# 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
