# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ZAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ZAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ZAP1/seqs-shuffled # positives: 860 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ZAP1/seqs-centered (Sat Jan 18 12:36:11 PST 2020) # negatives: 860 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ZAP1/seqs-shuffled (Sat Jan 18 12:36:11 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 12:52:44 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 0.317 C 0.184 G 0.181 T 0.318 MOTIF TAAGGCR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 85 6 4.3e-020 1.4e-015 # TAAGGCG CGCCTTA 63 3 2.2e-016 7.2e-012 # TAAGGCA TGCCTTA 24 3 2.2e-005 7.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 87 E= 1.4e-015 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 0.275862 0.000000 0.724138 0.000000 MOTIF TCGAACCB DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 69 3 3.6e-018 1.2e-013 # TCGAACCC GGGTTCGA 32 1 3.0e-009 9.7e-005 # TCGAACCG CGGTTCGA 25 2 2.4e-006 7.9e-002 # TCGAACCT AGGTTCGA 12 0 2.3e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 69 E= 1.2e-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 0.463768 0.362319 0.173913 MOTIF CCCANACA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCCANACA TGTNTGGG 88 12 1.6e-016 5.3e-012 # CCCATACA TGTATGGG 39 3 1.9e-009 6.2e-005 # CCCACACA TGTGTGGG 34 8 2.8e-005 9.1e-001 # CCCAAACA TGTTTGGG 13 2 3.6e-003 1.2e+002 # CCCAGACA TGTCTGGG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 116 E= 5.3e-012 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 0.112069 0.491379 0.060345 0.336207 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 ACTBGGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 55 1 3.3e-016 1.1e-011 # ACTTGGCC GGCCAAGT 29 0 1.5e-009 4.7e-005 # ACTCGGCC GGCCGAGT 24 0 5.1e-008 1.6e-003 # ACTGGGCC GGCCCAGT 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 1.1e-011 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 0.381818 0.200000 0.418182 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 MOTIF CCGTACAY DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCGTACAY RTGTACGG 45 2 4.7e-012 1.5e-007 # CCGTACAT ATGTACGG 32 1 3.0e-009 9.6e-005 # CCGTACAC GTGTACGG 13 1 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 1.5e-007 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 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 0.276596 0.000000 0.723404 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 47 3 1.1e-011 3.4e-007 # GCGCTACC GGTAGCGC 30 1 1.2e-008 3.7e-004 # GCTCTACC GGTAGAGC 17 2 3.4e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 3.4e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.638298 0.361702 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 AGTGGTTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTW WAACCACT 49 4 1.9e-011 6.2e-007 # AGTGGTTA TAACCACT 30 1 1.2e-008 3.7e-004 # AGTGGTTT AAACCACT 19 3 4.0e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 6.2e-007 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.612245 0.000000 0.000000 0.387755 MOTIF AYTRCGCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AYTRCGCC GGCGYART 44 1 7.6e-013 2.4e-008 # ATTGCGCC GGCGCAAT 13 0 1.2e-004 3.7e+000 # ACTGCGCC GGCGCAGT 12 0 2.3e-004 7.5e+000 # ACTACGCC GGCGTAGT 9 0 1.9e-003 6.1e+001 # ATTACGCC GGCGTAAT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.4e-008 1.000000 0.000000 0.000000 0.000000 0.000000 0.477273 0.000000 0.522727 0.000000 0.000000 0.000000 1.000000 0.431818 0.000000 0.568182 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 MOTIF RAARAAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RAARAAAA TTTTYTTY 170 82 1.1e-009 3.5e-005 # GAAGAAAA TTTTCTTC 31 6 1.7e-005 5.5e-001 # GAAAAAAA TTTTTTTC 69 32 9.7e-005 3.1e+000 # AAAGAAAA TTTTCTTT 58 25 1.4e-004 4.3e+000 # AAAAAAAA TTTTTTTT 85 45 1.7e-004 5.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 202 E= 3.5e-005 0.628713 0.000000 0.371287 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.599010 0.000000 0.400990 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 1.000000 0.000000 0.000000 0.000000 MOTIF GCCGTKAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCCGTKAC GTMACGGC 24 0 5.1e-008 1.6e-003 # GCCGTTAC GTAACGGC 17 0 7.0e-006 2.2e-001 # GCCGTGAC GTCACGGC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.291667 0.708333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGGAGAY DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GTGGAGAY RTCTCCAC 24 0 5.1e-008 1.6e-003 # GTGGAGAT ATCTCCAC 13 0 1.2e-004 3.7e+000 # GTGGAGAC GTCTCCAC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.6e-003 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 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 0.440000 0.000000 0.560000 MOTIF ACACSC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACACSC GSGTGT 92 35 7.9e-008 2.5e-003 # ACACCC GGGTGT 60 25 6.4e-005 2.0e+000 # ACACGC GCGTGT 32 11 8.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 122 E= 2.5e-003 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 0.737705 0.262295 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGCGWGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 23 0 1.0e-007 3.2e-003 # AAGCGTGA TCACGCTT 14 0 5.8e-005 1.8e+000 # AAGCGAGA TCTCGCTT 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-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 0.391304 0.000000 0.000000 0.608696 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCAYAAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCCAYAAC GTTRTGGC 23 0 1.0e-007 3.2e-003 # GCCATAAC GTTATGGC 13 0 1.2e-004 3.7e+000 # GCCACAAC GTTGTGGC 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.434783 0.000000 0.565217 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 RAAATA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST RAAATA TATTTY 337 240 4.5e-007 1.4e-002 # AAAATA TATTTT 235 173 2.7e-004 8.4e+000 # GAAATA TATTTC 131 85 5.1e-004 1.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 408 E= 1.4e-002 0.669118 0.000000 0.330882 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GAGACCW DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GAGACCW WGGTCTC 27 2 6.8e-007 2.1e-002 # GAGACCA TGGTCTC 15 1 2.5e-004 7.6e+000 # GAGACCT AGGTCTC 12 1 1.7e-003 5.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 MOTIF TGTTGWA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST TGTTGWA TWCAACA 75 28 1.0e-006 3.2e-002 # TGTTGTA TACAACA 36 11 1.4e-004 4.5e+000 # TGTTGAA TTCAACA 40 18 2.3e-003 7.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 3.2e-002 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 0.519481 0.000000 0.000000 0.480519 1.000000 0.000000 0.000000 0.000000 MOTIF GTATGAC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GTATGAC GTCATAC 26 2 1.3e-006 4.0e-002 # GTATGAC GTCATAC 26 2 1.3e-006 4.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 4.0e-002 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTAGACC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACTAGACC GGTCTAGT 23 1 1.3e-006 4.0e-002 # ACTAGACC GGTCTAGT 23 1 1.3e-006 4.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.0e-002 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 0.000000 0.000000 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 103.00 seconds