# DREME 4.12.0 # command: dreme -p UPINTRON_293_U1AMO_sorted_ext.fa -n lastpas-ext.fa -oc U1AMO_upintronsites_vs_LastPAS_norc -norc -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: Tue Jan 16 15:20:29 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 WCCAGCCTGG DREME-1 # Word RC Word Pos Neg P-value E-value # BEST WCCAGCCTGG CCAGGCTGGW 48 48 2.2e-018 1.4e-012 # TCCAGCCTGG CCAGGCTGGA 33 31 1.6e-013 1.0e-007 # ACCAGCCTGG CCAGGCTGGT 15 17 3.5e-006 2.3e+000 letter-probability matrix: alength= 4 w= 10 nsites= 48 E= 1.4e-012 0.312500 0.000000 0.000000 0.687500 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TKTTATTGCT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TKTTATTGCT AGCAATAAMA 17 8 3.6e-010 2.3e-004 # TTTTATTGCT AGCAATAAAA 13 8 2.4e-007 1.5e-001 # TGTTATTGCT AGCAATAACA 4 0 3.0e-004 1.9e+002 letter-probability matrix: alength= 4 w= 10 nsites= 18 E= 2.3e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CAGAGYGAGACT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAGAGYGAGACT AGTCTCRCTCTG 19 13 1.0e-009 6.4e-004 # CAGAGTGAGACT AGTCTCACTCTG 10 6 5.6e-006 3.6e+000 # CAGAGCGAGACT AGTCTCGCTCTG 9 7 5.5e-005 3.5e+001 letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 6.4e-004 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 0.473684 0.000000 0.526316 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF TGCAGTSA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TGCAGTSA TSACTGCA 41 77 1.3e-009 8.6e-004 # TGCAGTGA TCACTGCA 30 58 3.6e-007 2.3e-001 # TGCAGTCA TGACTGCA 11 19 9.7e-004 6.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 8.6e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.268293 0.731707 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGAGGCHGAGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GGAGGCHGAGG CCTCDGCCTCC 26 31 1.9e-009 1.2e-003 # GGAGGCTGAGG CCTCAGCCTCC 15 16 2.1e-006 1.4e+000 # GGAGGCCGAGG CCTCGGCCTCC 9 14 1.7e-003 1.1e+003 # GGAGGCAGAGG CCTCTGCCTCC 5 5 5.6e-003 3.6e+003 letter-probability matrix: alength= 4 w= 11 nsites= 29 E= 1.2e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.172414 0.310345 0.000000 0.517241 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 0.000000 1.000000 0.000000 MOTIF TCACTTGAVC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TCACTTGAVC GBTCAAGTGA 14 6 7.7e-009 4.9e-003 # TCACTTGAGC GCTCAAGTGA 8 4 2.7e-005 1.7e+001 # TCACTTGAAC GTTCAAGTGA 3 1 8.2e-003 5.2e+003 # TCACTTGACC GGTCAAGTGA 3 1 8.2e-003 5.2e+003 letter-probability matrix: alength= 4 w= 10 nsites= 15 E= 4.9e-003 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 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 0.200000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TCAAMAAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TCAAMAAAA TTTTKTTGA 29 48 4.7e-008 3.0e-002 # TCAAAAAAA TTTTTTTGA 21 40 1.7e-005 1.1e+001 # TCAACAAAA TTTTGTTGA 8 8 4.2e-004 2.7e+002 letter-probability matrix: alength= 4 w= 9 nsites= 29 E= 3.0e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.724138 0.275862 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 GAKCGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GAKCGC GCGMTC 30 52 5.9e-008 3.8e-002 # GATCGC GCGATC 16 25 2.9e-005 1.9e+001 # GAGCGC GCGCTC 14 27 4.8e-004 3.0e+002 letter-probability matrix: alength= 4 w= 6 nsites= 30 E= 3.8e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.466667 0.533333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 1873.64 seconds