# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ZAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ZAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ZAP1/seqs-shuffled # positives: 486 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ZAP1/seqs-centered (Sat Jan 18 14:34:45 PST 2020) # negatives: 486 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ZAP1/seqs-shuffled (Sat Jan 18 14:34:45 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 14:43:59 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 0.292 C 0.208 G 0.210 T 0.290 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 153 10 8.3e-040 2.2e-035 # GGTTCGA TCGAACC 111 5 3.0e-030 7.8e-026 # GGTTCAA TTGAACC 42 5 6.0e-009 1.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 153 E= 2.2e-035 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 0.274510 0.000000 0.725490 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 78 3 1.6e-021 4.2e-017 # CCATACAT ATGTATGG 32 1 2.4e-009 6.3e-005 # CCGTACAT ATGTACGG 27 0 5.1e-009 1.3e-004 # CCGTACAC GTGTACGG 15 1 2.4e-004 6.1e+000 # CCATACAC GTGTATGG 10 1 5.6e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 89 E= 4.2e-017 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.516854 0.000000 0.483146 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.292135 0.000000 0.707865 MOTIF AGTGGTH DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTH DACCACT 90 11 2.0e-018 5.3e-014 # AGTGGTT AACCACT 56 7 1.9e-011 4.8e-007 # AGTGGTA TACCACT 33 3 7.1e-008 1.8e-003 # AGTGGTC GACCACT 12 1 1.6e-003 4.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 103 E= 5.3e-014 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 0.320388 0.116505 0.000000 0.563107 MOTIF ACCRACT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 66 5 7.8e-016 2.0e-011 # ACCAACT AGTTGGT 48 4 2.3e-011 6.0e-007 # ACCGACT AGTCGGT 18 1 3.3e-005 8.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 2.0e-011 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.731343 0.000000 0.268657 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 MOTIF AARAAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AARAAA TTTYTT 259 138 1.7e-015 4.2e-011 # AAAAAA TTTTTT 205 102 6.8e-013 1.7e-008 # AAGAAA TTTCTT 114 56 6.2e-007 1.6e-002 letter-probability matrix: alength= 4 w= 6 nsites= 381 E= 4.2e-011 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.713911 0.000000 0.286089 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 MOTIF ATAGTKTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 31 0 2.8e-010 7.1e-006 # ATAGTTTA TAAACTAT 17 0 6.6e-006 1.6e-001 # ATAGTGTA TACACTAT 14 0 5.6e-005 1.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 7.1e-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 0.451613 0.548387 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAAGGCR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 48 6 6.3e-010 1.6e-005 # TAAGGCG CGCCTTA 34 4 1.9e-007 4.7e-003 # TAAGGCA TGCCTTA 15 2 1.1e-003 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 1.6e-005 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 0.291667 0.000000 0.708333 0.000000 MOTIF AGAYCGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGG CCGRTCT 40 4 4.3e-009 1.1e-004 # AGATCGG CCGATCT 24 2 4.1e-006 1.0e-001 # AGACCGG CCGGTCT 16 2 6.0e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 1.1e-004 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 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CABACGC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CABACGC GCGTVTG 48 7 2.7e-009 6.6e-005 # CAGACGC GCGTCTG 15 1 2.4e-004 5.8e+000 # CACACGC GCGTGTG 20 4 6.8e-004 1.7e+001 # CATACGC GCGTATG 13 2 3.5e-003 8.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 6.6e-005 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.416667 0.312500 0.270833 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 CCCATKC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCCATKC GMATGGG 46 7 8.9e-009 2.2e-004 # CCCATGC GCATGGG 25 3 1.1e-005 2.6e-001 # CCCATTC GAATGGG 21 4 3.9e-004 9.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 2.2e-004 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 0.000000 0.000000 0.543478 0.456522 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 3 3.7e-008 9.1e-004 # ATGGCAAC GTTGCCAT 24 2 4.1e-006 1.0e-001 # ATGGCATC GATGCCAT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 9.1e-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 0.705882 0.000000 0.000000 0.294118 0.000000 1.000000 0.000000 0.000000 MOTIF ACCCADAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACCCADAC GTHTGGGT 31 2 4.2e-008 1.0e-003 # ACCCAGAC GTCTGGGT 12 0 2.3e-004 5.6e+000 # ACCCAAAC GTTTGGGT 11 1 3.0e-003 7.4e+001 # ACCCATAC GTATGGGT 11 1 3.0e-003 7.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.0e-003 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 0.314286 0.000000 0.342857 0.342857 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CKTTGGGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 23 0 9.1e-008 2.2e-003 # CGTTGGGC GCCCAACG 15 0 2.7e-005 6.6e-001 # CTTTGGGC GCCCAAAG 8 0 3.8e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.652174 0.347826 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGATCGAA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GGATCGAA TTCGATCC 25 1 3.0e-007 7.3e-003 # GGATCGAA TTCGATCC 25 1 3.0e-007 7.3e-003 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.3e-003 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 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACATCASG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACATCASG CSTGATGT 21 0 3.8e-007 9.2e-003 # ACATCACG CGTGATGT 14 0 5.6e-005 1.3e+000 # ACATCAGG CCTGATGT 7 0 7.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.2e-003 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTCACGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTCACGA TCGTGAGT 21 0 3.8e-007 9.2e-003 # ACTCACGA TCGTGAGT 21 0 3.8e-007 9.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.2e-003 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 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 CGCGKGC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CGCGKGC GCMCGCG 27 2 5.9e-007 1.4e-002 # CGCGTGC GCACGCG 15 1 2.4e-004 5.7e+000 # CGCGGGC GCCCGCG 12 1 1.6e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 1.4e-002 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 0.444444 0.555556 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCAKAAG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATCAKAAG CTTMTGAT 24 1 5.9e-007 1.4e-002 # ATCAGAAG CTTCTGAT 12 0 2.3e-004 5.5e+000 # ATCATAAG CTTATGAT 12 1 1.6e-003 3.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-002 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 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCAASAGA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CCAASAGA TCTSTTGG 29 3 9.0e-007 2.2e-002 # CCAACAGA TCTGTTGG 14 0 5.6e-005 1.3e+000 # CCAAGAGA TCTCTTGG 15 3 3.5e-003 8.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 2.2e-002 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 0.000000 0.000000 0.482759 0.517241 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 ACGGKGAA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACGGKGAA TTCMCCGT 26 2 1.1e-006 2.7e-002 # ACGGGGAA TTCCCCGT 13 0 1.1e-004 2.7e+000 # ACGGTGAA TTCACCGT 13 2 3.5e-003 8.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.7e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 AGTSTGGC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST AGTSTGGC GCCASACT 19 0 1.6e-006 3.8e-002 # AGTCTGGC GCCAGACT 11 0 4.6e-004 1.1e+001 # AGTGTGGC GCCACACT 8 0 3.8e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.8e-002 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 0.578947 0.421053 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 MOTIF ATGGYCA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST ATGGYCA TGRCCAT 41 9 1.6e-006 3.9e-002 # ATGGTCA TGACCAT 26 6 2.2e-004 5.2e+000 # ATGGCCA TGGCCAT 15 3 3.5e-003 8.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 3.9e-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 0.365854 0.000000 0.634146 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 67.71 seconds