# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ARR1/seqs-shuffled # positives: 570 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ARR1/seqs-centered (Sun Jan 19 02:22:59 PST 2020) # negatives: 570 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ARR1/seqs-shuffled (Sun Jan 19 02:22:59 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:37:24 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 0.204 G 0.203 T 0.295 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 120 5 8.9e-033 2.7e-028 # GGTTCGA TCGAACC 100 3 2.0e-028 6.0e-024 # GGCTCGA TCGAGCC 20 0 8.0e-007 2.4e-002 # GGATCGA TCGATCC 25 2 2.2e-006 6.8e-002 letter-probability matrix: alength= 4 w= 7 nsites= 121 E= 2.7e-028 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.099174 0.000000 0.719008 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 CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 54 2 6.5e-015 1.9e-010 # CTCGGCCA TGGCCGAG 24 0 4.7e-008 1.4e-003 # CTTGGCCA TGGCCAAG 19 1 1.7e-005 5.2e-001 # CTGGGCCA TGGCCCAG 11 1 3.0e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 1.9e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.444444 0.203704 0.351852 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-3 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 52 2 2.7e-014 7.9e-010 # TTAAGGCG CGCCTTAA 29 1 2.1e-008 6.1e-004 # CTAAGGCG CGCCTTAG 13 0 1.1e-004 3.4e+000 # GTAAGGCG CGCCTTAC 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 7.9e-010 0.000000 0.250000 0.192308 0.557692 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 AAAAAWAW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWAW WTWTTTTT 142 52 5.2e-013 1.6e-008 # AAAAAAAT ATTTTTTT 71 26 1.0e-006 3.1e-002 # AAAAAAAA TTTTTTTT 60 20 2.0e-006 6.0e-002 # AAAAATAA TTATTTTT 40 13 9.6e-005 2.9e+000 # AAAAATAT ATATTTTT 26 6 2.2e-004 6.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 159 E= 1.6e-008 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.610063 0.000000 0.000000 0.389937 1.000000 0.000000 0.000000 0.000000 0.553459 0.000000 0.000000 0.446541 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 36 0 8.2e-012 2.4e-007 # GCGCTACC GGTAGCGC 24 0 4.7e-008 1.4e-003 # GCTCTACC GGTAGAGC 12 0 2.3e-004 6.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 2.4e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 CCCATDC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 58 11 1.4e-009 4.0e-005 # CCCATAC GTATGGG 25 3 1.1e-005 3.3e-001 # CCCATTC GAATGGG 18 4 2.0e-003 5.9e+001 # CCCATGC GCATGGG 17 5 7.9e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 4.0e-005 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 0.000000 0.000000 0.000000 1.000000 0.426230 0.000000 0.278689 0.295082 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 67 16 2.1e-009 6.0e-005 # AGTGGTT AACCACT 44 8 1.1e-007 3.3e-003 # AGTGGTA TACCACT 36 8 9.0e-006 2.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 83 E= 6.0e-005 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 0.445783 0.000000 0.000000 0.554217 MOTIF GAWTTGAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GAWTTGAA TTCAAWTC 35 3 2.1e-008 6.2e-004 # GAATTGAA TTCAATTC 19 2 9.8e-005 2.8e+000 # GATTTGAA TTCAAATC 16 1 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 6.2e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.542857 0.000000 0.000000 0.457143 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 32 2 2.3e-008 6.8e-004 # ATGGCAAC GTTGCCAT 19 1 1.7e-005 5.1e-001 # ATGGCATC GATGCCAT 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.8e-004 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 0.593750 0.000000 0.000000 0.406250 0.000000 1.000000 0.000000 0.000000 MOTIF CCGTGSA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 30 2 8.7e-008 2.5e-003 # CCGTGGA TCCACGG 18 1 3.4e-005 9.8e-001 # CCGTGCA TGCACGG 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.5e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCKCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TGGCKCA TGMGCCA 30 2 8.7e-008 2.5e-003 # TGGCGCA TGCGCCA 19 1 1.7e-005 5.0e-001 # TGGCTCA TGAGCCA 11 1 3.0e-003 8.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.5e-003 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 0.000000 0.633333 0.366667 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 23 0 9.5e-008 2.7e-003 # CGTGCTAA TTAGCACG 12 0 2.3e-004 6.6e+000 # CGTGTTAA TTAACACG 11 0 4.7e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.7e-003 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 0.521739 0.000000 0.478261 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 ATCGTRAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATCGTRAG CTYACGAT 22 0 1.9e-007 5.6e-003 # ATCGTGAG CTCACGAT 15 0 2.8e-005 8.0e-001 # ATCGTAAG CTTACGAT 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.6e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.318182 0.000000 0.681818 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GYCAGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GYCAGA TCTGRC 61 19 6.0e-007 1.7e-002 # GCCAGA TCTGGC 32 7 2.7e-005 7.7e-001 # GTCAGA TCTGAC 30 12 3.4e-003 9.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 63 E= 1.7e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.507937 0.000000 0.492063 0.000000 1.000000 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 MOTIF MGCGCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST MGCGCA TGCGCK 50 13 8.0e-007 2.3e-002 # CGCGCA TGCGCG 26 5 7.9e-005 2.3e+000 # AGCGCA TGCGCT 25 8 2.0e-003 5.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 52 E= 2.3e-002 0.500000 0.500000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATTAASAG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 29 3 9.5e-007 2.7e-002 # ATTAAGAG CTCTTAAT 17 2 3.3e-004 9.4e+000 # ATTAACAG CTGTTAAT 12 1 1.6e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 2.7e-002 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 0.413793 0.586207 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 61.83 seconds