# DREME 5.3.3
#     command: dreme -oc ../result/final_prediction/GM12878/inference_raw/DREME/RankLinear1.0_10_SMAD1/ -k 8 -m 5 -e 1000 -verbosity 1 -p ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/SMAD1.fasta
#   positives: 250 from ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/SMAD1.fasta (Sat Feb 12 17:37:26 EST 2022)
#   negatives: 250 from shuffled positives
#        host: c22n12.farnam.hpc.yale.internal
#        when: Sat Feb 12 18:28:55 EST 2022

MEME version 5.3.3

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 0.237 C 0.259 G 0.259 T 0.245


MOTIF CCTGGCAC DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCTGGCAC   GTGCCAGG         10          1   5.4e-003   1.4e+001
#         CCTGGCAC   GTGCCAGG         10          1   5.4e-003   1.4e+001

letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 1.4e+001
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
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF GCCAAGAA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    GCCAAGAA   TTCTTGGC          7          0   7.5e-003   1.9e+001
#         GCCAAGAA   TTCTTGGC          7          0   7.5e-003   1.9e+001

letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.9e+001
0.000000 0.000000 1.000000 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
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 0.000000


MOTIF ACTTGGCA DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ACTTGGCA   TGCCAAGT          5          0   3.1e-002   7.8e+001

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 7.8e+001
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
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AGAAACTG DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AGAAACTG   CAGTTTCT          5          0   3.1e-002   7.7e+001

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 7.7e+001
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 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 1.000000 0.000000


MOTIF CTGGCAGC DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CTGGCAGC   GCTGCCAG          5          0   3.1e-002   7.6e+001

letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 7.6e+001
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 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


# Stopping reason: target motif count reached
#    Running time: 0.67 seconds