# DREME 4.12.0 # command: dreme -p UPINTRON_293_U1AMO_sorted_ext.fa -n lastpas-ext.fa -oc U1AMO_upintronsites_vs_LastPAS/ -mink 4 -maxk 12 -m 20 # positives: 988 from UPINTRON_293_U1AMO_sorted_ext.fa (Thu Jan 11 12:18:24 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 22:20:17 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 59 104 3.8e-014 2.1e-008 # CCAGGCTGGA TCCAGCCTGG 43 83 1.0e-009 5.6e-004 # CCAGGCTGGT ACCAGCCTGG 16 21 6.1e-006 3.4e+000 letter-probability matrix: alength= 4 w= 10 nsites= 60 E= 2.1e-008 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 0.716667 0.000000 0.000000 0.283333 MOTIF CAGAGYGAGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CAGAGYGAGA TCTCRCTCTG 33 40 1.7e-011 9.4e-006 # CAGAGTGAGA TCTCACTCTG 17 20 1.1e-006 6.1e-001 # CAGAGCGAGA TCTCGCTCTG 16 20 4.0e-006 2.2e+000 letter-probability matrix: alength= 4 w= 10 nsites= 33 E= 9.4e-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 0.484848 0.000000 0.515152 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 GASCAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GASCAAAA TTTTGSTC 54 132 6.2e-009 3.4e-003 # GACCAAAA TTTTGGTC 31 51 1.4e-008 7.9e-003 # GAGCAAAA TTTTGCTC 23 83 9.7e-003 5.3e+003 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 3.4e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.581818 0.418182 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 CCTCARCCTCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCTCARCCTCC GGAGGYTGAGG 22 23 6.8e-009 3.8e-003 # CCTCAGCCTCC GGAGGCTGAGG 18 22 7.9e-007 4.3e-001 # CCTCAACCTCC GGAGGTTGAGG 4 1 1.3e-003 7.3e+002 letter-probability matrix: alength= 4 w= 11 nsites= 22 E= 3.8e-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 0.181818 0.000000 0.818182 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 8.4e-009 4.6e-003 # CTTGAGCCC GGGCTCAAG 11 10 1.9e-005 1.1e+001 # CTTGAACCC GGGTTCAAG 12 16 1.0e-004 5.5e+001 letter-probability matrix: alength= 4 w= 9 nsites= 24 E= 4.6e-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 AAGAGRAAAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGAGRAAAAGA TCTTTTYCTCTT 10 1 1.5e-008 7.9e-003 # AAGAGAAAAAGA TCTTTTTCTCTT 6 1 3.2e-005 1.7e+001 # AAGAGGAAAAGA TCTTTTCCTCTT 4 0 3.0e-004 1.6e+002 letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 7.9e-003 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 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGWATC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGWATC GATWCG 45 103 2.5e-008 1.4e-002 # CGAATC GATTCG 23 34 2.7e-007 1.5e-001 # CGTATC GATACG 22 69 2.9e-003 1.6e+003 letter-probability matrix: alength= 4 w= 6 nsites= 46 E= 1.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.521739 0.000000 0.000000 0.478261 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCTATGATY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCTATGATY RATCATAGC 12 3 7.9e-009 4.3e-003 # GCTATGATC GATCATAGC 6 1 3.2e-005 1.7e+001 # GCTATGATT AATCATAGC 6 2 1.1e-004 6.2e+001 letter-probability matrix: alength= 4 w= 9 nsites= 12 E= 4.3e-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 MOTIF GAARCTC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GAARCTC GAGYTTC 75 235 5.2e-008 2.8e-002 # GAAACTC GAGTTTC 47 149 2.2e-005 1.2e+001 # GAAGCTC GAGCTTC 28 92 1.5e-003 8.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 2.8e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.623377 0.000000 0.376623 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 # Stopping reason: E-value threshold exceeded # Running time: 3058.87 seconds