# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CUP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CUP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CUP2/seqs-shuffled # positives: 619 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CUP2/seqs-centered (Sun Jan 19 03:16:26 PST 2020) # negatives: 619 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CUP2/seqs-shuffled (Sun Jan 19 03:16:26 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 03:31:53 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 0.294 C 0.206 G 0.206 T 0.294 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 103 3 3.1e-029 9.2e-025 # CGGTTCGA TCGAACCG 35 0 1.8e-011 5.3e-007 # GGGTTCGA TCGAACCC 42 2 2.9e-011 8.8e-007 # GAGTTCGA TCGAACTC 15 1 2.4e-004 7.2e+000 # CAGTTCGA TCGAACTG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 103 E= 9.2e-025 0.000000 0.446602 0.553398 0.000000 0.252427 0.000000 0.747573 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 TAAGGCR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 73 5 1.0e-017 3.1e-013 # TAAGGCG CGCCTTA 58 3 4.6e-015 1.4e-010 # TAAGGCA TGCCTTA 18 2 1.8e-004 5.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 3.1e-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 0.226667 0.000000 0.773333 0.000000 MOTIF ACCCANAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 62 2 2.5e-017 7.4e-013 # ACCCATAC GTATGGGT 30 1 1.1e-008 3.2e-004 # ACCCAAAC GTTTGGGT 13 0 1.1e-004 3.4e+000 # ACCCACAC GTGTGGGT 12 0 2.3e-004 6.9e+000 # ACCCAGAC GTCTGGGT 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 7.4e-013 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 0.183099 0.183099 0.197183 0.436620 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 60 3 1.2e-015 3.4e-011 # CTCGGCCA TGGCCGAG 31 0 3.2e-010 9.4e-006 # CTGGGCCA TGGCCCAG 11 0 4.7e-004 1.4e+001 # CTTGGCCA TGGCCAAG 18 3 6.8e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 3.4e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.516667 0.183333 0.300000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 42 1 2.5e-012 7.4e-008 # GCGCTACC GGTAGCGC 26 0 1.1e-008 3.4e-004 # GCTCTACC GGTAGAGC 16 1 1.3e-004 3.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 7.4e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.619048 0.380952 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 40 1 1.0e-011 3.0e-007 # ATGGCAAC GTTGCCAT 29 1 2.1e-008 6.2e-004 # ATGGCATC GATGCCAT 12 0 2.3e-004 6.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 3.0e-007 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 0.707317 0.000000 0.000000 0.292683 0.000000 1.000000 0.000000 0.000000 MOTIF GTMCGGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTMCGGA TCCGKAC 49 4 1.5e-011 4.5e-007 # GTACGGA TCCGTAC 35 3 2.2e-008 6.5e-004 # GTCCGGA TCCGGAC 14 1 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 4.5e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.725490 0.274510 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 TTGGGCB DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TTGGGCB VGCCCAA 55 7 4.6e-011 1.4e-006 # TTGGGCG CGCCCAA 16 0 1.4e-005 4.1e-001 # TTGGGCC GGCCCAA 22 2 1.5e-005 4.5e-001 # TTGGGCT AGCCCAA 17 5 8.0e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 1.4e-006 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.385965 0.298246 0.315789 MOTIF AARAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AARAAA TTTYTT 283 174 8.7e-011 2.5e-006 # AAAAAA TTTTTT 196 117 1.5e-007 4.5e-003 # AAGAAA TTTCTT 156 85 2.2e-007 6.4e-003 letter-probability matrix: alength= 4 w= 6 nsites= 410 E= 2.5e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.617073 0.000000 0.382927 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 MOTIF ACCAYTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACCAYTA TARTGGT 69 15 2.8e-010 8.0e-006 # ACCACTA TAGTGGT 44 7 3.4e-008 9.9e-004 # ACCATTA TAATGGT 26 8 1.3e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 8.0e-006 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 0.619718 0.000000 0.380282 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GAMTTGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GAMTTGA TCAAKTC 50 8 3.8e-009 1.1e-004 # GAATTGA TCAATTC 31 5 4.9e-006 1.4e-001 # GACTTGA TCAAGTC 20 3 2.2e-004 6.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 1.1e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.607843 0.392157 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAGAT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAGAT ATCTT 221 131 9.0e-009 2.6e-004 # AAGAT ATCTT 221 131 9.0e-009 2.6e-004 letter-probability matrix: alength= 4 w= 5 nsites= 270 E= 2.6e-004 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 MOTIF GTGATAGY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 33 2 1.2e-008 3.5e-004 # GTGATAGC GCTATCAC 19 1 1.8e-005 5.0e-001 # GTGATAGT ACTATCAC 15 1 2.4e-004 6.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 3.5e-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 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 0.558824 0.000000 0.441176 MOTIF CGTGGMG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGTGGMG CKCCACG 32 2 2.4e-008 6.8e-004 # CGTGGAG CTCCACG 19 2 9.9e-005 2.8e+000 # CGTGGCG CGCCACG 13 0 1.1e-004 3.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 6.8e-004 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.593750 0.406250 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTGAGCT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 0 9.7e-008 2.7e-003 # ACTGAGCT AGCTCAGT 23 0 9.7e-008 2.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.7e-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 0.000000 0.000000 1.000000 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 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 62.42 seconds