# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-shuffled # positives: 709 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-centered (Sat Jan 18 05:58:46 PST 2020) # negatives: 709 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-shuffled (Sat Jan 18 05:58:46 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:14:59 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 0.291 C 0.212 G 0.210 T 0.287 MOTIF GRNTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRNTCGAA TTCGANYC 122 11 3.2e-027 1.1e-022 # GGATCGAA TTCGATCC 23 0 9.9e-008 3.4e-003 # GAATCGAA TTCGATTC 23 3 3.8e-005 1.3e+000 # GGCTCGAA TTCGAGCC 16 1 1.3e-004 4.4e+000 # GAGTCGAA TTCGACTC 18 2 1.8e-004 6.4e+000 # GACTCGAA TTCGAGTC 12 0 2.3e-004 8.0e+000 # GATTCGAA TTCGAATC 13 1 8.7e-004 3.0e+001 # GGTTCGAA TTCGAACC 16 3 2.1e-003 7.2e+001 # GGGTCGAA TTCGACCC 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 122 E= 1.1e-022 0.000000 0.000000 1.000000 0.000000 0.508197 0.000000 0.491803 0.000000 0.377049 0.229508 0.229508 0.163934 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 MOTIF GCCWTAAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 43 0 5.9e-014 2.0e-009 # GCCTTAAC GTTAAGGC 32 0 1.6e-010 5.6e-006 # GCCATAAC GTTATGGC 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.0e-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 0.255814 0.000000 0.000000 0.744186 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 ARAAAAWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAWA TWTTTTYT 140 51 1.7e-012 5.9e-008 # AAAAAATA TATTTTTT 55 10 2.8e-009 9.6e-005 # AGAAAAAA TTTTTTCT 54 19 1.6e-005 5.5e-001 # AAAAAAAA TTTTTTTT 64 26 2.2e-005 7.6e-001 # AGAAAATA TATTTTCT 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 163 E= 5.9e-008 1.000000 0.000000 0.000000 0.000000 0.674847 0.000000 0.325153 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 0.650307 0.000000 0.000000 0.349693 1.000000 0.000000 0.000000 0.000000 MOTIF AACCACTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACCACTW WAGTGGTT 34 0 3.9e-011 1.3e-006 # AACCACTT AAGTGGTT 22 0 2.0e-007 6.9e-003 # AACCACTA TAGTGGTT 12 0 2.3e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.3e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.352941 0.000000 0.000000 0.647059 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 1 9.0e-011 3.1e-006 # GCGCTACC GGTAGCGC 24 1 6.5e-007 2.2e-002 # GCTCTACC GGTAGAGC 13 0 1.2e-004 3.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 3.1e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.648649 0.351351 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 AGACCRC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGACCRC GYGGTCT 45 4 2.3e-010 7.7e-006 # AGACCAC GTGGTCT 29 3 1.0e-006 3.4e-002 # AGACCGC GCGGTCT 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 7.7e-006 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 0.644444 0.000000 0.355556 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACTKGGC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 40 4 5.4e-009 1.8e-004 # AACTTGGC GCCAAGTT 30 3 5.4e-007 1.8e-002 # AACTGGGC GCCCAGTT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.8e-004 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 AGAYCGGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGGG CCCGRTCT 25 1 3.3e-007 1.1e-002 # AGATCGGG CCCGATCT 14 1 4.6e-004 1.6e+001 # AGACCGGG CCCGGTCT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-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 0.000000 0.440000 0.000000 0.560000 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 MOTIF AGMAGAT DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGMAGAT ATCTKCT 48 12 9.9e-007 3.4e-002 # AGCAGAT ATCTGCT 23 6 1.0e-003 3.5e+001 # AGAAGAT ATCTTCT 25 8 2.1e-003 7.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 3.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.520833 0.479167 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 TCGSCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TCGSCCA TGGSCGA 38 7 1.1e-006 3.7e-002 # TCGGCCA TGGCCGA 24 5 2.4e-004 8.1e+000 # TCGCCCA TGGGCGA 14 2 2.0e-003 6.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 3.7e-002 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 0.368421 0.631579 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 # Stopping reason: E-value threshold exceeded # Running time: 49.54 seconds