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 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 26 2 1.2e-006 4.0e-002 # ATCGTGAG CTCACGAT 16 1 1.3e-004 4.1e+000 # ATCTTGAG CTCAAGAT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-002 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 0.615385 0.384615 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GMTTAACA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GMTTAACA TGTTAAKC 26 2 1.2e-006 4.0e-002 # GATTAACA TGTTAATC 13 1 8.7e-004 2.8e+001 # GCTTAACA TGTTAAGC 13 1 8.7e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-002 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 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 1.000000 0.000000 0.000000 0.000000 MOTIF AACAARGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AACAARGC GCYTTGTT 23 1 1.3e-006 4.0e-002 # AACAAGGC GCCTTGTT 11 0 4.7e-004 1.5e+001 # AACAAAGC GCTTTGTT 12 1 1.6e-003 5.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.0e-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 1.000000 0.000000 0.000000 0.000000 0.521739 0.000000 0.478261 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 63.57 seconds