# DREME 4.10.2 # command: dreme -rna -oc motif.Puf3p -p Puf3p.s # positives: 1236 from Puf3p.s (Wed Oct 28 11:24:33 AEST 2015) # negatives: 1236 from shuffled positives # host: IMB12-010665 # when: Wed Oct 28 11:37:12 AEST 2015 MEME version 4.10.2 ALPHABET "RNA" RNA-LIKE A "Adenine" CC0000 C "Cytosine" 0000CC G "Guanine" FFB300 U "Uracil" 008000 N "Any base" = ACGU X = ACGU . = ACGU V "Not U" = ACG H "Not G" = ACU D "Not C" = AGU B "Not A" = CGU M "Amino" = AC R "Purine" = AG W "Weak" = AU S "Strong" = CG Y "Pyrimidine" = CU K "Keto" = GU T = U END ALPHABET Background letter frequencies (from dataset): A 0.333 C 0.171 G 0.145 U 0.352 MOTIF UGUAHAUA DREME # Word Pos Neg P-value E-value # BEST UGUAHAUA 316 32 2.1e-068 1.2e-063 # UGUAAAUA 161 13 5.4e-036 3.2e-031 # UGUAUAUA 124 16 2.9e-023 1.7e-018 # UGUACAUA 47 3 1.3e-011 7.5e-007 letter-probability matrix: alength= 4 w= 8 nsites= 337 E= 1.2e-063 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.480712 0.139466 0.000000 0.379822 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF YAUAUAWA DREME # Word Pos Neg P-value E-value # BEST YAUAUAWA 207 69 2.3e-019 1.3e-014 # UAUAUAUA 128 37 5.1e-014 3.0e-009 # CAUAUAUA 52 12 1.6e-007 9.7e-003 # UAUAUAAA 47 23 2.5e-003 1.5e+002 # CAUAUAAA 23 9 9.6e-003 5.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 261 E= 1.3e-014 0.000000 0.295019 0.000000 0.704981 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.233716 0.000000 0.000000 0.766284 1.000000 0.000000 0.000000 0.000000 MOTIF GAARR DREME # Word Pos Neg P-value E-value # BEST GAARR 549 365 1.1e-014 6.2e-010 # GAAGA 172 93 1.7e-007 9.8e-003 # GAAAA 290 193 5.2e-007 3.1e-002 # GAAGG 88 43 3.4e-005 2.0e+000 # GAAAG 149 111 7.6e-003 4.5e+002 letter-probability matrix: alength= 4 w= 5 nsites= 759 E= 6.2e-010 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.635046 0.000000 0.364954 0.000000 0.683794 0.000000 0.316206 0.000000 MOTIF YUYUUC DREME # Word Pos Neg P-value E-value # BEST YUYUUC 381 237 1.3e-011 7.5e-007 # CUCUUC 65 22 1.5e-006 8.4e-002 # UUUUUC 213 140 1.7e-005 9.4e-001 # UUCUUC 106 68 1.8e-003 9.9e+001 # CUUUUC 88 56 3.8e-003 2.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 500 E= 7.5e-007 0.000000 0.310000 0.000000 0.690000 0.000000 0.000000 0.000000 1.000000 0.000000 0.338000 0.000000 0.662000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GSUGSU DREME # Word Pos Neg P-value E-value # BEST GSUGSU 90 34 1.3e-007 7.3e-003 # GGUGGU 24 4 8.3e-005 4.6e+000 # GCUGGU 33 12 1.1e-003 6.3e+001 # GCUGCU 25 9 4.3e-003 2.4e+002 # GGUGCU 25 10 8.0e-003 4.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 104 E= 7.3e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.548077 0.451923 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.480769 0.519231 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF YAUGUA DREME # Word Pos Neg P-value E-value # BEST YAUGUA 165 89 2.9e-007 1.6e-002 # UAUGUA 118 61 6.0e-006 3.3e-001 # CAUGUA 56 30 2.9e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 181 E= 1.6e-002 0.000000 0.309392 0.000000 0.690608 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 15.23 seconds