# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT3/seqs-shuffled # positives: 894 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT3/seqs-centered (Sat Jan 18 18:53:46 PST 2020) # negatives: 894 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT3/seqs-shuffled (Sat Jan 18 18:53:46 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 19:08:38 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 0.296 C 0.206 G 0.205 T 0.293 MOTIF GGTTCGAB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGAB VTCGAACC 70 5 1.5e-016 5.2e-012 # GGTTCGAC GTCGAACC 21 0 4.2e-007 1.5e-002 # GGTTCGAT ATCGAACC 29 3 1.1e-006 3.8e-002 # GGTTCGAG CTCGAACC 20 2 5.5e-005 2.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 70 E= 5.2e-012 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.285714 0.414286 MOTIF CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 67 7 3.8e-014 1.3e-009 # CGCCTTA TAAGGCG 49 3 2.9e-012 1.0e-007 # CGCGTTA TAACGCG 18 4 2.1e-003 7.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 68 E= 1.3e-009 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 0.720588 0.279412 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 CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 53 3 2.0e-013 7.1e-009 # CTCGGCCA TGGCCGAG 25 1 3.4e-007 1.2e-002 # CTTGGCCA TGGCCAAG 18 2 1.9e-004 6.7e+000 # CTGGGCCA TGGCCCAG 10 0 9.5e-004 3.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 7.1e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.471698 0.188679 0.339623 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 CGGTADC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGGTADC GHTACCG 60 8 1.3e-011 4.7e-007 # CGGTAGC GCTACCG 24 2 4.6e-006 1.6e-001 # CGGTAAC GTTACCG 23 3 3.9e-005 1.4e+000 # CGGTATC GATACCG 14 3 6.2e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 4.7e-007 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 1.000000 0.000000 0.000000 0.000000 0.377049 0.000000 0.393443 0.229508 0.000000 1.000000 0.000000 0.000000 MOTIF SAAGAAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST SAAGAAA TTTCTTS 115 41 2.4e-010 8.5e-006 # GAAGAAA TTTCTTC 60 21 5.4e-006 1.9e-001 # CAAGAAA TTTCTTG 55 20 2.3e-005 8.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 118 E= 8.5e-006 0.000000 0.474576 0.525424 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 TAGTGGTW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 41 3 5.4e-010 1.9e-005 # TAGTGGTA TACCACTA 22 1 2.5e-006 9.0e-002 # TAGTGGTT AACCACTA 19 2 1.0e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.9e-005 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 0.000000 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 0.536585 0.000000 0.000000 0.463415 MOTIF ACCCAYAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCCAYAC GTRTGGGT 37 2 1.0e-009 3.6e-005 # ACCCATAC GTATGGGT 23 2 8.6e-006 3.0e-001 # ACCCACAC GTGTGGGT 14 0 5.8e-005 2.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 3.6e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.384615 0.000000 0.615385 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AARTCAGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AARTCAGA TCTGAYTT 29 1 2.3e-008 8.2e-004 # AAGTCAGA TCTGACTT 19 1 1.8e-005 6.5e-001 # AAATCAGA TCTGATTT 10 0 9.5e-004 3.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 8.2e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.344828 0.000000 0.655172 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAAGATTK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAAGATTK MAATCTTG 32 2 2.7e-008 9.5e-004 # CAAGATTT AAATCTTG 24 2 4.6e-006 1.6e-001 # CAAGATTG CAATCTTG 8 0 3.8e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.5e-004 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 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 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 MOTIF CTATCACR DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 31 2 5.2e-008 1.8e-003 # CTATCACA TGTGATAG 18 1 3.5e-005 1.2e+000 # CTATCACG CGTGATAG 13 1 8.8e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.8e-003 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 0.580645 0.000000 0.419355 0.000000 MOTIF AGAWG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGAWG CWTCT 363 256 6.5e-008 2.3e-003 # AGAAG CTTCT 233 163 4.1e-005 1.4e+000 # AGATG CATCT 176 114 4.3e-005 1.5e+000 letter-probability matrix: alength= 4 w= 5 nsites= 476 E= 2.3e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.592437 0.000000 0.000000 0.407563 0.000000 0.000000 1.000000 0.000000 MOTIF CCGTACAY DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCGTACAY RTGTACGG 28 1 4.6e-008 1.6e-003 # CCGTACAT ATGTACGG 20 1 9.5e-006 3.2e-001 # CCGTACAC GTGTACGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.6e-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 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 0.285714 0.000000 0.714286 MOTIF CTCTMCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 30 2 9.9e-008 3.4e-003 # CTCTCCCA TGGGAGAG 16 1 1.3e-004 4.4e+000 # CTCTACCA TGGTAGAG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.4e-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 0.466667 0.533333 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 CGRTGAAA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGRTGAAA TTTCAYCG 32 3 1.7e-007 5.6e-003 # CGGTGAAA TTTCACCG 22 2 1.6e-005 5.5e-001 # CGATGAAA TTTCATCG 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 5.6e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGCYCTG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGCYCTG CAGRGCT 29 2 1.9e-007 6.4e-003 # AGCTCTG CAGAGCT 17 1 6.8e-005 2.3e+000 # AGCCCTG CAGGGCT 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 6.4e-003 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 0.413793 0.000000 0.586207 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACGATGGS DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACGATGGS SCCATCGT 22 0 2.1e-007 7.1e-003 # ACGATGGC GCCATCGT 11 0 4.7e-004 1.6e+001 # ACGATGGG CCCATCGT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.1e-003 1.000000 0.000000 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 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 0.500000 0.500000 0.000000 MOTIF AGAAARAA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AGAAARAA TTYTTTCT 55 14 2.1e-007 7.2e-003 # AGAAAGAA TTCTTTCT 16 0 1.4e-005 4.8e-001 # AGAAAAAA TTTTTTCT 42 14 9.4e-005 3.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 7.2e-003 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.724138 0.000000 0.275862 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGSCACCG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AGSCACCG CGGTGSCT 21 0 4.2e-007 1.4e-002 # AGGCACCG CGGTGCCT 14 0 5.8e-005 2.0e+000 # AGCCACCG CGGTGGCT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 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 0.000000 0.000000 1.000000 0.000000 MOTIF CACTTKCG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 27 2 6.8e-007 2.3e-002 # CACTTTCG CGAAAGTG 15 1 2.5e-004 8.3e+000 # CACTTGCG CGCAAGTG 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.444444 0.555556 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 109.58 seconds