# DREME 5.3.3
#     command: dreme -oc ../result/final_prediction/GM12878/inference_raw/DREME/RankLinear1.0_10_NRF1/ -k 8 -m 5 -e 1000 -verbosity 1 -p ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/NRF1.fasta
#   positives: 250 from ../result/final_prediction/GM12878/fasta/RankLinear1.0_10/NRF1.fasta (Sat Feb 12 17:37:08 EST 2022)
#   negatives: 250 from shuffled positives
#        host: c22n06.farnam.hpc.yale.internal
#        when: Sat Feb 12 18:29:50 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 0.141 C 0.349 G 0.377 T 0.133


MOTIF GCGCAKGC DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    GCGCAKGC   GCMTGCGC         41          6   2.4e-008   5.6e-005
#         GCGCAGGC   GCCTGCGC         24          2   3.2e-006   7.7e-003
#         GCGCATGC   GCATGCGC         18          4   1.8e-003   4.3e+000

letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 5.6e-005
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 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.585366 0.414634
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF ATGCGCAG DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ATGCGCAG   CTGCGCAT          6          0   1.5e-002   3.4e+001

letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 3.4e+001
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 1.000000 0.000000 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


MOTIF CGCACGCG DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CGCACGCG   CGCGTGCG         10          2   1.8e-002   4.1e+001

letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 4.1e+001
0.000000 1.000000 0.000000 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
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF CAGCCGCA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CAGCCGCA   TGCGGCTG          4          0   6.2e-002   1.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.4e+002
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 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF CAGGCGCA DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CAGGCGCA   TGCGCCTG          4          0   6.2e-002   1.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.4e+002
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 1.000000 0.000000
0.000000 1.000000 0.000000 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


# Stopping reason: target motif count reached
#    Running time: 0.63 seconds