# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/seqs-shuffled # positives: 971 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/seqs-centered (Sat Jan 18 15:00:11 PST 2020) # negatives: 971 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/seqs-shuffled (Sat Jan 18 15:00:11 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 15:15:37 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 0.300 C 0.202 G 0.197 T 0.301 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 119 8 2.9e-028 1.0e-023 # GGTTCGA TCGAACC 100 5 2.2e-025 7.8e-021 # GGATCGA TCGATCC 27 3 3.6e-006 1.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 1.0e-023 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.000000 0.800000 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 88 7 5.2e-020 1.8e-015 # TGTATGGG CCCATACA 39 1 2.6e-011 9.1e-007 # TGTACGGA TCCGTACA 33 4 4.4e-007 1.5e-002 # TGTACGGG CCCGTACA 11 0 4.7e-004 1.7e+001 # TGTATGGA TCCATACA 14 2 2.0e-003 7.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 100 E= 1.8e-015 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 0.460000 0.000000 0.540000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 73 3 2.7e-019 9.3e-015 # CTCGGCCA TGGCCGAG 36 0 1.0e-011 3.7e-007 # CTTGGCCA TGGCCAAG 25 3 1.2e-005 4.3e-001 # CTGGGCCA TGGCCCAG 12 0 2.4e-004 8.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 9.3e-015 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.493151 0.164384 0.342466 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 BTAAGGCG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 69 6 2.0e-015 7.2e-011 # TTAAGGCG CGCCTTAA 40 3 1.1e-009 3.7e-005 # CTAAGGCG CGCCTTAG 17 1 6.8e-005 2.4e+000 # GTAAGGCG CGCCTTAC 12 2 6.3e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 69 E= 7.2e-011 0.000000 0.246377 0.173913 0.579710 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 48 1 5.0e-014 1.8e-009 # GCGCTACC GGTAGCGC 34 1 7.9e-010 2.8e-005 # GCTCTACC GGTAGAGC 14 0 5.8e-005 2.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 1.8e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.708333 0.291667 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 AGAARA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGAARA TYTTCT 306 172 9.5e-013 3.3e-008 # AGAAAA TTTTCT 236 126 8.2e-011 2.9e-006 # AGAAGA TCTTCT 105 56 3.5e-005 1.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 374 E= 3.3e-008 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 0.727273 0.000000 0.272727 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 50 5 6.3e-011 2.2e-006 # TAGTGGTA TACCACTA 29 3 1.1e-006 3.7e-002 # TAGTGGTT AACCACTA 21 2 3.0e-005 1.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 2.2e-006 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 0.580000 0.000000 0.000000 0.420000 MOTIF CAWAACCG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CAWAACCG CGGTTWTG 39 2 2.8e-010 9.5e-006 # CATAACCG CGGTTATG 21 1 5.0e-006 1.7e-001 # CAAAACCG CGGTTTTG 18 1 3.6e-005 1.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 9.5e-006 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.461538 0.000000 0.000000 0.538462 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 0.000000 0.000000 1.000000 0.000000 MOTIF CRCCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 142 61 9.6e-010 3.3e-005 # CACCCA TGGGTG 94 43 3.8e-006 1.3e-001 # CGCCCA TGGGCG 50 19 9.5e-005 3.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 218 E= 3.3e-005 0.000000 1.000000 0.000000 0.000000 0.756881 0.000000 0.243119 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 CTATCACR DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 31 1 6.1e-009 2.1e-004 # CTATCACG CGTGATAG 17 0 7.1e-006 2.4e-001 # CTATCACA TGTGATAG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.1e-004 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.451613 0.000000 0.548387 0.000000 MOTIF TTACRTAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TTACRTAA TTAYGTAA 47 7 7.6e-009 2.6e-004 # TTACATAA TTATGTAA 28 5 2.9e-005 9.9e-001 # TTACGTAA TTACGTAA 19 2 1.0e-004 3.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 2.6e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.583333 0.000000 0.416667 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATTAASAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 32 2 2.8e-008 9.4e-004 # ATTAAGAG CTCTTAAT 21 1 5.0e-006 1.7e-001 # ATTAACAG CTGTTAAT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.4e-004 1.000000 0.000000 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 0.343750 0.656250 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTCTCSCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSCA TGSGAGAG 28 1 4.6e-008 1.6e-003 # CTCTCCCA TGGGAGAG 18 1 3.6e-005 1.2e+000 # CTCTCGCA TGCGAGAG 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.6e-003 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.642857 0.357143 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKTCTGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCKTCTGA TCAGAMGC 27 1 9.1e-008 3.1e-003 # GCTTCTGA TCAGAAGC 14 0 5.8e-005 2.0e+000 # GCGTCTGA TCAGACGC 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.1e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.481481 0.518519 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 23 0 1.0e-007 3.6e-003 # AGATCGGG CCCGATCT 14 0 5.8e-005 2.0e+000 # AGATCGTG CACGATCT 9 0 1.9e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.6e-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 0.000000 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 0.608696 0.391304 0.000000 0.000000 1.000000 0.000000 MOTIF ATSTGTTG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATSTGTTG CAACASAT 32 3 1.7e-007 5.7e-003 # ATCTGTTG CAACAGAT 15 1 2.5e-004 8.4e+000 # ATGTGTTG CAACACAT 17 2 3.4e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.468750 0.531250 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCGGGSA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 22 0 2.1e-007 7.2e-003 # CGCGGGCA TGCCCGCG 11 0 4.7e-004 1.6e+001 # CGCGGGGA TCCCCGCG 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.2e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAAC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAAC GTTGCCAT 25 1 3.5e-007 1.2e-002 # ATGGCAAC GTTGCCAT 25 1 3.5e-007 1.2e-002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.2e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GATGATRA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST GATGATRA TYATCATC 25 1 3.5e-007 1.2e-002 # GATGATGA TCATCATC 14 0 5.8e-005 2.0e+000 # GATGATAA TTATCATC 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.2e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.440000 0.000000 0.560000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 24 1 6.8e-007 2.3e-002 # ACTGAGCT AGCTCAGT 24 1 6.8e-007 2.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.3e-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 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 MOTIF GRCCACGA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST GRCCACGA TCGTGGYC 20 0 8.6e-007 2.9e-002 # GACCACGA TCGTGGTC 13 0 1.2e-004 4.0e+000 # GGCCACGA TCGTGGCC 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.9e-002 0.000000 0.000000 1.000000 0.000000 0.650000 0.000000 0.350000 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTGGAGAY DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GTGGAGAY RTCTCCAC 23 1 1.3e-006 4.5e-002 # GTGGAGAT ATCTCCAC 12 0 2.4e-004 8.0e+000 # GTGGAGAC GTCTCCAC 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.5e-002 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 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 0.478261 0.000000 0.521739 # Stopping reason: E-value threshold exceeded # Running time: 133.29 seconds