# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/seqs-shuffled # positives: 452 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/seqs-centered (Sat Jan 18 17:38:22 PST 2020) # negatives: 452 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/seqs-shuffled (Sat Jan 18 17:38:22 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:46:52 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 0.297 C 0.205 G 0.202 T 0.296 MOTIF CTBGGCCA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 69 1 3.9e-021 1.0e-016 # CTCGGCCA TGGCCGAG 37 0 3.4e-012 8.8e-008 # CTTGGCCA TGGCCAAG 20 1 8.6e-006 2.3e-001 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 5.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 69 E= 1.0e-016 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.536232 0.173913 0.289855 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 SGGTTCRA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCRA TYGAACCS 76 4 6.2e-020 1.6e-015 # GGGTTCGA TCGAACCC 32 1 2.3e-009 6.0e-005 # CGGTTCGA TCGAACCG 24 1 5.8e-007 1.5e-002 # GGGTTCAA TTGAACCC 13 2 3.5e-003 9.0e+001 # CGGTTCAA TTGAACCG 7 0 7.6e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 76 E= 1.6e-015 0.000000 0.407895 0.592105 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 0.263158 0.000000 0.736842 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 82 9 1.4e-017 3.6e-013 # CGCCTTA TAAGGCG 65 6 8.5e-015 2.2e-010 # CGCGTTA TAACGCG 17 3 1.2e-003 3.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 3.6e-013 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 0.792683 0.207317 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 CCRTACA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 79 8 2.0e-017 5.1e-013 # CCGTACA TGTACGG 40 2 9.1e-011 2.3e-006 # CCATACA TGTATGG 45 6 3.8e-009 9.8e-005 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 5.1e-013 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.547368 0.000000 0.452632 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 1.000000 0.000000 0.000000 0.000000 MOTIF CABACGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CABACGC GCGTVTG 46 2 1.4e-012 3.5e-008 # CAGACGC GCGTCTG 16 0 1.3e-005 3.4e-001 # CATACGC GCGTATG 13 0 1.1e-004 2.8e+000 # CACACGC GCGTGTG 17 2 3.2e-004 8.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 3.5e-008 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.369565 0.347826 0.282609 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 GTGATAR DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTGATAR YTATCAC 51 5 1.7e-011 4.3e-007 # GTGATAG CTATCAC 32 2 2.1e-008 5.3e-004 # GTGATAA TTATCAC 19 3 3.7e-004 9.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 4.3e-007 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.365385 0.000000 0.634615 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 2 9.1e-011 2.3e-006 # ATGGCAAC GTTGCCAT 29 1 1.9e-008 4.7e-004 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.3e-006 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 0.707317 0.000000 0.000000 0.292683 0.000000 1.000000 0.000000 0.000000 MOTIF CTCTHCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTCTHCC GGDAGAG 45 4 1.6e-010 3.9e-006 # CTCTACC GGTAGAG 16 1 1.2e-004 3.1e+000 # CTCTCCC GGGAGAG 17 2 3.2e-004 8.1e+000 # CTCTTCC GGAAGAG 12 1 1.6e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 3.9e-006 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 1.000000 0.355556 0.377778 0.000000 0.266667 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TACACTAW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TACACTAW WTAGTGTA 33 1 1.2e-009 2.9e-005 # TACACTAT ATAGTGTA 27 1 7.4e-008 1.9e-003 # TACACTAA TTAGTGTA 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.9e-005 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.205882 0.000000 0.000000 0.794118 MOTIF CRCCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 82 25 1.9e-009 4.8e-005 # CACCCA TGGGTG 56 14 7.6e-008 1.9e-003 # CGCCCA TGGGCG 28 11 4.0e-003 1.0e+002 letter-probability matrix: alength= 4 w= 6 nsites= 100 E= 4.8e-005 0.000000 1.000000 0.000000 0.000000 0.710000 0.000000 0.290000 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 AGCKCGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGCKCGC GCGMGCT 32 1 2.3e-009 5.7e-005 # AGCGCGC GCGCGCT 17 0 6.5e-006 1.6e-001 # AGCTCGC GCGAGCT 15 1 2.3e-004 5.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 5.7e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.531250 0.468750 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 TCAKAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TCAKAA TTMTGA 99 38 8.3e-009 2.0e-004 # TCAGAA TTCTGA 57 19 3.1e-006 7.6e-002 # TCATAA TTATGA 44 20 1.3e-003 3.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 104 E= 2.0e-004 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 0.557692 0.442308 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TACCACTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TACCACTA TAGTGGTA 24 0 4.4e-008 1.1e-003 # TACCACTA TAGTGGTA 24 0 4.4e-008 1.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-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 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 TGGCGCAR DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TGGCGCAR YTGCGCCA 24 0 4.4e-008 1.1e-003 # TGGCGCAA TTGCGCCA 12 0 2.3e-004 5.5e+000 # TGGCGCAG CTGCGCCA 12 0 2.3e-004 5.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-003 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 MOTIF AARAAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AARAAA TTTYTT 209 131 5.7e-008 1.4e-003 # AAAAAA TTTTTT 146 91 2.1e-005 5.1e-001 # AAGAAA TTTCTT 105 58 3.2e-005 7.6e-001 letter-probability matrix: alength= 4 w= 6 nsites= 292 E= 1.4e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.660959 0.000000 0.339041 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 ACTGAGCT DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 0 8.9e-008 2.1e-003 # ACTGAGCT AGCTCAGT 23 0 8.9e-008 2.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.1e-003 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 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 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CACGGTGM DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 22 0 1.8e-007 4.3e-003 # CACGGTGA TCACCGTG 11 0 4.6e-004 1.1e+001 # CACGGTGC GCACCGTG 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.3e-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 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 0.500000 0.500000 0.000000 0.000000 MOTIF ATCSTTG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATCSTTG CAASGAT 19 0 1.6e-006 3.7e-002 # ATCCTTG CAAGGAT 11 0 4.6e-004 1.1e+001 # ATCGTTG CAACGAT 8 0 3.8e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 3.7e-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 0.666667 0.333333 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 # Stopping reason: E-value threshold exceeded # Running time: 56.90 seconds