# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MSS11/seqs-shuffled # positives: 801 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MSS11/seqs-centered (Sat Jan 18 20:24:01 PST 2020) # negatives: 801 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MSS11/seqs-shuffled (Sat Jan 18 20:24:01 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 20:38:12 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 0.212 T 0.284 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 115 11 6.9e-025 2.4e-020 # GGTTCGA TCGAACC 94 6 7.8e-023 2.7e-018 # GGATCGA TCGATCC 26 6 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 2.4e-020 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.206897 0.000000 0.000000 0.793103 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 ATGTAYGG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 59 0 5.7e-019 2.0e-014 # ATGTATGG CCATACAT 34 0 4.1e-011 1.4e-006 # ATGTACGG CCGTACAT 30 0 7.1e-010 2.4e-005 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 2.0e-014 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 0.455882 0.000000 0.544118 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 54 3 9.4e-014 3.2e-009 # CTCGGCCA TGGCCGAG 26 0 1.2e-008 4.2e-004 # CTTGGCCA TGGCCAAG 17 2 3.4e-004 1.2e+001 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 3.2e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.481481 0.203704 0.314815 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-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 38 1 4.7e-011 1.6e-006 # GCGCTACC GGTAGCGC 24 1 6.6e-007 2.3e-002 # GCTCTACC GGTAGAGC 14 0 5.8e-005 2.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.6e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.631579 0.368421 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 ATAGTKTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 43 3 1.4e-010 4.8e-006 # ATAGTGTA TACACTAT 26 1 1.7e-007 5.9e-003 # ATAGTTTA TAAACTAT 17 2 3.4e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 4.8e-006 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 0.604651 0.395349 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCANAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 58 10 5.6e-010 1.9e-005 # ACCCATAC GTATGGGT 17 1 6.7e-005 2.3e+000 # ACCCACAC GTGTGGGT 17 2 3.4e-004 1.2e+001 # ACCCAGAC GTCTGGGT 14 2 2.0e-003 6.9e+001 # ACCCAAAC GTTTGGGT 17 5 8.1e-003 2.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 66 E= 1.9e-005 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 0.257576 0.272727 0.196970 0.272727 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCCTTAAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAAC GTTAAGGC 34 1 7.5e-010 2.6e-005 # GCCTTAAC GTTAAGGC 34 1 7.5e-010 2.6e-005 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.6e-005 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 0.000000 0.000000 1.000000 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 GGYTATCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 31 1 5.8e-009 2.0e-004 # GGCTATCA TGATAGCC 18 1 3.5e-005 1.2e+000 # GGTTATCA TGATAACC 13 0 1.2e-004 4.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.0e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.580645 0.000000 0.419355 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGSTCTCC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CGSTCTCC GGAGASCG 24 0 5.0e-008 1.7e-003 # CGGTCTCC GGAGACCG 15 0 2.9e-005 9.8e-001 # CGCTCTCC GGAGAGCG 9 0 1.9e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.7e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 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 1.000000 0.000000 0.000000 MOTIF CCGKGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGKGC GCMCGG 70 21 5.7e-008 1.9e-003 # CCGTGC GCACGG 43 14 5.9e-005 2.0e+000 # CCGGGC GCCCGG 27 10 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 72 E= 1.9e-003 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 0.375000 0.625000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCTB DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCTB VAGAT 428 322 7.0e-008 2.4e-003 # ATCTT AAGAT 238 179 4.7e-004 1.6e+001 # ATCTG CAGAT 155 109 1.2e-003 4.1e+001 # ATCTC GAGAT 138 99 3.7e-003 1.3e+002 letter-probability matrix: alength= 4 w= 5 nsites= 601 E= 2.4e-003 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 0.000000 0.241265 0.281198 0.477537 MOTIF AAGCGWGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 23 0 1.0e-007 3.3e-003 # AAGCGTGA TCACGCTT 15 0 2.9e-005 9.3e-001 # AAGCGAGA TCTCGCTT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.3e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.347826 0.000000 0.000000 0.652174 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AASGATG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AASGATG CATCSTT 58 15 1.1e-007 3.7e-003 # AACGATG CATCGTT 35 9 4.3e-005 1.4e+000 # AAGGATG CATCCTT 23 6 1.1e-003 3.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 3.7e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.603448 0.396552 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 AARAAAW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 276 179 4.8e-008 1.6e-003 # AAAAAAA TTTTTTT 140 80 8.4e-006 2.7e-001 # AAGAAAA TTTTCTT 84 49 9.9e-004 3.2e+001 # AAAAAAT ATTTTTT 122 82 1.7e-003 5.5e+001 # AAGAAAT ATTTCTT 47 24 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 353 E= 1.6e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.643059 0.000000 0.356941 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 0.589235 0.000000 0.000000 0.410765 MOTIF ACTARACC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTARACC GGTYTAGT 30 3 5.6e-007 1.8e-002 # ACTAGACC GGTCTAGT 17 1 6.7e-005 2.2e+000 # ACTAAACC GGTTTAGT 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.8e-002 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 0.433333 0.000000 0.566667 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 ACRCCAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACRCCAC GTGGYGT 36 6 1.1e-006 3.4e-002 # ACGCCAC GTGGCGT 21 2 3.0e-005 9.5e-001 # ACACCAC GTGGTGT 15 4 9.3e-003 3.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.416667 0.000000 0.583333 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 MOTIF ACGAWACC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACGAWACC GGTWTCGT 26 2 1.3e-006 4.1e-002 # ACGAAACC GGTTTCGT 17 2 3.4e-004 1.1e+001 # ACGATACC GGTATCGT 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 4.1e-002 1.000000 0.000000 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 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 89.59 seconds