# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MOT3/seqs-shuffled # positives: 1007 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MOT3/seqs-centered (Fri Jan 17 22:36:48 PST 2020) # negatives: 1007 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MOT3/seqs-shuffled (Fri Jan 17 22:36:48 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:50:28 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 0.316 C 0.185 G 0.181 T 0.319 MOTIF TCGAACCB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 73 1 1.1e-021 3.6e-017 # TCGAACCC GGGTTCGA 36 1 2.0e-010 7.0e-006 # TCGAACCG CGGTTCGA 22 0 2.1e-007 7.2e-003 # TCGAACCT AGGTTCGA 15 0 2.9e-005 9.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 3.6e-017 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.493151 0.301370 0.205479 MOTIF AASCACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AASCACT AGTGSTT 85 16 2.2e-013 7.6e-009 # AACCACT AGTGGTT 64 10 2.1e-011 7.3e-007 # AAGCACT AGTGCTT 21 6 2.8e-003 9.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 7.6e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.755814 0.244186 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 MOTIF CCRTACA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 78 14 1.1e-012 3.6e-008 # CCATACA TGTATGG 55 8 2.8e-010 9.5e-006 # CCGTACA TGTACGG 30 6 3.0e-005 1.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 93 E= 3.6e-008 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.655914 0.000000 0.344086 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 ARAAAAD DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAD HTTTTYT 468 323 2.3e-011 7.7e-007 # AAAAAAG CTTTTTT 148 85 7.1e-006 2.4e-001 # AGAAAAA TTTTTCT 139 79 1.1e-005 3.5e-001 # AAAAAAA TTTTTTT 201 133 2.9e-005 9.6e-001 # AGAAAAG CTTTTCT 65 30 1.5e-004 5.2e+000 # AGAAAAT ATTTTCT 81 46 8.7e-004 2.9e+001 # AAAAAAT ATTTTTT 182 139 5.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 624 E= 7.7e-007 1.000000 0.000000 0.000000 0.000000 0.589744 0.000000 0.410256 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 0.347756 0.000000 0.283654 0.368590 MOTIF CCAACTKG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCAACTKG CMAGTTGG 42 2 3.8e-011 1.3e-006 # CCAACTTG CAAGTTGG 29 1 2.4e-008 8.0e-004 # CCAACTGG CCAGTTGG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.318182 0.681818 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 32 1 3.1e-009 1.0e-004 # GCGCTACC GGTAGCGC 20 0 8.7e-007 2.9e-002 # GCTCTACC GGTAGAGC 12 1 1.7e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 1.0e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.625000 0.375000 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 GTGGTMTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTGGTMTA TAKACCAC 32 1 3.1e-009 1.0e-004 # GTGGTCTA TAGACCAC 20 0 8.7e-007 2.9e-002 # GTGGTATA TATACCAC 12 1 1.7e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 1.0e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.375000 0.625000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACACCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACACCCA TGGGTGT 49 8 8.9e-009 3.0e-004 # ACACCCA TGGGTGT 49 8 8.9e-009 3.0e-004 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 3.0e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 39 5 5.3e-008 1.8e-003 # ATGGCAAC GTTGCCAT 26 4 2.6e-005 8.8e-001 # ATGGCATC GATGCCAT 13 1 8.9e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 1.8e-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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF SAAGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 395 286 1.7e-007 5.8e-003 # GAAGA TCTTC 220 160 3.8e-004 1.3e+001 # CAAGA TCTTG 220 167 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 5 nsites= 505 E= 5.8e-003 0.000000 0.504950 0.495050 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 AAAGCGWG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 25 1 3.5e-007 1.1e-002 # AAAGCGTG CACGCTTT 15 1 2.5e-004 8.0e+000 # AAAGCGAG CTCGCTTT 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 MOTIF TAYATACA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TAYATACA TGTATRTA 43 7 7.6e-008 2.4e-003 # TATATACA TGTATATA 33 7 1.8e-005 5.8e-001 # TACATACA TGTATGTA 10 1 5.8e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.4e-003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.232558 0.000000 0.767442 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCTTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCCTTA TAAGGC 71 24 4.1e-007 1.3e-002 # GCCTTA TAAGGC 71 24 4.1e-007 1.3e-002 letter-probability matrix: alength= 4 w= 6 nsites= 71 E= 1.3e-002 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 MOTIF AGCACGGW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGCACGGW WCCGTGCT 20 0 8.7e-007 2.8e-002 # AGCACGGT ACCGTGCT 11 0 4.8e-004 1.5e+001 # AGCACGGA TCCGTGCT 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-002 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.450000 0.000000 0.000000 0.550000 MOTIF MCCGGAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST MCCGGAA TTCCGGK 42 9 1.3e-006 4.1e-002 # ACCGGAA TTCCGGT 28 5 2.9e-005 9.3e-001 # CCCGGAA TTCCGGG 15 4 9.3e-003 3.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 4.1e-002 0.651163 0.348837 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 1.000000 0.000000 0.000000 0.000000 MOTIF GMTTAACA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GMTTAACA TGTTAAKC 23 1 1.3e-006 4.2e-002 # GCTTAACA TGTTAAGC 13 0 1.2e-004 3.8e+000 # GATTAACA TGTTAATC 10 1 5.8e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.2e-002 0.000000 0.000000 1.000000 0.000000 0.434783 0.565217 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 100.28 seconds