# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ZAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ZAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ZAP1/seqs-shuffled # positives: 519 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ZAP1/seqs-centered (Fri Jan 17 21:51:41 PST 2020) # negatives: 519 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ZAP1/seqs-shuffled (Fri Jan 17 21:51:41 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:02:31 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 0.204 G 0.204 T 0.295 MOTIF GRDTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRDTCGAA TTCGAHYC 113 3 4.6e-033 1.3e-028 # GAATCGAA TTCGATTC 29 0 1.2e-009 3.4e-005 # GGATCGAA TTCGATCC 29 0 1.2e-009 3.4e-005 # GAGTCGAA TTCGACTC 21 1 4.5e-006 1.2e-001 # GGGTCGAA TTCGACCC 15 0 2.8e-005 7.5e-001 # GATTCGAA TTCGAATC 12 1 1.6e-003 4.4e+001 # GGTTCGAA TTCGAACC 12 1 1.6e-003 4.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 113 E= 1.3e-028 0.000000 0.000000 1.000000 0.000000 0.522124 0.000000 0.477876 0.000000 0.513274 0.000000 0.318584 0.168142 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 MOTIF TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 81 4 2.5e-021 6.9e-017 # TGTATGGG CCCATACA 37 0 3.7e-012 1.0e-007 # TGTACGGA TCCGTACA 32 2 2.2e-008 6.1e-004 # TGTACGGG CCCGTACA 11 0 4.6e-004 1.3e+001 # TGTATGGA TCCATACA 12 2 6.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 94 E= 6.9e-017 0.000000 0.000000 0.000000 1.000000 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 0.468085 0.000000 0.531915 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.489362 0.000000 0.510638 0.000000 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 88 12 4.5e-017 1.2e-012 # AGTGGTT AACCACT 60 7 1.6e-012 4.3e-008 # AGTGGTA TACCACT 40 5 2.2e-008 5.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 103 E= 1.2e-012 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 0.388350 0.000000 0.000000 0.611650 MOTIF RAAAAAR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RAAAAAR YTTTTTY 206 98 9.4e-014 2.5e-009 # GAAAAAA TTTTTTC 93 40 5.2e-007 1.4e-002 # AAAAAAA TTTTTTT 126 65 6.5e-007 1.7e-002 # AAAAAAG CTTTTTT 80 46 8.1e-004 2.2e+001 # GAAAAAG CTTTTTC 31 14 6.9e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 267 E= 2.5e-009 0.640449 0.000000 0.359551 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 1.000000 0.000000 0.000000 0.000000 0.647940 0.000000 0.352060 0.000000 MOTIF CRCCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 99 28 5.5e-012 1.4e-007 # CACCCA TGGGTG 64 18 5.5e-008 1.5e-003 # CGCCCA TGGGCG 38 11 4.9e-005 1.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 1.4e-007 0.000000 1.000000 0.000000 0.000000 0.663866 0.000000 0.336134 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 CAACTKGG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 40 0 4.2e-013 1.1e-008 # CAACTTGG CCAAGTTG 29 0 1.2e-009 3.2e-005 # CAACTGGG CCCAGTTG 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.1e-008 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 0.000000 1.000000 0.000000 0.000000 0.275000 0.725000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AASGCG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AASGCG CGCSTT 99 30 3.1e-011 7.9e-007 # AAGGCG CGCCTT 66 21 2.4e-007 6.3e-003 # AACGCG CGCGTT 33 9 1.0e-004 2.6e+000 letter-probability matrix: alength= 4 w= 6 nsites= 100 E= 7.9e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.330000 0.670000 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 CGCGCTHC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGCGCTHC GDAGCGCG 32 1 2.5e-009 6.3e-005 # CGCGCTAC GTAGCGCG 24 0 4.5e-008 1.2e-003 # CGCGCTTC GAAGCGCG 11 1 3.0e-003 7.7e+001 # CGCGCTCC GGAGCGCG 8 0 3.8e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.3e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.562500 0.125000 0.000000 0.312500 0.000000 1.000000 0.000000 0.000000 MOTIF AGAYCGGG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGGG CCCGRTCT 30 1 9.9e-009 2.5e-004 # AGATCGGG CCCGATCT 18 1 3.3e-005 8.5e-001 # AGACCGGG CCCGGTCT 12 0 2.3e-004 5.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.5e-004 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 0.400000 0.000000 0.600000 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 1.000000 0.000000 MOTIF CCATCGTK DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCATCGTK MACGATGG 26 0 1.1e-008 2.7e-004 # CCATCGTG CACGATGG 13 0 1.1e-004 2.9e+000 # CCATCGTT AACGATGG 13 0 1.1e-004 2.