# DREME 4.12.0 # command: dreme -p UPINTRON_Union.fa -n lastpas-ext.fa -oc Both_upintronsites_vs_LastPAS/ -mink 4 -maxk 12 -m 20 # positives: 1028 from UPINTRON_Union.fa (Thu Jan 11 12:43:36 PST 2018) # negatives: 6520 from lastpas-ext.fa (Thu Jan 11 13:12:21 PST 2018) # host: compute-1-13.local # when: Sun Jan 14 23:13:16 PST 2018 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 0.293 C 0.176 G 0.187 T 0.344 MOTIF CCAGGCTGGW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCAGGCTGGW WCCAGCCTGG 62 104 7.8e-015 4.4e-009 # CCAGGCTGGA TCCAGCCTGG 46 83 1.6e-010 8.9e-005 # CCAGGCTGGT ACCAGCCTGG 16 21 9.7e-006 5.5e+000 letter-probability matrix: alength= 4 w= 10 nsites= 63 E= 4.4e-009 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 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.730159 0.000000 0.000000 0.269841 MOTIF CAGAGYGAGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CAGAGYGAGA TCTCRCTCTG 35 40 3.6e-012 2.0e-006 # CAGAGCGAGA TCTCGCTCTG 18 20 5.1e-007 2.9e-001 # CAGAGTGAGA TCTCACTCTG 17 20 1.8e-006 1.0e+000 letter-probability matrix: alength= 4 w= 10 nsites= 35 E= 2.0e-006 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 1.000000 0.000000 0.000000 0.514286 0.000000 0.485714 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 MOTIF CGRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGRA TYCG 401 1930 1.5e-009 8.6e-004 # CGAA TTCG 260 1176 5.6e-008 3.2e-002 # CGGA TCCG 210 1043 3.0e-004 1.7e+002 letter-probability matrix: alength= 4 w= 4 nsites= 562 E= 8.6e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.523132 0.000000 0.476868 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCTCARCCTCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCTCARCCTCC GGAGGYTGAGG 23 22 2.0e-009 1.1e-003 # CCTCAGCCTCC GGAGGCTGAGG 19 21 2.3e-007 1.3e-001 # CCTCAACCTCC GGAGGTTGAGG 4 1 1.5e-003 8.3e+002 letter-probability matrix: alength= 4 w= 11 nsites= 23 E= 1.1e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.173913 0.000000 0.826087 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTTGARCCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTTGARCCC GGGYTCAAG 23 26 1.6e-008 8.9e-003 # CTTGAGCCC GGGCTCAAG 11 10 2.7e-005 1.5e+001 # CTTGAACCC GGGTTCAAG 12 16 1.4e-004 7.7e+001 letter-probability matrix: alength= 4 w= 9 nsites= 24 E= 8.9e-003 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 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 MOTIF GASCAAAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GASCAAAA TTTTGSTC 54 131 1.7e-008 9.2e-003 # GACCAAAA TTTTGGTC 29 50 1.9e-007 1.0e-001 # GAGCAAAA TTTTGCTC 25 83 4.7e-003 2.5e+003 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 9.2e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.454545 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 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCTATGATY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCTATGATY RATCATAGC 12 3 1.2e-008 6.3e-003 # GCTATGATC GATCATAGC 6 1 3.9e-005 2.1e+001 # GCTATGATT AATCATAGC 6 2 1.4e-004 7.4e+001 letter-probability matrix: alength= 4 w= 9 nsites= 12 E= 6.3e-003 0.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 # Stopping reason: E-value threshold exceeded # Running time: 2419.31 seconds