# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/seqs-shuffled # positives: 762 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/seqs-centered (Sat Jan 18 19:54:05 PST 2020) # negatives: 762 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/seqs-shuffled (Sat Jan 18 19:54:05 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 20:09:30 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 0.301 C 0.197 G 0.200 T 0.303 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 115 13 1.7e-023 5.7e-019 # GGTTCGA TCGAACC 85 4 4.3e-022 1.4e-017 # GGTTCAA TTGAACC 31 9 2.9e-004 9.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 5.7e-019 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 0.267241 0.000000 0.732759 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF BTAAGGCG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 60 1 8.3e-018 2.7e-013 # TTAAGGCG CGCCTTAA 36 1 1.9e-010 6.0e-006 # CTAAGGCG CGCCTTAG 14 0 5.7e-005 1.9e+000 # GTAAGGCG CGCCTTAC 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 2.7e-013 0.000000 0.233333 0.166667 0.600000 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 CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 67 6 5.6e-015 1.8e-010 # CTCGGCCA TGGCCGAG 32 2 2.6e-008 8.4e-004 # CTTGGCCA TGGCCAAG 23 3 3.9e-005 1.3e+000 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 5.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 1.8e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.477612 0.179104 0.343284 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 SAAGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 409 272 1.1e-012 3.4e-008 # CAAGA TCTTG 228 149 1.7e-006 5.6e-002 # GAAGA TCTTC 237 157 1.8e-006 5.8e-002 letter-probability matrix: alength= 4 w= 5 nsites= 581 E= 3.4e-008 0.000000 0.500861 0.499139 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 MOTIF CTATCACR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 38 0 2.3e-012 7.1e-008 # CTATCACA TGTGATAG 20 0 8.4e-007 2.6e-002 # CTATCACG CGTGATAG 18 0 3.4e-006 1.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 7.1e-008 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 0.526316 0.000000 0.473684 0.000000 MOTIF CGGTABC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGGTABC GVTACCG 51 4 4.9e-012 1.5e-007 # CGGTAGC GCTACCG 28 3 1.9e-006 5.9e-002 # CGGTATC GATACCG 11 0 4.7e-004 1.5e+001 # CGGTACC GGTACCG 12 1 1.6e-003 5.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 1.5e-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 0.000000 0.235294 0.549020 0.215686 0.000000 1.000000 0.000000 0.000000 MOTIF CCCATDC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 65 10 9.2e-012 2.9e-007 # CCCATGC GCATGGG 19 0 1.7e-006 5.3e-002 # CCCATAC GTATGGG 31 6 1.7e-005 5.2e-001 # CCCATTC GAATGGG 20 4 7.1e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 2.9e-007 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 0.000000 0.000000 1.000000 0.480000 0.000000 0.253333 0.266667 0.000000 1.000000 0.000000 0.000000 MOTIF CGRTGAAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGRTGAAA TTTCAYCG 33 0 8.2e-011 2.5e-006 # CGGTGAAA TTTCACCG 20 0 8.4e-007 2.6e-002 # CGATGAAA TTTCATCG 13 0 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.5e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.411765 0.000000 0.588235 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 TCYGTACA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TCYGTACA TGTACRGA 30 0 7.0e-010 2.1e-005 # TCCGTACA TGTACGGA 24 0 5.0e-008 1.5e-003 # TCTGTACA TGTACAGA 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.1e-005 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.764706 0.000000 0.235294 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 MOTIF ACACTATA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 25 0 2.4e-008 7.5e-004 # ACACTATA TATAGTGT 25 0 2.4e-008 7.5e-004 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.5e-004 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTARACC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACTARACC GGTYTAGT 32 2 2.6e-008 8.0e-004 # ACTAGACC GGTCTAGT 18 0 3.4e-006 1.1e-001 # ACTAAACC GGTTTAGT 14 2 2.0e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.0e-004 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 0.437500 0.000000 0.562500 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 ATGGCAWC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 42 6 3.3e-008 1.0e-003 # ATGGCAAC GTTGCCAT 30 4 2.5e-006 7.6e-002 # ATGGCATC GATGCCAT 12 2 6.3e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.0e-003 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 0.714286 0.000000 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 MOTIF GCTCTMCC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCTCTMCC GGKAGAGC 27 1 8.7e-008 2.7e-003 # GCTCTACC GGTAGAGC 16 1 1.3e-004 3.9e+000 # GCTCTCCC GGGAGAGC 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.7e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.592593 0.407407 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCTTCY DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCTTCY RGAAGC 86 32 1.2e-007 3.8e-003 # GCTTCT AGAAGC 42 13 4.3e-005 1.3e+000 # GCTTCC GGAAGC 46 20 7.4e-004 2.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 95 E= 3.8e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.505263 0.000000 0.494737 MOTIF ACCCAMAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACCCAMAC GTKTGGGT 24 1 6.5e-007 2.0e-002 # ACCCACAC GTGTGGGT 13 0 1.2e-004 3.5e+000 # ACCCAAAC GTTTGGGT 11 1 3.1e-003 9.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.0e-002 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 0.423077 0.576923 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACGCSACA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACGCSACA TGTSGCGT 20 0 8.4e-007 2.5e-002 # ACGCGACA TGTCGCGT 11 0 4.7e-004 1.4e+001 # ACGCCACA TGTGGCGT 9 0 1.9e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.5e-002 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 0.450000 0.550000 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 MOTIF GCYAGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GCYAGA TCTRGC 76 29 1.2e-006 3.5e-002 # GCCAGA TCTGGC 48 17 5.5e-005 1.7e+000 # GCTAGA TCTAGC 30 12 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 78 E= 3.5e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.615385 0.000000 0.384615 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 AGTCAKAC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 2 1.3e-006 3.8e-002 # AGTCATAC GTATGACT 14 1 4.6e-004 1.4e+001 # AGTCAGAC GTCTGACT 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.8e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.461538 0.538462 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTGAGCTA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 23 1 1.3e-006 3.8e-002 # CTGAGCTA TAGCTCAG 23 1 1.3e-006 3.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.8e-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 # Stopping reason: E-value threshold exceeded # Running time: 91.45 seconds