# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--GAL11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--GAL11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--GAL11/seqs-shuffled # positives: 816 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--GAL11/seqs-centered (Sat Jan 18 17:22:47 PST 2020) # negatives: 816 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--GAL11/seqs-shuffled (Sat Jan 18 17:22:47 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:36:40 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 0.299 C 0.205 G 0.200 T 0.297 MOTIF GTTCGABY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGABY RVTCGAAC 89 3 2.4e-024 8.2e-020 # GTTCGATC GATCGAAC 24 1 6.6e-007 2.2e-002 # GTTCGATT AATCGAAC 22 1 2.5e-006 8.5e-002 # GTTCGACT AGTCGAAC 15 1 2.5e-004 8.3e+000 # GTTCGAGC GCTCGAAC 11 0 4.7e-004 1.6e+001 # GTTCGACC GGTCGAAC 9 0 1.9e-003 6.5e+001 # GTTCGAGT ACTCGAAC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 89 E= 8.2e-020 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.269663 0.213483 0.516854 0.000000 0.494382 0.000000 0.505618 MOTIF TBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TBGGCCA TGGCCVA 78 9 8.1e-016 2.7e-011 # TCGGCCA TGGCCGA 37 2 9.8e-010 3.3e-005 # TGGGCCA TGGCCCA 20 3 2.2e-004 7.5e+000 # TTGGCCA TGGCCAA 21 4 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 2.7e-011 0.000000 0.000000 0.000000 1.000000 0.000000 0.474359 0.256410 0.269231 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 ACCCABAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 67 8 1.7e-013 5.6e-009 # ACCCATAC GTATGGGT 33 0 8.4e-011 2.8e-006 # ACCCAGAC GTCTGGGT 14 1 4.7e-004 1.6e+001 # ACCCACAC GTGTGGGT 23 7 2.4e-003 8.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 108 E= 5.6e-009 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 0.000000 0.555556 0.129630 0.314815 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AARAARA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AARAARA TYTTYTT 258 133 2.3e-013 7.5e-009 # AAGAAAA TTTTCTT 95 41 7.8e-007 2.6e-002 # AAAAAAA TTTTTTT 133 75 1.1e-005 3.5e-001 # AAGAAGA TCTTCTT 38 11 5.7e-005 1.9e+000 # AAAAAGA TCTTTTT 71 36 3.1e-004 1.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 311 E= 7.5e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.610932 0.000000 0.389068 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.694534 0.000000 0.305466 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCWTAAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 49 2 3.0e-013 9.8e-009 # GCCTTAAC GTTAAGGC 37 2 9.8e-010 3.2e-005 # GCCATAAC GTTATGGC 13 0 1.2e-004 3.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 9.8e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.260000 0.000000 0.000000 0.740000 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 GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 43 1 1.5e-012 4.9e-008 # GCGCTACC GGTAGCGC 32 1 3.0e-009 9.8e-005 # GCTCTACC GGTAGAGC 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 4.9e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.744186 0.255814 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 AGTGGTWW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWW WWACCACT 54 9 1.6e-009 5.3e-005 # AGTGGTTT AAACCACT 13 0 1.2e-004 3.8e+000 # AGTGGTTA TAACCACT 23 4 1.4e-004 4.6e+000 # AGTGGTAA TTACCACT 18 3 7.0e-004 2.3e+001 # AGTGGTAT ATACCACT 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 66 E= 5.3e-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 0.454545 0.000000 0.000000 0.545455 0.621212 0.000000 0.000000 0.378788 MOTIF ATCCGKAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATCCGKAC GTMCGGAT 31 1 5.9e-009 1.9e-004 # ATCCGTAC GTACGGAT 24 1 6.6e-007 2.2e-002 # ATCCGGAC GTCCGGAT 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 1.9e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.212121 0.787879 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 48 8 1.4e-008 4.7e-004 # TGGCGCA TGCGCCA 27 4 1.4e-005 4.8e-001 # TGGCGTA TACGCCA 22 4 2.4e-004 8.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 4.7e-004 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 1.000000 0.000000 0.000000 0.551020 0.000000 0.448980 1.000000 0.000000 0.000000 0.000000 MOTIF CKATCAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CKATCAC GTGATMG 40 5 2.7e-008 8.9e-004 # CTATCAC GTGATAG 27 3 3.5e-006 1.2e-001 # CGATCAC GTGATCG 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 8.9e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.325000 0.675000 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 MOTIF CGTTGCCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCCA TGGCAACG 24 0 5.0e-008 1.6e-003 # CGTTGCCA TGGCAACG 24 0 5.0e-008 1.6e-003 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.6e-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 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 1.000000 0.000000 0.000000 0.000000 MOTIF ARCAGAT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ARCAGAT ATCTGYT 46 9 1.4e-007 4.6e-003 # AGCAGAT ATCTGCT 26 2 1.3e-006 4.2e-002 # AACAGAT ATCTGTT 23 7 2.4e-003 7.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 4.6e-003 1.000000 0.000000 0.000000 0.000000 0.460000 0.000000 0.540000 0.000000 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 0.000000 0.000000 0.000000 1.000000 MOTIF GCGCCTKA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCGCCTKA TMAGGCGC 26 1 1.7e-007 5.6e-003 # GCGCCTTA TAAGGCGC 24 1 6.6e-007 2.2e-002 # GCGCCTGA TCAGGCGC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.6e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.153846 0.846154 1.000000 0.000000 0.000000 0.000000 MOTIF CKTTGGGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 22 0 2.1e-007 6.7e-003 # CGTTGGGC GCCCAACG 12 0 2.3e-004 7.6e+000 # CTTTGGGC GCCCAAAG 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.7e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.454545 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 ATACAACA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATACAACA TGTTGTAT 21 0 4.2e-007 1.4e-002 # ATACAACA TGTTGTAT 21 0 4.2e-007 1.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 1.4e-002 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 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCAM DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGACCAM KTGGTCT 41 8 7.0e-007 2.3e-002 # AGACCAC GTGGTCT 28 6 8.4e-005 2.7e+000 # AGACCAA TTGGTCT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 2.3e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.317073 0.682927 0.000000 0.000000 MOTIF CTMATAAC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTMATAAC GTTATKAG 23 1 1.3e-006 4.2e-002 # CTAATAAC GTTATTAG 15 1 2.5e-004 8.0e+000 # CTCATAAC GTTATGAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.652174 0.347826 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 90.95 seconds