# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/seqs-shuffled # positives: 405 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/seqs-centered (Sat Jan 18 15:54:15 PST 2020) # negatives: 405 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/seqs-shuffled (Sat Jan 18 15:54:15 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:01:02 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 0.308 C 0.195 G 0.192 T 0.305 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 66 1 2.8e-020 7.1e-016 # TGTACGGA TCCGTACA 26 0 9.8e-009 2.5e-004 # TGTATGGG CCCATACA 28 1 3.6e-008 9.1e-004 # TGTATGGA TCCATACA 12 0 2.2e-004 5.7e+000 # TGTACGGG CCCGTACA 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 77 E= 7.1e-016 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.454545 0.000000 0.545455 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.506494 0.000000 0.493506 0.000000 MOTIF ACCRACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 63 3 6.0e-017 1.5e-012 # ACCAACT AGTTGGT 49 2 1.4e-013 3.6e-009 # ACCGACT AGTCGGT 14 1 4.4e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 63 E= 1.5e-012 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.222222 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 AACCACTH DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AACCACTH DAGTGGTT 55 1 1.2e-016 3.0e-012 # AACCACTC GAGTGGTT 20 0 7.5e-007 1.9e-002 # AACCACTA TAGTGGTT 17 0 6.4e-006 1.6e-001 # AACCACTT AAGTGGTT 20 1 8.4e-006 2.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 3.0e-012 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 0.298246 0.350877 0.000000 0.350877 MOTIF RGTTCGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 43 3 8.3e-011 2.1e-006 # GGTTCGA TCGAACC 33 1 1.1e-009 2.7e-005 # AGTTCGA TCGAACT 14 2 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 2.1e-006 0.279070 0.000000 0.720930 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 CACGS DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACGS SCGTG 118 47 3.1e-010 7.8e-006 # CACGG CCGTG 66 24 1.6e-006 4.0e-002 # CACGC GCGTG 63 26 2.1e-005 5.3e-001 letter-probability matrix: alength= 4 w= 5 nsites= 129 E= 7.8e-006 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 0.488372 0.511628 0.000000 MOTIF AMACCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AMACCCA TGGGTKT 46 6 1.8e-009 4.5e-005 # ACACCCA TGGGTGT 30 2 7.6e-008 1.8e-003 # AAACCCA TGGGTTT 18 4 1.9e-003 4.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 4.5e-005 1.000000 0.000000 0.000000 0.000000 0.380000 0.620000 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 TCAGWA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TCAGWA TWCTGA 77 23 3.6e-009 8.7e-005 # TCAGAA TTCTGA 53 13 1.3e-007 3.0e-003 # TCAGTA TACTGA 26 10 4.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 86 E= 8.7e-005 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 1.000000 0.000000 0.639535 0.000000 0.000000 0.360465 1.000000 0.000000 0.000000 0.000000 MOTIF AGMGCG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGMGCG CGCKCT 52 11 2.8e-008 6.6e-004 # AGCGCG CGCGCT 24 4 7.0e-005 1.7e+000 # AGAGCG CGCTCT 28 8 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 53 E= 6.6e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.528302 0.471698 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 MOTIF ATAGTKTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 31 2 3.9e-008 9.2e-004 # ATAGTGTA TACACTAT 17 0 6.4e-006 1.5e-001 # ATAGTTTA TAAACTAT 14 2 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 9.2e-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 0.548387 0.451613 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 30 2 7.6e-008 1.8e-003 # ATGGCAAC GTTGCCAT 19 2 9.3e-005 2.2e+000 # ATGGCATC GATGCCAT 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 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 0.633333 0.000000 0.000000 0.366667 0.000000 1.000000 0.000000 0.000000 MOTIF CAAGAAAW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAAGAAAW WTTTCTTG 25 1 2.8e-007 6.7e-003 # CAAGAAAT ATTTCTTG 13 0 1.1e-004 2.6e+000 # CAAGAAAA TTTTCTTG 12 1 1.6e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 6.7e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.480000 0.000000 0.000000 0.520000 MOTIF CCTTGTTR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCTTGTTR YAACAAGG 21 0 3.7e-007 8.6e-003 # CCTTGTTG CAACAAGG 13 0 1.1e-004 2.6e+000 # CCTTGTTA TAACAAGG 8 0 3.8e-003 8.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 8.6e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.380952 0.000000 0.619048 0.000000 MOTIF GCCWTAGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAGA TCTAWGGC 21 0 3.7e-007 8.6e-003 # GCCTTAGA TCTAAGGC 11 0 4.6e-004 1.1e+001 # GCCATAGA TCTATGGC 10 0 9.2e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 8.6e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.000000 0.000000 0.523810 0.000000 0.000000 0.000000 1.000000 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 ACCACTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACCACTA TAGTGGT 24 1 5.6e-007 1.3e-002 # ACCACTA TAGTGGT 24 1 5.6e-007 1.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 1.3e-002 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 1.000000 0.000000 0.000000 0.000000 MOTIF GGCTAYC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GGCTAYC GRTAGCC 23 1 1.1e-006 2.6e-002 # GGCTATC GATAGCC 15 1 2.3e-004 5.4e+000 # GGCTACC GGTAGCC 8 0 3.8e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 2.6e-002 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.347826 0.000000 0.652174 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 42.66 seconds