view test-data/dreme_output_test1.txt @ 13:4eb02864e5df draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b

# DREME 4.12.0
#     command: dreme -o ./dreme_test1_out -p dreme_test_sites.fa -norc -rna -s 1
#   positives: 1000 from dreme_test_sites.fa (Thu Apr 26 15:09:03 CEST 2018)
#   negatives: 1000 from shuffled positives
#        host: ThinkPad-T450s
#        when: Thu May 03 13:22:29 CEST 2018

MEME version 4.12.0

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 0.221 C 0.245 G 0.221 U 0.312


MOTIF UUYUCY DREME-1

#             Word        Pos        Neg    P-value    E-value
# BEST      UUYUCY        387        210   2.6e-018   1.2e-013
#           UUUUCC        147         75   1.8e-007   8.1e-003
#           UUUUCU        155         94   2.2e-005   1.0e+000
#           UUCUCU         94         51   1.3e-004   6.1e+000
#           UUCUCC         75         42   1.1e-003   5.0e+001

letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.294118 0.000000 0.705882
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.474946 0.000000 0.525054


MOTIF YAGG DREME-2

#             Word        Pos        Neg    P-value    E-value
# BEST        YAGG        600        416   1.1e-016   5.1e-012
#             CAGG        441        304   1.5e-010   6.6e-006
#             UAGG        232        165   1.1e-004   4.7e+000

letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012
0.000000 0.692308 0.000000 0.307692
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 GAAGAW DREME-3

#             Word        Pos        Neg    P-value    E-value
# BEST      GAAGAW         81         22   8.2e-010   3.4e-005
#           GAAGAU         45          7   2.4e-008   9.9e-004
#           GAAGAA         40         16   7.9e-004   3.3e+001

letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.494382 0.000000 0.000000 0.505618


MOTIF SMUGGA DREME-4

#             Word        Pos        Neg    P-value    E-value
# BEST      SMUGGA        110         47   9.1e-008   3.7e-003
#           GAUGGA         22          6   1.7e-003   7.1e+001
#           GCUGGA         33         14   3.6e-003   1.5e+002
#           CCUGGA         32         15   8.6e-003   3.5e+002
#           CAUGGA         29         13   9.1e-003   3.7e+002

letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003
0.000000 0.529412 0.470588 0.000000
0.428571 0.571429 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
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 13.95 seconds