# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SFL1/seqs-shuffled # positives: 939 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SFL1/seqs-centered (Sun Jan 19 00:19:00 PST 2020) # negatives: 939 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SFL1/seqs-shuffled (Sun Jan 19 00:19:00 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:32:53 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 0.299 C 0.202 G 0.201 T 0.298 MOTIF GRTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRTTCGA TCGAAYC 94 3 9.6e-026 3.4e-021 # GGTTCGA TCGAACC 87 2 8.8e-025 3.1e-020 # GATTCGA TCGAATC 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 3.4e-021 0.000000 0.000000 1.000000 0.000000 0.085106 0.000000 0.914894 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 GCCTTAMC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 53 2 2.1e-014 7.5e-010 # GCCTTAAC GTTAAGGC 37 2 1.0e-009 3.6e-005 # GCCTTACC GGTAAGGC 16 0 1.4e-005 5.0e-001 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 7.5e-010 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 0.698113 0.301887 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTTCYW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTTCYW WRGAAG 356 200 1.7e-015 6.0e-011 # CTTCTT AAGAAG 154 87 2.3e-006 8.2e-002 # CTTCTA TAGAAG 85 42 5.0e-005 1.7e+000 # CTTCCT AGGAAG 81 44 4.0e-004 1.4e+001 # CTTCCA TGGAAG 85 56 7.0e-003 2.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 432 E= 6.0e-011 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 0.405093 0.000000 0.594907 0.400463 0.000000 0.000000 0.599537 MOTIF AACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGG CCMAGTT 75 12 4.5e-013 1.6e-008 # AACTTGG CCAAGTT 46 9 1.5e-007 5.2e-003 # AACTGGG CCCAGTT 29 3 1.1e-006 3.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 1.6e-008 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 0.381579 0.618421 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 1 6.4e-012 2.2e-007 # GCGCTACC GGTAGCGC 24 1 6.8e-007 2.3e-002 # GCTCTACC GGTAGAGC 17 0 7.1e-006 2.4e-001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.2e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.585366 0.414634 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 ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 39 2 2.7e-010 9.4e-006 # ATGGCAAC GTTGCCAT 26 0 1.3e-008 4.3e-004 # ATGGCATC GATGCCAT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 9.4e-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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGGTWA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWA TWACCACT 40 3 1.0e-009 3.6e-005 # AGTGGTTA TAACCACT 22 2 1.6e-005 5.5e-001 # AGTGGTAA TTACCACT 18 1 3.5e-005 1.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.6e-005 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 0.450000 0.000000 0.000000 0.550000 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCAB DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGACCAB VTGGTCT 66 16 5.6e-009 1.9e-004 # AGACCAC GTGGTCT 27 4 1.5e-005 5.1e-001 # AGACCAT ATGGTCT 21 6 2.8e-003 9.6e+001 # AGACCAG CTGGTCT 20 6 4.4e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 1.9e-004 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.385714 0.285714 0.328571 MOTIF ATATRTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATATRTA TAYATAT 60 13 6.3e-009 2.2e-004 # ATATATA TATATAT 33 7 1.8e-005 6.0e-001 # ATATGTA TACATAT 29 6 5.1e-005 1.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 2.2e-004 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 0.000000 1.000000 0.553846 0.000000 0.446154 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATCYGAT DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AATCYGAT ATCRGATT 27 1 9.1e-008 3.1e-003 # AATCCGAT ATCGGATT 16 1 1.3e-004 4.4e+000 # AATCTGAT ATCAGATT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.1e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.592593 0.000000 0.407407 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CCAAAGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCAAAGC GCTTTGG 32 3 1.7e-007 5.7e-003 # CCAAAGC GCTTTGG 32 3 1.7e-007 5.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 5.7e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 26 1 1.8e-007 6.0e-003 # GTGATAGT ACTATCAC 13 0 1.2e-004 4.0e+000 # GTGATAGC GCTATCAC 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 6.0e-003 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 0.518519 0.000000 0.481481 MOTIF TCTCCACR DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TCTCCACR YGTGGAGA 29 2 1.9e-007 6.5e-003 # TCTCCACG CGTGGAGA 15 0 2.9e-005 9.8e-001 # TCTCCACA TGTGGAGA 14 2 2.0e-003 6.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.5e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.482759 0.000000 0.517241 0.000000 MOTIF RCTGCTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST RCTGCTA TAGCAGY 38 6 3.6e-007 1.2e-002 # GCTGCTA TAGCAGC 22 3 7.1e-005 2.4e+000 # ACTGCTA TAGCAGT 16 3 2.1e-003 7.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.2e-002 0.380952 0.000000 0.619048 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGATTTC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AAGATTTC GAAATCTT 28 2 3.6e-007 1.2e-002 # AAGATTTC GAAATCTT 28 2 3.6e-007 1.2e-002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.2e-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 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TTTCGGTW DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TTTCGGTW WACCGAAA 35 5 5.4e-007 1.8e-002 # TTTCGGTA TACCGAAA 16 1 1.3e-004 4.4e+000 # TTTCGGTT AACCGAAA 19 4 1.2e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.8e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.457143 0.000000 0.000000 0.542857 MOTIF AATSTTCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AATSTTCT AGAASATT 30 3 5.8e-007 2.0e-002 # AATCTTCT AGAAGATT 20 2 5.6e-005 1.9e+000 # AATGTTCT AGAACATT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.0e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 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 0.000000 1.000000 MOTIF ACAYCAGA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACAYCAGA TCTGRTGT 20 0 8.6e-007 2.9e-002 # ACACCAGA TCTGGTGT 10 0 9.5e-004 3.2e+001 # ACATCAGA TCTGATGT 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.9e-002 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 0.500000 0.000000 0.500000 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 GKTCAAGA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST GKTCAAGA TCTTGAMC 26 2 1.3e-006 4.4e-002 # GGTCAAGA TCTTGACC 16 2 6.2e-004 2.1e+001 # GTTCAAGA TCTTGAAC 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.4e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.615385 0.384615 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 113.51 seconds