# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CIN5/seqs-shuffled # positives: 831 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CIN5/seqs-centered (Sun Jan 19 00:43:31 PST 2020) # negatives: 831 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CIN5/seqs-shuffled (Sun Jan 19 00:43:31 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:58:09 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 0.317 C 0.184 G 0.179 T 0.320 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 87 9 2.7e-018 8.7e-014 # GGTTCGA TCGAACC 75 5 4.6e-018 1.5e-013 # GGATCGA TCGATCC 20 4 7.2e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 87 E= 8.7e-014 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.183908 0.000000 0.000000 0.816092 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 TBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TBGGCCA TGGCCVA 70 9 1.2e-013 4.0e-009 # TCGGCCA TGGCCGA 31 1 5.9e-009 1.9e-004 # TGGGCCA TGGCCCA 16 2 6.2e-004 2.0e+001 # TTGGCCA TGGCCAA 23 6 1.1e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 4.0e-009 0.000000 0.000000 0.000000 1.000000 0.000000 0.442857 0.228571 0.328571 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 AGAARA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGAARA TYTTCT 277 156 7.9e-012 2.6e-007 # AGAAAA TTTTCT 209 115 3.5e-009 1.1e-004 # AGAAGA TCTTCT 88 47 1.5e-004 4.9e+000 letter-probability matrix: alength= 4 w= 6 nsites= 341 E= 2.6e-007 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 0.736070 0.000000 0.263930 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF BTAAGGCG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 45 4 2.5e-010 7.9e-006 # TTAAGGCG CGCCTTAA 23 2 8.5e-006 2.7e-001 # CTAAGGCG CGCCTTAG 11 1 3.1e-003 9.9e+001 # GTAAGGCG CGCCTTAC 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 7.9e-006 0.000000 0.244444 0.244444 0.511111 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 0.000000 0.000000 1.000000 0.000000 MOTIF TAYRTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TAYRTA TAYRTA 210 113 1.1e-009 3.4e-005 # TATATA TATATA 92 45 1.8e-005 5.6e-001 # TACGTA TACGTA 40 13 1.1e-004 3.4e+000 # TACATA TATGTA 108 69 1.2e-003 3.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 257 E= 3.4e-005 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.377432 0.000000 0.622568 0.626459 0.000000 0.373541 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 39 3 1.9e-009 6.0e-005 # TAGTGGTA TACCACTA 21 2 3.0e-005 9.4e-001 # TAGTGGTT AACCACTA 18 1 3.5e-005 1.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 6.0e-005 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.538462 0.000000 0.000000 0.461538 MOTIF CKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CKCTACC GGTAGMG 40 5 2.7e-008 8.6e-004 # CGCTACC GGTAGCG 24 2 4.6e-006 1.4e-001 # CTCTACC GGTAGAG 16 3 2.1e-003 6.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 8.6e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 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 CCMCGCG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCMCGCG CGCGKGG 23 0 1.0e-007 3.2e-003 # CCCCGCG CGCGGGG 13 0 1.2e-004 3.7e+000 # CCACGCG CGCGTGG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.434783 0.565217 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 0.000000 1.000000 0.000000 MOTIF ACSGATG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACSGATG CATCSGT 31 3 3.0e-007 9.5e-003 # ACCGATG CATCGGT 16 1 1.3e-004 4.0e+000 # ACGGATG CATCCGT 15 2 1.1e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 9.5e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.457143 0.542857 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 CACGGTGM DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 21 0 4.2e-007 1.3e-002 # CACGGTGA TCACCGTG 12 0 2.3e-004 7.4e+000 # CACGGTGC GCACCGTG 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.428571 0.000000 0.000000 MOTIF CCYAAACA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCYAAACA TGTTTRGG 21 0 4.2e-007 1.3e-002 # CCTAAACA TGTTTAGG 13 0 1.2e-004 3.6e+000 # CCCAAACA TGTTTGGG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.619048 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 31 4 1.4e-006 4.4e-002 # ATGGCAAC GTTGCCAT 18 2 1.9e-004 5.8e+000 # ATGGCATC GATGCCAT 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 4.4e-002 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 0.580645 0.000000 0.000000 0.419355 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 67.40 seconds