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.7e-004 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 0.000000 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 0.500000 0.500000 MOTIF GTGATAGY DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 29 1 2.0e-008 5.0e-004 # GTGATAGC GCTATCAC 16 0 1.4e-005 3.4e-001 # GTGATAGT ACTATCAC 13 1 8.6e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.0e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.551724 0.000000 0.448276 MOTIF CTCTMCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 25 0 2.2e-008 5.6e-004 # CTCTCCCA TGGGAGAG 16 0 1.4e-005 3.4e-001 # CTCTACCA TGGTAGAG 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 5.6e-004 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 0.360000 0.640000 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 GTTCGAGY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTTCGAGY RCTCGAAC 22 0 1.9e-007 4.8e-003 # GTTCGAGC GCTCGAAC 14 0 5.6e-005 1.4e+000 # GTTCGAGT ACTCGAAC 8 0 3.8e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.8e-003 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.636364 0.000000 0.363636 MOTIF ACRGATG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACRGATG CATCYGT 25 1 3.1e-007 7.7e-003 # ACGGATG CATCCGT 16 0 1.4e-005 3.4e-001 # ACAGATG CATCTGT 10 1 5.7e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 7.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.384615 0.000000 0.615385 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCAARAGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CCAARAGA TCTYTTGG 25 1 3.1e-007 7.7e-003 # CCAAGAGA TCTCTTGG 14 1 4.5e-004 1.1e+001 # CCAAAAGA TCTTTTGG 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.7e-003 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 0.000000 0.440000 0.000000 0.560000 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 MOTIF TAATCAKA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TAATCAKA TMTGATTA 25 1 3.1e-007 7.7e-003 # TAATCATA TATGATTA 14 1 4.5e-004 1.1e+001 # TAATCAGA TCTGATTA 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.7e-003 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.440000 0.560000 1.000000 0.000000 0.000000 0.000000 MOTIF AYTGCGC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AYTGCGC GCGCART 28 2 3.1e-007 7.9e-003 # ATTGCGC GCGCAAT 16 1 1.2e-004 3.1e+000 # ACTGCGC GCGCAGT 12 1 1.6e-003 4.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 7.9e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTWGACC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 28 2 3.1e-007 7.9e-003 # CTAGACC GGTCTAG 13 0 1.1e-004 2.8e+000 # CTTGACC GGTCAAG 15 2 1.1e-003 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 7.9e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.464286 0.000000 0.000000 0.535714 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 MOTIF CACGGYG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 37 6 5.1e-007 1.3e-002 # CACGGTG CACCGTG 25 5 1.3e-004 3.3e+000 # CACGGCG CGCCGTG 12 1 1.6e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.3e-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 0.000000 1.000000 0.000000 0.000000 0.324324 0.000000 0.675676 0.000000 0.000000 1.000000 0.000000 MOTIF GGAWTTGA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GGAWTTGA TCAAWTCC 32 4 6.6e-007 1.7e-002 # GGAATTGA TCAATTCC 19 2 9.7e-005 2.4e+000 # GGATTTGA TCAAATCC 13 2 3.5e-003 8.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 1.7e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.593750 0.000000 0.000000 0.406250 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGTTGWA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST TGTTGWA TWCAACA 43 10 1.6e-006 4.0e-002 # TGTTGTA TACAACA 21 3 1.2e-004 3.0e+000 # TGTTGAA TTCAACA 22 7 3.6e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 4.0e-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 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 MOTIF AGACTGWA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST AGACTGWA TWCAGTCT 19 0 1.6e-006 4.0e-002 # AGACTGTA TACAGTCT 10 0 9.3e-004 2.3e+001 # AGACTGAA TTCAGTCT 9 0 1.9e-003 4.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.0e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.473684 0.000000 0.000000 0.526316 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 71.84 seconds