# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/seqs-shuffled # positives: 825 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/seqs-centered (Sat Jan 18 02:30:40 PST 2020) # negatives: 825 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/seqs-shuffled (Sat Jan 18 02:30:40 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 02:45:53 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 0.197 G 0.203 T 0.302 MOTIF SGGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 59 0 5.9e-019 2.0e-014 # GGGTTCGA TCGAACCC 39 0 1.1e-012 4.0e-008 # CGGTTCGA TCGAACCG 20 0 8.5e-007 2.9e-002 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 2.0e-014 0.000000 0.338983 0.661017 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 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 MOTIF ACTBGGCC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 49 0 8.5e-016 2.9e-011 # ACTTGGCC GGCCAAGT 26 0 1.2e-008 4.2e-004 # ACTCGGCC GGCCGAGT 23 0 1.0e-007 3.5e-003 # ACTGGGCC GGCCCAGT 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 2.9e-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 0.408163 0.142857 0.448980 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 GCCTTAMC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 48 3 5.3e-012 1.8e-007 # GCCTTAAC GTTAAGGC 33 1 1.5e-009 5.2e-005 # GCCTTACC GGTAAGGC 15 2 1.1e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 1.8e-007 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.687500 0.312500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATAGTKTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 46 3 2.0e-011 6.8e-007 # ATAGTGTA TACACTAT 25 0 2.5e-008 8.5e-004 # ATAGTTTA TAAACTAT 21 3 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 6.8e-007 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.543478 0.456522 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAW WTGCCAT 56 8 1.4e-010 4.7e-006 # ATGGCAA TTGCCAT 35 6 1.9e-006 6.5e-002 # ATGGCAT ATGCCAT 22 2 1.6e-005 5.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 4.7e-006 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 0.603448 0.000000 0.000000 0.396552 MOTIF GGWAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GGWAGA TCTWCC 112 39 1.9e-010 6.6e-006 # GGAAGA TCTTCC 69 21 9.3e-008 3.2e-003 # GGTAGA TCTACC 46 18 2.4e-004 8.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 120 E= 6.6e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.000000 0.400000 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 AAGARA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAGARA TYTCTT 256 159 2.3e-008 7.8e-004 # AAGAAA TTTCTT 193 124 1.0e-005 3.4e-001 # AAGAGA TCTCTT 79 45 9.8e-004 3.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 289 E= 7.8e-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 1.000000 0.000000 0.000000 0.000000 0.712803 0.000000 0.287197 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GACTSTTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 25 0 2.5e-008 8.3e-004 # GACTCTTA TAAGAGTC 13 0 1.2e-004 3.9e+000 # GACTGTTA TAACAGTC 12 0 2.3e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.3e-004 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 0.520000 0.480000 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 CCVTACA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCVTACA TGTABGG 54 12 4.9e-008 1.6e-003 # CCGTACA TGTACGG 23 5 4.1e-004 1.4e+001 # CCCTACA TGTAGGG 17 4 3.4e-003 1.2e+002 # CCATACA TGTATGG 16 4 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 1.6e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.298246 0.298246 0.403509 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 ACYGGGG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACYGGGG CCCCRGT 31 2 5.1e-008 1.7e-003 # ACTGGGG CCCCAGT 20 1 9.4e-006 3.2e-001 # ACCGGGG CCCCGGT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 1.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.354839 0.000000 0.645161 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 MOTIF AKACGCG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AKACGCG CGCGTMT 27 1 8.8e-008 3.0e-003 # ATACGCG CGCGTAT 13 0 1.2e-004 3.9e+000 # AGACGCG CGCGTCT 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 3.0e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.518519 0.481481 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 MOTIF TGGTCWA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGGTCWA TWGACCA 59 16 1.7e-007 5.7e-003 # TGGTCTA TAGACCA 28 6 8.4e-005 2.8e+000 # TGGTCAA TTGACCA 31 10 6.3e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 5.7e-003 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 1.000000 0.000000 0.000000 0.524590 0.000000 0.000000 0.475410 1.000000 0.000000 0.000000 0.000000 MOTIF AGCGCSC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGCGCSC GSGCGCT 29 2 1.9e-007 6.2e-003 # AGCGCGC GCGCGCT 14 0 5.8e-005 1.9e+000 # AGCGCCC GGGCGCT 15 2 1.1e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 6.2e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.517241 0.482759 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 31 3 3.0e-007 1.0e-002 # GGCTATCA TGATAGCC 18 2 1.9e-004 6.2e+000 # GGTTATCA TGATAACC 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.0e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.580645 0.000000 0.419355 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 MOTIF ACTTCWAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTTCWAA TTWGAAGT 25 1 3.4e-007 1.1e-002 # ACTTCAAA TTTGAAGT 12 0 2.3e-004 7.8e+000 # ACTTCTAA TTAGAAGT 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.480000 0.000000 0.000000 0.520000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCTTTGK DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GCTTTGK MCAAAGC 53 14 5.5e-007 1.8e-002 # GCTTTGG CCAAAGC 26 5 8.4e-005 2.8e+000 # GCTTTGT ACAAAGC 30 9 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 56 E= 1.8e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.464286 0.535714 MOTIF ACTGAGCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 20 0 8.5e-007 2.8e-002 # ACTGAGCT AGCTCAGT 20 0 8.5e-007 2.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-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 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 # Stopping reason: E-value threshold exceeded # Running time: 90.31 seconds