# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ARR1/seqs-shuffled # positives: 475 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ARR1/seqs-centered (Sat Jan 18 11:02:47 PST 2020) # negatives: 475 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ARR1/seqs-shuffled (Sat Jan 18 11:02:47 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 11:11:52 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 0.205 G 0.205 T 0.293 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 114 10 1.3e-026 3.3e-022 # GGTTCGA TCGAACC 94 7 8.8e-023 2.3e-018 # AGTTCGA TCGAACT 26 3 5.8e-006 1.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 114 E= 3.3e-022 0.201754 0.000000 0.798246 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 ACCACTV DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACTV BAGTGGT 87 5 2.2e-022 5.6e-018 # ACCACTA TAGTGGT 46 1 1.1e-013 2.9e-009 # ACCACTC GAGTGGT 31 3 2.5e-007 6.5e-003 # ACCACTG CAGTGGT 11 1 3.0e-003 7.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 88 E= 5.6e-018 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.522727 0.352273 0.125000 0.000000 MOTIF CCVTACA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCVTACA TGTABGG 93 9 8.1e-021 2.1e-016 # CCATACA TGTATGG 50 5 3.5e-011 9.0e-007 # CCGTACA TGTACGG 41 3 3.7e-010 9.5e-006 # CCCTACA TGTAGGG 11 1 3.0e-003 7.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 2.1e-016 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.517857 0.098214 0.383929 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 TAAGGCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 72 5 1.1e-017 2.8e-013 # TAAGGCG CGCCTTA 58 1 1.7e-017 4.4e-013 # TAAGGCA TGCCTTA 16 4 5.5e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 2.8e-013 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 0.216216 0.000000 0.783784 0.000000 MOTIF AACTKGGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 40 0 3.9e-013 9.7e-009 # AACTTGGC GCCAAGTT 30 0 5.8e-010 1.5e-005 # AACTGGGC GCCCAGTT 10 0 9.3e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 9.7e-009 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 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 0 3.5e-012 8.8e-008 # GCGCTACC GGTAGCGC 25 0 2.2e-008 5.4e-004 # GCTCTACC GGTAGAGC 12 0 2.3e-004 5.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 8.8e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.675676 0.324324 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 CDCCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CDCCCA TGGGHG 109 38 8.4e-011 2.1e-006 # CACCCA TGGGTG 55 20 1.6e-005 4.1e-001 # CGCCCA TGGGCG 32 9 1.6e-004 4.1e+000 # CTCCCA TGGGAG 26 9 2.6e-003 6.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 127 E= 2.1e-006 0.000000 1.000000 0.000000 0.000000 0.535433 0.000000 0.259843 0.204724 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 GGTCTCY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GGTCTCY RGAGACC 36 2 1.5e-009 3.6e-005 # GGTCTCC GGAGACC 22 2 1.5e-005 3.6e-001 # GGTCTCT AGAGACC 14 0 5.5e-005 1.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 3.6e-005 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.578947 0.000000 0.421053 MOTIF AAAAAAAK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAAK MTTTTTTT 87 28 2.0e-009 4.9e-005 # AAAAAAAT ATTTTTTT 54 15 5.6e-007 1.4e-002 # AAAAAAAG CTTTTTTT 34 16 6.4e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 95 E= 4.9e-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 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 0.000000 0.000000 0.368421 0.631579 MOTIF CACATYAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 27 0 5.1e-009 1.2e-004 # CACATCAC GTGATGTG 17 0 6.6e-006 1.6e-001 # CACATTAC GTAATGTG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.2e-004 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.629630 0.000000 0.370370 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAASGATG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 30 1 9.6e-009 2.3e-004 # CAACGATG CATCGTTG 20 1 8.7e-006 2.1e-001 # CAAGGATG CATCCTTG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.3e-004 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 0.666667 0.333333 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 1.000000 0.000000 MOTIF TGGCGYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 40 5 2.0e-008 4.9e-004 # TGGCGCA TGCGCCA 21 2 2.7e-005 6.7e-001 # TGGCGTA TACGCCA 19 3 3.7e-004 9.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 4.9e-004 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 0.000000 1.000000 0.000000 0.000000 0.525000 0.000000 0.475000 1.000000 0.000000 0.000000 0.000000 MOTIF ATAGTKTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 32 2 2.2e-008 5.2e-004 # ATAGTGTA TACACTAT 17 1 6.4e-005 1.5e+000 # ATAGTTTA TAAACTAT 15 1 2.4e-004 5.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.2e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.531250 0.468750 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGMAGAT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGMAGAT ATCTKCT 37 5 1.3e-007 3.1e-003 # AGCAGAT ATCTGCT 17 1 6.4e-005 1.5e+000 # AGAAGAT ATCTTCT 20 4 6.8e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 3.1e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.540541 0.459459 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 MOTIF AGATCGKG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 25 1 3.0e-007 7.2e-003 # AGATCGGG CCCGATCT 15 1 2.4e-004 5.7e+000 # AGATCGTG CACGATCT 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.2e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTWGACC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTWGACC GGTCWAGT 21 0 3.8e-007 9.2e-003 # ACTAGACC GGTCTAGT 13 0 1.1e-004 2.7e+000 # ACTTGACC GGTCAAGT 8 0 3.8e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.2e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.619048 0.000000 0.000000 0.380952 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 CACGGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CACGGA TCCGTG 40 8 9.5e-007 2.3e-002 # CACGGA TCCGTG 40 8 9.5e-007 2.3e-002 letter-probability matrix: alength= 4 w= 6 nsites= 41 E= 2.3e-002 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGARTCAT DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AGARTCAT ATGAYTCT 23 1 1.2e-006 2.8e-002 # AGAGTCAT ATGACTCT 13 1 8.5e-004 2.0e+001 # AGAATCAT ATGATTCT 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.434783 0.000000 0.565217 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 0.000000 1.000000 MOTIF GATTWGAA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 31 4 1.2e-006 2.8e-002 # GATTAGAA TTCTAATC 18 3 6.6e-004 1.6e+001 # GATTTGAA TTCAAATC 13 1 8.5e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.8e-002 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 0.580645 0.000000 0.000000 0.419355 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 61.76 seconds