# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--GAL11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--GAL11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--GAL11/seqs-shuffled # positives: 721 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--GAL11/seqs-centered (Sat Jan 18 18:11:02 PST 2020) # negatives: 721 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--GAL11/seqs-shuffled (Sat Jan 18 18:11:02 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:27:20 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 0.209 G 0.204 T 0.291 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 109 15 1.6e-020 5.3e-016 # GGTTCGA TCGAACC 87 10 1.0e-017 3.4e-013 # AGTTCGA TCGAACT 29 5 1.6e-005 5.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 109 E= 5.3e-016 0.238532 0.000000 0.761468 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 ACTYGGCC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACTYGGCC GGCCRAGT 42 0 1.2e-013 4.2e-009 # ACTCGGCC GGCCGAGT 24 0 4.9e-008 1.7e-003 # ACTTGGCC GGCCAAGT 24 0 4.9e-008 1.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 4.2e-009 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 0.547619 0.000000 0.452381 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 49 2 2.7e-013 9.1e-009 # GCCTTAAC GTTAAGGC 38 2 4.8e-010 1.6e-005 # GCCTTACC GGTAAGGC 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 9.1e-009 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 0.775510 0.224490 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTWGACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 38 1 4.5e-011 1.5e-006 # CTTGACC GGTCAAG 19 0 1.7e-006 5.7e-002 # CTAGACC GGTCTAG 19 1 1.8e-005 6.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.5e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 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 CCAAVAGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCAAVAGA TCTBTTGG 47 4 6.3e-011 2.1e-006 # CCAACAGA TCTGTTGG 14 0 5.7e-005 1.9e+000 # CCAAGAGA TCTCTTGG 16 1 1.3e-004 4.3e+000 # CCAAAAGA TCTTTTGG 17 3 1.2e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.1e-006 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 0.361702 0.297872 0.340426 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 TTTCTTB DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 156 69 1.4e-010 4.8e-006 # TTTCTTC GAAGAAA 69 22 1.8e-007 6.1e-003 # TTTCTTT AAAGAAA 63 33 1.0e-003 3.4e+001 # TTTCTTG CAAGAAA 40 17 1.3e-003 4.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 175 E= 4.8e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.394286 0.228571 0.377143 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 30 0 6.8e-010 2.3e-005 # ATGGCAAC GTTGCCAT 19 0 1.7e-006 5.7e-002 # ATGGCATC GATGCCAT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.3e-005 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 0.633333 0.000000 0.000000 0.366667 0.000000 1.000000 0.000000 0.000000 MOTIF AAAWATAW DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AAAWATAW WTATWTTT 84 25 1.7e-009 5.5e-005 # AAAAATAT ATATTTTT 28 7 2.2e-004 7.3e+000 # AAAAATAA TTATTTTT 36 12 2.9e-004 9.8e+000 # AAATATAA TTATATTT 19 4 1.2e-003 4.0e+001 # AAATATAT ATATATTT 13 2 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 91 E= 5.5e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.670330 0.000000 0.000000 0.329670 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.626374 0.000000 0.000000 0.373626 MOTIF GCKCTACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 34 3 4.4e-008 1.5e-003 # GCGCTACC GGTAGCGC 22 2 1.6e-005 5.2e-001 # GCTCTACC GGTAGAGC 12 1 1.6e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.647059 0.352941 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 CTCTCSC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSC GSGAGAG 27 1 8.6e-008 2.9e-003 # CTCTCCC GGGAGAG 16 0 1.4e-005 4.7e-001 # CTCTCGC GCGAGAG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.9e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.592593 0.407407 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGKGTAAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGKGTAAC GTTACMCT 21 0 4.1e-007 1.4e-002 # AGTGTAAC GTTACACT 13 0 1.2e-004 3.8e+000 # AGGGTAAC GTTACCCT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 1.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.409091 0.590909 0.000000 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 MOTIF CGCGGGSA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 24 1 6.5e-007 2.2e-002 # CGCGGGGA TCCCCGCG 15 1 2.4e-004 8.1e+000 # CGCGGGCA TGCCCGCG 9 0 1.9e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGCGWGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 20 0 8.3e-007 2.8e-002 # AAGCGAGA TCTCGCTT 11 0 4.7e-004 1.6e+001 # AAGCGTGA TCACGCTT 9 0 1.9e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-002 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 0.550000 0.000000 0.000000 0.450000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGMGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACTGMGC GCKCAGT 34 5 9.1e-007 3.0e-002 # ACTGAGC GCTCAGT 21 3 1.2e-004 4.1e+000 # ACTGCGC GCGCAGT 13 2 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 3.0e-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 0.000000 0.000000 1.000000 0.000000 0.617647 0.382353 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 23 1 1.3e-006 4.2e-002 # GTGATAGT ACTATCAC 14 1 4.6e-004 1.5e+001 # GTGATAGC GCTATCAC 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 4.2e-002 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 0.416667 0.000000 0.583333 # Stopping reason: E-value threshold exceeded # Running time: 74.30 seconds