# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/seqs-shuffled # positives: 935 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/seqs-centered (Sat Jan 18 08:19:59 PST 2020) # negatives: 935 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/seqs-shuffled (Sat Jan 18 08:19:59 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 08:34:58 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 0.298 C 0.206 G 0.202 T 0.294 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 112 10 1.5e-024 5.3e-020 # GGTTCGA TCGAACC 80 3 1.9e-021 6.8e-017 # GGTTCAA TTGAACC 32 7 3.0e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 5.3e-020 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 57 2 1.4e-015 4.8e-011 # ATGTACGG CCGTACAT 28 0 3.0e-009 1.1e-004 # ATGTATGG CCATACAT 34 2 7.4e-009 2.6e-004 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 4.8e-011 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.447761 0.000000 0.552239 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AARAAAWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 191 74 3.0e-015 1.1e-010 # AAAAAAAA TTTTTTTT 93 34 3.0e-008 1.0e-003 # AAGAAAAA TTTTTCTT 60 15 4.5e-008 1.6e-003 # AAGAAATA TATTTCTT 26 7 6.0e-004 2.1e+001 # AAAAAATA TATTTTTT 52 30 8.6e-003 3.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 214 E= 1.1e-010 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.621495 0.000000 0.378505 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 0.663551 0.000000 0.000000 0.336449 1.000000 0.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 54 3 1.1e-013 3.7e-009 # CCTTAACC GGTTAAGG 37 3 7.2e-009 2.5e-004 # CCATAACC GGTTATGG 17 0 7.1e-006 2.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 3.7e-009 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.314815 0.000000 0.000000 0.685185 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 0.000000 1.000000 0.000000 0.000000 MOTIF ACCACTAH DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCACTAH DTAGTGGT 43 2 1.9e-011 6.6e-007 # ACCACTAA TTAGTGGT 16 0 1.4e-005 5.0e-001 # ACCACTAT ATAGTGGT 12 0 2.4e-004 8.3e+000 # ACCACTAC GTAGTGGT 15 2 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 6.6e-007 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 0.372093 0.348837 0.000000 0.279070 MOTIF ACTYGGCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACTYGGCC GGCCRAGT 40 2 1.4e-010 4.9e-006 # ACTTGGCC GGCCAAGT 27 1 9.1e-008 3.2e-003 # ACTCGGCC GGCCGAGT 22 1 2.6e-006 8.9e-002 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 4.9e-006 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 0.475000 0.000000 0.525000 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 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 42 4 1.7e-009 6.1e-005 # GCGCTACC GGTAGCGC 29 2 1.9e-007 6.7e-003 # GCTCTACC GGTAGAGC 13 2 3.6e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 6.1e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.690476 0.309524 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 ACCCANAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 67 16 3.4e-009 1.2e-004 # ACCCATAC GTATGGGT 16 1 1.3e-004 4.5e+000 # ACCCACAC GTGTGGGT 27 9 1.8e-003 6.3e+001 # ACCCAAAC GTTTGGGT 16 3 2.1e-003 7.4e+001 # ACCCAGAC GTCTGGGT 15 4 9.3e-003 3.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 112 E= 1.2e-004 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 0.142857 0.580357 0.133929 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CATYACGC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CATYACGC GCGTRATG 28 1 4.6e-008 1.6e-003 # CATCACGC GCGTGATG 13 0 1.2e-004 4.1e+000 # CATTACGC GCGTAATG 15 1 2.5e-004 8.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.6e-003 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 0.464286 0.000000 0.535714 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 MOTIF AGAAATCT DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGAAATCT AGATTTCT 24 0 5.1e-008 1.8e-003 # AGAAATCT AGATTTCT 24 0 5.1e-008 1.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-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 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 0.000000 0.000000 1.000000 MOTIF TCCACGGW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TCCACGGW WCCGTGGA 23 0 1.0e-007 3.6e-003 # TCCACGGT ACCGTGGA 13 0 1.2e-004 4.1e+000 # TCCACGGA TCCGTGGA 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.6e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.434783 0.000000 0.000000 0.565217 MOTIF CTWGACC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 52 12 1.5e-007 5.1e-003 # CTAGACC GGTCTAG 31 5 5.4e-006 1.9e-001 # CTTGACC GGTCAAG 21 7 6.0e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 5.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.596154 0.000000 0.000000 0.403846 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 CWGACGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CWGACGC GCGTCWG 33 4 4.3e-007 1.5e-002 # CAGACGC GCGTCTG 18 2 1.9e-004 6.5e+000 # CTGACGC GCGTCAG 15 2 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.5e-002 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.000000 0.454545 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTCCMTTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTCCMTTA TAAKGGAG 23 1 1.3e-006 4.5e-002 # CTCCCTTA TAAGGGAG 11 0 4.7e-004 1.6e+001 # CTCCATTA TAATGGAG 12 1 1.7e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.5e-002 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 0.521739 0.478261 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 # Stopping reason: E-value threshold exceeded # Running time: 86.57 seconds