# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/seqs-shuffled # positives: 489 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/seqs-centered (Sat Jan 18 12:25:25 PST 2020) # negatives: 489 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/seqs-shuffled (Sat Jan 18 12:25:25 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 12:35:11 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 0.298 C 0.203 G 0.204 T 0.294 MOTIF CCAYAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCAYAC GTRTGG 111 23 2.6e-017 7.2e-013 # CCACAC GTGTGG 55 9 5.7e-010 1.6e-005 # CCATAC GTATGG 61 14 5.7e-009 1.6e-004 letter-probability matrix: alength= 4 w= 6 nsites= 131 E= 7.2e-013 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 0.442748 0.000000 0.557252 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TCGAACCB DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 61 2 3.4e-017 9.1e-013 # TCGAACCC GGGTTCGA 29 0 1.2e-009 3.3e-005 # TCGAACCG CGGTTCGA 25 2 2.2e-006 5.9e-002 # TCGAACCT AGGTTCGA 7 0 7.6e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 61 E= 9.1e-013 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 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 0.475410 0.409836 0.114754 MOTIF TBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TBGGCCA TGGCCVA 75 7 6.7e-017 1.8e-012 # TCGGCCA TGGCCGA 39 2 1.9e-010 5.2e-006 # TTGGCCA TGGCCAA 21 3 1.2e-004 3.2e+000 # TGGGCCA TGGCCCA 16 2 6.0e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 1.8e-012 0.000000 0.000000 0.000000 1.000000 0.000000 0.513158 0.210526 0.276316 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-4 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 58 3 3.2e-015 8.7e-011 # TTAAGGCG CGCCTTAA 34 1 6.0e-010 1.6e-005 # CTAAGGCG CGCCTTAG 13 1 8.5e-004 2.3e+001 # GTAAGGCG CGCCTTAC 11 1 3.0e-003 8.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 8.7e-011 0.000000 0.224138 0.189655 0.586207 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 ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 38 0 1.7e-012 4.6e-008 # ATGGCAAC GTTGCCAT 27 0 5.2e-009 1.4e-004 # ATGGCATC GATGCCAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 4.6e-008 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 0.710526 0.000000 0.000000 0.289474 0.000000 1.000000 0.000000 0.000000 MOTIF ACCACTAV DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCACTAV BTAGTGGT 40 2 9.7e-011 2.6e-006 # ACCACTAC GTAGTGGT 14 0 5.6e-005 1.5e+000 # ACCACTAA TTAGTGGT 18 2 1.8e-004 4.7e+000 # ACCACTAG CTAGTGGT 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.6e-006 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 0.450000 0.350000 0.200000 0.000000 MOTIF ATCCGTRC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATCCGTRC GYACGGAT 35 1 3.0e-010 7.9e-006 # ATCCGTAC GTACGGAT 26 0 1.1e-008 2.8e-004 # ATCCGTGC GCACGGAT 11 1 3.0e-003 8.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 7.9e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.692308 0.000000 0.307692 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 28 0 2.5e-009 6.7e-005 # CTATCACA TGTGATAG 15 0 2.7e-005 7.3e-001 # CTATCACG CGTGATAG 13 0 1.1e-004 3.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 6.7e-005 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 0.535714 0.000000 0.464286 0.000000 MOTIF GCKCTACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 35 2 2.9e-009 7.7e-005 # GCGCTACC GGTAGCGC 23 1 1.2e-006 3.1e-002 # GCTCTACC GGTAGAGC 12 1 1.6e-003 4.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 7.7e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.657143 0.342857 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 CACGGTGM DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 25 0 2.2e-008 5.8e-004 # CACGGTGA TCACCGTG 14 0 5.6e-005 1.5e+000 # CACGGTGC GCACCGTG 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 5.8e-004 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 0.560000 0.440000 0.000000 0.000000 MOTIF AAGTGRT DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAGTGRT AYCACTT 37 4 2.9e-008 7.7e-004 # AAGTGGT ACCACTT 24 2 4.1e-006 1.1e-001 # AAGTGAT ATCACTT 14 2 1.9e-003 5.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 7.7e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.368421 0.000000 0.631579 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AAGCGWGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 23 0 9.1e-008 2.4e-003 # AAGCGTGA TCACGCTT 13 0 1.1e-004 3.0e+000 # AAGCGAGA TCTCGCTT 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.4e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.434783 0.000000 0.000000 0.565217 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTCTCSCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSCA TGSGAGAG 22 0 1.9e-007 4.9e-003 # CTCTCCCA TGGGAGAG 15 0 2.7e-005 7.2e-001 # CTCTCGCA TGCGAGAG 7 0 7.6e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.9e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.681818 0.318182 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGCGAS DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CACGCGAS STCGCGTG 21 0 3.8e-007 1.0e-002 # CACGCGAC GTCGCGTG 11 0 4.6e-004 1.2e+001 # CACGCGAG CTCGCGTG 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.0e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.523810 0.476190 0.000000 MOTIF CTGAGCTA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 20 0 7.8e-007 2.1e-002 # CTGAGCTA TAGCTCAG 20 0 7.8e-007 2.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.1e-002 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 1.000000 0.000000 0.000000 0.000000 MOTIF TTGTTGWA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TTGTTGWA TWCAACAA 23 1 1.2e-006 3.1e-002 # TTGTTGAA TTCAACAA 14 1 4.5e-004 1.2e+001 # TTGTTGTA TACAACAA 9 0 1.9e-003 4.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.1e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.608696 0.000000 0.000000 0.391304 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 54.72 seconds